Immortal Yeast: a week's worth of research -

A week ago, I was curious - can we make an immortal yeast?

I wasn't sure. In 5 minutes of thinking, it seemed potentially doable (on the order of a 5+ year scale project for a hardworking technical team, but testable along the way).

It would also be the first time humanity made an organism immortal. Not counting human cells or pre-existing immortal species.

But I wasn't really sure. So, I decided to do a bit of looking into the question.

tl;dr - It's not obviously infeasible. Good researchers in the field don't see obvious reasons it wouldn't work. There are some potential issues (for example, would bud scars = dumb upper cap on replicative lifespan). There are also a few potential hacks that might work surprisingly well (for example, sporulating yeast to regenerate them - thanks to those who sent this paper). It might be worth doing chronological vs replicative lifespan to get around the bud scar issue + using some marker of metabolic activity. The best way to use 'the power of yeast genetics' would be to do a genetic screen - a knockout screen was done, but you could still do a mutant or over expression screen.

I feel kind of unsatisfied, though. What I want is a clear idea of what causes this aging and how to reverse it. Instead, there are ~49 things that the literature notes are linked to yeast, and our best response is still 'screen every gene in the genome'. What I'd love is a list of physically plausible hypotheses to chase down, and some feeling that there wasn't an enormous amount of uncharacterized dark matter that could actually be the core problem.

I'd also love tiny nanobots that can move atoms wherever I want them, so I guess the universe doesn't really care about my desires. Ah well.

Stuff I did:

#1 - Try to build a mental model of what it 'feels' like to be a yeast cell

This sounds kind of weird, but I have a hard time thinking about biology if I can't see the atoms. book.bionumbers.org is my personal 'Young Lady's Primer', so I went on their database and got ~806 bionumbers that correspond to yeast. I've included them in Appendix 3 below - I haven't Anki'd all these yet, but they were a useful reference when trying to get an intuition for yeast. I also just sat in a big room for ~2 hours thinking* about the consequences of each of the things we see change with aging. For example, aged cells seem to increase in size - how would this affect the concentration of everything? Does protein expression and metabolite transport correspondingly increase? Do mitochondria increase proportionately in volume, if not, would every protein see a decrease in average ATP concentration available? Are there more membrane proteins, or does their density increase? Were the transcriptional studies that looked at this normalized in a way that we could even tell re net vs just relative protein expression?

And on and on. I've included a list of questions for all the hallmarks at the bottom of this page, complete with a bunch of #notsatisfied tags. At some point I'll probably just make my aging Roam graph public, would be easier to see the full context that way.

#2 - Go through the literature to understand what people currently think

My takeaway:

- It's labor-intensive to manually do replicative yeast lifespans, and (aside from maybe Calico) the field doesn't yet have a very robust system for doing this at high-scale. There are lots of labs working on the problem with candidate approaches (microfluidics, genetics).

- Sporulation (a way to 'regenerate' yeast) looks promising! I have some unanswered questions (sporulation efficiency declines with age, so is this a selection artifact?), but Angelika Amon and Elçin Ünal might have addressed them. Maybe it's worth carefully optimizing the amount and timing of Ndt80 expression, given that the young cells only lived a bit longer?

- There are lots of candidate damage types relevant to aging (see Appendix 2), but no consensus on which are the most important.

- Yeast cells age in variable ways, and most measurements are population-wide.

#3 - Ask a bunch of questions about what the consequences might be of yeast aging in different ways.

Normally, I'd put more work into using the mental model from #1 to come up with new plausible things that could be going wrong with yeast, in addition to those from the literature. But this week was pretty busy, so as a first pass I just took the list of 49 hallmarks that had been published in a review and went through those. It feels bad and wrong to not have done more thinking about the physical modeling though.

I've included the list of hallmarks (Appendix 1), and the questions generated by them below (Appendix 2).

To sum things up - I'm still curious about this!

If I had infinite time, my next step would be to think more about being a yeast cell* and the kinds of things that could go wrong with age. Then, I'd try to do more concrete thought experiments inspired by a subset of the questions in Appendix 2. I'd carefully investigate the sporulation regeneration biology, and think a bit about mother/daughter asymmetric damage segregation (despite that potentially being not as actively regulated as people thought).

If I were a practicing yeast geneticist working towards a PhD, I might also start just trying to design some kind of experiment. But I'm not sure thinking about the problem more first would actually be a bad idea, despite having a huge personal tendency to overanalyze things.

Ultimately, if we had single atom pushers and microscopes that could see where all the stuff was, exactly, this would obviously be a cool problem to work on. Another constraint I didn't talk about is what we can do about all of this. Our 'stuff we can do' space seems to be 1) change the environment (temperature/pH/pressure/metabolites/etc), 2) give a small molecule or 3) express a protein. Yeast being a unicellular organism doesn't (that I know) open up amazing new ways to manipulate it, although I'm curious if I'm missing something interesting here. Particularly things that are physically possible but not yet implemented. So, proteins are still our most expressive and complex nanobots for doing what we want, in this scenario. I don't know enough about expected progress in protein engineering over the coming decade to know whether that should be an optimistic or pessimistic update on the ability to fix stuff that we directly know is going wrong and should be fixed.

Anyway. That's all from me. If you're interested in working on/thinking about this problem, I'd love to hear from you! (info@longevity.vc), even if just to shoot around all the confusing bits of it.

Deep thanks to Mark McCormick, Martin Borsch Jensen, Adam Marblestone and Reuben Saunders for technical discussions that helped clarify some of the above, even though the opinions represented above are obviously just my wrong-headed and fuzzy attempt to understand the problem and not any kind of direct representation of their opinions on the topic!

*my way of thinking about this is to pretend I am a yeast cell, and think about what I would feel like and what I would worry about as I got bigger. That sounds hard to explain in a non-crazy way on paper, so maybe I'll make a video about it at some point. It also may just be a totally ineffectual way of thinking about problems, who knows.

Appendix 1 (extracted manually from Janssens and Veenhoff 2016, Figure 1)

Hallmark	Reference
Cell size increases	Lee et al 2012
Vacuole size increases	Lee et al 2012
Decreased resistance to mutagen (EMS)	Kale and Jazwinski 1996
Increased stress resistance (and trehalose production gene)	levy et al 2012
Vacuolar pH decreases	Hughes and Gottshling 2012
Oxidative protein damage (increased carbony llevels)	Aguilaniu et al 2003
Decreased retention of oxidatively damaged proteins	Aguilaniu et al 2003
Increased histone H4K16 acetylation	Dang et al 2009
Decreased histone H3K56 acetylation	Dang et al 2009
Mitochondrial redox potential declines	McFaline-Figueroa et al 2011
Decreased mitochondrial membrane potnetial	Hughes and Gottshling 2012
Altered nuclear pore complexes	Lord et al 2015
Increased resistance to UV at age 8	Kale and Jazwinski 1996
Decreased Multidrug REsistance Transporter (Tpo1) activity	Eldakak et al 2010
Increased gluconeogenesis	Lin et al 2001
Decreased glycolysis	Lin et al 201
Occurrence of HSP104 foci	Unal et al 2011
Increased ROS levels (in 22% of population)	Lam et al 2011
Mitochondrial fragmentation	Hughes and Gottshling 2012
Aggregation of carbonyl-damaged proteins (HSP104 associated)	Erjavec et al 2007
Stress reporter MSN2/4 levels increase	Xie et al 2012
Reduced sporulation efficiency 16.7% instead of 69.8%	Boselli et al 2009
Loss of silencing at chromosome ends	Kim et al 1996
Detetable levels of ERCs	Lindstrom et al 2011
Enlarged nucleolus	Unal et al 2011
Daughters can be born as petites (lacking mtDNA)	Veatch et al 2009
Detection of glucose/energy-metabolism protein changes	Reverter-Branchat et al 2004
Detection of osidative stress response proteins	Reverter-Branchat et al 2004
Invagination of vacuolar membranes	Tang et al 2008
Over 50% of population has a random (nonaxial) budding pattern	Jazwinski et al 1998
Increase sterility mating frequency drops to 25% from 78%	Muller 1985
Accumulated ERCs	Sinclair and Guarente 1997
ROS detected to be localized at mitochondria	Laun et al 2001
Age-associated sterility	Smeal et al 1996
10-15% reduced lifespan of daughters	Kennedy et al 1994
Increase of cells with a G2/M DNA content (population level)	Feser et al 2010
Histone mRNA levels increase	Feser et al 2010
Histone protein levels decrease	Feser et al 2010
Increased ROS levels (in 22% of population)	Xie et al 2012
Chance of symmetric divisions between mother and daughter	Kennedy et al 1994
Amplification of the right segment of chromosome XII in 15% of cells	Hu et al 2014
Significant decrease of DNA breaks	Hu et al 2014
Two fold increase of retrotransposon DNA content	Hu et al 2014
Genomic translocations in rDNA	Hu et al 2014
Genomic translocations in mtDNa	Hu et al 2014
Four fold increase of mtDNA content	Hu et al 2014
Fuzzier nucleosome positioning	Hu et al 2014
Histone occupancy reduced 50%	Hu et al 2014
Decreased pheromone response 35% of cells respond to pheromone	Smeal et al 1996

Appendix 2 (written using Hallmarks from Appendix 1)

Standard questions (default apply to all of the below, in addition to specific questions)
- [[standard quantitative questions]]
  - By how much does this occur?
  - How do we know it occurs?
  - What genes control this phenotype when expressed?
    - How do they control this phenotype, physically?
  - Does inducing this specific phenotype in a non-aging organism lead to faster death?
  - Has anyone reversed this phenotype?
  - 4 most relevant publications showing this
  - What correlated things would you expect to see if this were true?
  - What physically causes this?
  - At what age was it first noticed?
  - Does it appear in all members of the population? Has a single-cell analysis been done?
  - How does it change over the lifetime of the organism?
  - Does this have predictive power for death?
  - Does this impair an obvious necessary function of the organism? To what degree?
  - What is the variability in this phenotype?
- [[organelle quantitative questions]]
  - Diameter
  - Shape
  - How many in a cell
  - Lipid composition
  - Membrane protein composition
  - Internal composition
    - Density
    - pH
    - Macromolecular breakdown
  - What is it continuous with
    - How leaky is it to this thing
  - What is the flux of what across the cell membrane?
  - How was it first discovered?
  - What do we know that it does, today?
  - How do we look at it? How has that changed?
  - What is it tethered to?
  - What does it exchange membrane with?
  - What bounces off its cell surface by temporarily binding but stays on the outside?
  - How variable is it between cells?
  - How often it fuses with itself
    - How often it fissions with itself
    - How often it fuses/fissions with other organelles
  - Can we isolate it from the cell?
  - Under what conditions do the above parameters really change?
  - What are the major labs that study this?
  - What are recently published techniques about this? What techniques would all labs want with regard to this?
- [[protein quantitative questions]]
  - What is the protein concentration in the cell?
  - How is it degraded? At what rate is it degraded?
  - Does the protein lose function over time?
    - What causes this if so?
  - How much is it expressed?
  - What environmental signals do we know to change this protein concentration?
  - What directly turns on and off expression of the mRNA for this protein?
  - What known post-translational modifications does this protein have?
  - How does expression change with time?
  - How many genes encode for this protein?
Cell size increases
- By how much does this occur?
- How do we know it occurs?
- What genes control this phenotype when expressed?
  - How do they control this phenotype, physically?
- Does inducing this specific phenotype in a non-aging organism lead to faster death?
- Has anyone reversed this phenotype?
- 4 most relevant publications showing this
  - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167394
- What correlated things would you expect to see if this were true?
  - Do things increase or decrease in concentration?
    - https://science.sciencemag.org/content/338/6108/822.abstract
  - Do old yeast take in nutrients in the same way? Is the flux higher?
  - When they get bigger does their composition change? Are they more dilute?
  - What does their cell surface look like?
    - Is it stretched?
    - Is it the same thickness?
    - Did they make more of it?
    - Is the protein density different?
    - Is the organelle density different?
  - Does the nucleus also get bigger?
  - Do the cells get a bit bigger after each division? Is there a gene that can modulate that size difference?
  - Does the bud scar have anything to do with it?
  - Is it the cell wall vs inside of the cell
  - Do you ever see a bud come from the middle of a scar?
  - Does the cell wall become more porous at all?
    - What does it mean for the cell wall to become porous, what has holes in it?
    - How many proteins thick is the cell wall?
    - When something buds off, how does the cell wall deal with that?
      - If you got rid of all the chitin would the cell wall be okay?
      - How stiff is the cell wall in an older cell?
      - What is the pressure like of an older cell, does it get more or less?
      - pH?
      - How is an old cell transcriptionally and protein-wise different from a young cell?
      - Why can’t an old cell make another daughter?
      - Do daughters know how old the mother is?
      - Do cells ever try to half-make a daughter and fail?
      - Can you regenerate an old cell right when it really thinks it can’t make daughters anymore?
      - How long can a cell just still be metabolically active after it stops making daughters?
      - Do cells have some specific thing that happens at death like increased porosity or no more transcription?
  - How often do spores die?
    - Quiescent cells?
- What physically causes this?
- At what age was it first noticed?
- Does it appear in all members of the population? Has a single-cell analysis been done?
- How does it change over the lifetime of the organism?
- Does this have predictive power for death?
- Does this impair an obvious necessary function of the organism? To what degree?
- What is the variability in this phenotype?
Vacuole size increases
- When does this start happening? Do the number of lipids change? Does the pressure change? Does everything inside of it get more dilute? How continuous is the vacuole with the cytosol? What causes the increase of size? Does the vacuole divide to create a new daughter vacuole? How is the new daughter vacuole created if not? What proteins are in the vacuole membrane, and what lipids? Can we isolate vacuoles? How big is a vacuole (~2um?). How much does vacuole size vary with cell size? How does it vary with conditions cells have experienced? How does it vary with age? Do any things obviously accumulate in the vacuole with age? What genes regulate vacuole size? Does the vacuole ever break open? How is the inside of the vacuole different from the outside? How was the vacuole first discovered? Do cells ever have multiple vacuoles? Do mutant cells ever have multiple vacuoles? What structure is the vacuole derived from? How is the vacuole made? Are there vacuole-specific proteins? What is the flux of things across the vacuole membrane? How does the vacuole relate to the outside of the cell? What is the vacuole analogous to in humans? Can cells exchange vacuoles? Do vacuoles play any role in cell-cell signaling? What other organelles do vacuoles signal to? What are vacuoles tethered to in the cell?
Decreased resistance to mutagen (EMS)
- [[standard quantitative questions]]
- What does it look like to have decreased resistance to a mutagen?
  - Does it mean death in response is increased?
  - Is DNA more damaged in response?
  - What other things are more damaged in response?
- What is EMS physically binding to?
- What does the DNA repair pathway look like in cells that have been treated with EMS?
  - What does the [[yeast DNA repair pathway questions]] look like in general? How well have we characterized it?
  - How does resistance to mutagenesis change with age?
- How do other DNA repair pathways change with aging? How does mutation load change with aging?
- By how much does EMS increase the average amount of mutagenesis?
- How was EMS first discovered?
  - What else does it do?
Increased stress resistance (and trehalose production gene)
- What kind of stress is the cell more resistant to?
- Does this continue through the end of life, monotonically? What kinds of stress is the cell less resistant to?
- How is stress resistance measured?
  - Instant death?
  - Lifespan?
  - Ability to turn on genes in annotated stress-response pathways?
- What is the therapeutic window for stress resistance?
- How much additional resource does the cell put towards increased stress resistance?
  - Is this physiologically relevant? Could the cell maintain this normally?
- What kinds of stresses does the cell normally encounter?
- Why is the cell physically more stress resistant?
Vacuolar pH decreases
- See vacuolar questions above
- Does the vacuole have a proton pump?
  - If so, do it's levels change with age?
- Does the vacuole fuse with things?
- Can protons diffuse across the vacuole membrane?
- What can reverse the phenotype of vacuolar pH decreasing?
- If you put alkaline in the vacuole, what does it do?
- What would decreasing pH be expected to do to protein function of things in vacuole?
- What other things in vacuole are regulated by pH?
- How was it discovered that enzymes more active in a low pH-environment might be less liable to harm a cell if released?
Oxidative protein damage (increased carbonyl levels)
- How is oxidative protein damage defined?
- How is oxidative protein damage measured?
- In which compartments does it increase?
- Where would oxidative protein damage be likely to occur?
- What agents oxidatively damage proteins?
  - Do these agents increase in frequency?
  - Does their location correlate to protein oxidation?
- What does oxidative protein damage mean?
- Are there non-oxidative forms of protein damage?
  - If so, do those also increase?
- What is the baseline rate of protein oxidation?
- What is the baseline rate of fixing protein oxidation?
  - How is protein oxidation fixed?
  - Is it directly recognized?
- Does oxidatively damaged protein net increase over time with age? When does this start to happen if so?
- How much can one protein be oxidatively damaged?
  - Beside the protein doing its normal thing less efficiently, what is bad about protein oxidative damage?
- What other things get oxidatively damaged in a cell?
  - What other ways are there to structurally impair things?
- Does oxidatively damaged protein aggregate?
- Does the cell have specific pathways for recognizing and eliminating oxidative damage?
- Is oxidative damage used by the cell for anything?
- Do any cellular reactions directly cause oxidative damage?
- Do any things not get oxidatively damaged that we would expect to see oxidatively damaged?
  - On a population scale, are all things oxidatively damaged roughly equally?
- Are parts of the cell particularly protected from oxidative damage?
- What are the most common oxidative damage-causing agents in a cell? How are they generated or how do they get in?
- Does the cell ever make more oxidative stress for a certain purpose?
- What is the half-life of agents that cause oxidative stress?
Decreased retention of oxidatively damaged proteins
- What are all the things that are asymmetrically segregated?
Increased histone H4K16 acetylation
- How do levels of histone acetylases/deacetylases/methylases change over time?
- Could you predict histone modification changes from net changes in enzymes which modify histones? If not, what might cause the gap?
- How do all histone marks change with age? How would you expect this to change DNA structure?
- Can you predict gene expression from histone marks? If not, how do histone marks give you more information than gene expression? Maybe a better overall heuristic for average gene expression over a certain time period - but potentially you could just measure this?
- What are all known yeast histone marks?
- How do they vary?
  - How often do they vary appreciably?
  - How do they vary during cell replication?
  - Do they vary on the order of minutes, hours, months?
- Do yeast have a DNA methylation age clock? If not, how useful are histone marks to predicting age?
- How do we look at histone marks? What would this method not catch? Can we correlate this to DNA structure and gene expression?
- How do histone marks physically affect gene expression?
  - Do they recruit other proteins? What are those proteins if so?
- How prevalent are the substrates of histone marks? Does their concentration ever limit the reaction?
- At a given time, how many histone-modifying enzymes are bound to DNA? How does this change with time? What DNA sequence controls where they bind?
- In what other ways is yeast DNA modified?
- Does yeast DNA have a 3D structure? How is this regulated?
- Have we done Hi-C in yeast? How else would you look at 3D DNA structure.
- Are histone modifications relevant for anything besides modulating gene expression?
  - Should it be possible for there to be a methylation clock but not a gene expression clock for aging?
- #notsatisfied
Decreased histone H3K56 acetylation
Mitochondrial redox potential declines
- What does the redox potential of the mitochondria mean?
- How is this related to mitochondrial function?
- #notsatisfied
Decreased mitochondrial membrane potential
- What causes the observed decrease in mitochondrial membrane potential in yeast?
- Does the membrane get more leaky?
- Does cytosol pH concentration change in a way that increases pH in the intermembrane space?
- Is there a decrease in net activity of the proteins in the membrane that should maintain this potential?
- Is there a decrease in density of proteins that should maintain this gradient?
- Does the mitochondria get bigger with cell age?
  - If so, does protein expression for complexes to maintain mitochondrial pH incease?
    - If not, does the ratio of protein complex activity to maintain pH with the size of the intermembrane space go down?
    - Would this decrease correspond to the difference in intermembrane potential?
  - Does mtDNA copy # increase?
- #notsatisfied
Altered nuclear pore complexes
- How many NPCs are there in a nucleus?
- Are they homogenously distributed?
- How often are NPCs turned over? How are they degraded?
  - How are NPCs damaged?
- How are nuclear pore complexes altered?
- Does their number decrease?
- Does the nucleus increase in size with age?
  - Does NPC expression increase proportionately if so?
  - What would regulate this?
- What activity do NPCs modulate? What goes through them? Are there different kinds of NPCs?
- Do NPCs have subunits? Can they be arranged in different ways? Does this change with age if so?
- Are nuclear pore complexes found anywhere except for the nucleus?
- How are nuclear pore complexes made? Where do they go to get to the nucleus?
  - If they need to go to non-nuclear places, are those places affected with age?
- Do nuclear pore complexes have post-translational modifications? What are they if so?
- How many different nuclear pore complex types are there?
- Do nuclear pore complexes do any active things? Do they bind to anything? What is associated to them?
- How do we track nuclear pore complexes?
- Do NPCs play any structural role in the cell?
- How were they first discovered? How were they first characterized?
- What does NPC complex expression respond to?
- Does the relative ratio of NPC complex parts change with age (and is it possible for the complex to have different stoichiometry?)
  - Does the expression of the different NPC components change in proportion to each other with age?
  - Does it always change in the same way if so?
- #notsatisfied
Increased resistance to UV at age 8
- What does it mean to have increased resistance to UV?
- Are certain stress response pathways turned on more?
- Is there less mutation?
- #notsatisfied
Decreased Multidrug REsistance Transporter (Tpo1) activity
- How do all genes change with age?
- What class of drugs does Tpo1 modulate resistance to?
- What are all the drug transporters in yeast? Do they all decrease in activity with age?
- Does Tpo1 have decreased expression, or decreased activity?
- [[protein quantitative questions]]
- #notsatisfied
Increased gluconeogenesis
- How much glycogen do yeast store?
- What % of glucose in yeast is in glycogen?
  - How much does this vary with environmental conditions?
  - What environmental conditions regulate this?
- Do yeast continuously do gluconeogenesis?
  - When do they do it if not?
- #notsatisfied
Decreased glycolysis
- By how much does glycolysis decrease with age?
- What is the flux through the glycolysis pathway normally, in glucose / second?
- What other pathways take metabolites from the glycolysis pathway? How do they very?
- What regulates glycolysis?
  - Is there one or a set of trasncription factors that proportionally regulate the expresion of glycolysis proteins?
  - Does the relevant amount of proteins in glycolysis change with age?
- What causes the decrease in glycolysis? Are all protein components expressed at the same amount?
  - Are all protein components expressed at the same density?
- Do all protein components function as efficiently as they did?
  - How do proteins in the glycolysis pathway get damaged?
  - What is the average damage level of a protein in the glycolysis pathway with aging?
  - Does the cytosol change with age?
    - If so, would that change affect the function of these proteins?
- Do the balances of metabolites for each of the reactions change over time?
  - How so?
- How do we measure the decrease in glycolysis with age?
- Does glucose density in the cell change with age?
  - What transports glucose into/out of the cell? Does that change with age?
- How does the end product of glycolysis change in concentration with age?
- #project is it possible to work backwards from the change in concentration of the metabolites involved in each reaction, to see if the rate of any of the proteins involved would be expected to change with time?
- #notsatisfied #otherreasons #mapfullpathway
Occurrence of HSP104 foci
- What is an HSP104 foci?
- How big are these foci?
- How many are there?
- Do all cells have them?
  - If not, what % of cells have them?
- How does the occurrence of HSP104 foci change with age?
- How many proteins are in them?
- What characterizes a protein in this state?
- Do any proteins or processes degrade HSP104 foci?
- Do all cells get HSP104 foci?
- Are these foci ever excreted?
- How are HSP104 foci segregated between mother and daughter cell?
- Do they have any proposed functional role?
- How were they first identified?
- Where are the foci located in the cell?
  - Are they tethered to anything?
  - Does anything bind to them?
- How are HSP104 foci characterized?
- Are foci inherited?
- How do foci grow?
- What is the baseline # of HSP104 proteins in a cell?
  - Does this number or concentration remain the same with age?
    - If not, how does it change?
- Does the concentration or number of HSP104 proteins in a cell that are not in foci remain the same independent of foci?
- Do any other proteins form foci?
- What is the rate of foci growth?
  - What cellular factors does this rely upon?
- What proteins form prions in the cell? What controls this?
- #notsatisfied #prionquestions
Increased ROS levels (in 22% of population)
- What is ROS? How many chemical structures are covered by this word?
- By how much does ROS increase? What does this look like over age?
- How would you expect this to affect protein oxidation levels?
  - Do you see this effect?
- What causes the increase in ROS levels?
  - Do we know what things create ROS?
  - If we know some of them, does their level of activity increase with age?
- Are there some cells in which ROS does not increase?
- Should mitochondrial stress in some way be proportional to ROS production?
- What quenches ROS once it is produced?
  - How do these processes work?
- #notsatisfied #moremechanismquestions
Mitochondrial fragmentation
- How is this measured?
- By how much does this increase?
  - How many fragments do you see, with age?
- Does this happen across cells?
- Does mitochondrial fragmentation affect mitochondrial efficiency, or is the internal membrane surface area essentially the same?
- Does mitochondrial fragmentation increase the flux of metabolites from the cytosol?
  - Is there ever a delay here?
- Are there any cells in which more fusion is instead detected?
- Does mitochondrial composition change with age?
- When does the mitochondria fragment normally?
- Is mitochondrial fragmentation thought to provide some kind of functional benefit?
- What proteins might regulate mitochondrial fragmentation?
- #notsatisfied
Aggregation of carbonyl-damaged proteins (HSP104 associated)
- How is aggregation of carbonyl-damaged proteins detected?
- What does it mean for a protein to be carbonyl-damaged?
- What is the approximate level of carbonyl-damaged proteins in the cell?
  - How much carbonyl damage does the average protein have?
    - What is the variability in this?
  - Is it normally in the same place?
  - What other kinds of damage occur to proteins?
- Can yeast remove carbonyl damage from proteins?
  - How, if so?
  - How active is this pathway normally?
- #notsatisfied
Stress reporter MSN2/4 levels increase
- What does this mean
- #notsatisfied
Reduced sporulation efficiency 16.7% instead of 69.8%
- What is sporulation efficiency?
- If sporulation efficiency decreases, does this mean that cells that do sporulate are selected to maybe be more healthy?
  - #sporulation
- #notsatisfied
Loss of silencing at chromosome ends
- How much is silencing lost?
- Does this result in new expression?
  - What does the expressed RNA do, if so?
- Does this render the chromosome ends more liable to some form of DNA reorganization?
  - What, if so?
- #notsatisfied #physicalquestions
Detetable levels of ERCs
- What is an ERC?
- How big is it?
- Is the sequence always the same?
- How many ERCs are there in a young cell?
  - How many in an old cell?
- Do ERCs increase in all cells?
- Is there any correlation between ERC # and probability of death?
- Do any mutants not show ERC increase?
- Do ERCs replicate independently of the genome?
- Could any enzymes extract ORIs from ERCs if so?
- At what rate do ERCs divide?
  - Is this the same between budding and non-budding cells?
- In cells with a lot of ERCs, what % of the cell volume is taken up by ERCs?
- #notsatisfied #physicalquestions
Enlarged nucleolus
- What is the nucleolus?
- What characterizes the nucleolus?
- By how much does it increase in size?
- Is there just one?
- What adds in mass to the nucleolus to make it increase in size?
  - Does the average amount of each normal component of a nucleolus increase by the same proportionate amount?
- #notsatisfied #moremechanismquestions
Daughters can be born as petites (lacking mtDNA)
- How often are daughters born as petites?
  - How does this increase with age?
- Do petites have a different replicative or chronological lifespan to normal?
- What does mitochondrial flux in a petit look like vs normal?
- #nosatisfied
Detection of glucose/energy-metabolism protein changes
- What does this mean?
Detection of oxidative stress response proteins
- Which proteins?
- By how much do the increase?
- [[protein quantitative questions]]
Invagination of vacuolar membranes
- What physically causes this?
- By how much do they invaginate?
- Is there a structure holding them in place?
- How many invaginations are there in the membrane?
- Are they equally spread across the membrane?
- Does this cause an increased flux over the vacuolar membrane?
- #notsatisfied #physicalquestions
Over 50% of population has a random (nonaxial) budding pattern
- What is the normal budding pattern?
  - What enforces it?
  - Are these proteins and metabolites expressed at the same concentration in aged cells?
  - If you look at the cells that do and don't show this non-axial pattern, is this related to the expression of proteins and metabolites in the relevant pathway?
- #notsatisfied
Increase sterility mating frequency drops to 25% from 78%
- Can repeated attempts at mating with the same yeast eventually lead to mating?
- Does the expression of any gene fix this?
- Does increased concentration of any mating factors fix this?
- Are there any obvious phenotypes in the morphology of cells that cannot mate?
- #notsatisfied #moremechanismquestions
Accumulated ERCs
- See ERC questions above
ROS detected to be localized at mitochondria
- See ROS questions above
- Is ROS normally not in mitochondria?
- Does the ratio of ROS in the mitochondria vs not change?
- Is the ROS in the inner compartment, or the intermembrane compartment?
- Can ROS diffuse between the cytosol and the intermembrane compartment?
Age-associated sterility
- see mating questions above
- #notsatisfied
10-15% reduced lifespan of daughters
- Does this always happen?
- Does this happen for the spores of certain aged cells?
- Does this happen to all old cells?
- What correlates to this?
- Do the daughters that show this phenotype have some phenotype in common?
- #notsatisfied #morephenotypequestions #physicalquestions
Increase of cells with a G2/M DNA content (population level)
- What is a G2/M DNA content?
- #notsatisfied #physicalquestions
Histone mRNA levels increase
- By how much do mRNA concentrations increase?
- Do all histone mRNA levels increase?
- Are there associated transcription factors whose levels have increased?
- Has the concentration increased?
- What have they increased relative to?
- #notsatisfied
Histone protein levels decrease
- By how much do histone protein levels decrease?
- Do all histone protein levels decrease?
- Are there fewer nucleosomes in the cell?
- Is there generally more expression of genes in the cell?
- Is there more degradation of histone proteins? Is there less translation of histone mRNA?
- #notsatisfied #moremechanismquestions #physicalquestions
Increased ROS levels (in 22% of population)
- see ROS questions above
Chance of symmetric divisions between mother and daughter
- What does a symmetric division mean?
- Is there a pathway that causes this? Could this be induced in a mother from youth?
- #notsatisfied #moremechanismquestions
Amplification of the right segment of chromosome XII in 15% of cells
- By how much is it amplified?
- Are other chromosome segments amplified?
- Do these cells have higher mortality?
- #notsatisfied #moremechanismquestions
Significant decrease of DNA breaks
- How many DNA breaks are there normally?
- By how much is this decreased?
- How are DNA breaks detected?
- Is it clear whether the baseline level of DNA breaks occurring is decreased, or the rate at which they are fixed increases?
- Do DNA breaks seem to correlate with some measure of transcriptional activity in DNA?
- Could DNA breaks actually be increasing in some way?
- #notsatisfied #moremechanismquestions
Two fold increase of retrotransposon DNA content
- What is the baseline level of retrotransposon activity?
- How many retrotransposons are there normally?
- is it the same in all cells?
- Does retrotransposon level predict death in some way?
- Are retrotransposons particularly present in some part of the cell?
- Would the increase in retrotransposon activity be likely to result in some amount of gene disruption?
  - How much, if so?
- #notsatisfied #moremechanismquestions
Genomic translocations in rDNA
- What is this?
- #notsatisfied #moremechanismquestions
Genomic translocations in mtDNA
- What is this?
- #notsatisfied
- #moremechanismquestions
Four fold increase of mtDNA content
- Is this related to an increase in mitochondrial size?
- Is this true in all cells?
- Does this change the density of mtDNA in mitochondria?
- Is there any corresponding increase in mtDNA protein expression?
- What proteins are on mtDNA but not the nucleus?
- How is mtDNA divided between mother and daughter?
- How does the mutation load of mtDNA change with time?
- Is mtDNA tethered to anything?
- Is there any mtDNA outside of the mitochondria?
- In young mutants with increased mtDNA, what phenotype do we see?
- #reallynotsatisfied #moremechanismquestions #physicalquestions
Fuzzier nucleosome positioning
- What does this mean?
  - Does this mean more movement in nucleosome positioning?
- By how much has this increased?
- Is it true of all nucleosomes?
- Is it related to transcriptional activity at the site?
- #notsatisfied
Histone occupancy reduced 50%
- What does this mean?
- #notsatisfied #moremechanismquestions
Decreased pheromone response 35% of cells respond to pheromone
- What does this mean?
- By how much is it decreased?
- Does this correspond to anything interesting in those cells with the decreased response?
- Are the cells with decreased mating response more likely to show sterility than those without?
- What protein normally detects pheromone?
- Does the concentration of this protein change with age?
- What does the cell normally do in response to pheromone?
- How much pheromone do older cells secrete?
- #notsatisfied #moremechanismquestions
Concepts
- [[yeast DNA repair pathway questions]]
  - How many proteins are known to be part of the yeast DNA repair pathway?
  - How many different ways is DNA repaired?
    - What do each of these different ways do?
    - What is the efficiency of each of these different ways?
    - What is the rate at which errors are repaired incorrectly in each of these different ways?
  - What is the baseline rate of DNA mutation in non-budding cells?
    - In budding cells?
      - What is the error rate of the normal yeast DNA polymerase?
      - How does DNA repair machinery affect this?
      - Are there less error-prone DNA polymerases?
      - Do we know of any essentially perfect DNA polymerases?
        
        If not, why not?
        
        Is there a source of thermal noise that prevents this?
      - Is there a tradeoff between speed and fidelity in DNA replication? If not, is there another tradeoff?
    - What causes DNA mutation in non-replicating cells?
  - How do we measure the baseline rate of mutagenesis?
    - What mutagensis would this obviously not catch, if any?
  - What causes mutagenesis?
    - Are UV rays relevant here? If so, if we shield yeast from UV rays, what happens?
    - Is thermal noise related to bond strength relevant? If we used nucleotides with a higher differnetial in bond strength, what would happen? Would there be negative effect related to the change in energy required to unzip DNA across the cell?
  - Are parts of DNA more targeted for mutagenesis than others?
  - Is there asymmetric seggregation of chromatids between mother and daughter?
  - Is DNA somehow repaired more during sporulation or budding?
  - If you could specify any machine in order to make DNA less liable to mutagenesis, what would you specify?
    - Is it possible for us to make this?
  - What DNA repair enzymes are people trying to make?
  - #project how does the division of yeast relate to how mutagenic it is?
    - How do populations of yeast diverge genetically over time?
    - How many mutations on average does it take for a yeast to become unable to divide?
    - How many mutations on average does a non-dividing yeast have per second or hour?
    - How many mutations does a dividing yeast have per division?
    - What is the ratio between the two?
    - Are important regions of the genome more protected?
    - How often does a yeast in a population become unable to divide further because of a mutation?
      - Is this ever fixed?
    - Are mutations to DNA repair or lethal mutations the only mutations that seem irreverslble?
      - Is there still a way to reverse them?
    - How often does a cell get better because it mutates?
    - Is mutation used for any non-obvious purpose? How important is it to allow a yeast population to adapt? How often does the genome of a population shift? How often in a way that seems selected for?
    - Given the above, when would a non-dividing cell be expected to die, on average? Is that what we see?
    - Does mutation rate change depending on rate of metabolism? What other things affect mutation rate?
  - Do yeast pass plasmids to each other?
Other
- What other things are there in the cell that could increase, but aren't covered by the above?

Appendix 3 (pulled from https://bionumbers.hms.harvard.edu/search.aspx, extracted with pandas read_html)

bion_id

Properties

Organism

Value

Range

Units

Reference

Reference PubMed ID

Primary Source

Primary Source PubMed ID

Measurement Method

Comments

Entered By

Keywords

179

100202

median length of a yeast RNA molecule

Budding yeast Saccharomyces cerevisiae

1474

nucleotides

Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365â1374. 2005

15758206

Wang et al. 2002 Arava et al. 2003 Ghaemmaghami et al. 2003 Huh et al. 2003).

Ron Milo - Admin

ribonucleic acid, transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

180

100203

Median cost of precursor synthesis per nucleotide [~P]

Budding yeast Saccharomyces cerevisiae

49.3

ATP

Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365â1374. 2005

15758206

Wang et al. 2002 Arava et al. 2003 Ghaemmaghami et al. 2003 Huh et al. 2003).

derived from the base composition of yeast-coding regions, in units of phosphate bonds (ATP)

Ron Milo - Admin

nucleic acid, Adenosine TriPhosphate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

181

100204

Median mRNA abundance

Budding yeast Saccharomyces cerevisiae

1.2

unitless

Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365â1374. 2005

15758206

Wang et al. 2002 Arava et al. 2003 Ghaemmaghami et al. 2003 Huh et al. 2003).

Ron Milo - Admin

copy number, messenger ribonucleic acid,transcript,transcriptome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

182

100205

Median mRNA half life

Budding yeast Saccharomyces cerevisiae

min

Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30 99(9):5860-5 free online article p.5862 left column 2nd paragraph

11972065

Abstract: "By using DNA microarrays, researchers precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II." P.5860 left column bottom paragraph: "Determination of mRNA Decay by Transcriptional Shut-Off Assay: [Yeast strain] Y262 was grown in 500 ml of yeast extract/peptone/dextrose (YPD) medium at 24°C to OD600 â¼0.5. The temperature of the culture was abruptly shifted to 37°C by adding an equal volume of YPD medium that had been prewarmed to 49°C. Aliquots of the culture (100 ml) were removed at 0, 5, 10, 15, 20, 30, 40, 50, and 60 min after the temperature shift. Cells were rapidly harvested on a nitrocellulose filter (Whatman no. 141109) followed by immediate freezing in liquid N2. Total RNA was prepared from cells harvested at each time point by hot phenol extraction (ref 16)." P.5860 right column bottom paragraph: "A nonlinear least squares model was fit to determine the decay rate constant (k) and half-life (t1/2) of each mRNA. The decay rate constant, k, is the value that minimized Si = 1,n[y(ti) - exp(-k×ti)]^2, where y(t) is the mRNA abundance at time t and the summation is taken over all observations for the particular mRNA. The half-life is t1/2 = ln2/k. The goodness of fit of the decay model for each gene was assessed with the F statistic (ref 20), based on the null hypothesis that the data fit a first-order decay model. A bootstrap method was used to calculate confidence intervals for both t1/2 and k (ref 21)."

P.5862 left column 2nd paragraph: "The half-lives of the 4,687 mRNAs analyzed varied widely, ranging from ~3 min to more than 90 min, with a mean of 23 min (BNID 105511) and median of 20 min (Fig. 2A). No simple correlation was found between the decay rates of mRNAs and their abundance (Cor. Coeff. = 0.06), the size of the ORF (Cor. Coeff. = â0.01), codon adaptation index (Cor. Coeff. = 0.04), or the density of ribosomes bound to the mRNA (Cor. Coeff. = 0.08) (Y. Arava, D.H., and P.O.B., unpublished data) (http://www-genome.stanford.edu/turnover)."

Ron Milo - Admin

constant, decay, degradation, messenger ribonucleic acid, transcript, transcriptome

183

100206

Median length of a yeast protein

Budding yeast Saccharomyces cerevisiae

385

Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365â1374. 2005

15758206

Wang et al. 2002 Arava et al. 2003 Ghaemmaghami et al. 2003 Huh et al. 2003).

For average length of 466 aa see BNID 105224

Ron Milo - Admin

size, macromolecule, polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

184

100207

Median cost of precursor synthesis per amino acid [~P]

Budding yeast Saccharomyces cerevisiae

30.3

ATP

Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365â1374. 2005

15758206

Wang et al. 2002 Arava et al. 2003 Ghaemmaghami et al. 2003 Huh et al. 2003).

The energy currency Wagner uses is the activated (high-energy) phosphate bond [~P]. The median length of a yeast protein is 385 amino acids (BNID 100206), with a combined biosynthesis and polymerization cost of 30.3 [~P] per amino acid.

Ron Milo - Admin

Energy cost, building block,monomer, protein, synthesis,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

185

100208

Median protein abundance

Budding yeast Saccharomyces cerevisiae

2460

Copies/cell

Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365â1374. 2005

15758206

Wang et al. 2002 Arava et al. 2003 Ghaemmaghami et al. 2003 Huh et al. 2003).

Ron Milo - Admin

macromolecule, enzyme, polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

214

100237

Number of genes

Budding yeast Saccharomyces cerevisiae

6604

ORF

SGD-Saccharomyces cerevisiae Genome, Saccharomyces cerevisiae Genome Snapshot, database http://www.yeastgenome.org/cache/genomeSnapshot.html retrieved June 22nd 2017

Top of page in link: "The Genome Snapshot, updated daily, provides information on the annotation status of the Saccharomyces cerevisiae genome. All data displayed on this page are available in one or more files on SGDâs download site. The YeastMine tool can be used to retrieve chromosomal features that match specific criteria." 6604 genes as of June 22nd 2017. 5885 genes according to Goffeau et al 1996, PMID 8849441. For 5616 protein coding genes see BNID 105444

Ron Milo - Admin

heredity, Genome, genetics

217

100240

Number of tRNA genes

Budding yeast Saccharomyces cerevisiae

299

unitless

http://www.yeastgenome.org/cache/genomeSnapshot.html

Better ref is needed

Ron Milo - Admin

aminoacylation, transfer ribonucleic acid,ribozyme<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

220

100243

Number of rRNA genes

Budding yeast Saccharomyces cerevisiae

~150

genes

M. Nomura, Regulation of ribosome biosynthesis in Escherichia coli and Saccharomyces cerevisiae: diversity and common principles. J Bacteriol. 1999 Nov181(22):6857-64. p.6862 left column top paragraph

10559149

P.6862 left column top paragraph: "There are three features of ribosomal DNA (rDNA) transcription in most eukaryotes that distinguish it clearly from rRNA synthesis in prokaryotes: (i) the use of a specific Pol I, (ii) the presence of tandemly repeated rRNA genes, and (iii) the presence of the nucleolus. Regarding the number of rRNA genes, E. coli has seven, four of which are located fairly close to the origin of replication but are not tandemly connected, whereas the yeast S. cerevisiae carries about 150 in tandem repeats."

Ron Milo - Admin

ribosomal ribonucleic acid phosphatase

229

100252

Percent of total transcription devoted to ribosomal RNA

Budding yeast Saccharomyces cerevisiae

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999 Nov24(11):437-40

10542411

Ron Milo - Admin

rRNA, fraction, ribosome, translation, machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

232

100255

RNA to DNA ratio

Budding yeast Saccharomyces cerevisiae

Unitless

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999 Nov24(11):437-40

10542411

Ron Milo - Admin

ribunucleic acid, deoxyribonucleic acid, nucleic acid, polymerase, Transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

235

100258

Fraction of total RNA that is ribosomal RNA

Budding yeast Saccharomyces cerevisiae

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999 Nov24(11):437-40

10542411

Ron Milo - Admin

rRNA, fraction, ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

238

100261

Percent of total RNA that is tRNA

Budding yeast Saccharomyces cerevisiae

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999 Nov24(11):437-40 p.437 left column bottom paragraph

10542411

See percent of rRNA/total RNA in yeast in range 80%-85% BNID 105192

Ron Milo - Admin

Fraction, transfer ribonucleic acid, ribozyme<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

239

100262

Diffusion rate of Phosphoglycerate kinase

Budding yeast Saccharomyces cerevisiae

63.8

Table link - http://bionumbers.hms.harvard.edu/files/Hydrodynamic%20properties%20of%20proteins%20of%20known%20structure.pdf

µm^2/sec

Squire PG, Himmel ME. Hydrodynamics and protein hydration. Arch Biochem Biophys. 1979 Aug196(1):165-77. p.167 table 1

507801

Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration

P.168 left column 4th paragraph: "The mean value for the 21 proteins (2-22) in Table I, is 0.53 g H2O/g protein, but the most remarkable observation is the extreme diversity of values calculated from hydrodynamic data of high quality on proteins of known dimensions."

Ron Milo - Admin

transferase enzyme, glycolysis

241

100264

Percent of total RNA that is mRNA

Budding yeast Saccharomyces cerevisiae

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999 Nov24(11):437-40 p.437 left column bottom paragraph

10542411

"The ratio of RNA to DNA in a rapidly growing cell of S. cerevisiae is 50:1 (indeed, the original name for RNA was âyeast nucleic acidâ). The approximate distribution of RNA is 80% rRNA, 15% tRNA and 5% mRNA." For mRNA fraction of total RNA of Ë3% (in unspecified organism) see Han & Lillard 2000 PMID 10994967 p.4076 right column 2nd paragraph

Ron Milo - Admin

messenger ribonucleic acid, fraction, Transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

243

100266

Number of cells in colony in YPD

Budding yeast Saccharomyces cerevisiae

1400000

Cells/colony

Joseph SB, Hall DW. Spontaneous mutations in diploid Saccharomyces cerevisiae: more beneficial than expected. Genetics. 2004 Dec168(4):1817-25 p.1820 right column top paragraph

15611159

P.1818 left column 4th paragraph: "MA [mutation-accumulation] line establishment and propagation: One hundred fifty-one MA lines were established from the ancestor. Each MA line was grown on YPD solid medium (1% yeast extract, 2% peptone, 2% dextrose, and 2% agar) at 30° and passaged by single-cell transfer." P.1818 right column 2nd paragraph: "[Researchers] estimated the average number of generations assuming exponential growth from counts of the number of cells per colony. The number of cells per colony was estimated approximately every seven transfers by choosing a single colony from each of 10 petri dishes. [They] then suspended the colony in 1 ml of water and estimated cell density using a hemacytometer. (Reichert Bright Line, 0.1 mm depth)."

P.1820 right column top paragraph: "For forty-eight of the 50 passages, average colony size was estimated to be 1.4×10^6 cells, which represents ~20.4 generations between passages, or one cell division every 141 min." YPD Medium is a blend of peptone, yeast extract, and dextrose in optimal proportions for growing most Saccharomyces cerevisiae strains.

Ron Milo - Admin

growth, concentration, YEPD, Yeast Extract Peptone Dextrose

244

100267

Number of ribosomes

Budding yeast Saccharomyces cerevisiae

187000

±56000 table link - http://bionumbers.hms.harvard.edu/files/Cellular%20RNA%20content%20and%20proportion%20of%20total%20RNA%20that%20is%20rRNA%20from%20several%20studies%2C%20and%20calculation%20of%20the%20cellular%20ribosome%20content.pdf

Ribosomes/cell

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 162:87 p6/14 table 1

18925958

[30] Warner JR. The economics of ribosome biosynthesis in yeast, Trends Biochem Sci. 1999 Nov24(11):437-40 and see refs beneath table

10542411

(For primary source [30], value of 200000 ribosomes/cell) Based on comparison of the size of the genome (1.4×10^7 bp) with the RNA in a ribosome (5469 nucleotides), and using ratio of DNA to rRNA

(For von der Haar ref above p.5 right column bottom paragraph:) "The RP [ribosomal protein] abundance distribution in figure 2 shows a mean abundance of 227,000 RPs per cell. Independent estimates for the cellular ribosome content have been generated by analysing the abundance of ribosomal RNA (rRNA) species in several studies [25-30], with reported values ranging from 150,000 to 350,000 copies of ribosomal RNA per cell for fast-growing haploid yeast strains. All of these studies were relying on relatively inaccurate estimates for the molecular weights of rRNAs derived from gel electrophoreses, and much of the variation in reported rRNA abundances derives from the fact that different estimates for this parameter were used. However, these studies also report the raw data for total cellular RNA content and the proportion of RNA that is rRNA, and rRNA abundances are therefore here re-calculated from these raw data based on the exact rRNA molecular weights from now available sequence information (table 1). The resulting estimate of 187,000 ± 56,000 rRNA copies per yeast cell can be usefully compared to the distribution of RP abundances in figure 2." See note under table. 300,000 ribosomes per generation given by Phizicky et al., 2010 PMID 20810645 p.1832 right column top paragraph (BNID 113860)

Ron Milo - Admin

translation machinery

247

100270

Characteristic generation time in rich medium

Budding yeast Saccharomyces cerevisiae

~100

minutes

JR Warner,The economics of ribosome biosynthesis in yeast,Trends Biochem Sci. 1999 Nov24(11):437-40. p.437 left column bottom paragraph

10542411

"Comparison of the size of the genome (1.4×10^7 bp) with the RNA in a ribosome (5469 nucleotides) shows that there are nearly 200,000 ribosomes per cell (Fig. 1a). With a generation time of ~100 min, the cell must produce 2000 ribosomes per min." Can reach ~70 minutes under ideal conditions (see BNID 101747). For 99 min see BNID 101310. See BNID 104 360

Ron Milo - Admin

doubling, division, Growth, cell cycle<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

251

100276

Gene duplication rate per gene per billion years

Budding yeast Saccharomyces cerevisiae

0.035

0.01 - 0.06

gene^-1*billion years^-1

Gao LZ, Innan H. Very low gene duplication rate in the yeast genome. Science. 2004 Nov 19 306(5700):1367-70.

15550669

A very low duplication rate in comparison to other organisms. For a general rate of gene duplication of 1%/gene/million years see Lewin, Genes IX p.101 fig.6.4

Ron Milo - Admin

DNA, genome, genotype<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

254

100279

Molecular mass of Phosphoglycerate kinase

Budding yeast Saccharomyces cerevisiae

45800

Table link - http://bionumbers.hms.harvard.edu/files/Hydrodynamic%20properties%20of%20proteins%20of%20known%20structure.pdf

Dalton

Squire PG, Himmel ME. Hydrodynamics and protein hydration. Arch Biochem Biophys. 1979 Aug196(1):165-77. p.167 table 1

507801

Calculated from covalent structure

Ron Milo - Admin

transferase, glycolysis, molecular weight, MW, Da, kDa

396

100427

Median haploid cell volume

Budding yeast Saccharomyces cerevisiae

±2

µm^3

Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M. Systematic identification of pathways that couple cell growth and division in yeast. Science. 2002 Jul 19 297(5580):395-400 p.398 table 1 bottom row 3rd column from left

12089449

(Supplementary material 1st paragraph:) "Cultures were grown overnight in XY medium (2% peptone, 1% yeast extract, 0.01% adenine, 0.02% tryptophan) containing 2% glucose, diluted ~300-fold into fresh medium and grown for at least 5 hours (which corresponded to three population doublings for wild-type) at 30°C to a final density of 0.3-3×10^7 cells/mL, a cell density range in which wild-type size distributions do not vary. To obtain each size distribution, 100µL of culture was diluted into 10mL of IsotonII, sonicated gently for 10s to disperse aggregated cells, and analyzed with a Coulter Channelizer Z2 (Beckman-Coulter). Cell size distributions were saved in a tabular form, as a function of cell counts in each of 256 size bins."

Doubling time of 87±6 min. For mean volume of 37 µm^3 see BNID 100430. See BNID 103715, 105103.

Ron Milo - Admin

unicellular eukaryote, Size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

399

100430

Mean haploid cell volume in exponential phase grown in YEP+glucose at 30°

Budding yeast Saccharomyces cerevisiae

31.1 - 40.6 Table Link - http://bionumbers.hms.harvard.edu/files/Population%20doubling%20time%2C%20percent%20budded%20cells%2C%20and%20mean%20cell%20volume%20for%20different%20batch%20culture%20media1.pdf

µm^3

Tyson CB, Lord PG, Wheals AE. Dependency of size of Saccharomyces cerevisiae cells on growth rate. J Bacteriol. 1979 Apr138(1):92-8. p.93 table 1

374379

The mean volume of a haploid yeast cell in exponential phase growing in YEP+Glucose at 30° [for composition of YEP see p.93 left column top paragraph]. Taken from cultures with different doubling times in range 75-84.2 min

P.93 left column bottom paragraph: "The data in Table 1 clearly show that mean size increases with growth rate, especially at the faster growth rates. There is a consistent relationship between cell size and growth rate for any one medium even when doubling times vary due to differences in separate batches of media." P.94 left column 2nd paragraph: "The percentage of budded cells decreases as growth rate decreases (Table 1), as has been observed before (refs 7, 22), and it is possible to calculate the duration of the budded phase using equation 5 (see Appendix)." For median cell volume of 42±2 µm^3 see BNID 100427. See table link for cell volumes on other media, BNID 105103.

Ron Milo - Admin

size

402

100433

Number of Zn ions in YPD

Budding yeast Saccharomyces cerevisiae

80000000

Unitless

Eide et al. Genome Biology 2005

Mike Springer

404

100435

Number of Se ions in YPD

Budding yeast Saccharomyces cerevisiae

60000000

Unitless

Eide et al. Genome Biology 2005

Mike Springer

406

100437

Number of S ions in YPD

Budding yeast Saccharomyces cerevisiae

500000000

Unitless

Eide et al. Genome Biology 2005

Mike Springer

408

100439

Number of P ions in YPD

Budding yeast Saccharomyces cerevisiae

5000000000

Unitless

Eide et al. Genome Biology 2005

Mike Springer

410

100441

Number of Ni ions in YPD

Budding yeast Saccharomyces cerevisiae

20000000

Unitless

Eide et al. Genome Biology 2005

Mike Springer

412

100443

Number of Na ions in YPD

Budding yeast Saccharomyces cerevisiae

200000000

Unitless

Eide et al. Genome Biology 2005

Mike Springer

414

100445

Number of Mn ions in YPD

Budding yeast Saccharomyces cerevisiae

500000

unitless

Eide et al. Genome Biology 2005

Mike Springer

416

100447

Nuclear volume (average)

Budding yeast Saccharomyces cerevisiae

2.9

µm^3

Jorgensen P, Edgington NP, Schneider BL, Rupes I, Tyers M, Futcher B. The size of the nucleus increases as yeast cells grow. Mol Biol Cell. 2007 Sep18(9):3523-32.

17596521

Morphometry: Image processing software (Particles8 Plus at http://rsb.info.nih.gov/ij/plugins/index.html) Image processing takes an image as an input and yields 1) another image - take a grayscale image and produce a color image, and (2) set of parameters as output- sphericity (minimal radius/maximal radius), Aspect ratio (feret (width)/breadth), etc.

SD 2% glucose medium, wild-type haploid cells. For fraction of nucleus out of total cell volume in yeast see BNID 104 708 and in HeLa cell see comments section of BNID 101402

Paul Jorgensen

Nucleus, Size, organelle<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

418

100451

Cell diameter

Budding yeast Saccharomyces cerevisiae

~3-6

µm

Ahmad MR, Nakajima M, Kojima S, Homma M, Fukuda T. The effects of cell sizes, environmental conditions, and growth phases on the strength of individual W303 yeast cells inside ESEM. IEEE Trans Nanobioscience. 2008 Sep7(3):185-93 DOI: 10.1109/TNB.2008.2002281 abstract

18779098

Abstract: "[Investigators] performed in situ measurements of mechanical properties of individual W303 wild-type yeast cells were performed by using an integrated environmental scanning electron microscope (ESEM)-nanomanipulator system."

Abstract: "Compression experiments to penetrate the cell walls of single cells of different cell sizes (about 3-6µm diameter), environmental conditions (600 Pa and 3 mPa), and growth phases (early log, mid log, late log and saturation) were conducted." See BNID 103896

Paul Jorgensen

radius, Dimensions, Sizes

419

100452

Cell volume

Budding yeast Saccharomyces cerevisiae

µm^3

Roskams and Rodgers, LabRef

Paul Jorgensen

Size,unicellular eukaryote<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

423

100457

Mutation rate per base pair per replication

Budding yeast Saccharomyces cerevisiae

2.20E-10

Table link - http://bionumbers.hms.harvard.edu/files/Mutation%20rates%20per%20genome%20per%20replication%20in%20microbes%20with%20DNA%20chromosomes.pdf

mutation/bp/replication

Drake JW, Charlesworth B, Charlesworth D, Crow JF. Rates of spontaneous mutation. Genetics. 1998 Apr148(4):1667-86. p.1670 table 4

9560386

The typical procedure is to estimate C (the reciprocal of the efficiency of mutation detection), then to calculate the mutant frequency f, then the mutation rate µt of the measured target sequence, then the mutation rate µbp of the average base pair (dividing µt by the size of the target sequence), then the mutation rate µg of the entire genome (multiplying µbp by the number of base pairs per genome).

"Mutation rates in DNA-based microbes: Rates of spontaneous mutation in this class of organisms were last surveyed in Drake (1991) and are summarized in Table 4 using a few updated values for genome sizes. Unlike the experimental and theoretical limits to the accuracy of the RNA-virus values, the DNA-microbe values were determined in well-studied systems using robust calculations, and the individual values are likely to be accurate to within two-fold. Table 4 shows that µb and G vary inversely and smoothly over nearly four orders of magnitude while µg remains constant. Given the paucity of general, constant values in evolutionary processes, this particular constant is strikingly robust." For description of parameters see http://bionumbers.hms.harvard.edu/files/Parameters%20used%20in%20describing%20the%20mutation%20process.pdf

Ron Milo - Admin

base, DNA, Mutation, Mutation Rates, pair, rate, replication<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

424

100458

Mutation rate per genome per replication

Budding yeast Saccharomyces cerevisiae

0.0027

Table link - http://bionumbers.hms.harvard.edu/files/Mutation%20rates%20per%20genome%20per%20replication%20in%20microbes%20with%20DNA%20chromosomes.pdf

mutation/genome/replication

Drake JW, Charlesworth B, Charlesworth D, Crow JF. Rates of spontaneous mutation. Genetics. 1998 Apr148(4):1667-86. p.1670 table 4

9560386

Ron Milo - Admin

DNA, genome, Mutation, Mutation Rates, rate, replication<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

425

100459

Genome Size

Budding yeast Saccharomyces cerevisiae

12100000

Base pairs

Goffeau A et al., Life with 6000 genes. Science. 1996 Oct 25 274(5287):546, 563-7. p. 564 table 2

8849441

P.546 left column: "The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through an international effort involving some 600 scientists in Europe, North America, and Japan. It is the largest genome to be completely sequenced so far (as of 1996, a record that [researchers] hope will soon be bettered) and is the first complete genome sequence of a eukaryote. A number of public data libraries nucleotide and protein sequence data from each of the 16 yeast chromosomes (refs 1-16) have been established (Table 1)."

Abstract: "The complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history." 12,068kbp according to table 2, top row, right-most value. The Budding yeast genome has 12,157,105 base pairs [12,071,326 Nuclear+85,779 mitochondrial] as of June 21st 2015 according to SGD http://www.yeastgenome.org/cache/genomeSnapshot.html

Ron Milo - Admin

DNA, heredity, genetic material

456

100490

Median cell size of a diploid budding yeast in glucose medium (S288c background)

Budding yeast Saccharomyces cerevisiae

µm^3

12089449

Paul Jorgensen

size, unicellular eukaryote<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

457

100491

Mean nuclear volume of a haploid budding yeast in glucose medium (S288c background)

Budding yeast Saccharomyces cerevisiae

2.9

±0.9

µm^3

Jorgensen P, Edgington NP, Schneider BL, Rupes I, Tyers M, Futcher B. The size of the nucleus increases as yeast cells grow. Mol Biol Cell. 2007 Sep18(9):3523-32. p.3527 table 2 top row

17596521

"Strains were propagated to log phase in synthetic medium with the indicated carbon source, and the area (A) of a nuclear cross-section was determined for n cells. All strains were in the S288c background and were congenic except at the noted alleles. Nuclear volume (V) was estimated under the assumption that each nucleus was spherical. Cell volume distributions were directly measured with a Coulter particle analyzer and a representative distribution was analyzed. The mean and SD of each distribution were calculated." Estimation from microscopic cross-sectional area

Value in range is SD

Paul Jorgensen

nucleus, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

611

100647

Number of metabolites and metabolic reactions in genome-scale reconstructed metabolic network

Budding yeast Saccharomyces cerevisiae

584 metabolites: 1175 reactions

Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003 Feb13(2):244-53 abstract, p.247 left column bottom paragraph & table 2

12566402

Abstract: "The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments and the environment were included."

Abstract: "A total of 708 structural open reading frames (ORFs) were accounted for in the reconstructed network, corresponding to 1035 metabolic reactions. Further, 140 reactions were included on the basis of biochemical evidence resulting in a genome-scale reconstructed metabolic network containing 1175 metabolic reactions and 584 metabolites." P.247 left column bottom paragraph: "The metabolic reconstruction process resulted in a network that consisted of 1175 metabolic reactions and 584 metabolites (Table 2)."

Paul Jorgensen

metabolites, metabolic compounds, metabolome, metabolomics, in silico model

612

100648

ORF transcriptome: expression levels, half lives and transcriptional freqency

Budding yeast Saccharomyces cerevisiae

Database link - http://tinyurl.com/5kbovl

http://web.wi.mit.edu/young/pub/orf_transcriptome.txt

Ron Milo - Admin

mRNA,levels,abundance,absolute,copies<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

869

104995

Number of distinct proteins in proteome

Budding yeast Saccharomyces cerevisiae

6237

Unitless

Müller A, MacCallum RM, Sternberg MJ. Structural characterization of the human proteome. Genome Res. 2002 Nov 12 (11):1625-41. Table link - http://bionumbers.hms.harvard.edu/files/Proteome%20size%20and%20number%20of%20proteins%20in%20each%20structural%20class%20in%20model%20organisms.pdf

12421749

A valuable tool in exploiting three-dimensional information is the databases of protein structure in which domains with similar three-dimensional architecture are grouped together. Here, we use the structural classification of proteins (SCOP)(Conte et al. 2000). In SCOP, protein domains of known structure that are likely to be homologs are grouped by an expert into a common superfamily based on their structural similarity together with functional and evolutionary considerations. SCOP is widely regarded as an accurate assess-ment of which domains are homologs. However, SCOP remains subjective and one cannot exclude the possibility that two domains placed within the same superfamily only share a common fold as a result of convergent evolution and therefore are not homologous.

Key words give superfamilies of SCOP (Structural Classification of Proteins). See value of 6,340 proteins in budding yeast in BNID 105464 table link - http://bionumbers.hms.harvard.edu/files/Numbers%20and%20mean%20lengths%20for%20proteins%20and%20pseudogenes%20in%20four%20eukaryotes.pdf

Uri M

SCOP, superfamily, budding yeast, Classic zinc finger, Immunoglobulin, EGF/laminin, P-loop containing nucleotide triphosphate, hydrolases, Fibronectin type III, Cadherin, RNA-binding domain, Protein kinase-like (PK-like), Hemeodomain-like, Spectrin repeat, PH domain-like, SH3 domain, EF-hand, Ankyrin repeat, Complement control module/SCR domain, PDZ domain-like, Ligand-binding domain of low-density lipoprotein receptor, Tetratricopeptide repeat (TPR), -finger domain, Trp-Asp repeat (WD-repeat), domain (Calcium/lipid-binding* domain, CaLB), NAD(P)-binding Rossmann-fold domains, ARM repeat, SH2 domain, Thioredoxin-like, C-type lectin-like, Glucocorticoid receptor-like (DNA-binding domain), ConA-like lectins/glucanases, Actin-like, ATPase domain, No. distinct proteins in proteome, No. distinct superfamilies in proteome, enzyme<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

871

104997

Turgor pressure (exponentially phase)

Budding yeast Saccharomyces cerevisiae

0.05

0.01

MPa

Martinez de Marañon I, Marechal PA, Gervais P. Passive response of Saccharomyces cerevisiae to osmotic shifts: cell volume variations depending on the physiological state. Biochem Biophys Res Commun. 1996 Oct 14 227(2):519-23.

8878546

jannis

turgor, osmotic, stress<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

872

104998

Turgor pressure (stationary phase)

Budding yeast Saccharomyces cerevisiae

0.2

0.04

MPa

8878546

jannis

turgor, osmotic, stress<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

951

105078

Mass of DNA in haploid cell (conditions of growth unknown)

Budding yeast Saccharomyces cerevisiae

0.017

Table link - http://bionumbers.hms.harvard.edu/files/Size%20and%20composition%20of%20yeast%20cells.pdf

pg/cell

Sherman F. Getting started with yeast. Methods Enzymol. 2002 350: 3-41. p.15 table V

12073320

P.15 bottom paragraph: "The sizes of haploid and diploid cells vary with the phase of growth (ref 64) and from strain to strain. Typically, diploid cells are 5 × 6µm ellipsoids and haploid cells are 4µm diameter spheroids (BNID 108257, 108258). The volumes and gross composition of yeast cells are listed in Table V. During exponential growth, haploid cultures tend to have higher numbers of cells per cluster compared to diploid cultures. Also, haploid cells have buds that appear adjacent to the previous one, whereas diploid cells have buds that appear at the opposite pole (ref 66)." pg=Picogram=10^-12 gram. P.15 2nd paragraph: ""Normal" laboratory haploid strains have a doubling time of 90 min in YPD medium and approximately 140 min in synthetic media during the exponential phase of growth." Optimal growth temperature for yeast is 30°C. See BNID 105079,105080,105081,105082,105083

Uri M

deoxyribonucleic acid, weight

952

105079

Mass of DNA in diploid cell (conditions of growth unknown)

Budding yeast Saccharomyces cerevisiae

0.034

Table link - http://bionumbers.hms.harvard.edu/files/Size%20and%20composition%20of%20yeast%20cells.pdf

pg/cell

Sherman F. Getting started with yeast. Methods Enzymol. 2002 350: 3-41. p.15 table V

12073320

P.15 bottom paragraph: "The sizes of haploid and diploid cells vary with the phase of growth (ref 64) and from strain to strain. Typically, diploid cells are 5 × 6µm ellipsoids and haploid cells are 4µm diameter spheroids (BNID 108257, 108258). The volumes and gross composition of yeast cells are listed in Table V. During exponential growth, haploid cultures tend to have higher numbers of cells per cluster compared to diploid cultures. Also, haploid cells have buds that appear adjacent to the previous one, whereas diploid cells have buds that appear at the opposite pole (ref 66)." pg=Picogram=10^-12 gram. The sizes of haploid and diploid cells vary with the phase of growth and from strain to strain. Optimal growth temperature for yeast is 30°C. See BNID 105078,105080,105081,105082,105083

Uri M

deoxyribonucleic acid, genetic material, content, DNA, weight

953

105080

Mass of RNA in diploid cell (conditions of growth unknown)

Budding yeast Saccharomyces cerevisiae

1.9

pg/cell

Sherman F. Getting started with yeast. Methods Enzymol. 2002 350: 3-41. Table link - http://bionumbers.hms.harvard.edu/files/Size%20and%20composition%20of%20yeast%20cells.pdf

12073320

pg=Picogram=10^-12 gram. The sizes of haploid and diploid cells vary with the phase of growth and from strain to strain. Optimal growth temperature for yeast is 30°C. See BNID 105078,105079,105081,105082,105083

Uri M

ribonucleic acid,weight<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

954

105081

Mass of RNA in haploid cell (conditions of growth unknown)

Budding yeast Saccharomyces cerevisiae

1.2

Table link - http://bionumbers.hms.harvard.edu/files/Size%20and%20composition%20of%20yeast%20cells.pdf

pg/cell

Sherman F. Getting started with yeast. Methods Enzymol. 2002 350: 3-41. p.11 table V

12073320

pg=Picogram=10^-12 gram. "Normal" laboratory haploid strains have a doubling time of 90 min in YPD medium and approximately 140 min in synthetic media during the exponential phase of growth. Optimal growth temperature for yeast is 30°C. See BNID 105078,105079,105080,105082,105083

Uri M

weight, ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

955

105082

Mass of protein in haploid cell (conditions of growth unknown)

Budding yeast Saccharomyces cerevisiae

pg/cell

Sherman F. Getting started with yeast. Methods Enzymol. 2002 350: 3-41. Table link - http://bionumbers.hms.harvard.edu/files/Size%20and%20composition%20of%20yeast%20cells.pdf

12073320

Uri M

weight<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

956

105083

Mass of protein in diploid cell (conditions of growth unknown)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Size%20and%20composition%20of%20yeast%20cells.pdf

pg/cell

Sherman F. Getting started with yeast. Methods Enzymol. 2002 350: 3-41. p.15 table V

12073320

P.15 bottom paragraph: "The sizes of haploid and diploid cells vary with the phase of growth (ref 64) and from strain to strain. Typically, diploid cells are 5 x 6-µm ellipsoids and haploid cells are 4-µm diameter spheroids (ref 65). The volumes and gross composition of yeast cells are listed in Table V. During exponential growth, haploid cultures tend to have higher numbers of cells per cluster compared to diploid cultures. Also, haploid cells have buds that appear adjacent to the previous one, whereas diploid cells have buds that appear at the opposite pole (ref 66)." pg=Picogram=10^-12 gram. The sizes of haploid and diploid cells vary with the phase of growth and from strain to strain. Optimal growth temperature for yeast is 30°C. See BNID 105078,105079,105080,105081,105082

Uri M

Ribonucleic acid, content, macromolecule, weight

963

105090

Median mutational variance in gene expression

Budding yeast Saccharomyces cerevisiae

4.70E-05

(Substitution/generation)^2

Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. Genetic properties influencing the evolvability of gene expression. Science. 2007 Jul 6 317(5834):118-21

17525304

Researchers performed a mutation-accumulation (MA) experiment (Fig. 1A) in S. cerevisiae in order to isolate the contribution of the mutational process to gene expression evolution.With serial transfer of random colonies, they accumulated spontaneous mutations by maintaining parallel lines with effective population sizes of ~10 individuals. The lines diverged from an isogenic common ancestor for 4000 generations. They estimated the Vm of gene expression for genes that showed significant statistical differences (Bayesian posterior probability > 0.99) in expression among any pair of the four MA lines by using logtransformed relative expression levels.

The rate of phenotypic evolution due to mutation alone can be measured by the mutational variance (Vm), which is defined as the increase in the variance of a trait introduced by mutations each generation. It can be calculated from the variance of traits among MA (mutation accumulation) lines. For haploid asexual organisms, Vm = 2sb^2/t, where sb^2 is the between-line variance and t is the number of generations. See BNID 105091

Uri M

mutation, selection, gene alteration, DNA<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

967

105094

Volume of cell occupied by water

Budding yeast Saccharomyces cerevisiae

Jerry W. King, Gary R, Supercritical fluid technology in oil and lipid chemistry, 1996, American Oil Chemists' Society, p.303 2nd paragraph

Masamichi Kamihira, Masayuki Taniguchi and Takeshi Kobayashi, Sterilization of microorganisms with supercritical carbon dioxide, Agric. Biol Chem., 51 (2), 407-412, 1987 p.410 left column bottom paragraph

P.303 2nd paragraph: "Table 14.11 shows the results of sterilizing enzyme preparations with SC-CO2 at 20 MPa and 35ËC for 2 h. After wet E. coli (water content: 74%) or bakerâs yeast (water content: 68%) was mixed with crude, dry Î±-amylase or lipase at a weight ratio of 9:1, the microorganisms in the enzyme preparations could be sterilized with SC-CO2." For water fraction by volume in E. coli and mammalian cell see BNID 100044 and 103960 respectively. For water fraction by mass in yeast see BNID 103689

Uri M

content, H2O, universal solvent

975

105102

Fraction of cells that budded for different batch culture media

Budding yeast Saccharomyces cerevisiae

Table Link - http://bionumbers.hms.harvard.edu/files/populationtyson1978.pdf

Tyson CB, Lord PG, Wheals AE. Dependency of size of Saccharomyces cerevisiae cells on growth rate. J Bacteriol. 1979 Apr138(1):92-8.

374379

The mean size and percentage of budded cells of a wild-type haploid strain of Saccharomyces cerevisiae grown in batch culture over a wide range of doubling times (tau) have been measured using microscopic measurements and a particle size analyzer.

Smallest fraction of cells that budded 36.7% on MM1+glycerol. Largest fraction of cells that budded 88.6% on YEP+glucose.

Uri M

%, YEP, fructose, glucose, sucrose, mannose, maltose, raffinose, sorbitol, gluconate, galactose, glycerol, mannitol, trehalose, MM1, MM2, MM3, MM4, EMM, acetate, citric acid, phthalate, generation, time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

976

105103

Mean cell volume for different batch culture media

Budding yeast Saccharomyces cerevisiae

Table Link - http://bionumbers.hms.harvard.edu/files/populationtyson1978.pdf

Tyson CB, Lord PG, Wheals AE. Dependency of size of Saccharomyces cerevisiae cells on growth rate. J Bacteriol. 1979 Apr138(1):92-8. p.93 table 1

374379

P.93 left column bottom paragraph: "The data in Table 1 clearly show that mean size increases with growth rate, especially at the faster growth rates. There is a consistent relationship between cell size and growth rate for any one medium even when doubling times vary due to differences in separate batches of media." P.94 left column 2nd paragraph: "The percentage of budded cells decreases as growth rate decreases (Table 1), as has been observed before (refs 7, 22), and it is possible to calculate the duration of the budded phase using equation 5 (see Appendix)." Smallest volume 15.9 µm^3 on YEP+sorbitol medium. Greatest volume 42.5 µm^3 on YEP+fructose. See BNID 100427, 100430

Uri M

999

105126

Concentration of steady-state free Ca(2+) in endoplasmic reticulum

Budding yeast Saccharomyces cerevisiae

µM

Strayle J, Pozzan T, Rudolph HK. Steady-state free Ca(2+) in the yeast endoplasmic reticulum reaches only 10 microM and is mainly controlled by the secretory pathway pump pmr1. EMBO J. 1999 Sep 1 18(17):4733-43.

10469652

Researchers developed a yeast ER Ca2+ probe based on aequorin, a Ca2+ photoprotein that emits light when exposed to Ca2+ in the presence of its prosthetic group coeleterazine.

Article describes in vivo measurements of free Ca2+ in the lumen of the yeast ER using a protein chimera which consists of the Ca2+ sensitive photoprotein aequorin fused onto Stt3, an ER resident oligosaccharyl transferase subunit. Measurements with this sensor reveal a steady state free Ca2+ level of ~10µM for the yeast ER, a concentration significantly lower than free Ca2+ in the mammalian ER. See BNID 103966, 101700

Uri M

calcium, ER, organelle, metal ion, cofactor, coenzyme, signal transduction<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1047

105175

Distance between ER membranes

Budding yeast Saccharomyces cerevisiae

±5

Bernales S, McDonald KL, Walter P. Autophagy counterbalances endoplasmic reticulum expansion during the unfolded protein response. PLoS Biol. 2006 Nov4(12):e423. p.2313 left column

17132049

Thin section electron microscopy

"The spacing between ER membranes was significantly increased in the expanded unfolded protein response (UPR)-induced ER (ER membrane distance=31±5nm in control cells versus 48±6nm in UPR-induced cells)."

Uri M

Endoplasmic reticulum, organelle, secretory protein pathway<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1061

105189

Half-life of yeGFP-ssrA

Budding yeast Saccharomyces cerevisiae

104

±19

min

Grilly C, Stricker J, Pang WL, Bennett MR, Hasty J. A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae. Mol Syst Biol. 2007 3: 127.

17667949

Integration of yeGFP-ssrA into CGD699 yeast strain. Researchers used a microfluidic platform tailored for single-cell fluorescence measurements.

This half-life is the result of growth-related dilution (note that the doubling time of the batch culture grown on galactose was approximately 125 min)

Uri M

green fluorescent protein, reporter enzyme, tag sequence<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1062

105190

Half-life of yeGFP-ssrA with expressed E. coli ClpXP protease

Budding yeast Saccharomyces cerevisiae

22-91

min

Grilly C, Stricker J, Pang WL, Bennett MR, Hasty J. A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae. Mol Syst Biol. 2007 3: 127. abstract & p.3 right column 2nd paragraph

17667949

Abstract: "Here, [investigators] use components of the Escherichia coli degradation machinery to construct a Saccharomyces cerevisiae strain that allows for tunable degradation of a tagged protein. Using a microfluidic platform tailored for single-cell fluorescence measurements, [they] monitor protein decay rates after repression using an ssrA-tagged fluorescent reporter." P.2 left column bottom paragraph: "[Investigators] have constructed a S. cerevisiae strain (CGD699) that allows tunable degradation of a tagged protein. To accomplish this, [they] expressed a modified E. coli ClpXP protease in yeast under the control of a repressible promoter."

Abstract: "[Investigators] observe a half-life ranging from 91 to 22 min, depending on the level of activation of the degradation genes." P.3 right column 2nd paragraph: "Previous studies have used exponential fits to characterize the halfâlife of the reporter. [Investigators] found that modeling decay as arising from a set of enzymatic MichaelisâMenten reactions led to excellent agreement between model and experiment (see below). However, in order to systematically compare with the previous fluorescent reporter degradation studies, [they] chose to first analyze the fluorescence trajectories with exponential fits that were reasonably accurate (Figure 3B). From these fits, [they] were able to calculate the mean halfâlife for each concentration of IPTG [Isopropyl Î²-D-1-thiogalactopyranoside], as shown in Figure 3C. The halfâlife decreases from a value of 91 min for no IPTG to 22 min for media containing 5 mM IPTG."

Uri M

green fluorescent protein, reporter enzyme, tag sequence, half life

1064

105192

Proportion of total RNA that is rRNA

Budding yeast Saccharomyces cerevisiae

80-85 table link - http://bionumbers.hms.harvard.edu/files/Cellular%20RNA%20content%20and%20proportion%20of%20total%20RNA%20that%20is%20rRNA%20from%20several%20studies%2C%20and%20calculation%20of%20the%20cellular%20ribosome%20content.pdf

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 16 2:87 p.6/14 table 1

18925958

List of refs in table

Analysis of protein abundance datasets

Table gives ribosome/cell value of 187000±56000 (BNID 100267). See proportion of tRNA/total RNA in yeast of 15% BNID 100261

Uri M

protein synthesis, ribosome, ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1085

105213

Error rate of RNA pol III determined solely by selectivity

Budding yeast Saccharomyces cerevisiae

0.00018

correct/incorrect nucleotide

Alic N, Ayoub N, Landrieux E, Favry E, Baudouin-Cornu P, Riva M, Carles C. Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription. Proc Natl Acad Sci U S A. 2007 Jun 19 104(25):10400-5 abstract

17553959

P.10400 right column bottom paragraph: "In this study, [investigators] examined nucleotide misincorporation by cleavage-competent and cleavage-deficient S. cerevisiae Pol III ternary complexes at a specific position on a tRNA gene. The results define the strategies used by a eukaryotic RNA Pol with high intrinsic cleavage activity to ensure the accuracy of its transcription. [They] used computational methods to combine the experimental observations and predict the steady-state error rate of Pol III and to demonstrate the equally high contribution of proofreading and nucleotide selectivity to the overall fidelity of Pol III."

Abstract: "Determination of relative rates of the reactions producing correct and erroneous transcripts at a specific position on a tRNA gene, combined with computational methods, demonstrated that Pol III has a highly efficient proofreading activity increasing its transcriptional fidelity by a factor of 10^3 over the error rate determined solely by selectivity (1.8×10^-4)." See BNID 103453, 105213

Uri M

transcription, fidelity, mutation, RNA polymerase

1086

105214

RNA pol III fidelity-determined by selectivity and proofreading activity

Budding yeast Saccharomyces cerevisiae

10^3 times the error rate determined solely by selectivity

correct/incorrect nucleotide

17553959

Selectivity was measured as ratio between incorporation of correct to incorrect nucleotide to tRNA gene, 1.8×10^-4 (BNID 105213). Fidelity is the product of selectivity and proofreading. See figure 5 and equation 3. Pol III?, an Incomplete form of Pol III lacking RNA-cleavage activity, can quantitatively incorporate an incorrect nucleotide.

"Determination of relative rates of the reactions producing correct and erroneous transcripts at a specific position on a tRNA gene, combined with computational methods, demonstrated that Pol III has a highly efficient proofreading activity increasing its transcriptional fidelity by a factor of 10^(3) over the error rate determined solely by selectivity (1.8×10^(-4) [BNID 105213])." Proofreading decreases transcription error rate a 1000 fold.

Uri M

transcription, mutation, RNA polymerase, error rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1088

105216

Misincorporation rate in translation in CAT III mutant

Budding yeast Saccharomyces cerevisiae

5e-6 - 2e-5

Mismatched/matched amino acid

Stansfield I, Jones KM, Herbert P, Lewendon A, Shaw WV, Tuite MF. Missense translation errors in Saccharomyces cerevisiae. J Mol Biol. 1998 Sep 11 282(1):13-24. p.19 right column top paragraph and p.20 right column bottom paragraph

9733638

Measurement of inactivating mutants of type III chloramphenicol acetyl transferase mutants.

"In order for active CAT enzyme to be produced from the Ala195 mutant allele of CATIII, on the assumption that such a missense error arises through inaccuracy of mRNA decoding, a non-cognate interaction is required between tRNAGUGHis and the GCU Ala codon at position 195, an event that requires mispairing at both the first and the second positions and a G·U wobble pairing at the third position (Figure 2). The unlikely occurrence of such an error made it all the more surprising that a His misincorporation frequency of 2×10^-5 was detected using the Ala195 CATIII allele (Figure 4), a frequency approximately three times the basal His misincorporation event measured using the Tyr195 allele." "The obvious inference from the S. cerevisiae measurements presented here is that not only is the translational missense error frequency substantially lower than the corresponding E. coli value, but the underlying and contributory transcriptional error frequency must also be at least less than 0.5×10^-5, again lower than the prokaryote estimates. Can Saccharomyces (and other eukaryotes?) be regarded as intrinsically more accurate transcribers and translators than E. coli (or other prokaryotes)? An examination of other codon-specific missense error frequency estimates in E. coli would indicate that yeast does not necessarily exhibit a lesser global error frequency. For example, expression in E. coli of the identical CATIII alleles employed in this study yielded estimates for the histidine substitution for tyrosine of 0.5×10^-5 (Lewendon et al., 1994), identical to estimates made here for the same error in yeast. Histidine substitution for alanine at CATIII codon 195 in E. coli occurs at a frequency of 1×10^-6, again a value comparable to the yeast estimate (Lewendon et al., 1994)." 0.000005 for His195(CAC)>Tyr195(UAC) mutant. 0.00002 for His195(CAC)>Ala195(GCU) mutant.

Uri M

CAT III, missense error, mutation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1096

105224

Size of average protein

Budding yeast Saccharomyces cerevisiae

467

±29 table link - http://bionumbers.hms.harvard.edu/files/Numbers%20and%20mean%20lengths%20for%20proteins%20and%20pseudogenes%20in%20four%20eukaryotes.pdf

Amino acids

Harrison PM, Milburn D, Zhang Z, Bertone P, Gerstein M. Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Res. 2003 Feb 1 31(3):1033-7. table 1 p.1035

12560500

Value of 466 given in Lodish et al, Molecular Cell Biology 2000, 3.1 Hierarchical Structure of Proteins, 6th paragraph under heading 'The Amino Acids Composing Proteins Differ Only in Their Side Chains': "The 6225 known and predicted proteins encoded by the yeast genome have an average molecular weight (MW) of 52,728 and contain, on average, 466 amino acid residues." Value of 415 aa given in Drummond et al., 2005 PMID 16176987 p.14340 left column 2nd paragraph: "At the canonical ribosomal error rate of 5 errors per 10,000 codons translated (ref 35), â19% of average length yeast proteins (415 aa) contain a missense error, and these errors may cause misfolding (ref 36)." Page link - http://tinyurl.com/yd5mt43 For protein median length of 385 aa see BNID 100206.

Uri M

proteome, polypeptide

1097

105225

Translation rate of amino acid codons

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Translation%20rate%20of%20codons%20in%20yeast.pdf

Gilchrist MA, Wagner A. A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J Theor Biol. 2006 Apr 21 239(4):417-34 Supplemental data table S1

16171830

1)T. Ikemura, Codon usage and transfer-RNA content in unicellular and multicellular organisms, Mol. Biol. Evol. 2 (1985), pp. 13â34. (2) R. Percudani, A. Pavesi and S. Ottonello, Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae, J. Mol. Biol. 268 (1997), pp. 322â330. (3) H. Akashi, Translational selection and yeast proteome evolution, Genetics 164 (2003), pp. 1291â1303

3916708, 9159473, 12930740

Range: 0.965 aa/sec (Leu, CUU) - 27.0 aa/sec (Gly, GGC), ~30-fold difference. Sørensen et al 1989 PMID 2474074 report a sixfold difference between codon translation rates in E. coli.

Uri M

ala, arg, asn, asp, cys, gln, gly, his, ile, leu, lys, met, phe, pro, ser, thr, trp, tyr, val, codon, anticodon, protein synthesis, polypeptide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1100

105228

Molecular biology and genetics database SGD

Budding yeast Saccharomyces cerevisiae

Database link - http://www.yeastgenome.org

Department of Genetics at the School of Medicine, Stanford University.

SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.

Uri M

gene, genome, protein, chromosome map, sgd<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1119

105247

Estimated protein concentration in biosynthetic pathways

Budding yeast Saccharomyces cerevisiae

× /4.7

Liebermeister W, Klipp E. Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. Theor Biol Med Model. 2006 Dec 15 3: 42. Table link - http://bionumbers.hms.harvard.edu/files/Empirical%20parameter%20ranges.pdf

17173670

Enzyme concentrations were roughly guessed from protein molecule numbers in the yeast S. cerevisiae, measured in a GFP assay [Huh et al, PMID 14562095]. The range is calculated by dividing and multiplying the geometric mean by the exponent of the standard deviation of the natural logarithm, 4.7. 0.000036/4.7=7.7nM. 0.000036×4.7=170nM.

Uri M

biosynthesis, enzyme kinetics<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1120

105248

Typical empirical protein concentration in biosynthetic pathways

Budding yeast Saccharomyces cerevisiae

2480

× /4.7

Copies/cell

17173670

Enzyme concentrations were roughly guessed from protein molecule numbers in the yeast S. cerevisiae, measured in a GFP assay [Huh et al, PMID 14562095]. To convert molecule numbers into concentrations, researchers assumed a spherical cell of radius 6 µm. The protein concentration reads c= Number of molecules/(Number Avogadro ×Vcell) M, with Avogadro's constant NA=6.022×10^23 and the cell volume measured in litres. The range is calculated by dividing and multiplying the geometric mean by the exponent of the standard deviation of the natural logarithm, 4.7. 2480/4.7=528copies/cell. 2480×4.7=11,656 copies/cell.

Uri M

biosynthesis, kinetic model<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1366

100941

Kcat of glycogen Synthetase

Budding yeast Saccharomyces cerevisiae

27300

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Glycogen synthetase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1374

100950

Kcat of Glycogen phosphorylase

Budding yeast Saccharomyces cerevisiae

33750

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Yeast,Glycogen phosphorylase A,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1375

100951

Kcat of Glycogen phosphorylase

Budding yeast Saccharomyces cerevisiae

9750

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Yeast,Glycogen phosphorylase B,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1383

100959

Kcat of Glucokinase

Budding yeast Saccharomyces cerevisiae

7600

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Yeast,Glucokinase,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1386

100962

Kcat of Phosphoglucomutase

Budding yeast Saccharomyces cerevisiae

13300

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Yeast,Phosphoglucomutase,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1410

100986

Cell concentration for culture with OD600 of 1

Budding yeast Saccharomyces cerevisiae

30000000

Cells/ml

Audra Day, Colette Schneider, and Brandt L. Schneider,chapter 6- Yeast Cell Synchronization, Methods Mol Biol. 2004 241: 55-76. p.73 bullet 17.

14970646

[3] Short protocols in molecular biology, Fred Ausubel et al., 5th ed. Vol. 2 Wiley, New York. pp. 13-9

P.73 bullet 17: "Cell density is most accurately determined with a Z2 Coulter Counter Channelyzer. However, a spectrophotometer and OD600 absorbance readings can be substituted. One OD600 is equivalent to approx 3×10^7 cells/mL (primary source). However, OD600 absorbance readings are sensitive to the size of cells. In block-and-release protocols, where cell size increases dramatically, OD600 absorbance readings will increase whereas the cell number does not."

Best to measure at OD<1 to insure linearity. Value depends on strain and conditions to a factor of several fold.

Ron Milo - Admin

optical density, absorbance, od

1411

100987

Cell concentration for culture with OD660 of 1

Budding yeast Saccharomyces cerevisiae

18500000

cell/ml

http://www.pangloss.com/seidel/Protocols/ODvsCells.html

"Several measurements of Saccharomyces cerevisiae strain YPH499 gave an Cell/OD600 relationship of 4-9x10^7 cells/ml per OD600. According to Current Protocols: OD600 of 1.0 is roughly 3x10^7 cells/ml." Notice -this is at 660nm and not at 600nm.

Ron Milo - Admin

optical density<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1412

100988

Kcat of Hexokinase

Budding yeast Saccharomyces cerevisiae

83200

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Hexokinase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1415

100991

Kcat of Phosphoglucoisomerase

Budding yeast Saccharomyces cerevisiae

80300

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Phosphoglucoisomerase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1422

100998

Kcat of Phosphofructokinase

Budding yeast Saccharomyces cerevisiae

50100

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Phosphofructokinase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1430

101006

Kcat of Triosephosphate isomerase

Budding yeast Saccharomyces cerevisiae

1000000

1/min

Triosephosphate isomerase from Yeast. Krietsch WKG. Meth. Enzymol. 41, 434-438.1975.

not available online

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Triosephosphate isomerase, Kcat, Yeast,tim<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1431

101007

Kcat of Aldolase

Budding yeast Saccharomyces cerevisiae

12500

1/min

Fructose diphosphate aldolase. Rutter WJ , Hunsley JR et al. Meth. Enzymol. 9, 479-498. 1966..

not available online

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Aldolase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1437

101013

Kcat of GA3P dehydrogenase

Budding yeast Saccharomyces cerevisiae

60000

1/min

Glyceraldehyde-3-phosphate dehydrogenase from yeast. Byers LD. Methods Enzymol. 198289 Pt D:326-35.

PMID: 6755173

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

GA3P dehydrogenase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1439

101015

Kcat of 3PGA kinase

Budding yeast Saccharomyces cerevisiae

43500

1/min

3-Phosphoglycerate kinase from bovine liver and yeast. Kulbe KD, Bojanovski M. Methods Enzymol. 198290 Pt E:115-20.

PMID: 6759851

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

3PGA kinase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1446

101022

Kcat of PGA mutase

Budding yeast Saccharomyces cerevisiae

120600

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

PGA mutase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1451

101027

Kcat of Enolase

Budding yeast Saccharomyces cerevisiae

17600

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Enolase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1459

101035

Kcat of Pyruvate kinase

Budding yeast Saccharomyces cerevisiae

71400

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Pyruvate kinase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1461

101037

Kcat of F1,6-biphosphatase

Budding yeast Saccharomyces cerevisiae

9500

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

F1,6-biphosphatase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1467

101043

Kcat of G6P dehydrogenase

Budding yeast Saccharomyces cerevisiae

86800

1/min

Albe KR, Butler MH, Wright BE., Cellular concentrations of Enzymes and Their Substrates, J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Glucose-6-phosphate dehydrogenase, G6P, Kcat, Yeast,turnover number<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1471

101047

Kcat of 6PG dehydrogenase

Budding yeast Saccharomyces cerevisiae

4200

1/min

.Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

6PG dehydrogenase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1473

101049

Kcat of R5P isomerase

Budding yeast Saccharomyces cerevisiae

12000

1/min

.Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

R5P isomerase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1474

101050

Kcat of Ru5P 3-Epimerase

Budding yeast Saccharomyces cerevisiae

12000

1/min

.Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Ru5P 3-Epimerase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1476

101052

Kcat of Transketolase

Budding yeast Saccharomyces cerevisiae

6800

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Transketolase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1479

101055

Kcat of Transaldolase A

Budding yeast Saccharomyces cerevisiae

4150

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Transaldolase A,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1480

101056

Kcat of Transaldolase B

Budding yeast Saccharomyces cerevisiae

2900

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Transaldolase B,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1483

101059

Kcat of Gal1P Uridyltransferase

Budding yeast Saccharomyces cerevisiae

59200

1/min

Uridine diphosphate glucose-4-epimerase and galactose-1-phosphate uridylyltransferase from Saccharomyces cerevisiae. Fukasawa T, Segawa T, Nogi Y. Methods Enzymol. 198289 Pt D:584-92.

PMID: 6292668

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Gal1P Uridyltransferase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1484

101060

Kcat of Galactokinase

Budding yeast Saccharomyces cerevisiae

3300

1/min

Galactokinase from Saccharomyces cerevisiae. Wilson DB, Schell MA. Methods Enzymol. 198290 Pt E:30-5.

PMID: 6759857

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Galactokinase,Kcat,Yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1529

101107

Kcat of Asp transaminase

Budding yeast Saccharomyces cerevisiae

45200

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Asp transaminase,Yeast,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1532

101110

Kcat of Glu dehydrogenase(NAD)

Budding yeast Saccharomyces cerevisiae

8050

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Glu dehydrogenase(NAD),Yeast,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1533

101111

Kcat of Glu dehydrogenase(NADP)

Budding yeast Saccharomyces cerevisiae

22250

1/min

Albe KR, Butler MH, Wright BE. Cellular concentrations of Enzymes and Their Substrates,J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Assumed molecular mass

Sudhakaran Prabakaran, Ruchi Chauhan

Glu dehydrogenase(NADP), Yeast, Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1544

101122

Kcat of GSSG reductase

Budding yeast Saccharomyces cerevisiae

18000

1/min

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

GSSG reductase, Glutathione disulfide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1547

101125

Kcat of Ornithine decarboxylase

Budding yeast Saccharomyces cerevisiae

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Ornithine decarboxylase,Yeast,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1559

101137

Kcat of Pyruvate carboxylase

Budding yeast Saccharomyces cerevisiae

3900

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Assumed molecular mass, kcat for subunit

Sudhakaran Prabakaran, Ruchi Chauhan

Pyruvate carboxylase, Yeast, Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1565

101143

Kcat of UDPG 4-epimerase

Budding yeast Saccharomyces cerevisiae

3900

1/min

Uridine diphosphate glucose-4-epimerase and galactose-1-phosphate uridylyltransferase from Saccharomyces cerevisiae. Fukasawa T, Segawa T, Nogi Y. Methods Enzymol. 198289 Pt D:584-92.

PMID: 6292668

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

UDPG 4-epimerase,Yeast,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1566

101144

Kcat of PDC

Budding yeast Saccharomyces cerevisiae

232000

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

PDC,Yeast,Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1572

101150

Kcat of Citrate synthase

Budding yeast Saccharomyces cerevisiae

17600

1/min

Cellular concentrations of Enzymes and Their Substrates, K.R. Albe et al, 1990, Journal of Theoretical Biology

PMID: 2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Assumed molecular mass

Sudhakaran Prabakaran, Ruchi Chauhan

Citrate synthase, Yeast, Kcat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1575

101153

Kcat of Isocitrate dehydrogenase

Budding yeast Saccharomyces cerevisiae

10680

1/min

Albe KR, Butler MH, Wright BE., Cellular concentrations of Enzymes and Their Substrates, J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

The values were calculated based on values mentioned in the Tables 1 and 2 of the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Isocitrate dehydrogenase, Yeast, Kcat, enzyme, turnover number,IDH,citric acid cycle<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1616

101194

concentration of ADP

Budding yeast Saccharomyces cerevisiae

320-1300

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Lagunas R, Gancedo C. Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae. Eur J Biochem. 1983 Dec 15137(3):479-83. and Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast.Biochimie. 197355(2):205-11.

6229402, 4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

ADP, Yeast, Intracellular metabolite concentrations, Adenosine diphosphate, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1617

101195

concentration of ATP

Budding yeast Saccharomyces cerevisiae

1100-1900

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

6229402 and 4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

ATP, Yeast, Intracellular metabolite concentrations, Adenosine triphosphate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1618

101196

concentration of F1-6-biphosphate

Budding yeast Saccharomyces cerevisiae

1700-4500

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

6229402 and 4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

F1-6-biphosphate,Yeast,Intracellular metabolite concentrations<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1619

101197

concentration of alpha-KG

Budding yeast Saccharomyces cerevisiae

200-5000

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

6229402 and 4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

alpha-KG,Yeast,Intracellular metabolite concentrations<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1620

101198

Concentration of AMP

Budding yeast Saccharomyces cerevisiae

170-300

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 1973 55(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

AMP, Yeast, Intracellular metabolite concentrations, Adenosine monophosphate, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1621

101199

concentration of Ala

Budding yeast Saccharomyces cerevisiae

7000 - 25000

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Ala,Yeast,Intracellular metabolite concentrations,Alanine,concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1622

101200

concentration of Arg

Budding yeast Saccharomyces cerevisiae

18000

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Arg,Yeast,Intracellular metabolite concentrations,Arginine<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1623

101201

concentration of Asp

Budding yeast Saccharomyces cerevisiae

3000 - 13000

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Asp, Yeast, Intracellular metabolite concentrations, Aspartic acid, concentrations<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1624

101202

Concentration of citrate

Budding yeast Saccharomyces cerevisiae

700

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Citric acid, Intracellular metabolite<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1625

101203

Concentration of Citrulline

Budding yeast Saccharomyces cerevisiae

5000

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

a-amino acid, Intracellular metabolite, urea cycle, ammonia excretion<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1626

101204

concentration of G1P

Budding yeast Saccharomyces cerevisiae

1-100

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

G1P, Yeast, Intracellular metabolite concentrations, Glucose 1-phosphate, glucose 1 phosphate, glucose<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1627

101205

concentration of glutamate

Budding yeast Saccharomyces cerevisiae

15000 - 35000

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Glu,Yeast,Intracellular metabolite concentrations,Glutamic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1628

101206

concentration of Gln

Budding yeast Saccharomyces cerevisiae

15000 - 35000

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Gln, Yeast, Intracellular metabolite concentrations, Glutamine<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1629

101207

Concentration of NAD

Budding yeast Saccharomyces cerevisiae

1000-1600

Î¼M

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 1973 55(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

NAD, Yeast, Intracellular metabolite concentrations, Nicotinamide adenine dinucleotide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1630

101208

Concentration of NADP

Budding yeast Saccharomyces cerevisiae

20-150

Î¼M

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 1973 55(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

NADP, Yeast, Intracellular metabolite concentrations, Nicotinamide adenine dinucleotide phosphate, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1631

101209

Concentration of NADPH

Budding yeast Saccharomyces cerevisiae

50-150

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Intracellular metabolite concentrations, Nicotinamide adenine dinucleotide phosphate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1632

101210

concentration of NH3

Budding yeast Saccharomyces cerevisiae

30000

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

NH3,Yeast,Intracellular metabolite concentrations,Ammonia,concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1633

101211

Concentration of OAA

Budding yeast Saccharomyces cerevisiae

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

OAA, Yeast, Intracellular metabolite concentrations, Oxaloacetic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1634

101212

concentration of Ornithine

Budding yeast Saccharomyces cerevisiae

7000

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Ornithine, Yeast, Intracellular metabolite concentrations, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1635

101213

concentration of 6PG

Budding yeast Saccharomyces cerevisiae

100-300

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

6PG, Yeast, Intracellular metabolite concentrations, 6-Phosphogluconate, phosphogluconate, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1636

101214

concentration of UDPG

Budding yeast Saccharomyces cerevisiae

300

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

Gancedo JM, Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie. 197355(2):205-11.

4578278

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

UDPG, Yeast, Intracellular metabolite concentrations, uridine diphosphate glucose<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1637

101215

Concentration of DHAP

Budding yeast Saccharomyces cerevisiae

330

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

Lagunas R, Gancedo C. Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae. Eur J Biochem. 1983 Dec 15 137(3):479-83.

6229402

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Intracellular metabolite, Dihydroxyacetone phosphate,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1638

101216

concentration of F6P

Budding yeast Saccharomyces cerevisiae

650

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Lagunas R, Gancedo C. Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae. Eur J Biochem. 1983 Dec 15137(3):479-83.

6229402

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

F6P,Yeast,Intracellular metabolite concentrations,fructose 6-phosphate,fructose 6 phosphate,concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1639

101217

concentration of G 6P

Budding yeast Saccharomyces cerevisiae

2300

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Lagunas R, Gancedo C. Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae. Eur J Biochem. 1983 Dec 15137(3):479-83.

6229402

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

G 6P, Yeast, Intracellular metabolite concentrations, Glucose 6-phosphate, glucose 6 phosphate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1640

101218

Concentration of Pi

Budding yeast Saccharomyces cerevisiae

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

Lagunas R, Gancedo C. Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae. Eur J Biochem. 1983 Dec 15 137(3):479-83.

6229402

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Pi, Yeast, Intracellular metabolite concentrations, inorganic phosphate, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1641

101219

concentration of PEP

Budding yeast Saccharomyces cerevisiae

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Lagunas R, Gancedo C. Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae. Eur J Biochem. 1983 Dec 15137(3):479-83.

6229402

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

PEP, Yeast, Intracellular metabolite concentrations, Phosphoenolpyruvate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1642

101220

concentration of Pyruvate

Budding yeast Saccharomyces cerevisiae

1600

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Lagunas R, Gancedo C. Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae. Eur J Biochem. 1983 Dec 15137(3):479-83.

6229402

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

Pyruvate,Yeast,Intracellular metabolite concentrations<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1643

101221

concentration of GA3P

Budding yeast Saccharomyces cerevisiae

400-1200

microM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Ottaway JH, Mowbray J. The role of compartmentation in the control of glycolysis. Curr Top Cell Regul. 197712:107-208.

140783

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

GA3P,Yeast,Intracellular metabolite concentrations,Glyceraldehyde-3-phosphate,glyceraldehyde 3 phosphate,concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1644

101222

Concentration of 2PGA

Budding yeast Saccharomyces cerevisiae

420-1100

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22 143(2):163-95.

2200929

Ottaway JH, Mowbray J. The role of compartmentation in the control of glycolysis. Curr Top Cell Regul. 1977 12:107-208.

140783

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

2PGA, Yeast, Intracellular metabolite concentrations, 2-phosphyglycerate, 2 phosphyglycerate, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1645

101223

concentration of 3PGA

Budding yeast Saccharomyces cerevisiae

100-260

µM

Albe KR, Butler MH, Wright BE. Cellular concentrations of enzymes and their substrates. J Theor Biol. 1990 Mar 22143(2):163-95.

2200929

Ottaway JH, Mowbray J. The role of compartmentation in the control of glycolysis. Curr Top Cell Regul. 197712:107-208.

140783

The values were calculated based on values mentioned in the cited literature

Sudhakaran Prabakaran, Ruchi Chauhan

3PGA, Yeast, Intracellular metabolite concentrations, 3-phosphyglycerate, 3 phosphyglycerate, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1692

101270

Number of subunits in the F0 oligomer of ATPase in mitochondria

Budding yeast Saccharomyces cerevisiae

unitless

Seelert H et al. Proton-powered turbine of a plant motor. Nature. 2000 May 25 405(6785):418-9 p.418 right column

10839529

Stock D, Leslie AG, Walker JE. Molecular architecture of the rotary motor in ATP synthase. Science. 1999 Nov 26 286(5445):1700-5.

10576729

(Primary source:) An electron density map obtained from crystals of a subcomplex of yeast mitochondrial ATP synthase

differs in bacteria, yeast and plants

Ron Milo - Admin

ATP, protons, chemiosmotic<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1731

101310

Doubling time of haploid cell

Budding yeast Saccharomyces cerevisiae

±1 Table link - http://bionumbers.hms.harvard.edu/files/Comparison%20between%20colony%20doubling%20time%20and%20doubling%20time%20predicted%20from%20measurements%20of%20growth%20rate%20of%20individual%20cells.pdf

minutes

Talia, S. D., J. M. Skotheim, J. M. Bean, E. D. Siggia, and F. R. Cross, 2007. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature 448:947â951. DOI: 10.1038/nature06072 Supplementary information p. 20 table S12

17713537

P.947 right column 3rd paragraph: "When [researchers] quantified total red fluorescence per cell as described [ref 24], [they] found exponential growth in single cells (Fig. 2a Supplementary Information), as deduced previously from pulse-labelling of size-selected populations [ref 25]. The single-cell growth rate Î± is moderately variable, but its average agrees well with the bulk culture growth rate (Fig. 2b, Supplementary Table 12)." Media and temperature dependent. Although unspecified, the growth media appears to be glucose according to following sentence from p. 16 in supplementary information (bottom paragraph): "Glycerol/ethanol supports a much slower growth rate than glucose (170 min compared to 100 min doubling time)..." For doubling time of haploid mother cell from the same article see BNID 104360. For 100 min in rich medium see BNID 100270.

Ben Marks

cell division, growth rate, cell cycle, generation time

1753

101333

Coefficient of Variance of Generation Time

Budding yeast Saccharomyces cerevisiae

0.18

unitless

Siegal-Gaskins D, Crosson S. Tightly regulated and heritable division control in single bacterial cells. Biophys J. 2008 Aug95(4):2063-72 p. 2068 table 2

18469083

Talia, S. D., J. M. Skotheim, J. M. Bean, E. D. Siggia, and F. R. Cross, 2007. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature 448:947 â U12.

17713537

Ben Marks

cell division, division control, division rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1758

101338

Number of NPCs (Nuclear Pore Complexes) during G1 phase

Budding yeast Saccharomyces cerevisiae

±16

unitless

Winey M, Yarar D, Giddings TH Jr, Mastronarde DN. Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes. Mol Biol Cell. 1997 Nov8(11):2119-32. p. 2124 table 1

9362057

Researchers created 3D reconstructions of entire nuclei from electron micrographs of serial thin sections to determine the number, surface density, and distribution of NPCs throughout the cell cycle of the budding yeast S. cerevisiae.

Mean±SD

Ben Marks

phase, cell cycle, nucleus<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1759

101339

Number of NPCs (Nuclear Pore Complexes) during S phase

Budding yeast Saccharomyces cerevisiae

117

±16.8

unitless

9362057

Ben Marks

complex, NPC, phase, cell cycle, nucleus, pores, complexes, nuclear<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1760

101340

Number of NPCs (Nuclear Pore Complexes) during early mitosis

Budding yeast Saccharomyces cerevisiae

142

±16.4

unitless

9362057

Ben Marks

phase, cell cycle, nucleus<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1761

101341

Number of NPCs (Nuclear Pore Complexes) during late anaphase

Budding yeast Saccharomyces cerevisiae

137

±29.2

unitless

9362057

Ben Marks

phase, cell cycle, nucleus,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1762

101342

Surface area of nucleus during late anaphase

Budding yeast Saccharomyces cerevisiae

13.8

±1.62

µm^2

Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes. Winey M, Yarar D, Giddings TH Jr, Mastronarde DN. Mol Biol Cell. 1997 Nov8(11):2119-32. Table 1

9362057

Ben Marks

phase, cell cycle, area<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1763

101343

Surface area of nucleus during early mitosis

Budding yeast Saccharomyces cerevisiae

12.5

±1.50

µm^2

9362057

Computer-aided reconstruction of entire nuclei from electron micrographs of serially sectioned cells.

Ben Marks

phase, cell cycle, area, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1764

101344

Surface area of nucleus during S phase

Budding yeast Saccharomyces cerevisiae

8.3

±1.92

µm^2

9362057

Ben Marks

phase, cell cycle, size, area<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1765

101345

surface area of nucleus during G1 phase

Budding yeast Saccharomyces cerevisiae

7.4

+-1.15

um^2

9362057

Ben Marks

phase, cell cycle,size,area<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1766

101346

Density of NPCs (Nuclear Pore Complexes) during G1 phase

Budding yeast Saccharomyces cerevisiae

11.6

±2.35

NPC/Î¼m^2

9362057

Ben Marks

complex, NPC, phase, cell cycle, nucleus, pores, complexes, nuclear<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1767

101347

Density of NPCs (Nuclear Pore Complexes) during S phase

Budding yeast Saccharomyces cerevisiae

14.6

±2.72

NPC/µm^2

9362057

Ben Marks

phase, cell cycle, nucleus<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1768

101348

Density of NPCs (Nuclear Pore Complexes) during early mitosis

Budding yeast Saccharomyces cerevisiae

11.4

±1.55

NPC/µm^2

9362057

P.2122 left column 2nd paragraph: "[Researchers] created 3D reconstructions of entire nuclei from electron micrographs of serial thin sections to determine the number, surface density, and distribution of NPCs [Nuclear Pore Complexes] throughout the cell cycle of the budding yeast S. cerevisiae."

P.2122 right column bottom paragraph to p.2124 left column: "The IMOD program [a tool for analyzing and viewing three-dimensional biological image data] was used to extract various parameters from the 32 models of yeast nuclei. These values include the number of NPCs per nucleus, as well as the volume and surface area of each nucleus (Table 1). Surface area was determined from a mesh of triangles over the surface of the nuclear models (Figure 2, see MATERIALS AND METHODS). By using the surface area and NPC values for each nucleus, an average NPC density (NPC/Î¼m^2 of nuclear envelope) was derived (Table 1). The number of NPCs observed in models of individual nuclei ranged from 65 in a G1 cell (Table 1, model 1) to 182 NPCs in a late anaphase cell (Table 1, model 32). The surface area of the nuclei ranged from 5.5 Î¼m^2 in a G1 cell to 16.9 Î¼m^2 in a late anaphase cell (Table 1, models 5 and 30, respectively). The volume of the nuclei ranged from 1.3 Î¼m^3 in a S-phase cell to 4.0 Î¼m^3 in a mitotic cell (Table 1, models 12 and 24, respectively). The trend toward increasing numbers in later stages of the cell cycle is reversed for average NPC density per Î¼m^2 of nuclear envelope, which ranged from 8.2 NPCs/Î¼m^2 in a late anaphase cell to 18 NPCs/Î¼m^2 in a S-phase cell (Table 1, models 27 and 15, respectively)."

Ben Marks

phase, cell cycle, nucleus

1769

101349

Density of NPCs (Nuclear Pore Complexes) during late anaphase

Budding yeast Saccharomyces cerevisiae

±1.86

NPC/µm^2

9362057

Ben Marks

phase, cell cycle, nucleus,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1770

101350

Surface area of nuclei during late anaphase

Budding yeast Saccharomyces cerevisiae

13.8

±1.62

µm^2

9362057

Ben Marks

size, phase, cell cycle, nucleus

1771

101351

Volume of nuclei during early mitosis

Budding yeast Saccharomyces cerevisiae

3.1

±0.62

µm^3

9362057

Ben Marks

phase, cell cycle, nucleus<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1772

101352

Volume of nuclei during S phase

Budding yeast Saccharomyces cerevisiae

2.13

±0.72

µm^3

9362057

Ben Marks

phase, cell cycle, nucleus<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1773

101353

Volume of nuclei during G1 phase

Budding yeast Saccharomyces cerevisiae

1.76

±0.41

µm^3

9362057

Ben Marks

phase, cell cycle, nucleus

1813

101395

Number of nuclear pores per nucleus

Budding yeast Saccharomyces cerevisiae

119

pores/nucleus

Maul GG, Deaven L. Quantitative determination of nuclear pore complexes in cycling cells with differing DNA content. J Cell Biol. 1977 Jun73(3):748-60. p. 752 table 1

406262

[17] Hartwell LH. Periodic density fluctuation during the yeast cell cycle and the selection of synchronous cultures. J Bacteriol. 1970 Dec104(3):1280-5.

16559104

P.749 right column top paragraph: "Yeast (Saccharomyces cerevisiae) was grown according to Hartwell (primary source) at 24°C or with the same medium but containing 20% glycerol. After several days, the yeast adapted to this condition but grew very slowly. Determinations of nuclear diameter by phase-contrast microscopy, of height by electron microscopy, and of pore frequency by freeze-etching were done on cells during the exponential growth phase (48 h after plating)." P.753 right column 3rd paragraph: "[Investigators] decided to extend the number of different cell lines and select them according to different DNA content. Table I provides the summary of the data collected during this extended investigation, and reveals an obvious increase in nuclear surface with increasing DNA content: this increase is not proportional, however."

P.751 right column 2nd paragraph: "The numbers in Table I represent the corrected values. Briefly, the indentation at the cytocenter results in a nuclear shape similar to the shape of an indented ball. Since most cells will appear round when the indentation is parallel to the optical axis, the volume will be extremely overestimated if the formula for a sphere is used."

Ben Marks

nucleus, pore

1814

101396

Volume of Nucleus

Budding yeast Saccharomyces cerevisiae

3.3

µm^3

Maul GG, Deaven L. Quantitative determination of nuclear pore complexes in cycling cells with differing DNA content. J Cell Biol. 1977 Jun73(3):748-60. p. 752 table 1

406262

Yeast (Saccharomyces cerevisiae) was grown according to Hartwell (17) at 24°C or with the same medium but containing 20% glycerol. After several days, the yeast adapted to this condition but grew very slowly. Determinations of nuclear diameter by phase-contrast microscopy, of height by electron microscopy, and of pore frequency by freeze-etching were done on cells during the exponential growth phase (48 h after plating). For determination of nuclear size the short and long axis of 50 live cells were measured and averaged separately.

Ben Marks

nuclear, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

1831

101413

Concentration of dTTP in a 42fL yeast cell, cells measured asychronously

Budding yeast Saccharomyces cerevisiae

µM

Koç A, Wheeler LJ, Mathews CK, Merrill GF. Hydroxyurea arrests DNA replication by a mechanism that preserves basal dNTP pools. J Biol Chem. 2004 Jan 2 279(1):223-30 DOI: 10.1074/jbc.M303952200 p.225 left column top paragraph

14573610

DNA polymerase-based enzymatic assay, HPLC

P.225 left column top paragraph: "Assuming a cell volume of 42 fl (ref 34 BNID 100427), the concentrations of dTTP, dATP, dCTP, and dGTP were 70, 44, 18, and 15 Î¼m, respectively." Note that this value is for asynchronous cultures, dNTP levels increase several fold at S-phase

Paul Jorgensen

deoxyribonucleotides, dNTP, dNTPs

1832

101414

Concentration of dATP in a 42fL yeast cell, measured from an asyncrhonous population

Budding yeast Saccharomyces cerevisiae

µM

14573610

DNA polymerase-based enzymatic assay, HPLC

P.225 left column top paragraph: "Assuming a cell volume of 42 fl (ref 34 BNID 100427), the concentrations of dTTP, dATP, dCTP, and dGTP were 70, 44, 18, and 15 Î¼m, respectively." Note: This value is measured from asynchronous cells, dNTP levels increase several fold during S-phase

Paul Jorgensen

dNTPs, NTPs, dNTP, deoxyribonucleotide

1833

101415

Concentration of dCTP in a 42fL yeast cell, measured from an asyncrhonous population

Budding yeast Saccharomyces cerevisiae

µM

14573610

DNA polymerase-based enzymatic assay, HPLC

P.225 left column top paragraph: "Assuming a cell volume of 42 fl (ref 34 BNID 100427), the concentrations of dTTP, dATP, dCTP, and dGTP were 70, 44, 18, and 15 Î¼m, respectively." Note: This value is measured from asynchronous cells, dNTP levels increase several fold during S-phase

Paul Jorgensen

dNTPs, NTPs, dNTP, deoxyribonucleotide

1834

101416

Concentration of dGTP in a 42fL yeast cell, measured from an asyncrhonous population

Budding yeast Saccharomyces cerevisiae

µM

14573610

DNA polymerase-based enzymatic assay, HPLC

P.225 left column top paragraph: "Assuming a cell volume of 42 fl (ref 34 BNID 100427), the concentrations of dTTP, dATP, dCTP, and dGTP were 70, 44, 18, and 15 Î¼m, respectively." Note: This value is measured from asynchronous cells, dNTP levels increase several fold during S-phase

Paul Jorgensen

dNTPs, NTPs, dNTP, deoxyribonucleotide

1835

101417

Concentration of rUTP in a yeast cell

Budding yeast Saccharomyces cerevisiae

0.34

14573610

[40] Exinger F, Lacroute F. 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr Genet. 1992 Jul22(1):9-11 [41] Larsson C et al., Glycolytic flux is conditionally correlated with ATP concentration in Saccharomyces cerevisiae: a chemostat study under carbon- or nitrogen-limiting conditions. J Bacteriol. 1997 Dec179(23):7243-50.

1611672, 9393686

Calculated from published data

P.229 right column bottom paragraph: "The mechanism for replication arrest when RNR [ribonucleotide reductase] is inhibited remains unknown. If RNR inhibition resulted in significant expansion of the rNTP pools, it is possible that an increased rNTP/dNTP ratio might result in misincorporation of ribonucleotides into DNA and thereby trigger a replication arrest. However, the rNTP pools in yeast, calculated from published data to be 0.34 mM rUTP, 2 mM rATP, 0.26 mM rCTP, and 0.34 mM rGTP (primary sources), are 5â90-fold greater than the corresponding dNTP pools (Fig. 1B) (refs 15, 18) and are therefore unlikely to be affected by the presence or absence of a relatively small flux of rNDPs through RNR."

Paul Jorgensen

NTPs, ribonucleotide, nucleotide

1836

101418

Concentration of rATP in a yeast cell

Budding yeast Saccharomyces cerevisiae

14573610

1611672, 9393686

Calculated from published data

Paul Jorgensen

NTPs, ribonucleotide, nucleotide

1837

101419

Concentration of rCTP in a yeast cell

Budding yeast Saccharomyces cerevisiae

0.26

14573610

1611672, 9393686

Calculated from published data

Paul Jorgensen

NTPs, ribonucleotide, nucleotide

1838

101420

Concentration of rGTP in a yeast cell

Budding yeast Saccharomyces cerevisiae

0.34

14573610

1611672, 9393686

Calculated from published data

Paul Jorgensen

NTPs, ribonucleotide, nucleotide, GTP

1849

101431

The ratio of protein to DNA in highly purified yeast nuclei from budding yeast

Budding yeast Saccharomyces cerevisiae

Unitless

Aris, J.P. & Blobel G. Isolation of yeast nuclei. Meth. Enz. 194:735 (1991) p.741 2nd paragraph

2005821

[22] O.H. Lowry, N.J. Rosebrough, A.L. Farr, R.J. Randall, Protein measurement with the Folin phenol reagent. J. Biol. Chem., 193 (1951), p. 265 [23] G. Ceriotti, Determination of nucleic acids in animal tissues. J. Biol. Chem., 214 (1955), p. 59

14907713, 14367363

P.741 2nd paragraph: "A simple way to evaluate the isolation of nuclei is to view the nuclei directly in the Ficoll suspension by light microscopy. Nuclei appear dark, with the crescent-shaped nueleolus sometimes evident (Fig. 1c). Membrane(s) associated with nuclei may be visible (Fig. 1c, lower left). Electron microscopy reveals that nuclei isolated from two Ficoll gradients are substantially free of contamination (Fig. 1a,b). [Investigators] have routinely observed smooth membrane in contact with nuclei and believe this may reflect regions of intimate contact between the nucleus and vacuole, which are often seen in micrographs of yeast cells and spheroplasts (not shown). The protein-to-DNA mass ratio of this preparation is approximately 20:1 as determined by standard methods (primary sources)."

Paul Jorgensen

nuclei, nucleus, size

1914

105337

Minimal generation time (on YEP+fructose)

Budding yeast Saccharomyces cerevisiae

Table Link - http://bionumbers.hms.harvard.edu/files/populationtyson1978.pdf

min

Tyson CB, Lord PG, Wheals AE. Dependency of size of Saccharomyces cerevisiae cells on growth rate. J Bacteriol. 1979 Apr138(1):92-8.

374379

Uri M

growth, doubling, yeast extract peptone<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2021

105444

Number of protein-coding genes

Budding yeast Saccharomyces cerevisiae

5616

Table link - http://bionumbers.hms.harvard.edu/files/Gene%20sets%2C%20homology%2C%20tandem%20repeats%20and%20ohnologs.pdf

genes

Byrne KP, Wolfe KH. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 2005 Oct15(10):1456-61 Supplemental table 1

16169922

Abstract: "[Researchers] developed the Yeast Gene Order Browser to facilitate visual comparisons and computational analysis of synteny relationships in yeasts."

P.1457 left column bottom paragraph: "Gene content is highly conserved, with 89%-96% of the genes in each genome having a homolog in at least one of the other species [of yeast](Supplemental Table 1). About 6%-8% of genes remain in singleton pillars in each post-WGD [whole Genome Duplication event] species. The majority of these are located in subtelomeric regions and are often members of multigene families (so [researchers] can be fairly sure that they are real genes), but they lack well-defined orthologs in other species. For example, in S. cerevisiae there are 352 genes in singleton pillars, and 213 of them are within 20 genes of the end of a chromosome." For total gene number of 6,606 see BNID 100237. See value of 6,340 proteins in BNID 105464 table link - http://bionumbers.hms.harvard.edu/files/Numbers%20and%20mean%20lengths%20for%20proteins%20and%20pseudogenes%20in%20four%20eukaryotes.pdf

Uri M

heredity, Genome, genetics, DNA, proteome

2027

105450

Retrotransposition rate of plasmid containing wild-type scZorro3 retrotransposon

Budding yeast Saccharomyces cerevisiae

2.00E-06

events/cells plated

Dong C, Poulter RT, Han JS. LINE-like retrotransposition in Saccharomyces cerevisiae. Genetics. 2009 Jan181(1):301-11

18957700

scZorro3 is controlled by the GAL1 inducible promoter, and an antisense reporter (mHIS3AI) interrupted with an intron on the scZorro3 sense strand is placed in the 3'-UTR. Only after scZorro3 transcription, splicing, and reverse trascription/integration does the marker produce functional HIS3 protein (fig 1b). When placed on a high-copy plasmid and introduced into S. cerevisiae, this led to scZorro3-dependent HIS+ colony formation (Figure 1C), indicating that retrotransposition occurred. To examine scZorro3 retrotransposition from a more ânaturalâ habitat, researchers integrated scZorro3mHIS3AI into chromosome II, along with mutants predicted to abolish the function of activities required for L1 retrotransposition. Under the conditions of their assay, wild-type scZorro3 retrotransposed with a frequency of ~2×10^-6 events/cells plated.

Zorro3 is a member of the L1 clade of non-LTR retrotransposons from the distantly related Candida albicans that is known to be active for retrotransposition in its host (Goodwin et al. 2007, PMID: 17683538)

Uri M

LINE-1, Long interspersed nuclear element, transposon, mobile genetic element, reverse transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2048

105471

Number of base pairs in mitochondrial genome

Budding yeast Saccharomyces cerevisiae

85779

Foury F, Roganti T, Lecrenier N, Purnelle B. The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 1998 Dec 4 440(3):325-31. abstract & p.325 right column bottom paragraph

9872396

"A library was constructed from sheared mtDNA fragments inserted in the EcoRV site of Bluescript SK vector and random DNA sequencing of 0.5â0.7 kb fragments was performed by automatic sequencing using Bigdye terminators."

"The mtDNA sequence of strain FY1679, an isogenic derivative of S288C, is 85,779 bp in length and assembles into a circular contig (Fig. 1, right, Table 1 and Table 2)." p.325 left column bottom paragraph:"The yeast mitochondrial genome contains the genes for cytochrome c oxidase subunits I, II and III (cox1, cox2 and cox3), ATP synthase subunits 6, 8 and 9 (atp6, atp8 and atp9), apocytochrome b (cytb), a ribosomal protein (var1) and several intron-related open reading frames (ORFs) 9 and 10." I.e., The DNA molecule encodes 8 proteins (7 for oxidative phosphorylation and 1 ribosomal protein)

stirling

DNA, genetic material, mitochondria, mitochondrion<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2064

105487

Comparison between colony doubling time and doubling time predicted from measurements of growth rate of individual cells of haploids, diploids and tetraploids

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Comparison%20between%20colony%20doubling%20time%20and%20doubling%20time%20predicted%20from%20measurements%20of%20growth%20rate%20of%20individual%20cells.pdf

17713537

P.947 left column bottom paragraph: "[Researchers] measured times from cytokinesis to budding (G1) and from budding to cytokinesis in haploids, diploids or tetraploids (mothers and daughters), using time-lapse fluorescence microscopy of strains expressing Myo1 tagged with green fluorescent protein (Myo1âGFP)." P.950 left column paragraph above bottom: "Strain and plasmid constructions: Standard methods were used throughout. All strains are W303-congenic. All integrated constructs were characterized by Southern blot analysis. Cells were prepared for time-lapse microscopy as described (ref 24, Bean et al. 2006 PMID 16387649). [Researchers] observed growth of microcolonies with fluorescence time-lapse microscopy at 30°C using a Leica DMIRE2 inverted microscope with a Ludl motorized XY stage. Images were acquired every 3min for cells grown in glucose and every 6min for cells grown in glycerol/ethanol with a Hamamatsu Orca-ER camera. [They] used custom Visual Basic software integrated with ImagePro Plus to automate image acquisition and microscope control."

Media and temperature dependent. Although unspecified, the growth media appears to be glucose according to following sentence from p.16 in supplementary information: "Glycerol/ethanol supports a much slower growth rate than glucose (170 min compared to 100 min doubling time)..." See BNID 101310, 104360. For 100 min in rich medium see BNID 100270

Uri M

cell division, growth rate, cell cycle

2084

105507

Half life of ribosomal protein rps6b mRNA

Budding yeast Saccharomyces cerevisiae

±2

min

Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30 99(9):5860-5 p. 5861 fig. 1B

11972065

mRNA decay profile determined by quantitative microarray analysis gave a value of 24±2min (calculated half-life and 95% confidence interval). Northern analysis quantified with a PhosphorImager gave value of ~17min, Fig 1C .

The 131 ribosomal protein mRNAs analyzed in this study had remarkably similar half-lives, with t1/2=22±6min, BNID 104743

Uri M

ribosome, translation machinery, messenger ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2085

105508

Half life of Phosphoglycerate kinase 1 (PGK1) mRNA

Budding yeast Saccharomyces cerevisiae

53-98

min

Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30 99(9):5860-5 p. 5861 fig. 1B

11972065

mRNA decay profile determined by quantitative microarray analysis gave a value of 70min range 53-98min (calculated half-life and 95% confidence interval). Northern analysis quantified with a PhosphorImager gave value >90min, Fig 1C .

Uri M

transferase enzyme, glycolysis, messenger ribonucleic acid, transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2086

105509

Half life of ACT1 mRNA

Budding yeast Saccharomyces cerevisiae

±8

min

Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30 99(9):5860-5 p. 5861 fig. 1B

11972065

mRNA decay profile determined by quantitative microarray analysis (calculated half-life and 95% confidence interval)

ACT1 is the only actin structural gene in yeast (Wertman et al., 1992 PMID 1427032)

Uri M

globular, cytoskeletal protein, messenger ribonucleic acid, transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2087

105510

Median mRNA decay constant

Budding yeast Saccharomyces cerevisiae

0.00056

sec^-1

Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365â1374. 2005 p. 1366 left column, bottom paragraph

15758206

1) Wang et al., Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30 99(9):5860-5 (2) Arava et al., Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2003 Apr 1 100(7):3889-94 (3) Ghaemmaghami et al., Global analysis of protein expression in yeast. Nature. 2003 Oct 16 425(6959):737-41. (4) Huh et al., Global analysis of protein localization in budding yeast. Nature. 2003 Oct 16 425(6959):686-91.

11972065, 12660367, 14562106, 14562095

The value is calculated from published information (primary sources) on yeast genes and their expression.

Uri M

transcript, degradation, gene expression<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2088

105511

Mean mRNA half life

Budding yeast Saccharomyces cerevisiae

~3 - >90

min

11972065

P.5862 left column 2nd paragraph: "The half-lives of the 4,687 mRNAs analyzed varied widely, ranging from ~3 min to more than 90 min, with a mean of 23 min and median of 20 min (BNID 100205)(Fig. 2A). No simple correlation was found between the decay rates of mRNAs and their abundance, (Cor. Coeff. = 0.06), the size of the ORF (Cor. Coeff. = â0.01), codon adaptation index (Cor. Coeff. = 0.04), or the density of ribosomes bound to the mRNA (Cor. Coeff. = 0.08) (Y. Arava, D.H., and P.O.B., unpublished data) (http://www-genome.stanford.edu/turnover)." Note-Pérez-Ortín et al., 2007 PMID 17379352 p.253 right column 2nd paragraph give range from 3 to 300 min

Uri M

constant, decay, degradation, messenger ribonucleic acid, transcript, transcriptome

2089

105512

Half lives of mRNAs and of Poly(A) of mRNAs of 4687 genes

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/mRNA%20half%20lives%20for%204%2C687%20genes%20Wang%202003.xlsx

Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30 99(9):5860-5 (free online article) supporting site, please see primary source

11972065

http://www-genome.stanford.edu/turnover/data.shtml

By using DNA microarrays, researchers precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II: Yeast was grown on YPD at 24 degrees celsius, transferred to a similar medium at 49 degrees and 0, 5, 10, 15, 20, 30, 40, 50, and 60 min after the temperature shift harvested on a nitrocellulose filter followed by liquid nitrogen freezing and total RNA extraction by hot phenol extraction. A nonlinear least squares model was fit to determine the decay rate constant (k) and half-life (t1/2) of each mRNA. The decay rate constant, k, is the value that minimized Si = 1,n[y(ti) - exp(-k×ti)]^2, where y(t) is the mRNA abundance at time t and the summation is taken over all observations for the particular mRNA. The half-life is t1/2 = ln2/k. The goodness of fit of the decay model for each gene was assessed with the F statistic (ref 20 in article), based on the null hypothesis that the data fit a first-order decay model. A bootstrap method was used to calculate confidence intervals for both t1/2 and k (ref 21 in article). To examine the global relationship between poly(A) shortening and mRNA turnover, researchers made a separate series of measurements of the fate of each mRNA, using an anchored oligo(dT) primer (5'-T20VN-3'), rather than random primers, in the cDNA probe synthesis. This approach allowed them to track specifically the mRNAs that retained poly(A) tails of sufficient length to allow priming. The poly(A)+ mRNA decay half-lives, as defined in their assay, were distributed within a narrower range and were significantly shorter (peak at 10â15 min) than the overall mRNA decay half-lives (Fig. 2A).

Look at 'Data' sheet in Excel file. Note, in 'Data' sheet column BF has half lives with greater values than column DM and thus BF would seem to be overall mRNA half life and DM the Poly(A) half life. However, the designation in the table (DE and BE) says the opposite, which seems to be in error. Column B gives gene name and protein function.

Uri M

constant, decay, degradation, messenger ribonucleic acid, transcript, transcriptome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2204

105627

Volume of nuclei during late anaphase

Budding yeast Saccharomyces cerevisiae

2.83

±0.53

µm^3

9362057

Uri M

phase, cell cycle, nucleus<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2250

105673

Intracellular copper concentration

Budding yeast Saccharomyces cerevisiae

µM

Rae TD, Schmidt PJ, Pufahl RA, Culotta VC, O'Halloran TV. Undetectable intracellular free copper: the requirement of a copper chaperone for superoxide dismutase. Science. 1999 Apr 30 284(5415):805-8. p. 805

10221913

Elemental analysis of hydrolyzed cells was measured by inductively coupled plasma-atomic emission spectroscopy (AtomScan ICP-AES).

Calculated from copper atoms/cell, table 1 p. 806: 3.9×10^5[Cu/cell]/6×10^23[Cu/mole]/10^-14[liter/cell]=6.5×10^-5MË70µM. The majority is in bound state.

Uri M

Cu, trace metal, SY1699<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2251

105674

Number of copper atoms in cell

Budding yeast Saccharomyces cerevisiae

390000

±20000

unitless

10221913

Elemental analysis of hydrolyzed cells was measured by inductively coupled plasma-atomic emission spectroscopy (AtomScan ICP-AES).

SY1699 (wildtype strain). Corresponds to 70µM (BNID 105673).

Uri M

Cu, trace metal,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2257

105680

Intracellular free iron pool

Budding yeast Saccharomyces cerevisiae

12.8

±1.4

µM

Srinivasan C, Liba A, Imlay JA, Valentine JS, Gralla EB. Yeast lacking superoxide dismutase(s) show elevated levels of "free iron" as measured by whole cell electron paramagnetic resonance. J Biol Chem. 2000 Sep 22 275(38):29187-92. p.29188 right column 3rd paragraph

10882731

The procedure for electron paramagnetic resonance (EPR) spectroscopy sample preparation was adapted from (Keyer et al., 1996, PMID 8942986)

A total iron conc. of ~175µM is given in fig.1 p.29189

Uri M

Ferric concentration, Fe<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2323

105746

Percentage of cells with shmoo formation after 2hours of 50 nM Î± pheromone treatment

Budding yeast Saccharomyces cerevisiae

Qi M, Elion EA. Formin-induced actin cables are required for polarized recruitment of the Ste5 scaffold and high level activation of MAPK Fus3. J Cell Sci. 2005 Jul 1 118(Pt 13):2837-48 p.2843 left column 2nd paragraph

15961405

(Differential) Nomarski Interference Contrast microscopy (DIC/NIC)

See p.2841 right column top paragraph for value of 90% shmoo formation after 2 hours of exposure to a factor

Uri M

mating yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2404

101458

Average gene length

Budding yeast Saccharomyces cerevisiae

1.4

Krebs, Goldstein & Kilpatrick, Lewin's Genes XI, 2014, Jones & Bartlett Learning, p.89 left column top paragraph

P.89 left column top paragraph: "The average yeast gene is 1.4 kb long, and very few are longer than 5 kb." For median length of RNA molecule of 1474 nucleotides see BNID 100202. For mRNA length of ~2kb see Oeffinger M et al. PMID 22387213 p.501 right column 3rd paragraph

Ben Marks

genes, size

2586

101698

Heat of combustion of S. cerevisiae grown in batch culture on glucose

Budding yeast Saccharomyces cerevisiae

-21.39

±0.33

kJ/g dry weight

Larsson C, Blomberg A, Gustafson L. Use of Microcalorimetric Monitoring in Establishing Continuous Energy Balances and in Continuous Determinations of Substrate and Product Concentrations of Batch-Grown Saccharomyces cerevisiae. Biotechnology and Bioengineering. 1991. 38(5) pp.447-458 DOI: 10.1002/bit.260380503 p.453 right column 2nd paragraph

18604803

Abstract: "Energy balance calculations were performed for different physiological states during batch growth of Saccharomyces cerevisiae with glucose as carbon and energy source."

P.453 right column 2nd paragraph: "Elemental Composition and Heat of Combustion of the Dry Biomass: The elemental composition of the cells showed small variations during batch growth between different physiological states (data not shown). Consequently, the heat of combustion values, calculated from the elemental composition (refs 9, 14) , showed a small standard deviation (SD ±0.38 kJ/g(af) dry weight, n = 4), which were within the same range as for the standard deviation between parallel samples from a specific physiological state (see below). This variation in the heat of combustion of the biomass affected the energy balance calculations by maximally 1%. Therefore, the experimentally determined heat of combustion value of -21.39±0.33 kJ/g(af) dry weight (±SD, n = 4) of stationary phase cells has been used for all energy balance calculations. The corresponding elemental composition of stationary phase cells (CH1.71O0.52N0.17), which gives a unit carbon formula weight (UCFW) of 24.4 g/C-mol, was used in the continuous substrate and product calculations presented later. These values are in agreement with data previously reported in the literature (refs 5, 9)."

Phil Mongiovi

microcalorimetry, energy

2621

101733

Number of rRNA genes

Budding yeast Saccharomyces cerevisiae

140

genes

Schweizer, E. MacKechnie, C. Halverson,HO. The Redundancy of Ribosomal and Transfer RNA Genes in Saccharomyces cerevisiae. J. Mol. Biol. 1969. 40, 261-277. abstract, p.269 bottom paragraph, p.271 table 4 & p.274 2nd paragraph

5365012

Abstract 1st paragraph: "DNA-RNA hybridization studies have been performed to determine the number of 4, 18 and 26 s RNA cistrons present in purified nuclear and mitochondrial DNA of Saccharomyces cerevisiae."

Abstract 3rd paragraph: "Assuming a genome size of yeast nuclear DNA of 1.25×10^10 daltons, the hybridization data correspond to 140 cistrons for ribosomal RNA and to 320 to 400 cistrons for transfer RNA. With the possible exception of a minor homology between 18 and 26 s ribosomal RNA, the competition experiments indicate that there are separate cistrons for all three classes of RNA." P.269 bottom paragraph: "If one accepts a nuclear genome size in yeast of 1.25x10^10 daltons (Teuro, unpublished results), the extent of hybridization between nuclear DNA and ribosomal RNA is consistent with 140 cistrons for each 18 and 26 s rRNA (Table 4)." P.274 2nd paragraph: "Evidence is presented that S. cerevisiae nuclear DNA contains 140 cistrons for both 18 and 26 s ribosomal RNA and 320 to 400 cistrons for total transfer RNA. No homology was detected between either class of RNA and mitochondrial DNA." For ~150 genes see French et al., 2003 PMID 12588976 p.1559 left column 2nd paragraph

Phil Mongiovi

rRNA genes, rRNA, rDNA, yeast, ribosomal RNA

2625

101737

Catalytic Rate of transporter HXT7

Budding yeast Saccharomyces cerevisiae

197

glucose molecules/sec

Ye L, Berden JA, van Dam K, Kruckeberg AL. Expression and activity of the Hxt7 high-affinity hexose transporter of Saccharomyces cerevisiae. Yeast. 2001 Sep 30 18(13):1257-67. p.1265 left column 2nd paragraph

11561293

"Glucose uptake was assayed as described (Walsh et al., 1994) at five concentrations of D-U- (14C)-glucose [1, 2.5, 5, 10 and 25 mM (371, 297, 148, 74 and 30 MBq/mol, respectively)]. The data were fit to the MichaelisâMenten equation using ENZFITTER software (Elsevier-Biosoft). Total cell protein was measured by the method of Lowry (Lowry et al., 1951) using a COBAS Auto-analyzer (Roche) after digestion of cells overnight in 1 N NaOH. Bovine serum albumin was used as a standard. Cell number was determined by counting at least 1000 cells with a haemocytometer."

"The cellular abundance of the Hxt7::GFP chimera and the glucose transport activity mediated by that protein were used to calculate the catalytic centre activity of Hxt7 for glucose. For the first time point (mid-exponential phase), the Hxt7::GFP cell suspension contained 0.61 mg total cell protein/ ml, giving a relationship of 4.5 pmol Hxt7::GFP/mg total cell protein. The Vmax for glucose transport of these cells, 53 nM/min/mg total cell protein, was divided by this value, resulting in an estimate of 197/s for the catalytic-centre activity of Hxt7::GFP." See BNID 101737, 101738

Ben Marks

glucose, transport, glucose transporter, Kcat, turnover<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2626

101738

Catalytic Rate of transporter HXT7 in cells that have undergone the diauxic shift

Budding yeast Saccharomyces cerevisiae

237

glucose molecules/sec

11561293

"The cellular abundance of the Hxt7::GFP chimera and the glucose transport activity mediated by that protein were used to calculate the catalytic centre activity of Hxt7 for glucose." "For the second time point (diauxic shift), the Hxt7::GFP cell suspension contained 0.57 mg total cell protein/ml, giving a relationship of 7.0 pmol Hxt7::GFP/mg total cell protein. The Vmax for glucose transport of these cells, 99 nmoles/min/mg total cell protein, was divided by this value, resulting in an estimate of 237/s for the catalytic centre activity of Hxt7::GFP."

The cellular abundance of the Hxt7::GFP chimera and the glucose transport activity mediated by that protein were used to calculate the catalyticcentre activity of Hxt7 for glucose. For the second time point (diauxic shift), the Hxt7::GFP cell suspension contained 0.57 mg total cell protein/ml, giving a relationship of 7.0 pmol Hxt7::GFP/mg total cell protein. The Vmax for glucose transport of these cells, 99 nmoles/min/mg total cell protein, was divided by this value, resulting in an estimate of 237/s for the catalytic centre activity of Hxt7::GFP. See BNID 101737, 101739

Ben Marks

glucose, transport, glucose transporter, Kcat, turnover, gfp<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2627

101739

Catalytic Rate of transporter HXT2

Budding yeast Saccharomyces cerevisiae

glucose molecules/sec

Kruckeberg AL, Ye L, Berden JA, van Dam K. Functional expression, quantification and cellular localization of the Hxt2 hexose transporter of Saccharomyces cerevisiae tagged with the green fluorescent protein. Biochem J. 1999 Apr 15 339 ( Pt 2):299-307. abstract, p. 303 left column, top sentence & p.306 left column bottom paragraph

10191260

"To investigate further the properties and regulation of Hxt2 researchers have tagged it with the green fluorescent protein (GFP) of Aequorea victoria. GFP matures after translation to be an intrinsically fluorescent protein." "[Investigators] have constructed an Hxt2-GFP fusion protein for use as a reporter of Hxt2 expression, abundance and localization within the yeast cell."

"[Investigators] calculated from the fluorescence level and transport kinetics that induced cells had 1.4x10^5 Hxt2-GFP molecules per cell, and that the catalytic-centre activity of the Hxt2-GFP molecule in vivo is 53 s-1 at 30° C." "The cellular abundance of the Hxt2-GFP chimaera and the glucose transport activity mediated by that protein were used to calculate the catalytic-centre activity for glucose of the transporter. The Hxt2-GFP cell suspension contained 0.61 mg of total cell protein/ml, giving a relationship of 32 pmol of Hxt2-GFP/mg of total cell protein. The Vmax for glucose transport of these cells, 103 nmol/min per mg of total cell protein (Table 3) was divided by this value, resulting in an estimate of 53 s^-1 for the catalytic-centre activity of Hxt2-GFP. All of the Hxt2-GFP in the cells seemed to be at the plasma membrane when examined by fluorescence microscopy (results not shown)." "By quantifying the emission from GFP in the fusion protein [investigators] were able to determine a value for the catalytic-centre activity of Hxt2-GFP in vivo. [They] estimate that under inducing conditions each hxt-null cell transformed with single-copy HXT2-GFP has 1.4×10^5 Hxt2 molecules in the plasma membrane and that the transporter has a catalytic-centre activity at 30 °C of 53 s^-1. To [their] knowledge this is the first empirical estimate of a catalytic centre activity for a yeast hexose transport protein. It assumes that all Hxt2-GFP molecules were actively transporting glucose and is therefore a minimum estimate." See BNID 101737, 101738

Ben Marks

glucose, transport, glucose transporter, Kcat, turnover, green fluorescence protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2635

101747

Population doubling time, percent budded cells, and mean cell volume for different batch culture media

Budding yeast Saccharomyces cerevisiae

Table Link - http://bionumbers.hms.harvard.edu/files/Population%20doubling%20time%2C%20percent%20budded%20cells%2C%20and%20mean%20cell%20volume%20for%20different%20batch%20culture%20media1.pdf

Tyson CB, Lord PG, Wheals AE. Dependency of size of Saccharomyces cerevisiae cells on growth rate. J Bacteriol. 1979 Apr138(1):92-8. p. 93 table 1

374379

Shortest generation time 71 min on YEP+fructose medium. Longest generation time 477 min on EMM+acetate+phtalate. See BNID 104360,100270

Ben Marks

2658

101771

Number of H+ needed to synthesize one ATP

Budding yeast Saccharomyces cerevisiae

4.333

H+/ATP

Rich, PR. The molecular machinery of Keilin's respiratory chain. Biochem Soc Trans. 2003 Dec31(Pt 6):1095-105.

14641005

The motor unit of ATP synthase requires 10 H+ to complete a full rotation, which results in the generation of three ATP. For each ATP, the energy of an additional proton is required to transport the substrates and products across the mitochondrial membrane. 13/3 is approximately 4.3 H+/ATP.

Phil Mongiovi

TCA cycle, aerobic respiration, glucose oxidation, ATP, H+, hydrogen ions, protons, ATP synthase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2668

101781

abundance of H+ ATPase protein

Budding yeast Saccharomyces cerevisiae

1260000

molecules/cell

Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature. 2003. 425(6959) pp.737-41.

14562106

This number is found in the supplemental data. It is the protein encoded by the pma1 gene.

Phil Mongiovi

proton, H+, ion transporter<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2679

101794

"Rule of thumb" for cell volume

Budding yeast Saccharomyces cerevisiae

µm^3

"Physical Biology of the Cell", Rob Phillips, Jane Kondev and Julie Theriot (2009). Page 26

See BNID 100427, 105103, 103704, 100 430

Ben Marks

size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2680

101795

"Rule of thumb" for cell mass

Budding yeast Saccharomyces cerevisiae

"Physical Biology of the Cell", Rob Phillips, Jane Kondev and Julie Theriot (2009). Page 26 table 1.1 Rules of thumb for biological estimates

P.25 3rd paragraph: "The quantitative rules of thumb in Table 1.1 will serve as the basis of [investigators'] rough numerical estimates that could be carried out using a stick in the sand without reference to books, papers, or tables of data. Where do these numbers come from? Each comes from the results of a long series of experimental measurements of many different kinds."

Ben Marks

weight, cellular mass, size

2681

101796

"Rule of thumb" for diameter of cells

Budding yeast Saccharomyces cerevisiae

µm

"Physical Biology of the Cell", Rob Phillips, Jane Kondev and Julie Theriot (2009). Page 26

See BNID 100451, 103896

Ben Marks

radius, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2682

101797

Rule of thumb for generation time of cell (cell cycle)

Budding yeast Saccharomyces cerevisiae

200

min

Physical Biology of the Cell, Rob Phillips, Jane Kondev and Julie Theriot (2009). Page 26

Se BNID 101747, 101310, 105487, 104 360

Ben Marks

doubling time,growth rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2686

101801

Empirical elemental formula for biomass

Budding yeast Saccharomyces cerevisiae

C:H(1.613):O(0.557):N(0.158)

von Stockar, U. Liu, J. Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth. 1999. Biochim Biophys Acta. 1412(3) p.198 table 4

10482783

[33] J.A. Roels, Energetics and Kinetics in Biotechnology, Elsevier, Amsterdam, 1983. [38] Edwin H. Battley, Robert L. Putnam, Juliana Boerio-Goates, Heat capacity measurements from 10 to 300 K and derived thermodynamic functions of lyophilized cells of Saccharomyces cerevisiae including the absolute entropy and the entropy of formation at 298.15 K, Thermochim. Acta 298 (1997) 37-46. doi:10.1016/S0040-6031(97)00108-1 [39] Edwin H. Battley, An empirical method for estimating the entropy of formation and the absolute entropy of dried microbial biomass for use in studies on the thermodynamics of microbial growth, Thermochim. Acta 326 (1999) 7-15. doi:10.1016/S0040-6031(98)00584-X

P.198 left column bottom paragraph: "The entropy can be directly determined using low-temperature calorimetry. The first to apply this technique to microbial biomass were Battley et al. [primary source 38]. They measured the heat capacity of lyophilized Saccharomyces cerevisiae cells over a temperature range of 10â300 K, and consequently determined the entropy of the dried biomass. Assuming that the entropy of hydration and the residual entropy of biomass are small enough to be neglected, the Gibbs energy of combustion is calculated to be â515.0 kJ/C-mol. More recently, Battley [primary source 39] proposed an empirical method to estimate the entropy of the biomass based on the atomic entropies of the atoms comprising the biomass. As he showed, this method gives very good accuracy as compared to the values calculated based on the experimentally determined entropies. The results of the reported work on the entropies and Gibbs energies of combustion of biomass are summarized in Table 4."

P.198 right column 2nd paragraph: "As seen in Table 4, the Gibbs energy of combustion for S. cerevisiae that was determined using the experimental value of entropy is within 1% of the value estimated with Roelsâ correlation, or Battleyâs empirical method. Therefore, it is hypothesized that the Gibbs energy of combustion for other microorganisms may also be estimated by using Roelsâ correlation or Battleyâs method without introducing large error in the calculation of Gibbs energy changes. In most cases, the value for average biomass (â541.2 kJ/C-mol) may be used, though some further error might be introduced." This means that for every mole of carbon, there are 1.613 moles of hydrogen, 0.557 moles of oxygen and 0.158 moles of nitrogen. There are also 0.012 moles of phosphorus, 0.003 of sulfur, 0.003 of magnesium, 0.022 of potassium and 0.001 of calcium.

Phil Mongiovi

per mole Carbon, C-mols, molecular weight, composition, molecular mass

2723

101845

Protein levels

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/yeastproteinabundances.xls

protein molecules/cell

Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature. 2003. 425(6959) pp.737-41. doi:10.1038/nature02046 Supplementary Data (Excel table)

14562106

"Cultures (1.7 ml) of tagged strains were grown in 96-well format to log phase, and total cell extracts were examined by SDSâpolyacrylamide gel electrophoresis (PAGE)/western blot analysis as described in Supplementary Information."

More than 3000 protein levels. This table is the Supplemental Data from the reference. The proteins are ordered by gene name, but could be sorted based on abundance using the function on Excel.

Phil Mongiovi

abundance, proteins, TAP, TAP tagging, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2738

101860

Peak intracellular concentration of acetate in respiratory phase

Budding yeast Saccharomyces cerevisiae

Xu Z, Tsurugi K. A potential mechanism of energy-metabolism oscillation in an aerobic chemostat culture of the yeast Saccharomyces cerevisiae. FEBS J. 2006 273(8):1696-709

16623706

Yeast were grown at 30C with glucose as the carbon source. The number is taken from figure 2c of the reference.

Phil Mongiovi

acetate, intracellular concentration, yeast

2780

101902

Rate of glucose-induced proton efflux

Budding yeast Saccharomyces cerevisiae

0.687

±0.077

nmol of H+/min/mg yeast

Holyoak et al. Activity of the plasma membrane H(+)-ATPase and optimal glycolytic flux are required for rapid adaptation and growth of Saccharomyces cerevisiae in the presence of the weak-acid preservative sorbic acid. 1996. Appl Environ Microbiol. 62(9): p.3162.

8795204

determined from the rate of proton extrusion into unbuffered water.

at pH 5.7 in late-exponential phase growth at 30 degrees C. This proton flux is primarily, if not completely through the plasma membrane H+ ATPase. Approximating the mass of 1 cell as 60pg, there are about 17 million yeast cells in 1 mg. The calculation 0.687nmol*6.02E23/17 million gives a value of about 24 million H+ per cell per min, or 400,000 H+ per cell per second.

Phil Mongiovi

proton efflux, H+, protons, H+ ATPase, plasma membrane ATPase, acid efflux, glucose-induced acid efflux, proton pump, proton pump rate, pump rates, transport rates<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2803

101928

Properties of yeast glycolytic enzymes (protein abundance, mRNA abundance, and flux)

Budding yeast Saccharomyces cerevisiae

Table Link - http://bionumbers.hms.harvard.edu/files/transcriptproteinflux.jpg

Dan G Fraenkel. The top genes: on the distance from transcript to function in yeast glycolysis. Current Opinion in Microbiology 2003, 6:198â201

12732312

Ben Marks

mrna, protein, flux, HXK1, 2, GLK1, PGI1, PFK1, 2, FBA1, TPI1, TDH1-3, PGK1, GPM1, ENO1, 2, PYK1, PDC1, 5, ADH1, ADH2, PFK26, 27, FBP1, ZWF1,transcriptome,proteome,metabolome,metabolite,glycolysis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2861

101986

Length of flanking homologous regions required for gene targeting through homologous recombination in yeast

Budding yeast Saccharomyces cerevisiae

â¥30

Manivasakam P, Weber SC, McElver J, Schiestl RH. Micro-homology mediated PCR targeting in Saccharomyces cerevisiae. Nucleic Acids Res. 1995, 23:2799-800. p.2800 right column bottom paragraph

7651842

P.2799 left column top paragraph: "In the present study, [investigators] determined the amount of homology required for targeted integration of DNA fragments into the yeast genome. The procedure described here facilitates the manipulation of the yeast genome and eliminates the need to clone sequences homologous to a target site. In addition, this method is useful for applications in which only limited sequence information of the target is available. The procedure comprises of: (i) production of PCR primers to amplify a selectable marker containing flanking homology to the target of choice (ii) transformation of yeast cells and (iii) selection of integrants."

P.2800 right column bottom paragraph: "In summary, [investigators] have defined the minimum amount of homology required for efficient homologous integration in S. cerevisiae. Homology of 30 bp on each side of a selectable marker is sufficient to obtain a large fraction of targeted integration events. This information can be applied to the economical design of primers for yeast genome modification by microhomology mediated PCR targeting."

Irina

homologous recombination, gene targeting, homologous integration, homologous arm

2883

102009

Replication errors per genome

Budding yeast Saccharomyces cerevisiae

0.002

Unitless

X. Sunney Xie, Paul J. Choi, Gene-Wei Li, Nam Ki Lee, and Giuseppe Lia, 'Single-Molecule Approach to Molecular Biology in Living Bacterial Cells', Annu. Rev. Biophys. 2008. 37:p.419

18573089

Drake JW, A constant rate of spontaneous mutation in DNA-based microbes.Proc Natl Acad Sci U S A. 1991 Aug 1588(16):7160-4

1831267

A nearly invariant microbial mutation rate appears to have evolved.

Uri M

DNA,mutation,CANI.,target,microbe,spontaneous,rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

2987

102126

GC content

Budding yeast Saccharomyces cerevisiae

38.3

Wood et al. The genome sequence of Schizosaccharomyces pombe. 2002. Nature 415, 871-880. P.872 right column 4th paragraph

11859360

P.872 right column 4th paragraph: "Gene density is similar for chromosomes I and II, with one gene every 2,483 and 2,457 bp respectively, but is less dense for chromosome III, at one gene every 2,790 bp. This is not due to differences in the average length of the genes, which are similar (1,407â1,446 bp) for all three chromosomes (Table 1). Protein-coding genes are absent from the centromeres, although tRNA genes are found in these regions. Gene density is also lower at the telomeres. The gene density for the complete genome is one gene every 2,528 bp, compared with one gene every 2,088 bp for S. cerevisiae. The protein-coding sequence is predicted to occupy 60.2% (57% excluding introns) of the sequenced portion of the S. pombe genome, compared with 71% in S. cerevisiae (70.5% excluding introns). The overall guanine and cytosine (GC) content is 36.0%, compared with 38.3% in S. cerevisiae, and for the protein-coding portion is identical in the two yeasts at 39.6%." A better reference is needed.

Phil Mongiovi

GC contents, guanine, cytosine

3053

105836

Levels of polyP in mitochondria

Budding yeast Saccharomyces cerevisiae

0.022-0.44 table link - http://bionumbers.hms.harvard.edu/files/Levels%20of%20polyP%20inmitochondria%20of%20S.%20cerevisiae.pdf

µmol P/mg protein

Kulakovskaya TV, Lichko LP, Vagabov VM, Kulaev IS. Inorganic polyphosphates in mitochondria. Biochemistry (Mosc). 2010 Jul75(7):825-31. http://tinyurl.com/zcyv76s p.826 table 1

20673205

[25] Pestov NA, Kulakovskaya TV, Kulaev IS. Inorganic polyphosphate in mitochondria of Saccharomyces cerevisiae at phosphate limitation and phosphate excess. FEMS Yeast Res. 2004 Mar4(6):643-8. [26] Pestov, N. A. (2004) Polyphosphates and Exopolyphosphatases of Mitochondria of Yeast Saccharomyces cerevisiae: PhD Thesis [in Russian], Pushchino. [27] Andreeva NA, Kulakovskaya TV, Kulakovskaya EV, Kulaev IS. Polyphosphates and exopolyphosphatases in cytosol and mitochondria of Saccharomyces cerevisiae during growth on glucose or ethanol under phosphate surplus. Biochemistry (Mosc). 2008 Jan73(1):65-9.

15040953, 18294131

P.826 right column 2nd paragraph: "Later, the polyP from isolated mitochondria of S. cerevisiae was studied by chemical extraction with 0.5 N HClO4 [perchloric acid] and electrophoresis in polyacrylamide gel [primary sources]."

P.826 right column 2nd paragraph: "[Promitochondria] contained polyP at a level strongly dependent on Pi concentration in the culture medium (Table 1)." P.826 right column 3rd paragraph: "Under phosphate overplus, this level was nearly twofold higher than in the complete medium without preliminary Pi starvation (Table 1). The chain length of acid_soluble polyP of mitochondria was estimated by electrophoresis. Under Pi limitation, their polyP level was too low to be detected by this method. The chain length was <15 phosphate residues. This is close to the value determined by 31P_NMR [ref 24]. Under phosphate overplus, the mitochondrial polyP chains became longer. At the same time, polyP accumulation in mitochondria was not observed during cultivation on ethanol under aeration, even under polyP overplus in the cells [primary source 27]. Their content was extremely low (Table 1)."

Uri M

inorganic polyphosphates, mitochondrion

3054

105837

Levels of polyP (polyP1,2,3,4,5) in mitochondria in cells grown on glucose and ethanol

Budding yeast Saccharomyces cerevisiae

51.7-468 Glucose: 63-320 Ethanol

µmolP/g dry biomass

Kulakovskaya TV, Lichko LP, Vagabov VM, Kulaev IS. Inorganic polyphosphates in mitochondria. Biochemistry (Mosc). 2010 Jul75(7):825-31. p.829 table 3 table link - http://bit.ly/bXZ39C

20673205

Vagabov VM, Trilisenko LV, Kulakovskaya TV, Kulaev IS. Effect of a carbon source on polyphosphate accumulation in Saccharomyces cerevisiae. FEMS Yeast Res. 2008 Sep8(6):877-82.

18647178

Five separate fractions of polyP have been obtained from the cells grown on glucose and ethanol under phosphate overplus.

Uri M

inorganic polyphosphates, mitochondrion, polyp1, polyp2, polyp3, polyp4, polyp5<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3055

105838

Properties of mitochondrial fractions obtained from strains grown on glucose, stationary growth phase

Budding yeast Saccharomyces cerevisiae

Table link - http://bit.ly/cXrGBP

Kulakovskaya TV, Lichko LP, Vagabov VM, Kulaev IS. Inorganic polyphosphates in mitochondria. Biochemistry (Mosc). 2010 Jul75(7):825-31. p.829 table 4

20673205

Pestov NA, Kulakovskaya TV, Kulaev IS. Effects of inactivation of the PPN1 gene on exopolyphosphatases, inorganic polyphosphates and function of mitochondria in the yeast Saccharomyces cerevisiae. FEMS Yeast Res. 2005 Jun5(9):823-8. DOI: 10.1016/j.femsyr.2005.03.002

15925310

The goal of primary source study was to compare the effects of inactivation of the PPX1 and PPN1 genes on polyP metabolism and mitochondrial function in S. cerevisiae. The respiratory control ratio was measured by means of an oxygen electrode (Estabrook 1967, doi:10.1016/0076-6879(67)10010-4)

Uri M

inorganic polyphosphates, mitochondrion, endopolyphosphatase, Exopolyphosphatase, hydrolase, Respiratory control, Phosphorus/Oxygen ratio, parent strain<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3056

105839

Fraction of PolyP located in mitochondria

Budding yeast Saccharomyces cerevisiae

Beauvoit, B., Rigonlet, M., Guerin, B., and Canioni, P. Polyphosphates as a source of high energy phosphates in yeast mitochondria: A 31P NMR study, FEBS letters Volume 252, Issues 1-2, July 1989, Pages 17-21 p.20 right column top sentence doi:10.1016/0014-5793(89)80882-8

31P NMR (nuclear magnetic resonance)

average length of 14±1 residues per chain. Note-Kulakovskaya et al., 2010 PMID 20673205 give fraction of PolyP in mitochondria in range of 7%-10%. See BNID 103449, 103450

Uri M

inorganic polyphosphates, mitochondrion<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3057

105840

Fraction of phosphate in form of PolyP

Budding yeast Saccharomyces cerevisiae

Langen, P., Liss, E. and Lohmann, K. (1962) in: Acides Ribonucleiques et Polyphosphates: Structures, Synthese et Fonctions, Colloq. Int. CNRS, Strasbourg, pp.603-612, CNRS Paris.

In Saccharomyces cerevisiae, the poly(P) account for about 37% of the total phosphate content and consist of linear chains with 20 phosphates units or even more (primary source)

Uri M

inorganic polyphosphates, content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3058

105841

Duration of yeast metabolic cycle (YMC)

Budding yeast Saccharomyces cerevisiae

0.667 to 10.0

hours

Laxman S, Sutter BM, Tu BP. Behavior of a metabolic cycling population at the single cell level as visualized by fluorescent gene expression reporters. PLoS One. 2010 Sep 7 5(9):e12595. p. 1 left column doi:10.1371/journal.pone.0012595

20830298

5) Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science. 2005 Nov 18 310(5751):1152-8 (6) Tu BP, McKnight SL. Metabolic cycles as an underlying basis of biological oscillations. Nat Rev Mol Cell Biol. 2006 Sep7(9):696-701 (7) Tu BP, McKnight SL. The yeast metabolic cycle: insights into the life of a eukaryotic cell. Cold Spring Harb Symp Quant Biol. 2007 72: 339-43.

16254148, 16823381, 18419291

When yeast cells are grown to a high density, starved for a short period, and then continuously fed low concentrations of glucose using a chemostat, the cell population becomes highly synchronized and undergoes robust oscillations in oxygen consumption termed yeast metabolic cycles (YMC) (primary sources). Such cycles can range anywhere from 40 minutes to over 10 hours depending on the continuous glucose concentration. Numbers of primary sources correspond to numbers of references in article.

Uri M

periodicity, oscillation, oscillatory behavior, period, duration, time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3059

105842

Fraction of genes expressed periodically during 4â5 hour yeast metabolic cycle

Budding yeast Saccharomyces cerevisiae

20830298

Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science. 2005 Nov 18 310(5751):1152-8

16254148

(primary source) To understand the molecular basis of these metabolic cycles, researchers performed microarray analysis of gene expression and assessed whether any genes were expressed periodically.

Note-although ref cites primary source, value wasn't located there. Instead on p.1158 left column 2nd paragraph of primary source the following value appears: "mRNAs for over 60% of annotated yeast transcription factors fluctuated in abundance as a function of the YMC (yeast metabolic cycle)". See BNID 105843

Uri M

periodicity, oscillation, oscillatory behavior, period, duration, time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3060

105843

Classification of periodic genes

Budding yeast Saccharomyces cerevisiae

Table link - http://bit.ly/bkwnaU

Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science. 2005 Nov 18 310(5751):1152-8 1153 table 1 DOI: 10.1126/science.1120499

16254148

To understand the molecular basis of the yeast metabolic cycles (YMC), researchers performed microarray analysis of gene expression and assessed whether any genes were expressed periodically.

Genes encoding proteins associated with energy, metabolism, and protein synthesis were overrepresented in the list of periodic genes. Moreover, characterization of the periodic genes with the yeast proteome localization data (Huh et al., 2003 PMID 14562095) indicated that gene products localized to the mitochondria, cell periphery, and bud neck tended to be expressed periodically. See BNID 105842

Uri M

periodicity, oscillation, oscillatory behavior, period, duration, time, Energy, metabolism, Protein synthesis, Mitochondria, Cell periphery, Bud neck, Transcription, Protein binding, Protein fate, Nucleolus, Early Golgi, Nuclear periphery, Localization, function, yeast metabolic cycle<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3112

105895

Fraction of consumed glucose molecules that enter the pentose phosphate pathway

Budding yeast Saccharomyces cerevisiae

16.2 Batch culture 44.2 Chemostat

Gombert AK, Moreira dos Santos M, Christensen B, Nielsen J. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J Bacteriol. 2001 Feb183(4):1441-51. p.1448 right column top paragraph

11157958

Metabolic network analysis was performed by combining labeling experiments with mathematical modelling (Christensen et al., 2000 PMID 10592531)

In this way, it was possible to compare cells growing in a chemostat at steady state, with a speci?c growth rate of 0.1h^-1, with cells growing in a batch cultivation, with µmax=0.37h^-1, in a quantitative fashion.

Uri M

pp pathway,catabolism,glucose repression,central carbon metabolism<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3153

105936

Cell composition in chemostat and in batch culture

Budding yeast Saccharomyces cerevisiae

Table link - http://tinyurl.com/6b6m4gx

11157958

11) Ertugay, N., and H. Hamamci. 1997. Continuous cultivation of bakerâs yeast: change in cell composition at different dilution rates and effect of heat stress on trehalose level. Folia Microbiol. 42:463â467. (21). Ku¨enzi, M. T., and A. Fiechter. 1972. Regulation of carbohydrate composition of Saccharomyces cerevisiae under growth limitation. Arch. Mikrobiol. 84:254â265. (30) Nissen, T., U. Schulze, J. Nielsen, and J. Villadsen. 1997. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 143:203â218. (32) O¨ stling, J., and H. Ronne. 1998. Negative control of the Mig1p repressor by Snf1-dependent phosphorylation in the absence of glucose. Eur. J. Biochem. 252:162â168. (33) Oura, E. 1972. The effect of aeration on the growth energetics and biochemical composition of bakerâs yeast, with an appendix: reactions leading to the formation of yeast cell material from glucose and ethanol. Ph.D. thesis. Helsinki University, Helsinki, Finland. (41) van Gulik, W. M., and J. J. Heijnen. 1995. A metabolic network stoichiometry analysis of microbial growth and product formation. Biotechnol. Bioeng. 48:681â698. (43) Verduyn, C. 1991. Physiology of yeasts in relation to biomass yields. Antonie Leeuwenhoek 60:325â353.

9438349, 4559459, 9025295, 9523726, 18623538, 1807201

Cells grown in a chemostat at steady state, with a speci?c growth rate of 0.1h^-1, and cells grown in a batch cultivation, with µmax=0.37h^-1.

Uri M

protein, lipid, carbohydrate, lipid, ashes, content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3192

105975

Intracellular pH of stationary phase cells suspended in water

Budding yeast Saccharomyces cerevisiae

5.5

±0.17

Unitless

Cimprich P, Slavík J, Kotyk A. Distribution of individual cytoplasmic pH values in a population of the yeast Saccharomyces cerevisiae. FEMS Microbiol Lett. 1995 Aug 1 130(2-3):245-51 p.248 right column top paragraph and fig.3a

7649447

Fluorescence spectroscopy of an intracellular dye subjected to excitation at two different wavelengths.

Range is standard deviation. Full width at half maximum (of the Gaussian) is 0.4 pH units. n=80

Uri M

acidity, H+ concentration, cytoplasm<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3193

105976

Intracellular pH of stationary phase cells after 15 min in strong buffer

Budding yeast Saccharomyces cerevisiae

±0.15

Unitless

7649447

Fluorescence spectroscopy of an intracellular dye subjected to excitation at two different wavelengths.

Fifteen minutes after resuspension in a strong buffer (0.2 M TEPA) the distribution was slightly narrower than stationary phase (BNID 105975)-full width at half maximum (of the Gaussian) is 0.36 instead of 0.4pH units. Range is standard deviation. n=60

Uri M

acidity, H+ concentration, cytoplasm<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3194

105977

Intracellular pH of lag phase cells suspended in water

Budding yeast Saccharomyces cerevisiae

5.15

±0.18

Unitless

7649447

Fluorescence spectroscopy of an intracellular dye subjected to excitation at two different wavelengths.

Range is standard deviation. Full width at half maximum (of the Gaussian) is 0.42 pH units. n=60. The same pH distribution was found also for resting cells.

Uri M

acidity, H+ concentration, cytoplasm, resting cells<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3195

105978

Intracellular pH of exponential phase cells suspended in water

Budding yeast Saccharomyces cerevisiae

5.25

±0.18

Unitless

7649447

Fluorescence spectroscopy of an intracellular dye subjected to excitation at two different wavelengths.

Range is standard deviation. Full width at half maximum (of the Gaussian) is 0.42 pH units. n=60.

Uri M

acidity, H+ concentration, cytoplasm, resting cells<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3196

105979

pH range into which 99% of the population in different conditions of growth would be included

Budding yeast Saccharomyces cerevisiae

0.9 to 1.1

pH units

7649447

Fluorescence spectroscopy of an intracellular dye subjected to excitation at two different wavelengths.

Corresponding to full width at half maximum (of the Gaussian) of 0.36 to 0.42pH units. For the different growth conditions see BNID 105975, 105976, 105977, 105978

Uri M

acidity, H+ concentration, cytoplasm<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3234

106017

Concentration of several proposed regulatory metabolites of the Pasteur effect in aerobiosis and anaerobiosis

Budding yeast Saccharomyces cerevisiae

Table link - http://bit.ly/hZVGI4

Lagunas R, Gancedo C. Role of phosphate in the regulation of the Pasteur effect in Saccharomyces cerevisiae. Eur J Biochem. 1983 Dec 15 137(3):479-83. p.481 table 3 http://kirschner.med.harvard.edu/files/bionumbers/Concentration%20of%20several%20proposed%20regulatory%20metabolites%20of%20the%20Pasteur%20effect%20in%20aerobiosis%20and%20anaerobiosis%20in%20yeast.pdf

6229402

"[Investigators] measured the levels of a series of metabolites possibly related to the Pasteur effect in cultures which showed the effect and compared them with those measured in cultures that did not show it. A group of metabolites was formed by glycolytic intermediates (Table 2) and other by metabolites that have been implicated as possible regulators in the Pasteur effect (Table 3). Included in this latter group are fructose 2,6-bisphosphate and 2-oxoglutarate, this last compound being the product of an enzyme potentially implicated in the Pasteur effect [4]."

See notes beneath table

Uri M

Fructose2, 6bisPhosphate, ATP, ADP, AMP, Citrate, 2-Oxoglutarate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3235

106018

Concentration of Fructose 2,6-bisphosphate in glucose medium, aerobic growth

Budding yeast Saccharomyces cerevisiae

1.2

±0.2

µM

6229402

Fructose 2,6-bisphosphate was determined with pyrophosphate: fructose-6-phosphate phosphotransferase from potato tubers as described by van Schaftingen et al. [1982, PMID 6297885]. See note beneath table

Measured upon transfer to resting medium.

Uri M

Fructose2, 6bisPhosphate, glycolysis, metabolite, Fru-2, 6-P2<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3236

106019

Concentration of phosphate in glucose medium, aerobic growth

Budding yeast Saccharomyces cerevisiae

±1

6229402

Phosphate was determined by the method of Lowry and Lopez [1946, PMID 21018750]. See note beneath table

Measured upon transfer to resting medium.

Uri M

Pi, inorganic phosphate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3237

106020

Concentration of ATP in glucose medium, aerobic growth

Budding yeast Saccharomyces cerevisiae

1.9

±0.1

6229402

Spectrophotometric methods [Bergmeyer, H. U. (1974)]. See note beneath table

Measured upon transfer to resting medium.

Uri M

adenosine triphosphate, energy currency<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3238

106021

Concentration of ADP in glucose medium, aerobic growth

Budding yeast Saccharomyces cerevisiae

0.32

±0.02

6229402

Spectrophotometric methods [Bergmeyer, H. U. (1974)]. See note beneath table

Measured upon transfer to resting medium.

Uri M

adenosine diphosphate, nucleotide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3239

106022

Concentration of AMP in glucose medium, aerobic growth

Budding yeast Saccharomyces cerevisiae

0.19

±0.02

6229402

Spectrophotometric methods [Bergmeyer, H. U. (1974)]. See note beneath table

Measured upon transfer to resting medium.

Uri M

adenosine monophosphate, nucleotide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3240

106023

Concentration of citrate in glucose medium, aerobic growth

Budding yeast Saccharomyces cerevisiae

5.2

±0.5

6229402

Spectrophotometric methods [Bergmeyer, H. U. (1974)]. See note beneath table

Measured upon transfer to resting medium.

Uri M

citric acid,metabolite<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3241

106024

Concentration of 2-oxoglutarate in glucose medium, aerobic growth

Budding yeast Saccharomyces cerevisiae

±0.2

6229402

Spectrophotometric methods [Bergmeyer, H. U. (1974)]. See note beneath table

Measured upon transfer to resting medium.

Uri M

a-Ketoglutaric acid,metabolite<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3403

106186

Mean information content (number of base pairs) in transcription factor sequence

Budding yeast Saccharomyces cerevisiae

13.8

Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 2009 Oct25(10):434-40. p.436 right column 2nd paragraph

19815308

Yeast TF motifs have a mean information content of I=13.8 bits, which is below the required Imin~24 bits (BNID 106185), but represents a smaller information deficiency (IminâI~10 bits) than that of the multicellular eukaryotes (IminâI~18 bits).

Uri M

nucleic acid, DNA, information theory, saccharomyces, budding yeast,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3408

106191

Decrease in diffusion coefficient of 2 proteins in cytoplasm compared to dilute solution

Budding yeast Saccharomyces cerevisiae

Fold

Pielak GJ, Li C, Miklos AC, Schlesinger AP, Slade KM, Wang GF, Zigoneanu IG. Protein nuclear magnetic resonance under physiological conditions. Biochemistry. 2009 Jan 20 48(2):226-34. p.227 right column 1st paragraph

19113834

Williams SP, Haggie PM, Brindle KM. 19F NMR measurements of the rotational mobility of proteins in vivo. Biophys J. 1997 Jan72(1):490-8.

8994636

19F NMR,nuclear magnetic resonance

Uri M

diffusion rate, glycolytic enzymes, phosphoglycerate kinase, hexokinase, aqueous solution,cytosol<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3415

106198

Total number of proteins per cell

Budding yeast Saccharomyces cerevisiae

~5e+7

Molecules/cell

Futcher B, Latter GI, Monardo P, McLaughlin CS, Garrels JI. A sampling of the yeast proteome. Mol Cell Biol. 1999 Nov19(11):7357-68. p.7358 left column 4th paragraph

10523624

A haploid yeast cell contains about 4×10^-12g of protein (refs 1, 15). Assuming a mean protein mass of 50kDa, there are about 50×10^6 molecules of protein per cell. 6×10^23[proteins/mole]×4×10^ -12[gram]/50000[gram/mole]=~50×10^6proteins

P.7358 left column 4th paragraph: "A haploid yeast cell contains about 4×10^-12g of protein (refs 1, 15). Assuming a mean protein mass of 50 kDa, there are about 50×10^6 molecules of protein per cell. There are about 1.8 methionines per 10kDa of protein mass, which implies 4.5×10^8 molecules of methionine per cell (neglecting the small pool of free Met). [Researchers] measured (i) the counts per minute in each spot on the 2D gels, (ii) the total number of counts on each gel (by integrating counts over the entire gel), and (iii) the total number of counts loaded on the gel (by scintillation counting of the original sample). Thus, [they] know what fraction of the total incorporated radioactivity is present in each spot. After correcting for the methionine (and cysteine [see below]) content of each protein, [they] calculated an absolute number of protein molecules based on the fraction of radioactivity in each spot and on 50×10^6 total molecules per cell." See BNID 104313

Uri M

concentration, content, abundance

3418

106201

Number of mRNAs and proteins per cell

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20proteins%20and%20mRNA%20per%20cell.pdf

Futcher B, Latter GI, Monardo P, McLaughlin CS, Garrels JI. A sampling of the yeast proteome. Mol Cell Biol. 1999 Nov19(11):7357-68. p.7361 table 1 and p.7362 table 2

10523624

Two-dimensional (2D) gel electrophoresis

The relative abundance of proteins was measured in glucose and ethanol media. See table 2 (beneath table 1) for functions of proteins listed in Table 1

Uri M

concentration, content, abundance, transcript, enzyme, Carbohydrate metabolism, Adh1, Adh2, Cit2, Eno1, Eno2, Fba1, Hxk1, 2, Icl1, Pdb1, Pdc1, Pfk1, Pgi1, Pyc1, Tal1, Tdh2, Tdh3, Tpi1, Protein synthesis Efb1, Eft1, 2, Prt1, Rpa0, Tif1, 2, Yef3, Heat shock Hsc82, Hsp60, Hsp82, Hsp104, Kar2, Ssa1, Ssa2, Ssb1, 2, Ssc1, Sse1, Sti1, Amino acid synthesis Ade1, Ade3, Ade5, 7, Arg4, Gdh1, Gln1, His4, Ilv5, Lys9, Met6, Pro2, Ser1, Trp5, Adk1, Ald6, Atp2, Bmh1, Bmh2, Cdc48, Cdc60, Erg20, Gpp1, Gsp1, Ipp1, Lcb1, Mol1, Pab1, Psa1, Rnr4, Sam1, Sam2, Sod1, Uba1, YKL056, YLR109, YMR116<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3419

106202

Number of proteins per mRNA

Budding yeast Saccharomyces cerevisiae

4000

Proteins/transcript

Futcher B, Latter GI, Monardo P, McLaughlin CS, Garrels JI. A sampling of the yeast proteome. Mol Cell Biol. 1999 Nov19(11):7357-68. p.7360 right column 2nd paragraph and p.7361 table 1 Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20proteins%20and%20mRNA%20per%20cell.pdf

10523624

Estimates of mRNA abundance for each gene have been made by SAGE (Velculescu et al., 1997 PMID 9008165) and by hybridization of cRNA to oligonucleotide arrays (Wodicka et al., 1997 PMID 9415887). These data on mRNA and protein abundance (Table 1) suggest that for each mRNA molecule, there are on average 4,000 molecules of the cognate protein.

See BNID 104185

Uri M

3430

106213

Number of spurious transcription factor binding sites per genome

Budding yeast Saccharomyces cerevisiae

10^2 to 10^4

Spurious sites per transcription factor

Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 2009 Oct25(10):434-40. p.437 left column 2nd paragraph

19815308

Using information theory and simulations, researchers estimate the lower bound of the number of such spurious sites or hits as h=2^(Imin-I), with an average spacing s=2^I between them

Assuming 0 to 80% chromatinization. See BNID 106212

Uri M

nucleic acid, DNA, information theory, chromatin,nonfunctional binding<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3435

106218

Translation parameters calculated in model

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Translational%20parameters%20calculated%20in%20model.pdf

Siwiak M, Zielenkiewicz P. A comprehensive, quantitative, and genome-wide model of translation.PLoS Comput Biol. 2010 Jul 29 6(7):e1000865. p.3 out of 12 table 1

20686685

Researchers developed a model to measure the absolute, translational activity at the level of individual genes.

See parameter annotation beneath table

Uri M

protein synthesis,transcript half life,transcript life time,translation,ribosome,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3441

106224

Ribosome efficiency

Budding yeast Saccharomyces cerevisiae

8.8 fast growing cells: 5.2 slow growing cells

aa/sec/ribosome

Waldron C, Jund R, Lacroute F. Evidence for a high proportion of inactive ribosomes in slow-growing yeast cells. Biochem J. 1977 Dec 15 168(3):409-15. p.411 table 1

343781

The times required to synthesize polypeptides of different molecular weights were determined from the kinetics of incorporation of a radioactive amino Acid.

Nitrogen source of fast growing cells (0.54 doublings/hour) was (NH4)2SO4. Nitrogen source of slow growing cells (0.31 doublings/hour) was L-Proline

Uri M

translation, protein synthesis rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3442

106225

Total amount of protein in cell

Budding yeast Saccharomyces cerevisiae

4.9e-12 to 6.4e-12

Grams

Siwiak M, Zielenkiewicz P. A comprehensive, quantitative, and genome-wide model of translation.PLoS Comput Biol. 2010 Jul 29 6(7):e1000865. p.5 out of 15 left column 2nd paragraph

20686685

16) von der Haar T, McCarthy JE. Intracellular translation initiation factor levels in Saccharomyces cerevisiae and their role in cap-complex function. Mol Microbiol. 2002 Oct46(2):531-44. (35) Baroni MD, Martegani E, Monti P, Alberghina L. Cell size modulation by CDC25 and RAS2 genes in Saccharomyces cerevisiae.Mol Cell Biol. 1989 Jun9(6) :2715-23.

12406227, 2548086

4.9×10^-12 g from primary source [16], 6.4×10^-12 g from primary source [35]. Siwiak et al. in this study estimated that the total mass of proteins in a yeast cell is around 2.2×10^-12 g.

Uri M

protein content, weight, mass<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3443

106226

Total number of trancripts in cell

Budding yeast Saccharomyces cerevisiae

36000

unitless

Siwiak M, Zielenkiewicz P. A comprehensive, quantitative, and genome-wide model of translation.PLoS Comput Biol. 2010 Jul 29 6(7):e1000865. p.11 out of 15 right column 2nd paragraph

20686685

"Two reports provide an independent, yet coherent, estimation of the total number of ribosomes: 187,000±56,000 [BNID 100267] and 200,000 [ref 57] molecules per cell. In this study, [researchers] decided to set W to 200,000. The value of 85% was established for the parameter p, as stated in experimental studies [refs 61,62]. The number of all transcripts in a cell is more problematic. Many contemporary studies assume that a yeast cell contains 15,000 mRNAs per cell on average [refs 27,63], which is based on estimations done over 30 years ago [ref 64]. Current research, based on more up-to-date techniques (e.g., in situ hybridisation or GATC-PCR) argues that the number should be at least doubled [ref 65] or even quadrupled [ref 62]. [Researchers] decided to use the value of X situated between these estimates and equal to 36,000. This number was also confirmed by other studies [Miura et al., 2008 PMID 19040753 p.9 right column 2nd paragraph & p.10 left column 2nd paragraph, method-Generalized Adaptor-Tagged Competitive PCR (GATC-PCR)]." See BNID 102988, 103023

Uri M

mRNA content, macromolecule<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3444

106227

Translational parameters calculated for 14 genes coding proteins of the 20S yeast proteasome

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Translational%20parameters%20calculated%20for%2014%20genes%20coding%20proteins%20of%20the%2020S%20yeast%20proteasome.pdf

Siwiak M, Zielenkiewicz P. A comprehensive, quantitative, and genome-wide model of translation.PLoS Comput Biol. 2010 Jul 29 6(7):e1000865. Supplementary material Table S3

20686685

See description of parameters above table.

Uri M

transcripts per cell, protein, ribosome density, translation initiation, elongation, mRNA half-life, life time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3445

106228

Number of transcripts and proteins per cell of expressed genes

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20transcripts%20and%20proteins%20per%20cell%20of%20expressed%20genes.pdf

Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999 Mar19(3):1720-30. pp.1723-1724 table 1

10022859

Protein expression levels were quantified by metabolic labeling of the yeast proteins to a steady state, followed by 2DE (two-dimensional gel electrophoresis) and liquid scintillation counting of the selected, separated protein species. mRNA quantitation by serial analysis of gene expression (SAGE).

Uri M

Protein, abundance, mRNA abundance, gene expression, CPR1, EGD2, YKL056C, YER067W, YLR109W, ATP7, GUK1, SAR1, TSA1, EFB1, SOD2, HSP26, ADK1, YKL117W, TFS1, URA5, GSP1, RPS5, MRP8, RPE1, RPS3, VMA4, TPI1, PRE8, YHR049W, YNL010W, GPM1, HOR2, YST1, PUP2, YMR226C, DPM1, PRE4, PRB, BMH1, OMP2, GPP1, ILV6, IPP1, HIS1, SPE3, ADE1, SEC14, URA1, BEL1, YDL124W, TDH1, CAR1, TDH2, APA1, YJR105W, YJR105W, ADH2, ADH1, TAL1, IDH2, ILV5, BAT1, QCR2, FBA1, HOM2, PSA1, YNL134C, BAT2, ERG10, TOM40, CYS3, DYS1, SER1, ERG6, YBR025C, TIF1, PGK1, CAR2, IDP1, IDP2, ENO1, ENO2, COR1, AAT2, WTM1, MET17, LYS9, SUP45, PRO2, TEF2, YDR190C, YEL047C, TUB2, LPD1, SHM2, YFR044C, HXK2, GYP6, ALD6, ADE, PYK1, YEL071W, PDI1, GLK1, ATP1, CYS4, ARO8, CYB2, FRS2, ZWF1, THR4, SRV2, VMA2, ACH1, PDC1, 38 CCT8, PDC5, ICL1, ILV3, PGM2, PAB1, STI1, SSB1, LEU4, SSA2, YKL029C, GRS1, MET6, EFT1, ADE3, MCM3<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3482

106265

Number of tRNA molecules and ribosomes in yeast cells growing in different media

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20tRNA%20molecules%20and%20ribosomes%20in%20yeast%20cells%20growing%20in%20different%20media1.pdf

Waldron C, Lacroute F. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol. 1975 Jun122(3):855-65. p.862 table 4

1097403

Total RNA from cells growing in different media was analyzed by electrophoresis. From estimates of the tRNA fraction and of total RNA content researchers could calculate the number of tRNA molecules per cell in each growth medium

See table 1, at bottom of table link, beneath table 4, for composition of growth media and growth rates. See notes beneath table

Uri M

Growth rate, tRNA, ribosome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3483

106266

Number of tRNA molecules in cells growing on glucose and casein hydrolysate

Budding yeast Saccharomyces cerevisiae

3300000

Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20tRNA%20molecules%20and%20ribosomes%20in%20yeast%20cells%20growing%20in%20different%20media1.pdf

tRNA/cell

Waldron C, Lacroute F. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol. 1975 Jun122(3):855-65. p.862 table 4

1097403

See table 1, beneath table 4 in table link for composition of growth media and growth rates

Uri M

Growth rate,tRNA,ribosome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3484

106267

Comparison of estimated mRNA synthesis rates

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Comparison%20of%20estimated%20mRNA%20synthesis%20rates%20for%20intron%20containing%20and%20non-intron-containing%20ribosomal%20protein%20and%20non%20ribosomal%20proteins.pdf

Ares M Jr, Grate L, Pauling MH. A handful of intron-containing genes produces the lion's share of yeast mRNA. RNA. 1999 Sep5(9):1138-9. p.1139 table 1

10496214

Holstege et al., Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998 Nov 25 95(5):717-28.

9845373

Researchers separated yeast genes into intron-containing and intron-lacking classes and summed the estimated number of mRNAs synthesized each hour in each class.

Note-link beneath table doesn't work

Uri M

transcript,mRNA,gene<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3492

106275

Molecular mass of V- ATPases

Budding yeast Saccharomyces cerevisiae

650 peripheral V1 domain: 260 integral V0 domain

kDa

Inoue T, Wilkens S, Forgac M. Subunit structure, function, and arrangement in the yeast and coated vesicle V-ATPases. J Bioenerg Biomembr. 2003 Aug35(4):291-9. p.292 left column 1st paragraph

14635775

Nishi T, Forgac M. The vacuolar (H+)-ATPasesnature's most versatile proton pumps. Nat Rev Mol Cell Biol. 2002 Feb3(2):94-103. AND Zhang, J., Feng, Y., and Forgac, M. (1994). J. Biol. Chem. 269, 23518â 23523.

11836511

V1 is in cytoplasm, Vo in the membrane

Uri M

Vacuolar-type H+-ATPase, molecular weight, ATP synthase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3506

106289

Number of c-rings in ATPase (equivalent to number of protons translocated/rotation)

Budding yeast Saccharomyces cerevisiae

Unitless

Stock D, Leslie AG, Walker JE. Molecular architecture of the rotary motor in ATP synthase. Science. 1999 Nov 26 286(5445):1700-5. p.1701 left column bottom sentence

10576729

X-ray scattering techniques

Uri M

ATP synthase, pmf, proton motif force, H+,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3516

106299

Cell concentration for culture at stationary phase with OD600 of 1 at 10°C

Budding yeast Saccharomyces cerevisiae

9000000

Cells/ml

Margesin R. Effect of temperature on growth parameters of psychrophilic bacteria and yeasts. Extremophiles. 2009 Mar13(2):257-62 p.261 fig.2 right bottom graph

19057843

P.258 right column 2nd paragraph: "Culture turbidity (optical density) was measured spectrophotometrically a 600 nm (OD600). Numbers of viable cells were determined by the plate count method on the bacterial or yeast medium as described above, solidified with agar (15 g/l). Colony-forming units (cfu) were counted after 2 days at 25°C (Pedobacter heparinus, Saccharomyces cerevisiae), 3 days at 20°C (Pedobacter piscium, P.heparinus, Leucosporidiella creatinivora), or after 5 days at 15°C (Rhodotorula glacialis). Only plates containing 30â300 colonies were used for statistically valid enumeration (Koch 1994)." Value extracted visually from fig. 2

The optical density of yeast and bacterial cultures is due to light scattering, not absorption. Therefore it is sensitive to the geometry of the detector relative to the cuvette, as well as the size and shape of the cells. You really have to calibrate each spectrophotometer for each strain.

Uri M

optical density, absorbance, od

3517

106300

Cell concentration for culture at stationary phase with OD600 of 1 at 20°C

Budding yeast Saccharomyces cerevisiae

11000000

Cells/ml

Margesin R. Effect of temperature on growth parameters of psychrophilic bacteria and yeasts. Extremophiles. 2009 Mar13(2):257-62 p.261 fig.2 right bottom graph

19057843

Culture turbidity (optical density) was measured spectrophotometrically a 600 nm (OD600). Numbers of viable cells were determined by the plate count method on the bacterial or yeast medium. Value extracted manually from fig. 2

Uri M

optical density, absorbance, od<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3518

106301

Cell concentration for culture at stationary phase with OD600 of 1 at 30°C

Budding yeast Saccharomyces cerevisiae

8000000

Cells/ml

Margesin R. Effect of temperature on growth parameters of psychrophilic bacteria and yeasts. Extremophiles. 2009 Mar13(2):257-62 p.261 fig.2 right bottom graph

19057843

"Culture turbidity (optical density) was measured spectrophotometrically a 600 nm (OD600). Numbers of viable cells were determined by the plate count method on the bacterial or yeast medium as described above, solidified with agar (15 g/l). Colony-forming units (cfu) were counted after 2 days at 25°C (Pedobacter heparinus, Saccharomyces cerevisiae), 3 days at 20°C (Pedobacter piscium, P. heparinus, Leucosporidiella creatinivora), or after 5 days at 15°C (Rhodotorula glacialis). Only plates containing 30â300 colonies were used for statistically valid enumeration (Koch 1994)." Value extracted visually from fig. 2

Uri M

optical density, absorbance, od<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3519

106302

Maximum OD600 of cells in YPGal medium

Budding yeast Saccharomyces cerevisiae

6.87

±0.07

Unitless

Boccazzi P, Zhang Z, Kurosawa K, Szita N, Bhattacharya S, Jensen KF, Sinskey AJ. Differential gene expression profiles and real-time measurements of growth parameters in Saccharomyces cerevisiae grown in microliter-scale bioreactors equipped with internal stirring. Biotechnol Prog. 2006 May-Jun22(3):710-7. p.714 left column 5th paragraph

16739953

OD600 data for biomass determination were obtained from transmission measurements using an orange LED (Epitex L600- 10V, 600 nm, Kyoto, Japan).

The composition of YPD is 10 g/L yeast extract (Difco, BD Diagnostic Systems, Franklin Lakes, NJ), 5 g/L peptone (Difco), 10 g/L glucose (Sigma-Aldrich, St. Louis, MO), and 50 mg/L streptomycin (Sigma-Aldrich). YPGal is identical to YPD except that 10 g/L galactose (Sigma-Aldrich) was substituted for glucose.

Uri M

optical density,absorbance,od<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3520

106303

Maximum OD600 of cells in YPD medium

Budding yeast Saccharomyces cerevisiae

5.2

±0.2

Unitless

16739953

P.712 right column: "OD600 data for biomass determination were obtained from transmission measurements using an orange LED (Epitex L600-10V, 600 nm, Kyoto, Japan)."

P.714 left column 7th paragraph: "In YPD medium, cells reached a maximum OD600 of 5.2 ((0.2) with a pH and DO concentration of 6.6 ((0.1) and 42.1 ((8.7)%, respectively (Figure 3)." P.711 right column 3rd paragraph: "The composition of YPD is 10 g/L yeast extract (Difco, BD Diagnostic Systems, Franklin Lakes, NJ), 5 g/L peptone (Difco), 10 g/L glucose (Sigma-Aldrich, St. Louis, MO), and 50 mg/L streptomycin (Sigma-Aldrich)."

Uri M

optical density, absorbance, od

3552

106335

Degree of reduction of substrates and products and C-molar enthalpies of respiration and C-molar enthalpy of ethanol fermentation

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Degree%20of%20reduction%20of%20substrates%20and%20products%20and%20C-molar%20enthalpies%20of%20respiration%20and%20C-molar%20enthalpy%20of%20ethanol%20fermentation1.pdf

18604803

See refs beneath table

A mathematical model and direct calorimetry. See notes beneath table

Uri M

microcalorimetry, energy, Acetic acid, glucose, Glycerol, Ethanol, Ammonium ion<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3553

106336

Cumulative heat yields and cumulative growth yields at different phases of growth for non-pH-adjusted cultures

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Cumulative%20heat%20yields%20and%20cumulative%20growth%20yields%20of%20S.%20cerevisiae%20at%20different%20phases%20of%20growth%20for%20non-pH-adjusted%20cultures1.pdf

18604803

Abstract: "Energy balance calculations were performed for different physiological states during batch growth of Saccharomyces cerevisiae with glucose as carbon and energy source...By mathematical modeling and direct monitoring on-line of the rate of heat production, continuous calculations of (1) glucose consumption, and (3) biomass production were performed, and were shown to correlate closely with measured values for the continuously changing growth process."

P.456 right column bottom paragraph: "The heat of ethanol fermentation is small compared with the heat of respiration with glucose as the energy source. Theoretically, the former gives -16.2 kJ/C-mol of glucose and the latter -468.7 kJ/C-mol of glucose, when calculated for a real biologic process taking part in an aqueous environment (Table I). Respiration of ethanol gives an even higher value, i.e., -678.7 kJ/C-mol of ethanol (Table I). However, these values imply only catabolism, i.e., that the carbon and energy source is totally fermented or oxidized and to no part conserved as biomass. Therefore, the value of the heat yield (AQx) is also dependent on the actual growth yield, which for S. cerevisiae is lowest during the respire-fermentative growth (Table II). Respiro-fermentative growth of S. cerevisiae indeed gave the lowest heat yields (Table II), which is in agreement with the early results of Battley [ref 3] and with recent results with Kluyveromyces fragilis, for which the heat yield fell continuously to lower values while the catabolism was increasingly shifted to a fermentative mode [ref 31]."

Uri M

microcalorimetry, energy, glucose, Ethanol, Respiro-fermentative, respiration, fermentation

3554

106337

Energy recovery at different phases of growth for non-pH-adjusted cultures

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Energy%20recovery%20(ER%3B%20mean%20of%20two%20experiments)%20at%20different%20phases%20of%20growth%20for%20non-pH-adjusted%20cultures.pdf

hours

18604803

P.448 left column 3rd paragraph: "A mathematical model and direct calorimetry, as the only continuous on-line measurement, was used for the continuous indirect determination of biomass production, substrate consumption, and intermediate product formation and consumption."

P.454 right column 3rd paragraph: "The energy balances that were attained are expressed in Table III as energy recovery. (ER = The sum of the energy contents of the products divided by the energy contents of the substrates substrates and products have been considered to be in the actual thermodynamic state. For explanation, see Theory and Calculations.) The calculated ER values are dependent on the chosen reference state, which is why it is important in the evaluation of such data to clearly define the reference state used (see Theory and Calculations). With the reference state used in this study, however, no major component of the system is overlooked if ER is close to one."

Uri M

microcalorimetry, energy, Respiro-fermentative, respiration, fermentation

3555

106338

Energy balances during growth on glucose without pH adjustment

Budding yeast Saccharomyces cerevisiae

Figure link - http://bionumbers.hms.harvard.edu/files/Energy%20balances%20during%20growth%20of%20S.%20cerevisiae%20on%20glucose%20without%20pH%20adjustment1.pdf

18604803

A mathematical model and direct calorimetry. See note beneath figure 6

Uri M

microcalorimetry, energy, Respiro-fermentative, respiration, fermentation, biomass, integrated heat, glucose, ethanol, acetate, glycerol,substrate,product<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3568

106351

Dwell time of a transcript at the transcription site in nucleus

Budding yeast Saccharomyces cerevisiae

290

±30

Sec

Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science. 2011 Apr 22 332(6028):475-8. p.476 right column bottom paragraph

21512033

An idealized fluorescence time trace for transcription of a single pre-mRNA can be described by an autocorrelation function G(t), which is a discrete autocorrelation over all the transition probabilities for RNAPII

The variables are the total dwell time of a transcript (T), which includes elongation and termination, and the transcript initiation rate (c).

Uri M

RNA polymerase, transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3569

106352

Transcription initiation events at POL1 promoter during the active period in the cell cycle

Budding yeast Saccharomyces cerevisiae

1.3

±0.72

Min^-1

Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science. 2011 Apr 22 332(6028):475-8. p.477 left column

21512033

Although the POL1 promoter is only active during a certain stage of the cell cycle, initiation events during this active period are stochastic and uncorrelated and occur with a frequency c=1.3±0.72min-1.

Uri M

RNA polymerase, transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3570

106353

Mean dwell time of transcripts at transcription site during G1

Budding yeast Saccharomyces cerevisiae

770±260 PP7- MDN1 transncript: 140±30 MDN1-PP7 transcript

Sec

21512033

The total dwell time of a transcript (T), includes elongation and termination, and the transcript initiation rate (c).

Uri M

RNA polymerase, transcription, cell cycle<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3571

106354

Transcription initiation rate during G1

Budding yeast Saccharomyces cerevisiae

0.16±0.07 PP7- MDN1 transncript: 0.24±0.1 MDN1-PP7 transcript

Min^-1

21512033

Uri M

RNA polymerase, transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3572

106355

Velocity of RNAPII on MDN1 during G1

Budding yeast Saccharomyces cerevisiae

±8

bases/sec

21512033

In late S/G2 phase, PP7-MDN1 velocity was 46±6.2 bases per second.

Uri M

RNA polymerase, transcription rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3573

106356

Volume of nucleus

Budding yeast Saccharomyces cerevisiae

10.3

±3.7

Î¼m^3

21512033

Volume measurements and three-dimensional rendering of Mbp1-GFP were carried out using the Imaris x64 software package (Bitplane AG)

Uri M

nuclear size, dimension<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3575

106358

Growth rate anaerobically on xylose only

Budding yeast Saccharomyces cerevisiae

0.12

Hours^-1

Pitkänen JP, Rintala E, Aristidou A, Ruohonen L, Penttilä M. Xylose chemostat isolates of Saccharomyces cerevisiae show altered metabolite and enzyme levels compared with xylose, glucose, and ethanol metabolism of the original strain. Appl Microbiol Biotechnol. 2005 Jun67(6):827-37 p.835 left column top paragraph

15630585

Sonderegger M, Sauer U. Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microbiol. 2003 Apr69(4):1990-8.

12676674

(Primary source abstract:) Researchers developed a selection procedure for the evolution of strains that are capable of anaerobic growth on xylose alone.

For growth rate of 0.025Hours^-1 on xylose aerobically see Madhavan et al, 2009 PMID 19125247 p.1039 right column 3rd paragraph

Uri M

doubling time, generation time, minimal medium, recombinant yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3576

106359

Growth rate on minimal medium at 30ºC

Budding yeast Saccharomyces cerevisiae

0.37

Hours^-1

Narendranath NV, Thomas KC, Ingledew WM. Effects of acetic acid and lactic acid on the growth of Saccharomyces cerevisiae in a minimal medium. J Ind Microbiol Biotechnol. 2001 Mar26(3):171-7. p.173 fig.2

11420658

Growth was measured turbidometrically using a Klett Summerson colorimeter (Klett Manufacturing, New York, NY) equipped with a no. 66 red filter (420-660 nm).

Value extracted manually and is average of Alltech and ATCC strains, fig.2.

Uri M

divison, doubling, generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3711

102323

Steady-state biomass concentration

Budding yeast Saccharomyces cerevisiae

2.7

g/L

Ertugay, N. and Hamamci, H. Continuous cultivation of bakers' yeast: change in cell composition at different dilution rates and effect of heat stress on trehalose level. 1997. Folia Microbiol. 42(5):463-467.

9438349

This number is valid for dilution rates up to 0.3/h. Beyond this rate the biomass concentration decreases rapidly.

Phil Mongiovi

biological material<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3712

102324

Fermentation yield

Budding yeast Saccharomyces cerevisiae

0.45

g biomass produced per g glucose consumed

9438349

âThe effects of dilution rate and heat stress at a specified dilution rate on the cell composition of continuously cultured bakers' yeast were studied. The cell composition of the yeast was determined in terms of RNA, total protein and the saccharides trehalose and glycogen. The medium composition was determined in terms of residual sucrose (as glucose equivalents), phosphate and ammonia.â

"The fermentation yield (g biomass produced per g glucose consumed) was constant up to a dilution rate of 0.3/h with a value of 0.45 and then it decreased with increasing dilution rate (Fig. 1)."

Phil Mongiovi

3713

102325

Trehalose content

Budding yeast Saccharomyces cerevisiae

8.6-33

mg per g biomass

9438349

The amount of trehalose decreases through this range (i.e. from 33 to 8.6 mg/g biomass) as the dilution rate increases from 0.1/h to 0.4/h.

Phil Mongiovi

starch, polysaccharide, sugar, storage<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3714

102326

Glycogen content

Budding yeast Saccharomyces cerevisiae

93-150

mg per g biomass

9438349

The amount of glycogen decreases through this range (i.e. from 150 to 93 mg/g biomass) as the dilution rate increases from 0.1/h to 0.4/h.

Phil Mongiovi

starch, polysaccharide, sugar, storage<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3715

102327

RNA content

Budding yeast Saccharomyces cerevisiae

93-113

mg per g biomass

9438349

"The effects of dilution rate and heat stress at a specified dilution rate on the cell composition of continuously cultured bakers' yeast were studied. The cell composition of the yeast was determined in terms of RNA, total protein and the saccharides trehalose and glycogen. The medium composition was determined in terms of residual sucrose (as glucose equivalents), phosphate and ammonia."

"As the dilution rate was increased from 0.1 to 0.4/h at 0.05 intervals the steady-state trehalose content decreased from 33 to 8.6 mg/g biomass, and glycogen content from 150 to 93 mg/g biomass. On the other hand, the protein content increased from 420 to 530 mg/g biomass and the RNA content from 93 to 113 mg/g biomass."

Phil Mongiovi

cell composition<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3716

102328

Protein content

Budding yeast Saccharomyces cerevisiae

420-530

mg per g biomass

9438349

Phil Mongiovi

cell composition<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3843

102473

Ribosome volume according to partial specific volume and molecular mass of RNA and protein

Budding yeast Saccharomyces cerevisiae

3750

nm^3

Menetret JF et al., The structure of ribosome-channel complexes engaged in protein translocation. Mol Cell. 2000 Nov6(5):1219-32. p.1231 left column 2nd paragraph

11106759

"The threshold representing 100% of the ribosomal volume was chosen on the basis of calculated and experimentally measured partial specific volumes and the known mass of ribosomal protein and RNA. The 100% ribosomal volumes used in this work were 3.75×10^6Å^3 (yeast) and 4×10^6Å^3 (mammals)."

Uri M

size, translation machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3846

102476

Number of proteins in ribosome

Budding yeast Saccharomyces cerevisiae

unitless

Planta RJ, Mager WH. The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast. 1998 Mar 3014(5):471-7.

9559554

Putative ribosomal protein genes were selected primarily on the basis of the sequence similarity of their products with ribosomal proteins from other eukaryotic organisms, in particular the rat.

large subunit 46 proteins small subunit 32 proteins. 59 of the 78 protein genes are duplicated.

Uri M

large,small,subunit,protein,gene<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3866

102498

Number of proteins in small subunit of ribosome

Budding yeast Saccharomyces cerevisiae

unitless

Planta RJ, Mager WH. The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast. 1998 Mar 3014(5):pp. 472 table 1

9559554

Putative ribosomal protein genes were selected primarily on the basis of the sequence similarity of their products with ribosomal proteins from other eukaryotic organisms, in particular the rat.

78 proteins in ribosome. large subunit 46 proteins small subunit 32 proteins. 59 of the 78 protein genes are duplicated. of the 137 genes 99 have introns

Uri M

large,small,subunit,protein,gene<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3867

102499

Length of RNA of 16S subunit of small subunit of ribosome

Budding yeast Saccharomyces cerevisiae

1800

nucleotides

Neil R. Voss. 2006 'Geometric Studies of RNA and Ribosomes, and Ribosome Crystallization' Table 5.1 pp. 130 link - http://bionumbers.hms.harvard.edu/files/Molecular%20composition%20of%20ribosomes%20from%20several%20organisms.jpg

primary reference needed. Thesis link - http://www.yale.edu/moorelab/thesis/voss06-large.pdf

Uri M

rrna, sequence, nucleotide, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3868

102500

Length of RNA of 5S subunit of large subunit of ribosome

Budding yeast Saccharomyces cerevisiae

118

nucleotides

primary reference needed

Uri M

rrna, sequence, nucleotide, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3869

102501

Length of RNA of 5.8S subunit of large subunit of ribosome

Budding yeast Saccharomyces cerevisiae

159

nucleotides

primary reference needed

Uri M

3870

102502

Length of RNA of 25S subunit of large subunit of ribosome

Budding yeast Saccharomyces cerevisiae

3550

nucleotides

primary reference needed. Thesis link - http://www.yale.edu/moorelab/thesis/voss06-large.pdf

Uri M

ribonucleic acid,rna,translation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3895

102527

Time between starvation and expression of meiosis genes

Budding yeast Saccharomyces cerevisiae

12.4

±2.4

hours

Nachman I, Regev A, Ramanathan S. Dissecting timing variability in yeast meiosis. Cell. 2007 Nov 2 131(3):pp. 548 fig. 3A

17981121

research followed up to 4000 single cells at 5â10 min intervals under a fluorescent microscope for 18â45 hr as they underwent meiosis. External factors (temperature, nutrient flow) were kept constant and uniform across cells.

This stage, the precommitment interval, is highly variable from cell to cell whereas the postcommitment interval is far less variable (see BNID 102528)

Uri M

precommitment, interval, early, meiosis, genes, yfp, yellow, fluorescent, protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3896

102528

Duration of both meiotic divisions

Budding yeast Saccharomyces cerevisiae

0.6

±0.2

hours

Nachman I, Regev A, Ramanathan S. Dissecting timing variability in yeast meiosis. Cell. 2007 Nov 2131(3):pp. 548 fig. 3A

17981121

Research followed up to 4000 single cells at 5â10 min intervals under a fluorescent microscope for 18â45 hr as they underwent meiosis. External factors (temperature, nutrient flow) were kept constant and uniform across cells.

The precommitment interval is highly variable from cell to cell (see BNID 102527) whereas this stage, the postcommitment interval, is far less variable

Uri M

precommitment, interval, early, meiosis, genes, yfp, yellow, fluorescent, protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3900

102532

Glutathione concentration

Budding yeast Saccharomyces cerevisiae

mg/l

Cha JY, Park JC, Jeon BS, Lee YC, Cho YS. Optimal fermentation conditions for enhanced glutathione production by Saccharomyces cerevisiae FF-8. J Microbiol. 2004 Mar42(1):51-5. p.52 left column bottom paragraph & p.54 left column 3rd paragraph

15357293

P.51 right column top paragraph: "Saccharomyces cerevisiae FF-8, a glutathione producing yeast strain, was established in [investigators'] laboratory (Park et al., 2003). FF-8 was aerobically grown in 500 ml flask containing 100 ml of YM medium consisting of 1.0% glucose, 0.5% peptone, 0.3% yeast extract, and 0.3% malt extract, at pH 6.0 for 24 h at 30ËC." P.51 right column bottom paragraph: "The harvested yeast cells were suspended in 0.2 M phosphate buffer (pH 7.2) and disrupted by sonication. The disrupted cells were then removed by centrifugation, and glutathione concentration in the supernatant was measured using published methods (Cohn et al., 1966), by measuring the absorbance of reaction solutions at 412 nm using a spectrophotometer (UV mini 1240, Shimadzu, Japan)."

P.52 left column bottom paragraph: "Yeast strains such as S. cerevisiae and Candida utilis have been reported to produce glutathione (Wei, 2003 Alfafara et al., 1992). [Investigators] have previously reported that S. cerevisiae FF-8, a glutathione producing strain, was isolated from Korean Traditional Rice Wine. Glutathione production by S. cerevisiae FF-8 under optimal culture conditions in YM medium was 90 mg/l." P.54 left column 3rd paragraph: "The glutathione concentration produced by S. cerevisiae FF-8 using this medium significantly increased by 2.27-fold [to 204 mg/l] compared to the 90 mg/l achieved in YM medium."

Uri M

ym, ff8, ff-8, glutathione, production

3934

102566

Keq for complete kinetic mechanism of homoisocitrate dehydrogenase

Budding yeast Saccharomyces cerevisiae

0.45

Lin Y, Alguindigue SS, Volkman J, Nicholas KM, West AH, Cook PF. Complete kinetic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae. Biochemistry. 2007 Jan 2346(3):890-8.

17223711

The Keq for the overall reaction measured directly using the change in NADH as a probe, calculated using fixed concentrations of the other reactants and 2.3 mM a-Ka (see eq. 12)

The Keq calculated from the Haldane relationship using the kinetic constants given in Table 1 and eq. 13 is 0.68 ± 0.03 M.

Uri M

nad,nadh,Mg-homoisocitrate,complex,MgHIc,alpha aminoadipate,pathway,lysine,synthesis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3935

102567

Dissociation constant of the Mg-homoisocitrate complex (MgHIc)

Budding yeast Saccharomyces cerevisiae

±2

Lin Y, Alguindigue SS, Volkman J, Nicholas KM, West AH, Cook PF. Complete kinetic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae. Biochemistry. 2007 Jan 2346(3):890-8.

17223711

Determination of the Mg-HIc Dissociation Constant by 1H NMR. A plot of the change in chemical shift vs. Mg2+ concentration was used

Uri M

NADH, NAD, Mg-homoisocitrate, complex, MgHIc, alpha aminoadipate, pathway, lysine, synthesis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3936

102568

Decrease in velocity of the reaction when isocitrate replaces homoisocitrate as substrate

Budding yeast Saccharomyces cerevisiae

216

Fold

Lin Y, Alguindigue SS, Volkman J, Nicholas KM, West AH, Cook PF. Complete kinetic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae. Biochemistry. 2007 Jan 2346(3):890-8.

17223711

Determination of the Mg-HIc Dissociation Constant by 1H NMR

In contrast to HIc, the uncomplexed form of isocitrate and Mg2+ bind to the enzyme, unlike the situation with MgHIc.

Uri M

nad,nadh,Mg-homoisocitrate,complex,MgHIc,alpha aminoadipate,pathway,lysine,synthesis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3944

102576

Combined molecular mass of six subunits of origin recognition complex

Budding yeast Saccharomyces cerevisiae

414

kDa

Lee DG, Bell SP. Architecture of the yeast origin recognition complex bound to origins of DNA replication. Mol Cell Biol. 1997 Dec17(12):7159-68.

9372948

Six ORC subunits comprising orc are referred to as Orc1p through Orc6p (in order of decreasing mass), and all six proteins are essential for the viability of yeast cells. DNA binding domain of ORC requires the coordinate action of five of the six ORC subunits.

Uri M

DNA, replication, initiation, site, orc,molecular weight, molecular mass, MW, Da, kDa<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3945

102577

Length of DNA sequence required to stabilize origin recognition complex

Budding yeast Saccharomyces cerevisiae

Lee DG, Bell SP. Architecture of the yeast origin recognition complex bound to origins of DNA replication. Mol Cell Biol. 1997 Dec17(12):pp. 7160

9372948

See BNID 106930

Uri M

DNA, replication, initiation, site, orc, cdc6, mcm, autonomous, replication, sequence, ARS, orc-dna, binding<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

3946

102578

Number of subunits in origin recognition complex

Budding yeast Saccharomyces cerevisiae

unitless

Lee DG, Bell SP. Architecture of the yeast origin recognition complex bound to origins of DNA replication. Mol Cell Biol. 1997 Dec17(12):7159-68.

9372948

Uri M

DNA,replication,initiation,site,orc<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4016

102660

Affinity of MHC class I heavy chain to calreticulin

Budding yeast Saccharomyces cerevisiae

µM

Peaper DR, Cresswell P. Regulation of MHC class I assembly and peptide binding. Annu Rev Cell Dev Biol. Annu Rev Cell Dev Biol. 2008 24:343-68. :pp. 350

18729726

Wearsch PA, Jakob CA, Vallin A, Dwek RA, Rudd PM, Cresswell P. Major histocompatibility complex class I molecules expressed with monoglucosylated N-linked glycans bind calreticulin independently of their assembly status. J Biol Chem. 2004 Jun 11 279(24):25112-21.

15056662

recombinant expression system

Uri M

mhc, major, histocompatibility, complex, HLA, human, calreticulin, human, e. coli<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4017

102661

Dissociation constant of the calreticulin/ERp57

Budding yeast Saccharomyces cerevisiae

Peaper DR, Cresswell P. Regulation of MHC class I assembly and peptide binding. Annu Rev Cell Dev Biol. 200824:pp. 350

18729726

Frickel EM, Riek R, Jelesarov I, Helenius A, Wuthrich K, Ellgaard L. TROSY-NMR reveals interaction between ERp57 and the tip of the calreticulin P-domain. Proc Natl Acad Sci U S A. 2002 Feb 1999(4):1954-9

11842220

ELISA, Isothermal Titration Microcalorimetry (ITC),NMR spectroscopy

The lectin chaperone calreticulin (CRT) assists the folding and quality control of newly synthesized glycoproteins in the endoplasmic reticulum (ER). It interacts with ERp57, a thiol-disulfide oxidoreductase that promotes the formation of disulfide bonds in glycoproteins bound by CRT.

Uri M

hc,MHC , class I ,complex ,major,histocompatibility,complex,HLA,human,calreticulin,human,e. coli,thiol-disulfide, oxidoreductase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4183

102973

Number of YFP detectable in single cell

Budding yeast Saccharomyces cerevisiae

350

molecules

Gordon A, Colman-Lerner A, Chin TE, Benjamin KR, Yu RC, Brent R. Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Methods. 2007 Feb4(2):175-81.

17237792

Microscope-based cytometry, open-source software tools and statistical routines.

Uri M

yellow fluorescence protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4184

102974

YFP maturation time

Budding yeast Saccharomyces cerevisiae

±7

min

Gordon A, Colman-Lerner A, Chin TE, Benjamin KR, Yu RC, Brent R. Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Methods. 2007 Feb4(2):175-81. p.178 right column 3rd paragraph & fig. 4B

17237792

P.178 right column 2nd paragraph: "[Researchers] quantified maturation time [refs 22,23] for YFP (wild-type GFP with mutations S65G,V68L,S72A,T203Y) and a cyan fluorescent protein derivative (CFP wild-type GFP with mutations F64L,S65T,Y66W,N146I,M153T,V163A), in individual S. cerevisiae at 25°C (ref. 3 Supplementary Note). [They] induced fluorescent protein synthesis by addition of pheromone to cells with integrated constructs in which the fluorescent protein replaced the PRM1 ORF, allowed transcription and translation to proceed for 30 min, then added cycloheximide to block translation. Cells reached maximum fluorescence by 3 h after translation stop (Fig. 4a) and photobleaching-corrected fluorescence (Supplementary Note) remained stable for up to 24 h (data not shown), indicating that under these conditions protein degradation was negligible."

P.178 right column 3rd paragraph: "Although individual cells varied in the total amount of YFP by a factor of four (Fig. 4a), there was little cell-to-cell variation in the maturation rates (Fig. 4b coefficient of variation o 0.1 Supplementary Note). [Researchers] performed an identical analysis for CFP (data not shown). In yeast under these conditions, YFP and CFP form mature fluorophores at similar rates, with average halftimes for maturation of 39 ± 7 and 49 ± 9 min, respectively (Supplementary Note)."

Uri M

yellow fluorescence protein, jellyfish Aequorea victoria

4196

102988

Total mRNA per cell

Budding yeast Saccharomyces cerevisiae

12200

6100-18300

copies/cell

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 16 2: 87 doi: 10.1186/1752-0509-2-87. p.8 of 14 right column 2nd paragraph

18925958

Analysis of Yeast datasets

"Although the total mass of cellular RNA cannot be calculated in the same way because non-coding mRNA regions for each gene contribute to the molecular weight but are not accurately known, the total number of mRNAs in the dataset can easily be calculated as about 12,200, with 95% confidence limits between 6,100 and 18,300 mRNAs per cell. This compares to experimental estimates of about 15,000 poly(A) tailed RNAs per cell generated experimentally [BNID 104312]. In two important aspects, the curated dataset thus approaches estimates from available experimental data."

Zeev Waks

transcript, transcription, messenger ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4218

103011

Number of mRNA transcripts of 80 percent of expressed genes in cell

Budding yeast Saccharomyces cerevisiae

0.1-2

copies/cell

Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998 Nov 25 95(5):717-28. p.718 left column 2nd paragraph

9845373

High-density oligonucleotide arrays (HDAs) were used to determine the effects of mutations in these components genome wide

These 80 percent include many essential genes

Uri M

gene, expression, transcriptome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4219

103012

Average speed of RNA Polymerase

Budding yeast Saccharomyces cerevisiae

0.81

±0.07

kb/min

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71. p.1269 left column 2nd paragraph

19011635

Abstract:"Using an in situ hybridization [FISH] approach that detects single mRNA molecules, [investigators] measured mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells." See fig. 8a: Synthesis time was plotted against the length of the gene. The slope of the line gives (polymerase speed)^-1

"The distribution of nascent chains further implies a synthesis time uniquely determined from the fit. If plotted against the effective length of the gene, the inverse slope provides the average speed of RNA polymerase: 0.81±0.07 kb minute-1 (Fig. 8a)." "The elongation speed is slower than the elongation speed measured from a Gal promoterâdriven gene, measured at 2 kb/min. A velocity of 2 kb/min (BNID 103016), however, does not fit [investigators'] data, suggesting that different elongation speeds exist for different classes of gene."

Uri M

FISH, fluorescence in situ hybridization, transcription, rate, KAP104, DOA1, MDN1, POL1, PDR5<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4220

103013

Average number of MDN1 mRNA per cell

Budding yeast Saccharomyces cerevisiae

6.1

copies/cell

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71.

19011635

an in situ hybridization (FISH) approach that detects single mRNA molecules, mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells was measured.

Uri M

FISH,fluorescence in situ hybridization,transcription,transcript,MDN1,midasin homolog<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4221

103014

Average number of KAP104 mRNA per cell

Budding yeast Saccharomyces cerevisiae

4.9

copies/cell

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71.

19011635

an in situ hybridization (FISH) approach that detects single mRNA molecules, mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells was measured.

Uri M

FISH,fluorescence in situ hybridization,transcription,transcript,kap104,nucleocytoplamic,transport<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4222

103015

Average number of DOA1 mRNA per cell

Budding yeast Saccharomyces cerevisiae

2.6

Copies/cell

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71.

19011635

an in situ hybridization (FISH) approach that detects single mRNA molecules, mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells was measured.

Uri M

FISH, fluorescence in situ hybridization, transcription, transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4223

103016

RNA Polymerase II elongation rate on a GAL promoter driven gene

Budding yeast Saccharomyces cerevisiae

kb/min

Mason PB, Struhl K. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo.Mol Cell. 2005 Mar 18 17(6):831-40. p.832 left column 2nd paragraph

15780939

the level of Pol II association at various positions within the large (8 kb) and nonessential YLR454 gene whose expression is driven by the rapidly regulated GAL1 promoter was measured.

Uri M

transcription, GAL1-YLR454 gene<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4230

103023

Number of mRNA transcripts per cell

Budding yeast Saccharomyces cerevisiae

~60,000

copies/cell

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71. p.1269 right column top paragraph

19011635

"...an in situ hybridization (FISH) approach that detects single mRNA molecules, mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells." "To achieve single-transcript resolution, [researchers] adapted a FISH technique previously described in mammalian cells [ref 22 PMID 9554849]."

"As shown in Supplementary Table 4 online, the genes used in this study show a three- to six-fold higher expression than that determined previously (ref 12, Holstege et al, Cell 1998 pubmed 9845373, report a value of 15000 mRNA transcripts per cell). This would correct the number of transcripts to around 60,000 mRNAs per cell and indicates that the yeast transcriptome is more active than initially thought." See BNID 104312

Uri M

ribonucleic acid, transcription, macromolecule, polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4231

103025

Percent of ribosomes associated with mRNA

Budding yeast Saccharomyces cerevisiae

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71.

19011635

an in situ hybridization (FISH) approach that detects single mRNA molecules, mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells was measured. See fig. 8a: Synthesis time was plotted against the length of the gene. The slope of the line gives (polymerase speed)^-1

There are 2*10^5 ribosomes in a yeast cell (Bion 100267). This value is similar to (Arava 2003, pubmed 12660367) which found 71 percent of ribosomes associated with mRNA for 5701 genes

Uri M

FISH, fluorescence in situ hybridization, transcription, rate, KAP104, DOA1, MDN1, POL1, PDR5<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4232

103026

Ratio of mRNA nucleotides per ribosome on average

Budding yeast Saccharomyces cerevisiae

154

nucleotides

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71.

19011635

This value is termed 'ribosome density'. It is similar to that found by (Arava, 2003, pubmed 12660367), which was 1 ribosome per 156 nts

Uri M

FISH, fluorescence in situ hybridization, transcription, rate, KAP104, DOA1, MDN1, POL1, PDR5, ribosome, density, transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4233

103027

Number of amino acids in Alpha factor mating pheromone

Budding yeast Saccharomyces cerevisiae

Amino acids

Chen P, Sapperstein SK, Choi JD, Michaelis S. Biogenesis of the Saccharomyces cerevisiae mating pheromone a-factor. J Cell Biol. 1997 Jan 27 136(2):251-69. Figure link - http://tinyurl.com/yzur3ms

9015298

The mature a factor is 12 amino acids long, flanked by 21 amino acids on the N terminal and CaaX box (3 amino acids) on the C terminal. See figure link for sequence.

Uri M

MFA1 peptide MFA1 Alpha factor mating pheromone Yeast, shmoo, conjugation, haploid cell<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4234

103028

Molecular mass of Alpha factor mating pheromone

Budding yeast Saccharomyces cerevisiae

1682

Dalton

http://www.genwaybio.com/product_info.php?products_id=83056

Better ref needed

Sequence: {TRP} {HIS} {TRP} {LEU} {GLN} {LEU} {LYS} {PRO} {GLY} {GLN} {PRO} {MET} {TYR}. Formula: C82H114N20O17S

Uri M

MFA1 peptide MFA1 Alpha factor mating pheromone Yeast, shmoo, conjugation, haploid cell, molecular weight, molecular mass, MW, Da, kDa<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4268

106439

Density of cells arrested in various stages of the cell cycle

Budding yeast Saccharomyces cerevisiae

1.0846 G1: 1.1049 S: 1.0998 metaphase

g/mL

Bryan AK, Goranov A, Amon A, Manalis SR. Measurement of mass, density, and volume during the cell cycle of yeast. Proc Natl Acad Sci U S A. 2010 Jan 19 107(3):999-1004 p.1000 right column bottom paragraph

20080562

"To determine how cell density correlates with the cell cycle, [researchers] measured the distributions of buoyant mass and volume in budding yeast populations." Cells arrested in G1 by treatment with the pheromone alpha factor...Cells arrested in S phase by the replication inhibitor hydroxyurea...cells arrested in metaphase by the microtubule inhibitor nocodazole (NOC)"

Cells arrested in G1 1.0846±0.0043g/mL. Cells arrested in S phase 1.1049±0.0024g/mL. Cells arrested in metaphase 1.0998±0.0049g/mL. The density of asynchronous budding yeast in researchers' strain background, W303, was 1.1029±0.0026g/mL. See BNID 103876

Uri M

size, volume<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4277

106448

Median protein length

Budding yeast Saccharomyces cerevisiae

379

Table link - http://bionumbers.hms.harvard.edu/files/Median%20protein%20lengths%20in%20eukaryotic%2C%20bacterial%20and%20archaeal%20organisms.pdf

Amino acids

Brocchieri L, Karlin S. Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res. 2005 Jun 10 33(10):3390-400 table 2 pp.3392-3

15951512

Researchers examined proteomes from 5 eukaryotic species, 16 archaeal species and 67 bacterial species. They evaluated results using the set of proteins classified in the COG (Clusters of Orthologous Groups of proteins) database and the set of genomic proteins included in the Pfam database of functional/structural domain alignments verified by human intervention (Pfam-A).

Uri M

yeast, proteome, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4338

106510

Number of free protons in the cytosol of a single cell (volume 48µm^3) at a pH of 7

Budding yeast Saccharomyces cerevisiae

3000

Protons

Orij R, Brul S, Smits GJ. Intracellular pH is a tightly controlled signal in yeast. Biochim Biophys Acta. 2011 Mar 21 1st page left column

21421024

Sherman F. Getting started with yeast. Methods Enzymol. 2002 350: 3-41 AND Perktold A, Zechmann B, Daum G, Zellnig G. Organelle association visualized by three-dimensional ultrastructural imaging of the yeast cell. FEMS Yeast Res. 2007 Jun7(4):629-38 AND Orij R, Postmus J, Ter Beek A, Brul S, Smits GJ. In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth. Microbiology. 2009 Jan155(Pt 1):268-78.

12073320, 17419771, 19118367

There are 10^-7mol protons in a liter, i.e. in 10^15µm^3. Calculating amount in 48µm^3: 48µm^3×10^-7mol/10^15µm^3=48×10^-22mole protons. Multiply by Avogadro's number: 48×10^-22mole×6×10^-23protons/mole=2880protons

Uri M

hydrogen ion, acidity, cytoplasm<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4339

106511

Concentration of inorganic phosphate (Pi)

Budding yeast Saccharomyces cerevisiae

Orij R, Brul S, Smits GJ. Intracellular pH is a tightly controlled signal in yeast. Biochim Biophys Acta. 2011 Oct1810(10):933-44. doi: 10.1016/j.bbagen.2011.03.011. p.933 left column

21421024

van Eunen K. et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60

20067525

"The pH of a solution is defined as the negative logarithm of the hydrogen ion activity in water. If [investigators] assume the inside of a yeast cell to be a watery solution, [they] can estimate the number of free protons in the cytosol of a single cell (48 µm^3 [refs 1,2] at a pH of 7 [ref 3]) at no more than ~3000. In contrast, global analysis of protein expression in yeast tells us that the number of protein molecules in a cell is in the order of millions [ref 4]. Each of these proteins has multiple protonatable groups which can either donate or take up a proton. In addition, acidic metabolites are also in excess compared to free protons. For instance, the concentration of inorganic phosphate (Pi) in yeast cells is estimated at around 50 mM [primary source], five orders of magnitude higher than that of protons. This difference in the numbers of free protons and potential buffer molecules is important for [investigatorsâ] perception of pHi." See BNID 106019

Uri M

inorganic phosphate, cytoplasm, phosphoric acid.<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4343

106515

Fraction of wildtype ATPase activity that is required for growth

Budding yeast Saccharomyces cerevisiae

Orij R, Brul S, Smits GJ. Intracellular pH is a tightly controlled signal in yeast. Biochim Biophys Acta. 2011 Mar 21 5th page right column 2nd paragraph

21421024

Ambesi A, Miranda M, Petrov VV, Slayman CW. Biogenesis and function of the yeast plasma-membrane H(+)-ATPase. J Exp Biol. 2000 Jan203(Pt 1):155-60.

10600684

Uri M

proton pump, ATPase, membrane protein,H+-ATPase Pma1p<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4344

106516

Range of medium pH values in which wild-type yeast can grow

Budding yeast Saccharomyces cerevisiae

2.5 to 8.5

Unitless

Orij R, Brul S, Smits GJ. Intracellular pH is a tightly controlled signal in yeast. Biochim Biophys Acta. 2011 Mar 21 7th page right column top paragraph

21421024

T.M. Matthews, C. Webb, Culture systems, in: M.F. Tuite, S.G. Oliver (Eds.), Saccharomyces (Biotechnology Handbooks), Plenum Press, New York, 1991, pp. 249â282.

Wild-type yeast can grow at medium pH values ranging from 2.5 to 8.5, while growth and fermentation kinetics are unaffected between 3.5 and 6.0 (primary source)

Uri M

acidity<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4345

106517

pH of peroxysomal lumen

Budding yeast Saccharomyces cerevisiae

8.2

Unitless

Orij R, Postmus J, Ter Beek A, Brul S, Smits GJ. In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth. Microbiology. 2009 Jan155(Pt 1):268-78. p.268 right column top paragraph

19118367

van Roermund CW, de Jong M, IJlst L, van Marle J, Dansen TB, Wanders RJ, Waterham HR. The peroxisomal lumen in Saccharomyces cerevisiae is alkaline. J Cell Sci. 2004 Aug 15 117(Pt 18):4231-7.

15316083

(Primary Source, abstract:) researchers used two different pH-sensitive yellow fluorescent proteins targeted to the peroxisome by virtue of a C-terminal SKL

p.268 right column top paragraph: "The pH of the peroxisomal lumen is reported to be 8.2 this coincides with the pH optimum for most peroxisomal enzymes, which lies between 8 and 9 (primary Source)."

Uri M

peroxysome, organelle, acidity

4365

106538

Ribosome synthesis rate

Budding yeast Saccharomyces cerevisiae

2000

Ribosomes/min

Huber A. et al., Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L. EMBO J. 2011 Jul 5. doi: 10.1038/emboj.2011.221 p.1 right column top paragraph

21730963

Better ref needed. Same value given in Warner 1999 PMID 10542411 p.437 right column top paragraph. See BNID 103187, 110022

Uri M

molecular machine, translation machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4384

106557

The nucleus/cytoplasm volume ratios in mutant and wild-type cells

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/The%20Nucleus-Cytoplasm%20volume%20ratios%20in%20mutant%20and%20wild-type%20cells.pdf

Webster MT, McCaffery JM, Cohen-Fix O. Vesicle trafficking maintains nuclear shape in Saccharomyces cerevisiae during membrane proliferation. J Cell Biol. 2010 Dec 13 191(6):1079-88 p.1085 table II

21135138

Electron microscopy

The ratios are the same in mutant as in wildtype cells

Uri M

nuclear, cytoplasmic, volume, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4385

106558

Nucleus and nucleolus sizes of different strains

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Nucleus%20and%20nucleolus%20sizes%20of%20different%20strains.pdf

Therizols P, Duong T, Dujon B, Zimmer C, Fabre E. Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres. Proc Natl Acad Sci U S A. 2010 Feb 2 107(5):2025-30. Supporting information p.8 table S4

20080699

Fluorescence microscopy

See note beneath table

Uri M

radius, diameter, nuclear volume, nucleoplasmic volume<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4523

106696

Numbers of budded and unbudded parents and daughter cells at different doubling times

Budding yeast Saccharomyces cerevisiae

Taqble link - http://bionumbers.hms.harvard.edu/files/Numbers%20of%20budded%20and%20unbudded%20parents%20and%20daughter%20cells%20at%20different%20doubling%20times.pdf

Lord PG, Wheals AE. Asymmetrical division of Saccharomyces cerevisiae. J Bacteriol. 1980 Jun142(3):808-18. p.810 table 1

6991494

Cell counts and volume were determined by using a model 111 LTS Electrozone/ Celloscope (Particle Data Inc., Elmhurst, Ill.) fitted with a 60µm orifice tube.

Uri M

growth rate, division, generation time,glucose,fructose,mannose,raffinose,cellobiose,galactose,glycerol,sorbitol,mannitol,yep,yeast extract peptone,emm,edinburgh minimal medium<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4590

106763

Number of mRNA transcripts per cell

Budding yeast Saccharomyces cerevisiae

26000

mRNAs/cell

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. p.2 left column bottom paragraph

21103382

Miura F, Kawaguchi N, Yoshida M, Uematsu C, Kito K, Sakaki Y, Ito T. Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs. BMC Genomics. 2008 Nov 29 9 :574 AND Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 Jun 6 320(5881):1344-9.

19040753, 18451266

(1st primary source abstract:)"[Researchers] conceived an idea of competitive PCR between genomic DNA and cDNA." (2nd primary source abstract:) "[Researchers] developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome."

"[Researchers] used an updated total amount of mRNA molecules per yeast cell that has been corrected from that previously used (15000 molecules from [Hereford et al., 1977 PMID 321129]) to more recent and precise calculations obtained from massive parallel sequencing and competitive PCR transcriptome measurements: 26000 molecules from [primary sources]." See BNID 102988, 103023

Uri M

transcriptome, messenger ribonucleic acid, transcripts abundance, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4591

106764

Whole dataset of the nascent transcription rate

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Whole%20dataset%20of%20the%20nascent%20transcription%20rate.pdf

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. Supplementary analysis and references. table S1

21103382

Whole dataset of the nascent TR obtained in this work and other transcription parameters

The nascent (TR) and the indirect transcription rates (TR indirect) are presented computed from [Wang et al., 2002 PMID 11972065]. Both data are shown before and after the correction used to compensate the dilution effect.

Uri M

transcriptome,messenger ribonucleic acid,transcripts abundance,concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4592

106765

Whole dataset of the nascent transcription rate (production rate per gene)

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/Whole%20dataset%20of%20the%20nascent%20transcription%20rate.xlsx

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. Supplementary analysis and references. table S1

21103382

Whole dataset of the nascent TR obtained in this work and other transcription parameters

Uri M

transcriptome, messenger ribonucleic acid, transcripts abundance, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4593

106766

Median transcription rate

Budding yeast Saccharomyces cerevisiae

0.12

mRNA molecules/min

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. p.5 left column 2nd paragraph

21103382

P.1 right column botom paragraph: "[Researchers] [ref 10] and others [refs 11,12] developed genomic variants of the well-known run-on technique [ref 13] to evaluate the nascent TR (transcription rate) for most genes. In this technique (GRO, Genomic Run-on), elongating RNA pol molecules, that conserve the RNA, are forced to incorporate radioactive UTP for a short length."

p.5 left column 2nd paragraph: "The distribution of the TR values (Figure 3) is similar to a log-normal as shown in most cases by the expression datasets, being the median TR about 0.12 mRNA molecules/min (equivalent to 7 mRNAs/hour). Furthermore, 90% of the genes have TRs between 2.33 and 29.7 mRNAs/hour and, if [researchers] assume that the 4670 genes for which [they] have data are representative of the 5796 non-dubious ORFs, the total transcription for RNA pol II in a yeast cell growing in standard conditions is about 60200 mRNAs/h. By assuming the known datum that RNA polymerase molecules transcribe at 25 nt/s [ref 30], then the median RNA pol II density inside the genes is 0.078 molecules/kb."

Uri M

transcriptome, messenger ribonucleic acid, transcript

4594

106767

Transcription rate of 90% of the genes

Budding yeast Saccharomyces cerevisiae

2.33 and 29.7

mRNA molecules/hour

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. p.5 left column 2nd paragraph

21103382

Researchers developed genomic variants of the well-known run-on technique to evaluate the nascent TR (transcription rate) for most genes. In this technique (GRO, Genomic Run-on), elongating RNA pol molecules, that conserve the RNA, are forced to incorporate radioactive UTP for a short length.

If researchers assume that the 4670 genes for which they have data are representative of the 5796 non-dubious ORFs, the total transcription for RNA pol II in a yeast cell growing in standard conditions is about 60200 mRNAs/h.

Uri M

transcriptome, messenger ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4595

106768

Median RNAP II density inside the genes

Budding yeast Saccharomyces cerevisiae

0.078

Molecules/kb

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. p.5 left column 2nd paragraph

21103382

By assuming the known datum that RNA polymerase molecules transcribe at 25 nt/s [Edwards et al., 1991 PMID 1985924], then the median RNA pol II density inside the genes is 0.078 molecules/kb. Corresponds to an average of 0.096 molecules/gene.

Uri M

transcription, messenger ribonucleic acid, RNA polymerase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4596

106769

Number of genes that have >1 molecule of elongating RNA pol II/gene

Budding yeast Saccharomyces cerevisiae

Gene

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. p.7 right column 2nd paragraph

21103382

The statistical distribution shows that less than 1% of yeast genes have >1 molecule of elongating RNA pol II/gene.

Uri M

transcription, messenger ribonucleic acid, RNA polymerase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4597

106770

Fraction of RNA pol II molecules that are associated with chromatin

Budding yeast Saccharomyces cerevisiae

60 to 80

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. p.8 left column top paragraph

21103382

Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT. Regulation of TATA-binding protein dynamics in living yeast cells. Proc Natl Acad Sci U S A. 2008 Sep 9 105(36):13304-8

18765812

FRAP (fluorescence recovery after photobleaching)

Uri M

transcription,messenger ribonucleic acid,RNA polymerase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4598

106771

Nascent transcription rate datasets from different physiological conditions

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Nascent%20TR%20datasets%20from%20to%20other%20physiological%20conditions.pdf

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. Supplementary analysis and references. table S2

21103382

Researchers used previously published GRO (Genomic Run-on) datasets to expand the change from cells growing in glucose to galactose [García-Martínez 2004 PMID 15260981] oxidative stress [Molina-Navarro 2008 PMID 18424442] and osmotic stress [Romero-Santacreu 2009 PMID 19369426]

Uri M

transcriptome, messenger ribonucleic acid, transcripts abundance, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4599

106772

Percentage of transcription rate devoted to compensate the dilution effect due to the cell growth

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Percentage%20of%20TR%20devoted%20to%20compensate%20the%20dilution%20effect%20due%20to%20the%20cell%20growth.pdf

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. Supplementary analysis and references. table S3

21103382

The TR necessary to compensate the dilution is computed using the RA (mRNA amount) and a generation time of 113 minutes.

As the TR (transcription rate) necessary to compensate the dilution is computed independently to the nascent TR some values show percentage greater than 100% or are negative. In those cases we have arbitrarily substituted the values to either 100% or 0%, meaning that the TR devoted to compensate the dilution is much larger (100%) or negligible (0%) in respect to the TR devoted to compensate the degradation.

Uri M

transcriptome, messenger ribonucleic acid, transcripts abundance, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4600

106773

Nascent transcription rate datasets from different physiological conditions (production rate per gene)

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/Nascent%20TR%20datasets%20from%20to%20other%20physiological%20conditions.xlsx

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. Supplementary analysis and references. table S2

21103382

Uri M

transcriptome, messenger ribonucleic acid, transcripts abundance, concentration

4601

106774

Percentage of transcription rate (production rate per gene) devoted to compensate the dilution effect due to the cell growth

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/Percentage%20of%20TR%20devoted%20to%20compensate%20the%20dilution%20effect%20due%20to%20the%20cell%20growth.xlsx

Pelechano V, Chávez S, Pérez-Ortín JE. A complete set of nascent transcription rates for yeast genes. PLoS One. 2010 Nov 16 5(11):e15442. Supplementary analysis and references. table S3

21103382

The TR necessary to compensate the dilution is computed using the RA (mRNA amount) and a generation time of 113 minutes.

Uri M

transcriptome, messenger ribonucleic acid, transcripts abundance, concentration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4604

106777

Effect of glucosamine complex and its different constituents (at 5mg/ml) on H+ extrusion

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Effect%20of%20glucosamine%20complex%20and%20its%20different%20constituents%20on%20H%2B%20extrusion.pdf

Dillemans M, Appelboom T, Van Nedervelde L. Yeast as a model system for identification of metabolic targets of a 'glucosamine complex' used as a therapeutic agent of osteoarthritis. Biomed Pharmacother. 2008 Nov62(9):645-50 p.648 table 1

18662850

Researchers examined the effect of a 15 h cell preincubation with glucosamine complex or its different constituents at a concentration of 5 mg/ml, on cellular protonsâ extrusion in extracellular environment after glucose addition.

Uri M

Proton efflux, glucosamine complex, MSM, methylsulfonylmethane, Ribes nigrum, black currant, silicon,amino sugar<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4709

106883

ECFP maturation time

Budding yeast Saccharomyces cerevisiae

±9

min

17237792

P.178 right column 2nd paragraph: "[Researchers] quantified maturation time [refs 22,23] for YFP (wild-type GFP with mutations S65G,V68L,S72A,T203Y) and a cyan fluorescent protein derivative (CFP wild-type GFP with mutations F64,S65T,Y66W,N146I,M153T,V163A), in individual S. cerevisiae at 25°C (ref. 3 Supplementary Note). [They] induced fluorescent protein synthesis by addition of pheromone to cells with integrated constructs in which the fluorescent protein replaced the PRM1 ORF, allowed transcription and translation to proceed for 30 min, then added cycloheximide to block translation. Cells reached maximum fluorescence by 3 h after translation stop (Fig. 4a) and photobleaching-corrected fluorescence (Supplementary Note) remained stable for up to 24 h (data not shown), indicating that under these conditions protein degradation was negligible."

Uri M

yellow fluorescence protein, jellyfish Aequorea victoria

4742

106916

Fraction of genome that is expressed under normal growth conditions

Budding yeast Saccharomyces cerevisiae

Benjamin Lewin, Genes IX, Jones and Bartlett Publishers, 2008 p.93 right column bottom paragraph

~4,500 genes

Uri M

gene expression, constitutive genes, housekeeping genesis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4756

106930

Length of essential Aâ¢T origin of replication sequence

Budding yeast Saccharomyces cerevisiae

Benjamin Lewin, Genes VIII 2004, p.359 "key concepts" text box

An ARS (autonomously replicating sequence) extends for ~50 bp and includes a consensus sequence (A) and additional elements (B1-B3). See BNID 102577 Note-Méchali 2010 PMID 20861881 p.728 right column bottom paragraph:"Saccharomyces cerevisiae ORCs specifically recognize a 12 bp consensus sequence (ref 4), but Schizosaccharomyces pombe and metazoan ORCs do not exhibit sequence specificity (refs 5,6)."

Uri M

replication, DNA synthesis, polymerization, origin, autonomously replicating sequence<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4828

103043

Number of atoms in phenylalanine tRNA

Budding yeast Saccharomyces cerevisiae

1652

Atoms

Neil R. Voss. 2006 'Geometric Studies of RNA and Ribosomes, and Ribosome Crystallization' Table 3.4 pp. 97

Primary ref under table 3.4 in ref. pdb entry lehz

X ray diffraction

Uri M

size, rna, yeast, transfer rna, complexes of life<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4829

103044

Shell volume of phenylalanine tRNA

Budding yeast Saccharomyces cerevisiae

36049

Table link - http://bionumbers.hms.harvard.edu/files/Solvent%20properties%20for%20several%20different%20macromolecules.jpg

Å^3

Neil R. Voss. 2006 'Geometric Studies of RNA and Ribosomes, and Ribosome Crystallization' Table 3.4 pp. 97

Shi and Moore 2000. The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited. RNA. 2000 Aug6(8):1091-105. PDB entry lehz

10943889

a computer program that uses the rolling probe algorithm to obtain a shell. The algorithm can generate an infinite number of surfaces for a macromolecule simply by varying the radius of probe used.

The âshellâ of a macromolecule is the limiting surface used to distinguish the interior of the macromolecule from its exterior. The shell volume is the volume inside that surface. for further definition see section 3.2.2 page 52 of ref link- http://www.yale.edu/moorelab/thesis/voss06-large.pdf

Uri M

size, fractional, solvent, volume, ribosome, rna, purple bacterium Azoarcus sp. BH72, group I self-splicing intron, complexes of life<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4845

103060

Number of atoms in 20S proteasome

Budding yeast Saccharomyces cerevisiae

49676

Table link - http://bionumbers.hms.harvard.edu/files/Solvent%20properties%20for%20several%20different%20macromolecules.jpg

Atoms

Neil R. Voss. 2006 'Geometric Studies of RNA and Ribosomes, and Ribosome Crystallization' Table 3.4 pp. 97

Groll M, Ditzel L, Löwe J, Stock D, Bochtler M, Bartunik HD, Huber R. Structure of 20S proteasome from yeast at 2.4 A resolution. Nature. 1997 Apr 3 386(6624):463-71. PDB entry 1ryp

9087403

X ray diffraction

Uri M

size, fractional, protein degradation, proteolysis, ubiquitin-proteasome system, complexes of life<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4846

103061

Shell volume of 20S proteasome

Budding yeast Saccharomyces cerevisiae

1260000

Å^3

Neil R. Voss. 2006 'Geometric Studies of RNA and Ribosomes, and Ribosome Crystallization' Table 3.4 pp. 97 link - http://bionumbers.hms.harvard.edu/files/Solvent%20properties%20for%20several%20different%20macromolecules.jpg

Groll M, Ditzel L, Löwe J, Stock D, Bochtler M, Bartunik HD, Huber R. Structure of 20S proteasome from yeast at 2.4 A resolution. Nature. 1997 Apr 3 386(6624):463-71. PDB entry 1ryp

9087403

a computer program that uses the rolling probe algorithm to obtain a shell. The algorithm can generate an infinite number of surfaces for a macromolecule simply by varying the radius of probe used.

Uri M

size, fractional, protein degradation, proteolysis, complexes of life<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4852

103067

Number of mitochondria in non budding cell grown on glucose

Budding yeast Saccharomyces cerevisiae

2.3

mitochondria/cell

Visser W, van Spronsen EA, Nanninga N, Pronk JT, Gijs Kuenen J, van Dijken JP. Effects of growth conditions on mitochondrial morphology in Saccharomyces cerevisiae. Antonie Van Leeuwenhoek. 1995 67(3):243-53. p.247 table 1

7778893

Confocal-scanning laser microscopy ( CSLM) techniques CSLM allows the generation of high resolution, three-dimensional images of living cells

Uri M

size, growth condition, anaerobic growth, fermentable substrate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4853

103068

Number of mitochondria in budding cell grown on glucose

Budding yeast Saccharomyces cerevisiae

3.2

Table link - http://bionumbers.hms.harvard.edu/files/Effect%20of%20growth%20substrate%20on%20morphology%20of%20S.%20cerevisiae%20cells%20and%20mitochondria.pdf

mitochondria/cell

7778893

"[Researchers] used the vital stain for mitochondria methylpyridinium iodine (DASPMI), a fluorescent, non-toxic stain for mitochondria (Bereiter-Hahn 1976: Bereiter-Hahn et al. 1983), combined with confocal scanning laser microscopy (CSLM) (Brakenhoff et al. 1979, 1985, 1989). CSLM allows the generation of high resolution, three-dimensional images of living cells, without the disadvantage of conventional fluorescence microscopy: i.e., the strong out-of-focus fluorescence light which reduces the contrast of images made at high magnifications."

"The most striking observation concerned the number of mitochondria, which was approximately ten-fold higher in ethanol-grown cells than in cells grown on glucose (Table 1). Although the number of mitochondria was different, the mitochondrial volume in ethanol-and glucose-grown cells was approximately the same (Table 1). This implies that mitochondria in ethanol-grown cultures have a much larger surface area than those in glucose-grown cells...In [researchers'] study, the different mitochondrial number and morphology observed in ethanol-and glucose-grown cells did not significantly affect the fraction of the cellular volume occupied by the mitochondria (6-7%, Table 1)." See notes above & beneath table. Note-Graziewicz MA et al., 2006 PMID 16464011 p.384 left column write that "Several hundred mitochondria can be present in individual cells."

Uri M

size, growth condition, anaerobic growth, fermentable substrate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4854

103069

Effect of growth substrate on morphology of cells and mitochondria

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Effect%20of%20growth%20substrate%20on%20morphology%20of%20S.%20cerevisiae%20cells%20and%20mitochondria.pdf

7778893

Uri M

size, growth condition, anaerobic growth, non-fermentable substrate,ethanol,glucose<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4855

103070

Number of mitochondria in budding cell grown on ethanol

Budding yeast Saccharomyces cerevisiae

20-30 table link - http://bionumbers.hms.harvard.edu/files/Effect%20of%20growth%20substrate%20on%20morphology%20of%20S.%20cerevisiae%20cells%20and%20mitochondria.pdf

mitochondria/cell

7778893

"The most striking observation concerned the number of mitochondria, which was approximately ten-fold higher in ethanol-grown cells than in cells grown on glucose (Table 1). Although the number of mitochondria was different, the mitochondrial volume in ethanol-and glucose-grown cells was approximately the same (Table 1). This implies that mitochondria in ethanol-grown cultures have a much larger surface area than those in glucose-grown cells...In [researchers'] study, the different mitochondrial number and morphology observed in ethanol-and glucose-grown cells did not significantly affect the fraction of the cellular volume occupied by the mitochondria (6-7%, Table 1)." Note-Graziewicz MA et al., 2006 PMID 16464011 p.384 left column write that "Several hundred mitochondria can be present in individual cells."

Uri M

size, growth condition, anaerobic growth, non-fermentable substrate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4856

103071

Maximum respiratory capacity in anaerobic conditions

Budding yeast Saccharomyces cerevisiae

Î¼mole oxygen/g dry weight/min

7778893

Shake-flask cultivation,Chemostat cultivation,The maximum respiratory capacity of culture samples was measured polarographically with a Clark type oxygen electrode (Yellow Springs Instruments Inc., Yellow Springs, Ohio, USA) at 30 degrees C.

Upon aeration of a previously anaerobic chemostat culture, the maximum respiratory capacity increased from 10 to 70 µmole oxygen/g dry weight/min within 10 h.

Uri M

size, growth condition, anaerobic growth, mitochondria, respiration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4857

103072

Maximum respiratory capacity in aerobic conditions

Budding yeast Saccharomyces cerevisiae

umole oxygen/((g^-1 dry weight)*(min^-1))

7778893

Upon aeration of a previously anaerobic chemostat culture, the maximum respiratory capacity increased from 10 to 70 umole.min-1.g dry weight-1 within 10 h.

Uri M

size, growth condition, aerobic growth,mitochondria,respiration<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4858

103074

Increase in cell volume upon shift from anaerobic to aerobic conditions

Budding yeast Saccharomyces cerevisiae

7778893

Shake-flask cultivation,Chemostat cultivation,in a glucose-limited chemostat culture. Cell-size measurements were performed with a Coulter counter

Although the dry weight per cell appeared to be fairly constant during the transition, the cell volume increased by ca. 40%, suggesting that the water content of the cells increased (Table 2). Change occurred over a 25-hour period.

Uri M

size, growth condition, anerobic, aerobic growth<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4880

103097

Rate of DNA transfer from mitochondria to nucleus

Budding yeast Saccharomyces cerevisiae

2.00E-05

1/(cell×generation)

Thorsness PE, Fox TD. Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae. Nature. 1990 Jul 26 346(6282):376-9 p.377 right column 3rd paragraph and p.378 table 2

2165219

A yeast strain with mitochondria that contained only sequences derived from a defined plasmid was generated using high velocity microprojectile bombardment.

Movement of DNA in the opposite direction, from nucleus to mitochondria, is apparently at least 100,000 times slower

Uri M

endosymbiotic theory, ura+<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4984

103207

Actin mRNA

Budding yeast Saccharomyces cerevisiae

±5

transcripts / cell

Needleman RB, Kaback DB, Dubin RA, Perkins EL, Rosenberg NG, Sutherland KA, Forrest DB, Michels CA. MAL6 of Saccharomyces: a complex genetic locus containing three genes required for maltose fermentation. Proc Natl Acad Sci U S A. 1984 May81(9):2811-5.

6371820

Brian.C.Haynes

transcript,messenger RNA,transcriptome,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4989

103213

Lifetime of cortical clathrin patches

Budding yeast Saccharomyces cerevisiae

73.8

±31.5

sec

Kaksonen M, Toret CP, Drubin DG. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell. 2005 Oct 21123(2):305-20.Click here to read

16239147

TIRF (total internal reflection fluorescence) imaging of Clc1-GFP in combination with simultaneous epifluorescence imaging of Abp1-RFP,enabled visualization of cortical clathrin patches that partially colocalized with Abp1-RFP patches

Uri M

endocytic protein, pathway, endocytosis, coat formation, red fluorescence protein, total internal reflection fluorescence<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4990

103214

Distance of movement off cell surface before disappearance of clathrin coated vesicle

Budding yeast Saccharomyces cerevisiae

200

Kaksonen M, Toret CP, Drubin DG. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell. 2005 Oct 21123(2):305-20.Click here to read

16239147

multicolor real-time fluorescence microscopy and particle tracking algorithms

The endocytic proteins Sla1p, Pan1p (Eps15 homolog), and Sla2p (Hip1R homolog) appear at the plasma membrane after Las17p, and they move together approximately 200 nm off the cell surface. The disappearance most probably results from the internalization of the coat.

Uri M

endocytic protein, pathway, endocytosis, coat formation, clathrin/actin-mediated endocytosis, Sla1p, Pan1p, Eps15 homolog, Sla2p, Hip1R homolog,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4991

103215

Number of endocytic sites on cell surface

Budding yeast Saccharomyces cerevisiae

0.43

±0.15

Patches/µm^2

Kaksonen M, Toret CP, Drubin DG. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell. 2005 Oct 21123(2):305-20.Click here to read

16239147

Approximately spherical single and large budded cells with unpolarized patches were scored for each strain. Surface area of individual cells was estimated as an average of sphere surface areas calculated from four diameters (at 0°, 45°, 90°, and 135°) measured from maximum intensity projections.

Uri M

endocytic protein, pathway, endocytosis, coat formation, clathrin/actin-mediated endocytosis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4992

103218

Reduction in number of endocytic sites on cell surface in clathrin mutants compared to wild type

Budding yeast Saccharomyces cerevisiae

50-75

Percent

Kaksonen M, Toret CP, Drubin DG. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell. 2005 Oct 21123(2):305-20.Click here to read

16239147

TIRF microscopy and epifluorescence. Approximately spherical single and large budded cells with unpolarized patches were scored for each strain. Surface area of individual cells was estimated as an average of sphere surface areas calculated from four diameters (at 0°, 45°, 90°, and 135°) measured from maximum intensity projections.

Uri M

endocytic protein, pathway, endocytosis, coat formation, clathrin/actin-mediated endocytosis,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4993

103219

Lifetime of patch formed by End3-GFP in endocytic pathway

Budding yeast Saccharomyces cerevisiae

30.2

±4.2

sec

Kaksonen M, Toret CP, Drubin DG. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell. 2005 Oct 21 123(2):305-20.

16239147

TIRF microscopy and epifluorescence. Researchers quantitatively analyzed the spatial and temporal localization of the C-terminal GFP fusions of each protein expressed from its endogenous locus

End3-GFP initially formed an immotile patch that later moved about 200 nm toward the cell center while it was dissipating (Figures 3B and 3C). The onset of the inward movement corresponded with the arrival of Abp1-RFP at the End3-GFP patch (Figure 3D). Thus, End3p behaves like Sla1p, Pan1p, and Sla2p (Kaksonen et al., 2003). Since these proteins move like clathrin, they are likely associated with the vesicle coat.

Uri M

actin, clathrin, coat formation, clathrin/actin-mediated endocytosis, green fluorescence protein, EH domain protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4994

103220

Lifetime of patch formed by Bbc1-GFP endocytic pathway

Budding yeast Saccharomyces cerevisiae

9.6

±1.1

sec

Kaksonen M, Toret CP, Drubin DG. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell. 2005 Oct 21123(2):305-20.Click here to read

16239147

TIRF microscopy and epifluorescence. Researchers quantitatively analyzed the spatial and temporal localization of the C-terminal GFP fusions of each protein expressed from its endogenous locus

Bbc1-GFP patches had a short lifetime of 9.6 ± 1.1 s and stayed immotile at the cell surface throughout their lifetime

Uri M

actin, clathrin, coat formation, clathrin/actin-mediated endocytosis, green fluorescence protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4995

103221

Lifetime of patch formed by Rvs161-GFP in endocytic pathway

Budding yeast Saccharomyces cerevisiae

12.1

±3.3

sec

Kaksonen M, Toret CP, Drubin DG. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell. 2005 Oct 21123(2):305-20.Click here to read

16239147

TIRF microscopy and epifluorescence. Researchers quantitatively analyzed the spatial and temporal localization of the C-terminal GFP fusions of each protein expressed from its endogenous locus

Rvs161-GFP and Rvs167-GFP also appeared at patches very transiently (12.1 ± 3.3 and 10.2 ± 1.4 s respectively Figure 3A). These proteins were initially immotile, then moved and immediately dissipated from the patch (Figures 3B and 3C). The patch centroids moved only about 100 nm, and the movement took place in less than 0.5 s

Uri M

actin, clathrin, coat formation, clathrin/actin-mediated endocytosis, green fluorescence protein, Rvs167-GFP, endocytic protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

4996

103222

Lifetime of endocytic protein Cap1-GFP

Budding yeast Saccharomyces cerevisiae

18.8

±2.1

sec

Kaksonen M, Toret CP, Drubin DG. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell. 2005 Oct 21123(2):305-20.Click here to read

16239147

TIRF microscopy and epifluorescence. Researchers quantitatively analyzed the spatial and temporal localization of the C-terminal GFP fusions of each protein expressed from its endogenous locus

Uri M

actin, clathrin, coat formation, clathrin/actin-mediated endocytosis, green fluorescence protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5008

103234

Constant rate of actin filament movement from cell cortex to cell center

Budding yeast Saccharomyces cerevisiae

45.3

±4.6

nm/sec

Kaksonen M, Sun Y, Drubin DG. A pathway for association of receptors, adaptors, and actin during endocytic internalization. Cell. 2003 Nov 14115(4):475-87.

14622601

fluorescence recovery after photobleaching, FRAP

Uri M

endocytosis, endocytic pathway<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5009

103235

Distance covered by Abp1p and Arc15p from cell surface in endocytic pathway

Budding yeast Saccharomyces cerevisiae

500-1000

Kaksonen M, Sun Y, Drubin DG. A pathway for association of receptors, adaptors, and actin during endocytic internalization. Cell. 2003 Nov 14115(4):475-87.

14622601

Uri M

endocytosis,endocytic pathway,Actin-binding protein,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5010

103236

average apparent speed of the Sla1p patches during the motile phase

Budding yeast Saccharomyces cerevisiae

nm/sec

Kaksonen M, Sun Y, Drubin DG. A pathway for association of receptors, adaptors, and actin during endocytic internalization. Cell. 2003 Nov 14115(4):475-87.

14622601

six yeast proteins involved in endocytosis were tagged with GFP spectral variants and analyzed their localization and dynamics in living cells using multicolor wide field epifluorescence microscopy.

Value observed in the plane of focus

Uri M

endocytosis, endocytic pathway, actin related protein,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5011

103237

Speed of the abp1p patches during the final fast phase of endocytosis

Budding yeast Saccharomyces cerevisiae

230

nm/sec

Kaksonen M, Sun Y, Drubin DG. A pathway for association of receptors, adaptors, and actin during endocytic internalization. Cell. 2003 Nov 14 115(4):475-87.

14622601

six yeast proteins involved in endocytosis were tagged with GFP spectral variants and analyzed their localization and dynamics in living cells using multicolor wide field epifluorescence microscopy.

abp1p is one of three activator proteins of the ARP2/3 complex, which is a major nucleator of actin filaments, essential for yeast endocytosis

Uri M

endocytosis, endocytic pathway, actin binding protein, Arp2/3, actin cytoskeleton, nucleation, cortical patches<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5023

103250

Length of adenosine tail

Budding yeast Saccharomyces cerevisiae

55-90

nucleotides

Tian B, Hu J, Zhang H, Lutz CS. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 2005 Jan 1233(1):201-12.

15647503

Uri M

polyadenylation, 3 prime, transcript, mrna<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5121

103351

ATP yield per substrate in fermentation

Budding yeast Saccharomyces cerevisiae

Byung Hong Kim, Geoffrey Michael Gadd. Bacterial Physiology and Metabolism. Cambridge University Press. pp. 188

glucose as substrate

Ron Milo - Admin

5187

103417

Hill coefficient of PolyA polymerase

Budding yeast Saccharomyces cerevisiae

1.6

Unitless

Sillero MA, De Diego A, Osorio H, Sillero A. Dinucleoside polyphosphates stimulate the primer independent synthesis of poly(A) catalyzed by yeast poly(A) polymerase. Eur J Biochem. 2002 Nov269(21):5323-9.

12392566

Poly(A) polymerase from yeast was prepared. One unit of enzyme is the amount that incorporates 1 nmol of ATP (as AMP) into an acid insoluble form in 1 min at 37 °C. After incubation at 30 degrees or 37 degrees, the reaction mixtures were analyzed by TLC or HPLC

As value>1, this is a positively cooperative reaction: Once one ligand molecule is bound to the enzyme, its affinity for other ligand molecules increases.

Uri M

poly adenine polymerase, transcript, 3 prime,pola tail<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5188

103418

Km of PolyA polymerase

Budding yeast Saccharomyces cerevisiae

0.308

±0.12

12392566

Km calculated for S[0.5] (substrate at half of Vmax)

Uri M

poly adenine polymerase, transcript, 3 prime, pola tail<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5189

103419

Km of PolyA polymerase in presence of Gp4G

Budding yeast Saccharomyces cerevisiae

0.063

±0.012

12392566

Km calculated for S[0.5] (substrate at half of Vmax). The presence of Gp4G or Ap4A changed the kinetic from sigmoidal to hyperbolic,

Uri M

5190

103420

Km of PolyA polymerase in presence of Ap4A

Budding yeast Saccharomyces cerevisiae

0.17

±0.025

12392566

Km calculated for S[0.5] (substrate at half of Vmax). The presence of Gp4G or Ap4A changed the kinetic from sigmoidal to hyperbolic,

Uri M

5195

103426

Lipid-phosphorus concentration

Budding yeast Saccharomyces cerevisiae

0.137

mg P/mg dry cell

Katchman BJ, Fetty WO. Phosphorus metabolism in growing cultures of Saccharomyces cerevisiae. J Bacteriol. 1955 Jun69(6):607-15.

14392115

Total phosphorus was estimated colorimetrically after conversion of the sample to orthophosphate by digestion with perchloric acid for 1 hour at 130-160 C. Lipid-phosphorus fraction: Two milliliter aliquots of a 30 ml alcohol-ether extract are pipetted into 25 ml volumetric flasks, a few drops of water are added, and the organic solvents are evaporated on a boiling water bath. One milliliter of 70 per cent perchloric acid is added, and the sample is digested at 130-160 C as for the total phosphorus determination.

Uri M

logarithmic phase, metabolism<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5196

103427

Concentration of phosphorus in DNA

Budding yeast Saccharomyces cerevisiae

0.05

mg P/mg dry cell

Katchman BJ, Fetty WO. Phosphorus metabolism in growing cultures of Saccharomyces cerevisiae. J Bacteriol. 1955 Jun69(6):607-15.

14392115

Total phosphorus was estimated colorimetrically after conversion of the sample to orthophosphate by digestion with perchloric acid for 1 hour at 130-160 C.

P in values denotes Phosphorus

Uri M

logarithmic phase, metabolism, deoxyribose nucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5197

103428

Fraction of total genes regulated by phosphoinositide-specific phospholipase

Budding yeast Saccharomyces cerevisiae

Demczuk A, Guha N, Nguyen PH, Desai P, Chang J, Guzinska K, Rollins J, Ghosh CC, Goodwin L, Vancura A. Saccharomyces cerevisiae phospholipase C regulates transcription of Msn2p-dependent stress-responsive genes. Eukaryot Cell. 2008 Jun7(6):967-79.

18375619

DNA array experiments with plc1 delta strains

Uri M

Plc1p, inositol polyphosphates, (InsPs), Phosphatidylinositol phosphates, phospholipid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5198

103429

Number of orthophosphates in polyphosphate chains

Budding yeast Saccharomyces cerevisiae

200

Unitless

Vagabov VM, Trilisenko LV, Kulaev IS. Dependence of inorganic polyphosphate chain length on the orthophosphate content in the culture medium of the yeast Saccharomyces cerevisiae. Biochemistry (Mosc). 2000 Mar65(3):349-54.

10739478

Successive treatment of biomass with cold diluted perchloric acid, salt, and then weak alkali

Uri M

inorganic polyphosphates,(polyP), polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5199

103430

Increase in PolyP3 levels 2 hours after starvation

Budding yeast Saccharomyces cerevisiae

400

Fold

10739478

The polyP3 fraction is involved in the maintenance of the fine structural organization of the yeast cell wall. This suggests that the cells primarily restore normal function of the cell surface disrupted during the phosphate starvation.

Uri M

inorganic polyphosphates,(polyP),polymer,Sodium tripolyphosphate, (Na5P3O10),overcompensation,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5200

103431

Length of polyphosphate chain in orthophosphate fraction at pH 4.5

Budding yeast Saccharomyces cerevisiae

25-55

Orthophosphate units

10739478

The yeast is first cultivated for 4 h in a complete Rider medium containing 9 mM Pi and 111 mM glucose as a carbon source. Then the cells are placed on the same medium except depleted of Pi under sterile conditions and the culture is grown during 7 h. Further, the cells are again placed on fresh complete medium, where the culture is growing for 2 and 4 h. The degree of polymerization (n) of polyP fractions was estimated from the areas of 31P-NMR-spectral peaks. As seen from Fig. 2, the polyphosphates of the acid-soluble fraction can be separated into two sub-fractions by precipitation with barium salt first at pH 4.5 and then at pH 8.2.

The orthophosphate fraction is the acid soluble fraction

Uri M

inorganic polyphosphates, (polyP), polymer,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5201

103432

Pi concentration in polyphosphates

Budding yeast Saccharomyces cerevisiae

5798

µg P/g dry cell weight

10739478

The yeast is first cultivated for 4 h in a complete Rider medium containing 9 mM Pi and 111 mM glucose as a carbon source. Phosphate concentration was estimated according to Berenblum and Chain in the modification of Weil-Malherbe and Green (ref 16 of article). To determine dry weight, aliquots of cell suspensions were applied on filters preliminary brought to a constant weight by drying under vacuum at 85°C and dried to a constant weight under the same conditions.

Uri M

inorganic polyphosphates, (polyP), polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5202

103433

PolyP2 concentration in polyphosphates

Budding yeast Saccharomyces cerevisiae

3800

µg P/g dry cell weight

10739478

P.350 right column 4th paragraph: "Phosphate concentration was estimated according to Berenblum and Chain in the modification of Weil-Malherbe and Green (ref 16)." P.350 right column 5th paragraph: "To determine dry weight, aliquots of cell suspensions were applied on filters preliminary brought to a constant weight by drying under vacuum at 85°C and dried to a constant weight under the same conditions." P.350 right column 8th paragraph: "The yeast is first cultivated for 4 h in a complete Rider medium containing 9 mM Pi and 111 mM glucose as a carbon source (point A)." Extracted visually from Fig. 1. a).

P.351 caption to Fig1.A: "PolyP [inorganic linear polyphosphate] content in the cells of S. cerevisiae under different conditions of their cultivation: PolyP content in the cells of S. cerevisiae under different conditions of their cultivation." P.351 right column bottom paragraph: "A comparison of polyP content in the yeast before phosphate starvation (point A) and after the transfer of the culture to the fresh complete medium (point C) indicates that super-accumulation is not characteristic for all polyP fractions. As seen from Fig. 1a, the maximal accumulation under the conditions in question is observed for the polyP3 (almost 5-fold) and polyP5 (more than 8-fold) fractions."

Uri M

inorganic polyphosphates, (polyP), polymer, pyrophosphoric acid, (H4P2O7)

5203

103434

PolyP3 concentration in polyphosphates

Budding yeast Saccharomyces cerevisiae

3250

µg P/g dry cell weight

10739478

Measured manually from Fig. 1. a) PolyP content in the cells of S. cerevisiae under different conditions of their cultivation

Uri M

inorganic polyphosphates, (polyP), polymer, tripolyphosphoric acid, (H5P3O10)<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5204

103435

PolyP4 concentration in polyphosphates

Budding yeast Saccharomyces cerevisiae

2900

µg P/g dry cell weight

10739478

Measured manually from Fig. 1. a) PolyP content in the cells of S. cerevisiae under different conditions of their cultivation

Uri M

inorganic polyphosphates, (polyP), polymer, tetrapolyphosphoric acid, H6P4O13<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5205

103436

PolyP5 concentration in polyphosphates

Budding yeast Saccharomyces cerevisiae

500

µg P/g dry cell weight

10739478

Measured manually from Fig. 1. a) PolyP content in the cells of S. cerevisiae under different conditions of their cultivation

Uri M

inorganic polyphosphates, (polyP), polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5206

103437

Total polyphosphates concentration

Budding yeast Saccharomyces cerevisiae

16250

µg P/g dry cell weight

10739478

Uri M

inorganic polyphosphates, (polyP), polymer

5212

103443

Increse in weight after 7 hours of growth on Pi depleted medium

Budding yeast Saccharomyces cerevisiae

Fold

10739478

The yeast is first cultivated for 4 h in a complete Rider medium containing 9 mM Pi and 111 mM glucose as a carbon source.Then the cells are placed on the same medium except depleted of Pi under sterile conditions and the culture is grown during 7 h. To determine dry weight, aliquots of cell suspensions were applied on filters preliminary brought to a constant weight by drying under vacuum at 85°C and dried to a constant weight under the same conditions.

Almost complete polyP utilization of absolutely all fractions is seen within 7 h of phosphate starvation.

Uri M

inorganic polyphosphates,(polyP),polymer,orthophosphate,logarithmic growth phase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5213

103444

Length of polyphosphate chain in orthophosphate fraction at pH 8.2

Budding yeast Saccharomyces cerevisiae

8-20

Pi units

10739478

The yeast is first cultivated for 4 h in a complete Rider medium containing 9 mM Pi and 111 mM glucose as a carbon source.Then the cells are placed on the same medium except depleted of Pi under sterile conditions and the culture is grown during 7 h. The degree of polymerization (n) of polyP fractions was estimated from the areas of 31P-NMR-spectral peaks. As seen from Fig. 2, the polyphosphates of the acid-soluble fraction can be separated into two sub-fractions by precipitation with barium salt first at pH 4.5 and then at pH 8.2.

The orthophosphate fraction is the acid soluble fraction

Uri M

inorganic polyphosphates, (polyP), polymer, orthophosphate, Pyrophosphoric acid, diphosphoric acid, H4P2O7,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5214

103445

Length of polyphosphate chain in PolyP2 fraction

Budding yeast Saccharomyces cerevisiae

13-48

Pi units

10739478

This is the salt-soluble fraction (polyP2). Measured manually from figure 2

Uri M

inorganic polyphosphates, (polyP), polymer, H4P2O7, Pyrophosphoric acid, PPi, diphosphoric acid,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5215

103446

Length of polyphosphate chain in PolyP3 fraction

Budding yeast Saccharomyces cerevisiae

70-116

Pi units

10739478

This is an alkali-soluble fraction (polyP3). Measured manually from fiigure 2

Uri M

inorganic polyphosphates,(polyP),polymer,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5216

103447

Length of polyphosphate chain in PolyP4 fraction

Budding yeast Saccharomyces cerevisiae

125-200

Pi units

10739478

This is an alkali-soluble fraction (polyP4). Measured manually from fiigure 2

Uri M

inorganic polyphosphates,(polyP),polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5217

103448

Increase in length of polyphosphate chain in PolyP2 fraction during 20 fold decrease of weight following Phosphorus depletion

Budding yeast Saccharomyces cerevisiae

Fold

10739478

This is the salt-soluble fraction (polyP2). The length of the chains increased to n=40-45 Pi units

Uri M

inorganic polyphosphates,(polyP),polymer,H4P2O7,Pyrophosphoric acid,PPi,diphosphoric acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5218

103449

Fraction of PolyP localized at the cell surface

Budding yeast Saccharomyces cerevisiae

20-30

10739478

Vagabov, V. M. (1988) Biosynthesis of Carbohydrate Components of Yeast Cell Wall [in Russian], NTsBI Akad. Nauk SSSR, Pushchino. AND Kulaev, I. S., Vagabov, V. M., and Shabalin, Yu. A. (1987) in Phosphate Metabolism and Cellular Regulation in Microorganisms (Torriani-Gorini, A., Rothman, F. G., Silver, S., Wright, A., and Yagil, E., eds.) American Society for Microbiology, Washington, pp. 233-238.

The content of this polyP may comprise 20-30% of the total amount of cell polyP depending on the conditions of cultivation. See BNID 103450, 105839

Uri M

inorganic polyphosphates, (polyP), polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5219

103450

Fraction of PolyP localized in the vacuoles

Budding yeast Saccharomyces cerevisiae

10739478

See BNID 103449, 105839

Uri M

inorganic polyphosphates, (polyP), polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5220

103451

Pi concentration in polyphosphates following 7 hours of phosphorus depletion

Budding yeast Saccharomyces cerevisiae

1054

µg P/g dry cell weight

10739478

This represents a decrease greater than 5 fold compared to complete medium (see bion 103432)

Uri M

inorganic polyphosphates, (polyP), polymer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5286

103518

Percent of genome that is intergenic DNA

Budding yeast Saccharomyces cerevisiae

18583475

Uri M

noncoding DNA<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5289

103521

Rate of overall mutations (including non deleterious)

Budding yeast Saccharomyces cerevisiae

0.32

mutation/(genome*cell division)

Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, Thomas WK. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A. 2008 Jul 8105(27):9272-7. Table 3 table link - http://bionumbers.hms.harvard.edu/files/Comparisons%20of%20mutation%20rates%20per%20cell%20division%20in%20yeast%2C%20nematode%2C%20fly%20and%20human.pdf

18583475

1. Baer CF, 2. et al. (2006) Cumulative effects of spontaneous mutations for fitness in Caenorhabditis: Role of genotype, environment and stress. Genetics 174:1387â1395.

16888328

Analyses are based on an examination of parallel MA lines of a key model system, the yeast Saccharomyces cerevisiae. The initially isogenic lines were passed through 200 single-cell bottlenecks on a 3- to 4-day cycle of clonal growth for a total of Ë4,800 cell divisions per line. Spontaneous mutations were accumulated in 32 independent sets of haploid lines, 8 in each of four series, AâD, all initiated from the same clonal parent derived from a single laboratory stock, FY10 (leu2?1, ura3â52, MATa)

0.0041 base substitutions, 0.0002 small insertion/deletions in complex sequence, 0.0019 microsatellite mutations, and 0.3094 homopolymer mutations.

Uri M

yeast Saccharomyces cerevisiae, microsatellite, homopolymeric region, base substitution, insertion, deletion, mitochondria<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5292

103524

Number of tRNA types in cell

Budding yeast Saccharomyces cerevisiae

273

tRNA types

Man O, Pilpel Y. Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nat Genet. 2007 Mar39(3):415-21.

17277776

The tRNA gene copy numbers were obtained by applying the tRNAscan-SE software version 1.1 (Lowe and Eddy 1997), which uses a hidden Markov model (HMM)-based approach to the genome sequences.

Uri M

transfer RNA<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5310

103543

Redox potential of cytosolic glutathione

Budding yeast Saccharomyces cerevisiae

-289

Østergaard H, Tachibana C, Winther JR. Monitoring disulfide bond formation in the eukaryotic cytosol. J Cell Biol. 2004 Aug 2 166(3):337-45. abstract & p.339 table I

15277542

"[Investigators] apply a previously designed GFP-based sensor for disulfide bond formation (Ostergaard et al., 2001) to study the cytosolic thiol-disulfide redox status." Using a genetically encoded glutathione-specific redox probe the concentrations of GSH and GSSG in the yeast cytosol have been estimated

"For the first time a genetically encoded probe is used to determine the redox potential specifically of cytosolic glutathione. We find it to be -289mV, indicating that the glutathione redox status is highly reducing and corresponds to a cytosolic GSSG level in the low micromolar range." Table 1-Cytosolic redox potentials (E'cytosol) were calculated from the pulse-chase end point redox distributions given in Figs. 2 and 3 and an E°' of â265 mV for rxYFP

Uri M

thiolate anion, protein thiols, redox, SH, PSH, thiolâdisulfide, glutathione, green fluorescent protein, glutaredoxin, redox, oxidation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5315

103548

Concentration of glutathione disulfide GSSG in cytosol

Budding yeast Saccharomyces cerevisiae

µM

Østergaard H, Tachibana C, Winther JR. Monitoring disulfide bond formation in the eukaryotic cytosol. J Cell Biol. 2004 Aug 2166(3):337-45.

15277542

Using a genetically encoded glutathione-specific redox probe the concentrations of GSH and GSSG in the yeast cytosol have been estimated

Estimates of absolute concentrations of GSH and GSSG are based on only two assumptions: (1) a cytosolic pH between 6.7 and 7.3 and (2) the absence of other catalysts than glutaredoxin 1 and 2. Although no direct evidence has been found for the latter, it seems, however, highly reasonable given the slow equilibration kinetics observed in the glr1 grx1 grx2 triple knockout. It should also be emphasized that the presence of additional redox catalysts would imply an even lower cytosolic GSSG concentration than the one estimated here. If the GSH concentration of this mutant is close to that of the wild type, as supported by whole cell measurements, we find the cytosolic GSSG concentration of the wild type to be surprisingly low, ~4 µM.

Uri M

thiolate anion, protein thiols, redox, SH, PSH, thiolâdisulfide, glutathione, green fluorescent protein, glutaredoxin, redox, oxidation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5380

103613

Concentration of alpha Agglutinin after induction by alpha mating factor

Budding yeast Saccharomyces cerevisiae

10000

molecules/cell

Lipke PN, Kurjan J. Sexual agglutination in budding yeasts: structure, function, and regulation of adhesion glycoproteins.Microbiol Rev. 1992 Mar56(1):180-94. Table 1

1579109

a-Agglutinin binds its glycoprotein ligand a-agglutinin, expressed on the surface of cells of mating-type a.

Uri M

alpha-Agglutinin, glycoprotein ligand a-agglutinin, mating pheromone, alpha mating factor, cell adhesion<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5381

103614

Concentration of agglutinins on cell surface after expression upregulation by pheromone

Budding yeast Saccharomyces cerevisiae

0.001

Zhao H, Shen ZM, Kahn PC, Lipke PN. Interaction of alpha-agglutinin and a-agglutinin, Saccharomyces cerevisiae sexual cell adhesion molecules. J Bacteriol. 2001 May183(9):2874-80.

11292808

Shen, Z. M., L. Wang, H. Zhao, J. Kurjan, J. Pike, and P. N. Lipke. Delineation of functional regions within the subunits of the Saccharomyces cerevisiae cell adhesion molecule a-agglutinin. J Biol Chem. 2001 May 11276(19):15768-75

11278672

a-Agglutinin binds its glycoprotein ligand a-agglutinin, expressed on the surface of cells of mating-type a. Binding is tight, with a Kd near 10-9 M and an extremely slow dissociation rate

Uri M

alpha-Agglutinin, glycoprotein, ligand a-agglutinin, mating pheromone, alpha mating factor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5382

103615

External concentration of alpha mating factor required for half maximal cell division arrest

Budding yeast Saccharomyces cerevisiae

0.25

Moore SA. Comparison of dose-response curves for alpha factor-induced cell division arrest, agglutination, and projection formation of yeast cells. Implication for the mechanism of alpha factor action. J Biol Chem. 1983 Nov 25 258(22):13849-56. p.13852 right column 4th paragraph and p.13851 table 1

6358212

yeast MATa cells respond to alpha pheromone by undergoing several inducible responses: the arrest of cell division, the production of a cell surface agglutinin, and the formation of one or more projections on the cell surface commonly termed the "shmoo" morphology. Dose-response curves were determined for each of these inducible responses as a function of alpha factor concentration. Two new cell division arrest assays were devised here and are the N4/NO and the %UBh assays.

This dose is nearly the same as that at which cells exhibit a half-maximal response for agglutination induction (0.1nM, bion 103616)

Uri M

alpha-pheromone, cell cycle arrest, sex mating pheromone, alpha mating factor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5383

103616

External concentration of alpha mating factor required for half maximal induction of agglutination

Budding yeast Saccharomyces cerevisiae

0.1

6358212

This value is nearly the same as that at which cells exhibit a half-maximal response for cell division arrest (0.25 nM, bion 103615)

Uri M

alpha-agglutinin, cell cycle arrest, sex mating pheromone, alpha mating factor, cell adhesion,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5384

103617

Cellular concentration of Alpha factor mating pheromone

Budding yeast Saccharomyces cerevisiae

28900

molecules/cell

http://www.genwaybio.com/product_info.php?products_id=83056

Better ref needed

Uri M

MFA1 peptide MFA1, Alpha factor mating pheromone Yeast,shmoo,conjugation,haploid cell,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5385

103618

External concentration of alpha mating factor required for half maximal 'shmoo' formation

Budding yeast Saccharomyces cerevisiae

6358212

This value is 2 orders of magnitude higher than that at which cells exhibit a half-maximal response for cell division arrest (0.25 nM, bion 103615) and a half-maximal response for agglutination response (0.1 nM, Bion 103616)

Uri M

projection formation,cell cycle arrest,sex mating pheromone,alpha mating factor,cell adhesion<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5424

103657

RNA polymerase III elongation rate

Budding yeast Saccharomyces cerevisiae

21-22

nt/sec

Matsuzaki H, Kassavetis GA, Geiduschek EP. Analysis of RNA chain elongation and termination by Saccharomyces cerevisiae RNA polymerase III. J Mol Biol. 1994 Jan 28 235(4):1173-92. abstract, p.1180 left column bottom paragraph & p.1187 right column bottom paragraph

8308883

In vitro transcription and transcript release. p.1175 left column 3rd paragraph:"Autoradiograms were scanned with a laser densitometer and analyzed with the aid of a software package developed by AMBIS (san diego)."

Abstract:"RNA chain elongation through assembled transcription complexes was uneven but relatively rapid: at 20°C with 1 mM NTPs, the fastest RNA chains elongated at an average rate of 29 nucleotides (nt)/second, and the median RNA chains elongated at 21 to 22 nt/second on average." "An average RNA chain elongation rate of 21 to 22 nt/second at 1 mM NTPs could be derived for the median RNA chain from Figure 2(d), as already mentioned, and an extrapolated value of 7.2 nt/second at 100µM NTPs from Figure 2(c)." "[Investigators] have found that RNA chain elongation by Pol III is also uneven. The yeast Pol III in vitro system has a relatively high rate of chain elongation: at 20°C, with 1 mM NTPs, the fastest chains elongate at 29 nt/seconds and the median elongation rate is 21 to 22 nt/seconds."

Uri M

transcription, mrna, speed, base pairs, nucleotide, polymerization<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5425

103658

Decrease in RNA polymerase III elongation rate at 0 degrees celsius

Budding yeast Saccharomyces cerevisiae

Fold

Matsuzaki H, Kassavetis GA, Geiduschek EP. Analysis of RNA chain elongation and termination by Saccharomyces cerevisiae RNA polymerase III. J Mol Biol. 1994 Jan 28235(4):1173-92.

8308883

In vitro transcription and transcript release. Autoradiograms were scanned with a laser densitometer and analyzed with the aid of a software package developed by AMBIS (san diego)

RNA chain elongation through assembled transcription complexes was uneven but relatively rapid: at 20 degrees C with 1 mM NTPs, the fastest RNA chains elongated at an average rate of 29 nucleotides (nt)/second, and the median RNA chains elongated at 21 to 22 nt/second on average. At 0 degrees celsius rate decreased 30-fold

Uri M

translation, mrna, speed, base pairs, nucleotide, polymerization,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5719

107283

Statistics of proteins and complexes

Budding yeast Saccharomyces cerevisiae

Figure - http://bionumbers.hms.harvard.edu/files/Statistics%20of%20proteins%20and%20complexes.pdf

Gavin et al., Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002 Jan 10 415(6868):141-7. p.142 fig.2

11805826

The purified protein assemblies were separated by denaturing gel electrophoresis, individual bands were digested by trypsin, analysed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and identified by database search algorithms.

Uri M

ER, Golgi, vesicles, Mitochondria, Cytoplasm, Nucleus, membrane, Transcription, DNA, maintenance, chromatin structure, Signalling, Cell polarity, structure, Cell cycle, Intermediate and, energy metabolism, Membrane biogenesis, turnover, Protein, RNA transport, RNA metabolism, Protein synthesis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5731

107295

Subcellular localization of 2,744 proteins

Budding yeast Saccharomyces cerevisiae

47% cytoplasmic: 27% nuclear/nucleolar: 13% mitochondrial: 13% exocytic

Kumar A et al., Subcellular localization of the yeast proteome. Genes Dev. 2002 Mar 15 16(6):707-19. abstract

11914276

High-throughput immunolocalization of tagged gene products

Exocytic=(including proteins of the endoplasmic reticulum and secretory vesicles). Similarly, Huh et al. 2003 PMID 14562095 presented the localization of 4,156 proteins to 22 subcellular compartments in yeast showing that 43% were cytoplasmic, 35% nuclear and 13% mitochondrial.

Uri M

mitochondria, proteome, nucleus, nucleoli, nucleolus, cytoplasm<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5763

107327

Binding constant of ribosome to CrPV IGR IRES element

Budding yeast Saccharomyces cerevisiae

21.7

±1.7

Jack K et al., rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. Mol Cell. 2011 Nov 18 44(4):660-6. p.662 fig.1C

22099312

Steady-state filter-binding assays

CrPV IRES=cricket paralysis virus internal ribosome entry site

Uri M

association, dissociation constant,kinetics<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5764

107328

Length of genome

Budding yeast Saccharomyces cerevisiae

Yanamoto T, Miyamoto A, Ikeda K, Hatano T, Matsuzaki H. The relationship between chromosomal positioning within the nucleus and the SSD1 gene in Saccharomyces cerevisiae. Biosci Biotechnol Biochem. 2011 75(9):1713-21 p.1713 left column top paragraph

21897045

Wente, Gasse and Caplan "The molecular and cellular biology of the yeast Saccharomyces, volume 3 cell cycle and cell biology", eds. Pringle, Broach and Jones, Cold Spring Harbor Laboratory Press, Cold Spring Harbor pp.471-546 (1997)

In eukaryotic cells, very large chromosomal DNAs are efficiently packed within the nucleus. A haploid cell of the budding yeast S. cerevisiae contains 16 chromosomal DNAs with a total length of ~14Mb, equivalent to 5mm (primary source).

Uri M

length, size, genome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5765

107329

Fraction of mitochondrial division events that are spatially linked to sites of ER-mitochondrial contact

Budding yeast Saccharomyces cerevisiae

Friedman JR, Lackner LL, West M, DiBenedetto JR, Nunnari J, Voeltz GK. ER tubules mark sites of mitochondrial division. Science. 2011 Oct 21 334(6054):358-62 p.360 right column bottom paragraph

21885730

Researchers examined the role of ER in mitochondrial division by using fluorescence microscopy in live yeast cells transformed with an ER marker (GFP-HDEL) and mito-dsRed to image the behavior of ER and mitochondria simultaneously over time.

n=112

Uri M

endoplasmic reticulum,mitochondria, division, mitochondrion,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5767

107331

Mitotic recombination rate

Budding yeast Saccharomyces cerevisiae

2.30E-05

2.1e-5 to 3.0e-5

Recombinations per Mitosis

Sheltzer et al., Aneuploidy drives genomic instability in yeast. Science. 2011 Aug 19 333(6045):1026-30. p.1028 fig.3C

21852501

Researchers quantified the fraction of cells that contained DSBs in seven phleomycin-sensitive disomes by monitoring Rad52âgreen fluorescent protein (Rad52-GFP) foci, which localize to sites of recombinational repair.

Range is 95% confidence interval

Uri M

DNA, nucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5768

107332

Mutation frequencies at CAN1

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Mutation%20frequencies%20at%20CAN1.pdf

Sheltzer et al., Aneuploidy drives genomic instability in yeast. Science. 2011 Aug 19 333(6045):1026-30. Supporting online material p.43/63 Supplemental Table S1

21852501

In order to define the molecular mechanism underlying the increased mutation rate in aneuploid cells, researchers sequenced the CAN1 allele from 133 wild-type and 404 disomic canavanine-resistant isolates

Uri M

DNA, nucleic acid, Basepair, substitutions, Frameshifts, Complex, Events, Transitions, Transversions, Insertions, Deletions<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5769

107333

Fraction of the DSB repair events in mitotic cells that result in a crossover

Budding yeast Saccharomyces cerevisiae

~10 to 15

Agmon N, Yovel M, Harari Y, Liefshitz B, Kupiec M. The role of Holliday junction resolvases in the repair of spontaneous and induced DNA damage. Nucleic Acids Res. 2011 Sep 1 39(16):7009-19 p.7015 right column 2nd and bottom paragraphs

21609961

Inbar,O., Liefshitz,B., Bitan,G. and Kupiec,M. (2000) The relationship between homology length and crossing over during the repair of a broken chromosome. J. Biol. Chem., 275, 30833â30838. AND Borts,R.H. and Haber,J.E. (1987) Meiotic recombination in yeast: alteration by multiple heterozygosities. Science, 237, 1459â1465 AND Lee,P.S., Greenwell,P.W., Dominska,M., Gawel,M., Hamilton,M. and Petes,T.D. (2009) A fine-structure map of spontaneous mitotic crossovers in the yeast Saccharomyces cerevisiae. PLoS Genet., 5, e1000410 AND Bzymek,M., Thayer,N.H., Oh,S.D., Kleckner,N. and Hunter,N. (2010) Double Holliday junctions are intermediates of DNA break repair. Nature, 464, 937â941.

10924495, 2820060, 19282969, 20348905

DSB=Double Strand Breaks

Uri M

DNA damage<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5785

107349

Percentage of RNA-polymerase-II-mediated transcription initiation events that involve ribosomal protein (RP) genes

Budding yeast Saccharomyces cerevisiae

JR Warner,The economics of ribosome biosynthesis in yeast,Trends Biochem Sci. 1999 Nov24(11):437-40. p.437 right column top paragraph

10542411

"As the RP [ribosomal protein] mRNAs are relatively short-lived compared with other mRNAs (Ref. 9 PMID 10409730), an estimated 50% of the RNA-polymerase- II-mediated transcription initiation events involve RP genes."

Uri M

transcription, ribosome, translation machinery, mRNA<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5786

107350

Fraction of ribosomes that are present in the polysomes

Budding yeast Saccharomyces cerevisiae

<85

Piques et al., Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol. 2009 5: 314 p.2 left column 2nd paragraph

19888209

Uri M

translation machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5845

107409

Amplitude of local periodic nanoscale motions

Budding yeast Saccharomyces cerevisiae

±0.5

Reguera G. When microbial conversations get physical. Trends Microbiol. 2011 Mar19(3):105-13. p.106 left column top paragraph

21239171

Pelling AE, Sehati S, Gralla EB, Valentine JS, Gimzewski JK. Local nanomechanical motion of the cell wall of Saccharomyces cerevisiae. Science. 2004 Aug 20 305(5687):1147-50.

15326353

Atomic force microscopy

Using the sensitivity of an atomic force microscope to probe cellular nanomechanics in an acoustically insulated environment,Pelling et al. demonstrated that the cell wall of single, living cells of Saccharomyces cerevisiae exhibited local periodic nanoscale motions of similar average amplitude (3.0±0.5nm), yet variable, temperature-dependent frequencies (0.9â1.6 kHz)

Uri M

oscillation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5846

107410

Activation energy of oscillations of single cells

Budding yeast Saccharomyces cerevisiae

kJ/mol

Reguera G. When microbial conversations get physical. Trends Microbiol. 2011 Mar19(3):105-13. p.106 left column top paragraph

21239171

Pelling AE, Sehati S, Gralla EB, Valentine JS, Gimzewski JK. Local nanomechanical motion of the cell wall of Saccharomyces cerevisiae. Science. 2004 Aug 20 305(5687):1147-50.

15326353

Atomic force microscopy

The oscillations of single cells had activation energies (58 kJ/mol) and velocities similar to those reported for cytoskeleton motors.

Uri M

oscillation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5847

107411

Magnitude of the forces behind cell oscillation

Budding yeast Saccharomyces cerevisiae

~10

Reguera G. When microbial conversations get physical. Trends Microbiol. 2011 Mar19(3):105-13. p.106 left column top paragraph

21239171

Pelling AE, Sehati S, Gralla EB, Valentine JS, Gimzewski JK. Local nanomechanical motion of the cell wall of Saccharomyces cerevisiae. Science. 2004 Aug 20 305(5687):1147-50.

15326353

Atomic force microscopy

The magnitude of the forces (~10 nN) was such that it would have required the concerted action of several molecular motors, as expected of a dedicated system that transmitted the metabolic status of the cell as mechanical vibration and sound.

Uri M

oscillation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5849

107413

Acoustic frequency range of signals emitted by cells

Budding yeast Saccharomyces cerevisiae

0.9 to 1.6

kHz

Reguera G. When microbial conversations get physical. Trends Microbiol. 2011 Mar19(3):105-13. p.107 left column 2nd paragraph

21239171

Pelling AE, Sehati S, Gralla EB, Valentine JS, Gimzewski JK. Local nanomechanical motion of the cell wall of Saccharomyces cerevisiae. Science. 2004 Aug 20 305(5687):1147-50.

15326353

Atomic force microscopy

the acoustic frequency ranges of signals emitted by yeast cells (0.9â1.6 kHz) [primary source] differ substantially from the signals emitted by colonies of B. subtilis (8â43 kHz)

Uri M

sound, physical signal<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

5997

107562

Relative cell volumes and buoyant densities in cell fractions

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Relative%20cell%20volumes%20and%20buoyant%20densities%20in%20cell%20fractions%20separated%20bv%20Percoll%20equilibrium%20centrifugation.pdf

Baldwin WW, Kubitschek HE. Buoyant density variation during the cell cycle of Saccharomyces cerevisiae. J Bacteriol. 1984 May158(2):701-4. p.702 table 1

6373726

P.702 note above table 1: "Relative cell volumes and buoyant densities in cell fractions separated by Percoll equilibrium centrifugation."

P.704 left column 2nd paragraph: "The results in Fig. 3 provide an explanation for the observation that the range of cell volumes shown in Table 1 was only about 60% of the expected twofold range of cell volumes from birth to division. The top fraction of the band in an equilibrium gradient would be relatively homogeneous, composed mainly of doublet cells with a value of V/Vb close to 2. The top fraction in Table 1 has a value of 1.96, which is in good agreement with this expected value. The bottom fraction, however, would be composed mainly of a mixture of cells of three classes, singlets, one-quarter relative bud diameter, and one-half relative bud diameter. Although the value of V/Vb for singlets should approach 1, the corresponding relative volumes of the other classes will be larger than 1 (Table 1)."

Uri M

size

6000

107565

Kinetics of glucoamylase production in batch and continuous cultures

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Kinetics%20of%20glucoamylase%20production%20in%20batch%20cultures%20and%20continuous%20cultures.pdf

Kilonzo PM, Margaritis A, Bergougnou MA. Plasmid stability and kinetics of continuous production of glucoamylase by recombinant Saccharomyces cerevisiae in an airlift bioreactor. J Ind Microbiol Biotechnol. 2009 Sep36(9):1157-69. p.1162 table 1 and p.1165 table 2

19504139

The selective YNBG medium contained 6.7 g/l yeast nitrogen base (YNB) without amino acids (Sigma), 0.04 g/l L-histidine (Sigma) and 20 g/l D-glucose. Free cell concentration was measured by dry weight and optical density methods.

The specific growth rate, yields and productivity for the culture grown on glucose are summarized in Table 1. The effect of dilution rate on cell yield, product yield, specific GA production, volumetric productivity and specific productivity are shown in Table 2.

Uri M

growth rate, selective, non-selective<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6001

107566

Cell concentrations in fibrous-bed bioreactors

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Cell%20Concentrations%20in%20Fibrous-Bed%20Bioreactors.pdf

Yang ST, Shu CH. Kinetics and stability of GM-CSF production by recombinant yeast cells immobilized in a fibrous-bed bioreactor. Biotechnol Prog. 1996 Jul-Aug12(4):449-56. p.454 table 3

8987473

Cell concentration was determined by measuring the optical density at 660 nm (OD660) of the cell suspension in a 1.5-mL polystyrene cuvette (with a light path of 10 mm) and comparing the measured value to a standard curve.

The concentrations of immobilized cells and free cells in fibrous-bed bioreactors at the end of each reactor study are listed in Table 3. See note beneath table

Uri M

immobilized cells, suspended free cells,density,fiber,liquid volume,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6019

107584

Amino acid usage versus aerobic expression data across the entire proteome

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Amino%20acid%20usage%20versus%20aerobic%20expression%20data%20across%20the%20entire%20proteome.pdf

Raiford DW, Heizer EM Jr, Miller RV, Akashi H, Raymer ML, Krane DE. Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae? J Mol Evol. 2008 Dec67(6):621-30. p.624 table 1

18937004

The approach taken to calculate biosynthetic costs was first employed by Craig and Weber (1998), and by Akashi and Gojobori (2002 PMID 11904428), and it exploited the near-universality of biosynthetic pathways to determine the number of high energy phosphate bonds (~PO4) required to synthesize amino acids.

Uri M

Glu, Gln, Ala, Gly, Pro, Ser, Asp, Asn, Arg, Thr, Cys, His, Val, Lys, Met, Leu, IIe, Tyr, Phe, Trp<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6020

107585

Amino acid usage versus anaerobic expression data across the entire proteome

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Amino%20acid%20usage%20versus%20anaerobic%20expression%20data%20across%20the%20entire%20proteome.pdf

18937004

P.623 left column bottom paragraph: "The approach taken to calculate biosynthetic costs was first employed by Craig and Weber (1998), and by Akashi and Gojobori (2002 PMID 11904428), and it exploited the near-universality of biosynthetic pathways to determine the number of high energy phosphate bonds (~PO4) required to synthesize amino acids."

P.628 left column 2nd paragraph: "The most biosynthetically expensive amino acid utilizing anaerobic costs is Met, which also exhibits no significant trend (Table 2). The other aromatic amino acids (Tyr and Phe) which also are aerobically biosynthetically expensive generally show no significant trend in usage vs. expression data acquired under aerobic conditions (Tyr has a significant negative trend with respect to aerobic transcript abundance however, the Mantel-Haenszel statistic is not significant, indicating that the trend is not consistent across functional categories) (Tables 1 and 2). Additionally, there are several amino acids with a low biosynthetic cost that exhibit negative correlations with all three expressivity measures (Ser for anaerobic costs and Arg, Asn, Cys, His, and Ser, e.g., for aerobic) (Tables 1 and 2)."

Uri M

Glu, Gln, Ala, Gly, Pro, Ser, Asp, Asn, Arg, Thr, Cys, His, Val, Lys, Met, Leu, IIe, Tyr, Phe, Trp

6044

107609

Diameter of vacuole

Budding yeast Saccharomyces cerevisiae

2.1

±0.6

Î¼m

Michaillat L, Baars TL, Mayer A. Cell-free reconstitution of vacuole membrane fragmentation reveals regulation of vacuole size and number by TORC1. Mol Biol Cell. 2012 Mar23(5):881-95. p.882 right column top paragraph

22238359

Electron microscopy

"Fragmentation reactions incubated in the absence of ATP contained many intact vacuoles (d = 2.1 ± 0.6 µm), visible as large circular structures with an electron-translucent, white lumen."

Uri M

diameter, radius<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6081

103689

Fraction of cell mass that is water

Budding yeast Saccharomyces cerevisiae

60.4

±0.2 table link - http://bionumbers.hms.harvard.edu/files/Contents%20of%20intracellular%20water%20(Wi%20)%20in%20cells%20of%20S.cerevisiae%20and%20Arthrobacter%20sp..pdf

Illmer P, Erlebach C, Schinner F. A practicable and accurate method to differentiate between intra- and extracellular water of microbial cells. FEMS Microbiol Lett. 1999 Sep 1 178(1):135-9. p.138 table 1

10483732

P.136 right column 3rd & 4th paragraphs: "An infra-red balance (Mettler LP16) which was interfaced to a computer was used for the investigation. Weight was measured automatically every 6 s till no further change in weight could be recognised (about 40 min after starting). The basic assumption of the method is that drying of microbial cells occurs during two phases (Fig. 1). First, the more volatile extracellular water We is lost. Not before this fraction is completely evaporated, the intracellular water Wi starts to vaporise. The change between the two phases (the so-called critical point, CP) can be detected in the form of a small bulge. This change in drying behaviour should be caused by the membrane and/or the cell wall as this briefly protects Wi against evaporation...[Researchers] used the second derivation (f"(x)) to determine the CP. As can be deduced from Fig. 1, the CP must be located between two inflection points (f"(x)=0) and should be characterised by a minimum of f"(x) which indicates a minimum radius of curvature of the original curve." See primary source [7] [Uribelarrea, J.L., Pacaud, S., Goma, G. (1985) New method for measuring the cell water content by thermogravimetry. Biotechnol. Lett. 7, 75â80] for more details of method.

P.137 left column bottom paragraph: "Wi values relative to DM [dry matter] of S. cerevisiae and Arthrobacter sp. are given in Table 1. Percentages of DM per g of fresh weight are not presented as these values vary to a great extent depending mainly on the sample preparation. However, the total water contents are about 10% higher than the more exact data given in Table 1 and thus correspond better with data from literature, where usually no differentiation between intra- and extracellular water is made [refs 1,2]." P.138 left column top paragraph: "From [primary source 7, see bottom of Method], the Wi of S. cerevisiae was calculated to be 1.1 g/g DM which is beyond the results shown in Table 1. However, growth conditions (nutrition, incubation time and temperature) differ from the ones used within the present investigation and may therefore be responsible for the difference [ref 9]. Quiros et al. ([ref 3]) calculated the Wi of Streptomyces antibioticus to be 0.81 and 1.56 ml/g DM for dormant spores and vegetative mycelium, respectively. This again indicates the great variability depending on the stage of growth even within a species." For water fraction by volume in E. coli, yeast and mammalian cell see BNID 100044, 105094, 103960, respectively

Uri M

content, H2O, weight, fluid, liquid

6087

103696

Diameter of NPC (Nuclear Pore Complex)

Budding yeast Saccharomyces cerevisiae

9362057

This value is somewhat smaller than the diameter of vertebrate NPC, 120 nm

Uri M

complex, NPC, phase, cell cycle, nucleus, pores, complexes, nuclear, porin, nucleoplasm<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6088

103697

Number of times a cell divides prior to death

Budding yeast Saccharomyces cerevisiae

30-50

divisions

Powell CD, Quain DE, Smart KA. Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology. 2003 Nov149(Pt 11):3129-37.

14600225

Mortimer RK, Johnston JR. Life span of individual yeast cells. Nature. 1959 Jun 20 183(4677):1751-2.

13666896

See BNID 105586

Uri M

generation time, senesence, lifespan, offspring

6089

103698

Polyploid cell diameter, surface area and volume

Budding yeast Saccharomyces cerevisiae

Table link - http://tinyurl.com/d8ydxn

Powell CD, Quain DE, Smart KA. Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology. 2003 Nov149(Pt 11):3129-37. Table 1

14600225

BB11 cell dimensions were determined using the confocal microscope measure function. Cell surface area and volume were calculated assuming that cells were prolate ellipsoidal spherical with a smooth cell surface.

Table gives Relationship between age and cell size in BB11 polyploid strain. Values for haploid and diploid strains demonstrated to be considerably lower.

Uri M

size, generation,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6090

103699

Polyploid cell diameter

Budding yeast Saccharomyces cerevisiae

6.4

+-0.2

Powell CD, Quain DE, Smart KA. Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology. 2003 Nov149(Pt 11):3129-37. Table 1

14600225

Table link - http://tinyurl.com/d8ydxn

BB11 cell dimensions were determined using the confocal microscope measure function.

Value for cell that has not yet divided. As cell divides, size increases. Table gives Relationship between age and cell size in BB11 polyploid strain. Values for haploid and diploid strains demonstrated to be considerably lower.

Uri M

size, generation, BB11 strain,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6091

103700

Polyploid cell surface area

Budding yeast Saccharomyces cerevisiae

133.9

±9.5

µm^2

Powell CD, Quain DE, Smart KA. Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology. 2003 Nov149(Pt 11):3129-37. Table 1

14600225

Table link - http://tinyurl.com/d8ydxn

Uri M

size, generation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6092

103701

Polyploid cell volume

Budding yeast Saccharomyces cerevisiae

153.6

±16.5

µm^3

Powell CD, Quain DE, Smart KA. Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology. 2003 Nov149(Pt 11):3129-37. Table 1 table link - http://tinyurl.com/d8ydxn

14600225

Table link - http://tinyurl.com/d8ydxn

Uri M

size, generation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6093

103702

Relationship between cell age and birth scar size

Budding yeast Saccharomyces cerevisiae

Table Link - http://tinyurl.com/ctq3os

Powell CD, Quain DE, Smart KA. Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology. 2003 Nov149(Pt 11):3129-37. Table 2

14600225

Saccharomyces cerevisiae reproduces asexually by budding and as a consequence of this process both mother and daughter cell retain chitinous scar tissue at the point of cytokinesis. Daughter cells exhibit a frail structure known as the birth scar, while mother cells display a more persistent bud scar.

Uri M

diameter, cell surface area, birth scar, bud scar, cytokinesis, generation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6094

103703

Birth scar diameter

Budding yeast Saccharomyces cerevisiae

3.4

Table Link - http://tinyurl.com/ctq3os

µm

Powell CD, Quain DE, Smart KA. Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology. 2003 Nov149(Pt 11):3129-37. p.3133 Table 2

14600225

Value is average of virgin and generations 2, 4, and 6. Saccharomyces cerevisiae reproduces asexually by budding and as a consequence of this process both mother and daughter cell retain chitinous scar tissue at the point of cytokinesis. Daughter cells exhibit a frail structure known as the birth scar, while mother cells display a more persistent bud scar. Value was calculated as mean of birth scar diameters of cells that divided 0,2,4 & 6 times

Uri M

diameter, cell surface area, birth scar, cytokinesis, generation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6095

103704

Diploid cell volume

Budding yeast Saccharomyces cerevisiae

26-74

Î¼m^3

Powell CD, Quain DE, Smart KA. Chitin scar breaks in aged Saccharomyces cerevisiae. Microbiology. 2003 Nov149(Pt 11):3129-37. Table 1

14600225

Woldringh CL, Huls PG, Vischer NO. Volume growth of daughter and parent cells during the cell cycle of Saccharomyces cerevisiae a/alpha as determined by image cytometry. J Bacteriol. 1993 May175(10):3174-81.

8491731

The pattern of volume growth of Saccharomyces cerevisiae a/alpha was determined by image cytometry for daughter cells and consecutive cycles of parent cells. An image analysis program was specially developed to measure separately the volume of bud and mother cell parts and to quantify the number of bud scars on each parent cell.

X2180 diploid strain

Uri M

size, X2180<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6096

103705

Total mitochondria surface area in cell

Budding yeast Saccharomyces cerevisiae

chemically fixed cell 29: cryofixed cell 32 table link - http://bionumbers.hms.harvard.edu/files/Total%20organelle%20surface%20area%20and%20organelle%20volume%20per%20cell.pdf

µm^2

Perktold A, Zechmann B, Daum G, Zellnig G. Organelle association visualized by three-dimensional ultrastructural imaging of the yeast cell. FEMS Yeast Res. 2007 Jun7(4):629-38. p.634 table 2

17419771

Abstract: "...a computer aided method was employed to generate three-dimensional ultrastructural reconstructions of chemically and cryofixed yeast cells."

P.633 left column: "Due to different surface areas of organelles, however, the number of associations per defined organelle surface area was regarded as a more relevant measure for the affinity between two compartments (Table 2)." P.634 left column: "As can be seen from Tables 1 and 2, however, the method of fixation not only affected the shape of cell organelles as a result of alterations in surface area and volume, but also the number of organelle associations." P.634 right column top paragraph: "The calculated ratios of associations per organelle surface area (Table 2) demonstrated high association rates between lipid particles/mitochondria, ER/mitochondria and lipid particles/nucleus." See notes above and beneath table

Uri M

size, mitochondrion, organelle

6097

103706

Total lipid particle volume in cell

Budding yeast Saccharomyces cerevisiae

0.4

Table link - http://bionumbers.hms.harvard.edu/files/Total%20organelle%20surface%20area%20and%20organelle%20volume%20per%20cell.pdf

um^3

Perktold A, Zechmann B, Daum G, Zellnig G. Organelle association visualized by three-dimensional ultrastructural imaging of the yeast cell. FEMS Yeast Res. 2007 Jun7(4):629-38. p.634 table 2

17419771

Abstract: "...a computer aided method was employed to generate three-dimensional ultrastructural reconstructions of chemically and cryofixed yeast cells."

Uri M

size, organelle

6105

103715

Final replicative volume-volume of cell that can no longer replicate

Budding yeast Saccharomyces cerevisiae

160-539

µm^3

Zadrag-Tecza R, Kwolek-Mirek M, Bartosz G, Bilinski T. Cell volume as a factor limiting the replicative lifespan of the yeast Saccharomyces cerevisiae. Biogerontology. 2008 Nov 5. Table 2

18985429

Final replicative volume-volume of cell that can no longer replicate. In a population, cells cease to bud after various number of cell cycles but attaining a similar final volume.

Uri M

size, aging<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6106

103716

Ratio between volume of daughter and mother cell in first budding

Budding yeast Saccharomyces cerevisiae

0.5-0.7

Unitless

Zadrag-Tecza R, Kwolek-Mirek M, Bartosz G, Bilinski T. Cell volume as a factor limiting the replicative lifespan of the yeast Saccharomyces cerevisiae. Biogerontology. 2008 Nov 5. Table 2

18985429

Cell volume was estimated by analysis of microscopic images recorded every each five cell divisions during a routine procedure of determination of replicative lifespan. Images were captured with a Nikon Eclipse E200 microscope with 20× objective, equipped with a Sony digital camera. Diameter of the cell was measured using a MicroImage 3.0 software. Cell diameter (d) was measured in four times in various planes for each cell and the mean value was used for calculations. It was assumed that each cell has a regular shape similar to a sphere and the cell volume was calculated as 4/3p(d/2)3.

In a population, cells cease to bud after various number of cell cycles. The ratio of volumes of the bud and the mother cell in the wild-type strains studied was 0.50â0.70 in the first budding decreasing to about 0.28 in the last buddings.

Uri M

size, aging,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6169

103783

Total organelle surface area and organelle volume per cell

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Total%20organelle%20surface%20area%20and%20organelle%20volume%20per%20cell.pdf

Perktold A, Zechmann B, Daum G, Zellnig G. Organelle association visualized by three-dimensional ultrastructural imaging of the yeast cell. FEMS Yeast Res. 2007 Jun7(4):629-38. p.634 table 2

17419771

Abstract: "...a computer aided method was employed to generate three-dimensional ultrastructural reconstructions of chemically and cryofixed yeast cells."

Uri M

size, mitochondrion, organelle, ER, endoplasmic reticulum, lipid particle, mitochondrion, nucleus, PM, plasma membrane, vacuole.

6177

103791

Growth rate on different nitrogen sources

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Growth%20of%20S.%20cerevisiae%20at%20pH%206.1%20on%20different%20nitrogen%20sources.pdf

Soupene E, Ramirez RM, Kustu S. Evidence that fungal MEP proteins mediate diffusion of the uncharged species NH(3) across the cytoplasmic membrane. Mol Cell Biol. 2001 Sep21(17):5733-41 p.5736 table 2

11486013

Cells were grown in medium 164 with glucose (3%) as the carbon source and different nitrogen sources at the concentrations indicated in table. Cell Concentrations estimated by Optical Density

at pH 6.1

Uri M

Methylammonium, ammonium, permeases, (MEP), mep1, mep2, mep3, doubling time, generation time, Glutamate, Proline, Arginine, Urea, NH4Cl<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6217

103831

Percent of genome that is transposable elements

Budding yeast Saccharomyces cerevisiae

3.1

Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 1998 May8(5):464-78

9582191

Full chromosome sequences were obtained from the Saccharomyces Genome Database (http://genome-www.stanford. edu/Saccharomyces/). Large chromosome sequences were segmented and formatted for use with software from the Genetics Computer Group (GCG) (Devereux et al. 1984).

Overall, retrotransposon sequences constitute >377 kb or 3.1% of the genome. The lack of evidence in the genome sequence for non-LTR-retrotransposons or any of the classes of transposable elements that replicate through DNA intermediates, prompted substituting "retrotransposons" with "transposable elements" in the property name

Uri M

jumping genes,junk DNA<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6257

103872

Terminal velocity of Budding yeast "free falling" in water - a theoretical estimate

Budding yeast Saccharomyces cerevisiae

equivalent to ~3 hours to fall 1 cm

µm/sec

Calculation analogous to the one given in "Random walks in biology" Howard Berg, Princeton University Press, 1993 pp.62

uses the equation v=mg/6*pi*eta*R, where v is the terminal velocity, eta is the viscosity, m is the effective mass after subtracting the effect of bouyancy by subtracting the volume * density of water.

Assumes the cell is a sphere of radius 2 micron and density 1.1 (BNID 103876). Viscosity of water 0.001 Pascal*Sec. Please comment if you know of experimental values in the literature

Ron Milo - Admin

floating, yeast<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6261

103876

Cell density at osmotic pressure of 0 bar

Budding yeast Saccharomyces cerevisiae

1.0952

±0.011

g/ml

M. Reuß, D. Josic, M. Popovic, and W.K. Bronn, Viscosity of Yeast Suspensions, European J. Appl. Microbiol. Biotechnol. 8, 167-175 (1979)

The mean density of the yeast cells was computed from Rho biomass=Rho suspension (1- (volume fraction of cells))/volume fraction of cells, eq. 7

suspended in distilled water. The mean density of yeast cells will also depend on the osmotic pressure. This value for (Posm = 0 bar, 1 bar = 100 kPa (kilopascals)) Extrapolated from figure 4. See BNID 106439

Uri M

osmolarity<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6262

103877

Maximum volume fraction of cells in distilled water

Budding yeast Saccharomyces cerevisiae

0.63

Unitless

M. Reuß, D. Josic, M. Popovic, and W.K. Bronn, Viscosity of Yeast Suspensions, European J. Appl. Microbiol. Biotechnol. 8,167175 (1979)

Calculated from equations 8 and 9

This maximum value corresponds roughly to the arithmetic mean of the values for cubic and rhombohedric arrangements of spheres in close packing

Uri M

packing, density<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6281

103896

Cell diameter of yeast grown in YEPG medium at 60% DO2

Budding yeast Saccharomyces cerevisiae

5.55

±0.1

µm

Teerapatr Srinorakutara, Determination of yeast cell wall thickness and cell diameter using new methods, Journal of Fermentation and Bioengineering Volume 86, Issue 3, 1998, Pages 253-260 p.257 table 2

P.253 left column 2nd paragraph: "In order to test the reliability of cell diameter measurements by the micromanipulation technique, in this work the diameters of yeast cells both in shake-flask cultivation and 2 l fermentor cultivation were determined using various methods, including the micromanipulation technique, Coulter counting, and image analysis (both directly from fermentation samples and from TEM [Transmission Electron Microscopy] micrographs). The results were compared and a discussion is presented in this paper."

S. cerevisiae Yg grown in YEPG medium at 60% DO2. See BNID 100451

Uri M

radius, Dimensions, Sizes

6311

103926

Ratio between volume of daughter and mother cell in last budding of yeast

Budding yeast Saccharomyces cerevisiae

0.28

Unitless

Zadrag-Tecza R, Kwolek-Mirek M, Bartosz G, Bilinski T. Cell volume as a factor limiting the replicative lifespan of the yeast Saccharomyces cerevisiae. Biogerontology. 2008 Nov 5. Table 2

18985429

Uri M

size,aging<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6336

103951

Cell membrane and wall combined thickness

Budding yeast Saccharomyces cerevisiae

180

150-200

M Milani et al, Differential Two Colour X-Ray Radiobiology of Membrane/Cytoplasm Yeast Cells, TMR Large-Scale Facilities Access Programme Technical report January 1998 University of Milan, Italy Table link - http://tinyurl.com/da5lly

In order to precisely characterise their morphological structure before irradiation (hence allowing a precise dosimetry), yeast cells have been analysed with different experimental techniques including: optical microscopy, TEM, X-ray microscopy and Coulter Counter. Researchers wanted to measure the cell average radius ro, the total membrane and wall thickness DS, and the nucleus radius rN.

Uri M

size, width,<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6337

103952

Nuclear radius

Budding yeast Saccharomyces cerevisiae

0.95

µm

"In order to precisely characterise their morphological structure before irradiation (hence allowing a precise dosimetry), yeast cells have been analysed with different experimental techniques including: optical microscopy, TEM, X-ray microscopy and Coulter Counter. Researchers wanted to measure the cell average radius ro, the total membrane and wall thickness DS, and the nucleus radius rN."

For nuclear diameter of ~2µm see Yanamoto et al., 2011 PMID 21897045 p.1713 left column top paragraph

Uri M

size, diameter, nucleus, nuclei, organelle<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6338

103953

Cell radius

Budding yeast Saccharomyces cerevisiae

2.58

±0.54

µm

Uri M

size, diameter<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6382

103998

Size of 'replication factory'-replication foci in nucleus

Budding yeast Saccharomyces cerevisiae

180-280

Kitamura E, Blow JJ, Tanaka TU. Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell. 2006 Jun 30 125(7):1297-308 p.1305 right column 4th paragraph

16814716

Green fluorescent protein, time-lapse microscopy

Uri M

polymerization, euchromatin, chromatin, size, diameter<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6392

104008

Percent of proteins that contain potential zinc binding domains

Budding yeast Saccharomyces cerevisiae

Eide DJ. The molecular biology of metal ion transport in Saccharomyces cerevisiae. Annu Rev Nutr. 1998 18:441-69.

9706232

Analysis of the S. cerevisiae genome sequence indicated that almost 3% of all yeast proteins (i.e. >150 of approximately 6000 total genes) contain potential zinc binding domains (DJ Eide, unpublished observation).

Uri M

trace metal,Percent<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6396

104012

Cellular copper content

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Atomic%20absorption%20measurement%20of%20cellular%20copper%20content.pdf

Lin CM, Kosman DJ. Copper uptake in wild type and copper metallothionein-deficient Saccharomyces cerevisiae. Kinetics and mechanism. J Biol Chem. 1990 Jun 5 265(16):9194-200

2188974

Atomic absorption spectrophotometry

See BNID 105673

Uri M

trace metal, CUP1delta,Cu<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6397

104013

Km for copper uptake in wildtype cell

Budding yeast Saccharomyces cerevisiae

4.4

±0.4

µM

Lin CM, Kosman DJ. Copper uptake in wild type and copper metallothionein-deficient Saccharomyces cerevisiae. Kinetics and mechanism. J Biol Chem. 1990 Jun 5 265(16):9194-200 p.9195 right column bottom paragraph

2188974

Atomic absorption spectrophotometry

Uri M

trace metal, CUP1delta<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6398

104014

Vmax for copper uptake in wildtype cell

Budding yeast Saccharomyces cerevisiae

0.21

±0.007

nmol copper/min/mg protein

Lin CM, Kosman DJ. Copper uptake in wild type and copper metallothionein-deficient Saccharomyces cerevisiae. Kinetics and mechanism. J Biol Chem. 1990 Jun 5 265(16):9194-200 p.9195 right column

2188974

Atomic absorption spectrophotometry

Uri M

trace metal, CUP1delta<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6399

104015

Cellular copper content in copper free medium

Budding yeast Saccharomyces cerevisiae

7.2

±0.4 Table link - http://bionumbers.hms.harvard.edu/files/Atomic%20absorption%20measurement%20of%20cellular%20copper%20content.pdf

nmol copper/mg protein

Lin CM, Kosman DJ. Copper uptake in wild type and copper metallothionein-deficient Saccharomyces cerevisiae. Kinetics and mechanism. J Biol Chem. 1990 Jun 5 265(16):9194-200 p.9196 table 1

2188974

Atomic absorption spectrophotometry

After 2 hours in a copper free medium

Uri M

trace metal, CUP1delta<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6400

104016

Cellular copper content in medium of 5µM copper

Budding yeast Saccharomyces cerevisiae

16.8

±1.1 Table link - http://bionumbers.hms.harvard.edu/files/Atomic%20absorption%20measurement%20of%20cellular%20copper%20content.pdf

nmol copper/mg protein

Lin CM, Kosman DJ. Copper uptake in wild type and copper metallothionein-deficient Saccharomyces cerevisiae. Kinetics and mechanism. J Biol Chem. 1990 Jun 5 265(16):9194-200 p.9196 table 1

2188974

atomic absorption spectrophotometry

After 2 hours in a 5 µM copper medium

Uri M

trace metal, CUP1delta<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6532

104150

Range of protein concentration

Budding yeast Saccharomyces cerevisiae

50-1300000

proteins/cell

P Picotti, A Kuemmel, R Costenoble, H Lam, D Campbell, LN Mueller, M Heinemann, E Deutsch, U Sauer, B Domon, and R Aebersold, Analysis of the S. cerevisiae metabolic network by targeted proteomics 2008 http://www.wiley-vch.de/vch/journals/2120/not2wis/HUPO_abstracts/S9.pdf

Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature. 2003 Oct 16 425(6959):737-41

14562106

(Primary source) To facilitate global protein analyses, researchers have created a Saccharomyces cerevisiae fusion library where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location. Through immunodetection of the common tag, they obtain a census of proteins expressed during log-phase growth and measurements of their absolute levels.

Equivalent to ~1nM-30uM. Primary source finds that the abundance of proteins ranges from fewer than 50 to more than 10^6 molecules per cell.

Uri M

peptide, enzyme, amount<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6533

104151

Average and median half life of protein

Budding yeast Saccharomyces cerevisiae

â43

min

Belle A, Tanay A, Bitincka L, Shamir R, O'Shea EK. Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A. 2006 Aug 29 103(35):13004-9 p.13004 right column 4th paragraph

16916930

Abstract: "Using an epitope-tagged strain collection, [researchers] measured the half-life of >3,750 proteins in the yeast proteome after inhibition of translation."

P.13004 right column 4th paragraph: "[Researchers] measured the half-life of 3,751 proteins and found the distribution of half-lives to be approximately log-normal, with a mean and median half-life of Ë43 min (Fig. 1C). The distribution deviates from log-normal in that [they] observe an unexpected number of very unstable proteins (161 proteins with a half-life of <4 min), consistent with the idea that degradation may determine the abundance of these proteins." See BNID 102058, 104386

Uri M

peptide, enzyme, tau, degradation, median

6534

104152

Half life of proteins

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Half%20life%20measurement%20of%20Budding%20yeast%20proteins.pdf

Belle A, Tanay A, Bitincka L, Shamir R, O'Shea EK. Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A. 2006 Aug 29103(35):13004-9

16916930

Using an epitope-tagged strain collection, researchers measured the half-life of >3,750 proteins in the yeast proteome after inhibition of translation.

Researchers measured the half-life of 3,751 proteins and found the distribution of half-lives to be approximately log-normal, with a mean and median half-life of ~43 min (Fig. 1C)

Uri M

peptide,enzyme,tau,YGL252C, RTG2 , YGR204W, ADE3 , YLR103C, CDC45 , YNL127W , YJL069C , YAL005C SSA1 119 77 YDR101C , YDR194C ,MSS, YDL174C ,DLD1 , YGL234W ,ADE5, YLR289W ,GUF1 , YHL007C, STE20 , YER103W, SSA4 , YPR019W ,CDC54 , YML056C, IMD4 , YGL234W ,ADE5, YDL190C ,UFD2 , YOR335C ,ALA1 , YOR076C , YDR243C, PRP28 , YLR427W , YJL209W ,CBP1 , YLR028C ,ADE16 , YOL113W ,SKM1 , YLL026W, HSP104 , YIL137C , YHR015W, MIP6 , YPR190C ,RPC82 , YML082W , YPR135W, CTF4 , YGL107C , YJL154C ,VPS35 , YPR141C, KAR3 , YMR277W, FCP1 , YDR356W ,NUF1 , YPR091C , YPL040C, ISM1 , YGR246C, BRF1 , YIL017C ,VID28 , YGL125W ,MET13 , YMR125W, STO1 , YML054C ,CYB2 , YKL185W, ASH1, YBR260C, RGD1 , YML042W, CAT2 , YIL130W , YOL025W, LAG2 , YIL075C, RPN2 , YCR084C, TUP1 , YHR120W, MSH1 , YGL060W, YKL005C , YIL155C ,GUT2 , YNL118C ,DCP2 , YBR169C ,SSE2 , YMR287C, MSU1 , YOL117W , YPR008W , YGL227W, VID30 , YOR350C, MNE1 , YML109W ,ZDS2 , YDL227C, HO , YOL090W, MSH2 , YPL084W ,BRO1 , YKR036C, CAF4 , YMR019W ,STB4 , YKL134C , YJL057C ,IKS1 , YGR162W ,TIF4631 , YJL128C ,PBS2 , YCR088W, ABP1 , YIL101C, XBP1 , YPL007C, TFC8 , YNL008C , YLR060W, FRS1 , YKR089C , YER075C, PTP3 , YFR040W ,SAP155 , YNL218W , YDL220C, CDC13 , YMR227C ,TAF67 , YOL066C, RIB2 , YBR017C, KAP104 , YGL113W, SLD3 , YER049W , YIL056W , YAR014C ,BUD14 , YMR120C, ADE17 , YGR287C , YPR179C ,PLO1 , YER088C ,DOT6 , YKR002W, PAP1 , YGR100W ,MDR1 , YKL135C,APL2 37 71 YCR038C ,BUD5 , YLR234W, TOP3 , YML023C , YPR111W, DBF20 , YLR369W, SSQ1 , YNL047C , YDL113C , YKL048C, ELM1 , YOR207C, RET1 , YDR389W ,SAC7 , YKL032C ,IXR1 , YPL086C, ELP3 , YOR147W , YDR137W, RGP1 , YDR294C, DPL1 , YAL011W , YLR117C, CLF1 , YNL023C, FAP1 , YEL032W ,MCM3 , YDR144C, MKC7 , YNL308C ,KRI1 , YBR212W, NGR1 , YPL263C, KEL3 , YDR307W , YGR140W CBF2 29 101 YBR123C ,TFC1 , YOR308C ,SNU66 , YLR299W ,ECM38 , YMR288W, HSH155 , YNL094W , YNL197C ,WHI3 , YMR080C ,NAM7 , YLR002C , YGR068C , YGR250C , YNL236W, SIN4 , YBR073W ,RDH54 , YLR429W ,CRN1 , YJL127C ,SPT10, YMR224C ,MRE11, YOR154W , YIL015W ,BAR1 , YOR299W, BUD7 , YGL066W , YOR349W ,CIN1 , YNL039W ,TFC5 , YEL007W, TOS9 , YGR186W ,TFG1 , YFR048W , YHR149C , YNL082W ,PMS1 , YGL099W, KRE35 , YBR289W ,SNF5 , YOR363C ,PIP2 , YER032W, FIR1 , YBR094W, YKL112W, ABF1<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6535

104153

Percent Composition (Dry Matter Basis) of Whole Yeast Cells (WY) and Phosphorylated Yeast Protein Concentrate (PPC)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Percent%20Composition%20(Dry%20Matter%20Basis)%20of%20Whole%20Yeast%20Cells%20(WY)%20and%20Phosphorylated%20Yeast%20Protein%20Concentrate%20(PPC).pdf

15884819

Water content, ashes, and crude protein (N X5.8) were determined according to the AOAC (ref 15) procedures. Total lipids were determined according to the Bligh and Dyer method (16). Soluble and insoluble fibers were quantified by treating the sample first with proteolytic enzymes (pepsin/pancreatin) to digest sample protein, followed by filtration to retain the insoluble fiber and precipitation of the soluble fiber from the filtrate with ethanol.

Uri M

protein, lipid, ashes, rna, soluble fiber, insoluble fiber, content, component<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6536

104154

Mineral Element content of Whole Yeast Cells (WY) and Phosphorylated Yeast Protein Concentrate (PPC)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Mineral%20Elements%20in%20the%20Whole%20Yeast%20Cells%20(WY)%20and%20Phosphorylated%20Yeast%20Protein%20Concentrate%20(PPC).pdf

15884819

Mineral composition was determined in a plasma spectrometer (ICP 2000 BAIRD simultaneous version) with an argon flame detector. Quantification was done by using a pure standard mixture of known concentration. Preparation of the samples for analysis was done according to the method of Angelucci and Mantovani (17) and IMO Industries Inc. (18).

Uri M

Na ,sodium, Ca ,calcium, Mg,magnesium,ion, P ,phosphorus, K ,potassium, Fe ,iron, Mn ,manganese, Zn ,zinc, Cu,copper<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6537

104155

Essential Amino Acid Profile and Score (EAE) of Whole Yeast Cells (WY) and Phosphorylated Yeast Protein Concentrate (PPC)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Essential%20Amino%20Acid%20Profile%20and%20Score%20(EAE)%20of%20Whole%20Yeast%20Cells%20(WY)%20and%20Phosphorylated%20Yeast%20Protein%20Concentrate%20(PPC).pdf

15884819

Amino acids were determined in an acidic hydrolysate (6 N HCl, 110 °C, 22 h) essentially according to the procedure of Spackman et al. (20) using a Dionex D-300 analyzer with cation exchange column and postcolumn ninhydrin reaction, using a Pierce standard amino acids mixture for quantification. Tryptophan was quantified in a Pronase (40 °C, 24 h) hydrolysate by the reaction with 4-dimethylaminobenzaldehyde (DAB), according to the method of Spies (21).

Essential Amino Acid Score (EAE). The EAE represents the smallest ratio of the most limiting essential amino acid in the protein under study with regard to the same amino acid of a reference standard. In this work the FAO/WHO (27) reference was used. Protein Digestibility Corrected Amino Acid Scoring (PDCAAS). This index is calculated by multiplying the EAE by the true protein digestibility (TD), normally expressed in percentage (28).

Uri M

protein, true digestibility, PTD, content, component, Corrected Amino Acid Scoring, (PDCAAS), methionine + half-cystine, valine, isoleucine, leucine, tyrosine + phenylalanine, lysine, histidine, tryptophan<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6538

104156

Fatty Acid Composition of Whole Yeast Cells (WY) and Phosphorylated Yeast Protein Concentrate (PPC)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Fatty%20Acid%20Composition%20of%20Whole%20Yeast%20Cells%20(WY)%20and%20Phosphorylated%20Yeast%20Protein%20Concentrate%20(PPC).pdf

15884819

Fatty acid composition was determined by gas-liquid chromatography after acidic interesterification with methanol, according to the procedure of Firestone (ref 22).

Uri M

caprylic ,content,composition, capric, hundecanoic , lauric , myristic , pentadecanoic , palmitic , palmitoleic , margaric , cis-10-heptadecenoic , stearic , elaidic , oleic , trans-linoleic , linoleic , R-linolenic , arachidic , behenic , arachidonic , eicosapentaenoic , docosahexaenoic , saturated , monounsaturated , polyunsaturated<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6539

104157

Cell composition of dry mass

Budding yeast Saccharomyces cerevisiae

Protein 39.6% Fiber 31.4% RNA 9% Ashes 4.6% Lipids 0.5% Other 14.9%

Yamada EA, Sgarbieri VC. Yeast (Saccharomyces cerevisiae) protein concentrate: preparation, chemical composition, and nutritional and functional properties. J Agric Food Chem. 2005 May 18 53(10):3931-6 p.3932 table 1 - http://bionumbers.hms.harvard.edu/files/Percent%20Composition%20(Dry%20Matter%20Basis)%20of%20Whole%20Yeast%20Cells%20(WY)%20and%20Phosphorylated%20Yeast%20Protein%20Concentrate%20(PPC).pdf

15884819

P.3932 left column 3rd paragraph: "Water content, ashes, and crude protein (N × 5.8) were determined according to the AOAC (Association of Official Analytical Chemists, ref 15) procedures. Total lipids were determined according to the Bligh and Dyer method (ref 16). Soluble and insoluble fibers were quantified by treating the sample first with proteolytic enzymes (pepsin/pancreatin) to digest sample protein, followed by filtration to retain the insoluble fiber and precipitation of the soluble fiber from the filtrate with ethanol."

P.3932 right column 6th paragraph: "The percent composition of WY [Whole Yeast Cells] and of PPC [Phosphorylated Yeast Protein Concentrate] is shown in Table 1. The protein contents of WY and of PPC of yeast from an ethanol distillery were lower than the one determined in the brewing industry yeast (ref 13)." P.3933 left column top paragraph: "As shown in Table 1 the content of RNA (10.4%) is quite high in the PPC."

Uri M

protein, lipid, ashes, rna, soluble fiber, insoluble fiber, content, component

6567

104185

Number of proteins/mRNA

Budding yeast Saccharomyces cerevisiae

5600

4,000 to 7,000

proteins/mRNA

Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan25(1):117-24. abstract, p.120 caption of fig.4b,e and p.121 right column 2nd paragraph

17187058

Abstract: "[Researchers] report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides."

P.121 right column 2nd paragraph: "Further, binning the measurements (Fig. 4b) indicates that the relationship between the numbers of protein and mRNA molecules has the form of a power law with an exponent close to one. Therefore, the distribution of individual proteins is also well fit by a linear relationship of [protein] = 5,600 × [mRNA], implying â¼5,600 proteins present per mRNA, which is somewhat higher than previous estimates [refs 20,35]. The logarithm of the ratio of proteins per mRNA is well modeled (R^2 = 0.98) by a normal distribution (Fig. 4c)." See BNID 106202

Uri M

Transcription, mRNA, proteins per mRNA, protein

6570

104188

Yeast protein abundances for rich and minimal media

Budding yeast Saccharomyces cerevisiae

Table link - http://tinyurl.com/mr2x6j

17187058

Researchers report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides.

Table contains data on >6000 yeast proteins

Uri M

peptide,enzyme<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6627

104245

Yeast protein abundances for rich and minimal media

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/Yeast%20proteins%20abundance%20data.xls

17187058

Table contains data on >6000 yeast proteins

Uri M

copies/cell, copies per cell, mRNA, protein, aromaticity, molecular weight,molecular mass,MW,Da,kDa<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6665

107654

Number of replication origin sites in OriDB database

Budding yeast Saccharomyces cerevisiae

613

279 Confirmed: 192 Likely: 142 Dubious

Replication origin sites

Nieduszynski CA, Hiraga S, Ak P, Benham CJ, Donaldson AD. OriDB: a DNA replication origin database. Nucleic Acids Res. 2007 Jan35(Database issue):D40-6 p.D42 left column 2nd paragraph

17065467

P.D41 right column 3rd paragraph: "Most of the information in the OriDB database is collated from four microarray-based studies, each of which produced a list of proposed origin sites (refs 24â27), and a fifth study which produced a list of confirmed origin sites (ref 12)."

P.D42 left column top paragraph: "âConfirmedâ origins are those have been cloned and tested by ARS [Autonomously Replicating Sequences] assay and/or have been detected by 2D gel analysis. âLikelyâ origin sites have been identified by two (or more) microarray studies but have not yet been confirmed. âDubiousâ origin sites are those identified by only one microarray study." P.D42 left column 2nd paragraph: "Data from additional studies will be added to the database as they become available. This process may result in the criteria described above âevolvingâ. The status of predicted origins will certainly change as more origin sites are experimentally verified. At the time of writing OriDB contains 613 replication origin sites (279 Confirmed 192 Likely and 142 Dubious)." Database site address - http://cerevisiae.oridb.org/

Uri M

transcription, translation

6667

107656

Protein and phosphorus contents of walls from yeast grown at different rates under various conditions of substrate limitation

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Protein%20and%20phosphorus%20contets%20of%20walls%20from%20yeast%20grown%20at%20different%20rates%20under%20various%20conditios%20of%20substrate%20limitation.pdf

McMurrough I, Rose AH. Effect of growth rate and substrate limitation on the composition and structure of the cell wall of Saccharomyces cerevisiae. Biochem J. 1967 Oct105(1):189-203. p.198 table 1

6056621

To study the effect of growth rate and substrate limitation on the composition and structure of the yeast cell wall, the yeast was grown in the chemostat at different dilution rates (D, which under steady state conditions equals the specific growth rate, µ) and under conditions in which the concentration of either glucose or NH4+ limited growth.

Uri M

Protein, Phosphorus, Glucose, ammonium, ammonia<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6668

107657

Estimated thickness of the spore wall

Budding yeast Saccharomyces cerevisiae

~120

Jiang H et al., Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy. Proc Natl Acad Sci U S A. 2010 Jun 22 107(25):11234-9 p.11236 right column 2nd paragraph

20534442

X-ray diffraction microscopy

Uri M

sporulation, width, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6669

107658

Average density of the yeast spore

Budding yeast Saccharomyces cerevisiae

~1.14

g/cm^3

Jiang H et al., Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy. Proc Natl Acad Sci U S A. 2010 Jun 22 107(25):11234-9 p.11236 right column bottom paragraph

20534442

By measuring the incident and diffracted X-ray intensities, researchers quantified the density of the reconstructed 3D image.

Uri M

sporulation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6670

107659

Length of mitochondria of yeast spore cell

Budding yeast Saccharomyces cerevisiae

~200 to 300

Jiang H et al., Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy. Proc Natl Acad Sci U S A. 2010 Jun 22 107(25):11234-9 p.11236 right column bottom paragraph

20534442

X-ray diffraction microscopy

Uri M

mitochondrion, diameter, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6671

107660

Nuclear volume of yeast spore cell

Budding yeast Saccharomyces cerevisiae

0.28

Î¼m^3

Jiang H et al., Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy. Proc Natl Acad Sci U S A. 2010 Jun 22 107(25):11234-9 p.11236 right column bottom paragraph

20534442

X-ray diffraction microscopy

"The nucleus exhibits a very high density with a volume of 0.28µm^3, which accounts for ~5% of the cell volume. A region near the center of the nucleus has the highest density in the cell, which is likely the nucleolus (Fig. 4B, Inset). The highest density is possibly related to the condensation of the chromatin. The nuclear size is regulated by several cellular functions such as nucleocytoplasmic transport, lipid metabolism, and ribosome biogenesis."

Uri M

nucleus, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6672

107661

Vacuole volume of yeast spore cell

Budding yeast Saccharomyces cerevisiae

~0.7

Î¼m^3

Jiang H et al., Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy. Proc Natl Acad Sci U S A. 2010 Jun 22 107(25):11234-9 p.11237 left column top paragraph

20534442

X-ray diffraction microscopy

The volume of the vacuole was determined to be ~0.7µm^3, which accounts for ~12% of the spore volume.

Uri M

vacuolar, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6685

107674

Secondary Structure Properties for 975, 1523 and 2777 nt RNAs

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Secondary%20Structure%20Properties%20for%20975%2C%201523%20and%202777%20nt%20RNAs.pdf

Gopal A, Zhou ZH, Knobler CM, Gelbart WM. Visualizing large RNA molecules in solution. RNA. 2012 Feb18(2):284-99. Supplementary table ST2

22190747

See note beneath table

Uri M

GC content,Minimum Free Energy,tree graphs<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6689

107678

Average length of mRNA

Budding yeast Saccharomyces cerevisiae

~1,250

nts

19040753

P.10 left column top paragraph: "The median lengths of 5'/3'-untranslated regions revealed by tiling array hybridization [ref 26] and RNA-Seq [ref 27] were reported to be 68 nt/91 nt and 50 nt/104 nt, respectively. Thus, the average length of mRNA is 1,500 nt, coincident with the previous estimate [ref 19]. However, it should be noted that a significant negative correlation was observed between expression level and ORF length in the budding yeast [ref 28]. Indeed, the average size of the yeast ORFs can be as short as 1,123 nt and 1,083 nt when weighted by the copy numbers calculated from signal intensity of high-density DNA microarray [ref 29] and GATC-PCR results, respectively. Thus, the average length of mRNA should be regarded as ~1,250 nt rather than 1,500 nt."

Uri M

length, base pairs

6691

107680

Immunoblotting measurements of abundances of key components

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Immunoblotting%20measurements%20of%20abundances%20of%20key%20components.pdf

Thomson TM et al., Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. Proc Natl Acad Sci U S A. 2011 Dec 13 108(50):20265-70. Supporting information p.18 of 21 Supplementary table S1

22114196

See refs beneath table

Quantitative immunoblotting

"After electrophoresis, [researchers] transferred all proteins to a blotting membrane. After equilibrating the gel in low SDS transfer buffer (39 mM glycine, 48 mM Tris base, 0.01% SDS, 20% methanol) for 15 min, [they] electrophoretically transferred proteins from the gel to a thick, small-pore PVDF membrane (Immobilon PSQ. Millipore) using the Criterion or mini-Protean blotter (Bio-Rad) as directed by the manufacturer (100 V for 40â60 min). After transfer, [they] incubated the membrane for 1 h in 1% blocking reagent (Roche) in Tris-buffered saline (TBS) (150 mM NaCl, 10 mM Tris·HCl, pH 7.5) and then incubated overnight at 4 °C with primary antibodies and 1% blocking reagent in TBS with 0.05% Tween20. Table S1 contains a list of the sources and dilutions of all antibodies except for the anti-GFP antibody (JL-8 mouse antibody, 1:2,000 dilution Clontech)."

Uri M

G protein-coupled receptor, g alpha, g beta, PAK kinase, Scaffold, MAPKKK binding partner, MAPK phosphatase, Transcriptional activator, Transcriptional repressor, Cell cycle inhibitor, Scaffold/MAPKK<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6692

107681

Cell to cell coefficient of variation (CV) of FP-tagged proteins

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Cell%20to%20cell%20coefficient%20of%20variation%20(CV)%20of%20FP-tagged%20proteins.pdf

Thomson TM et al., Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. Proc Natl Acad Sci U S A. 2011 Dec 13 108(50):20265-70. Supplementary table S2

22114196

See ref beneath table

Quantitative immunoblotting

Uri M

YFP-Ste5, Fus3-YFP, Ste7-YFP, CFP-Ste12, Dig1-YFP<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6693

107682

Model parameters of scaffold proteins

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Model%20parameters.pdf

Thomson TM et al., Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. Proc Natl Acad Sci U S A. 2011 Dec 13 108(50):20265-70. Supplementary table S3

22114196

See refs beneath table

Quantitative immunoblotting

Uri M

abundance, molecules per cell, k on, k off<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6700

107689

Upper limit to number of distinct NPC components

Budding yeast Saccharomyces cerevisiae

Components

Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol. 2000 Feb 21 148(4):635-51. p.644 right column 2nd paragraph

10684247

This indicates a surprisingly simple composition for such a massive structure (e.g., given ~75 different proteins in a ribosome), and is significantly lower than previous estimates (Rout and Wente, 1994). For value of ~30 different proteins to make up npc see Khmelinskii et al., 2012 PMID 22729030 p.709 right column 4th paragraph: "Each NPC [eukaryotic organism unspecified] comprises ~30 different proteins, called nucleoporins, that form pores in the nuclear envelope and control nucleocytoplasmic transport and nuclear organization (Fig. 3a). In organisms with open mitosis, NPCs disassemble when the nuclear envelope breaks down during cell division but are stable in nondividing cells." See Yang et al., 2017 PMID 28446921 p.1 2nd paragraph: "The nuclear pore complex (NPC) is the gateway of macromolecular trafficking between the nucleus and the cytoplasm (Xu and Meier, 2008). Being one of the largest multi-protein complexes in the cell, the NPC consists of multiple copies of ~30 different proteins known as nucleoporins (Nups), which are organized in an octagonal manner and symmetrically around the cylindrical axis of the NPC (Alber et al., 2007, Tamura et al., 2010, Tamura and Hara-Nishimura, 2013)."

Uri M

Nuclear pore complex, protein

6701

107690

Number of proteins in NPC (Nuclear Pore Complex)

Budding yeast Saccharomyces cerevisiae

â¥456

proteins

Alber F et al., Determining the architectures of macromolecular assemblies. Nature. 2007 Nov 29 450(7170):683-94. p.683 left column 2nd paragraph

18046405

Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol. 2000 Feb 21 148(4):635-51

10684247

Yeast NPCs are ~50 MDa structures built of multiple copies of some 30 different proteins (nucleoporins), totalling at least 456 protein molecules

Uri M

molecular machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6712

107701

Percent of total transcription that is rRNA polymerized by RNA pol I

Budding yeast Saccharomyces cerevisiae

~60

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999 Nov24(11):437-40 p.437 middle column 2nd paragraph

10542411

Woolford, J. L., Jr and Warner, J. R. (1991) in The Molecular and Cellular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics (Broach, J. R., Pringle, J. R. and Jones, E. W., eds), pp. 587â626, Cold Spring Harbor Laboratory Press

As estimated from the synthesis of PolyA- RNA, as well as from calculations based on RNA abundance and stability, the transcription of rRNA by RNA polymerase I (Pol I) appears to represent nearly 60% of the total transcription in the cell (primary source)

Uri M

rRNA, fraction, ribonucleic acid, RNA polymerase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6746

107735

Concentration of MAPK scaffold Ste5

Budding yeast Saccharomyces cerevisiae

~480 Table link - http://bionumbers.hms.harvard.edu/files/Immunoblotting%20measurements%20of%20abundances%20of%20key%20components.pdf

molecules/cell

Thomson TM et al., Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. Proc Natl Acad Sci U S A. 2011 Dec 13 108(50):20265-70. p.20266 left column 2nd paragraph and Supplementary table S1

22114196

See refs beneath table

Quantitative immunoblotting

The least abundant essential system protein, the MAPK scaffold Ste5, was present at ~480 molecules/cell.

Uri M

abundance<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6747

107736

Concentration of Ste7 protein

Budding yeast Saccharomyces cerevisiae

~920 Table link - http://bionumbers.hms.harvard.edu/files/Immunoblotting%20measurements%20of%20abundances%20of%20key%20components.pdf

molecules/cell

Thomson TM et al., Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. Proc Natl Acad Sci U S A. 2011 Dec 13 108(50):20265-70. p.20268 right column top paragraph and Supplementary table S1

22114196

See refs beneath table

Quantitative immunoblotting

Uri M

abundance<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6763

107752

Ion and elemental composition

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Inductively%20coupled%20plasma%20atomic%20emission%20spectroscopy%20elemental%20analysis%20of%20the%20biomass.pdf

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.750 table 1

20067525

"Inductively coupled plasma atomic emission spectroscopy elemental analysis of the biomass"

"First, the biomass composition was determined in samples from these cultures. Table 1 shows the measured amounts expressed in grams of element per kilogram of biomass, and the calculated intracellular concentrations (mM) of the measured elements." "The concentration of potassium calculated from the elemental analysis was approximately 340 mM (Table 1). Taking into account the experimental error, this is consistent with the literature values, which are between 290 and 310 mM [refs 15â17]."

Uri M

calcium, potassium, magnesium, sodium, phosphorus, sulfate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6764

107753

In vivo-like medium composition with various anion concentrations

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/In%20vivo-like%20medium%20composition%20with%20various%20anion%20concentrations.pdf

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.752 table 2

20067525

In this article, the Vertical Genomics Consortium, Yeast Systems Biology Network and STRENDA present a standardized in vivo-like assay medium for kinetic studies on cytosolic yeast enzymes.

See note above table

Uri M

calcium, potassium, magnesium, sodium, phosphorus, sulfate, glutamate, phosphate, pipes<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6765

107754

Vmax values measured under the optimized and the in vivo-like conditions in the absence of the phosphatase inhibitors

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Vmax%20values%20measured%20under%20the%20optimized%20and%20the%20in%20vivo-like%20conditions%20in%20the%20absence%20of%20the%20phosphatase%20inhibitors.pdf

mmol/min/gram protein

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.753 table 3

20067525

The Vmax of each enzyme was measured under conditions optimized for maximal activity

See note above and below table

Uri M

hexokinase, phosphoglucose isomerase, phosphofructokinase, aldolase, triosephosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, enolase, pyruvate kinase, pyruvate decarboxylase, alcohol dehydrogenase, enzyme kinetics<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6766

107755

Vmax values measured under the in vivo-like conditions (in the absence of the phosphatase inhibitors) and the maximal fluxes through the glycolytic and fermentative enzymes

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Vmax%20values%20measured%20under%20the%20in%20vivo-like%20conditions%20(in%20the%20absence%20of%20the%20phosphatase%20inhibitors)%20and%20the%20maximal%20fluxes%20through%20the%20glycolytic%20and%20fermentative%20enzymes.pdf

mmol/min/gram protein

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.754 table 4

20067525

The Vmax of each enzyme was measured under conditions optimized for maximal activity

See note above table

Uri M

hexokinase,phosphoglucose isomerase,phosphofructokinase,aldolase,triosephosphate isomerase,glyceraldehyde-3-phosphate dehydrogenase,3-phosphoglycerate kinase,enolase,pyruvate kinase,pyruvate decarboxylase,alcohol dehydrogenase,phosphoglycerate mutase,alcohol dehydrogenase,enzyme kinetics<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6767

107756

Potassium concentration

Budding yeast Saccharomyces cerevisiae

290 to 310

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.750 right column 3rd paragraph

20067525

Olz R, Larsson K, Adler L, Gustafsson L. Energy flux and osmoregulation of Saccharomyces cerevisiae grown in chemostats under NaCl stress. J Bacteriol. 1993 Apr175(8):2205-13. AND Roomans GM, Sevéus LA. Subcellular localization of diffusible ions in the yeast Saccharomyces cerevisiae: quantitative microprobe analysis of thin freeze-dried sections. J Cell Sci. 1976 Jun21(1):119-27. AND Sunder S, Singh AJ, Gill S, Singh B. Regulation of intracellular level of Na+, K+ and glycerol in Saccharomyces cerevisiae under osmotic stress. Mol Cell Biochem. 1996 May 24158(2):121-4.

8468281, 777014, 8817473

Uri M

ion, potassium, K+<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6768

107757

Free cytosolic phosphate concentration

Budding yeast Saccharomyces cerevisiae

10 - 75

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.751 left column top paragraph

20067525

[14] Wu L et al., Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN.PK 113-7D following a glucose pulse. Appl Environ Microbiol. 2006 May72(5):3566-77. [18] Auesukaree C, Homma T, Tochio H, Shirakawa M, Kaneko Y, Harashima S. Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccharomyces cerevisiae. J Biol Chem. 2004 Apr 23 279(17):17289-94. [19] Gonzalez B, de Graaf A, Renaud M, Sahm H. Dynamic in vivo (31)P nuclear magnetic resonance study of Saccharomyces cerevisiae in glucose-limited chemostat culture during the aerobic-anaerobic shift. Yeast. 2000 Apr16(6):483-97. [20] Greenfield NJ, Hussain M, Lenard J. Effects of growth state and amines on cytoplasmic and vacuolar pH, phosphate and polyphosphate levels in Saccharomyces cerevisiae: a 31P-nuclear magnetic resonance study. Biochim Biophys Acta. 1987 Dec 7 926(3):205-14 [21] Theobald U, Mohns J & Rizzi M (1996) Determination of in-vivo cytoplasmic orthophosphate concentration in yeast. Biotechnol Tech 10, 297â302. http://link.springer.com/article/10.1007/BF00173242

16672504, 14966138, 10790685, 3318934

"From the elemental analysis, [investigators] could only estimate the total concentration of phosphorus, which was ~300 mM. A substantial part of this is present in bound phosphate groups or in the form of polyphosphates. To estimate the free cytosolic phosphate concentration, [investigators] used values from the literature. A broad range was found, from 10 to 75 mM [primary sources]. As the growth conditions applied by Wu et al. [primary source 14] were almost identical to [their] growth conditions, [they] used their value of 50 mM. However, [they] note that varying the phosphate concentration between 10 and 75 mM did not affect the reported Vmax values (Fig. S1), as reported below."

Uri M

ion, phosphorus<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6769

107758

Sodium concentration

Budding yeast Saccharomyces cerevisiae

~20

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.751 left column 2nd paragraph

20067525

Olz R, Larsson K, Adler L, Gustafsson L. Energy flux and osmoregulation of Saccharomyces cerevisiae grown in chemostats under NaCl stress. J Bacteriol. 1993 Apr175(8):2205-13. AND Sunder S, Singh AJ, Gill S, Singh B. Regulation of intracellular level of Na+, K+ and glycerol in Saccharomyces cerevisiae under osmotic stress. Mol Cell Biochem. 1996 May 24158(2):121-4.

8468281, 8817473

Uri M

ion,sodium,Na+<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6771

107760

Estimated free magnesium concentration in cytosol

Budding yeast Saccharomyces cerevisiae

0.1 to 1.0

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.751 left column 3rd paragraph

20067525

Beeler T, Bruce K, Dunn T. Regulation of cellular Mg2+ by Saccharomyces cerevisiae. Biochim Biophys Acta. 1997 Jan 31 1323(2):310-8.

9042353

Uri M

ion, magnesium level, mg2+, cytoplasm<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6772

107761

Free cytosolic calcium concentration

Budding yeast Saccharomyces cerevisiae

0.05 and 0.5

Î¼M

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.751 right column 2nd paragraph

20067525

Miseta A, Fu L, Kellermayer R, Buckley J, Bedwell DM The Golgi apparatus plays a significant role in the maintenance of Ca2+ homeostasis in the vps33Delta vacuolar biogenesis mutant of Saccharomyces cerevisiae. J Biol Chem. 1999 Feb 26 274(9):5939-47. AND Nakajima-Shimada J, Iida H, Tsuji FI, Anraku Y. Monitoring of intracellular calcium in Saccharomyces cerevisiae with an apoaequorin cDNA expression system. Proc Natl Acad Sci U S A. 1991 Aug 1 88(15):6878-82.

10026219, 1862111

Values for free cytosolic calcium found in the literature are very low, between 0.05 and 0.5µM (primary sources)

Uri M

ion,magnesium level,mg2+<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6773

107762

Cytosolic pH

Budding yeast Saccharomyces cerevisiae

6.8

Unitless

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. doi: 10.1111/j.1742-4658.2009.07524.x. p.751 right column 3rd paragraph

20067525

P.756 left column 3rd paragraph: "For measurement of the cytosolic pH, S. cerevisiae strain ORY001 was used...This strain expresses a cytosolic pHluorin, which is a pH-sensitive mutant of the green fluorescent protein [ref 66]."

P.751 right column 3rd paragraph: "The measured cytosolic pH was 6.8. The pH chosen for [researchers] assay medium was therefore 6.8."

Uri M

acidity, cytoplasm

6774

107763

Intracellular concentration of glutamate (the most abundant amino acid in the cell)

Budding yeast Saccharomyces cerevisiae

~75

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.752 left column top paragraph

20067525

Canelas AB, Ras C, ten Pierick A, van Dam JC, Heijnen JJ & Van Gulik WM (2008) Leakage-free rapid quenching technique for yeast metabolomics. Metabolomics 4, 226â239.

Uri M

amino acid,Glutamic acid,level<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6775

107764

Total amino acid concentration in cell (see comments section for total/free amino acid concentration)

Budding yeast Saccharomyces cerevisiae

~150

van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. p.752 right column bottom paragraph

20067525

[47] Canelas AB, Ras C, ten Pierick A, van Dam JC, Heijnen JJ & Van Gulik WM (2008) Leakage-free rapid quenching technique for yeast metabolomics. Metabolomics 4, 226â239. [52] Hans MA, Heinzle E, Wittmann C. Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae. Biotechnol Bioeng. 2003 Apr 20 82(2):143-51.

12584756

P.752 right column bottom paragraph:"An additional reason for this choice is that the total amino acid concentration in the cell is â¼ 150 mm [primary sources], which compensates substantially, albeit not completely, for the lack of anions." Please note-ref states "total amino acid" whereas primary source [52] gives "free intracellular amino acid".

Uri M

amino acid, level

6776

107765

Characteristics of an oscillating culture of S. cerevisiae in continuous cultivation at D=0.22hour^-1

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Characteristics%20of%20an%20oscillating%20culture%20of%20S.%20cerevisiae%20in%20continuous%20cultivation%20at%20D%200.22%20per%20hour.pdf

Hans MA, Heinzle E, Wittmann C. Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae. Biotechnol Bioeng. 2003 Apr 20 82(2):143-51. p.148 table 1

12584756

Amino acids were derivatized with ortho-phthaldialdehyde (OPA), separated by HPLC using a Grom-Sil OPA-3 column (125 × 4 mm, Grom-Analytik, Herrenberg, Germany) and detected as isoindol-derivatives by fluorescence (Agilent Series 1100 Agilent Technologies, Waldbronn, Germany) with excitation at 330 nm and emission at 450 nm.

Uri M

Histidine, Phenylalanine, Tyrosine, Tryptophan, Serine, Glycine, Alanine, Valine, Leucine , Aspartate, Asparagine, Methionine, Threonine, Isoleucine, Glutamate, Glutamine, Lysine, Arginine, Trehalose, 2-Oxoglutarate, Pyruvate, Acetate, Dissolved oxygen, pH, Optical density<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6794

107785

Typical values of rate of ribosome progression at 30°C

Budding yeast Saccharomyces cerevisiae

7 to 8

amino acids/sec/translating ribosome

Piques et al., Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol. 2009 5: 314. doi: 10.1038/msb.2009.68. p.11 right column 3rd paragraph

19888209

Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2003 Apr 1 100(7):3889-94.

12660367

"Literature values for the rate of ribosome progression in eukaryotic cells vary from 1â8 amino acids per second per translating ribosome, depending on the cellular conditions and the mRNA (for reviews, see Ryazanov et al, 1991 Mathews et al, 2007), with typical values of 4â5 for animal cells at 25â26°C (e.g. Lodish and Jacobsen, 1972 Palmiter, 1974) and 7â8 for with yeast cells at 30°C (primary source)."

Uri M

translation, protein synthesis, polymerization<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6877

107871

Peptide chain elongation rate

Budding yeast Saccharomyces cerevisiae

2.8 to 10.0 Table link - http://bionumbers.hms.harvard.edu/files/Variation%20in%20the%20peptide%20chain%20elongation%20rate%20(PER)%2C%20the%20number%20of%20active%20ribosomes%20in%20the%20cell%20per%20one%20amino%20acid%20in%20the%20synthesised%20proteins%20(RSGR-PER%20).pdf

Amino acids per second per ribosome

Karpinets TV, Greenwood DJ, Sams CE, Ammons JT. RNA:protein ratio of the unicellular organism as a characteristic of phosphorous and nitrogen stoichiometry and of the cellular requirement of ribosomes for protein synthesis. BMC Biol. 2006 Sep 5 4: 30. p.5/10 table 3

16953894

[13] Waldron C, Lacroute F. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol. 1975 Jun122(3):855-65. [14] Boehlke KW, Friesen JD. Cellular content of ribonucleic acid and protein in Saccharomyces cerevisiae as a function of exponential growth rate: calculation of the apparent peptide chain elongation rate. J Bacteriol. 1975 Feb121(2):429-33.

1097403, 1089627

"The mass of ribosomal RNA per cell (mrRNA) measured in the studies of E. coli, S. coelicolor, M. bovis, S. cerevisiae (two studies), and N. crassa (Table 3) allowed [investigators] to estimate the cellular requirement of ribosomes for protein synthesis in the organisms as functions of the growth conditions by calculating the number of ribosomes and the peptide elongation rate (PER)."

Uri M

translation rate, speed<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6886

107880

Preferred nucleosome linker lengths

Budding yeast Saccharomyces cerevisiae

10.41n+4.6 or 10.47n+5.5

Brogaard K, Xi L, Wang JP, Widom J. A map of nucleosome positions in yeast at base-pair resolution. Nature. 2012 Jun 3. doi: 10.1038/nature11142. p.499 right column 3rd paragraph

22722846

Researchers developed a new, genome-wide mapping approach that directly determines nucleosome centre positions with single-base-pair resolution. It derives from earlier work in which localized hydroxyl radicals were used to map reconstituted mononucleosomes centre positions

If researchers add 1 or 2 bp uniformly to each linker length to account for over-stretching of nucleosome DNAs, the linker length will follow a form of 10.41n+4.6 bp or 10.47n+5.5 bp (for integer n) respectively by Fourier analysis (for linker lengths=60 bp).

Uri M

chromatin,DNA<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6928

107923

Biomass concentration for different strains

Budding yeast Saccharomyces cerevisiae

TMB3001 0.530: TMB3001C5 0.581: TMB3001C1 0.479

gDW/OD unit

Sonderegger M, Sauer U. Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microbiol. 2003 Apr69(4):1990-8. p.1991 right column 2nd paragraph from bottom

12676674

P.1991 right column 6th paragraph: "Determination of physiological parameters: In batch cultures, exponential growth rates were determined by log-linear regression of OD600 versus time with growth rate as the regression coefficient. The specific biomass yield (YX/S) was determined from a plot of the coefficient of linear regression of the biomass concentration (X) versus substrate concentration (S) during the exponential growth phase. The biomass concentration was estimated from predetermined correlations between OD600 and cellular dry weight during the mid-exponential growth phase of aerobic cultures grown on glucose for strains TMB3001, TMB3001C5, and TMB3001C1 (0.530, 0.581, and 0.479 g/OD600 unit, respectively). During the exponential growth phase, specific glucose and xylose uptake rates were calculated by determining the ratio of the growth rate to YX/S. Ethanol, xylitol, acetate, and glycerol yields were calculated by linear regression of by-product concentration versus S."

Uri M

dry weight

6939

107934

Translational diffusion coefficients simulated for bead models of tRNA Phe structures

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Translational%20diffusion%20coefficients%20(in%20units%20of%2010%5E-%207cm%5E2%20per%20s%20simulated%20for%20bead%20models%20of%20tRNA%20Phe%20structures.pdf

10^- 7cm^2/sec

Antosiewicz J, Porschke D. Effect of aminoacylation on tRNA conformation. Eur Biophys J. 1989 17(4):233-5. p.234 table 1

2612442

See notes beneath table

Uri M

diffusivity<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6940

107935

Diffusion coefficient of tRNA before and after aminoacylation

Budding yeast Saccharomyces cerevisiae

68.4±1 before: 58±2 after aminoacylation

Î¼m^2/sec

Potts RO, Ford NC Jr, Fournier MJ. Changes in the solution structure of yeast phenylalanine transfer ribonucleic acid associated with aminoacylation and magnesium binding. Biochemistry. 1981 Mar 17 20(6):1653-9. p.1656 right column 2nd paragraph

7013797

"The effect of aminoacylation on the structure of yeast phenylalanine tRNA was evaluated by laser light scattering."

"In contrast, however, the data obtained with the aminoacylated and nonacylated species generate different slopes and intercepts in 10 mM Mg2+ Aminoacylation results in a decrease in Do20,w from (6.84±0.10)X10^-7 to (5.8±0.2)X10^-7 cm2/s and an increase in the slope from (0.10±0.02) X10^-7 to (0.22±0.06)X10^-7(cm2/s)/(mg/mL). From the slope values, the average charge of nonacylated tRNAPhc is estimated to be 10±2e-, while the average charge of the aminoacylated form is 15±2e-, corresponding to an increase in negative charge of 5±2e-. Thus, while aminoacylation of tRNAPhe results in no changes in 1 mM Mg2+, an increase in negative charge and decrease in Do20,w are observed with the 10 mM Mg2+ condition."

Uri M

diffusivity, transfer ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6951

107946

Effect of carbon source on growth rate and volume at bud initiation

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Effect%20of%20carbon%20source%20on%20growth%20rate%20and%20volume%20at%20bud%20initiation.pdf

Johnston GC, Ehrhardt CW, Lorincz A, Carter BL. Regulation of cell size in the yeast Saccharomyces cerevisiae. J Bacteriol. 1979 Jan137(1):1-5. p.3 table 2

368010

To investigate the relation between growth rate and cell size at bud initiation, researchers examined cells grown both in chemostat and in batch cultures. Microscopy/Coulter counter.

When cells of AG1-7 were grown in media containing different carbon sources, growth rates varied by 2.5-fold (Table 2).

Uri M

volume, size, glucose, acetate, glycerol, growth rate, generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6952

107947

Effect of nitrogen source on growth rate of strain AGI- 7 and volume at bud initiation

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Effect%20of%20nitrogen%20source%20on%20growth%20rate%20of%20strain%20AGI-%207%20and%20volume%20at%20bud%20initiation.pdf

Johnston GC, Ehrhardt CW, Lorincz A, Carter BL. Regulation of cell size in the yeast Saccharomyces cerevisiae. J Bacteriol. 1979 Jan137(1):1-5. p.3 table 3

368010

To investigate the relation between growth rate and cell size at bud initiation, researchers examined cells grown both in chemostat and in batch cultures. Microscopy/Coulter counter.

Cell size at initiation of budding again was proportional to growth rate, and each successive round of budding was accompanied by an increase in the volume of the budding cell (Table 3).

Uri M

volume, size, proline, leucine, growth rate, generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6953

107948

Effect of altered growth rate on volume at bud initiation

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Effect%20of%20altered%20growth%20rate%20on%20volume%20at%20bud%20initiation.pdf

Johnston GC, Ehrhardt CW, Lorincz A, Carter BL. Regulation of cell size in the yeast Saccharomyces cerevisiae. J Bacteriol. 1979 Jan137(1):1-5. p.2 table 1

368010

To investigate the relation between growth rate and cell size at bud initiation, researchers examined cells grown both in chemostat and in batch cultures. Microscopy/Coulter counter. See note beneath table.

The volumes of cells of different bud scar classes initiating buds under steady-state growth conditions are shown in Table 1 and Fig. 2.

Uri M

volume, size, growth rate, generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

6954

107949

Effect of growth rate on the mean volumes of yeast cells grown under conditions of glucose limitation or NH4+ limitation

Budding yeast Saccharomyces cerevisiae

Figure link - http://bionumbers.hms.harvard.edu/files/Effect%20of%20growth%20rate%20on%20the%20mean%20volumes%20of%20yeast%20cells%20grown%20under%20conditions%20of%20glucose%20limitation%20or%20NH4%2B%20limitation.pdf

McMurrough I, Rose AH. Effect of growth rate and substrate limitation on the composition and structure of the cell wall of Saccharomyces cerevisiae. Biochem J. 1967 Oct105(1):189-203. p.200 figure 8

6056621

Calculations of the mean volumes of cells grown under various conditions of substrate limitation showed that these volumes were little affected by the nature of the limitation, although they were dependent on growth rate (Fig. 8).

Uri M

size, Glucose, ammonium, ammonia<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7076

108074

Kinesin-like protein KIF2C depolymerizes the minus end faster than the plus end by

Budding yeast Saccharomyces cerevisiae

1.7

±0.2

Fold

Varga V, Helenius J, Tanaka K, Hyman AA, Tanaka TU, Howard J. Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner. Nat Cell Biol. 2006 Sep8(9):957-62. p.958 left column bottom paragraph

16906145

To determine whether budding yeast Kip3p is a microtubule depolymerase, the full-length His-tagged protein was expressed in insect cells, purified to homogeneity and its activity measured in sedimentation assays.

Although MCAK acts at both ends, it depolymerizes the minus end 1.7±0.2 times faster than the plus end (mean ± s.d., n = 26).

Uri M

speed, velocity<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7077

108075

Microtubule growth rate

Budding yeast Saccharomyces cerevisiae

1.4

±0.4

Î¼m/min

Varga V, Helenius J, Tanaka K, Hyman AA, Tanaka TU, Howard J. Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner. Nat Cell Biol. 2006 Sep8(9):957-62. p.960 left column top paragraph

16906145

Tanaka K, Mukae N, Dewar H, van Breugel M, James EK, Prescott AR, Antony C, Tanaka TU. Molecular mechanisms of kinetochore capture by spindle microtubules. Nature. 2005 Apr 21 434(7036):987-94.

15846338

Because their speed was faster than the microtubule growth rate of 1.4±0.4µm/min (primary source), Kip3p spots always caught up with the ends of growing microtubules, leading to bright plus-end labelling (Fig. 4). See p.960 right column top paragraph for "typical microtubule growth rates of ~1µm/min"

Uri M

speed, velocity<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7079

108077

Velocity of movement of individual Kip3p-EGFP molecules

Budding yeast Saccharomyces cerevisiae

3.2

±0.3

Î¼m/min

Varga V, Leduc C, Bormuth V, Diez S, Howard J. Kinesin-8 motors act cooperatively to mediate length-dependent microtubule depolymerization. Cell. 2009 Sep 18 138(6):1174-83. p.1177 right column bottom paragraph

19766569

Single-molecule microscopy

The highest depolymerization rates measured during the saturation phases ranged from 2.5 to 4 µm/min in different experiments. This is similar to the velocity of movement of individual Kip3p-EGFP molecules measured under single-molecule conditions (3.2±0.3µm/min).

Uri M

speed,molecular motor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7080

108078

Concentration of Kip3p in vivo

Budding yeast Saccharomyces cerevisiae

~30

19766569

Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature. 2003 Oct 16 425(6959):737-41.

14562106

(primary source abstract:) Researchers created a Saccharomyces cerevisiae fusion library where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location.

The concentration of Kip3p in vivo is ~30 nM (700 molecules [Ghaemmaghami et al., 2003] in a volume of 20 to 40 µm^3 [Tyson et al., 1979]), though some molecules may not be active cellular microtubules are up to several microns long.

Uri M

contents, molecular motor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7142

108140

Thermodynamic analysis of central glycolysis in yeast

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Thermodynamic%20analysis%20of%20central%20glycolysis%20in%20yeast.pdf

Canelas AB, van Gulik WM, Heijnen JJ. Determination of the cytosolic free NAD/NADH ratio in Saccharomyces cerevisiae under steady-state and highly dynamic conditions. Biotechnol Bioeng. 2008 Jul 1 100(4):734-43. p.735 table 1

18383140

See notes beneath table. Thermodynamic analysis of glycolysis with published metabolite concentrations for Saccharomyces cerevisiae reveals positive ?rG's, in disagreement with the 2nd law of thermodynamics (Table I).

Uri M

fbp,3pg,atp,adp,pi,nad,nadh,gibbs free energy<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7143

108141

Steady-state intracellular concentrations of measured metabolites from aerobic glucose-limited cultures at D=0.1/hour

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Steady-state%20intracellular%20concentrations%20of%20measured%20metabolites%20from%20aerobic%20glucose-limited%20cultures%20at%20D%20of%200.1%20per%20h.pdf

18383140

The concentrations of the metabolic intermediates G6P, F6P, FBP, PEP, pyruvate, T6P, 6PG, G1P, M6P, oxoglutarate, succinate, fumarate, malate, and M1P, as well as the combined pools 2PG+3PG and citrate+isocitrate, were determined by ESI-LC-MS/MS (Van Dam et al., 2002). Quantification was based on IDMS (Mashego et al., 2004 Wu et al., 2005). The concentrations of NAD and NADH were determined by the spectrophotometric cycling method as described in Visser et al. (2004).

As shown in Table II, no significant differences were observed in the levels of all 17 measured metabolites, including NAD and NADH, between the two strains.

Uri M

g6p, f6p, fbp, 2pg, 3pg, pep, pyruvate, t6p, 6pg, g1p, m6p, citrate, isocitrate, oxoglutarate, succinate, fumarate, malate, m1p, nad, nadh, nicotinamide adenine dinucleotide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7146

108144

Influence of the NAD/NADH ratio on the thermodynamic feasibility of glycolysis

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Influence%20of%20the%20NAD-NADH%20ratio%20on%20the%20thermodynamic%20feasibility%20of%20glycolysis.pdf

18383140

To test whether the values obtained for the cytosolic free NAD/NADH ratio are realistic, researchers performed a thermodynamic analysis of central glycolysis. They focused particularly on the influence of the NAD/NADH ratio on the overall ?rG' of the steps between FBP and 3PG.

See notes beneath table.

Uri M

fbp, 3pg, atp, adp, pi, nicotinamide adenine dinucleotide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7147

108145

Cytosolic free NAD/NADH ratio under aerobic glucose-limited steady-state conditions at Î¼=0.1/h

Budding yeast Saccharomyces cerevisiae

101(±14) to 320(±45)

unitless

4711187

Under aerobic glucose-limited steady-state conditions at µ=0.1/h researchers obtained a cytosolic free NAD/NADH ratio between 101(±14) and 320(±45), assuming the cytosolic pH is between 7.0 and 6.5, respectively.

Uri M

Nicotinamide adenine dinucleotide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7148

108146

Total NAD/NADH ratio from the whole-cell concentrations of NAD and NADH

Budding yeast Saccharomyces cerevisiae

7.5

±2.5

unitless

18383140

Under aerobic glucose-limited steady-state conditions at µ=0.1/h researchers obtained a total NAD/NADH ratio of 7.5(±2.5) from the whole-cell concentrations of NAD and NADH. This value is in the range reported for S. cerevisiae under similar growth conditions (Theobald et al., 1997 Visser et al., 2004).

Uri M

Nicotinamide adenine dinucleotide, redox, ratio

7198

108196

Nucleic acid content of yeast cells growing in different media

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Nucleic%20acid%20content%20of%20yeast%20cells%20growing%20in%20different%20media.pdf

Waldron C, Lacroute F. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol. 1975 Jun122(3):855-65. p.859 table 2

1097403

See notes beneath table

"The RNA content per cell also decreased with decreasing growth rate, but in a manner that can best be represented by the curvilinear function shown in Fig. 3C. These measurements of RNA content were not corrected for the DNA labeled since DNA was only a small fraction of total nucleic acid (Table 2)." See table 1 p.856 for composition of media

Uri M

RNA, DNA, ribonucleic acid, deoxyribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7199

108197

Number of tRNA molecules per ribosome in yeast cells growing in different media

Budding yeast Saccharomyces cerevisiae

9.5 to 12.2 Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20tRNA%20molecules%20and%20ribosomes%20in%20yeast%20cells%20growing%20in%20different%20media1.pdf

tRNA/ribosome

Waldron C, Lacroute F. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol. 1975 Jun122(3):855-65. p.862 table 4

1097403

"Total RNA from cells growing in different media was analyzed by electrophoresis..." "From estimates of the tRNA fraction (fig.5B) and of total RNA content (fig.3C) [researchers] could calculate the number of tRNA molecules per cell in each growth medium (table 4). [They] could likewise calculate the number of ribosomes per cell, assuming that all rRNA is present in ribosomes (Table 4)."

See table 1, at bottom of table link, beneath table 4, for composition of growth media and growth rates. See notes beneath table

Uri M

RNA, transfer ribonucleic acid, ribosome, translation machinery, transfer RNA<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7201

108199

Biomass concentration, protein content of biomass, and metabolite concentrations during anaerobic glucose-limited chemostat growth

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Biomass%20concentration%2C%20protein%20content%20of%20biomass%2C%20and%20metabolite%20concentrations%20during%20anaerobic%20glucose-limited%20chemostat%20growth.pdf

Verduyn C, Postma E, Scheffers WA, van Dijken JP. Physiology of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J Gen Microbiol. 1990 Mar136(3):395-403. DOI: 10.1099/00221287-136-3-395 p.398 table 1

1975265

P.396 left column 5th paragraph: "Acetate, acetaldehyde, glycerol, succinate and glucose were determined with Boehringer test-kits 148261, 668613, 148270, 176281 and 676543, respectively."

P.398 left column 3rd paragraph: "When S. cerevisiae H1022 was grown at D=0.10/h, its biomass output was significantly higher than for CBS 8066 at the same dilution rate. Furthermore, acetate production was negligible during anaerobic growth of H1022 (Table 1). [Researchersâ] data confirm the original observations of Schatzmann (1975) with this strain. The protein content of H1022, however, was similar to that of CBS 8066. Also the patterns and quantities of minor byproducts (pyruvate, succinate etc.) were similar for both strains (Table 1)."

Uri M

glucose, Ethanol, Glycerol, Acetate, Succinate, Pyruvate

7202

108200

Cell composition

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Cell%20composition.pdf

11157958

"With the aim of obtaining precise values for batch cultivation parameters such as the maximum specific growth rate and the cell yield on glucose for both strains employed in this work, two batch cultivations were carried out in 4-liter bioreactors, i.e., one cultivation with each strain."

"In terms of metabolites drained for biosynthesis, two different cell compositions were considered in terms of macromolecules, one for each cultivation condition (Table 1). However, the composition of each type of macromolecule was assumed to be independent of the cultivation condition. Thus, the amino acid composition of a protein was assumed to be the same under both conditions and was taken from Oura (34)."

Uri M

protein, lipid, carbohydrate, rna, ashes, content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7203

108210

Biomass composition of S. cerevisiae grown on three different nitrogen sources

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Biomass%20composition%20of%20S.%20cerevisiae%20grown%20on%20three%20different%20nitrogen%20sources.pdf

Albers E, Larsson C, Lidén G, Niklasson C, Gustafsson L. Influence of the nitrogen source on Saccharomyces cerevisiae anaerobic growth and product formation. Appl Environ Microbiol. 1996 Sep62(9):3187-95. p.3192 table 4

8795209

Total protein content was determined with samples of freeze-dried cells (prepared as described previously [9]), resuspended in 3 ml of 1M NaOH, by a modified biuret method (34).

The results show that the nitrogen sources used have only a small influence on the cellular composition.

Uri M

protein, glycogen, trehalose, ash, carbon, Ammonium, Glutamic acid, Amino acid mixture<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7213

108220

Smallest known centromere

Budding yeast Saccharomyces cerevisiae

125

Zhang H, Dawe RK. Total centromere size and genome size are strongly correlated in ten grass species. Chromosome Res. 2012 May20(4):403-12 p.404 left column top paragraph

22552915

... the budding yeast Saccharomyces cerevisiae, ... has the smallest known centromere at 125 bp

Uri M

chromosome,sister chromatid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7279

104292

Half time for invertase inactivation at 30 MPa homogenization pressure

Budding yeast Saccharomyces cerevisiae

3414

min

Wojciech Bialas, Tomasz Jankowski High-pressure homogenisation of baker's yeast for the selective recovery of invertase, Electronic journal of Polish agricultural universities, 2007 Volume 10 Issue 2

The process of yeast cell disruption using a high-pressure double-valve pilot-scale homogeniser has been investigated for the selective release of invertase. The first-order kinetics was applied for the determination of the release rate of invertase and total proteins.

Invertase (beta-fructofuranosidase) is a sucrase enzyme. It catalyzes the hydrolysis (breakdown) of sucrose (table sugar) to fructose and glucose, usually in the form of inverted sugar syrup.

Uri M

enzyme, inactivation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7280

104293

Half time for invertase inactivation at 90 MPa homogenization pressure

Budding yeast Saccharomyces cerevisiae

min

Wojciech Bialas, Tomasz Jankowski High-pressure homogenisation of baker's yeast for the selective recovery of invertase, Electronic journal of Polish agricultural universities, 2007 Volume 10 Issue 2

Invertase (beta-fructofuranosidase) is a sucrase enzyme. It catalyzes the hydrolysis (breakdown) of sucrose (table sugar) to fructose and glucose, usually in the form of inverted sugar syrup.

Uri M

enzyme, inactivation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7281

104294

Association constant of alpha mating factor and receptor

Budding yeast Saccharomyces cerevisiae

2000000

1/(M*Sec)

Yi TM, Kitano H, Simon MI. A quantitative characterization of the yeast heterotrimeric G protein cycle. Proc Natl Acad Sci U S A. 2003 Sep 16100(19):10764-9

12960402

Researchers constructed strains possessing genomic copies of the FRET pairs CFP-GPA1 (Ga) and STE18-YFP (G?), which replaced their cognate genes. They observed the dose-dependent loss of FRET on a-factor addition, which was quantitated by fluorometer. The kinetics and dose response of G protein activation were measured and compared with the pheromone responsiveness of two downstream events, cell-cycle arrest, and transcriptional activation of pheromone-inducible genes. Finally, researchers fit the data to a mathematical model that furnishes a detailed description of the yeast heterotrimeric G protein cycle (Fig. 1) and also enables quantitative explanations of the data.

Uri M

g protein heterodimer,mating factor,mating response,ligand receptor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7282

104295

Dissociation constant of alpha mating factor and receptor

Budding yeast Saccharomyces cerevisiae

0.01

Sec^-1

Yi TM, Kitano H, Simon MI. A quantitative characterization of the yeast heterotrimeric G protein cycle. Proc Natl Acad Sci U S A. 2003 Sep 16100(19):10764-9

12960402

Uri M

g protein heterodimer,mating factor,mating response,ligand receptor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7283

104296

Degradation rate of alpha mating factor receptor

Budding yeast Saccharomyces cerevisiae

0.0004

molecules/cell/sec

Yi TM, Kitano H, Simon MI. A quantitative characterization of the yeast heterotrimeric G protein cycle. Proc Natl Acad Sci U S A. 2003 Sep 16100(19):10764-9

12960402

Uri M

g protein heterodimer,mating factor,mating response,ligand receptor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7284

104297

Number of alpha mating factor receptor

Budding yeast Saccharomyces cerevisiae

10000

molecules/cell

Yi TM, Kitano H, Simon MI. A quantitative characterization of the yeast heterotrimeric G protein cycle. Proc Natl Acad Sci U S A. 2003 Sep 16100(19):10764-9

12960402

Number estimated from Western blots and fluorescence quantification. Researchers constructed strains possessing genomic copies of the FRET pairs CFP-GPA1 (Ga) and STE18-YFP (G?), which replaced their cognate genes. They observed the dose-dependent loss of FRET on a-factor addition, which was quantitated by fluorometer. The kinetics and dose response of G protein activation were measured and compared with the pheromone responsiveness of two downstream events, cell-cycle arrest, and transcriptional activation of pheromone-inducible genes. Finally, researchers fit the data to a mathematical model that furnishes a detailed description of the yeast heterotrimeric G protein cycle (Fig. 1) and also enables quantitative explanations of the data.

Uri M

g protein heterodimer,mating factor,mating response,ligand receptor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7285

104298

Rate of activation of alpha mating factor receptor

Budding yeast Saccharomyces cerevisiae

1.00E-05

molecules/cell/sec

Yi TM, Kitano H, Simon MI. A quantitative characterization of the yeast heterotrimeric G protein cycle. Proc Natl Acad Sci U S A. 2003 Sep 16100(19):10764-9

12960402

G protein activation rate was determined from FRET time course and doseâresponse data. Researchers constructed strains possessing genomic copies of the FRET pairs CFP-GPA1 (Ga) and STE18-YFP (G?), which replaced their cognate genes. They observed the dose-dependent loss of FRET on a-factor addition, which was quantitated by fluorometer. The kinetics and dose response of G protein activation were measured and compared with the pheromone responsiveness of two downstream events, cell-cycle arrest, and transcriptional activation of pheromone-inducible genes. Finally, researchers fit the data to a mathematical model that furnishes a detailed description of the yeast heterotrimeric G protein cycle (Fig. 1) and also enables quantitative explanations of the data.

Uri M

g protein heterodimer, mating factor, mating response, ligand receptor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7286

104299

Number of fusion proteins expressed at the cell surface

Budding yeast Saccharomyces cerevisiae

100000

molecules/cell

Boder ET, Wittrup KD. Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol. 1997 Jun15(6):553-7

9181578

Uri M

antibody engineering, combinatorial library, surface display, affinity maturation,scFv<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7287

104300

Translation rate on culture of nitrogen bases and glucose

Budding yeast Saccharomyces cerevisiae

9.3

aa/sec

Bonven B, Gulløv K. Peptide chain elongation rate and ribosomal activity in Saccharomyces cerevisiae as a function of the growth rate. Mol Gen Genet. 1979 Feb 26 170(2):225-30.

372763

The peptide-chain elongation rate of Saccharomyces cerevisiae at two different growth rates was estimated by the kinetics of radioactive labelling of nascent and finished polypeptides as described by Gausing, 1972, and Young and Bremer, 1976.

At 30 degrees celsius in logarithmic phase

Uri M

ribosome, elongation, protein synthesis, polymerization<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7288

104301

Translation rate on culture of nitrogen bases and acetate

Budding yeast Saccharomyces cerevisiae

5.5

aa/sec

Bonven B, Gulløv K. Peptide chain elongation rate and ribosomal activity in Saccharomyces cerevisiae as a function of the growth rate. Mol Gen Genet. 1979 Feb 26 170(2):225-30.

372763

At 30 degrees celsius in logarithmic phase

Uri M

ribosome, elongation, protein synthesis, polymerization<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7290

104303

Quantification of Ribosome-associated Protein Biogenesis factors (RPBs) and ribosomes in a logarithmically growing yeast cell

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Quantification%20of%20RPBs%20and%20ribosomes%20in%20a%20logarithmically%20growing.pdf

17229726

Construction of Plasmids,Purification of His6-tagged Standard Proteins,Determination of Protein Concentrations,Antibodies and Immunoblotting Procedures,Quantification of Ribosomes and RPBs in Yeast Cells,In Vitro Transcription and Translation,Cross-linking of Nascent Polypeptides to RPBs,Purification of FLAG-tagged RNCs under Native Conditions,Generation of Non-translating and Translating Ribosomes

Uri M

trigger factor, peptide elongation, peptide transport, translation, Ribosome, Rps, Asc1, Rpl39, Rpl17, Ssb1/2, RAC, Ssz1, Zuo1, NAC, NAC, SRP, Srp54, Map1, Map2, NatA, Nat, Ard1, oligomer<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7291

104304

Number of 40S ribosomal protein S9 in a logarithmically growing yeast cell

Budding yeast Saccharomyces cerevisiae

315000

oligomers/cell

Raue U, Oellerer S, Rospert S. Association of protein biogenesis factors at the yeast ribosomal tunnel exit is affected by the translational status and nascent polypeptide sequence. J Biol Chem. 2007 Mar 16282(11):7809-16 Table link - http://bionumbers.hms.harvard.edu/files/Quantification%20of%20RPBs%20and%20ribosomes%20in%20a%20logarithmically%20growing.pdf

17229726

220000 Rps9 subunits/cell

Uri M

peptide elongation, translation, Ribosome,Rps9<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7292

104305

Number of Nascent Associated Polypeptide Complexes (NAC) in logarithmically growing yeast cell

Budding yeast Saccharomyces cerevisiae

400000

Copies/cell

17229726

1.25 NAC per 1 ribosome

Uri M

trigger factor, peptide elongation, peptide transport, translation, Ribosome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7293

104306

Number of methionine aminopeptidase1 (MAP1) in logarithmically growing yeast cell

Budding yeast Saccharomyces cerevisiae

20000

Copies/cell

17229726

Uri M

trigger factor,peptide elongation,peptide transport,translation,Ribosome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7294

104307

Number of Ssb1/2 in logarithmically growing yeast cell

Budding yeast Saccharomyces cerevisiae

280000

Copies/cell

17229726

0.891 Ssb 1/2 molecules to 1 ribosome

Uri M

trigger factor,peptide elongation,peptide transport,translation,Ribosome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7295

104308

Concentration of standard proteins

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Concentration%20of%20standard%20proteins.pdf

17229726

The concentration of each purified protein was determined by two independent methods. The amount of proteins applied to generate standard curves was calculated based on mean of the two values. Bradford-assay (Bio-Rad), DC protein-assay (Bio- Rad), and BCA-assay (Sigma) were performed according to the manufacturersâ manual with bovine serum albumin as a standard. The concentration of His6-Nat1 was determined with the DC proteinassay (Bio-Rad), which can be performed in the presence of detergent. The concentrations of His6- Asc1, His6-Ard1 and His6-Ssb1 were calculated from UV-absorption at 280 nm using molar extinction coefficients at 280 nm: e(His6-Asc1) = 71056 M-1 cm-1, e(His6- Ard1) = 23506 M-1 cm-1, and e(His6- Ssb1) = 19099 M-1 cm-1. Absorption at 280 nm could not be applied as a method for protein quantification when purification was performed under denaturing conditions, as urea interfered with measurements.

Uri M

His6-Rps9a, denatured, His6-Asc1, native, His6-Rpl39, His6-Rpl17a, His6-Nat1, His6-Ard1, His6-Map1, His6-Map2, RAC, His6-Ssb1, NAC, His6-Srp54, peptide elongation, peptide transport, translation, Ribosome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7296

104309

Protein production rate in haploid cell under fast growth conditions

Budding yeast Saccharomyces cerevisiae

13000

6500-19500

Proteins/cell/sec

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 162:87 p.8/14 right column 2nd paragraph

18925958

An examination of the accuracy of genome-wide expression datasets generated for Saccharomyces cerevisiae shows that the available datasets suffer from large random errors within studies as well as systematic shifts in reported values between studies, which make predictions of translational activity at the level of individual genes relatively inaccurate. In contrast, predictions of cell-wide translational activity are possible from such datasets with higher accuracy, and current datasets predict a production rate of about 13,000 proteins per haploid cell per second under fast growth conditions. This prediction is shown to be consistent with independently derived kinetic information on nucleotide exchange reactions that occur during translation, and on the ribosomal content of yeast cells. The predicted translation rates of 13,000 (6,500â19,500) proteins synthesised per second and of 6 (3â9) million peptide bonds (BNID 104314) being formed per second will form a useful benchmark against which emerging knowledge on the kinetics of relevant reactions can be interpreted.

Uri M

protein synthesis, translation, peptide synthesis, polymerization, ribosome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7297

104310

Cellular RNA content and proportion of total RNA that is rRNA

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Cellular%20RNA%20content%20and%20proportion%20of%20total%20RNA%20that%20is%20rRNA%20from%20several%20studies%2C%20and%20calculation%20of%20the%20cellular%20ribosome%20content.pdf

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 162:87 p.6/14 table 1

18925958

List of refs in table

Analysis of protein abundance datasets

Table gives ribosome/cell value of 187000±56000 (BNID 100267), proportion of rRNA/total RNA of 80%-85%. See BNID 100261

Uri M

protein synthesis, ribosome, ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7298

104311

Total RNA content per cell

Budding yeast Saccharomyces cerevisiae

7.10E-13

±1.9e-13 table link - http://bionumbers.hms.harvard.edu/files/Cellular%20RNA%20content%20and%20proportion%20of%20total%20RNA%20that%20is%20rRNA%20from%20several%20studies%2C%20and%20calculation%20of%20the%20cellular%20ribosome%20content.pdf

g/cell

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 16 2: 87 p.6 table 1

18925958

See refs beneath table

Analysis of protein abundance datasets. Value is average of several studies in table

P.5 right column bottom paragraph: "However, these studies also report the raw data for total cellular RNA content and the proportion of RNA that is rRNA, and rRNA abundances are therefore here re-calculated from these raw data based on the exact rRNA molecular weights from now available sequence information (table 1). The resulting estimate of 187,000 ± 56,000 rRNA copies per yeast cell can be usefully compared to the distribution of RP abundances in figure 2. Overall, the analysis of ribosomal protein abundance data thus supports the assumption generated from the pairwise study comparisons that individual datasets contain random errors in the reported values." Table gives value of 187000±56000 ribosomes/cell of (BNID 100267)

Uri M

ribosome, ribonucleic acid

7299

104312

Number of polyadenylated mRNA transcripts

Budding yeast Saccharomyces cerevisiae

~15,000

Copies/cell

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 162:87 p.8/14 right column 2nd paragraph

18925958

Hereford LM, Rosbash M. Number and distribution of polyadenylated RNA sequences in yeast. Cell. 1977 Mar10(3):453-62. p.457 note "f" beneath table 1

321129

(P.457 of primary source note "f" beneath table 1:)ââCopies per cellâ is calculated with the following assumptions. The size of the genome is 9x10^9daltons (Bicknell and Doublas, 1970). The RNA/DNA ratio is 50:1 (Hartwell, 1970). The percentage of poly(A)-containing RNA is 1.5 (estimated from the difference if the Crot1/2 values of Figures 5 and 8). The average size of yeast mRNA is 1500 nucleotides. There are therefore approximately 15,000 mRNA molecules per cell. Copies per cell=15,000x(%cDNA)/(number of sequences).â

"Although the total mass of cellular RNA cannot be calculated in the same way as proteins because non-coding mRNA regions for each gene contribute to the molecular weight but are not accurately known, the total number of mRNAs in the dataset can easily be calculated as about 12,200, with 95% confidence limits between 6,100 and 18,300 mRNAs per cell [BNID 102988]. This compares to experimental estimates of about 15,000 poly(A) tailed RNAs per cell generated experimentally [primary source]. In two important aspects, the curated dataset thus approaches estimates from available experimental data." See BNID 103023

Uri M

transcription, polyadenylation, polyA tail<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7300

104313

Sum of proteins per logarithmically growing haploid cell

Budding yeast Saccharomyces cerevisiae

53000000

3e+7 to 8e+7

Copies/cell

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 16 2:87 doi: 10.1186/1752-0509-2-87. p.8 of 14 right column 3rd paragraph

18925958

"The sum of proteins per cell predicted from the curated dataset is about 53 million proteins for a fast-growing haploid yeast cell, with 90% confidence limits of 30â80 million. From the local loss-rates for individual proteins through degradation, the global loss-rate through cell growth, and the local protein abundance data, protein synthesis rates can be calculated for each gene. The cell- wide sum of these rates amounts to about 13,000 (6,500â 19,500) proteins synthesised per cell per second on aver- age throughout the cell cycle, and, if translation initiation and termination are assumed to be loss-free processes, there must consequently also be about 13,000 translation initiation and translation termination events per cell per second." See BNID 106198

Uri M

enzyme, peptide, amount, number<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7301

104314

Frequency of translation elongation events

Budding yeast Saccharomyces cerevisiae

6000000

3E6-9E6

Events/cell/sec

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 162:87 p.8/14 right column 3rd paragraph

18925958

There must be about 13,000 translation initiation and translation termination events per cell per second. The frequency of translation elongation events can be calculated locally for each gene if the relevant ORF lengths are included in the calculations, the sum of these amounts to 6.0 (3â9) million elongation events per second per cell.

Uri M

protein synthesis, translation, peptide synthesis, polymerization, ribosome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7302

104315

Protein half life according to ORF name with measurement technique

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/Yeast%20protein%20half%20life%20and%20measurement%20technique.xlsx

min

von der Haar T. A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol. 2008 Oct 162: 87 Additional file 1

18925958

List of refs in column 'D' of table

See methods in column 'C' of table

"Excel spreadsheet containing the literature datasets for protein abundance and protein half-lives, and the full curated dataset."

Uri M

enzyme, degradation, Pulse-Chase Labelling, Gal-Promoter shut-off, Cycloheximide arrest<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7325

104338

Median promoter length

Budding yeast Saccharomyces cerevisiae

455

Kristiansson E, Thorsen M, Tamás MJ, Nerman O. Evolutionary forces act on promoter length: identification of enriched cis-regulatory elements. Mol Biol Evol. 2009 Jun26(6):1299-307 p.1301 left column 4th paragraph

19258451

Sequence Data and Analysis, Transcription Factor Binding Site Data and Phylogenetic Filtering, Three Tests for Enrichment of Transcription Factor Binding Sites

"The simplest definition of a gene's putative promoter region is the DNA sequence located 5' of the corresponding ORF and stretching to the upstream ORF. Extracting promoter regions for all genes according to this definition revealed the median length of all promoters in the S. cerevisiae genome is 455 bp and that the length of promoters varies greatly (fig. 1)."

Uri M

regulatory sequence, transcription, transcription factor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7343

104356

Acid soluble stable organic phosphorus

Budding yeast Saccharomyces cerevisiae

0.125

+-0.01

mg P/mg dry cell

KATCHMAN BJ, FETTY WO. Phosphorus metabolism in growing cultures of Saccharomyces cerevisiae. J Bacteriol. 1955 Jun69(6):607-15.

14392115

Total labile phosphorus must be heated in 1 N acid for 10-15 min at 100 C to effect quantitative hydrolysis. The orthophosphate from such hydrolyzed extracts was determined colorimetrically

P in values denotes Phosphorus. Stable organic-(total acid-soluble-P)-(total-P 10 min). Number of runs averaged is 51

Uri M

logarithmic phase, metabolism<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7344

104357

Average cell cycle periods for cells of different ploidy

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Average%20cell%20cycle%20periods%20for%20cells%20of%20different%20ploidy.pdf

Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature. 2007 Aug 23448(7156):947-51

17713537

Researchers measured times from cytokinesis to budding (G1) and from budding to cytokinesis in haploids, diploids or tetraploids (mothers and daughters), using time-lapse fluorescence microscopy of strains expressing Myo1 tagged with green fluorescent protein (Myo1âGFP).

Uri M

haploid, diploid, tetraploid, daughter, G1, mother, Budded, period, mother, Total, cycle, doubling time, generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7345

104358

Average G1 cell cycle period for haploid daughter cell

Budding yeast Saccharomyces cerevisiae

±2

min

Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature. 2007 Aug 23 448(7156):947-51 Table link - http://bionumbers.hms.harvard.edu/files/Average%20cell%20cycle%20periods%20for%20cells%20of%20different%20ploidy.pdf

17713537

n=158

Uri M

haploid, cell cycle, gap 1<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7346

104359

Average G1 cell cycle period for haploid mother cell

Budding yeast Saccharomyces cerevisiae

15.6

±0.5

min

Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature. 2007 Aug 23448(7156):947-51 Table link - http://bionumbers.hms.harvard.edu/files/Average%20cell%20cycle%20periods%20for%20cells%20of%20different%20ploidy.pdf

17713537

n=202

Uri M

haploid, cell cycle, gap 1<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7347

104360

Average total cell cycle period for haploid mother cell

Budding yeast Saccharomyces cerevisiae

±1 table link - http://bionumbers.hms.harvard.edu/files/Average%20cell%20cycle%20periods%20for%20cells%20of%20different%20ploidy.pdf

min

17713537

P.947 left column bottom paragraph: "[Researchers] measured times from cytokinesis to budding (G1) and from budding to cytokinesis in haploids, diploids or tetraploids (mothers and daughters), using time-lapse fluorescence microscopy [a technique wherein a camera that periodically takes photographs is attached to a microscope, imaging cellular or intracellular activity] of strains expressing Myo1 tagged with green fluorescent protein (Myo1âGFP)." GFP (Green Fluorescent Protein), a fluorescing molecule, is often used as a label. In this case GFP was fused (through genetic engineering) to another protein, Myo1, which forms a ring at the daughter cell's bud neck.

n=116. Although unspecified, the growth media appears to be glucose according to following sentence from p. 16 in supplementary information (bottom paragraph): "Glycerol/ethanol supports a much slower growth rate than glucose (170 min compared to 100 min doubling time)..." For doubling time of haploid cell from the same article see BNID 101310. See BNID 100270, 101747

Uri M

haploid, cell cycle, generation time, doubling time

7348

104361

Average total cell cycle period for haploid daughter cell

Budding yeast Saccharomyces cerevisiae

112

±3

min

Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature. 2007 Aug 23448(7156):947-51 Table link - http://bionumbers.hms.harvard.edu/files/Average%20cell%20cycle%20periods%20for%20cells%20of%20different%20ploidy.pdf

17713537

n=97

Uri M

haploid, cell cycle, generation time, doubling time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7349

104362

Average duration of cell cycle periods for wt haploid cells grown in glycerol-ethanol

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Average%20duration%20of%20cell%20cycle%20periods%20for%20wt%20haploid%20cells%20grown%20in%20glycerol-ethanol.pdf

17713537

Uri M

haploid,Budded,period,mother,Total,cycle,doubling time,generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7350

104363

Cell cycle period for wt haploid daughter cell grown in glycerol-ethanol

Budding yeast Saccharomyces cerevisiae

219

±3 table link - http://bionumbers.hms.harvard.edu/files/Average%20duration%20of%20cell%20cycle%20periods%20for%20wt%20haploid%20cells%20grown%20in%20glycerol-ethanol.pdf

min

17713537

Number of observations is 54. The table shows the mean +/- standard error of the mean in minutes with the number of observations reported in parenthesis.

Uri M

haploid, Budded, period, Total, cycle, doubling time, generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7351

104364

Cell cycle period for wt haploid mother cell grown in glycerol-ethanol

Budding yeast Saccharomyces cerevisiae

133

±2 Table link - http://bionumbers.hms.harvard.edu/files/Average%20duration%20of%20cell%20cycle%20periods%20for%20wt%20haploid%20cells%20grown%20in%20glycerol-ethanol.pdf

min

17713537

Number of observations is 84. The table shows the mean +/- standard error of the mean in minutes with the number of observations reported in parenthesis.

Uri M

haploid, Budded, period, Total, cycle, doubling time, generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7352

104365

Average cell cycle periods for different haploid strains

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Average%20cell%20cycle%20periods%20for%20different%20haploid%20strains.pdf

17713537

Uri M

haploid,Budded,period,mother,Total,cycle,doubling time,generation time,6xCLN3 ,6xCLN2 ,6xCLN3 6xCLN2<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7353

104366

Fraction of proteome that is expressed under normal growth conditions

Budding yeast Saccharomyces cerevisiae

Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature. 2003 Oct 16 425(6959):737-41 abstract

14562106

To facilitate global protein analyses, researchers have created a Saccharomyces cerevisiae fusion library where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location. Through immunodetection of the common tag, they obtain a census of proteins expressed during log-phase growth and measurements of their absolute levels.

Researchers find that about 80% of the proteome is expressed during normal growth conditions

Uri M

translation, gene expression, protein, enzyme, Percent<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7496

104512

Time for recovery of 90 percent of TATA Binding Protein (TBP) fluorescence signal

Budding yeast Saccharomyces cerevisiae

sec

Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT. Regulation of TATA-binding protein dynamics in living yeast cells. Proc Natl Acad Sci U S A. 2008 Sep 9 105(36):13304-8

18765812

To determine whether the dynamic behavior of the Pol II machinery in vivo is fundamentally different from that of Pol I and whether the static behavior of Pol II factors in vitro fully recapitulates their behavior in vivo, researchers used fluorescence recovery after photobleaching (FRAP). Signal noise resulting from the small size of the bleach spot combined with the relatively faint intranuclear YFP signals was overcome by collection of FRAP data from Ë30â100 individual cells.

Uri M

Yellow fluorescent protein, YFP, RNAP, RNA polymerase, Transcription Preinitiation Complex<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7497

104513

Time for complete recovery of TATA Binding Protein (TBP) fluorescence signal

Budding yeast Saccharomyces cerevisiae

sec

Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT. Regulation of TATA-binding protein dynamics in living yeast cells. Proc Natl Acad Sci U S A. 2008 Sep 9 105(36):13304-8

18765812

Uri M

Yellow fluorescent protein, YFP, RNAP, RNA polymerase, Transcription Preinitiation Complex<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7498

104514

Number of TATA Binding Protein (TBP) molecules per haploid cell

Budding yeast Saccharomyces cerevisiae

20000

Copies/cell

Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT. Regulation of TATA-binding protein dynamics in living yeast cells. Proc Natl Acad Sci U S A. 2008 Sep 9 105(36):13304-8

18765812

Borggrefe T, Davis R, Bareket-Samish A, Kornberg RD. Quantitation of the RNA polymerase II transcription machinery in yeast. J Biol Chem. 2001 Dec 14 276(50):47150-3 Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20selected%20protein%20molecules%20per%20yeast%20cell.pdf

11591727

(Primary source) Tandem Affinity Purification (TAP) tags and dot blot analysis have been used to measure the amounts of RNA polymerase II transcription proteins in crude yeast extracts.

Uri M

Gene regulation, RNA polymerase, Transcription Preinitiation Complex<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7499

104515

Number of RNA polymerase and general transcription factor protein molecules per haploid cell

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20selected%20protein%20molecules%20per%20yeast%20cell.pdf

Borggrefe T, Davis R, Bareket-Samish A, Kornberg RD. Quantitation of the RNA polymerase II transcription machinery in yeast. J Biol Chem. 2001 Dec 14 276(50):47150-3 p.47152 table II

11591727

Tandem Affinity Purification (TAP) tags and dot blot analysis have been used to measure the amounts of RNA polymerase II transcription proteins in crude yeast extracts.

"The results (Table II) showed the greatest abundance of RNA polymerase II, in keeping with its involvement in both the initiation and elongation of transcription. The level of TFIIF was nearly the same, as expected from its tight association with RNA polymerase II and from its likely role in both transcription initiation and elongation as well (ref 16)." Range of the 6 TF copies in table is 6,000-24,000 proteins/cell. Note-(1) Frank A. Robey, 'Use of capillary electrophoresis for binding studies' in James P Landers, Handbook of capillary electrophoresis, 1996, pp 598 writes: "...it is believed that there are only 10^3-10^4 molecules of transcription factors per cell nucleus,...". (2) Bolouri et al, 2003 PMID 12883007 give value of 300-10000 TF proteins/cell in sea urchin.

Uri M

Gene regulation, RNA polymerase, Transcription Preinitiation Complex, RNA polymerase II, (Rpb3), TFIIF (Tfg2), TFIIE (Tfa2), TFIIB (Sua7), TFIID (TBP), Mediator (Med8), TFIIH (Tfb3), Transcription factor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7500

104516

Number of RNA polymerase II (Rpb3) molecules per haploid cell

Budding yeast Saccharomyces cerevisiae

30000

Copies/cell

11591727

Tandem Affinity Purification (TAP) tags and dot blot analysis have been used to measure the amounts of RNA polymerase II transcription proteins in crude yeast extracts.

Uri M

Gene regulation, RNA polymerase, Transcription Preinitiation Complex<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7501

104517

Number of Mediator (Med8) molecules per haploid cell

Budding yeast Saccharomyces cerevisiae

6000

Copies/cell

11591727

Tandem Affinity Purification (TAP) tags and dot blot analysis have been used to measure the amounts of RNA polymerase II transcription proteins in crude yeast extracts.

The measurements showed comparable amounts of RNA polymerase II, TFIIE, and TFIIF, lower levels of TBP and TFIIB, and still lower levels of Mediator and TFIIH.

Uri M

Gene regulation,RNA polymerase,Transcription Preinitiation Complex,activation of transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7502

104518

"Rule of thumb" for transforming one molecule per cell to units of concentration

Budding yeast Saccharomyces cerevisiae

Calculated according to cell volume, please see Measurement Method

Calculated using Avogadro's constant according to cell volume of 50 µm^3= 5E-14liter (BNID 100452, 100 430). 1 particle/5E-14liter=X particles/liter>>X=2E13particles/liter. 2E13(particles/liter)/6E23(particles/mole) = ~3E-11M=~10 pM. Note: 3e-11M and 1e-11M are on same order of magnitude, allowing approximation.

pM=1e-12Molar. Value above means 1000 molecules/cell=10nM. For 1000molecules/cell=1nM (1molecule=1pM) concentration in eukaryotic cell see Luby-Phelps 2000 PMID 10553280 p.191 top paragraph (this order of magnitude difference than calculation above probably comes from consideration of larger eukaryotic cells).

Uri M

Dimension, size, volume, constant<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7504

104520

Average concentration of a protein in cell

Budding yeast Saccharomyces cerevisiae

0.4-1.4

µM

Calculated according to cell volume and average protein copy number, please see Measurement Method

Calculated manually from 2 sources: (1)[Ghaemmaghami et al PMID 14562106, BNID 101845] Average protein copy number is ~12100 (column C in table). Dividing by Avogadro's number and cell volume (50µm^3=5e-14 liter BNID 100 430,100452). ~12100/6e23mol^-1/5e-14liter ~ 0.4µM. (2) BNID 104245. Column W in Table link-http://bionumbers.hms.harvard.edu/files/Yeast%20proteins%20abundance%20data.xls. Average protein copy number is 41000. A similar calculation gives concentration of 1.4µM.

(To Ghaemmaghami et al PMID 14562106) Table gives more than 3000 protein levels. This table is the Supplemental Data from the reference. The proteins are ordered by gene name, but could be sorted based on abundance using the function on Excel. It is also possible to search for protein abundance by gene name at the yeastgfp site (BNID 100600). Note-Wagner (2005) gives median protein abundance of 2460 copies/cell (BNID 100208). Using this value in a similar calculation as in Measurement method one arrives at concentration of 8.2e-8M=~0.1µM. See BNID 105247 for concentration of 36nM.

Uri M

table, link, protein level, protein abundance, proteins, TAP, TAP tagging<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7509

104525

Rule of thumb' for time it takes a protein to diffuse across the cell

Budding yeast Saccharomyces cerevisiae

0.5

sec

Calculated according to yeast cell diameter and average protein diameter. Please see Measurement Method

Taking X, distance to be traveled, as 4.5µm (BNID 100 451) and D in cytoplasm, as 10µm^2/sec (D in cytoplasm is in the range of 5-15µm^2/sec, GFP-BNID 100 193, 40kda dextran, similar weight to protein, BNID 100198). According to equation of diffusion (in 3 dimensions): t diffusion=X^2/(6×D). (4.5µm)^2/60µm^2/sec=0.338secË0.5sec.

In cytoplasm there are solutes and D is smaller than in water (100µm^2/sec). D in water can be calculated from the Einstein-Stokes eq. D=KBT/6/p/?/R where R=2.5nm, typical protein radius. KB=Boltzmann's constant, ?=viscosity, 0.001 Pa×sec for water. (1.38×10^-23Kg×m^2×sec^-2×K^-1×300K)/ (6×3.14×0.001Kg×m^-1×sec^-1×2.5×10^-9m)= 8.8×10^-11m^2/sec=88µm^2secË100µm^2/sec

Uri M

diffusion, movement, peptide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7570

104588

Fraction of Cell wall out of total cell weight

Budding yeast Saccharomyces cerevisiae

Lesage G, Bussey H. Cell wall assembly in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 2006 Jun70(2):317-43. p.318 left column 3rd paragraph

16760306

[206] Nguyen TH, Fleet GH, Rogers PL. Composition of the cell walls of several yeast species. Appl Microbiol Biotechnol. 1998 Aug50(2):206-12.

9763691

(Primary source abstract:) "Cell walls, representing 26%-32% of the cell dry weight, were prepared from several strains of the yeasts Kloeckera apiculata, Debaryomyces hansenii, Zygosaccharomyces bailii, Kluyveromyces marxianus and Saccharomyces cerevisiae. Extraction of the walls with potassium hydroxide at 4 degrees C, followed by saturation of the alkali-soluble extract with ammonium sulphate gave fractions of mannoprotein, alkali-soluble glucan and alkali-insoluble glucan."

P.318 left column 3rd paragraph: "The S. cerevisiae cell wall represents ~30% of the dry weight of the cell and is composed largely of polysaccharides (~85%) and proteins (~15%) (primary source)."

Uri M

fungi, membrane, extra cellular matrix

7571

104589

Polysaccharide composition of Extracellular matrix

Budding yeast Saccharomyces cerevisiae

60% glucose: 8% mannose: 32% galactose

Beauvais A et al, Characterization of a biofilm-like extracellular matrix in FLO1-expressing Saccharomyces cerevisiae cells. FEMS Yeast Res. 2009 May9(3):411-9

19207290

Cell wall analysis-Total hexose determination was performed using the phenol sulphuric acid procedure with glucose as the standard (Dubois et al., 1956). Total hexosamine was measured after hydrolysis with 8 N HCl for 4 h at 100 °C (Johnson, 1971).

Cell wall composition is ~85% polysaccharides: 15% proteins (BNID 104590)

Uri M

fungi, membrane, extra cellular matrix<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7572

104590

Composition of Cell wall

Budding yeast Saccharomyces cerevisiae

~85% polysaccharides: ~15% proteins

Lesage G, Bussey H. Cell wall assembly in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 2006 Jun70(2):317-43. p.318 left column 3rd paragraph

16760306

[206] Nguyen TH, Fleet GH, Rogers PL. Composition of the cell walls of several yeast species. Appl Microbiol Biotechnol. 1998 Aug50(2):206-12.

9763691

P.318 left column 3rd paragraph: "The S. cerevisiae cell wall represents ~30% of the dry weight of the cell and is composed largely of polysaccharides (~85%) and proteins (~15%) (primary source)."

Uri M

fungi, membrane, extra cellular matrix

7573

104591

Effects of growth conditions on cell wall mass, chitin, mannan, b-glucans, b-1,6-glucan and on the sensitivity of whole cells to zymolyase

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Effects%20of%20growth%20conditions%20on%20cell%20wall%20mass%2C%20chitin%2C%20mannan%2C%20b-glucans%2C%20b-1%2C6-glucan%20and%20on%20the%20sensitivity%20of%20whole%20cells%20to%20zymolyase.pdf

Aguilar-Uscanga B, François JM. A study of the yeast cell wall composition and structure in response to growth conditions and mode of cultivation. Lett Appl Microbiol. 2003 37(3):268-74. p.270 table 1

12904232

Chemical and enzymatic methods were used to determine levels of beta-1,3-glucan and 1,6-glucan, mannan and chitin of the yeast cell wall, whereas the structure/resistance of the wall was qualitatively assessed by the sensibility to the lytic action by zymolyase.

Uri M

chitin, nitrogen limitation, pH, weight, extracellular matrix, Growth, Condition, Growth, rate, dry, Chitin, wall, Mannan, cell mass, (lg mg)1, b-glucan, b-1, 6-glucan, glucan, Zymolyase, Sensitivity, (MLR), YPD, YNB, CF, Glucose, Mannose, Sucrose, Maltose, Galactose, Ethanol<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7574

104592

Fraction of cell wall out of total cell mass when grown on YPD

Budding yeast Saccharomyces cerevisiae

24.5

±2.5 Table link - http://bionumbers.hms.harvard.edu/files/Effects%20of%20growth%20conditions%20on%20cell%20wall%20mass%2C%20chitin%2C%20mannan%2C%20b-glucans%2C%20b-1%2C6-glucan%20and%20on%20the%20sensitivity%20of%20whole%20cells%20to%20zymolyase.pdf

12904232

(Abstract:) "Chemical and enzymatic methods were used to determine levels of beta-1,3-glucan and 1,6-glucan, mannan and chitin of the yeast cell wall, whereas the structure/resistance of the wall was qualitatively assessed by the sensibility to the lytic action by zymolyase."

Dry weight. Growth rate µmax=0.42 hour^-1. BNID 104588 gives value of 30 percent of total cell dry weight

Uri M

Extracellular matrix, mass, dry weight<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7575

104593

Fraction of cell wall out of total cell mass when grown on ethanol

Budding yeast Saccharomyces cerevisiae

10.8

±1.5 Table link - http://bionumbers.hms.harvard.edu/files/Effects%20of%20growth%20conditions%20on%20cell%20wall%20mass%2C%20chitin%2C%20mannan%2C%20b-glucans%2C%20b-1%2C6-glucan%20and%20on%20the%20sensitivity%20of%20whole%20cells%20to%20zymolyase.pdf

12904232

Dry weight. Growth rate µmax=0.13 hour^-1. Please note that BNID 104588 gives value of 30 percent of total cell dry weight

Uri M

Extracellular matrix, mass, dry weight, Percent<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7656

104675

Rule of thumb for time it takes a small molecule (lactate) to diffuse across the cell

Budding yeast Saccharomyces cerevisiae

0.01

sec

Calculated according to yeast cell diameter. Please see Measurement Method

Taking X, distance to be traveled, as 4.5µm (BNID 100 451) and D of lactate in cytoplasm of erythrocyte in rat, 210 µm^2/sec BNID 104644. According to equation of diffusion (in 3 dimensions): t diffusion=X^2/(6×D). (4.5µm)^2/1260µm^2/sec=0.016secË0.01sec.

Uri M

lactic acid, diffusion, small molecule, metabolite<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7688

104708

Fraction of nuclear volume out of cell volume

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Summary%20of%20nuclear%20and%20cell%20size%20distributions%20in%20asynchronous%20cultures.pdf

Jorgensen P, Edgington NP, Schneider BL, Rupes I, Tyers M, Futcher B. The size of the nucleus increases as yeast cells grow. Mol Biol Cell. 2007 Sep18(9):3523-32. p.3527 table 2

17596521

Electron microscopy

P.3525 right column bottom paragraph: "Indeed, the cross-sectional nuclear areas measured in the small cell populations, and the large cell populations generated by CLN3 manipulation were significantly different from the nuclear areas measured in wild-type cells in the same medium (Figure 2A, Table 2, Student's t tests, p < 10^â15). The differences in the nuclear areas appeared to be roughly proportional to the differences in cell volume measured with a Coulter particle analyzer (Figure 2B). To estimate nuclear volumes, [investigators] assumed that the nuclei were spherical, which is true or nearly true (Winey et al., 1997). The N/C ratio determined from population averages was quite constant, such that nuclear volume was 6â8% of cell volume, even though these alterations in CLN3 activity generated twofold differences in average cell volume (Table 2)." See nuclear volume of 2.9 µm^3 BNID 100447, for fraction of nucleus out of total cell volume in HeLa see comments section of BNID 101402. For fraction of nucleus volume out of total erythrocyte volume in chicken see BNID 104642

Uri M

organelle, Nucleus, Size

7689

104709

Summary of nuclear and cell size distributions in asynchronous cultures

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Summary%20of%20nuclear%20and%20cell%20size%20distributions%20in%20asynchronous%20cultures.pdf

Jorgensen P, Edgington NP, Schneider BL, Rupes I, Tyers M, Futcher B. The size of the nucleus increases as yeast cells grow. Mol Biol Cell. 2007 Sep18(9):3523-32. p.3527 table 2

17596521

"All cells in a field were quantified unless they were undergoing anaphase or cytokinesis, that is, if they possessed an elongated nucleus or two separated nuclei. For all experiments, multiple cell fields were imaged. The resulting data were analyzed in Microsoft Excel (Redmond, CA) and in Matlab (MathWorks, Natick, MA). For volume estimates, it was assumed that nuclei and G1 cells were spherical and that measured areas were cross-sections through the centers of these spheres."

"The N/C [nucleus/cell] ratio determined from population averages was quite constant, such that nuclear volume was 6â8% of cell volume, even though these alterations in CLN3 activity generated twofold differences in average cell volume (Table 2)." Table gives values of nuclei and cell volumes for wild type and several mutant strains. See Nuclear volume of 2.9µm^3 BNID 100447

Uri M

average, Budding yeast Saccharomyces cerevisiae, Nuclear, Sizes, volume, Volumes, glucose, galactose, raffinose, GAL-1-CLN-3-1, whi5delta, sch9delta, sfp1delta<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7722

104742

Half life of histone mRNA

Budding yeast Saccharomyces cerevisiae

±2

min

Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002 Apr 30 99(9):5860-5 p.5862 right column 3rd paragraph

11972065

By using DNA microarrays, researchers precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II.

The half-lives of the 4,687 mRNAs analyzed varied widely, ranging from ~3 min to more than 90 min, with a mean of 23 min and median of 20 min. The nucleosome core is composed of four histone subunits, in equimolar proportions, assembled into an octamer (ref 29). The 4 distinguishable histone mRNAs have closely matched, rapid decay rates, with t1/2=7±2min

Uri M

nucleosome, transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7723

104743

Half life of ribosomal protein mRNA

Budding yeast Saccharomyces cerevisiae

±6

min

11972065

By using DNA microarrays, researchers precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II.

The half-lives of the 4,687 mRNAs analyzed varied widely, ranging from ~3 min to more than 90 min, with a mean of 23 min and median of 20 min. The ribosomal proteins are encoded by 137 different mRNAs (there are 59 duplicated genes) (ref 31). The 131 ribosomal protein mRNAs analyzed in this study had remarkably similar half-lives, with t1/2=22±6min

Uri M

ribosome, translation machinery, messenger ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7724

104744

Half life of mRNA of 20S proteasome core protein subunit

Budding yeast Saccharomyces cerevisiae

±3

min

11972065

By using DNA microarrays, researchers precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II.

The half-lives of the 4,687 mRNAs analyzed varied widely, ranging from ~3 min to more than 90 min, with a mean of 23 min and median of 20 min. The 20S proteasome core is a stoichiometric complex of 14 different protein subunits (ref 30). We were able to obtain good measurements of the decay of 13 of the 14 corresponding mRNAs all decayed at closely matched rates, with t1/2 = 13 ± 3 min

Uri M

protein degradation machinery, transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7725

104745

Average ratio of mRNA abundance to its respective protein abundance

Budding yeast Saccharomyces cerevisiae

4200-4800

proteins/mRNA

Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature. 2003. 425(6959) pp.737-41. Table link - http://bionumbers.hms.harvard.edu/files/yeastproteinabundances.xls

14562106

Overall, researchers observe a significant relationship between mRNA levels, as measured by an earlier microarray analysis of log-phase yeast (ref 25), and protein levels (Spearman rank correlation coefficient rs = 0.57). Very abundant mRNAs generally encode for abundant proteins, and the average protein per mRNA ratio remains remarkably constant throughout the full range of mRNA abundances (Fig. 4c, middle, and Supplementary Fig. S4). The average protein per mRNA ratio is 4,800 using this measure of mRNA levels, and is 4,200 using an alternative mRNA abundance measurement based on a microarray analysis comparing mRNA to genomic DNA levels (ref 26) (Supplementary Fig. S4). Note: a comparison of median protein abundance of 2460 copies/cell (BNID 100208) and median mRNA abundance of 1.2 copies/cell (BNID 100204)gives an mRNA/protein ratio greater by a factor of 2. Table link: More than 3000 protein levels. This table is the Supplemental Data from the reference. The proteins are ordered by gene name, but could be sorted based on abundance using the function on Excel.

Uri M

transcript, expression, messenger ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7726

104746

Half life of mRNA of trehalose phosphate synthase complex protein subunit

Budding yeast Saccharomyces cerevisiae

105

±12

min

11972065

By using DNA microarrays, researchers precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II.

The half-lives of the 4,687 mRNAs analyzed varied widely, ranging from ~3 min to more than 90 min, with a mean of 23 min and median of 20 min. The trehalose phosphate synthase complex plays an important role in carbohydrate metabolism and stress responses (refs 32, 33). The mRNAs encoding the four distinct subunits of this stoichiometric complex exhibited uniformly slow decay rates, with t1/2 =105±12 min

Uri M

degradation, transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7770

104790

Cleavage rate of pyrophosphate into Pi by Yeast inorganic pyrophosphatase

Budding yeast Saccharomyces cerevisiae

432.3

nmole Pi/min/ug PPi

Kent RB, Guterman SK. Pyrophosphate inhibition of rho ATPase: a mechanism of coupling to RNA polymerase activity. Proc Natl Acad Sci U S A. 1982 Jul 79(13):3992-6. Table 3

6125940

Preparation of p and Assay of ATPase, [tritium]Poly(C) Binding Assay, Kinetic Measurements, Pyrophosphatase Assays, Protein Determination,

Assay mixtures containing 0.05 ug of protein were incubated for 1 or 2 min. For PPi cleavage rate in E. coli by rho transcription termination factor See BNIDs 104788-9. See also BNID 104791

Uri M

polymerization, RNA, PPi<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7783

108248

Estimated number of mRNA molecules per cell

Budding yeast Saccharomyces cerevisiae

15000

Molecules/cell

Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999 Mar19(3):1720-30. p.1728 left column top paragraph

10022859

[16] Hereford LM, Rosbash M. Number and distribution of polyadenylated RNA sequences in yeast. Cell. 1977 Mar10(3):453-62.

321129

P.1727 right column bottom paragraph: "For the SAGE method, the error associated with a value increases with a decreasing number of transcripts per cell. The conclusions drawn from this study are dependent on the quality of the mRNA levels from previously published data (ref 35). Since more than 65% of the mRNA levels included in this study were calculated to 10 copies/cell or less (40% were less than 4 copies/cell), the error associated with these values may be quite large. The mRNA levels were calculated from more than 20,000 transcripts. Assuming that the estimate of 15,000 mRNA molecules per cell is correct (primary source), this would mean that mRNA transcripts present at only a single copy per cell would be detected 72% of the time (ref 35). The mRNA levels for each gene were carefully scrutinized, and only mRNA levels for which a high degree of confidence existed were included in the correlation value."

Uri M

transcript abundance, messenger ribonucleic acid

7790

108255

Doubling time of "normal" laboratory haploid strain

Budding yeast Saccharomyces cerevisiae

~90 in YPD [yeast extract peptone dextrose] medium: ~140 in synthetic media

Minutes

F. Sherman, Getting started with yeast, Methods Enzymol. 350, 3-41 (2002). p.15 2nd paragraph

12073320

P.15 2nd paragraph: ""Normal" laboratory haploid strains have a doubling time of ~90 minutes in YPD medium and ~140 minutes in synthetic media during the exponential phase of growth. However, strains with greatly reduced growth rates in synthetic media are often encountered. Usually strains reach a maximum density of 2 × 10^8 cells/ml in YPD medium. Titers 10 times this value can be achieved with special conditions, such as pH control, continuous additions of balanced nutrients, filtered-sterilized media, and extreme aeration that can be delivered in fermentors."

Uri M

division, generation time

7791

108256

Maximum density of strains in YPD [yeast extract peptone dextrose] medium

Budding yeast Saccharomyces cerevisiae

200000000

Cells/ml

F. Sherman, Getting started with yeast, Methods Enzymol. 350, 3-41 (2002). p.15 2nd paragraph

12073320

P.15 2nd paragraph: "Growth and Size: "Normal" laboratory haploid strains have a doubling time of approximately 90 min in YPD medium (see below) and approximately 140 min in synthetic media during the exponential phase of growth. However, strains with greatly reduced growth rates in synthetic media are often encountered. Usually strains reach a maximum density of 2×10^8 cells/ml in YPD medium. Titers 10 times this value can be achieved with special conditions, such as pH control, continuous additions of balanced nutrients, filtered-sterilized media, and extreme aeration that can be delivered in fermentors."

Uri M

concentration, growth

7792

108257

Size of (ellipsoid) diploid cell

Budding yeast Saccharomyces cerevisiae

5 Ñ 6

Î¼m

F. Sherman, Getting started with yeast, Methods Enzymol. 350, 3-41 (2002). p.15 bottom paragraph

12073320

[65] Mortimer RK. Radiobiological and genetic studies on a polyploid series (haploid to hexaploid) of Saccharomyces cerevisiae. Radiat Res. 1958 Sep9(3):312-26. doi: 10.2307/3570795

13579200

p.15 bottom paragraph: "The sizes of haploid and diploid cells vary with the phase of growth (ref 64) and from strain to strain. Typically, diploid cells are 5 × 6µm ellipsoids and haploid cells are 4µm diameter spheroids (primary source). The volumes and gross composition of yeast cells are listed in Table V. During exponential growth, haploid cultures tend to have higher numbers of cells per cluster compared to diploid cultures. Also, haploid cells have buds that appear adjacent to the previous one, whereas diploid cells have buds that appear at the opposite pole (ref 66)." The sizes of haploid and diploid cells vary with the phase of growth and from strain to strain.

Uri M

concentration

7793

108258

Diameter of (spheroid) haploid cell

Budding yeast Saccharomyces cerevisiae

Î¼m

F. Sherman, Getting started with yeast, Methods Enzymol. 350, 3-41 (2002). p.15 bottom paragraph

12073320

[65] Mortimer RK. Radiobiological and genetic studies on a polyploid series (haploid to hexaploid) of Saccharomyces cerevisiae. Radiat Res. 1958 Sep9(3):312-26. doi: 10.2307/3570795

13579200

P.15 bottom paragraph: "The sizes of haploid and diploid cells vary with the phase of growth (ref 64) and from strain to strain. Typically, diploid cells are 5 × 6µm ellipsoids and haploid cells are 4µm diameter spheroids (primary source). The volumes and gross composition of yeast cells are listed in Table V. During exponential growth, haploid cultures tend to have higher numbers of cells per cluster compared to diploid cultures. Also, haploid cells have buds that appear adjacent to the previous one, whereas diploid cells have buds that appear at the opposite pole (ref 66)." The sizes of haploid and diploid cells vary with the phase of growth and from strain to strain.

Uri M

size, radius, shape, dimension

7801

108266

Cell wall thickness

Budding yeast Saccharomyces cerevisiae

±15

T Srinorakutara, Determination of Yeast Cell Wall Thickness and Cell Diameter Using New Methods, Journal of Fermentation and Bioengineering, Volume 86, Issue 3, 1998, Pages 253â260 p.257 left column top paragraph and p.256 fig.5

Microscopic and TEM (transmission electron micrographs) observations. Recalculation of âtrueâ cell diameters and cell wall thickness was done using equations, written by Dr. Zhibing Zhang (School of Chemical Engineering, University of Birmingham, UK).

The corrected cell wall thickness obtained from various fermentation conditions in this study was approximately 70±15nm, which is consistent with that reported by Brady et al. (5).

Uri M

width, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7828

108293

Numbers of various organelles and cell components in individual cells

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Numbers%20of%20various%20organelles%20and%20cell%20components%20in%20individual%20S.%20cerevisiae%20cells.pdf

organelle or component/cell

Yamaguchi M, Namiki Y, Okada H, Mori Y, Furukawa H, Wang J, Ohkusu M, Kawamoto S. Structome of Saccharomyces cerevisiae determined by freeze-substitution and serial ultrathin-sectioning electron microscopy. J Electron Microsc (Tokyo). 2011 60(5):321-35. doi: 10.1093/jmicro/dfr052. p.325 table 1

21908548

P.322 left column 2nd paragraph: "Here, [Researchers] report the structome of S. cerevisiae strain S288c determined by freeze substitution and serial ultrathin-sectioning electron microscopy."

P.329 right column 3rd paragraph: "[Researchers] enumerated the total number of ribosome particles in S. cerevisiae cells the number ranged from 183,000 to 272,000 (Table 1). The number per unit volume of cytosol, however, was relatively constant at â¼20,000/µm^3 (Table 1)." P.331 left column 2nd & 3rd paragraphs: "Vacuoles, autophagosomes and multivesicular bodies: There were one to two vacuoles in a cell (Table 1). The total vacuolar volume in this stage was 0.1â0.9 µm^3 and occupied 1â5% of the cell volume (Table 2, Fig. 3). The ratio of total vacuolar volume in Cell 4â6 is shown in Fig. 6. One or two autophagosomes were present in this stage (Table 1) and occupied 0.01â0.1% of cell volume (Table 2). There were no multivesicular bodies in this stage (Table 1). Ribosomes and cytosol: There were 115,000â239,000 ribosome particles in this stage (Table 1). The number per unit volume of cytosol was â¼20,000/µm^3 (Table 1). Cytosol occupied â¼68% of the cell volume (Table 2)."

Uri M

Nucleus, Nucleolus, Spindle pole body, Mitochondria, ERs/Golgi apparatus, Vacuoles, Autophagosomes, Multivesicular bodies, Ribosomes, Small vesicles, Filasomes, Virus-like particles, Peroxisomes, Invaginations

7829

108294

Volumetric measurement of cells and cell components

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Volumetric%20measurement%20of%20S.%20cerevisiae%20cells%20and%20cell%20components.pdf

Î¼m^3

21908548

P.322 left column 2nd paragraph: "Here, [Researchers] report the structome of S. cerevisiae strain S288c determined by freeze substitution and serial ultrathin-sectioning electron microscopy."

P.327 right column bottom paragraph: "The nucleus, nuclear envelope, nuclear pore and nucleolus: The nucleus was enclosed by a double-layered nuclear envelope (Fig. 1i). The nucleus in interphase cell was spherical (Fig. 1i), â¼1.6 µm in diameter (Table 3) and â¼1.8 µm^3 in volume, occupying â¼10.5% of the cell volume (Table 2, Fig. 4). The nuclear envelope consisted of the outer and inner envelopes. Both measured â¼13 nm in thickness (Table 4). The nuclear pore was â¼94 nm in diameter (Table 3) and is known to function in the transport of substances between the nucleoplasm and cytoplasm [ref 15]. There was only one nucleolus in a nucleus (Table 1). The nucleolus was composed of densely packed granular materials (Fig. 1i) â¼0.4 µm^3 in volume and occupied â¼22% of the nuclear volume (Table 2)." P.329 right column bottom paragraph: "The volume of cytosol was calculated by subtracting the volume of all organelles and cell components (from cell wall to multivesicular bodies, but not nucleolus, in Table 2) from the cell volume. Cytosol occupied ~64% of the cell volume (Table 2, Fig. 4)." P.330 right column 6th paragraph: "The nucleus, nuclear envelope, nuclear pore and nucleolus: The nucleus was ~1.3 Î¼m^3 in volume and occupied ~10% of the cell volume (Table 2, Fig. 3), whereas the nucleolus was ~0.2 Î¼m^3 in volume and occupied ~16% of the nuclear volume (Table 2)." See notes beneath table

Uri M

Nucleus, Nucleolus, Mitochondria, ERs/Golgi apparatus, Vacuoles, Autophagosomes, Multivesicular bodies, cytosol, volume, size

7830

108295

Length and diameter of cell and various components

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Length%20and%20diameter%20of%20S.%20cerevisiae%20cell%20and%20various%20components.pdf

21908548

P.322 left column 2nd paragraph: "Here, [Researchers] report the structome of S. cerevisiae strain S288c determined by freeze substitution and serial ultrathin-sectioning electron microscopy."

P.327 right column bottom paragraph: "The nucleus, nuclear envelope, nuclear pore and nucleolus: The nucleus was enclosed by a double-layered nuclear envelope (Fig. 1i). The nucleus in interphase cell was spherical (Fig. 1i), â¼1.6 µm in diameter (Table 3) and â¼1.8 µm^3 in volume, occupying â¼10.5% of the cell volume (Table 2, Fig. 4). The nuclear envelope consisted of the outer and inner envelopes. Both measured â¼13 nm in thickness (Table 4). The nuclear pore was â¼94 nm in diameter (Table 3) and is known to function in the transport of substances between the nucleoplasm and cytoplasm [ref 15]." P.329 right column 2nd paragraph: "Multivesicular bodies were spherical membrane-bound organelles containing microvesicles (Fig. 1e) [refs 18,19]. These microvesicles were â¼39 nm in diameter (Table 3). Up to five multivesicular bodies were present in a cell (Table 1), having an average length and diameter of 206 and 186 nm, respectively (Table 3)." P.330 left column 4th paragraph: "Microtubules (Fig. 1m) had a diameter of ~25 nm (Table 3). Most microtubules were associated with the SPB [spindle pole body] and few were found in the cytoplasm. Microfilaments (Fig. 1n) were of ~7 nm thick (Table 3)."

Uri M

Cell, Nucleus, Nuclear pores, Spindle pole body, Mitochondria, Vacuoles, Autophagosomes, Multivesicular, bodies, Microvesicles in, multivesicular, bodies, Ribosomes, Small vesicles, Filasomes, Virus-like particle, Microtubules, Microfilaments, size

7831

108296

Membrane thickness of various organelles

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Membrane%20thickness%20of%20various%20organelles.pdf

21908548

P.322 left column 2nd paragraph: "Here, [Researchers] report the structome of S. cerevisiae strain S288c determined by freeze substitution and serial ultrathin-sectioning electron microscopy."

P.330 left column bottom paragraph to right column 2nd paragraph: "The plasma membrane and membrane systems: The plasma membrane was â¼15.6 nm thick and consisted of three leaflets (Fig. 1a, Table 4). The outer leaflet was electron dense, the middle leaflet was electron transparent and the inner leaflet was electron dense. They measured â¼4.6, 3.8 and 7.3 nm, respectively (Table 4). The plasma membrane was invaginated into cytoplasm in certain places (Fig. 1b). There were 20â45 invaginations in each cell (Table 1). Membranes of S. cerevisiae might be classified into two groups according to their thickness. The first group had a thickness of 16â19 nm (Table 4) and included the plasma membrane (Fig. 1a), vacuolar membrane (Fig. 1o), membranes of autophagosomes (Fig. 1d) and multivesicular body (Fig. 1e). The second group had a thickness of 13â14 nm (Table 4) and included the outer and inner nuclear envelope (Fig. 1m), ER/Golgi membranes (Fig. 1a and g) and mitochondrial outer membrane (Fig. 1c)."

Uri M

Plasma membrane, Vacuole, Autophagosome, Multivesicular body, Nuclear outer envelope, Nuclear inner envelope, ER/Golgi apparatus, Mitochondrial outer, membrane, size, width

7838

108303

Comparison of growth rates and rRNA synthesis rates in two FOB1 deletion strains in YPD medium

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Comparison%20of%20growth%20rates%20and%20rRNA%20synthesis%20rates%20in%20two%20FOB1%20deletion%20strains%20in%20YPD%20medium.pdf

French SL, Osheim YN, Cioci F, Nomura M, Beyer AL. In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol Cell Biol. 2003 Mar23(5):1558-68. p.1560 table 1

12588976

"Multiple chromatin spreads from multiple cultures of yeast cells were visualized for each strain, and two to four Miller spread preparations were quantitatively analyzed for each strain."

The top strain is control for number of rRNA genes. See notes beneath table.

Uri M

doubling time, division time, ribosomal rna<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7839

108304

Growth rates on different media

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Growth%20rates%20on%20different%20media.pdf

Waldron C, Lacroute F. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol. 1975 Jun122(3):855-65. p.856 table 1

1097403

"Growth of liquid cultures was monitored turbidimetrically in a Klett-Summerson colorimeter, using a red filter (about 670 nm) for medium C and a blue filter (about 430 nm) for the other media."

Uri M

glucose, fructose, lactose, ethanol, generation time, doubling time, division time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7843

108308

RNAPol I density (per rRNA gene)

Budding yeast Saccharomyces cerevisiae

one polymerase/132 nts

12588976

"These polymerase densities are similar to the average seen in the control yeast strain in our study: one polymerase/132 nt (Fig. 5)."

Uri M

transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7847

108312

Ratio between size of diploid and haploid cells

Budding yeast Saccharomyces cerevisiae

Unitless

Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ. Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell. 2004 Aug15(8):3841-62. p.3848 left column top paragraph

15169868

Lorincz, A., and Carter, B.L.A. (1979). Control of cell size at bud initiation in Saccharomyces cerevisiae. J. Gen. Microbiol. 113, 287â295. doi: 10.1099/00221287-113-2-287

"A diploid cell is twice as big as a haploid cell (primary source)".

Uri M

volume<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7848

108313

Concentration of Cln2

Budding yeast Saccharomyces cerevisiae

~50

Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ. Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell. 2004 Aug15(8):3841-62. p.3848 left column top paragraph

15169868

"From our model, the average value of [Cln2] over a full cycle is 1.25 au therefore, 1 au of Cln2 (or Clb2 or Sic1) corresponds to a concentration of ~40 nM, or 1200 molecules per haploid cell."

Uri M

cyclin protein,abundance<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7850

108315

Size and composition of yeast cells

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Size%20and%20composition%20of%20yeast%20cells.pdf

Sherman F. Getting started with yeast. Methods Enzymol. 2002 350: 3-41. p.15 table V

12073320

Uri M

deoxyribonucleic acid, genetic material, content, DNA, weight, volume, composition, wet weight, dry weight, RNA, protein, haploid, diploid

7852

108318

pH of vacuole

Budding yeast Saccharomyces cerevisiae

6.17

unitless

Preston RA, Murphy RF, Jones EW. Assay of vacuolar pH in yeast and identification of acidification-defective mutants. Proc Natl Acad Sci U S A. 1989 Sep86(18):7027-31. p.7029 right column 2nd paragraph

2674942

"...[Researchers] developed assays of vacuolar pH using flow cytometry and fluorescence microscopy, based on the pH-dependent fluorescence of 6-carboxyfluorescein (6-CF)."

"Cytometric analysis of wild-type cells labeled with 6-CF showed that vacuolar pH was maintained at 6.17 (SD = 0.07, n = 16) under several different conditions tested." pH of vacuole varies from <5 to 6.5 according to Li et al., 2009 PMID 18786576 p.654 left column bottom paragraph

Uri M

acidity, organelle<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7853

108319

Concentration of K+ of intact yeast cells and spheroplasts

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Concentration%20(mM)%20of%20K%2B%20of%20intact%20yeast%20cells.pdf

Martínez-Muñoz GA, Peña A. In situ study of K+ transport into the vacuole of Saccharomyces cerevisiae. Yeast. 2005 Jul 15 22(9):689-704. p.696 table 3

16034802

See note beneath table

Uri M

potassium content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7907

108373

Common limit on distance of cis-regulatory element away from the transcription start site

Budding yeast Saccharomyces cerevisiae

~800

base pairs

Turner JJ, Ewald JC, Skotheim JM. Cell size control in yeast. Curr Biol. 2012 May 8 22(9):R350-9. p.R350 left column 2nd paragraph

22575477

Dobi KC, Winston F. Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Mol Cell Biol. 2007 Aug27(15):5575-86

17526727

"...whereas metazoan cis regulatory elements are found thousands of base pairs away from the transcription start site, yeast elements are limited to ~800 base pairs upstream [primary source]."

Uri M

gene expression regulation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7909

108375

Coefficient of variation of haploid cell size at budding

Budding yeast Saccharomyces cerevisiae

~0.17

unitless

Turner JJ, Ewald JC, Skotheim JM. Cell size control in yeast. Curr Biol. 2012 May 8 22(9):R350-9. p.R351 left column 2nd paragraph

22575477

"For haploid cells, the coefficient of variation (standard deviation/mean) of S. pombe cell size at fission is ~0.06, while the coefficient of variation of S. cerevisiae cell size at budding is ~0.17"

Uri M

size,volume<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7910

108376

Daughter cell size as percent of mother cell size under nutrient limitation conditions

Budding yeast Saccharomyces cerevisiae

<20

Turner JJ, Ewald JC, Skotheim JM. Cell size control in yeast. Curr Biol. 2012 May 8 22(9):R350-9. p.R351 left column 3rd paragraph

22575477

Johnston GC, Pringle JR, Hartwell LH. Coordination of growth with cell division in the yeast Saccharomyces cerevisiae. Exp Cell Res. 1977 Mar 1 105(1):79-98.

320023

"Upon nutrient limitation, budding yeast will produce daughter cells less than 20% of the mother cell size [primary source]."

Uri M

size, volume<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

7919

108386

Lipid recovery of the 2-step lipid extraction procedure

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Lipid%20recovery%20of%20the%202-step%20lipid%20extraction%20procedure.pdf

Ejsing CS et al., Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry. Proc Natl Acad Sci U S A. 2009 Feb 17 106(7):2136-41 supplementary table S1

19174513

Lipid Analysis by Quadrupole Time-of-flight Mass Spectrometry (QSTAR Pulsar-i). Lipid Analysis by Linear Ion Trap-orbitrap Mass Spectrometry (LTQ Orbitrap).

Uri M

content,composition<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8099

108567

Thickness of subcellular membranes

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Thickness%20of%20Subcellular%20Membranes.pdf

Schneiter R et al., Electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis of the lipid molecular species composition of yeast subcellular membranes reveals acyl chain-based sorting/remodeling of distinct molecular species en route to the plasma membrane. J Cell Biol. 1999 Aug 23 146(4):741-54. p.746 table II

10459010

"[Researchers] measured membrane thickness of the different fractions on high magnification prints of electron micrographs. The values obtained from this analysis are listed in Table II."

Uri M

microsomes, organelle, Plasma membrane, Golgi membrane, width, size, Lipid particles, Vacuole, Outer mitochondrial membrane, Inner mitochondrial membrane<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8100

108568

Average thickness of subcellular and plasma membranes

Budding yeast Saccharomyces cerevisiae

7.1

±0.4 Table link - http://bionumbers.hms.harvard.edu/files/Thickness%20of%20Subcellular%20Membranes.pdf

10459010

"[Researchers] measured membrane thickness of the different fractions on high magnification prints of electron micrographs. The values obtained from this analysis are listed in Table II."

"The average thickness of the membranes was 7.1±0.4 nm. The plasma membrane was significantly thicker (9.2±0.4 nm), and the lipid particle membrane was significantly thinner (4.5±0.4 nm), as expected for a lipid monolayer that delineates the lipid particles (Leber et al., 1994)."

Uri M

8101

108569

Thickness of plasma membrane

Budding yeast Saccharomyces cerevisiae

9.2

±0.4 Table link - http://bionumbers.hms.harvard.edu/files/Thickness%20of%20Subcellular%20Membranes.pdf

10459010

"[Researchers] measured membrane thickness of the different fractions on high magnification prints of electron micrographs. The values obtained from this analysis are listed in Table II."

Uri M

Plasma membrane,size,width<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8102

108570

Thickness of lipid particle membrane

Budding yeast Saccharomyces cerevisiae

4.5

±0.4 Table link - http://bionumbers.hms.harvard.edu/files/Thickness%20of%20Subcellular%20Membranes.pdf

10459010

"[Researchers] measured membrane thickness of the different fractions on high magnification prints of electron micrographs. The values obtained from this analysis are listed in Table II."

Uri M

size,width<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8103

108571

Phospholipid and sterol composition of subcellular membranes

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Phospholipid%20and%20Sterol%20Composition%20of%20Subcellular%20Membranes.pdf

10459010

Nano-electrospray ionization tandem mass spectrometry (nano-ESI-MS/MS)

Uri M

microsomes,organelle,Plasma membrane,Golgi membrane,Lipid particles,Vacuole,Outer mitochondrial membrane,Inner mitochondrial membrane,Protein,Phospholipid, Ergosterol<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8104

108572

Phosphatidylserine species of yeast subcellular membranes

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/PS%20Species%20of%20Yeast%20Subcellular%20Membranes.pdf

10459010

Nano-electrospray ionization tandem mass spectrometry (nano-ESI-MS/MS)

Uri M

microsomes,organelle,Plasma membrane,Golgi membrane,Lipid particles,Vacuole,Outer mitochondrial membrane,Inner mitochondrial membrane<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8209

108677

YFP Maturation Time

Budding yeast Saccharomyces cerevisiae

±7

Minutes

Gordon, Andrew Colman-Lerner, Alejandro Chin, Tina E. et al. Single-cell quantification of molecules and rates using open-source microscope-based cytometry NATURE METHODS 4(2) pp.175-181 DOI: 10.1038/nmeth1008

17237792

Cycloheximide to block translation. Time-lapse microscopy.

Peccoud

yellow fluorescent protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8210

108678

CFP Maturation Time

Budding yeast Saccharomyces cerevisiae

±9

Minutes

17237792

Cycloheximide to block translation. Time-lapse microscopy.

Peccoud

8311

108780

Relationship of adenine content of yeast extract powders and final cell yields

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Relationship%20of%20Adenine%20Content%20of%20Yeast%20Extract%20Powders%20and%20Final%20Cell%20Yields%20of%20S.%20cerevisiae%20(884)%20Following%20Cultivation%20in%20YEHD%20Medium.pdf

VanDusen WJ, Fu J, Bailey FJ, Burke CJ, Herber WK, George HA. Adenine quantitation in yeast extracts and fermentation media and its relationship to protein expression and cell growth in adenine auxotrophs of Saccharomyces cerevisiae. Biotechnol Prog. 1997 Jan-Feb13(1):1-7. p.4 table 1

9041705

"As can be seen in Table 1, higher adenine levels in the yeast extract powders generally correlated with higher cell mass (dry cell weight, DCW) after a 72 h incubation."

Uri M

cell dry weight, adenine content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8364

108833

Cellular Cu budget

Budding yeast Saccharomyces cerevisiae

520000

atoms/cell

Finney LA, O'Halloran TV. Transition metal speciation in the cell: insights from the chemistry of metal ion receptors. Science. 2003 May 9 300(5621):931-6. p.932 left column bottom paragraph

12738850

[10] Rae TD, Schmidt PJ, Pufahl RA, Culotta VC, O'Halloran TV. Undetectable intracellular free copper: the requirement of a copper chaperone for superoxide dismutase. Science. 1999 Apr 30 284(5415):805-8.

10221913

P.932 left column bottom paragraph: "Free metal ions in the cytoplasm? Copper is one of the more toxic of the essential metals, so the proposal that the cellular Cu budget (in Saccharomyces cerevisiae, corresponding to 5.2×10^5 atoms per cell) operates on a âno free metalâ principle (primary source), employing metal ion chaperone proteins to allocate Cu to some targets, appeals to common sense." See BNID 108840

Uri M

copper, content

8371

108840

Intracellular copper concentration

Budding yeast Saccharomyces cerevisiae

1.3±0.2x10^6

atoms/cell

Meera R Raja, Scott R Waterman, Jin Qiu , Reiner Bleher, Peter R Williamson and Thomas V. O'Halloran, A copper hyperaccumulation phenotype correlates with pathogenesis in Cryptococcus neoformans, Metallomics. 2013 Apr5(4):363-71. doi: 10.1039/c3mt20220h. p.365 right column 2nd paragraph

23511945

[34] J. L. Wolford. Zinc Localization and Quantitation in Specialized Cells and Tissues. Northwestern University, Evanston, IL, 2006.

P.365 right column 2nd paragraph: "Copper quota of C. neoformans is higher than that of S. cerevisiae: [Investigators] next tested whether high levels of copper accumulation was a typical feature of fungal cell growth and compared the copper content in C. neoformans and the non-pathogenic yeast Saccharomyces cerevisiae. To minimize variances due to different media compositions, both of the cell types were grown in YPD media, which contains â¼400 nM copper as analyzed by ICP-MS ([Inductively coupled plasma mass spectrometry], data not shown). While S. cerevisiae contains 1.3 ± 0.2 × 10^6 atoms of copper per cell (primary source) the C. neoformans cells accumulated almost three times that amount of copper per cell, i.e. 3.7 ± 0.7 × 10^6 (Fig. 3). This pathogen clearly accumulates more copper than brewers yeast when grown in culture. To further elucidate whether C. neoformans also accumulates copper to high levels when growing within the cell host and test the copper homeostasis pathways involved, [they] next examined fungal isolates from mouse models." See BNID 108833

Uri M

Cu, content, composition

8474

108943

Size of cell

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Sizes%20of%20various%20cells.pdf

Î¼m

EMD Millipore: Introducing Scepterâ¢ 2.0 Cell Counter

Scepter Sensor Technology

Uri M

radius,diameter,length<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8648

109118

Density of narrow pores (similar to the CHIP28)

Budding yeast Saccharomyces cerevisiae

7×10^12

pores/cm^2

de Marañón IM, Gervais P, Molin P. Determination of cells' water membrane permeability: unexpected high osmotic permeability of Saccharomyces cerevisiae. Biotechnol Bioeng. 1997 Oct 5 56(1):62-70. doi: 10.1002/(SICI)1097-0290(19971005)56:1&lt62::AID-BIT7&gt3.0.CO2-T. p.68 right column 2nd paragraph

18636610

See eq.9 on p.68 right column

Uri M

membrane permeability,aquaporin<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8734

109204

Number of proteins with DNA-binding domains

Budding yeast Saccharomyces cerevisiae

245

Table link - http://bionumbers.hms.harvard.edu/files/Numbers%20of%20DNA-binding%20transcription%20factors%20in%20five%20organisms.pdf

Proteins

Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA. Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol. 2004 Jun14(3):283-91 p.286 table 1

15193307

See notes beneath table

Uri M

gene expression regulation, tf, dna binding domain, Transcription factors<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8738

109208

Number of copies of proteins per cell in budding yeast

Budding yeast Saccharomyces cerevisiae

Database link - http://yeastgfp.yeastgenome.org/

Molecules/cell

Yeast GFP fusion localization database http://yeastgfp.yeastgenome.org/

Wiki:"S. cerevisiae protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD [Saccharomyces Genome Database]."

Uri M

abundance, content, polypeptide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8741

109211

Number of RNA polymerase II holoenzyme in haploid yeast cells

Budding yeast Saccharomyces cerevisiae

2,000 to 4,000

molecules/cell

Lee TI, Young RA. Transcription of eukaryotic protein-coding genes. Annu Rev Genet. 2000 34 :77-137. p.109 3rd paragraph

11092823

Koleske AJ, Young RA. The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem Sci. 1995 Mar20(3):113-6.

7709429

"There are approximately 2000 to 4000 molecules of RNA polymerase II holoenzyme in haploid yeast cells (primary source)." Note-value wasn't located in primary source. For estimated ~1,000molecules/cell see PMID 8133894 p.467 right column 4th paragraph

Uri M

enzyme, abundance,rna polypeptide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8742

109212

Number of selected protein molecules in yeast cells

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20selected%20protein%20molecules%20in%20yeast%20cells.pdf

molecules/cell

Lee TI, Young RA. Regulation of gene expression by TBP-associated proteins. Genes Dev. 1998 May 15 12(10):1398-408. p.1402 table 2

9585500

See pointers to refs beneath table

Uri M

SRBs/RNA polymerase II holoenzyme, RNA polymerase II, TFIIF, TFIIB, TBP, TFIIA, TAFIs, TAFIIs, TAFIIIs, SAGA, Mot1, NC2, Nots, Nontranscriptional components, Ribosomes, Tubulin, ORC<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8814

109284

Percent of ARS Consensus Sequences that are functional (out of 12,000 ACS)

Budding yeast Saccharomyces cerevisiae

3.3

Cayrou C et al., Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res. 2011 Sep21(9):1438-49 p.1438 left column top paragraph

21750104

Nieduszynski CA, Knox Y, Donaldson AD. Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 2006 Jul 15 20(14):1874-9 p.1874 left column bottom paragraph

16847347

P.1438 left column top paragraph: "In Saccharomyces cerevisiae, Oris are identified by specific DNA elements, called Autonomous Replication Sequences (ARS), which have a common AT-rich 11-bp ARS Consensus Sequence (ACS). However, sequence specificity identifies potential Oris but does not determine their selection. Indeed, of the 12,000 ACS present in S. cerevisiae genome only 400 (3.3%) are functional (primary source)."

Uri M

DNA synthesis, polymerization

8918

109396

Number of mitochondria per unit volume

Budding yeast Saccharomyces cerevisiae

Haploid strain 0.85/Î¼m^3: Diploid strain 1.02/Î¼m^3

mitochondria/Î¼m^3

Posakony JW, England JM, Attardi G. Mitochondrial growth and division during the cell cycle in HeLa cells. J Cell Biol. 1977 Aug74(2):468-91. p.485 right column 2nd paragraph

885911

Grimes GW, Mahler HR, Perlman RS. Nuclear gene dosage effects on mitochondrial mass and DNA. J Cell Biol. 1974 Jun61(3):565-74.

4365780

"For the number of mitochondria per unit of cytoplasmic volume, these authors observed values of 0.85/µm^3 and 1.02/µm^3 (haploid and diploid strains, respectively)"

Uri M

content,mitochondria,mitochondrion<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8919

109397

Mitochondria volume

Budding yeast Saccharomyces cerevisiae

Haploid strain 0.16: Diploid strain 0.14

Î¼m^3

Posakony JW, England JM, Attardi G. Mitochondrial growth and division during the cell cycle in HeLa cells. J Cell Biol. 1977 Aug74(2):468-91. p.485 right column 2nd paragraph

885911

Grimes GW, Mahler HR, Perlman RS. Nuclear gene dosage effects on mitochondrial mass and DNA. J Cell Biol. 1974 Jun61(3):565-74.

4365780

"For the number of mitochondria per unit of cytoplasmic volume, these authors observed values of 0.85/µm^3 and 1.02/µm^3 (haploid and diploid strains, respectively) for the mean mitochondrial volume, the values were 0.16µm^3 and 0.14µm^3, respectively."

Uri M

content, mitochondria, mitochondrion<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8984

109462

Number of DNA, Gal4p, Gal180p and Gal3*p molecules in haploid yeast cells in different media

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20different%20molecules%20in%20haploid%20yeast%20cell.pdf

Venkatesh KV, Bhat PJ, Kumar RA, Doshi P. Quantitative model for Gal4p-mediated expression of the galactose/melibiose regulon in Saccharomyces cerevisiae. Biotechnol Prog. 1999 Jan-Feb15(1):51-7. p.54 table 1

9933513

See note beneath table

Uri M

content, composition, dna, gal4p, G80, Gal80p, G3*, Gal3*p<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8991

109469

Nucleic acid and protein content of S. cerevisiae, and cell volume

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Nucleic%20acid%20and%20protein%20content%20of%20S.%20cerevisiae%2C%20and%20cell%20volume.pdf

Weiss RL, Kukora JR, Adams J. The relationship between enzyme activity, cell geometry, and fitness in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1975 Mar72(3):794-8. p.796 table 1

1093169

P.795 right column 2nd paragraph: "Nucleic Acid and Protein Assays: DNA was extracted from a determined number of cells (1 to 5×10^9) with trichloroacetic acid as previously described (ref 4). DNA was determined in the trichloroacetic acid extract by a modified diphenylamine procedure (refs 12, 13). Standard curves were prepared with salmon sperm DNA (Mann). RNA was extracted and assayed as described by Ogur and Rosen (ref 14) with yeast RNA (Sigma) as a standard. Total protein was determined (ref 15) after extraction of a determined number of cells with 1 N NaOH for 24 hr, with bovine serum albumin as a standard."

P.795 right column bottom paragraph: "Macromolecular Composition: The macromolecular composition of haploid and diploid cells was examined during both unlimited and carbon-limited growth. Diploid cells under unlimited (all components of the medium present in excess) growth conditions have 1.57 the volume of haploid cells. However, when diploid cells are grown under conditions of carbon-limitation, they possess exactly the same volume as haploid cells (Table 1). Thus, by varying the conditions of the environment [investigators] can vary cell size independent of the level of ploidy. The DNA contents of such cells are shown in Table 1."

Uri M

DNA, RNA, total protein, size, haploid, diploid, composition

8992

109470

Amino-acid pools in S. cerevisiae

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Amino-acid%20pools%20in%20S.%20cerevisiae.pdf

Weiss RL, Kukora JR, Adams J. The relationship between enzyme activity, cell geometry, and fitness in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1975 Mar72(3):794-8. p.796 table 2

1093169

"The macromolecular composition of haploid and diploid cells was examined during both unlimited and carbon-limited growth."

Uri M

Tryptophan, Arginine, size, haploid, diploid, composition<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8993

109471

Specific activities of tryptophan synthetase and ornithine transcarbamylase

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Specific%20activities%20of%20tryptophan%20synthetase%20and%20ornithine%20transcarbamylase%20in%20S.%20cerevisiae.pdf

Weiss RL, Kukora JR, Adams J. The relationship between enzyme activity, cell geometry, and fitness in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1975 Mar72(3):794-8. p.797 table 3

1093169

"Activities of two enzymes...tryptophan synthetase and ornithine transcarbamylase, were...determined in haploid and diploid cells under the two environmental conditions."

Uri M

haploid, diploid, enzymatics<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8994

109472

Cell surface enzyme activity

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Cell%20surface%20enzyme%20activity%20in%20S.%20cerevisiae.pdf

Weiss RL, Kukora JR, Adams J. The relationship between enzyme activity, cell geometry, and fitness in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1975 Mar72(3):794-8. p.797 table 4

1093169

"For estimation of acid phosphatase activity cells were grown in chemostats, limiting growth with an organic source of phosphate (ß-glycerol phosphate). In order to estimate invertase activity cells were grown in flask culture, in minimal medium, with sucrose as the sole carbon source."

Uri M

haploid, diploid, enzymatics, Acid phosphatase, invertase, size, area, volume<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

8995

109473

Ratio between diploid/haploid cell volume under nonlimiting growth conditions (minimal medium)

Budding yeast Saccharomyces cerevisiae

1.57

Table link - http://bionumbers.hms.harvard.edu/files/Nucleic%20acid%20and%20protein%20content%20of%20S.%20cerevisiae%2C%20and%20cell%20volume.pdf

unitless

Weiss RL, Kukora JR, Adams J. The relationship between enzyme activity, cell geometry, and fitness in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1975 Mar72(3):794-8. Abstract and p.796 table 1

1093169

Uri M

volume,size,haploid,diploid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9051

109529

Percent of Genome that is Genic

Budding yeast Saccharomyces cerevisiae

73.5

Table link - http://bionumbers.hms.harvard.edu/files/Percentage%20of%20non-coding%20DNA%20in%20selected%20sequenced%20genomes.pdf

Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Annotating non-coding regions of the genome. Nat Rev Genet. 2010 Aug11(8):559-71. doi: 10.1038/nrg2814. p.569 table 2

20628352

Includes introns

Avi Flamholz

DNA content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9056

109534

Percent of Genome that is Exonic

Budding yeast Saccharomyces cerevisiae

72.9

Table link - http://bionumbers.hms.harvard.edu/files/Percentage%20of%20non-coding%20DNA%20in%20selected%20sequenced%20genomes.pdf

Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Annotating non-coding regions of the genome. Nat Rev Genet. 2010 Aug11(8):559-71. doi: 10.1038/nrg2814. p.569 table 2

20628352

Excludes introns

Avi Flamholz

DNA content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9057

109535

Rate of mating type switching in heterothallic yeast during mitotic growth

Budding yeast Saccharomyces cerevisiae

~1E-06

switches / generation

Strathern JN, Herskowitz I. Asymmetry and directionality in production of new cell types during clonal growth: the switching pattern of homothallic yeast. Cell. 1979 Jun17(2):371-81. p.371 right column 3rd paragraph

378408

Hawthorne DC. A deletion in yeast and its bearing on the structure of the mating type locus. Genetics. 1963 Dec48: 1727-9. AND Hicks JB, Herskowitz I. Interconversion of Yeast Mating Types I. Direct Observations of the Action of the Homothallism (HO) Gene. Genetics. 1976 Jun83(2):245-58.

14105103, 17248712

Yeasts carrying the "ho" allele are called "heterothallic" meaning that sexes reside in different individuals (with high probability). "Yeast strains differ in the stability of their mating type. In strains carrying the ho allele (âheterothallicâ strains), the MATa and MATa alleles are stable during mitotic growth, with changes from MATa to MATa and from MATa to MATa observed at low frequency (~10^-6) (primary sources)."

Avi Flamholz

sexual reproduction<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9110

109588

Time scales for half of the cells to respond to switching from noninducing medium (raffinose) to galactose

Budding yeast Saccharomyces cerevisiae

Wildtype 1.60: mutant 2.72

hours

Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD. Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet. 2006 Sep38(9):1082-7 p.1083 right column 2nd paragraph

16936734

"[Researchers] simulated and measured experimentally the time courses of the reporter responses in cells switched from noninducing medium (raffinose) to galactose."

"The fluorescence histograms from the time-course experiment (Fig. 3) demonstrate a transiently bimodal distribution of the response in the double-loop-knockout and a uniform rate of response in wild-type cells...[researchers] estimated the time scales for half of the cells to respond as 1.60 h for the wild-type and 2.72 h for the mutant."

Uri M

Gal operon, culture shift<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9111

109589

Molecules per unit volume

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Molecules%20per%20unit%20volume.pdf

16936734

"[Researchers] simulated and measured experimentally the time courses of the reporter responses in cells switched from noninducing medium (raffinose) to galactose."

From SI: âthe unit of volume is 3.57?10^-14 liters (a typical cell volume for haploid yeastâ¦). Similarly, âmolec" appearing as a unit in the kinetic constants for the model represents molecules per unit volume as defined aboveâ¦ [researchers] used the conversion factor of 4.65?10^-8 millimolar/(molec/cell).â See note beneath table

Uri M

Gal operon<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9112

109590

Gal4p molecules per unit volume

Budding yeast Saccharomyces cerevisiae

monomer 0.16: homodimer 308.9

molecules per unit volume

16936734

"[Researchers] simulated and measured experimentally the time courses of the reporter responses in cells switched from noninducing medium (raffinose) to galactose."

Uri M

Gal operon, transcription factor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9113

109591

Gal3p molecules per unit volume

Budding yeast Saccharomyces cerevisiae

4341

Table link - http://bionumbers.hms.harvard.edu/files/Molecules%20per%20unit%20volume.pdf

molecules per unit volume

16936734

"[Researchers] simulated and measured experimentally the time courses of the reporter responses in cells switched from noninducing medium (raffinose) to galactose."

Uri M

Gal operon, transcription factor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9114

109592

Gal80p monomer molecules per unit volume

Budding yeast Saccharomyces cerevisiae

Nucleus 0.1138: cytoplasm 0.1095

molecules per unit volume

16936734

"[Researchers] simulated and measured experimentally the time courses of the reporter responses in cells switched from noninducing medium (raffinose) to galactose."

Uri M

Gal operon, transcription factor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9115

109593

Gal80p homodimer molecules per unit volume

Budding yeast Saccharomyces cerevisiae

Nucleus 157: cytoplasm 157

molecules per unit volume

16936734

"[Researchers] simulated and measured experimentally the time courses of the reporter responses in cells switched from noninducing medium (raffinose) to galactose."

Uri M

Gal operon, transcription factor<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9173

109651

Biomass yield, residual substrate concentration, and protein content

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Biomass%20yield%2C%20residual%20substrate%20concentration%2C%20and%20protein%20content.pdf

Diderich JA et al., Glucose uptake kinetics and transcription of HXT genes in chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 1999 May 28 274(22):15350-9. p.15353 table II

10336421

P.15351 left column 2nd paragraph: "The aim of the present study was to investigate the regulation of hexose transport in S. cerevisiae under a wide range of defined growth conditions. Glucose transport kinetics were determined for cells grown at a fixed specific growth rate under different nutrient limitations and for cells from aerobic glucose limited chemostat cultures grown at various specific growth rates."

P.15352 right column bottom paragraph: "Other nutrient limitations were investigated in chemostat cultures grown at a fixed dilution rate of 0.10 h^-1. All aerobic hexose-limited cultures were completely respiratory at this dilution rate, as is evident from the absence of fermentation products in culture supernatants, a respiratory quotient close to 1, and a high biomass yield of 0.5 g of biomassâ¢(g of glucose)^-1 (Table II). The anaerobic glucose-limited cultures were completely fermentative, with specific rates of glucose consumption that were 5-fold higher than the aerobic cultures (Table II). Aerobic ethanol-limited cultures served as a reference situation in which no net hexose uptake occurred during growth (Table II)." See note above table

Uri M

Biomass yield, residual substrate concentration, protein content, specific rates (q) of oxygen consumption, carbon dioxide production, glucose consumption, and ethanol production in steady-state chemostat, cultures, S. cerevisiae, ethanol, fructose, galactose, glucose, aerobic, anaerobic

9174

109652

Maximum velocity and Michaelis constant (mM) of glucose transport by cells grown in aerobic glucose-limited chemostats

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Maximum%20velocity%20and%20Michaelis%20constant%20(mM)%20of%20glucose%20transport%20by%20cells%20grown%20in%20aerobic%20glucose-limited%20chemostats.pdf

Diderich JA et al., Glucose uptake kinetics and transcription of HXT genes in chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 1999 May 28 274(22):15350-9. p.15354 table III

10336421

"Glucose transport kinetics were determined for cells grown at a fixed specific growth rate under different nutrient limitations and for cells from aerobic glucose limited chemostat cultures grown at various specific growth rates."

"Cells grown at low dilution rates in aerobic glucose-limited chemostats generally displayed single-component high affinity glucose transport kinetics with a Km of approximately 1 mM (Table III)."

Uri M

velocity, glucose, michaelis menten kinetics, chemostat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9175

109653

Maximum velocity and Michaelis constant (mM) of glucose transport by cells grown in duplicate chemostats with various nutrient limitations at a dilution rate of 0.1 h^-1

Budding yeast Saccharomyces cerevisiae

Diderich JA et al., Glucose uptake kinetics and transcription of HXT genes in chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 1999 May 28 274(22):15350-9. p.15355 table IV

10336421

"The galactose-limited and anaerobic glucose-limited cultures (D=0.1 h^-1) displayed single-component high affinity glucose transport. All of the other cultures examined at this dilution rate displayed both high and low affinity kinetics (Table IV)."

Uri M

velocity, glucose, michaelis menten kinetics, chemostat<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9214

109700

Frequency of petite mutants displaying cytosolic inheritance pattern

Budding yeast Saccharomyces cerevisiae

% per generation

Clark-Walker, G. D., McArthur, C. R., & Daley, D. J. (1981). Does mitochondrial DNA length influence the frequency of spontaneous petite mutants in yeasts? Current Genetics, 4(1), 7â12. doi:10.1007/BF00376779

Avi Flamholz

petite, mutant, mitochondria, inheritance<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9315

109803

Comparison of the steady-state glucose consumption rate with the zero trans-influx kinetics of glucose transport and the intracellular glucose concentration in derepressed and repressed cells

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Comparison%20of%20the%20steady-state%20glucose%20consumption%20rate%20with%20the%20zero%20trans-influx%20kinetics%20of%20glucose%20transport.pdf

Teusink B, Diderich JA, Westerhoff HV, van Dam K, Walsh MC. Intracellular glucose concentration in derepressed yeast cells consuming glucose is high enough to reduce the glucose transport rate by 50%. J Bacteriol. 1998 Feb180(3):556-62. p.559 table 1

9457857

"[Researchers] developed a new method to measure intracellular glucose concentrations in cells metabolizing glucose, which compares glucose stereoisomers to correct for adhering glucose."

Uri M

Measured intracellular glucose concentration, glucose, consumption rate, Derepressed cells, Repressed cells<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9316

109804

Glucose concentration in derepressed cells

Budding yeast Saccharomyces cerevisiae

~1.5 Table link - http://bionumbers.hms.harvard.edu/files/Comparison%20of%20the%20steady-state%20glucose%20consumption%20rate%20with%20the%20zero%20trans-influx%20kinetics%20of%20glucose%20transport.pdf

9457857

Abstract: "To determine if this regulation of glucose transport might be a consequence of intracellular free glucose [investigators] developed a new method to measure intracellular glucose concentrations in cells metabolizing glucose, which compares glucose stereoisomers to correct for adhering glucose."

Abstract: "The intracellular glucose concentration was 1.5 mM, much higher than in most earlier reports." P.558 right column 2nd paragraph: "In the case of the derepressed cells described above, the calculated glucose consumption rate was very similar to the measured rate. Clearly, in derepressed cells consuming glucose, the intracellular glucose concentration is of sufficient magnitude to reduce the flux through the carrier by 50% (see Table 1). Further, the high-affinity transport system present in these cells is close to saturation at 13.3 and 34 mM extracellular glucose so it is not surprising that both the glucose consumption rates and the intracellular glucose concentrations were similar at these extracellular glucose concentrations (Table 1). Carryover of extracellular glucose, however, should differ greatly between these two cases, strongly suggesting that [investigators'] correction for carryover was effective."

Uri M

Measured intracellular glucose concentration, glucose, carbohydrate

9374

109862

Mitochondrial pH during exponential growth on glucose

Budding yeast Saccharomyces cerevisiae

7.5

pH units

19118367

Measured using mitochondrially targeted pH-sensitive GFP.

Avi Flamholz

9375

109863

Cytosolic pH during exponential growth on glucose

Budding yeast Saccharomyces cerevisiae

7.2

pH units

Orij, Rick, et al. "In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth." Microbiology 155.1 (2009): 268-278. doi: 10.1099/mic.0.022038-0. abstract, p.274 right column bottom paragraph & p.275 right column bottom paragraph

19118367

Measured using cytosolically targeted pH-sensitive GFP.

"The in vivo measurement allowed accurate determination of organelle-specific pH, determining a constant pHcyt of 7.2 and a constant pHmit of 7.5 in cells exponentially growing on glucose." "[Researchers] determined a pHcyt of 7.2±0.2 and a pHmit of 7.5±0.2 in cells growing on glucose. These specific pH values appear to be tightly regulated and maintained in a broad range of external pH values, ranging from pH 3.0 to 7.5 (Figs 2c, 5aâc and 6). Previously reported pHi values were lower (Bracey et al., 1998 Fernandes et al., 2003 Guldfeldt & Arneborg, 1998). This is most likely due to the methods used, which determine an average pH over whole cells including the vacuole. This will result in significantly lower values."

Avi Flamholz

9388

109876

Typical replicon size

Budding yeast Saccharomyces cerevisiae

~100

Koren A, Soifer I, Barkai N. MRC1-dependent scaling of the budding yeast DNA replication timing program. Genome Res. 2010 Jun20(6):781-90. doi: 10.1101/gr.102764.109. p.783 right column 3rd paragraph

20219942

"a distance of ~100 kb, [is] comparable to a typical replicon size"

Uri M

origin of replication<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9424

109913

Transcription elongation rate

Budding yeast Saccharomyces cerevisiae

~40 table link - http://bionumbers.hms.harvard.edu/files/Modeled%20Lifetimes%20and%20Processing%20Times%20for%20Pre-rRNA%20Intermediates%20Resolved%20by%20Metabolic%20Labeling.pdf

nts/sec

Kos M, Tollervey D. Yeast pre-rRNA processing and modification occur cotranscriptionally. Mol Cell. 2010 Mar 26 37(6):809-20. doi: 10.1016/j.molcel.2010.02.024. abstract and p.811 left column 4th paragraph and p.816 table 1 & p.817 right column 5th paragraph

20347423

P.817 right column 3rd paragraph: "[Researchers] report the development of techniques for sampling metabolically labeled yeast cells at 10 s intervals, and the use of the derived quantitative data to populate a mathematical model of the processing pathway."

P.817 right column 5th paragraph: "With this insight,the transcription time of 35S synthesis can be reliably determinedâfrom the time required to reach steady state, less the label equilibration time and the 35S life-time, which [researchers] knew to be very short (~10 s) (Venema and Tollervey, 1999). At 30°C in [researchers'] strain (which is derived from W303), this was found to be 170 s, corresponding to 40 nt/s."

Uri M

rna synthesis, speed

9425

109914

Modeled lifetimes and processing times for pre-rRNA intermediates resolved by metabolic labeling

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Modeled%20Lifetimes%20and%20Processing%20Times%20for%20Pre-rRNA%20Intermediates%20Resolved%20by%20Metabolic%20Labeling.pdf

Kos M, Tollervey D. Yeast pre-rRNA processing and modification occur cotranscriptionally. Mol Cell. 2010 Mar 26 37(6):809-20. doi: 10.1016/j.molcel.2010.02.024. p.816 table 1

20347423

"[Researchers] report the development of techniques for sampling metabolically labeled yeast cells at 10 s intervals, and the use of the derived quantitative data to populate a mathematical model of the processing pathway."

RTC=released transcript cleavage. NTC=nascent transcript cleavage. "Figure 4 shows the final fit of full model to the various prerRNAs and rRNAs obtained by manual adjustment of the initial parameters. Values of all parameters are listed in Table 1."

Uri M

rna synthesis, speed, transcription time, Elongation rate, Total time for 25S, RTC, 18S, via NTC, (released transcript cleavage, RTC)<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9447

109936

ATP turnover of proteasome

Budding yeast Saccharomyces cerevisiae

110

±12

ATP/min/26S

Henderson A, Erales J, Hoyt MA, Coffino P. Dependence of proteasome processing rate on substrate unfolding. J Biol Chem. 2011 May 20 286(20):17495-502. doi: 10.1074/jbc.M110.212027 abstract and p.17499 left column bottom paragraph & p.17500 table 2 & p.17501 left column bottom paragraph

21454622

"The ATPase activity reported as number of ATP molecules hydrolyzed per min per doubly-capped 26S proteasome particle...Proteasome ATPase activity was measured in a coupled assay (19, 20) in 25 mM HEPES (pH 7.5), 100 mM KCl, 20 mM MgCl2, 10% glycerol, 250 mU/ml LDH/pyruvate kinase (Sigma), 7.5 mM phospho(enol)pyruvic acid, 1 mM NADH, 2mM DTT, and 5mM ATP."

"ATP turnover was 110/min./proteasome, and was not markedly changed by substrate...The rate of ATP turnover was 110/proteasome/min. and varied modestly among several independently prepared lots."

Uri M

adenosine triphosphate, protein degradation rate, speed, proteasome, ATP hydrolysis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9469

109958

Mean sizes of peptides generated by Î±3âN and wild type core particle of proteasome

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Mean%20Sizes%20of%20Peptides%20Generated%20by%20a3%3FN%20and%20wild%20type%20core%20particle%20of%20proteasome.pdf

residues (amino acids)

Köhler A, Cascio P, Leggett DS, Woo KM, Goldberg AL, Finley D. The axial channel of the proteasome core particle is gated by the Rpt2 ATPase and controls both substrate entry and product release. Mol Cell. 2001 Jun7(6):1143-52. p.1149 table 1

11430818

"Mean sizes were calculated from the distributions of products obtained by size exclusion chromatography, assuming an average molecular weight of 110 Da for each residue."

"By combining the data for casein and ovalbumin, a mean length of 7.6 residues was obtained for products of wild-type CP, and for openchannel particles, 9.6. These differences were shown to be highly significant by the Mann-Whitney U test (for casein p0.01, for ovalbumin p0.001). An even larger relative difference was seen in the median peptide size (Table 1)."

Uri M

casein, ovalbumin, protein degradation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9509

109998

Direct sequencing estimates of mutation rate

Budding yeast Saccharomyces cerevisiae

3.30E-10

Table link - http://bionumbers.hms.harvard.edu/files/Direct%20sequencing%20estimates%20of%20mutation%20rates.pdf

mutations/site/generation

Kondrashov FA, Kondrashov AS. Measurements of spontaneous rates of mutations in the recent past and the near future. Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27 365(1544):1169-76. doi: 10.1098/rstb.2009.0286. p.1172 table 1

20308091

Lynch, M. et al. 2008 A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc. Natl Acad. Sci. USA 105, 9272â9277. (doi:10.1073/pnas. 0803466105)

18583475

"As far as quantitative estimates of mutation rate are concerned, a large fraction of them have been obtained in recent studies that use a multigeneration direct sequencing approach (table 1)."

See "comments" column.

Uri M

yeast, Saccharomyces cerevisiae, Mutation rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9510

109999

Direct sequencing estimates of mutation rate in mitochondrion (point mutations)

Budding yeast Saccharomyces cerevisiae

1.20E-08

Table link - http://bionumbers.hms.harvard.edu/files/Direct%20sequencing%20estimates%20of%20mutation%20rates.pdf

mutations/site/generation

20308091

Lynch, M. et al. 2008 A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc. Natl Acad. Sci. USA 105, 9272â9277. (doi:10.1073/pnas. 0803466105)

18583475

"As far as quantitative estimates of mutation rate are concerned, a large fraction of them have been obtained in recent studies that use a multigeneration direct sequencing approach (table 1)."

See "comments" column.

Uri M

yeast,Saccharomyces cerevisiae,Mutation rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9511

110000

Direct sequencing estimates of mutation rate in mitochondrion (indels)

Budding yeast Saccharomyces cerevisiae

7.50E-09

Table link - http://bionumbers.hms.harvard.edu/files/Direct%20sequencing%20estimates%20of%20mutation%20rates.pdf

mutations/site/generation

20308091

Lynch, M. et al. 2008 A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc. Natl Acad. Sci. USA 105, 9272â9277. (doi:10.1073/pnas. 0803466105)

18583475

"As far as quantitative estimates of mutation rate are concerned, a large fraction of them have been obtained in recent studies that use a multigeneration direct sequencing approach (table 1)."

See "comments" column.

Uri M

yeast,Saccharomyces cerevisiae,Mutation rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9528

110017

Phenotypic mutation rates

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Phenotypic%20mutation%20rates.pdf

mutations/genome/generation

Lang GI, Murray AW. Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae. Genetics. 2008 Jan178(1):67-82. doi: 10.1534/genetics.107.071506. p.70 table 2

18202359

"Typically, fluctuation assays are performed in test tubes however, to increase the throughput, [researchers] perform the assays in 96-well plates."

"Using the 96-well format [researchers] can vary the culture volume from 10 to 200 ml and can measure mutation rates over two orders of magnitude (Table 2)." See note beneath table

Uri M

phenotype, dna alteration, mutagenesis,alpha factor,a-factor,canavanine resistance,5-fluoroorotic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9529

110018

Mutation rates at URA3 and CAN1

Budding yeast Saccharomyces cerevisiae

3.8e-10 at URA3: 6.44e-10 at CAN1

1/bp/generation

Lang GI, Murray AW. Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae. Genetics. 2008 Jan178(1):67-82. doi: 10.1534/genetics.107.071506. p.68 right column top paragraph

18202359

"Typically, fluctuation assays are performed in test tubes: however, to increase the throughput, [researchers] perform the assays in 96-well plates."

"Combining...estimates of phenotypic mutation rates and locus-specific effective target sizes, [researchers] conclude that the per-base-pair mutation rates at URA3 and CAN1 are 3.80?10^-10 and 6.44?10^-10/bp/generation, respectively, suggesting that the mutation rate varies across the yeast genome."

Uri M

phenotype, dna alteration, mutagenesis, ura3, can1<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9530

110019

Transcription Fidelity In Vitro

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Rpb1-E1103G%20Mutation%20Decreases%20Transcription%20Fidelity%20In%20Vitro.pdf

Kireeva ML. et al., Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol Cell. 2008 Jun 6 30(5):557-66. doi: 10.1016/j.molcel.2008.04.017. p.561 table 1

18538654

P.561 caption beneath table 1: "TEC9 [elongation complex containing a 9 nt transcript] was obtained on the template 45C and chased with 5â500 mM CTP or 0.1â5 mM UTP. The error values for kpol and KD estimates were obtained from the hyperbolic fit as described in the Supplemental Experimental Procedures."

P.560 left column bottom paragraph: "Comparisons of incorporation and misincorporation rates at physiological concentrations of NTPs by the WT and mutant Pol II variants provide only an estimation of the impact of the mutation on transcription fidelity. Because the mutation may affect the polymerization rates and the affinity to the nucleotide substrate, fidelity is calculated as the ratio of kpol/KD for the correct NTP to kpol/KD for the incorrect substrate (Wong et al., 1991). The apparent maximal polymerization rate, kpol, and the apparent dissociation constant, KD, were obtained for the WT and E1103G Pol II from the hyperbolic dependence of the reaction rates on the NTP concentration as described in the Supplemental Experimental Procedures. The resulting parameters are shown in Table 1."

Uri M

ctp, utp, kpol, turnover rate, rna polymerase

9531

110020

Number of (2 major) modifications to pre-rRNA: methyl group additions and pseudouridylation

Budding yeast Saccharomyces cerevisiae

67 2'-O-ribose methylations: 44 pseudouridylations

modifications

Woolford JL Jr, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics. 2013 Nov195(3):643-81. doi: 10.1534/genetics.113.153197. p.649 left column 3rd paragraph

24190922

Balakin, A. G., L. Smith, and M. J. Fournier, 1996 The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86: 823â834. & Kiss-Laszlo, Z., Y. Henry, J. P. Bachellerie,M. Caizergues-Ferrer, and T. Kiss, 1996 Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85: 1077â1088. & Ganot, P., M. L. Bortolin, and T. Kiss, 1997 Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89: 799â809. & Liang, X. H., Q. Liu, and M. J. Fournier, 2009 Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays prerRNA processing. RNA 15: 1716â1728. & Watkins, N. J., and M. T. Bohnsack, 2012 The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. Wiley Interdiscip. Rev. RNA 3: 397â414.

8797828, 8674114, 9182768, 19628622, 22065625

"The two major classes of snoRNPs that modify the prerRNA are named for their respective conserved snoRNA sequence motifs (Kiss et al. 2010 Watkins and Bohnsack 2012). The box H/ACA snoRNPs catalyze pseudouridylation at 44 sites on the rRNA, while the box C/D snoRNPs catalyze 2'-O-ribose methylation at 67 sites (primary sources) (Figure 6 figure - http://bionumbers.hms.harvard.edu/files/Box%20H-ACA%20and%20box%20C-D%20snoRNAs%20target%20pre-RNA%20modification%20via%20base%20pairing.pdf ). For each class of snoRNPs, catalysis is carried out by an enzyme stably associated with the snoRNA and is guided by a short snoRNA sequence."

Uri M

rna modification, Small nucleolar RNAs, snoRNAs<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9532

110021

Percent of the transcripts produced by RNA polymerase II that encode ribosomal proteins and ribosome assembly factors

Budding yeast Saccharomyces cerevisiae

â¥60

Woolford JL Jr, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics. 2013 Nov195(3):643-81. doi: 10.1534/genetics.113.153197. p.645 left column top paragraph

24190922

"RNA polymerases I and III transcribe the rRNAs. The messenger (m)RNAs encoding rproteins and ribosome assembly factors comprise at least 60% of the transcripts produced by RNA polymerase II and ultimately translated by ribosomes."

Uri M

ribosome,mrna,rrna,transcription,protein translation machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9533

110022

Ribosome assembly rate in a rapidly growing cell

Budding yeast Saccharomyces cerevisiae

>2,000

ribosomes/min

Woolford JL Jr, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics. 2013 Nov195(3):643-81. doi: 10.1534/genetics.113.153197. p.645 left column top paragraph

24190922

Warner, J. R., 1999 The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24: 437â440.

10542411

"Not only is this construction project expensive, but also it must be completed many times and in a hurry! More than 2000 ribosomes are assembled each minute in a rapidly growing yeast cell (primary source)." See similar value in BNID 106538

Uri M

ribosome, protein translation machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9534

110023

RNA polymerase I transcription elongation rate

Budding yeast Saccharomyces cerevisiae

40 - 60

nts/sec

Woolford JL Jr, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics. 2013 Nov195(3):643-81. doi: 10.1534/genetics.113.153197. p.645 right column 3rd paragraph

24190922

French, S. L., Y. N. Osheim, F. Cioci, M. Nomura, and A. L. Beyer, 2003 In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol. Cell. Biol. 23: 1558â1568. & Kos, M., and D. Tollervey, 2010 Yeast pre-rRNA processing and modification occur cotranscriptionally. Mol. Cell 37: 809â820.

12588976, 20347423

"In a single typical yeast cell generation, an astonishing 200,000 ribosomes are produced. To achieve this, RNA polymerase I maintains an elongation rate of 40â 60 nt/sec (primary sources). The ribosome biogenesis machinery consisting of pre-rRNA processing and preribosome assembly factors must keep up this demanding rate of pre-rRNA synthesis." See BNID 109913

Uri M

ribosome, protein translation machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9535

110024

Percent of the 150 tandem repeats of the rDNA that are actively transcribed in a typical cell

Budding yeast Saccharomyces cerevisiae

~50

Woolford JL Jr, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics. 2013 Nov195(3):643-81. doi: 10.1534/genetics.113.153197. p.647 right column 2nd paragraph

24190922

Toussaint, M., G. Levasseur, M. Tremblay, M. Paquette, and A. Conconi, 2005 Psoralen photocrosslinking, a tool to study the chromatin structure of RNA polymerase Iâtranscribed ribosomal genes. Biochem. Cell Biol. 83: 449â459.

16094448

[Primary source abstract:] "...the technique of psoralen photocrosslinking has been used successfully both in vitro and in vivo."

"In a typical yeast cell, only about half of the 150 tandem repeats of the rDNA [BNID 100243] are being actively transcribed. The others are maintained in a transcriptionally inactive state. This ratio of active to inactive rDNA genes was discovered by their differential accessibility to the intercalator, psolaren (primary source). The actively transcribed rRNA genes are devoid of histones and are instead covered with the Hmo1 protein (analogous to UBF1 in mammals)."

Uri M

ribosome, protein translation machinery, fraction, transcription<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9536

110025

Number of different assembly factors (proteins) that participate in the formation of ribosomes in addition to ribosomal proteins

Budding yeast Saccharomyces cerevisiae

~200

different factors

Woolford JL Jr, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics. 2013 Nov195(3):643-81. doi: 10.1534/genetics.113.153197. p.652 left column bottom paragraph

24190922

"In addition to r-proteins, ~200 different assembly factors participate in the formation of ribosomes in yeast (Table 3 and Table 4). Most of these proteins are essential and conserved throughout eukaryotes, and all are present in assembling ribosomes. Yeast ribosome assembly factors were first discovered by classic or molecular genetic approaches (Fabian and Hopper 1987 Sachs and Davis 1990 Shuai and Warner 1991 Tollervey et al. 1991 Girard et al. 1992 Lee et al. 1992 Ripmaster et al. 1992 Jansen et al. 1993 Schmitt and Clayton 1993 Berges et al. 1994 Chu et al. 1994 Sun and Woolford 1994)." See BNID 112255

Uri M

ribosome synthesis, translation

9537

110027

Half-lives of specific mRNAs

Budding yeast Saccharomyces cerevisiae

3 to >90

min

Bregman A, Avraham-Kelbert M, Barkai O, Duek L, Guterman A, Choder M. Promoter elements regulate cytoplasmic mRNA decay. Cell. 2011 Dec 23 147(7):1473-83. doi: 10.1016/j.cell.2011.12.005. p.1473 right column 2nd paragraph

22196725

Wang, Y., Liu, C.L., Storey, J.D., Tibshirani, R.J., Herschlag, D., and Brown, P.O. (2002). Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99, 5860â5865.

11972065

(primary source abstract:) "By using DNA microarrays, [researchers] precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II."

"Two major cytoplasmic decay pathways exist. Both are initiated by shortening of the mRNA poly(A) tail. The mRNA can then be exonucleolytically degraded by the exosome from 3' to 5' or by the Xrn1p exonuclease from 5' to 3'. The latter pathway involves removal of the mRNA 5' cap (m(7)GpppN) (Decker and Parker, 1993), which is a prerequisite stage for Xrn1p activity (Coller and Parker, 2004 Larimer et al., 1992 Parker and Song, 2004). Although most yeast mRNAs are degraded by either or both of these pathways, the half-lives of specific mRNAs vary widely, ranging from 3 min to more than 90 min (primary source)."

Uri M

half life, halflife, transcript, degradation, half-life<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9538

110028

Percent of genes that Rap1p transcription activator activates

Budding yeast Saccharomyces cerevisiae

% of genes

22196725

"...a small cis-acting element consisting of two Rap1p-binding sites is required and sufficient to destabilize the transcript. Rap1p is a well-known transcription activator of highly transcribed genes (~5% of the yeast genes). [Researchers] found that depletion of Rap1p leads to the stabilization of mRNAs whose synthesis is activated by this protein. Thus, Rap1p plays a dual role in maintaining the level of specific mRNAs."

Uri M

gene expression, transcription, genome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9539

110029

S phase duration

Budding yeast Saccharomyces cerevisiae

~17

min

Koren A, Soifer I, Barkai N. MRC1-dependent scaling of the budding yeast DNA replication timing program. Genome Res. 2010 Jun20(6):781-90. doi: 10.1101/gr.102764.109. p.782 left column top paragraph

20219942

"The medium used was YPD (1% yeast extract, 2% peptone, 2% dextrose) with addition of Geneticin (200 mg/mL) (GIBCO) or nourseothricin (Nat) (100 mg/mL) (Werner Bioagents) when required. Cells were grown at 30°C."

"S phase duration ranged from ~17 min in wild-type cells to 79 min in the rnr1 mutant (Fig. 1E)"

Uri M

cell cycle, time, dna synthesis<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9638

110128

Molecular mass of DNA polymerases

Budding yeast Saccharomyces cerevisiae

68 to 430 Table link - http://bionumbers.hms.harvard.edu/files/DNA%20polymerases%20in%20Saccharomyces%20cerevisiae.pdf

kDa

Kawasaki Y, Sugino A. Yeast replicative DNA polymerases and their role at the replication fork. Mol Cells. 2001 Dec 31 12(3):277-85. p.278 table 1

11804324

ß (IV) is 68kDa and e (II) is 430kDa

Uri M

replication machinery,molecular weight,epsilon,beta,alpha,delta,phi,sigma,gamma,eta<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9649

110139

Transformation yield

Budding yeast Saccharomyces cerevisiae

1000000

transformants/Î¼g autonomously replicating plasmid DNA

Gietz RD, Schiestl RH. Frozen competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG method. Nat Protoc. 2007 2(1):1-4. doi:10.1038/nprot.2007.17 p.4 "anticipated results"

17401330

"[Researchers] describe a protocol for the production of frozen competent yeast cells that can be transformed with high efficiency using the lithium acetate/single-stranded carrier DNA/PEG method."

"This protocol will yield up to 1?10^6 transformants per µg of autonomously replicating plasmid DNA with a good transforming strain. Plasmids or DNA fragments requiring integration will be less efficient. The frozen competent yeast cells are stable for 6 months to a year with little loss in efficiency."

Uri M

transformation, microgram<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9659

110149

Mean DNA replication rate

Budding yeast Saccharomyces cerevisiae

2.9

0.5-11

kb/min

Sekedat MD, Fenyö D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT. GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol Syst Biol. 2010 6: 353. doi: 10.1038/msb.2010.8 p.2 left column 3rd paragraph

20212525

Raghuraman et al., Replication dynamics of the yeast genome. Science. 2001 Oct 5 294(5540):115-21. DOI: 10.1126/science.294.5540.115 p.119 right column bottom paragraph

11588253

Oligonucleotide microarrays

"A wide range of nucleotide incorporation rates (0.5â11 kb/min) were observed, with a mean of 2.9 kb/min (primary source), whereas a second study reported a comparable mean rate of DNA duplication of 2.8±1.0 kb/min (BNID 110150)." See primary source p.119 right column bottom paragraph:"As with origin activation times, a broad range of fork rates was observed (ref 32 therein), with a mean of 2.9 kb/min and a median of 2.3 kb/min (Fig. 7)."

Uri M

DNA polymerization, average speed<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9660

110150

Mean DNA replication rate

Budding yeast Saccharomyces cerevisiae

2.8

±1.0

kb/min

20212525

Yabuki N, Terashima H, Kitada K (2002) Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7: 781â789

12167157

"A microarray technology was applied to obtain a genome-wide profile of DNA replication and to classify early firing origins."

"A wide range of nucleotide incorporation rates (0.5â11 kb/min) were observed, with a mean of 2.9 kb/min (BNID 110149), whereas a second study reported a comparable mean rate of DNA duplication of 2.8±1.0 kb/min (primary source)."

Uri M

DNA polymerization, average speed<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9661

110151

Mean DNA replication rate

Budding yeast Saccharomyces cerevisiae

1.6

±0.3

kb/min

20212525

"[Researchers] adopted a complementary approach for assaying replication dynamics using whole genome time-resolved chromatin immunoprecipitation combined with microarray analysis of the GINS complex, an integral member of the replication fork."

"Once an active origin fires, the GINS complex moves at an almost constant rate of 1.6±0.3 kb/min. Its movement through the inter-origin regions is consistent with that of a protein complex associated with a smoothly moving replication fork. This progression rate is considerably lower and more tightly distributed than those inferred from previous genome-wide measurements assayed through nascent DNA production (BNID 110149, 110150)."

Uri M

DNA polymerization,average speed<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

9974

110465

Haploid cell volumes in the different cell cycle stages

Budding yeast Saccharomyces cerevisiae

G1 phase 10-50µm^3: S phase 20-60µm^3: G2 phase 40-80µm^3 M phase 60-100µm^3

µm^3

Uchida M, Sun Y, McDermott G, Knoechel C, Le Gros MA, Parkinson D, Drubin DG, Larabell CA. Quantitative analysis of yeast internal architecture using soft X-ray tomography. Yeast. 2011 Mar28(3):227-36. doi: 10.1002/yea.1834. p.230 right column

21360734

Abstract: "[Researchers] used soft X-ray tomography (SXT) a high-resolution, quantitative imaging technique to measure cell size and organelle volumes in yeasts."

P.230 right column: "In haploid cells, the cell volumes were within the range 10â50 µm^3 in G1, 20â60 µm^3 in S, 40â80 µm^3 in G2 and 60â100 µm^3 in M phase...A similar trend of cell volume distribution was also observed in diploid cells of another S. cerevisiae strain (ATCC200060 see supporting information, Figure S1)."

Uri M

gap, cell stage, synthesis, mitosis

9975

110466

Diploid cell volumes in the different cell cycle stages

Budding yeast Saccharomyces cerevisiae

G1 phase 20-60µm^3: S phase 30-80µm^3: G2 phase 50-140µm^3: M phase 70-140µm^3

µm^3

21360734

Abstract: "[Researchers] used soft X-ray tomography (SXT) a high-resolution, quantitative imaging technique to measure cell size and organelle volumes in yeasts."

P.230 right column: "In diploid cells, the cell volumes were within 20â60 µm^3 in G1, within 30â80 µm^3 in S, within 50â140 µm^3 in G2 and within 70â140 µm^3 in M phase...A similar trend of cell volume distribution was also observed in diploid cells of another S. cerevisiae strain (ATCC200060 see supporting information, Figure S1)."

Uri M

gap, cell stage, synthesis, mitosis, size

9976

110467

Minimum size requirement to be in G1 phase

Budding yeast Saccharomyces cerevisiae

haploid cell 10µm^3: diploid cell 20µm^3

µm^3

21360734

Abstract: "[Researchers] used soft X-ray tomography (SXT) a high-resolution, quantitative imaging technique to measure cell size and organelle volumes in yeasts."

P.230 right column: "The minimum size requirement to be in G1 phase was observed to be 10 µm^3 in haploid and 20 µm^3 in diploid cells."

Uri M

gap, cell stage, synthesis, mitosis, size

9977

110468

Fraction of nucleolus out of nucleus volume

Budding yeast Saccharomyces cerevisiae

21360734

Abstract: "[Researchers] used soft X-ray tomography (SXT)a high-resolution, quantitative imaging techniqueto measure cell size and organelle volumes in yeasts." P.230 right column: "The average cytosolic volume (Figure 2C) was calculated by combining the cell wall/membrane volume with the total volume of segmented organelles and then subtracting this combined volume from the total cell volume."

P.231 left column top paragraph: "On average, the nucleus occupied 6â11% of cell volume: the nucleolus occupied 20% of the nucleus: vacuole(s) occupied 3â14% of the cell and mitochondria and lipid bodies occupied 1â2% of the cell (Figure 3): therefore, the cytosol, other nonsegmented organelles, large macromolecular complexes, such as the ribosomes, and the cytoskeleton occupy the remaining 70% of cell volume."

Uri M

nucleus, nuclear volume, size, cell, rrna transcription

9978

110469

Fraction of organelles out of total cell volume

Budding yeast Saccharomyces cerevisiae

nucleus 6-11%: vacuole(s) 3â14%: mitochondria and lipid bodies 1â2%

21360734

Abstract: "[Researchers] used soft X-ray tomography (SXT) a high-resolution, quantitative imaging technique to measure cell size and organelle volumes in yeasts." P.230 right column bottom paragraph: "The average cytosolic volume (Figure 2C) was calculated by combining the cell wall/membrane volume with the total volume of segmented organelles and then subtracting this combined volume from the total cell volume."

Uri M

nucleus, nuclear volume, size, cell, rrna transcription

9979

110470

Fraction of cells that had bud scar(s) on the cell surface

Budding yeast Saccharomyces cerevisiae

no bud scar â67%: one bud scar 14%: two bud scars 12%: three to seven bud scars <6%

21360734

Abstract: "[Researchers] used soft X-ray tomography (SXT) a high-resolution, quantitative imaging technique to measure cell size and organelle volumes in yeasts." P.232 left column bottom paragraph: "To better understand cell size control and organelle inheritance during bud emergence and formation of the daughter cell, [researchers] measured cell and organelle volumes in daughter and mother cells separately. The bud scar(s) on the cell surface was readily identified (an example of bud scars is shown in the supporting information, Figure S2)."

P.232 right column: "In this study, about 67% of cells had no bud scar, 14% of cells had one bud scar, 12% of cells had two bud scars, and <6% of cells had three to seven bud scars."

Uri M

mitosis

10054

110545

Typical population doubling time

Budding yeast Saccharomyces cerevisiae

90 - 120

min

Khmelinskii A et al., Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Nat Biotechnol. 2012 Jun 24 30(7):708-14. doi: 10.1038/nbt.2281. Supporting Online Material p.S7 3rd paragraph

22729030

"...the population doubling time is typically between 90 and 120 min."

Uri M

generation time, division time, growth rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10055

110546

Maturation time for sfGFP (super folded GFP)

Budding yeast Saccharomyces cerevisiae

5.63

±0.82

min

22729030

"Maturation rate constants of sfGFP and mCherry were determined from the induction time course data in two steps (Supplementary Fig. 8a)."

"Maturation rate constants were calculated independently for each cell. Subsequently, final maturation rate constants were determined as medians values (n=35), considering only the sub-population of cells yielding a better than median ?^2 value in model fitting. The obtained maturation half-time [is]... T=5.63±0.82min for sfGFP (median±s.e.m.) (Supplementary Fig. 8a)."

Uri M

chromophore, green fluorescent protein<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10056

110547

Fraction of essential proteins that can accommodate a tag at the C- terminus (without loss of function)

Budding yeast Saccharomyces cerevisiae

~84

22729030

[8] Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. Global analysis of protein localization in budding yeast. Nature. 2003 Oct 16 425(6959):686-91 [9] Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature. 2003. 425(6959) pp.737-41

14562095, 14562106

Supporting Online Material p.S8 3rd paragraph: "C-terminal tagging â The experiments conducted in this study used synthetic constructs and endogenous yeast proteins tagged with mCherry-sfGFP mostly at the C-terminus. Although a tag can influence the marked protein, C-terminal tagging appears to have the lowest likelihood of interfering with protein function and ~84% of essential proteins (total of 1034 essential proteins) in S. cerevisiae can accommodate a tag at the C-terminus [primary sources]."

Uri M

polypeptide, genetic engineering, percent

10057

110548

Fraction of Ste5 in complex with the different MAPKs and quantification of relative MAPK abundances at different sites in yeast cells

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Quantification%20of%20relative%20MAPK%20abundances%20at%20different%20sites%20in%20yeast%20cells.pdf

Maeder CI, Hink MA, Kinkhabwala A, Mayr R, Bastiaens PI, Knop M. Spatial regulation of Fus3 MAP kinase activity through a reaction-diffusion mechanism in yeast pheromone signalling. Nat Cell Biol. 2007 Nov9(11):1319-26. p.1322 figure 3a & 3b

17952059

Fluorescence cross-correlation spectroscopy (FCCS) & Confocal photon-counting (APD, avalanche photodiode detectors) imaging

"Fig.3 (a) FCCS-measured fraction of Ste5 in complex with the different MAPKs. (b) Quantification of relative MAPK abundances at different sites in yeast cells using APD imaging and image analysis (see Methods). The relative abundance of the three kinases (Ste11, Ste7 and Fus3) versus the scaffold Ste5 in vegetative or pheromone stimulated cells is given at the cellular locations indicated in the schematic representations. Cells were stimulated with a-factor for 2.5â3 h. Error values indicate the s.e.m. Abundances at the shmoo tip were quantified in 20â60 cells." "Results for the MAPKs are shown as the relative molar abundances of each component versus Ste5 (Fig. 3a, b). The molar ratio of Ste11 to Ste5 was 0.2 at the shmoo tip and was, therefore, similar to that detected in the cytoplasm by FCCS (Fig. 3a, b)."

Uri M

signalling protein, ste11, ste7, fus3, vegetative cells, pheromone stimulated cells, mitogen-activated protein kinase, MAPK, cascade<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10059

110550

Protein content in a typical haploid yeast cell

Budding yeast Saccharomyces cerevisiae

4 - 5 (~50 million protein molecules/cell)

pg/cell

Carroll KM, Simpson DM, Eyers CE, Knight CG, Brownridge P, Dunn WB, Winder CL, Lanthaler K, Pir P, Malys N, Kell DB, Oliver SG, Gaskell SJ, Beynon RJ. Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach. Mol Cell Proteomics. 2011 Dec10(12):M111.007633. doi: 10.1074/mcp.M111.007633. p.4 right column 3rd paragraph

21931151

"Assuming 4â5 pg of protein from a typical haploid yeast cell and an average protein molecular weight of 50 kDa, this gives a total constituency of ~50 million protein molecules."

Uri M

composition, polypeptide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10061

110552

mCherry maturation half-times (two - step maturation model)

Budding yeast Saccharomyces cerevisiae

T1=16.9±7.3 T2=30.3±11.2

min

22729030

"Cells induced to express a non-degradable mCherry-sfGFP fusion (strain AK1212 carrying the Ubi-M-RR-mCherry-sfGFP construct, which contains two lysine-to-arginine mutations in the degron sequence) were imaged with a fluorescence microscope. Maturation rate constants of mCherry and sfGFP were determined by fitting theoretical maturation models to fluorescence intensity traces of single cells (see Section 1.2)."

"A two-step maturation model for mCherry fitted the data (maturation half-times: TmCherry,1=16.9±7.3min, TmCherry,2=30.3±11.2min, mean±s.d., n=35). Note that m (maturation rate constant)=ln(2)/T."

Uri M

chromophore,green fluorescent protein,maturation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10062

110553

Average protein molecular weight

Budding yeast Saccharomyces cerevisiae

kDa

21931151

Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., and Darnell J. (2000) Hierarchical Structure of Proteins. In Molecular Cell Biology, 4th Ed., W. H. Freeman, New York

"Assuming 4â5 pg of protein from a typical haploid yeast cell and an average protein molecular weight of 50 kDa, this gives a total constituency of ~50 million protein molecules."

Uri M

molecular mass, polypeptide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10063

110554

Glycolytic enzymes per cell

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/Glycolytic%20enzymes%20per%20cell.xls

molecules/cell

21931151

"[Researchers] developed the QconCAT approach for multiplexed absolute quantification (refs 6, 7). In brief, synthetic genes, optimized for heterologous expression in Escherichia coli, encode a single open reading frame that is a concatenation of tryptic peptides, each of which acts as an internal standard (a Q-peptide) for a defined protein. Each analyte protein is represented by at least one, but more preferably two (or more), Q-peptides."

"[Researchers] describe the quantification of enzymes of the glycolytic pathway in Saccharomyces cerevisiae, using the QconCAT strategy, quantifying 27 glycolytic proteins (including isoforms)."

Uri M

PDC1, pdc5, pdc6, adh1, adh2, adh3, adh4, adh5, adh6, tdh1, fba1, pfk1, pfk2, glycolysis, polypeptide<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10064

110555

Quantification of Individual Proteins by AMRT (accurate mass/retention time)

Budding yeast Saccharomyces cerevisiae

Excel table link - http://bionumbers.hms.harvard.edu/files/Quantification%20of%20Individual%20Proteins%20by%20AMRT%20(accurate%20mass-retention%20time).xls

molecules/cell

21931151

"The complete set of quantification data for the enzymes of the pathway are provided in supplemental Table V."

Uri M

FBA1 Fructose 1,6-bisphosphate aldolase, PDC1 Major of three pyruvate decarboxylase isozymes, ADH3 Mitochondrial alcohol dehydrogenase isozyme II, ADH4 Alcohol dehydrogenase type IV, TDH1 Glyceraldehyde-3-phosphate dehydrogenase, TDH3 Glyceraldehyde-3-phosphate dehydrogenase, TPI1 Triose phosphate isomerase, PGK1 3-phosphoglycerate kinase, PGI1 Glycolytic enzyme phosphoglucose isomerase, HXK2 Hexokinase isoenzyme 2, GPM1 Tetrameric phosphoglycerate mutase, GLK1 Glucokinase, ENO2 Enolase, Pyruvate kinase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10065

110556

Number of copies of hexokinase II

Budding yeast Saccharomyces cerevisiae

123000

molecules/cell

21931151

"...for Hexokinase 2 (M1 extract 1), [researchers] obtained 5.4 fmol on column (heavy:light ratio, approximately 20:1), which (combined with the other extracts) gave a total of 123,000 molecules/cell."

Uri M

enzyme abundance<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10066

110557

Number of copies of pyruvate decarboxylase

Budding yeast Saccharomyces cerevisiae

23400

molecules/cell

21931151

"Of the two peptides selected for Pdc6p, IATTGEWDALTTDSEFQK and LPVFDAPESLIK, the former was detected using an SRM [selected reaction monitoring] approach with 23,400 molecules/cell obtained corresponding to ~800 amol on column for the most abundant extract."

Uri M

enzyme abundance<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10082

110573

Measured mean vesicle (of endocytic pathway) diameter

Budding yeast Saccharomyces cerevisiae

Puchner EM, Walter JM, Kasper R, Huang B, Lim WA. Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory. Proc Natl Acad Sci U S A. 2013 Oct 1 110(40):16015-20. doi: 10.1073/pnas.1309676110 p.16017 right column 2nd paragraph

24043832

"Single-molecule superresolution microscopy methods, more commonly known as stochastic optical reconstruction microscopy (23) or photoactivated localization microscopy (24), are based on localizing individual photoactivatable fluorophores through fitting their point-spread functions."

Uri M

average length, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10165

110656

P/O ratios

Budding yeast Saccharomyces cerevisiae

0.71 - 2.4 table link - http://bionumbers.hms.harvard.edu/files/Almitrine%20effects%20on%20oxidative%20phosphorylation%20supported%20by%20different%20substrates.pdf

unitless

Rigoulet M, Ouhabi R, Leverve X, Putod-Paramelle F, Guérin B. Almitrine, a new kind of energy-transduction inhibitor acting on mitochondrial ATP synthase. Biochim Biophys Acta. 1989 Aug 3 975(3):325-9. p.327 table 1

2527061

"ATP/O stoichiometries with different respiratory substrates were determined from the average of phosphorylation rates vs. respiratory rates in two different systems: (i) ATP production was monitored either by glucose 6-phosphate formation in the presence of non-limiting amount of hexokinase, 1 mM MgCl2 and 10 mM glucose, or (ii) by labelled Pi incorporation in adenine nucleotides as described in Ref. 7. These two methods gave identical results indicating that neither contaminating ATPase activity nor adenylate kinase activity changed significantly the ATP synthesis rate estimations."

Heading of table is :"almitrine effects on oxidative phosphorylation supported by different substrates."

Uri M

adenosine triphosphate, oxygen,succinate,almitrine,nadh,glycerol-3-phosphate,2-oxoglutarate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10179

110670

Number of NPC (nuclear pore complexes) in a G1 cell nucleus

Budding yeast Saccharomyces cerevisiae

~90

NPCs/nucleus

Oeffinger M, Zenklusen D. To the pore and through the pore: a story of mRNA export kinetics. Biochim Biophys Acta. 2012 Jun1819(6):494-506. doi: 10.1016/j.bbagrm.2012.02.011. p.498 left column 2nd paragraph

22387213

[57] M. Winey, D. Yarar, T. Giddings, D. Mastronarde, Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three dimensional reconstruction from electron micrographs of nuclear envelopes, Mol. Biol. Cell 8 (1997) 2119â2132.

9362057

Cryo-electron microscopy (cryo-EM), or electron cryomicroscopy,

P.498 left column 2nd paragraph: "Reaching the nuclear periphery is the first step on the way out of the nucleus. Once mRNPs have reached the nuclear periphery, they have to encounter an NPC, interact with its structure and get access to the pore. Thus encountering a nuclear pore is the next step. The surface of the inner nuclear membrane is densely packed with nuclear pore complexes. Cyro-EM studies in yeast have shown that a G1 cell nucleus contains about 90 NPCs [primary source]."

Uri M

nucleus, nuclear pore complex, npc, diffusivity

10180

110671

Typical nuclear surface area

Budding yeast Saccharomyces cerevisiae

7.4

Î¼m^2

22387213

"Cyro-EM studies in yeast have shown that a G1 cell nucleus contains about 90 NPCs (nuclear pore complexes)[ref 57]. Considering a typical nuclear surface area of 7.4 µm^2 and a diameter of an NPC of 100µm [units in error, should be nm], one can calculate that NPCs account for about 10% of the total surface of the inner nuclear membrane [ref 58]."

Uri M

nucleus, nuclear area, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10181

110672

Fraction of the total surface of the inner nuclear membrane that NPCs account for

Budding yeast Saccharomyces cerevisiae

~10

22387213

M.P. Rout, G. Blobel, Isolation of the yeast nuclear pore complex, J. Cell Biol. 123 (1993) 771â783.

8227139

"Cyro-EM studies in yeast have shown that a G1 cell nucleus contains about 90 NPCs (nuclear pore complexes)[ref 57]. Considering a typical nuclear surface area of 7.4µm^2 and a diameter of an NPC of 100µm [units in error, should be nm], one can calculate that NPCs account for about 10% of the total surface of the inner nuclear membrane [primary source]."

Uri M

nucleus, nuclear pore complex, npc, diffusivity<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10182

110673

Nuclear diameter

Budding yeast Saccharomyces cerevisiae

µm

22387213

"The large size of nuclei in higher eukaryotes might therefore further decrease the rate of mRNA export compared to cells with smaller nuclei. The probability of an mRNP to find its way back to the periphery after bounding off the nuclear envelope will be significantly lower in cells with a large nucleus as compared to a yeast cell, where nuclei are small (2 µm in diameter) and an mRNA can move across it in a few seconds. However, mRNA diffusion behavior in yeast has not yet been measured."

Uri M

nucleus,diameter,length,radius,size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10183

110674

Diameter of volume within which chromatin loci diffuse

Budding yeast Saccharomyces cerevisiae

~0.5

µm

22387213

72) P. Heun, T. Laroche, K. Shimada, P. Furrer, S.M. Gasser, Chromosome dynamics in the yeast interphase nucleus, Science 294 (2001) 2181â2186. (73) A. Berger, G. Cabal, E. Fabre, T. Duong, H. Buc, U. Nehrbass, et al., High-resolution statistical mapping reveals gene territories in live yeast, Nat. Methods 5 (2008) 1031â1037. (74) A. Taddei, H. Schober, S.M. Gasser, The budding yeast nucleus, Cold Spring Harb. Perspect. Biol. 2 (2010) a000612.

11739961, 18978785, 20554704

"In yeast, chromatin is very mobile and most loci diffuse within a volume of around 0.5µm in diameter [primary sources]. This suggests that almost any gene can encounter the nuclear periphery passively once in a while to stay in close proximity to a nuclear pore, it simply would have to be tethered there by a factor that mediates the interaction between specific chromatin-associated factors and NPC [nuclear pore complex] components."

Uri M

nucleus,diameter,length,radius,size,chromatin,genetic material,locus<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10184

110675

Dimensions of NPCs (nuclear pore complexes)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Dimensions%20of%20Yeast%20NPCs.pdf

Rout MP, Blobel G. Isolation of the yeast nuclear pore complex. J Cell Biol. 1993 Nov123(4):771-83. p.779 table II

8227139

"Measurements were made on electron micrographs of NPCs in the highly enriched NPC fraction negatively stained with phosphotungstate (In isolated NPCs), or on thin section electron micrographs of NPCs in the enriched nuclei fraction (In nuclei). Each mean value is given with its standard deviation. Figures in brackets are the number of measurements made to obtain each mean value. A minus sign indicates that the measurement could not be made."

"Surprisingly, the measurements obtained from the NPCs within the context of the yeast nuclei were very similar to those obtained from the isolated NPCs (Table II), though they are in full agreement with the dimensions of NPCs as seen in preparations of yeast cells (Moor and Miihlethaler, 1963 Severs et al., 1976 Willison and Johnston, 1978 Byers, 1981)."

Uri M

size, diameter, length, radius, plug, Spoke radial length, NPC diameter, NPC thickness, Basket height<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10185

110676

Number of Phe-Gly (FG) nups (nucleoporins) that line the walls of the transport channel in each nuclear pore complex (NPC)

Budding yeast Saccharomyces cerevisiae

~160

FG nups/NPC

22387213

88) F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, et al., The molecular architecture of the nuclear pore complex, Nature 450 (2007) 695â701. (89) M. Rout, J. Aitchison, A. Suprapto, K. Hjertaas, Y. Zhao, B. Chait, The yeast nuclear pore complex: composition, architecture, and transport mechanism, J. Cell Biol. 148 (2000) 635â651.

18046406, 10684247

"In yeast, it has been shown that around 160 individual FG nups line the walls of the transport channel in each nuclear pore [primary sources]. FG nups are anchored to the core scaffold by the linker nups."

Uri M

nuclear pore complex, npc<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10186

110677

Dimensions of mRNP (messenger ribonucleoprotein)

Budding yeast Saccharomyces cerevisiae

length 20-30: width 5-7

22387213

108) J. Batisse, C. Batisse, A. Budd, B. Böttcher, E. Hurt, Purification of nuclear poly(A)- binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure, J. Biol. Chem. 284 (2009) 34911â34917.

19840948

"...the average length of a yeast mRNA is only about 2 kb, and nuclear mRNPs purified from yeast cells show a rod like shape with a length of 20â30 nm and a width of 5â7 nm [primary source]."

Uri M

nuclear pore complex,npc<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10187

110678

Number of mRNAs per cell

Budding yeast Saccharomyces cerevisiae

15,000-40,000

mRNAs/cell

22387213

78) F.C. Holstege, E.G. Jennings, J.J. Wyrick, T.I. Lee, C.J. Hengartner, M.R. Green, et al., Dissecting the regulatory circuitry of a eukaryotic genome, Cell 95 (1998) 717â728. (122) D. Zenklusen, D.R. Larson, R.H. Singer, Single-RNA counting reveals alternative modes of gene expression in yeast, Nat. Struct. Mol. Biol. 15 (2008) 1263â1271.

9845373, 19011635

Uri M

messenger ribonucleic acid<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10188

110679

Number of pre-ribosomes that cross each NPC (nuclear pore complex) per minute

Budding yeast Saccharomyces cerevisiae

~25

pre-ribosomes/NPC/min

22387213

J. Warner, The economics of ribosome biosynthesis in yeast, Trends Biochem. Sci. 24 (1999) 437â440.

10542411

"Pre-ribosomal subunits, the second large complexes are a slightly higher burden for the NPC to transport: it has been estimated that ~25 pre-ribosomes cross each NPC per minute [primary source]."

Uri M

translation machinery, translocation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10229

110720

Reverse potential for K+

Budding yeast Saccharomyces cerevisiae

E[rev] extrapolated -37mV: E[K] calculated -41mV

Gustin MC, Martinac B, Saimi Y, Culbertson MR, Kung C. Ion channels in yeast. Science. 1986 Sep 12 233(4769):1195-7. p.1196 right column 2nd paragraph & caption of fig.2c

2426783

"[Researchers] have begun to study the ion channels in the plasma membrane of yeast spheroplasts with the patch-clamp technique."

"Replacement of 100 mM K+ in the bath solution with 100 mM Na+ resulted in a small reduction in the slope conductance and a shift in the extrapolated Erev to -37 mV, close to the calculated EK of -41 mV (Fig. 2C)."

Uri M

voltage, electrical potential, potassium<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10247

110738

Chloride concentration in cytoplasm and in phosphate-rich cytoplasmic granules

Budding yeast Saccharomyces cerevisiae

>60

Coury LA, McGeoch JE, Guidotti G, Brodsky JL. The yeast Saccharomyces cerevisiae does not sequester chloride but can express a functional mammalian chloride channel. FEMS Microbiol Lett. 1999 Oct 15 179(2):327-32. p.327 right column top paragraph

10518733

Roomans, G.M. (1980) Localization of divalent cations in phosphate-rich cytoplasmic granules in yeast. Physiol. Plant. 48, 47-50 DOI: 10.1111/j.1399-3054.1980.tb03217.x

"Roomans found the chloride content in both the cytoplasm and in phosphate-rich cytoplasmic granules to be greater than 60 mM [primary source] however, the cells were aerated in distilled water for one day before RbCl or CsCl-loading."

Uri M

cl-, composition, anion, content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10305

110796

in silico P/O ratio for oxidation of NADH and FADH2 during growth on glucose

Budding yeast Saccharomyces cerevisiae

1.04

unitless

Famili I, Forster J, Nielsen J, Palsson BO. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A. 2003 Nov 11 100(23):13134-9. p.13135 right column 2nd paragraph

14578455

"The metabolic capabilities of the S. cerevisiae network were calculated by using flux balance analysis and linear optimization (14, 15, 27). For growth simulations, biomass synthesis (i.e., production of biosynthetic components at the physiological level) was selected as the objective function to be maximized, and optimization was done subject to stoichiometric, limited thermodynamics, and reaction capacity constraints by using established procedures (13â15). Optimization problems were solved by using the commercially available package LINDO (Lindo Systems, Chicago)."

"In the reconstructed network, which contains no proton leakage, 12.5 molecules of ATP are generated via the ETS [Electron Transport System]. As complete oxidation of glucose leads to donation of 12 electron pairs (10 NADH and 2 FADH2) to the electron transport chain, the in silico P/O ratio is 1.04 for oxidation of NADH and FADH2 during growth on glucose, i.e., 12.5/12=1.04, agreeing well with the measured value without including any proton leakage."

Uri M

phosphate, oxygen<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10306

110797

In vivo P/O ratio

Budding yeast Saccharomyces cerevisiae

â0.95

unitless

14578455

[28] Verduyn, C., Stouthamer, A. H., Scheffers, W. A. & van Dijken, J. P. A theoretical evaluation of growth yields of yeasts. (1991) Antonie Leeuwenhoek 59, 49â63.

2059011

Primary source abstract: "Growth yields of Saccharomyces cerevisiae and Candida utilis in carbon-limited chemostat cultures were evaluated... In vivo P/O-ratios can be calculated for aerobic growth on ethanol and acetate, provided that the gap between the theoretical and experimental ATP requirements as observed for growth on glucose is taken into account. This was done in two ways: via the assumption that the gap is independent of the growth substrate (i.e. a fixed amount of ATP bridges the difference between the theoretical and experimental values). alternatively, on the assumption that the difference is a fraction of the total ATP expenditure, that is dependent on the substrate."

P.13135 right column 2nd paragraph: "The in silico model can be used to assess network properties such as the P/O ratio and energy maintenance costs and to compute whole-cell functions. The efficiency of aerobic respiration is measured by the P/O ratio. Experimental studies of isolated mitochondria have shown that S. cerevisiae lacks site I proton translocation (primary source). Consequently, estimation of the maximum theoretical or ââmechanisticââ yield of the ETS [Electron Transport System] alone gives a P/O ratio of 1.5 for oxidation of NADH in S. cerevisiae grown on glucose (primary source). However, based on experimental measurements, it has been determined that the net in vivo P/O ratio is â0.95 (primary source)."

Uri M

phosphate, oxygen

10420

110912

Effect of the external pH on pHi [intracellular pH] of cells

Budding yeast Saccharomyces cerevisiae

Figure - http://bionumbers.hms.harvard.edu/files/Effect%20of%20the%20external%20pH%20on%20pHi%20of%20S.%20cerevisiae%20cells.pdf

unitless

Valli M et al., Intracellular pH distribution in Saccharomyces cerevisiae cell populations, analyzed by flow cytometry. Appl Environ Microbiol. 2005 Mar71(3):1515-21. doi: 10.1128/AEM.71.3.1515-1521.2005. p.1518 figure 4

15746355

"The cells were harvested in exponential (¦) and stationary phase (?), loaded with the fluorochrome, and incubated in McIlvaine buffers of different pH values. The mean values of pHi obtained from two independent experiments are plotted versus the external pH. Standard deviations are indicated."

"Figure 4 shows the mean values of two independent experiments. Interestingly, the cells derived from different growth phases behave significantly differently under the chosen condition at different pH values. By decreasing the external pH from 7.0 to 2.2, a progressive reduction of the pHi from 7.1 to 5.1 was observed in exponentially grown cells. In contrast, stationary cells, which were able to maintain the pHi constant at around 6.1 when the external pH was in the range of 7.0 to 5.5, experienced a drop in pHi to 5.5 as a consequence of a reduction of the external pH to 5.0. Further reductions in the external pH did not have any effect. In fact a pHi of 5.5 was maintained by the stationary cells even with decreasing pH values from 5.0 to 2.2."

Uri M

acidity, h+, proton, external pH, internal pH, cellular pH<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10421

110913

Growth rate at the beginning of growth phase, cytosolic pH=7.0

Budding yeast Saccharomyces cerevisiae

0.48

hour^-1

Orij R et al., Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH(c) in Saccharomyces cerevisiae. Genome Biol. 2012 Sep 10 13(9):R80. doi: 10.1186/gb-2012-13-9-r80. p.2 left column bottom paragraph

23021432

"[Researchers] assessed pHc in growing yeast cultures under batch conditions to reveal that pHc is not constant during growth. pHc was neutral in the beginning of the exponential growth phase, and then gradually dropped approximately 0.3 pH units in mid-to late exponential phase, before glucose was depleted. Upon glucose depletion pHc decreased to 5.5 (Figure 1a)."

"[Researchers] determined that the gradual reduction of pHc [cytosolic pH] from 7 to 6.7 during growth of the culture was a response to changes in the cellular environment, rather than a property of the cultured cells themselves: [researchers] took cell and culture supernatant samples from the beginning of the growth phase (where pHc was 7.0 and the specific growth rate 0.48 h^-1) and at the end of the growth phase, just prior to glucose depletion, when the pHc and growth rate were decreased." equivalent to doubling time of 1.44 hours

Uri M

doubling time, division time, generation time<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10435

110927

Cytosolic pH (pHc) dynamics during growth

Budding yeast Saccharomyces cerevisiae

Figure - http://bionumbers.hms.harvard.edu/files/pHc%20dynamics%20during%20growth.pdf

23021432

"Growth (filled triangles) and pHc (filled circles) were monitored during growth on glucose in microplates. Data points represent the average of 24 biological replicates, error bars represent standard deviations."

Uri M

acidity, pH, H+<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10459

110951

S. cerevisiae ferments sugars even under aerobic conditions when the glucose concentration in the medium is

Budding yeast Saccharomyces cerevisiae

>0.8

Karin Elbing, Christer Larsson, Roslyn M Bill, Eva Albers, Jacky L Snoep, Eckhard Boles, Stefan Hohmann, and Lena Gustafsson. Role of hexose transport in control of glycolytic flux in Saccharomyces cerevisiae. Appl. Environ. Microbiol., 70(9):5323â5330, 2004 p.5323 left column

15345416

[15] Fiechter, A., G. F. Fuhrmann, and O. Kappeli. 1981. Regulation of glucose metabolism in growing yeast cells. Adv. Microb. Physiol. 22: 123â183. [48] Verduyn, C., T. P. L. Zomerdijk, J. P. Van Dijken, and W. A. Scheffers. 1984. Continuous measurement of ethanol production by aerobic yeast suspension with an enzyme electrode. Appl. Microbiol. Biotechnol. 19: 181â185. http://tinyurl.com/jbgcv2x

7036694

p.5323 left column: "The ability of the yeast Saccharomyces cerevisiae to readily degrade sugars to ethanol and carbon dioxide (CO2) has been utilized by humans for several thousands of years for the fermentation of alcoholic beverages and bread baking. S. cerevisiae ferments sugars even under aerobic conditions when the glucose concentration in the medium exceeds 0.8 mM (primary sources). This causes diauxic growth in aerobic batch cultures: once glucose is consumed, the ethanol is oxidized to CO2 in a second, strictly respiratory growth phase."

Uri M

fermentation, respiratioon

10460

110952

Size of hexose transporters Hxt1 and Hxt7 (each)

Budding yeast Saccharomyces cerevisiae

570

amino acids

15345416

Kruckeberg AL. The hexose transporter family of Saccharomyces cerevisiae. Arch Microbiol. 1996 Nov166(5):283-92.

8929273

"For the generation of chimeras, [researchers] chose Hxt1 and Hxt7 because they are the dominating transporters for glucose metabolism and display the lowest and highest glucose affinity, respectively (5). Hxt1 and Hxt7 each have 570 amino acids. They are 72% identical and are predicted to consist of 12 membrane-spanning domains, with the amino and carboxy termini located in the cytosol (primary source)."

Uri M

sugar, transport<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10461

110953

Total biomass yield (including both glucose and ethanol catabolism)

Budding yeast Saccharomyces cerevisiae

0.3 g/[g of Glucose]

g/mol

15345416

"Since the C-molar biomass yield during respiration of glucose is higher than that during respiration of ethanol (8), the total biomass yield (including both glucose and ethanol catabolism) in the wild type reached only 54 g/mol (0.3 g/[g of Glucose])."

Uri M

growth<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10462

110954

Vmax and Km of glucose transport and specific growth rates

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Vmax%20and%20Km%20of%20glucose%20transport%20and%20specific%20growth%20rates.pdf

15345416

P.5328 left column bottom paragraph: "[Researchers] have constructed functional chimeras between the low and high-affinity transporters Hxt1 and Hxt7 in order to further understand how changes in glucose uptake affect yeast metabolism. [Their] series of strains displayed different rates of ethanol production, which correlated linearly with the maximal specific glucose consumption rates attained during exponential growth on glucose (Fig. 3). Hence, restricted glucose consumption, and consequently a reduced glycolytic rate, is a strong candidate for explaining the observed differences in ethanol yield. Restricted glucose consumption, in turn, is explained by different capacities of the glucose transporters. Indeed, the strains with the highest glucose uptake capacity (Vmax [Table 2], Vapp [Fig. 4]) showed the highest glucose consumption and ethanol production rates, and vice versa."

P.5326 right column 3rd paragraph: "Glucose transport in the different strains exhibited low (Km, 50 to 250 mM)- or medium- to high (Km, ca. 2 to 10 mM)-affinity kinetics (Table 2). The differences in gas profiles (Fig. 1) correlated with the kinetic differences of the chimeric glucose transporters (Table 2)." P.5327 left column bottom paragraph: "The use of [researchers'] strains with altered glucose transport capacity offers the possibility to study the control of glycolytic flux by glucose uptake. By using log-log plots according to the theory of metabolic control analysis, it is possible to determine to what extent an enzymatic step controls the steady-state rate of a pathway (refs 13, 20, 22). However, neither Vmax nor Vapp (Fig. 4) activities of the chimeric transporters can be used directly in an estimation of the control of glucose transport in wild-type S. cerevisiae. This is because the transporters not only have different Vmax values but also have different affinities (Km) for glucose (see table 2)." See notes beneath table

Uri M

growth rate, doubling time, division time, generation time

10494

110988

Diffusion constant of Fus3

Budding yeast Saccharomyces cerevisiae

4.2

µm^2/sec

17952059

Fluorescence correlation spectroscopy (FCS)

Uri M

signalling protein, difussivity, fus3<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10537

111031

Total amount of RNA per cell

Budding yeast Saccharomyces cerevisiae

by hot phenol method 1.32±0.03: by NaOH/PCA method 1.43±0.01

pg/cell

19040753

Total amount of cellular RNAs (pg per cell) was determined for three independent preparations of S288C cells grown in YPD medium [(1%(w/v) yeast extract/2%(w/v) Bacto peptone/ 2%(w/v) glucose)] using a modified hot-phenol method [PMID 8643554] and NaOH/PCA[perchloric acid] method [PMID 1097403].

Uri M

ribonucleic acid, content<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10538

111032

Summary of the expression state of genes measured in study and compared to literature

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Summary%20of%20the%20expression%20state%20of%20genes%20measured%20in%20this%20study%20and%20compared%20to%20literature.pdf

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71. Supplemental table 4

19011635

Holstege FC et al., Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998 Nov 25 95(5):717-28. & Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature. 2003. 425(6959) pp.737-41.

9845373, 14562106

"...an in situ hybridization (FISH) approach that detects single mRNA molecules, mRNA abundance and transcriptional activity within single Saccharomyces cerevisiae cells." See fig. 8a: Synthesis time was plotted against the length of the gene. The slope of the line gives (polymerase speed)^-1

Uri M

ribonucleic acid, transcription, macromolecule, polymer, MDN1, midasin homolog,DOA1, KAP104, POL1, PDR5<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10611

111106

Dimensions of tubular invaginations of the plasma membrane associated with actin patches

Budding yeast Saccharomyces cerevisiae

diameter 50nm: length â¤180nm

Sirotkin V, Berro J, Macmillan K, Zhao L, Pollard TD. Quantitative analysis of the mechanism of endocytic actin patch assembly and disassembly in fission yeast. Mol Biol Cell. 2010 Aug 15 21(16):2894-904. doi: 10.1091/mbc.E10-02-0157. p.2894 left column

20587778

Mulholland, J., Preuss, D., Moon, A., Wong, A., Drubin, D., and Botstein, D. (1994). Ultrastructure of the yeast actin cytoskeleton and its association with the plasma membrane. J. Cell Biol. 125, 381â391. & Idrissi, F. Z., Grotsch, H., Fernandez-Golbano, I. M., Presciatto-Baschong, C., Riezman, H., and Geli, M. I. (2008). Distinct acto/myosin-I structures associate with endocytic profiles at the plasma membrane. J. Cell Biol. 180, 1219â1232.

8163554, 18347067

"Clathrin-dependent endocytosis in yeast cells depends on the assembly of structures called actin patches (Kaksonen et al., 2006 Galletta and Cooper, 2009), which are associated with tubular invaginations of the plasma membrane 50 nm in diameter and up to 180 nm long in budding yeast (primary sources). The protein composition of actin patches evolves along a precisely timed pathway (Kaksonen et al., 2003, 2005 Sirotkin et al., 2005), beginning with recruitment of clathrin and endocytic adaptor proteins at the tip of a shallow invagination of the plasma membrane, followed by recruitment of activators of Arp2/3 complex to the base and side of the invagination (Kaksonen et al., 2003, 2005 Newpher et al., 2005 Idrissi et al., 2008)."

Uri M

size, radius<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10685

111180

Diameter of an autophagosome

Budding yeast Saccharomyces cerevisiae

400-900

Takeshige, Kazuhiko, et al. "Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction." The Journal of cell biology 119.2 (1992): 301-311 abstract

1400575

Abstract: "For determination of the physiological role and mechanism of vacuolar proteolysis in the yeast Saccharomyces cerevisiae, mutant cells lacking proteinase A, B, and carboxypeptidase Y were transferred from a nutrient medium to a synthetic medium devoid of various nutrients and morphological changes of their vacuoles were investigated. After incubation for 1 h in nutrient-deficient media, a few spherical bodies appeared in the vacuoles and moved actively by Brownian movement. These bodies gradually increased in number and after 3 h they filled the vacuoles almost completely. During their accumulation, the volume of the vacuolar compartment also increased. Electron microscopic examination showed that these bodies were surrounded by a unit membrane which appeared thinner than any other intracellular membrane."

Abstract: "The diameter of the bodies ranged from 400 to 900 nm."

yuvgilad

size, radius, length, vesicle

10692

111187

Flux of proteins entering the endoplasmic reticulum (ER) lumen

Budding yeast Saccharomyces cerevisiae

460

78-3700 molecules/second

molecules/second

Vincent, M., Whidden, M., & Schnell, S. (2014). Surveying the floodgates: estimating protein flux into the endoplasmic reticulum lumen in Saccharomyces cerevisiae. Frontiers in Physiology, 5, 444. doi:10.3389/fphys.2014.00444 abstract

25431559

Abstract: "In this work [investigators] carried out a meta-analysis to estimate the average and absolute flux of proteins into the endoplasmic reticulum lumen." Theoretical estimate. See reference for details.

Abstract: "[Investigators] estimate an average of 460 proteins enter the endoplasmic reticulum every second, with an absolute minimum and maximum flux of 78 and 3700 molecules per second, respectively."

mvincent

Sec61, endoplasmic reticulum, protein flux, protein import, translocon, unfolded protein response

10693

111188

Mutation rate and type in mutator strains - CAN1 and GCR

Budding yeast Saccharomyces cerevisiae

table link - http://bionumbers.hms.harvard.edu/files/mutation%20rate%20and%20type%20in%20mutator%20strains.pdf

gen-1

Serero A, Jubin C, Loeillet S, Legoix-Né P, Nicolas AG. Mutational landscape of yeast mutator strains, Proc Natl Acad Sci U S A. 2014 Feb 4 111(5):1897-902. doi: 10.1073/pnas.1314423111. p.1898 table 1

24449905

See refs beneath table

Dana BZ

10694

111191

mutation rate and type in mutator strains (mutational landscape)

Budding yeast Saccharomyces cerevisiae

table link - http://www.pnas.org/content/111/5/1897/T2.expansion.html

mutation/gen#

Serero A, Jubin C, Loeillet S, Legoix-Né P, Nicolas AG. (2014) Mutational landscape of yeast mutator strains, Proc Natl Acad Sci U S A.

24449905

Using NGS to find mutation rate and type after mutation accumulation experiment in yeast mutator strains pol32? and rad27? (replication), msh2? (mismatch repair, MMR), tsa1? (oxidative stress), mre11? (recombination), mec1? tel1? (DNA damage/S-phase checkpoints), pif1? (maintenance of the mitochondrial genome and telomere length), cac1? cac3? (nucleosome deposition), and clb5? (cell cycle progression)"

Dana BZ

landscape mutation mutatores yeast accumulation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10768

111265

Summary of information relevant to translation initiation factor gene expression

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Summary%20of%20information%20relevant%20to%20eIF%20gene%20expression.pdf

von der Haar T, McCarthy JE. Intracellular translation initiation factor levels in Saccharomyces cerevisiae and their role in cap-complex function. Mol Microbiol. 2002 Oct46(2):531-44 DOI: 10.1046/j.1365-2958.2002.03172.x p.535 table 1

12406227

See refs beneath table

"[Researchers'] estimates of the eIF [eukaryotic initiation factor] protein concentrations indicate that their respective copy numbers per cell are spread over approximately a 30-fold range (Fig. 2). Distinct efficiencies of gene expression will make a significant contribution to these different values. [They] have summarized information that can provide clues as to the operation of post-transcriptional mechanisms that might generate differential rates of expression of the eIF genes (Table 1)."

Uri M

protein content, mrna copy number, protein copy number, content, composition,transcript<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10856

111353

Specific cell volume

Budding yeast Saccharomyces cerevisiae

1-2

ml/g

Lamprecht, I., Schaarschmidt, B. & Welge, G. Microcalorimetric investigation of the metabolism of yeasts. V. Influence of ploidy on growth and metabolism. Radiation and environmental biophysics 13, 57-61 (1976) p.60 table 1

785530

The specific volume was estimated dividing the reported âcell volumeâ by the reported âcell dry weightâ in Table 1.

AVazquez

size,volume<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10864

111361

Mass fraction of nuclear pore complex made up of FG repeat

Budding yeast Saccharomyces cerevisiae

12-20

Frey S, and Görlich D (2007). A saturated FG-repeat hydrogel can reproduce the permeability properties of nuclear pore complexes. Cell 130, 512â523.

17693259

Rout, M. P., Aitchison, J. D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B. T. (2000). The Yeast Nuclear Pore Complex. J. Cell Biol. 148, 635â652.

10684247

Avi Flamholz

nuclear pore, fraction, percentage, percent, FG repeats<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10865

111362

Approximate volume of nuclear pore complex transporter region

Budding yeast Saccharomyces cerevisiae

30000

nm^3

Frey S, and Görlich D (2007). A saturated FG-repeat hydrogel can reproduce the permeability properties of nuclear pore complexes. Cell 130, 512â523.

17693259

Approximated from dimensions measured in Yang, Q., Rout, M. P., and Akey, C. W. (1998). Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. Mol. Cell 1, 223â234.

Avi Flamholz

nuclear pore, volume, yeast, dimensions<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10959

111456

Glutathione redox potential

Budding yeast Saccharomyces cerevisiae

~-320

Morgan B, Ezerina D, Amoako TN, Riemer J, Seedorf M, Dick TP. Multiple glutathione disulfide removal pathways mediate cytosolic redox homeostasis. Nat Chem Biol. 2013 Feb9(2):119-25. doi: 10.1038/nchembio.1142. p.119 right column bottom paragraph & p.120 left column top paragraph

23242256

"To determine the cytosolic EGSH, [investigators] introduced a Grx1-roGFP2 probe [ref 8] into wild-type BY4742 yeast cells. [They] confirmed cytosolic localization by fluorescence microscopy (Supplementary Results, Supplementary Fig. 1a). Consistent with previous observations [refs 9, 10], the cytosolic Grx1-roGFP2 probe was ~5% oxidized at steady state (Fig. 1a), which, using the published midpoint potential of roGFP2 of -280 mV [ref 7], indicates a cytosolic EGSH of -320 mV."

"In this study, [investigators] investigated the regulation and interplay of cytosolic glutathione homeostasis and subcellular GSSG distribution. In line with previous findings, [they] show that the cytosolic EGSH is highly reduced (~-320 mV)."

Uri M

GSH, glutathione<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10960

111457

GSH:GSSG molar ratio

Budding yeast Saccharomyces cerevisiae

50,000:1

GSH:GSSG

23242256

Uri M

GSH,glutathione, redox potential<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10968

111465

Glutathione redox potential measured using Grx1-roGFP2

Budding yeast Saccharomyces cerevisiae

-310 to -320

Morgan B, Sobotta MC, Dick TP. Measuring E(GSH) and H2O2 with roGFP2-based redox probes. Free Radic Biol Med. 2011 Dec 1 51(11):1943-51. doi: 10.1016/j.freeradbiomed.2011.08.035. p.1944 left column 3rd paragraph

21964034

[26] Braun, N. A. Morgan, B. Dick, T. P. Schwappach, B. The yeast CLC protein counteracts vesicular acidification during iron starvation. J. Cell Sci. 123: 2342â2350 2010. doi: 10.1242/jcs.068403.

20530571

P.1944 left column 2nd paragraph: "In this article [investigators] describe methods and considerations for the use of two fluorescence-based, genetically encoded probes that enable real-time, nondisruptive, and subcellular compartment-specific measurement of the redox potential of the GSH:GSSG redox couple (EGSH) and changes in H2O2 concentration. These probes are fusion proteins consisting of redox-active green fluorescent protein 2 (roGFP2) genetically fused to the redox enzymes human glutaredoxin-1 (Grx1), for measurement of EGSH, and Orp1 from Saccharomyces cerevisiae, for measurement of H2O2 as described previously [refs 24,25]."

P.1944 left column 3rd paragraph: "[Investigatorsâ] measurements of the cytosolic EGSH in S. cerevisiae using the Grx1-roGFP2 probe typically give values of between -310 and -320 mV([primary source] and unpublished data),which is consistent with a number of other studies employing genetically encoded fluorescent probes [refs 7,8,27â29]. Assuming a total glutathione concentration of 10 mM this would imply a GSH:GSSG of between 20,000:1 and 40,000:1. Thus, GSSG appears to be present only in nanomolar amounts in the cytosol, suggesting that original estimates of the GSH:GSSG in this compartment are wrong by 2 to 3 orders of magnitude."

Uri M

redox, anti oxidant, thiol

10969

111466

Cytosolic pH of Gef1 expressing cell

Budding yeast Saccharomyces cerevisiae

unitless

Braun NA, Morgan B, Dick TP, Schwappach B. The yeast CLC protein counteracts vesicular acidification during iron starvation. J Cell Sci. 2010 Jul 1 123(Pt 13):2342-50. doi: 10.1242/jcs.068403. p.2345 right column bottom paragraph

20530571

"Steady-state pH measurements of the cytosol, the Gef1- containing compartment and the vacuole were then performed with gef1 deletion strains expressing the different Gef1 variants (Fig. 5)."

"By homology, the only CLC protein of Saccharomyces cerevisiae, Gef1, belongs to this family of intracellular exchangers." "Expression of any Gef1 variant resulted in a cytosolic pH close to 6 (differences to the deletion strain are statistically significant with P <0.02). At the same time, the Gef1-containing compartment was slightly acidic with respect to the cytosol and the vacuolar lumen substantially more acidic (Fig. 5B,C,D,E), as expected for these acidifying compartments from the literature (Klionsky et al., 1992, Manolson et al., 1994, Martinez-Munoz and Kane, 2008, Plant et al., 1999, Rothman et al., 1989)."

Uri M

acidity, cytosol<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10973

111470

Degree to which overall transcription rate is slower in stationary phase compared to logarithmic phase

Budding yeast Saccharomyces cerevisiae

3 - 5

times slower

Lemons JM et al., Quiescent fibroblasts exhibit high metabolic activity. PLoS Biol. 2010 Oct 19 8(10):e1000514. doi: 10.1371/journal.pbio.1000514. p.1 right column top paragraph

21049082

Choder M (1991) A general topoisomerase I-dependent transcriptional repression in the stationary phase in yeast. Genes Dev 5: 2315â2326.

1660829

"In addition, the overall transcription rate is three to five times slower in stationary-phase than in logarithmic-phase cultures [primary source], and protein synthesis is reduced to approximately 0.3% of the rate in logarithmically growing cultures [BNID 111471]. Therefore, the quiescent cells within a stationary-phase culture of yeast likely represent an example of a quiescent cell that has significantly reduced its metabolic activity."

Uri M

transcription rate, mrna synthesis, quiescence, exponential phase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10974

111471

Percent of protein synthesis in stationary phase out of protein synthesis in logarithmic phase

Budding yeast Saccharomyces cerevisiae

~0.3

Lemons JM et al., Quiescent fibroblasts exhibit high metabolic activity. PLoS Biol. 2010 Oct 19 8(10):e1000514. doi: 10.1371/journal.pbio.1000514. p.1 right column top paragraph

21049082

Fuge EK, Braun EL, Werner-Washburne M (1994) Protein synthesis in longterm stationary-phase cultures of Saccharomyces cerevisiae. J Bacteriol 176: 5802â5813.

8083172

"In addition, the overall transcription rate is three to five times slower in stationary-phase than in logarithmic-phase cultures [BNID 111470], and protein synthesis is reduced to approximately 0.3% of the rate in logarithmically growing cultures [primary source]. Therefore, the quiescent cells within a stationary-phase culture of yeast likely represent an example of a quiescent cell that has significantly reduced its metabolic activity."

Uri M

protein synthesis, translation, quiescence, exponential phase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10981

111478

Median spindle model length

Budding yeast Saccharomyces cerevisiae

meiosis I 2.0µm: meiosis II 1.71µm table link - http://bionumbers.hms.harvard.edu/files/Spindle%20model%20lengths%20and%20microtubule%20composition.pdf

µm

Winey M, Morgan GP, Straight PD, Giddings TH Jr, Mastronarde DN. Three-dimensional ultrastructure of Saccharomyces cerevisiae meiotic spindles. Mol Biol Cell. 2005 Mar16(3):1178-88. p.1181 table 1

15635095

"Fluorescence imaging of meiotic spindles was done with a green fluorescent protein (GFP)-Tub1pâexpressing strain of SK1 (strain YUMY4B1). Cells were induced to sporulate synchronously as described in Straight et al. (2000). Live cells were imaged in samples taken at 6, 7, 8, 9, and 10 h from a sporulating culture at 30°C."

"Table 1 lists some basic parameters derived from the 35 wild-type meiotic spindle models, including microtubule numbers and spindle lengths. Microtubules are reported as being from one SPB [spindle pole body] or the other SPB, with some instances of âcontinuousâ microtubules. Microtubules are assigned to one SPB or the other by tracking the individual microtubule in serial sections until it ends at or within one section (~40 nm) of a SPB. The SPB proximal end of the microtubule is considered to be the minus-end such that the end in the nucleoplasm will be the plus-end. All microtubules can be tracked to a SPB, but a few microtubules have both ends close enough to each of the two SPBs that the polarity cannot be determined, and these microtubules are called continuous. These microtubules are expected to have a normal plus- and minus-end, and they are found in MI [meiosis I] and MII [meiosis II] spindles (Table 1), as well as mitotic spindles (Winey et al., 1995)."

Uri M

spindle body, microtubule, size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

10982

111479

Median microtubule number in spindle model

Budding yeast Saccharomyces cerevisiae

meiosis I 56.5: meiosis II 47.0 table link - http://bionumbers.hms.harvard.edu/files/Spindle%20model%20lengths%20and%20microtubule%20composition.pdf

microtubules

Winey M, Morgan GP, Straight PD, Giddings TH Jr, Mastronarde DN. Three-dimensional ultrastructure of Saccharomyces cerevisiae meiotic spindles. Mol Biol Cell. 2005 Mar16(3):1178-88. p.1181 table 1

15635095

Uri M

spindle body,microtubule,size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11010

111507

Speed of telomere motion

Budding yeast Saccharomyces cerevisiae

~0.05

µm/sec

Vermot J, Fraser SE, Liebling M. Fast fluorescence microscopy for imaging the dynamics of embryonic development. HFSP J. 2008 Jun2(3):143-55. doi: 10.2976/1.2907579. p.144 left column 2nd paragraph

19404468

Gasser S M (2002). âVisualizing chromatin dynamics in interphase nuclei.â Science 296, 1412â1416.10.1126/science.1067703

12029120

Primary source abstract:"Real-time fluorescence microscopy"

"Dynamic processes in cellular biology span a broad range of velocities and scales. Some examples of this diversity are the speed of cell migration [140â170 µm/h for neural crest cells (BNID 111506)], telomere motion in yeast [~0.05 µm/sec (primary source)], fast calcium waves [10â50 µm/sec (BNID 111508)], red blood cell motion in the developing cardio-vascular system of rodents [1â10 mm/s (BNID 111509)], and the frequency of beating cilia [3â40 Hz (BNID 111510)."

Uri M

rate, motility<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11044

111541

Composition of subunits of ribosome (see comments section for number of nts & aa)

Budding yeast Saccharomyces cerevisiae

large 60S subunit ~61% RNA 39% protein: small 40S subunit 54% RNA 46% protein

Verschoor A, Warner JR, Srivastava S, Grassucci RA, Frank J. Three-dimensional structure of the yeast ribosome. Nucleic Acids Res. 1998 Jan 15 26(2):655-61. p.655 left column bottom paragraph

9421530

"The yeast ribosome is composed of two subunits. The 60S subunit contains three RNA molecules: 25S RNA of 3392 nt, hydrogen bonded to the 5.8S RNA of 158 nt and associated with the 5S RNA of 121 nt. There are 42 proteins in the large subunit, plus two copies each of two acidic exchangeable proteins. Altogether there are 3671 nt and 7235 amino acids in the 60S subunit, giving it a ratio of ~61% RNA to 39% protein. The 40S subunit has a single RNA of 1798 nt and 32 proteins with a total of 4749 amino acids, giving it a ratio of 54% RNA to 46% protein."

Uri M

content, composition, translation machinery<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11045

111542

Dimensions of ribosome

Budding yeast Saccharomyces cerevisiae

height ~254 Å: width ~278 Å: thickness ~267 Å

Verschoor A, Warner JR, Srivastava S, Grassucci RA, Frank J. Three-dimensional structure of the yeast ribosome. Nucleic Acids Res. 1998 Jan 15 26(2):655-61. p.656 left column paragraph above bottom paragraph

9421530

p.656 left column 4th paragraph:"The 80S ribosome from S.cerevisiae has been reconstructed from 7470 individual ribosome images to a resolution of 35 Å according to the Fourier Shell Criterion measure, using a critical value of 0.5 (ref 14), corresponding to a signal-to-noise ratio of ~2 (ref 15). This value closely agreed with the value obtained by the 45° phase residual criterion used in previous studies. Low pass filtration to 35 Å and, for correction of the transfer function, Wiener filtration were then applied."

"The yeast ribosome is a bipartite structure that varies from roughly equidimensional to somewhat elongate depending on viewing angle (Fig. 1). In the orientation shown in Figure 1A the two subunits are seen side by side, 40S subunit on the left and 60S subunit on the right, with their âheadsâ at the top. In this view the height of the ribosome is ~254 Å, the width ~278 Å and the thickness ~267 Å. These height and width dimensions are 11â14% smaller than those calculated for the ribosome from a higher eukaryote, wheatgerm (ref 3), but greater than those for the 70S E.coli ribosome (Fig. 1). That the thickness dimension is significantly greater for the yeast structure than for wheatgerm could be a result of experimental differences (see Discussion)."

Uri M

structure, size, translation machinery, length<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11075

111572

Distance between the TATA box and TSS [Transcription Start Site] for TATA box-containing genes

Budding yeast Saccharomyces cerevisiae

40 - 120

Base pairs

Liu X, Bushnell DA, Kornberg RD. RNA polymerase II transcription: structure and mechanism. Biochim Biophys Acta. 2013 Jan1829(1):2-8. doi: 10.1016/j.bbagrm.2012.09.003. p.4 left column bottom paragraph

23000482

K. Struhl, Molecular mechanisms of transcriptional regulation in yeast, Annu. Rev. Biochem. 58 (1989) 1051â1077.

2673007

p.4 left column bottom paragraph:"The distance between the TATA box and TSS is almost always about 30 bp for TATA box-containing genes [BNID 111571]. Consistent with this, the structural model of the minimal open promoter complex constructed from the pol IIâTFIIB crystal structure defines a template strand path of approximately 30 residues from the TATA box to the catalytic site [ref 9] and [ref 10]. The notable exception is Saccharomyces cerevisiae, in which the distance from the TATA box to the TSS is 40â120 bp [primary source]."

Uri M

transcription, rna pol, rna polymerase, tata box<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11079

111576

Metabolic networks for growth

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Metabolic%20networks%20for%20growth%20of%20Saccharomyces%20cerevisiae.pdf

van Gulik WM, Heijnen JJ. A metabolic network stoichiometry analysis of microbial growth and product formation. Biotechnol Bioeng. 1995 Dec 20 48(6):681-98. p.683 table II

18623538

Abstract:"Using available biochemical information, metabolic networks have been constructed to describe the biochemistry of growth of Saccharomyces cerevisiae and Candida utilis on a wide variety of carbon substrates."

p.690 left column 4th paragraph:"However, the introduction of extra biochemical reactions into a network without the introduction of an equal number of extra compounds results in an increase of the degree of freedom of the system. To construct a metabolic network for growth on glucose and ethanol eight extra reactions + one extra net conversion rate (ethanol) were added to metabolic network, S2. With these reactions, three extra compounds were introduced (i.e., ethanol, acetaldehyde, and glyoxylate), and thus 9 - 3 = 6 extra degrees of freedom were introduced. Because the degree of freedom of network S2 with fixed values for the parameters K and d' is equal to 1, the degree of freedom of the resulting network, S5 (see Table II), for growth on glucose/ethanol mixtures is equal to 7. Because the only input variables are the consumption rates of glucose and ethanol network S5 is underdetermined." For biochemical reactions (pp.695-6) see http://bionumbers.hms.harvard.edu/files/Biochemical%20reactions.pdf

Uri M

metabolism, Glycolysis, citric acid cycle, PEP phosphotransferase, Pentose phosphate pathway, Glyoxylate shunt, Oxidative phosphorylation, Carbon substrates other than glucose, Transfer of I -carbon compounds, Transport, H+ ATPase, Amino acid synthesis, Amino acid polymerization, Nucleotide synthesis, RNA synthesis, ATP consumption for maintenance, Synthesis of fatty acids, Synthesis of glycogen und polysucchurides, Biomass formation<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11112

111610

Average length of a gene

Budding yeast Saccharomyces cerevisiae

Pérez-Ortín JE, Alepuz PM, Moreno J. Genomics and gene transcription kinetics in yeast. Trends Genet. 2007 23: 250â257. p.250 left column bottom paragraph

17379352

Dujon, B. (1996) The yeast genome project: what did we learn? Trends Genet. 12, 263â270

8763498

p.250 left column bottom paragraph:"...the time required to âreadâ a gene is not negligible: 25â50 seconds for 1 kb (the average length of a yeast gene [primary source])..."

Uri M

size,genetics<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11130

111628

Zinc concentration in vacuole (top value)

Budding yeast Saccharomyces cerevisiae

100

7×10^8 atoms of vacuolar zinc/cell

Simm C et al., Saccharomyces cerevisiae vacuole in zinc storage and intracellular zinc distribution. Eukaryot Cell. 2007 Jul6(7):1166-77. abstract & p.1171 left column top paragraph

17526722

p.1171 left column top paragraph:"Capacity of the vacuolar zinc store to sustain cell growth. The results shown in Fig. 1 and Table 1 indicate that yeast cells grown in high zinc can accumulate a large amount of vacuolar zinc. Based on these data, [investigators] estimated that cells grown in SD [synthetic defined] medium plus 1,000 µM ZnCl2 accumulate as much as 900 pmol vacuolar zinc/10^6 cells. This value corresponds to ~7×10^8 atoms of vacuolar zinc per cell. [Their] previous studies indicated that the threshold amount of total intracellular zinc required for cell growth is ~5×10^6 atoms of zinc per cell (ref 34)."

Uri M

ion, organelle, zinc<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11132

111630

Total number of zinc atoms per cell required for optimal growth

Budding yeast Saccharomyces cerevisiae

~1.5×10^7

zinc atoms/cell

Simm C et al., Saccharomyces cerevisiae vacuole in zinc storage and intracellular zinc distribution. Eukaryot Cell. 2007 Jul6(7):1166-77. p.1166 left column bottom paragraph

17526722

MacDiarmid, C. W., L. A. Gaither, and D. Eide. 2000. Zinc transporters that regulate vacuolar zinc storage in Saccharomyces cerevisiae. EMBO J. 19: 2845-2855.

10856230

p.1166 left column bottom paragraph:"In the yeast Saccharomyces cerevisiae, approximately 1.5×10^7 total zinc atoms per cell are required for optimal growth (primary source). This value is referred to as the âzinc quotaâ for yeast and probably represents the level required to optimally metalate zinc-dependent proteins in the cell (ref 40). Below that amount, cells grow more slowly. When zinc levels drop below a minimum threshold of ~5×10^6 atoms per cell, growth ceases altogether."

Uri M

enzyme, proteome<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11142

111640

Oxidative phosphorylation regime of yeast cells during lactate-limited growth

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Oxidative%20phosphorylation%20regime%20of%20yeast%20cells%20during%20lactate-limited%20growth.pdf

Dejean L, Beauvoit B, Guérin B, Rigoulet M. Growth of the yeast Saccharomyces cerevisiae on a non-fermentable substrate: control of energetic yield by the amount of mitochondria. Biochim Biophys Acta. 2000 Feb 24 1457(1-2):45-56. p.52 table 1

10692549

p.46 left column 2nd paragraph:"...[investigators] used a respirometric and on-line calorimetric approach to analyse the energetic balances and the control of energetic metabolism during growth phase transitions of batch grown S. cerevisiae with limiting amounts of a non-fermentable carbon source (lactate)."

p.52 left column bottom paragraph:"Like the basal and the uncoupled respiratory rates (see Fig. 7A,B), TET-insensitive oxygen uptake of cells decreased during the late exponential phase, to attain a minimal value in the stationary phase (Table 1). The ratio between the maximal oxygen uptake and the non-phosphorylating respiratory activity (JO[ClCCP] vs. JO[TET]) did not vary significantly with regard to the growth phase (between 3.3 and 3.5) (Table 1)." TET=triethyltin chloride. ClCCP=carbonyl cyanide m-chlorophenyl hydrazone. JO=Respiratory rates

Uri M

entropy,Early exponential, Late exponential, Stationary, growth phase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11143

111641

Mitochondrial activities of yeast cells throughout the culture period

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Mitochondrial%20activities%20of%20yeast%20cells%20throughout%20the%20culture%20period.pdf

10692549

p.53 left column bottom paragraph:"The uncoupled respiration of yeast cells measured with lactate 0.2% as respiratory substrate continuously declined during the growth period (Fig. 7B). Moreover, Table 2 shows that the maximal respiratory capacity (JOmax) measured in the presence of ClCCP and saturating amounts of lactate, glucose and ethanol (0.2%, 20 mM and 100 mM in the culture medium, respectively [ref 9]) also decreased during the transition from the early to the late exponential phase, as well as to the stationary phase. In this way, this growth phase-dependent modulation of the maximal respiratory capacity of yeast cells was investigated in relation to the mitochondrial enzyme content." ClCCP=carbonyl cyanide m-chlorophenyl hydrazone. JO=Respiratory rates

Uri M

entropy,Early exponential, Late exponential, Stationary, growth phase,citrate synthase,lactate dehydrogenase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11144

111642

Growth yields, basal respiratory activity and calculated ATP turnover rate of yeast cells during lactate-limited growth

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Growth%20yields%2C%20basal%20respiratory%20activity%20and%20calculated%20ATP%20turnover%20rate%20of%20yeast%20cells%20during%20lactate-limited%20growth.pdf

10692549

p.54 left column 2nd paragraph:"In this study, [investigators] used a microcalorimetric method allowing construction of an enthalpy balance of yeast cells batch grown with a respiratory substrate [ref 13] and [ref 15]. The main observation was that the part of lactate energy input conserved as biomass (the enthalpic growth yield or energetic yield) was approximately the same in the early and the late exponential growth phases (32±2% versus 37±3%) whereas growth rate and respiratory rate continuously decreased during this phase transition (Table 3)." JO=Respiratory rates

Uri M

entropy, Early exponential, Late exponential, Stationary, growth phase<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11146

111644

Cell yields, metabolic fluxes, and carbon recovery as a function of the dilution rate in aerobic, glucose-limited chemostat cultures

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Cell%20yields%2C%20metabolic%20fluxes%2C%20and%20carbon%20recovery%20as%20a%20function%20of%20the%20dilution%20rate%20in%20aerobic%2C%20glucose-limited%20chemostat%20cultures.pdf

Van Hoek P, Van Dijken JP, Pronk JT. Effect of specific growth rate on fermentative capacity of baker's yeast. Appl Environ Microbiol. 1998 Nov64(11):4226-33. p.4227 table 1

9797269

p.4226 right column bottom paragraph:"The aim of the present study was to assess the effect of specific growth rate on fermentative capacity in an industrial bakerâs yeast strain grown in aerobic, sugar-limited chemostat cultures. Furthermore, the effect of specific growth rate on in vitro activities of key glycolytic and fermentative enzymes was investigated in an attempt to identify correlations between fermentative capacity and enzyme levels."

p.4229 right column 4th paragraph:"Qualitatively, the patterns of biomass production and metabolite formation as a function of the specific growth rate of the industrial strain used in this study are similar to those reported for other S. cerevisiae strains (refs 1, 21, 24, 37). A notable difference involved the production of acetate and pyruvate, which has been reported to occur at dilution rates slightly below Dcrit in laboratory strains (refs 1, 21). In strain DS28911, acetate and pyruvate production were detected above D = 0.28 h^-1 (Table 1) only when ethanol production also became apparent (Table 1 Fig. 1A)."

Uri M

Yield, oxygen, carbon dioxide, glucose, ethanol, acetate, pyruvate, glycerol, Carbon recovery, flux<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11147

111645

Parameters used in growth model

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Parameters%20used%20in%20growth%20model.pdf

Sonnleitner B, Käppeli O. Growth of Saccharomyces cerevisiae is controlled by its limited respiratory capacity: Formulation and verification of a hypothesis. Biotechnol Bioeng. 1986 Jun28(6):927-37. p.930 table I

18555411

Abstract:"A novel mechanistic model for the growth of baker's yeast on glucose is presented. It is based on the fact that glucose degradation proceeds via two pathways under conditions of aerobic ethanol formation. Part is metabolized oxidatively and part reductively, with ethanol being the end product of reductive energy metabolism."

p.931 left column 4th paragraph:"The stationary behavior of the described model using parameters listed in Table I is shown in Figure 2 for considerably dilute media because the model-in the presented form-is not intended to formulate any inhibitory effects of ethanol."

Uri M

yield, oxygen glucose, hydrogen, nitrogen, carbon<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11174

111672

Number of Autonomous Replication Sequence elements (ARSs) in the genome

Budding yeast Saccharomyces cerevisiae

~200 - 400

ARSs/genome

Raghuraman et al., Replication dynamics of the yeast genome. Science. 2001 Oct 5 294(5540):115-21. DOI: 10.1126/science.294.5540.115 p.115 right column

11588253

Rivin CJ, Fangman WL. Replication fork rate and origin activation during the S phase of Saccharomyces cerevisiae. J Cell Biol. 1980 Apr85(1):108-15. & C. S. Newlon, W. Burke, in ICN-UCLA Symposium on Molecular and Cellular Biology (Academic Press, New York, vol. 19, 1980), pp. 399-409.

6767729

Abstract:"Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae."

p.115 middle column:"The replication of eukaryotic chromosomes is highly regulated. Replication is limited to the S phase of the cell cycle and within S phase, initiation of replication is controlled with respect to both location and time. The sites of initiation, called replication origins, have been best characterized in the budding yeast Saccharomyces cerevisiae, in which a functional assay based on plasmid maintenance has allowed identification of potential origins of replication [autonomous replication sequence elements (ARSs)]. There are estimated to be ~200 to 400 ARSs in the yeast genome (primary sources), and most, but not all, function as chromosomal origins (ref 3)."

Uri M

DNA polymerization, origin of replication, Autonomously replicating sequence<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11175

111673

Length of chromosomal origin of replication

Budding yeast Saccharomyces cerevisiae

~200

base pairs

Raghuraman et al., Replication dynamics of the yeast genome. Science. 2001 Oct 5 294(5540):115-21. DOI: 10.1126/science.294.5540.115 p.115 right column

11588253

Abstract:"Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae."

p.115 right column:"There are estimated to be ~200 to 400 ARSs [Autonomous Replication Sequence elements] in the yeast genome (BNID 111672), and most, but not all, function as chromosomal origins (ref 3). The few origins investigated at the sequence level usually encompass ~200 base pairs (bp), most contain a perfect match or a one-base mismatch to an 11-bp ARS consensus sequence (ACS) (refs 4, 5)."

Uri M

DNA polymerization, origin of replication, Autonomously replicating sequence, dna replication<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11176

111674

Duration of S (synthesis) phase in microarray experiment

Budding yeast Saccharomyces cerevisiae

~55

min

Raghuraman et al., Replication dynamics of the yeast genome. Science. 2001 Oct 5 294(5540):115-21. DOI: 10.1126/science.294.5540.115 p.118 right column bottom paragraph

11588253

Abstract:"Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae."

p.118 right column bottom paragraph:"S phase in the microarray experiment spans an interval of ~55 min. Although [investigators] have previously described origins as belonging to distinct âearlyâ or âlateâ classes, this genome-wide analysis reveals that origins really show a continuum of activation times (Fig. 5A). Most of the origin firings occur near mid-S."

Uri M

DNA polymerization, cell cycle, phase, dna replication<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11183

111681

Speed of DNA replication fork

Budding yeast Saccharomyces cerevisiae

3.7

kb/min

Raghuraman et al., Replication dynamics of the yeast genome. Science. 2001 Oct 5 294(5540):115-21. DOI: 10.1126/science.294.5540.115 p.120 left column top paragraph

11588253

Rivin CJ, Fangman WL. Replication fork rate and origin activation during the S phase of Saccharomyces cerevisiae. J Cell Biol. 1980 Apr85(1):108-15.

6767729

Abstract:"Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae."

p.119 right column bottom paragraph:"The rates of fork migration were measured by taking absolute values of the slopes of the lines connecting peaks and valleys (that is, origins and termini) in the replication profiles, ignoring the region immediately flanking each peak or valley (5 kb on either side), where local flattening of the curve introduces artifacts in the measurement of fork rates. As with origin activation times, a broad range of fork rates was observed (ref 32), with a mean of 2.9 kb/min and a median of 2.3 kb/min (Fig. 7). These values are close to a previous estimate of fork migration rates made for isogenic cells grown under similar culture conditions [3.7 kb/min (primary source)]. "

Uri M

dna replication,dna synthesis,speed,rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11192

111690

Average number of ribosomes loaded per mRNA message

Budding yeast Saccharomyces cerevisiae

ribosomes/mRNA message

Guet CC et al., Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Res. 2008 Jul36(12):e73. doi: 10.1093/nar/gkn329. p.4 right column bottom paragraph

18515347

Arava et al., Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2003 Apr 1 100(7):3889-94.

12660367

p.4 right column bottom paragraph:"...if [investigators] assume on average three ribosomes loaded per mRNA message (primary source), [they] find that the average translation rate for an individual ribosome is about eight amino acids per second. This rate is consistent with the translation rates of previous studies (refs 23,24)."

Uri M

ribosome, protein synthesis, speed<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11255

111753

Yields on glucose for an anaerobic, glucose-limited continuous culture at various dilution rates

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Yields%20on%20glucose%20for%20an%20anaerobic%2C%20glucose-limited%20continuous%20culture%20at%20various%20dilution%20rates.pdf

C-mol/(C-mol glucose)

Nissen TL et al., Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology. 1997 Jan143 ( Pt 1):203-18. p.208 table 2

9025295

p.208 left column top paragraph:"Table 2 summarizes the yields on glucose of the most important products in the anaerobic, glucose-limited continuous cultures. It is seen that about 80% (w/w) of the consumed glucose is converted into ethanol and carbon dioxide and that these yields are virtually independent of the specific growth rate. On a molar basis Ysc (1.63 mol/mol) is slightly higher than Ysetoh (1.49 mol/mol) since CO2 is formed not only in the synthesis of ethanol but also in a number of anabolic reactions. A little less than 10% (w/w) of the glucose is converted into biomass and another 10% (w/w) ends up as glycerol whereas approximately 1% (w/w) is converted into various organic acids. Ysx decreases slighty with increasing dilution rate whereas Ysgly increases. Yssuc is practically unaffected by the dilution rate whereas YSpyr and especially Ysace increase when the dilution rate is increased from 0.1 to 0.4/h. It is seen that the measured compounds can account for about 98 % (w/w) of the consumed glucose (c.f. Table 2)." For abbreviations see 'compound' column in table. See note above table

Uri M

glucose, metabolism, carbon dioxide, ethanol, biomass, glycerol, succinic acid, acetic acid, pyruvic acid, yield, growth rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11256

111754

Stoichiometric (Î³) and maintenance (m) coefficients for the glucose-limited continuous culture

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Stoichiometric%20(%3F)%20and%20maintenance%20(m)%20coefficients%20for%20the%20glucose-limited%20continuous%20culture.pdf

Nissen TL et al., Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology. 1997 Jan143 ( Pt 1):203-18. p.208 table 3

9025295

p.208 left column 2nd paragraph:"Table 3 lists the stoichiometric and the maintenance coefficients for ethanol, glucose and glycerol. It is observed that all the maintenance coefficients are very close to zero." p.209 left column top paragraph:"The decrease in Ysx observed by Verduyn et al. (1990) may be due to excess residual medium concentration of unsaturated fatty acids at high dilution rates which could lead to uncoupling of anabolic and catabolic processes (Viegas et al., 1989) and thus, a decrease in Ysx. However, the ? values listed in Table 3 are in good accordance with the values observed by Verduyn et al. (1990) at dilution rates lower than 0.20/h. Lidin et al. (1995) reports similar values although the maximum value of Ysx is found to be 0.09 g/g indicating that the culture may have been fed with a suboptimal concentration of unsaturated fatty acids." Ysx=Biomass. For abbreviations see 'compound' column in table 2 - http://bionumbers.hms.harvard.edu/files/Yields%20on%20glucose%20for%20an%20anaerobic%2C%20glucose-limited%20continuous%20culture%20at%20various%20dilution%20rates.pdf

Uri M

glucose, metabolism, carbon dioxide, ethanol, biomass, glycerol, succinic acid, acetic acid, pyruvic acid, yield, growth rate<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11257

111755

Cellular composition as a function of the dilution rate in a glucose limited culture

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Cellular%20composition%20of%20S.%20cerevisiae%20as%20a%20function%20of%20the%20dilution%20rate%20in%20a%20glucose%20limited%20culture.pdf

% (w/w)

Nissen TL et al., Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology. 1997 Jan143 ( Pt 1):203-18. p.210 table 4

9025295

p.209 left column 2nd paragraph:"Measurements of the cellular composition are necessary to structure the flux of carbon to biomass, and especially if the cellular composition changes with the operating conditions it is important to consider the differences in fluxes to the different macromolecular pools. In this study, the cellular composition was therefore determined at four different dilution rates (see Table 4). The most important variation in the cellular composition is that the amount of active machinery, i.e. protein and RNA, increases linearly with increasing dilution rate at the expense of carbohydrates. The cellular content of other components is virtually independent of the dilution rate. From Table 4 it is seen that the measurements can account for approximately 100% of the cell mass, but since the pool of e.g. glycolytic intermediates has not been measured, some of the analyses have a small overlap. However, the results indicate that no major cellular component has been left out. The values listed in Table 4 are in good accordance with previously reported values for the cellular composition of S. cerevisiae (Kuenzi & Fiechter, 1972 Oura, 1972 Watson, 1976 Waldron, 1977 Furukawa et al., 1983 Verduyn et al., 1990)."

Uri M

Metabolite, metabolism, Protein, Glycogen, Trehalose, Mannan, carbohydrates, RNA, DNA, Free amino acids, Lipid, Ash, content, composition<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11317

111865

Diameter of endocytic patch

Budding yeast Saccharomyces cerevisiae

50 - 300

Berro J, Pollard TD. Local and global analysis of endocytic patch dynamics in fission yeast using a new "temporal superresolution" realignment method. Mol Biol Cell. 2014 Nov 5 25(22):3501-14. doi: 10.1091/mbc.E13-01-0004. p.3502 left column 3rd paragraph

25143395

Kukulski W, Schorb M, Kaksonen M, Briggs JAG (2012) Plasma membrane reshaping during endocytosis is revealed by time-resolved electron tomography. Cell 150: 508â520

22863005

Time-resolved electron tomography

p.3502 left column 3rd paragraph:"Endocytic patches are diffraction-limited structures with a diameter between 50 and 300 nm in wild-type yeast cells (primary source). When imaged with a spinning-disk confocal microscope, the fluorescence signal of a patch protein is blurred by a three-dimensional Gaussian defined by the point-spread function of the microscope. In [investigatorsâ] setup, the full width at half maximum in the z-axis is ~360 nm. Consequently, one must image at least three consecutive confocal sections spaced 360 nm apart to collect virtually all (95%) of the fluorescence signal of an endocytic patch."

Uri M

endocytosis, size, length<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11318

111866

Surface area of endocytic vesicle

Budding yeast Saccharomyces cerevisiae

6400

±1,900

nm^2

Kukulski W, Schorb M, Kaksonen M, Briggs JAG (2012) Plasma membrane reshaping during endocytosis is revealed by time-resolved electron tomography. Cell 150: 508â520 doi: 10.1016/j.cell.2012.05.046. abstract & p.517 left column bottom paragraph

22863005

Abstract:"[Investigators] directly correlated fluorescence microscopy of key protein pairs with electron tomography. [They] systematically located 211 endocytic intermediates, assigned each to a specific time window in endocytosis, and reconstructed their ultrastructure in 3D. The resulting virtual ultrastructural movie defines the protein-mediated membrane shape changes during endocytosis in budding yeast."

Abstract:"Scission occurs on average 9 s after initial bending when invaginations are ~100 nm deep, releasing nonspherical vesicles with 6,400 nm^2 mean surface area." p.517 left column bottom paragraph:"The Entire Plasma Membrane Surface Is Internalized by Endocytosis in One Cell Cycle: The surface area of the vesicles was 6,400 nm^2 ± 1,900 nm^2, which represents the mean area of plasma membrane that is being internalized per endocytic event. Based on this number, and considering an average number of 0.43 actin patches per fl of cell volume (Karpova et al., 1998) and an actin patch lifetime of 15 s (Kaksonen et al., 2003), [investigators] estimated that a yeast cell of about 5 µm diameter internalizes its complete plasma membrane surface by endocytosis in about 100 min, corresponding to approximately one round of the budding yeast cell cycle."

Uri M

endocytosis,size<IMG SRC="/WF_SQL_XSRF.html"><IMG SRC="/WF_SQL_XSRF.html">

11394

111976

Typical number of vacuoles

Budding yeast Saccharomyces cerevisiae

1 - 10

vacuoles/cell

Chan YH, Marshall WF. Organelle size scaling of the budding yeast vacuole is tuned by membrane trafficking rates. Biophys J. 2014 May 6 106(9):1986-96. doi: 10.1016/j.bpj.2014.03.014. p.1986 right column 2nd paragraph

24806931

p.1986 right column 2nd paragraph:"The yeast vacuole presents an interesting model for organelle size scaling, as it carries out essential biochemical functions both in its lumen (degradation, storage) and at the limiting membrane (signaling). Therefore, the cell is likely to control both the organelleâs internal volume and surface area. Individual cells typically have 1â10 vacuoles that tend to be clustered (Fig. 1 A). Unlike other organelles such as the mitochondria that have a characteristic morphology that constrains the relationship between surface area and volume, yeast vacuoles can exhibit a range of morphologies."

Uri M

organelle,content

11395

111977

Vacuole-to-cell volume ratio

Budding yeast Saccharomyces cerevisiae

W303A strain 10±0.2%: BY4741 strain 7±0.2%: DDY904 strain 3â14%

24806931

Abstract:"In this study, [investigators] measure the vacuole-cell size scaling trends in budding yeast using optical microscopy and a novel, to [their] knowledge, image analysis algorithm."

p.1988 right column 2nd paragraph:"The discrepancies in absolute size measurements may be reflective of differences in strains. On the other hand, the vacuole-to-cell volume ratios in W303A and BY4741 were 10±0.2% and 7±0.2%, respectively, both of which fall within the range of 3â14% reported for strain DDY904, which shows that these ratios are consistent between these two studies."

Uri M

organelle,size

11396

111978

Average cell volume

Budding yeast Saccharomyces cerevisiae

untreated cells 86±2: rapamycin treated cells 130±7

µm^3

24806931

Abstract:"In this study, [investigators] measure the vacuole-cell size scaling trends in budding yeast using optical microscopy and a novel, to [their] knowledge, image analysis algorithm."

p.1990 left column 2nd paragraph:"Thus, both the reported enlargement of the vacuole and the fusion of vacuoles seen in rapamycin-treated cells may be a natural consequence of scaling. To test this possibility, vacuole size was measured in cells that were treated with rapamycin for 4 h. Untreated cells have an average cell size of 86±2µm^3, and rapamycin treated cells arrest and grow to a larger average size of 130±7µm^3 (p < 0.0001, Studentâs t-test)."

Uri M

organelle,size

11397

111979

Comparison of cell and vacuole size measurements

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Comparison%20of%20cell%20and%20vacuole%20size%20measurements.pdf

24806931

Uchida, M., Y. Sun,... C. A. Larabell. 2011. Quantitative analysis of yeast internal architecture using soft x-ray tomography. Yeast. 28: 227â236. doi: 10.1002/yea.1834.

21360734

Abstract:"In this study, [investigators] measure the vacuole-cell size scaling trends in budding yeast using optical microscopy and a novel, to [their] knowledge, image analysis algorithm."

p.1988 right column 2nd paragraph:"[Investigatorsâ] measurements of average cell and vacuole size in the W303A strain were generally larger, but values for BY4741 fell within reported size ranges (see Table S2), showing that the cell outline tracing and vacuole surface reconstruction methods give similar size distributions to reported values."

Uri M

organelle,size,volume,surface area

11566

112149

Average length of Okazaki fragment

Budding yeast Saccharomyces cerevisiae

~165

Michael Lynch and Georgi K. Marinov, The bioenergetic costs of a gene, PNAS 2015 doi: 10.1073/pnas.1514974112 http://www.pnas.org/content/early/2015/10/29/1514974112 Supplementary Materials p.1 right column bottom paragraph

[20] Smith DJ, Whitehouse I. 2012. Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483(7390):434-438. doi: 10.1038/nature10895.

22419157

Primary source abstract:"Using deep sequencing, [investigators] demonstrate that ligation junctions preferentially occur near nucleosome midpoints rather than in internucleosomal linker regions."

Supplementary Materials p.1 right column bottom paragraph:"But because Okazaki fragments in eukaryotes appear to be short - averaging ~165 bp in yeast [primary source], with similar values in human and other eukaryotes [refs 21-23], there are again generally large numbers of Okazaki fragments per inter-ORI [origin of replication] interval, so the investment in RNA primers and ligation on the leading strand is minor relative to that on the lagging strand and can be ignored."

Uri M

dna replication, dna synthesis, genome, okazaki fragment, lagging strand, mean, size

11675

112258

Single cell statistics of the wild type strain (mass doubling time ~100 min)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Single%20cell%20statistics%20of%20the%20wild%20type%20strain%20(mass%20doubling%20time%20~100%20min).pdf

min

Oguz C et al., A stochastic model correctly predicts changes in budding yeast cell cycle dynamics upon periodic expression of CLN2. PLoS One. 2014 May 9 9(5):e96726. doi: 10.1371/journal.pone.0096726. p.4 table 2

24816736

Abstract:"First, [investigators] estimate the model parameters using extensive data sets: phenotypes of 110 genetic strains, single cell statistics of wild type and cln3 strains. Optimization of stochastic model parameters is achieved by an automated algorithm [they] recently used for a deterministic cell cycle model. Next, in order to test the predictive ability of the stochastic model, [they] focus on a recent experimental study in which forced periodic expression of CLN2 cyclin (driven by MET3 promoter in cln3 background) has been used to synchronize budding yeast cell colonies."

P.3 right column top paragraph:"Table 1 shows that after parameter optimization (six generations of DE [differential evolution] or 120 function evaluations), cln3 statistics are captured much better by the model (39% reduction in the fitting error), while overall fitting error in terms of wild type statistics (not enforced during optimization) remain unchanged (Table 2). [Investigators] also capture the abundances of key cell cycle proteins within threefold of experimental values [ref 15], [ref 16] as shown in Table S8 [BNID 112259]. In addition, [they] note that the stochastic simulation statistics presented in Tables 1, 2, and S8 have coefficient of variation (CV) values of less than 10% (low variability) among 15 independent realizations." See notes beneath table

Uri M

duration, time, phase

11676

112259

Abundance of some key cell cycle proteins

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Protein%20abundances%20in%20budding%20yeast.pdf

proteins/cell

24816736

P.3 right column top paragraph:"[Investigators] also capture the abundances of key cell cycle proteins within threefold of experimental values [ref 15], [ref 16] as shown in Table S8. In addition, [they] note that the stochastic simulation statistics presented in Tables 1, 2, and S8 have coefficient of variation (CV) values of less than 10% (low variability) among 15 independent realizations." See note and ref beneath table

Uri M

content, polypeptide, Whi5, Net1, Cdc15, Tem1, Cln3, Cln2, Clb5, Clb2, CKI,Neuroepithelial cell-transforming gene 1 protein, inhibitor protein,Tumor endothelial marker 1,G1/S-specific cyclin Cln3,B-type, S-phase cyclins,cell cycle regulation,Cyclin-dependent kinase inhibitor protein

11890

112475

Kd values for Pho4p and Cbf1p

Budding yeast Saccharomyces cerevisiae

~10nM - 10µM

Fordyce PM et al., De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol. 2010 Sep28(9):970-5. doi: 10.1038/nbt.1675. p.972 right column top paragraph

20802496

[20] Maerkl, S.J. & Quake, S.R. A systems approach to measuring the binding energy landscapes of transcription factors. Science 315, 233â237 (2007).

17218526

Reference abstract: "[Investigators] present a microfluidics-based approach for de novo discovery and quantitative biophysical characterization of DNA target sequences. [They] validated [their] technique by measuring sequence preferences for 28 Saccharomyces cerevisiae transcription factors with a variety of DNA-binding domains, including several that have proven difficult to study by other techniques." Primary source abstract: "Measuring affinities of molecular interactions in high-throughput format remains problematic, especially for transient and low-affinity interactions. [Investigators] describe a high-throughput microfluidic platform that measures such properties on the basis of mechanical trapping of molecular interactions."

P.972 right column top paragraph: "The range of Kd values calculated here for Pho4p and Cbf1p agree with those measured in previous studies (~10 nMâ10 Î¼M) [primary source], validating [investigators'] approach." PMID 15111622 abstract:"Cbf1p is a basic-helix-loop-helix-zipper protein of Saccharomyces cerevisiae required for the function of centromeres and MET gene promoters, where it binds DNA via the consensus core motif CACRTG (R = A or G)." Pho4p is a transcriptional activator of the PHO regulon.

Uri M

michaelis menten kinetics, dissociation constant, binding energy, PHO regulon, Dual function helix-loop-helix protein

12213

112799

Biomass constituents of protein, carbohydrate, lipids, RNA & DNA

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Biomass%20constituents.pdf

Lange HC, Heijnen JJ. Statistical reconciliation of the elemental and molecular biomass composition of Saccharomyces cerevisiae. Biotechnol Bioeng. 2001 Nov 5 75(3):334-44. p.336 table I

11590606

Kockova´-Kratochvílova´ A. 1990. Yeast and yeast-like organisms. New York, VCH Publisher.

Abstract: "A systematic mathematical procedure capable of detecting the presence of a gross error in the measurements and of reconciling connected data sets by using the maximum likelihood principle is applied to the biomass composition data of yeast. The biomass composition of Saccharomyces cerevisiae grown in a chemostat under glucose limitation was analyzed for its elemental and for its molecular composition. Both descriptions initially resulted in conflicting results concerning the elemental composition, molecular weight, and degrees of reduction. The application of the statistical reconciliation method, based on elemental balances and equality relations, is used to obtain a consistent biomass composition."

P.336 right column 2nd paragraph: "The following premises are made for the macromolecule composition of yeast: their composition is independent of the growth rate. The carbohydrates can be described as polyhexoses with infinite linear chains. For the nucleic acids, a guanine and cytidine content of each 20% is assumed. Lipids are taken as 60% fat and 40% phospholipids the acyl groups are made up of palmitoleic, oleic, palmitic, and stearic acids in a ratio of 44:17:14:10, as reported for S. cerevisiae grown on synthetic media by Kockova´ (Kockova´-Kratochvílova´, 1990). One acyl group is substituted in the phospholipids with an average of 23, 62, and 16% of ethanolamine, choline, and serine, respectively, bound through a phosphate group. The protein composition was derived from the experimental analysis of the amino acids. The resulting elemental composition of each macromolecule is given in Table I."

Uri M

protein, carbohydrate, lipids, RNA, DNA, composition, content, element, elemental composition, carbon, hydrogen, nitrogen, oxygen, sulfur, potassium

12214

112800

Amino acid composition of the protein as measured (mol %)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Amino%20acid%20composition%20of%20the%20protein%20as%20measured%20(mol%20percent).pdf

mol %

Lange HC, Heijnen JJ. Statistical reconciliation of the elemental and molecular biomass composition of Saccharomyces cerevisiae. Biotechnol Bioeng. 2001 Nov 5 75(3):334-44. p.339 table IV

11590606

P.338 right column 3rd paragraph: "Measurements of the Molecular Biomass Composition: The relative abundance of each amino acid did not vary between the different cultures and the average measured value (Table IV) was taken to determine the elemental protein composition as CH1.581N0.275O0.318S0.003. Most measured values were within ±10% of the ones reported by Oura (1972), Chistyakova et al. (1982), and Schulze (1995). A distinction between free amino acids and protein was not attempted. Trials with pure proteins exhibited variations in total recovery due to different susceptibility to hydrolyzation since the ratios of amino acids were in agreement with the literature values. On average, 0.82 ± 5% of the protein was recovered thus, measurements of the biomass protein content were adjusted accordingly."

Uri M

content,composition,

12219

112805

Acetaldehyde concentration

Budding yeast Saccharomyces cerevisiae

0.1

Bekers KM, Heijnen JJ1, van Gulik WM. Determination of the in vivo NAD/NADH ratio in S. cerevisiae under anaerobic conditions using alcohol dehydrogenase as sensor reaction. Yeast. 2015 Jun 9. doi: 10.1002/yea.3078. p.544 left column top paragraph

26059529

Verduyn C, Postma E, Scheffers WA, Vandijken JP. 1990. Physiology of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J Gen Microbiol 136: 395â403. DOI: 10.1099/00221287-136-3-395

1975265

Primary source abstract: "The physiology of Saccharomyces cerevisiae CBS 8066 was studied in anaerobic glucose-limited chemostat cultures in a mineral medium supplemented with ergosterol and Tween 80."

P.544 left column top paragraph: "Assuming a protein content of 50% w/w, a concentration of 0.1 mM acetaldehyde (primary source) and a specific cell volume of 1.7 ml/gDW (BNID 112806), the turnover time of the intracellular acetaldehyde pool can be calculated to be < 0.01 s."

Uri M

organic chemical compound, MeCHO, content, abundance

12220

112806

Specific cell volume

Budding yeast Saccharomyces cerevisiae

1.7

ml/gDW

26059529

Canelas AB, Ras C, ten Pierick A, et al. 2011. An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data. Metab Eng 13: 294â306. doi: 10.1016/j.ymben.2011.02.005.

21354323

P.544 left column top paragraph: "Assuming a protein content of 50% w/w, a concentration of 0.1 mM acetaldehyde (BNID 112805) and a specific cell volume of 1.7 ml/gDW (primary source), the turnover time of the intracellular acetaldehyde pool can be calculated to be < 0.01 s."

Uri M

size

12221

112807

Concentrations of the intracellular metabolites involved in the lumped GAPDH and PGK reactions and their subsequent ratios for approximately the same biomass-specific glucose consumption rates under aerobic and anaerobic conditions

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Concentrations%20of%20the%20intracellular%20metabolites%20involved%20in%20the%20lumped%20GAPDH%20and%20PGK%20reactions%20and%20their%20subsequent%20ratios.pdf

26059529

Abstract: "In this work [investigators] quantified free NAD:NADH ratios in yeast under anaerobic conditions, using alcohol dehydrogenase (ADH) and the lumped reaction of glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase as sensor reactions."

P.554 right column bottom paragraph: "The lower free NAD:NADH ratio (more reduced redox status) under anaerobic conditions has some major implications for the intracellular levels of the metabolites involved in glycolysis. For reactions that operate close to equilibrium, as is the case for GAPDH, the mass action ratio is close to the Keq at all times. As a consequence, a decreasing free NAD:NADH ratio would result in a shift of the mass action ratio from the thermodynamic equilibrium, and will thus be compensated by the ratios of the other products and reactants involved in the reaction. Table 1 shows the intracellular concentrations of these metabolites under aerobic and anaerobic conditions for the same glycolytic flux (for a complete overview, see supporting information, Figures S3, S4 and S5). Measurements of the cytosolic Pi concentrations are not available, but from the results of Gonzalez et al. (2000) it can be expected that this concentration is about a factor of 1.5 higher for anaerobic compared to aerobic conditions." GAPDH=glyceraldehyde-3-phosphate dehydrogenase. PGK=3-phosphoglycerate kinase

Uri M

aerobic, anaerobic, gap, Glyceraldehyde 3-phosphate, 3pg, 3-Phosphoglyceric acid, adp, atp, nad, Nicotinamide adenine dinucleotide, nadh, intracellular, metabolite, level, concentration, ratio, glucose, ethanol

12409

113067

Estimated wild-type DNA replication fork velocity

Budding yeast Saccharomyces cerevisiae

2.3

previous estimates 1.6-3kb/min

kb/min

Gispan A, Carmi M, Barkai N. Model-based analysis of DNA replication profiles: Predicting replication fork velocity and initiation rate by profiling free-cycling cells. Genome Res. 2016 Dec 27. pii: gr.205849.116. doi: 10.1101/gr.205849.116 p.5 top paragraph http://tinyurl.com/goepccw

28028072

Sekedat MD, Fenyo D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT. 2010. GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol Syst Biol 6: 353. http://www.ncbi.nlm.nih.gov/pubmed/20212525 DOI: 10.1038/msb.2010.8 AND Yang SC, Rhind N, Bechhoefer J. 2010. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol Syst Biol 6: 404. http://www.ncbi.nlm.nih.gov/pubmed/20739926 DOI: 10.1038/msb.2010.61 AND Hyrien O, Goldar A. 2010. Mathematical modelling of eukaryotic DNA replication. Chromosom Res 18: 147â161. http://www.ncbi.nlm.nih.gov/pubmed/20205354. doi: 10.1007/s10577-009-9092-4 AND Yabuki N, Terashima H, Kitada K. 2002. Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7: 781â789. http://www.ncbi.nlm.nih.gov/pubmed/12167157 AND Raghuraman MK et al., 2001. Replication dynamics of the yeast genome. Science (80- ) 294: 115â121. http://www.ncbi.nlm.nih.gov/pubmed/11588253 DOI: 10.1126/science.294.5540.115

20212525, 20739926, 20205354, 12167157, 11588253

P.5 top paragraph: "Validating predicted changes in fork velocity and initiation capacity using time-resolved profiling: [Investigators] next wished to verify predicted changes in fork velocity or initiation capacity. This required an independent means for measuring these parameters. To this end, [they] profiled cells that progress synchronously through S phase. Cells were arrested at the end of G1 using Î±-factor, and were followed for sixty minutes upon release, with samples taken every three minutes for DNA sequencing. Synchronized progression was verified by DNA staining (Fig. 4A). Plotting DNA content as a function of chromosomal coordinates at different times showed the expected v-shape increase in DNA content around replication origins, capturing the symmetric progression of the replication fork (Fig. 4B)."

P.5 top paragraph: "Based on this pattern around well-characterized origins [see Measurement Method], [investigators] estimated wild-type fork velocity to be 2.3 kb/min, consistent with previous estimates (1.6-3 kb/min)(primary sources)."

Uri M

polymerization, speed

12445

113112

Lipid composition of peroxisomal membrane of oleate-grown S. cerevisiae

Budding yeast Saccharomyces cerevisiae

phosphatidylcholine 48.2%: phosphatidylethanolamine 22.9%: phosphatidylinositol 15.8%:cardiolipin 7%

Kohlwein SD, Veenhuis M, van der Klei IJ. Lipid droplets and peroxisomes: key players in cellular lipid homeostasis or a matter of fatstore 'em up or burn 'em down. Genetics. 2013 Jan193(1):1-50. doi: 10.1534/genetics.112.143362. p.18 right column 4th paragraph

23275493

Zinser E et al. Phospholipid synthesis and lipid composition of subcellular membranes in the unicellular eukaryote Saccharomyces cerevisiae. J Bacteriol. 1991 Mar173(6):2026-34.

2002005

P.18 right column 4th paragraph: "The lipid composition of oleate-grown S. cerevisiae peroxisomes has been determined by Zinser et al. (primary source). The peroxisomal membrane contains the major cellular phospholipidsâphosphatidylcholine (48.2%), phosphatidylethanolamine (22.9%), and phosphatidylinositol (15.8%)âbut also has a remarkably high cardiolipin content (7%). The relative abundance of cardiolipin is noteworthy since this lipid is synthesized in mitochondria (Henry et al. 2012). The other lipids are derived from the ER-however, the mechanisms by which these lipids reach the peroxisomes are not yet firmly established-some evidence suggests that this process involves vesicular transport both from the ER and from mitochondria (Braschi et al. 2010)."

Uri M

peroxisome, membrane, lipid bilayer, intracellular organelle

12455

113130

Neutral lipid metabolism enzymes and LD (Lipid Droplets)-associated proteins

Budding yeast Saccharomyces cerevisiae

Table - http://bionumbers.hms.harvard.edu/files/Neutral%20lipid%20metabolism%20enzymes%20and%20LD-associated%20proteins.pdf

23275493

See pointers to refs at bottom of table

P.15 left column 3rd paragraph: "Targeting of proteins to LDs-Unlike other proteins targeted to organelles, LD-associated proteins apparently do not harbor targeting consensus sequences as determined by primary structure comparison of LD-associated proteins. However, a common feature appears to be the presence of hydrophobic domains, although exceptions exist (Leber et al. 1998 Mullner et al. 2004 Grillitsch et al. 2011). As shown in Table 1, several of the LD-associated proteins contain even one or two (predicted) transmembrane domains, which appear to be incompatible with the generally accepted view that the LD surface is covered by a phospholipid monolayer. Thus it is unclear how these extended stretches of hydrophobic amino acids are accommodated in the LD surface layer. Also, numerous LD proteins lack hydrophobic stretches indicative of membrane-anchoring sequences altogether (Table 1), suggesting that their interaction with LDs may be indirect and through the interaction with LD-anchored proteins."

Uri M

peroxisome, membrane, lipid bilayer, intracellular organelle

12557

113252

Drop in intracellular pH upon a glucose or ethanol pulse to glucose-limited chemostat cultures

Budding yeast Saccharomyces cerevisiae

from 6.5 to 5.5

unitless

Karen van Eunen & Barbara M. Bakker, The importance and challenges of in vivo-like enzyme kinetics, Perspectives in Science, Volume 1, Issues 1â6, May 2014, Pages 126â130, http://dx.doi.org/10.1016/j.pisc.2014.02.011 pdf http://tinyurl.com/jyn59e8 p.128 right column 2nd paragraph

Kresnowati MT, Suarez-Mendez CM, van Winden WA, van Gulik WM, Heijnen JJ. Quantitative physiological study of the fast dynamics in the intracellular pH of Saccharomyces cerevisiae in response to glucose and ethanol pulses. Metab Eng. 2008 Jan10(1):39-54. DOI: 10.1016/j.ymben.2007.10.001

18054509

P.128 right column 2nd paragraph: "Intracellular pH is recognized as one of most important factors that affects enzyme activities. To complicate matters, it may change rapidly upon a change in the environment. For instance, the intracellular pH of yeast drops from 6.5 to 5.5 upon a glucose or ethanol pulse to glucose-limited chemostat cultures (primary source). To mimic this in vitro, it is required to measure the intracellular pH accurately under conditions of interest."

Uri M

growth medium, acidity, ph

12562

113258

Doubling time of yeast subjected to different nutrients and metabolic operations

Budding yeast Saccharomyces cerevisiae

1.4 - 11

hours

Papagiannakis A, Niebel B, Wit EC, Heinemann M. Autonomous Metabolic Oscillations Robustly Gate the Early and Late Cell Cycle. Mol Cell. 2017 Jan 19 65(2):285-295. doi: 10.1016/j.molcel.2016.11.018. p.286 right column 2nd paragraph

27989441

Abstract: "Using microfluidics, cell-cycle reporters, and single-cell metabolite measurements, [investigators] found that metabolism of budding yeast is a CDK-independent oscillator that oscillates across different growth conditions, both in synchrony with and also in the absence of the cell cycle. Using environmental perturbations and dynamic single-protein depletion experiments, [they] found that the metabolic oscillator and the cell cycle form a system of coupled oscillators, with the metabolic oscillator separately gating and maintaining synchrony with the early and late cell cycle."

P.286 right column 2nd paragraph: "To test whether metabolic cycles also occur in other growth conditions, [investigators] subjected yeast to different nutrients and metabolic operations (aerobic fermentation, respiration, and gluconeogenesis), which varied the doubling time in single cells from 1.4 to 11 hr. Despite these different metabolic operations, [they] consistently identified oscillations in the NAD(P)H and ATP levels (Figures S2EâS2J), demonstrating that the metabolic cycles occur regardless of growth conditions."

Uri M

generation time, division time, growth rate

12563

113259

Period of cycle of metabolic oscillator

Budding yeast Saccharomyces cerevisiae

3 - 25 most with periods of 12

hours

27989441

Supplemental Information p.10 caption to figure S3D: "(D) Histogram of the frequency distribution of the periods of 63 metabolic oscillations without budding from 14 cells growing on low glucose and exhibiting multiple subsequent oscillations without budding. The period of each oscillation was estimated from the time between two consecutive troughs. This data shows that the autonomous metabolic oscillator can cycle at broadly different periods ranging from 3 to 25 hours with periods of 12 hours occurring most frequently in cells without cell cycle on low glucose."

Uri M

generation time,division time,growth rate

12564

113260

Fraction of total population that persisted after being subjected to antifungal drug fluphenazine

Budding yeast Saccharomyces cerevisiae

~0.1

Gilad Yaakov, David Lerner, Kajetan Bentele, Joseph Steinberger and Naama Barkai, Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress, Nature Ecology & Evolution 1, Article number: 0016 (2017) doi:10.1038/s41559-016-0016 pdf http://bionumbers.hms.harvard.edu/files/Gilad2017.pdf p.1 left column top paragraph & 3rd paragraph

Abstract: "[Investigators] report that spontaneous DNA damage triggers persistence in Saccharomyces cerevisiae by activating the general stress response, providing protection against a range of harsh stress and drug environments."

P.1 left column top paragraph: "Phenotypic persisters are individual microbes that survive harsh treatments that kill the majority of their genetically identical sister cells (refs 1-11). Persistence has been described in many bacterial species, and was recently implicated in the ability of individual cancer cells to survive chemotherapy (refs 12,13). Revealing the stochastic event triggering persistence is a major challenge to eradicating this subpopulation. Drug persistence has not been described in budding yeast, but a small fraction of cells have been shown to survive harsh environmental stresses (refs 14-16). While survivors are always expected, [investigators] observed a clear signature of persistence when subjecting cells to the antifungal drug fluphenazine: following the initial rapid exponential decline in the fraction of living cells, death rate was significantly reduced, indicating a small subpopulation (~10^â3) of persisters (Fig. 1a)." P.1 left column 3rd paragraph: "[Investigators] examined whether high Hsp12 [Heat shock protein 12] expression predicts stress survival by sorting single cells expressing either high (top 0.1%, termed âextremeâ) or normal (the remaining 99.9%, termed âcontrolâ) Hsp12-GFP (green fluorescent protein) into 96-well plates (Fig. 1c), and monitoring their ability to survive and generate a colony in a range of harsh stresses. In unstressed conditions, cells expressing extreme Hsp12 levels survived less well than control cells. In sharp contrast, extreme cells better survived practically all stress exposures (Fig. 1d,e). To verify that extreme cells maintain their advantage under competitive conditions, [they] co-sorted differentially labelled extreme and control cells into the same well at different initial frequencies, and measured the relative fraction of their progenies at saturation."

Uri M

survival, extreme cells

12565

113261

Fraction of cells that died within 60 min of exposure to antifungal drug fluphenazine

Budding yeast Saccharomyces cerevisiae

cells with low Heat Shock Protein 12 (HSP12) 99%: cells with high HSP12 25%

Gilad Yaakov, David Lerner, Kajetan Bentele, Joseph Steinberger and Naama Barkai, Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress, Nature Ecology & Evolution 1, Article number: 0016 (2017) pdf http://bionumbers.hms.harvard.edu/files/Gilad2017.pdf doi:10.1038/s41559-016-0016 p.4 left column

P.2 right column bottom paragraph to p.4 right column: "Consistent with the idea that DNA damage triggers persistence, [investigators] find an increased fraction of persisters in strains showing elevated mutation rates, as indicated by higher fractions of extreme Hsp12-expressing cells with increased stress survival (Supplementary Fig. 4). To verify directly that DNA damage triggers persistence, [they] induced DSBs [double-strand breaks] by expressing a GAL1-inducible HO (homothallic switching) endonuclease in cells with a single HO cleavage site. Inducing HO led to the appearance of Rad52-GFP foci, followed by a delayed (~2âh) induction of Hsp12-mCherry (Fig. 2f,g and Supplementary Fig. 5). Subjecting cells to fluphenazine confirmed that cells became persisters (Fig. 2h and Supplementary Videos 5 and 6). While ~99% of cells with low Hsp12 died within 60âmin of exposure, only 25% of high Hsp12 cells died at that time, with survivors losing viability at a significantly lower rate (Fig. 2i). Nearly all survivors had Rad52 foci (Fig. 2h). [They] conclude that a severe DNA damage, such as DSB, triggers persistence in budding yeast."

Uri M

survival, extreme cells

12566

113263

Summary of mutations detected in control and extreme cells

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Summary%20of%20mutations%20detected%20in%20control%20and%20extreme%20cells.pdf

Gilad Yaakov, David Lerner, Kajetan Bentele, Joseph Steinberger and Naama Barkai, Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress, Nature Ecology & Evolution 1, Article number: 0016 (2017) pdf http://bionumbers.hms.harvard.edu/files/Gilad2017.pdf doi:10.1038/s41559-016-0016 p.5 table 1

[25] Lynch, M. et al. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc. Natl Acad. Sci. USA 105, 9272â9277 (2008). doi: 10.1073/pnas.0803466105. [27] Serero, A., Jubin, C., Loeillet, S., Legoix-Ne, P. & Nicolas, A. G. Mutational landscape of yeast mutator strains. Proc. Natl Acad. Sci. USA 111, 1897â1902 (2014). DOI: 10.1073/pnas.1314423111

18583475, 24449905

P.5 right column bottom paragraph: "Indels or SVs (structural variations) were found in 26 of the 412 extreme samples, compared with 6 out of the 315 control samples (Table 1)." P.6 left column 2nd paragraph: "The frequencies of mutations in [investigatorsâ] control samples are consistent with literature values (Table 1 and Supplementary Information) (primary sources 25, 27, ref 26). Estimating the mutation frequency of extreme cells is less straightforward, since cells are extreme only transiently, and their division time, while being extreme, is greatly prolonged (Fig. 2e). Lower and upper bounds are obtained, however, by respectively assuming that extreme samples differ from the control cells in all 23â25 divisions, or that they differ in only the last extreme division (Table 1). The extreme dynamics [they] describe suggest that this mutation frequency is closer to the upper bound, namely that a division which triggers cells to become extreme has ~5% chance of generating an indel or an SV." See notes beneath table

Uri M

survival, extreme cells, snps, single nucleotide polymorphism, indels, insertion, deletion, mutation, genetic material, DNA, rate, speed, DNA alteration, structural variation

12632

113361

Fraction of nascent polypeptides associated with Hsp70 SSB

Budding yeast Saccharomyces cerevisiae

~45

Wang F, Durfee LA, Huibregtse JM. A cotranslational ubiquitination pathway for quality control of misfolded proteins. Mol Cell. 2013 May 9 50(3):368-78. doi: 10.1016/j.molcel.2013.03.009. p.376 left column 2nd paragraph

23583076

F. Willmund et al., The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis, Cell, 152 (2013), pp. 196â209 doi: 10.1016/j.cell.2012.12.001.

23332755

Primary source abstract: "Here, [investigators] use a sensitive and global approach to define the cotranslational substrate specificity of the yeast Hsp70 SSB."

P.376 left column 2nd paragraph: "In yeast, Hsp70 SSB associates with approximately 45% of nascent polypeptides (primary source), consistent with the possibility that the relationship between nascent chain misfolding and ubiquitination may affect an incredibly broad range of cellular proteins."

Uri M

polypeptide, protein Folding., ribosome, heat shock protein

12633

113362

Fraction of polypeptides that are ubiquitinated in vivo

Budding yeast Saccharomyces cerevisiae

ribosome-bound nascent chains 1.1±0.07%: completed, newly made polypeptides 0.5±0.04%

Duttler S, Pechmann S, Frydman J. Principles of cotranslational ubiquitination and quality control at the ribosome. Mol Cell. 2013 May 9 50(3):379-93. doi: 10.1016/j.molcel.2013.03.010. p.381 right column top paragraph

23583075

P.381 left column bottom paragraph: "All ubiquitinated material was depleted after the first round of polyUb-affinity isolation (Figure S1F), demonstrating that the polyUb-affinity resin was not limiting in [investigatorsâ] experiments. Along with the experiments in Figures S1A and S1B, [they] conclude that the polyUb affinity approached used here quantitatively isolates polyubiquitinated polypeptides from the RNC [ribosome-nascent chain complex] fraction. The direct polyubiquitination of nascent chains was further confirmed in two additional experiments. First, 35S-nascent chains were released from purified RNCs, and then polyUb-affinity isolation was carried out after an additional round of sucrose cushion sedimentation for the separation of vacant ribosomes from the released nascent chains (Figure 1E, lane 6 Figure S2). This demonstrates that released nascent chains are directly captured by the polyUb-affinity resin. Second, [they] subjected isolated ribosome-35S-nascent chain complexes to a stringent salt wash (Fleischer et al., 2006) to remove associated factors prior to the ribosome dissociation step, and subsequent polyUb-affinity isolation confirmed that these salt-stripped nascent chains were ubiquitinated (Figure S1G, lanes 6 and 8 and lanes 10 and 12). Altogether, these experiments demonstrate that nascent chains are directly ubiquitinated while on the ribosome."

P.381 right column top paragraph: "Quantitative analysis showed that approximately 1.1% ± 0.07% (n = 59) of the ribosome-bound nascent chains and 0.5% ± 0.04% (n = 59) of completed, newly made polypeptides were ubiquitinated in vivo (Figure 1F). [Investigators] conclude that newly made proteins are ubiquitinated co- and post-translationally during synthesis."

Uri M

protein folding, protein degradation, proteasome, ubiquitin, translation, protein synthesis, ribosome

12634

113363

Number of Rkr1 proteins [involved in ubiquitin-mediated degradation of non-stop proteins and translationally stalled ER membrane proteins]

Budding yeast Saccharomyces cerevisiae

200

proteins/cell

23583075

P.388 right column bottom paragraph: "[Investigators'] analysis of RKR1 deletion strains suggests that only a relatively small fraction of ubiquitinated nascent chains arises from stalled or NS-mRNA-derived products (Bengtson and Joazeiro, 2010). This most likely reflects the robust nature of mRNA quality control (Doma and Parker, 2007), which rapidly eliminates aberrant mRNAs in an initial round of translation. Consistent with these findings, there are only 200 molecules of Rkr1 compared to 200,000 ribosomes per yeast cell (Ghaemmaghami et al., 2003 von der Haar, 2008 BNID 100267)."

Uri M

polypeptide, concentration, content, abundance

12635

113364

Excess of ribosomes over proteasomes in mammalian cells & yeast

Budding yeast Saccharomyces cerevisiae

fold

23583075

S.J. Russell, K.A. Steger, S.A. Johnston, Subcellular localization, stoichiometry, and protein levels of 26 S proteasome subunits in yeast, J. Biol. Chem., 274 (1999), pp. 21943â21952 AND T. von der Haar, A quantitative estimation of the global translational activity in logarithmically growing yeast cells, BMC Syst. Biol., 2 (2008), p. 87 doi: 10.1186/1752-0509-2-87.

10419517, 18925958

P.391 left column top paragraph: "Biological Impact of Cotranslational Ubiquitination on Cellular Homeostasis: It is interesting to consider the impact of the low levels of cotranslational ubiquitination on overall cellular homeostasis. Ribosomes are present in 10-fold excess over proteasomes in both yeast and mammalian cells (primary sources), and, thus, a steady flow of 2%â5% of ubiquitinated nascent chains represents a substantial burden for the proteasome pathway, even under nonstressed conditions, particularly because proteasomal degradation has similar processivity rates as translation (Henderson et al., 2011). This consideration may reconcile the seemingly contradictory observations that de novo folding is favored over degradation (Frydman and Hartl, 1996, Vabulas and Hartl, 2005) with findings that newly made proteins contribute significantly to proteasomal load (Kim et al., 2011) and to antigen presentation (Lelouard et al., 2004, Reits et al., 2000)."

Uri M

polypeptide degradation, translation machinery, concentration, content, abundance

12636

113365

Fraction of actively translated proteins that are bound to Hsp70 SSB

Budding yeast Saccharomyces cerevisiae

Willmund et al., The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis. Cell. 2013 Jan 17 152(1-2):196-209. doi: 10.1016/j.cell.2012.12.001. p.197 right column bottom paragraph

23332755

P.197 right column bottom paragraph: "SSB-associated nascent chains were identified through their mRNAs using three independent experiments carried out as biological replicates. The experiments were highly reproducible, as underscored by their high correlation coefficient (r = 0.92) following hierarchical clustering analysis (Figure S1F). Comparing the SSB-bound data set to both the Translatome and the cotranslational interactome of SRP [signal recognition particle] revealed clear differences in specificity between SSB and SRP as well as differences between the SSB interactome and the Translatome (Figure 1E). [Investigators'] data indicate that SSB does not bind to every nascent chain complex, allowing [them] to define âSSB-boundâ and ânon-SSB-boundâ data sets (Figure 1E, see also Figure 4A)."

P.197 right column bottom paragraph: "Hierarchical clustering and statistical analyses identified 1,990 mRNAs enriched in the SSB data set (herein SSB-bound) (Table S1), representing 65% of all actively translated proteins."

Uri M

protein folding, aggregation, heat shock protein

12637

113366

Fraction of nascent chains encoding cytosolic and nuclear proteins that are bound to Hsp70 SSB

Budding yeast Saccharomyces cerevisiae

~80

23332755

P.199 left column 2nd paragraph: "Systems-Level Analysis of SSB Specificity: [Investigators] next examined the overall characteristics of SSB-associated nascent polypeptides. In contrast to SRP, which binds secretory and membrane proteins, SSB preferentially binds to cytosolic and nuclear proteins (Figure 2C). The overlap between SSB-bound and SRP-bound nascent chains was negligible (Figure 2C, inset, Figure 1E). These results suggest that SSB and SRP binding to nascent polypeptides are mutually exclusive and that SSB binds to a large subset of approximately 80% of nascent chains encoding cytosolic and nuclear proteins (Figure 2D)."

Uri M

protein folding, aggregation, heat shock protein, nucleus, cytosol

12646

113375

Fraction of amino acid substitutions that lead to protein inactivation

Budding yeast Saccharomyces cerevisiae

20 - 65

Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A. 2005 Oct 4 102(40):14338-43. DOI: 10.1073/pnas.0504070102 p.14342 right column bottom paragraph

16176987

[37] Bloom JD et al., Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci U S A. 2005 Jan 18 102(3):606-11. DOI: 10.1073/pnas.0406744102 [45] Guo HH, Choe J, Loeb LA. Protein tolerance to random amino acid change. Proc Natl Acad Sci U S A. 2004 Jun 22 101(25):9205-10. DOI: 10.1073/pnas.0403255101

15644440, 15197260

P.14342 right column bottom paragraph: "How large are the costs underlying translational robustness? [Investigators] can make a crude general estimate. As mentioned above, â19% of average-length yeast proteins will contain a missense error at typical ribosomal error rates. For diverse proteins, 20-65% of amino acid substitutions lead to inactivation (primary sources), generally due to misfolding (primary source 37). Consequently, 4-12% of a typical protein species would be expected to misfold because of missense errors."

Uri M

evolution,speciation

12654

113384

Number of phosphorylation sites that regulate proteins with a biotechnologically interesting phenotype

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Number%20of%20p-sites%20that%20regulate%20proteins%20with%20a%20biotechnologically%20interesting%20phenotype.pdf

Vlastaridis P et al., The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism. G3 (Bethesda). 2017 Apr 3 7(4):1239-1249. doi: 10.1534/g3.116.037218. p.1245 table 2

28250014

P.1245 right column 2nd paragraph: "Identification of p-sites [phosphorylation sites] in proteins that have a biotechnologically interesting phenotype related to metabolism and molecule production: The Saccharomyces Genome Database has mined and stored phenotypes caused by various gene perturbations, such gene over/underexpression or even gene deletion. [Investigators] manually inspected the phenotypes and focused on the ones that, in [their] opinion, are biotechnologically interesting. These phenotype terms mapped to 850 proteins, of which 408 were phosphoproteins, harboring 2363 p-sites. These phosphoproteins were not all annotated as participating in metabolism. By applying a stringent criterion of HC [high confidence] p-sites situated within conserved domains, [they] identified 180 of them in 73 phosphoproteins. These findings are summarized in Table 2. Obviously, there exist a significant number of very good candidate p-sites that may regulate biotechnologically important phenotypes, especially those related to increased chemical compound excretion and increased respiratory growth. These candidates should be the initial targets of future studies, e.g., to examine the phenotypic impact of deleting specific p-sites. Due to the inherent technical and biological noise of phosphorylation data, prioritization of p-sites for detailed study is an important task (Beltrao et al. 2012, Xiao et al. 2016). Readers can perform their own customized prioritization on these data using File S1."

Uri M

posttranslational modification, ATP, energy currency of cell, chemical compound, excretion, fermentative growth, fermentative metabolism, growth rate, nutrient uptake, respiratory growth, respiratory metabolism

12731

113490

Fraction of genes containing introns

Budding yeast Saccharomyces cerevisiae

Gonczarowska-Jorge H, Zahedi RP, Sickmann A. The proteome of baker's yeast mitochondria. Mitochondrion. 2017 Mar33: 15-21. doi: 10.1016/j.mito.2016.08.007. p.15 left column bottom paragraph

27535110

Cherry JM et al., Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 2012 Jan40(Database issue):D700-5. doi: 10.1093/nar/gkr1029. AND Goffeau A et al., Life with 6000 genes. Science. 1996 Oct 25 274(5287):546, 563-7.

22110037, 8849441

P.15 left column bottom paragraph: "Saccharomyces cerevisiae (S. cerevisiae) is an ideal model organism for many cellular processes in eukaryotes and for method development (Karathia et al., 2011). It was the first eukaryote whose genome was sequenced, wherein 12.1 megabases define 6604 potential protein-encoding genes, where only 4% of the genes, mostly encoding ribosomal proteins, contain introns (primary sources). The circular and conserved mitochondrial DNA (mtDNA) map of the strain FY1679 is composed of 85,779 base pairs, containing genes for mitochondrial small and large ribosomal RNAs, transfer RNAs, as well as mitochondrial proteins, among those subunits of the respiratory chain complexes III (Cytb), IV (Cox1, Cox2, Cox3), and V (Atp6, Atp8, and Atp9), as well as one ribosomal protein (Var1). (de Zamaroczy and Bernardi, 1986, Foury et al., 1998)."

Uri M

genome, splicing, gene structure

12732

113491

Classification of the mitochondrial proteome

Budding yeast Saccharomyces cerevisiae

Figure - http://bionumbers.hms.harvard.edu/files/Classification%20of%20the%20mitochondrial%20proteome.pdf

Gonczarowska-Jorge H, Zahedi RP, Sickmann A. The proteome of baker's yeast mitochondria. Mitochondrion. 2017 Mar33: 15-21. doi: 10.1016/j.mito.2016.08.007. p.16 fig. 1

27535110

Sickmann A et al., The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A. 2003 Nov 11 100(23):13207-12 DOI: 10.1073/pnas.2135385100

14576278

P.16 left column bottom paragraph: "Thus the highly-purified mitochondria were subjected to different separation techniques (1D, 2D PAGE [polyacrylamide gel electrophoresis] and multidimensional liquid chromatography) and proteolytic digestion with different enzymes prior to LC-MS [Liquid chromatographyâmass spectrometry]. In 2006, this first comprehensive yeast mitochondrial proteome was further expanded through the use of more advanced LC [liquid chromatography] and LC-MS methods by Reinders et al. (2006), leading to the identification of 102 additional proteins and estimating that the total of 851 identified proteins would correspond to 84% of the mitochondrial proteome in the MITOP [mitochondria-related proteins] yeast database (Scharfe et al., 1999), which would then amount to 1000 proteins. As of May 2016, a total of 1187 genes in the Saccharomyces Genome Database (SGD) (Cherry et al., 2012) were assigned to mitochondria (see Fig. 1)." P.16 caption to figure 1: "The 1187 proteins that were assigned to mitochondria in SGD as of May 2016 were classified, based on Gene Ontology Terms. As in the first mitochondrial proteome from Sickmann et al. (primary source) with 749 proteins, the share of proteins that are related to maintenance and expression of the mitochondrial genome is surprisingly high (22% compared to 25%), whereas the share of proteins with still (rather) unknown function decreased from 25% to 10%."

Uri M

genome, energy, protein import, protein folding, protein processing, lipids, metabolism, mitochondrial genome maintenance, mitochondrial genome expression, protein kinase

12733

113492

Fraction of imported mitochondrial proteins that are degraded after import in logarithmically growing yeast

Budding yeast Saccharomyces cerevisiae

6 - 12

Gonczarowska-Jorge H, Zahedi RP, Sickmann A. The proteome of baker's yeast mitochondria. Mitochondrion. 2017 Mar33: 15-21. doi: 10.1016/j.mito.2016.08.007. p.18 right column top paragraph

27535110

Augustin S et al., Characterization of peptides released from mitochondria: evidence for constant proteolysis and peptide efflux. J Biol Chem. 2005 Jan 28 280(4):2691-9. DOI: 10.1074/jbc.M410609200

15556950

P.18 right column top paragraph: "Besides proteases that play a role in protein import such as Icp55, MPP or Oct1, maintaining mitochondrial homeostasis requires a dedicated protein turnover machinery. This is particularly relevant as the components of the respiratory chain are encoded by both the mitochondrial and the nuclear genome. Imbalanced regulation may result in protein accumulation to avoid wrong complex stoichiometries. Moreover, the production of reactive oxygen species (ROS) renders especially IMM (inner mitochondrial membrane) proteins susceptible to undergo oxidative damage (Baker et al., 2011). Indeed, it is estimated that in logarithmically growing yeast 6â12% of imported mitochondrial proteins are degraded after import (primary source). Consequently, mitochondria possesses their own protein turnover machinery, composed of proteases and chaperones, responsible to maintain homeostasis especially under stress conditions (Baker et al., 2011, Pellegrino et al., 2013)."

Uri M

ptm, posttranslational modification, protein degradation, protein turnover

12734

113493

Copy number of 2Î¼ plasmid

Budding yeast Saccharomyces cerevisiae

40 - 80

copies per haploid genome

Gnügge R, Rudolf F. Saccharomyces cerevisiae Shuttle vectors. Yeast. 2017 May34(5):205-221. doi: 10.1002/yea.3228 p.208 right column 2nd paragraph & p.210 right column 3rd paragraph

28072905

Clark-Walker GD, Miklos GL. 1974. Localization and quantification of circular DNA in yeast. Eur J Biochem 41: 359â365. AND Futcher AB, Cox BS. 1984. Copy number and the stability of 2-micron circle-based artificial plasmids of Saccharomyces cerevisiae. J Bacteriol 157: 283â290 AND Gerbaud C, Guerineau M. 1980. 2 micron plasmid copy number in different yeast strains and repartition of endogenous and 2 micron chimeric plasmids in transformed strains. Curr Genet 1: 219â228 DOI: 10.1007/BF00390947

4593580, 6361000, 24189662

P.208 right column 2nd paragraph: "Yeast episomal plasmids (YEps) are based on sequences from a natural yeast plasmid. This plasmid is present in most wild-type and laboratory S. cerevisiae strains and has a length of 6318 bp (Hartley and Donelson, 1980). Alluding to its contour size, it was termed 2Î¼m or 2Î¼ plasmid (Stevens and Moustacchi, 1971, Guerineau et al., 1971). The plasmid is cryptic, as it is not associated with any apparent phenotype and confers no selective advantage to its host cell, nevertheless, its loss is very rare (Futcher and Cox, 1983). The 2Î¼ plasmid persists in yeast cells with 40â80 copies per haploid genome (primary sources). The plasmid copies are not homogeneously distributed in the nucleus, but are found in a few clusters (Scott-Drew and Murray, 1998, Velmurugan et al., 2000)." P.210 right column 3rd paragraph: "YEps containing the complete 2Î¼ sequence achieve 40â80 copies per cell, which is comparable to the endogenous 2Î¼ plasmid copy number (primary source Futcher and Cox, 1984)."

Uri M

dna, genetic material

12741

113501

Fraction of cell divisions in which the endogenous 2Î¼ plasmid is lost

Budding yeast Saccharomyces cerevisiae

<0.01

Gnügge R, Rudolf F. Saccharomyces cerevisiae Shuttle vectors. Yeast. 2017 May34(5):205-221. doi: 10.1002/yea.3228 p.210 right column 2nd paragraph

28072905

Futcher AB, Cox BS. 1983. Maintenance of the 2 microns circle plasmid in populations of Saccharomyces cerevisiae. J Bacteriol 154: 612â622.

6341357

P.210 right column 2nd paragraph: "While the endogenous 2Î¼ plasmid is lost in less than 0.1â° of the cell divisions (primary source), YEps [Yeast episomal plasmids] have a higher plasmid loss frequency. YEps that are created by the insertion of heterologous sequences into the complete 2Î¼ plasmid are typically lost in about 1% of the cell divisions. YEps containing only the 2Î¼ ORI and STB [a cis-acting sequence] sequences have plasmid loss frequencies of 1â5% in cir+ cells and of up to 50% in cir0 cells if REP1 and REP2 expression in trans is absent (Christianson et al., 1992, Futcher and Cox, 1984). The increased plasmid loss frequency of YEps can be attributed to decreased replication or amplification propensities and burdening overexpression of marker genes and other heterologous genes (Rose and Broach, 1990, Cakar et al., 1999, Karim et al., 2013)."

Uri M

dna, genetic material

12743

113503

Fraction of genes regulated by Heat shock factor 1 (HSF1)

Budding yeast Saccharomyces cerevisiae

Pincus D. Size doesn't matter in the heat shock response. Curr Genet. 2017 May63(2):175-178. doi: 10.1007/s00294-016-0638-7. p.176 right column top paragraph

27502399

Hahn JS, Hu Z, Thiele DJ, Iyer VR (2004) Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol 24 :5249â5256 DOI: 10.1128/MCB.24.12.5249-5256.2004

15169889

P.176 right column top paragraph: "A previous report had suggested that Hsf1 regulates upward of 3 % of yeast genes (primary source), so [investigators] expected many transcripts to change upon Hsf1 nuclear depletion. Strikingly, however, only 18 genes showed both reduced transcription and total mRNA levels following rapamycin treatment under basal conditions (Fig. 1a). All of these 18 Hsf1-dependent genes (HDGs) showed strong Hsf1 binding peaks in their promoters as determined by ChIP-seq [wiki-[this] is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins], and all but one HDG encodes a chaperone or other proteostasis-related factor."

Uri M

transcription factor, protein, gene expression

12811

113581

Difference between catalyzed and uncatalysed reaction in which OMP decarboxylase turns its substrate over

Budding yeast Saccharomyces cerevisiae

order of magnitudes faster

Miller BG, Wolfenden R. Catalytic proficiency: the unusual case of OMP decarboxylase. Annu Rev Biochem. 2002 71: 847-85. DOI: 10.1146/annurev.biochem.71.110601.135446 abstract

12045113

Abstract: "5'-phosphate decarboxylase (ODCase) turns its substrate over with a half-time of 18 ms, in a reaction that proceeds in its absence with a half-time of 78 million years in neutral solution."

Uri M

enzyme kinetics

12930

113854

Quantitative analysis of cellular components (volume, volume percentage & surface area)

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Quantitative%20Analysis%20of%20Cellular%20Components.pdf

Wei D et al., High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy. Biotechniques. 2012 Jul53(1):41-8. doi: 10.2144/000113850 p.47 table 1

22780318

Abstract: "[Investigators] developed an approach for focused gallium-ion beam scanning electron microscopy with energy filtered detection of backscattered electrons to create near isometric voxels for high-resolution whole cell visualization. Specifically, this method allowed [them] to create three-dimensional volumes of high-pressure frozen, freeze-substituted Saccharomyces cerevisiae yeast cells with pixel resolutions down to 3 nm/pixel in x, y, and z, supported by both empirical data and Monte Carlo simulations." P.47 note beneath table 1: "Quantitative analysis of volume, volume percentage and surface area of cellular components segmented in Avizo software."

P.47 right column top paragraph: "The accurate reconstruction of organelles in an entire cell allowed [investigators] to quantify targeted cellular structures, including but not limited to volume, volume percentage and surface area of various organelles (Table 1)." P.47 right column bottom paragraph: "[Investigators'] overall goal to optimize conditions for high-resolution 3D reconstructions of entire single cells allowed [them] to quantify and understand the spatial distribution of numerous sub-cellular structures (Figure 2, Table 1)."

Uri M

Cellular component, volume, percentage, surface area, size, endoplasmic reticulum, nuclear envelope, heterochromatin, euchromatin, golgi apparatus, mitochondria, lipid droplets, vesicles, vacuoles, cell wall, organelle, fraction

12933

113860

tRNA, ribosomes and mRNAs produced per generation

Budding yeast Saccharomyces cerevisiae

tRNAs ~3,000,000: ribosomes 300,000: mRNAs ~60,000

1/generation

Phizicky EM, Hopper AK. tRNA biology charges to the front. Genes Dev. 2010 Sep 1 24(17):1832-60. doi: 10.1101/gad.1956510 p.1832 right column top paragraph

20810645

Ares M Jr, Grate L, Pauling MH. 1999. A handful of intron-containing genes produces the lion's share of yeast mRNA. RNA 5: 1138â1139 AND Waldron C, Lacroute F. 1975. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J Bacteriol 122: 855â865

10496214, 1097403

Primary source Waldron et al. abstract: "The RNA from cells growing in different media was analyzed by polyacrylamide gel electrophoresis."

P.1832 right column top paragraph: "tRNA and rRNA genes are highly transcribed, leading to the production in yeast of â¼3 million tRNAs per generation and 300,000 ribosomes (primary source Waldron and Lacroute 1975), compared with about 60,000 mRNAs (primary source Ares et al. 1999). Because of the energy devoted to tRNA and rRNA transcription, and because of the required coordination of tRNA and ribosome function, tRNA transcription via RNA polymerase III (Pol III) and rRNA transcription via Pol I need to be coordinated and regulated in response to cellular nutrient availability and other environmental information."

Uri M

transfer rna, translation machinery, transcripts, content, composition

12935

113864

GSH [glutathione] half-life under standard conditions

Budding yeast Saccharomyces cerevisiae

~90

min

Baudouin-Cornu P, Lagniel G, Kumar C, Huang ME, Labarre J. Glutathione degradation is a key determinant of glutathione homeostasis. J Biol Chem. 2012 Feb 10 287(7):4552-61. doi: 10.1074/jbc.M111.315705 abstract, p.4555 left column top paragraph & supplementary information p.15

22170048

Abstract: "Combining mathematical models and (35)S labeling, [investigators] analyzed Saccharomyces cerevisiae sulfur metabolism. This led [them] to the observation that GSH [glutathione] recycling is markedly faster than previously estimated. [They] set up additional in vivo assays and concluded that under standard conditions, GSH half-life is around 90 min."

P.4554 right column bottom paragraph: "Thus, [investigators'] model strongly suggests that the time required for converting half the concentration of total GSH into Cys ([cor]T1/2[GSH]) is around 90 min (supplemental information, Part1). Determination of GSH Half-livesâThe half-life of a molecule is usually defined as the time required to degrade 50% of the initial amount of this molecule (e.g. [cor]T1/2[GSH] for GSH, see above). For practical reasons, [they] also use in this work the notion of apparent half-life of GSH ([app]T1/2 [GSH]), which [they] define as the time required to incorporate into proteins 50% of the sulfur atoms of the initial pool of GSH."

Uri M

antioxidant, glutathione, turnover, tripeptide, halflife

12938

113868

GSH [glutathione] half-lives in cells grown under different conditions

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/GSH%20half-lives%20in%20cells%20grown%20under%20different%20conditions.pdf

22170048

P.4555 right column bottom paragraph: "The real degradation rate of GSH is faster than the rate measured in [investigators'] assay, as some of the [35S]Cys is converted back into [35S]GSH (Fig. 1). [They] evaluated the importance of Cys back-conversion into GSH using [35S]Cys labeling (Table 1). The [Prot]Cys/[Meta]Cys ratio thus measured gives an estimate of the relative importance of the fluxes coming from Cys to proteins and to other sulfur-containing metabolites. Using these additional data in small mathematical models, [they] calculated f[GSH], defined as the fraction of GSH converted into Cys in 1 min (Table 1, supplemental information, Part 4)."

Uri M

antioxidant,glutathione,turnover,tripeptide

12939

113869

GSH [glutathione] intracellular concentration in different conditions and genetic backgrounds

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/GSH%20intracellular%20concentration%20in%20different%20conditions%20and%20genetic%20backgrounds.pdf

22170048

P.4557 left column 2nd paragraph: "To complete this study, [investigators] measured GSH intracellular concentration in W303-1A cells grown in nitrogen-free medium and observed that this concentration is significantly increased (Table 2). This result is consistent with a recent study in Schizosaccharomyces pombe (ref 27) but contrasts with other data in Saccharomyces cerevisiae (ref 9)." P.4558 right column 2nd paragraph: "[Investigators] measured GSH concentration in WT, dug2Î, and dug3Î strains and found that under standard conditions, the amount of intracellular GSH in the degradation mutants is approximately twice that in the WT strain (Table 2). Interestingly, this is the concentration [they] find in [their] mathematical model by simply suppressing GSH degradation (flux p = 0, Fig. 2) and adapting GSH concentration to satisfy the steady state hypothesis."

Uri M

antioxidant,glutathione,turnover,tripeptide

12961

113956

Volume to surface area ratio in tubER (tubular Endoplasmic Reticulum), cecER (central cisternal ER), and pmaER (plasma membrane-associated ER)

Budding yeast Saccharomyces cerevisiae

tubER 7: cecER 9.2: pmaER 7.4

West M, Zurek N, Hoenger A, Voeltz GK. A 3D analysis of yeast ER structure reveals how ER domains are organized by membrane curvature. J Cell Biol. 2011 Apr 18 193(2):333-46. doi: 10.1083/jcb.201011039 p.335 figure 1H & p.336 left column 2nd paragraph

21502358

P.336 left column 2nd paragraph: "[Investigators] used [their] 3D models to calculate the lumenal volume to surface area (V/SA) ratios of all three ER domains. [They] measured the volume to surface area ratios for several regions in [their] models that were unambiguously tubER, cecER, and pmaER (Fig. 1 H, mean V/SA[tubER] = 7.0, V/SA[cecER] = 9.2, and V/SA[pmaER] = 7.4). [They] also calculated for comparison the volume to surface area ratios of 30- and 60-nm vesicles present in [their] samples (V/SA = 5.0 and 10.0, respectively). These data reveal that ER domain shape affects the lumenal volume to membrane surface area ratios. In yeast, the cecER has a larger volume to surface area ratio than tubER and pmaER, which suggests that tubER could be better suited for functions that require a lot of membrane surface area, whereas cecER may be adapted for lumenal processes."

Uri M

physical property, size, surface area, organelle

12963

113958

Fraction of plasma membrane that is pmaER (plasma membrane-associated Endoplasmic Reticulum)

Budding yeast Saccharomyces cerevisiae

20-40

21502358

Abstract: "[Investigators] analyzed the structure of yeast endoplasmic reticulum (ER) during six sequential stages of budding by electron tomography to reveal a three-dimensional portrait of ER organization during inheritance at a nanometer resolution. [They] have determined the distribution, dimensions, and ribosome densities of structurally distinct but continuous ER domains during multiple stages of budding with and without the tubule-shaping proteins, reticulons (Rtns) and Yop1."

P.343 right column bottom paragraph: "The pmaER has many surprising features. It is made up of both tubules and fenestrated cisternae, which are so tightly linked to the PM [plasma membrane] that ribosomes are excluded between the two membranes (Fig. 1, EâG). The pmaER covers â¼20â40% of the PM in wt cells (varies with bud size, Fig. 4 H). Direct contacts between the PM and pmaER membranes can occasionally be found when [investigators] search for them (Fig. S5 A). Together, these data reveal a large pmaERâPM domain that may be unavailable for processes like vesicle-directed endocytosis and secretion. Indeed, within [their] tomograms, [they] have only observed invaginations of the PM at regions of the PM that are not bound by the ER (for an example see Fig. S5 B). The proteins that maintain this pmaERâPM domain have not been identified."

Uri M

size, surface area, organelle

12972

114002

Heme (iron protoporphyrin IX) concentration

Budding yeast Saccharomyces cerevisiae

in cytosol 20 - 40nM: in nucleus & mitochondria <2.5nM: total ferrous heme in mitochondria ~30µM

Hanna DA et al., Heme dynamics and trafficking factors revealed by genetically encoded fluorescent heme sensors. Proc Natl Acad Sci U S A. 2016 Jul 5 113(27):7539-44. doi: 10.1073/pnas.1523802113 abstract & p.7539 left column bottom paragraph & p.7543 left column 4th paragraph & bottom paragraph

27247412

[28] Garber Morales J, et al. (2010) Biophysical characterization of iron in mitochondria isolated from respiring and fermenting yeast. Biochemistry 49(26):5436â5444 doi: 10.1021/bi100558z

20536189

Abstract: "Herein, [investigators] elucidate the nature and dynamics of LH (labile heme) using genetically encoded ratiometric fluorescent heme sensors in the unicellular eukaryote Saccharomyces cerevisiae."

Abstract: "[Investigators] find that the subcellular distribution of LH (labile heme) is heterogeneous, the cytosol maintains LH at â¼20-40 nM, whereas the mitochondria and nucleus maintain it at concentrations below 2.5 nM." P.7539 left column bottom paragraph: "Herein, [investigators] report genetically encoded ratiometric fluorescent heme sensors and deploy them in the unicellular eukaryote Saccharomyces cerevisiae (Bakerâs yeast) to elucidate the nature and dynamics of LH. [They] find that LH is buffered at a concentration of 20â40 nM in the cytosol and less than 2.5 nM in the nucleus and mitochondria." P.7543 left column bottom paragraph: "The mitochondria, which have a very high demand for heme and are the site of heme biosynthesis, have exceptionally low quantities of LH, less than 2.5 nM or fewer than one molecule. By comparison, total ferrous heme in the yeast mitochondria has been estimated to be â¼30 Î¼M, or â¼9,000 molecules (primary source). Taken together, this low amount of mitochondrial LH suggests that mitochondrial heme is tightly regulated and trafficked in a manner that limits its availability. This observation is consistent with the identification of mitochondrial heme metabolism complexes that traffic heme via transient proteinâprotein interactions, thereby circumventing the LH pool (ref 35)."

Uri M

cofactor, ferrous ion

12978

114013

Cell growth rate and vacuole growth rate

Budding yeast Saccharomyces cerevisiae

cell growth rate 4.9±2.0 Î¼m^3/min: vacuole growth rate 1.3±1.1 Î¼m^2/min

Chan YH et al., Organelle Size Scaling of the Budding Yeast Vacuole by Relative Growth and Inheritance. Curr Biol. 2016 May 9 26(9):1221-8. doi: 10.1016/j.cub.2016.03.020 Supplemental Information p.8 table S1

27151661

P.1225 left column bottom paragraph: "To determine whether population-wide vacuole-to-cell size scaling can arise from relative growth rates in the absence of feedback, [investigators] implemented a theoretical model of cell and vacuole growth in asymmetrically dividing cells (Figure 4A). To account for natural variation in cell and vacuole growth rates, [they] evaluated model predictions using Monte Carlo simulations to predict population-wide scaling distributions (Supplemental Experimental Procedures, Table S1)."

Supplemental Information p.9 bottom paragraph: "Cell and vacuole growth simulations â Simulations of cell and vacuole growth were programmed using MATLAB (MathWorks). To generate a wild-type population (Fig. 3B, center), the simulation was initialized with 10 1st-generation mother cells containing a vacuole. The ratio of vacuole surface area-to cell volume was set to the population average measured experimentally. The time step of the simulation was 10min, and instantaneous cell and vacuole growth rates were randomly chosen from a Gaussian distribution with mean and standard deviation calculated from experimental data (cell volume growth rate = 4.9 ± 2Î¼m^3/time step, vacuole surface area growth rate = 1.3 ± 1.1Î¼m^2/time step). 1st generation mothers without buds were considered to be in G1, and when they reached a size threshold of volume 40Î¼m^3, they would begin budding with a probability that increased linearly with mother size. During budding, cell and vacuole continued growing at the same rates as in G1, and this growth was localized to the bud cell to simulate wild-type behavior. Once the bud reached a volume threshold of 30Î¼m^3, a probability of cytokinesis was introduced which increased linearly with bud size. Cytokinesis split the mother and bud along with their vacuoles into two mother cells to undergo a new G1 and budding cycle. This process was repeated until at least 500 cells were produced, which represented 6 generations of cells, and cell and vacuole sizes were recorded for every cell (mother, bud, and total) at all timepoints. The values of parameters used for the simulations depicted in each of the panels in Fig. 4 are summarized in Table S1."

Uri M

size, development

12991

114036

Simulation parameters of the (microtubule and dynein) gliding assay [to be approved once article is peer-reviewd]

Budding yeast Saccharomyces cerevisiae

Table link - http://bionumbers.hms.harvard.edu/files/Simulation%20parameters%20of%20the%20(microtubule%20and%20dynein)%20gliding%20assay.pdf

Kunalika Jain, Neha Khetan, Chaitanya A. Athale, 'Switch-like' transition from random to directed motility of microtubules by a yeast dynein, Biorxiv 2017, doi: https://doi.org/10.1101/181404 p.24 table 1

See refs beneath table

P.14 2nd paragraph: "The model of microtubule and motor mechanics is based on previous reports (refs 34, 63-67). Specific aspects that were modified from previous work are described in the following sections. Parameters were taken from previous reports of experimental measurements, where available, and in their absence reasonable estimates were made (Table 1)." P.16 4th paragraph: "2D simulations were performed using Cytosim, a C++ based Langevin dynamics simulation engine (ref 64). Space was modeled as a square simulation box with periodic boundary conditions. The integration time was chosen to be smaller than the fastest time-scale (Table 1). The system consists of MT [microtubule] filaments of a fixed length (L) and a fixed number of motors determined by the density (Ïm). Both filaments and motors were randomly distributed in simulation space at the time of initialization."

Uri M

time step, Thermal energy, kBT, Viscosity, glycerol, MT, motor mechanics, MT bending modulus, Motor stiffness, Attachment distance, molecular distances, Attachment rate, Basal detachment rate, Basal motor velocity, Stall force, Motor density

13045

114150

Cell surface potential

Budding yeast Saccharomyces cerevisiae

-131

PláÅ¡ek J et al., A novel method for assessment of local pH in periplasmic space and of cell surface potential in yeast. J Bioenerg Biomembr. 2017 Jun49(3):273-279. doi: 10.1007/s10863-017-9710-3 abstract & p.276 right column 4th paragraph

28405872

Abstract: "Here [investigators] present a novel method enabling the assessment of local pH at the periplasmic membrane surface which can be directly related to the underlying cell surface potential. In this proof of concept study using Saccharomyces cerevisiae cells with episomally expressed pH reporter, pHluorin, intracellular acidification induced by the addition of the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP) was measured using synchronously scanned fluorescence spectroscopy (SSF)."

Abstract: "The cell surface potential was estimated to amount to -130 mV." P.276 right column 3rd paragraph: "The cell surface potential in yeast is negative due to the presence of anionic groups on the plasma membrane surface. Hence, cations including H+ tend to accumulate in the vicinity of the cell surface. The ratio between the surface cs and bulk concentration câ is related to the surface potential Ïs through an exponential Boltzmann factor (Ehrenberg 1986, Itoh 1979, Tsui et al. 1986) as follows: cS=câe^â[FÏS/(RT)] (eq.3) After converting the bulk and periplasmic pH values to corresponding H+ concentrations, the ratio cs/câ can be inserted into Eq. 3. [Investigators] obtained Ïs = â131 and â89 mV in a plain 25 mM MES-TEA buffer and in a buffer of high ionic strength (25 mM MES-TEA with 145 mM choline chloride and 5 mM KCl), respectively. In the other series of measurements using PCP [pentachlorophenol, a protonophore] instead of CCCP [carbonyl cyanide m-chlorophenylhydrazone, another protonophore] the estimated cell surface potential was Ïs = â113 mV."

Uri M

electric potential, membrane, lipid bilayer

13059

114179

Distributions of protein abundance and functional enrichment

Budding yeast Saccharomyces cerevisiae

Figure - http://bionumbers.hms.harvard.edu/files/Distributions%20of%20protein%20abundance%20and%20functional%20enrichment.pdf

Brandon Ho et al., Comparative analysis of protein abundance studies to quantify the Saccharomyces cerevisiae proteome, bioRxiv preprint first posted online Feb. 2, 2017, doi: https://doi.org/10.1101/104919 p.5 figure 3 and beneath it p.2 table 1

P.7 right column bottom paragraph: "Here [investigators] provide a comprehensive view of protein abundance in yeast by normalizing and combining 19 abundance datasets, collected by mass spectrometry (Lu et al. 2007, de Godoy et al. 2008, Lee et al. 2011, Thakur et al. 2011, Peng et al. 2012, Nagaraj et al. 2012, Kulak et al. 2014, Lawless et al. 2016), GFP fluorescence flow cytometry (Newman et. al. 2006, Lee et al. 2007, Davidson et al. 2011), GFP fluorescence microscopy (Tkach et al. 2012, Breker et al. 2013, Denervaud et al. 2013, Mazumder et al. 2013, Chong et al. 2015, Yofe et al. 2016), and western blotting (Ghaemmaghami et al. 2003)." See table 1, beneath figure, 3rd column from left

P.5 right column 2nd paragraph: "Genetic interaction networks have been extensively characterized in yeast, mapping genes and pathways into functional modules (Costanzo et al. 2016). [Investigators] used spatial analysis of functional enrichment (SAFE) (Baryshnikova 2016) to identify the regions of the genetic interaction similarity network (Costanzo et al. 2016) that are enriched for high and low abundance proteins in [their] normalized protein abundance dataset (Figure 3B). [They] found high abundance proteins were specifically overrepresented in network regions associated with cell polarity and morphogenesis, and with ribosome biogenesis (Figure 3B, orange). Low abundance proteins were overrepresented in the region associated with DNA replication and repair (Figure 3B, teal)." See table 1 beneath figure for details on the 19 studies depicted in figure

Uri M

protein abundance, quantity, content

13060

114180

Total range of protein copies per cell (75% of proteins quantified are present in range 1,000-10,000molecules/cell)

Budding yeast Saccharomyces cerevisiae

0 - 1.3×10^6

molecules/cell

P.8 left column top paragraph: "Collectively, [investigatorsâ] analysis suggests protein abundance in the yeast proteome ranges from zero to 1.3 x 10^6 molecules per cell. Interestingly, 75% of yeast proteins quantified are present at between 1000 and 10 000 molecules per cell, indicating that it is rare for proteins to be present at very high or very low copy numbers."

Uri M

protein abundance, quantity, content

13061

114181

Half-life of typical mRNA

Budding yeast Saccharomyces cerevisiae

~32

min

Geisberg et al., Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast. Cell. 2014 Feb 13 156(4):812-24. doi: 10.1016/j.cell.2013.12.026

24529382

Primary source abstract: "[Investigators] measured half-lives of 21,248 mRNA 3' isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process."

P.8 left column bottom paragraph: "What could account for this apparent discrepancy? First, the half-life of a typical mRNA (~32 minutes) (primary source) is short compared to the typical protein (~43 minutes) (Belle et al. 2006 BNID 104151), and so it might be expected that mRNA levels would show a more rapid response to stress than would protein levels."

Uri M

transcript, halflife, degradation, lifetime, messenger RNA

13062

114182

Protein abundance (download Excel supplemental tables from link below)

Budding yeast Saccharomyces cerevisiae

http://tinyurl.com/y7ua7t2q

P.5 left column top paragraph: "Conversion of GFP measurements to molecules per cell resulted in a unified dataset covering 97% of the yeast proteome (Table S3). Of the 5858 protein proteome, only 156 proteins were not detected in any study (Table S4). The 156 proteins are enriched for uncharacterized ORFs (hypergeometric p = 6.9×10^-81) and for genes involved in proton transport and glucose import (p = 5.9×10^-5 and p =0.0080, respectively). 353 proteins were detected in only a single study. In general, there is agreement in the molecules per cell for each protein among the data sets analyzed in [investigators'] study, with protein abundances ranging from 5 to 1.3×10^6 molecules per cell (Figure 2A and Table S3)." P.7 left column bottom paragraph: "Since the majority of proteins do not change in abundance in any given stress condition, [investigators] normalized GFP intensities from each study by the mode-shifting method and applied the same linear regression used previously to convert arbitrary units to protein molecules per cell (Table S6). [They] applied a cut-off for changes in protein abundance, corresponding to either a two-fold increase or a two-fold decrease (Table S7). At this cutoff, which is more conservative than that used in most of the individual studies, 1250 of 4263 proteins assessed change in abundance in at least one condition: 580 proteins increase in abundance, and 744 proteins decrease in abundance. The magnitude of abundance changes spans a range of 60-fold for increases and 57-fold for decreases (Table S7, the Lee et al. dataset was excluded from analysis of abundance decreases as its inclusion results in maximum âfold decreases that greatly exceed the dynamic range of GFP fluorescence detection that is evident in Figure 3)."

Uri M

proteome, quantity, abundance

13110

114272

Ribosome footprints

Budding yeast Saccharomyces cerevisiae

typical footprint 28-29: stalled at an mRNA 3â² end ~15: closely stacked diribosomes ~80

nucleotides

Joazeiro CAP, Ribosomal Stalling During Translation: Providing Substrates for Ribosome-Associated Protein Quality Control. Annu Rev Cell Dev Biol. 2017 Oct 6 33: 343-368. doi: 10.1146/annurev-cellbio-111315-125249 p.355 3rd paragraph

28715909

Guydosh NR, Green R. 2014. Dom34 rescues ribosomes in 3â² untranslated regions. Cell 156: 950â62 doi: 10.1016/j.cell.2014.02.006

24581494

P.355 3rd paragraph: "Likely to be critical in providing a more complete picture of endogenous pauses and stalls at the transcriptome level are computational methods aimed at improving resolution (Woolstenhulme et al. 2015), experimental manipulations to increase stalling or decrease rescue (Figure 5) (primary source, Guydosh & Green 2017), and the analysis of alternative footprint sizes (primary source, Guydosh & Green 2017). Although the typical footprint size of nonrotated, elongating ribosomes is 28â29 nt, stalled ribosomes may be associated with different footprint sizes, for example, ribosomes stalled at an mRNA 3' end protect â¼15 nt, and closely stacked diribosomes can protect â¼80 nt (primary source)."

Uri M

translation machinery, mRNA

13311

114945

Volume of cell

Budding yeast Saccharomyces cerevisiae

69µm^3 at growth rate 0.35h^-1: 52.6µm^3 averaged over seven growth rates

µm^3

Klis FM, de Koster CG, Brul S. Cell wall-related bionumbers and bioestimates of Saccharomyces cerevisiae and Candida albicans. Eukaryot Cell. 2014 Jan13(1):2-9. doi: 10.1128/EC.00250-13 p.3 table 2

24243791

[7] McMurrough I, Rose AH. 1967. Effect of growth rate and substrate limitation on the composition and structure of the cell wall of Saccharomyces cerevisiae. Biochem. J. 105: 189â203.

6056621

Uri M

dimension, size

13314

114948

Average cell volume of adult (at 120 min of growth)

Budding yeast Saccharomyces cerevisiae

67.5

µm^3

Bryan AK, Goranov A, Amon A, Manalis SR. Measurement of mass, density, and volume during the cell cycle of yeast. Proc Natl Acad Sci U S A. 2010 Jan 19 107(3):999-1004 Supporting Information Average of adult (at 120 min) cell volumes in Figures S2 and S4

20080562

Abstract: "The suspended microchannel resonator weighs single cells with a precision in mass of 0.1% for yeast. Here [investigators] use the suspended microchannel resonator with a Coulter counter to measure the mass, volume, and density of budding yeast cells through the cell cycle."

Volume of adult (age 120 min) extracted visually from figures S2A (~78µm^3) and S4A (~57µm^3)

Uri M

size, dimension

13315

114949

Cell volume

Budding yeast Saccharomyces cerevisiae

7.3

±3

µm^3

Haddad SA, Lindegren CC. A method for determining the weight of an individual yeast cell. Appl Microbiol. 1953 May1(3):153-6 p.155 table 1

13041190

P.156 right column bottom paragraph: "A method is presented by which the density of individual yeast cells can be calculated by the use of Stokes' law for falling spheres through a viscous fluid. From density measurements the weights of the respective individuals cells can be computed. A high degree of accuracy of the method is revealed by correlation studies of weights and volumes computed independently from experimental data."

In 'Range' is standard deviation

Uri M

size, dimension

13316

114950

Number of ribosomes

Budding yeast Saccharomyces cerevisiae

200000

ribosomes/cell

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999 Nov24(11):437-40 p.437 left column bottom paragraph

10542411

Electron microscopy P.438 caption to figure 1A: "A thin-section electron micrograph showing the density of ribosomes in the cytoplasm of Saccharomyces cerevisiae (courtesy of B. Byers, University of Washington). As much as 30â40% of the cytoplasmic volume is occupied by ribosomes (scale bar=100 µm)."

P.437 left column bottom paragraph: "Comparison of the size of the genome (1.4×10^7 bp) with the RNA in a ribosome (5469 nucleotides) shows that there are nearly 200,000 ribosomes per cell (Fig. 1a)."

Uri M

translation machinery, content, concentration

13317

114951

Number of ribosomes

Budding yeast Saccharomyces cerevisiae

~220,000

ribosomes/cell

21908548

Abstract: "[Investigators] have coined a new word, 'structome', by combining 'structure' and '-ome', and defined it as the 'quantitative and three-dimensional structural information of a whole cell at the electron microscopic level'. In the present study, [they] performed structome analysis of Saccharomyces cerevisiae, one of the most widely researched biological materials, by using freeze-substitution and serial ultrathin-sectioning electron microscopy."

Abstract: "[Investigators'] analysis revealed that there were one to three mitochondria, ~220 000 ribosomes in a cell, and 13-28 endoplasmic reticula/Golgi apparatus which do not form networks in the cytoplasm in the G1 phase."

Uri M

translation machinery, content, concentration

13383

115090

Protein abundance

Budding yeast Saccharomyces cerevisiae

range 0 - 750,000: median 2,622: 67% of proteins between 1,000 - 10,000

molecules/cell

Ho B, Baryshnikova A, Brown GW. Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome. Cell Syst. 2018 Feb 28 6(2):192-205.e3. doi: 10.1016/j.cels.2017.12.004 p.198 left column

29361465

Abstract: "[Investigators] evaluated 21 quantitative analyses of the S. cerevisiae proteome, normalizing and converting all measurements of protein abundance into the intuitive measurement of absolute molecules per cell."

P.198 right column: "With [investigatorsâ] unified dataset, [they] find that yeast protein abundance, when logarithmically transformed, is skewed toward high-abundance proteins (Figure 4C). Protein abundance ranges from zero to 7.5 × 10^5 molecules per cell, the median abundance is 2,622 molecules per cell, and 67% of proteins quantified exist between 1,000 and 10,000 molecules per cell (Figure 4C). Low-abundance proteins, the first decile, have abundances ranging from 3 to 822 molecules per cell, while high-abundance proteins, the tenth decile, have abundances ranging from 1.4 × 10^5 to 7.5 × 10^5. [Their] data suggest that protein copy number is maintained within a narrow range from which only a small portion of the proteome deviates." P.202 right column 2nd paragraph: "Collectively, [investigatorsâ] analyses indicate that protein abundance in the yeast proteome ranges from 3 to 7.5 × 10^5 molecules per cell, with a median abundance of 2,622 molecules per cell. [They] define the lowest abundance proteins as those present at 866 or fewer copies, and the highest abundance proteins as those with 14,938 or more copies."

Uri M

concentration, content, enzyme

13384

115091

Average protein mass

Budding yeast Saccharomyces cerevisiae

54580

29361465

P.198 right column bottom paragraph: "With an average protein mass of 54,580 Da, and mean logarithmic phase cell volume of 42µm^3 (Jorgensen et al., 2002), [investigators] calculate 7.9×10^7 protein molecules per cell." Please note: value of 54,580 Da wasn't found in Jorgensen et al., 2002 PMID 12089449.

Uri M

weight, molecular mass, polypeptide

13385

115092

Half-life of a typical mRNA

Budding yeast Saccharomyces cerevisiae

~32

min

29361465

Geisberg JV, Moqtaderi Z, Fan X, Ozsolak F, Struhl K. Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast. Cell. 2014 Feb 13 156(4):812-24. doi: 10.1016/j.cell.2013.12.026

24529382

P.202 left column 4th paragraph: "The apparent absence of a global protein response likely reflects the short half-life of a typical mRNA (~32 min) (primary source) compared with the considerably longer median protein half-life (8.8 hr [Christiano et al., 2014] 2.0 hr [Martin-Perez and Villen, 2015])."

Uri M

turnover, halflife, halflives, degradation

13386

115093

Median protein half-life

Budding yeast Saccharomyces cerevisiae

[Christiano et al., 2014] 8.8: [Martin-Perez and Villen, 2015] 2.0

hours

29361465

Christiano R, Nagaraj N, Fröhlich F, Walther TC. Global proteome turnover analyses of the Yeasts S. cerevisiae and S. pombe. Cell Rep. 2014 Dec 11 9(5):1959-1965. doi: 10.1016/j.celrep.2014.10.065 AND Martin-Perez M, Villén J. Feasibility of protein turnover studies in prototroph Saccharomyces cerevisiae strains. Anal Chem. 2015 Apr 787(7):4008-14. doi: 10.1021/acs.analchem.5b00264

25466257, 25767917

P.202 left column 4th paragraph: "The apparent absence of a global protein response likely reflects the short half-life of a typical mRNA (~32 min) (BNID 115092) compared with the considerably longer median protein half-life (8.8 hr [primary source Christiano et al., 2014] 2.0 hr [primary source Martin-Perez and Villen, 2015])."

Uri M

turnover, halflife, halflives, degradation, polypeptide

13387

115096

Lower limit for reliable detection of GFPs [Green Fluorescent Proteins]

Budding yeast Saccharomyces cerevisiae

~1,400

molecules/cell

29361465

P.202 right column 2nd paragraph: "In conclusion, [investigators] provide a comprehensive view of protein abundance in yeast by normalizing and combining 21 abundance datasets, collected by MS [Mass Spectrometry], GFP fluorescence flow cytometry, GFP fluorescence microscopy, and western blotting. Since cellular autofluorescence interferes with detection of GFP fluorescence, [they] find that the lower limit for reliable detection of GFP proteins corresponds to â¼1,400 molecules per cell. Above this threshold [they] found less variation among GFP-based studies than among MS studies, suggesting that although MS analyses provide the greatest sensitivity and dynamic range for protein measurements, the GFP-based measurements have greater precision."

Uri M

green fluorescent protein, fluorescence

13655

115810

Total cellular concentrations

Budding yeast Saccharomyces cerevisiae

glutamate â¼75: glutathione â¼15: ATP â¼2.5

Theillet FX et al., Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev. 2014 Jul 9 114(13):6661-714. doi: 10.1021/cr400695p p.6664 left column 3rd paragraph

24901537

[39] van Eunen K et al., Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J. 2010 Feb277(3):749-60. doi: 10.1111/j.1742-4658.2009.07524.x [67] Østergaard H, Tachibana C, Winther JR. Monitoring disulfide bond formation in the eukaryotic cytosol. J Cell Biol. 2004 Aug 2 166(3):337-45 DOI: 10.1083/jcb.200402120 [68] Ytting CK et al., Measurements of intracellular ATP provide new insight into the regulation of glycolysis in the yeast Saccharomyces cerevisiae. Integr Biol (Camb). 2012 Jan4(1):99-107. doi: 10.1039/c1ib00108f

20067525, 15277542, 22134619

Primary source [39] abstract: "â¦[investigators] have developed a single assay medium for determining enzyme-kinetic parameters in yeast." Primary source [67] abstract: "Here, [investigators] present a glutathione-specific green fluorescent protein-based redox probe termed redox sensitive YFP (rxYFP). Using yeast with genetically manipulated GSSG [oxidized glutathione] levels, [they] find that rxYFP equilibrates with the cytosolic glutathione redox buffer." Primary source [68] abstract: "[Investigators] have constructed a new nanobiosensor that can perform time-resolved measurements of intracellular ATP in intact cells."

p.6664 left column 3rd paragraph: "In the yeast S. cerevisiae, total cellular concentrations of glutamate, glutathione, and ATP are â¼75, â¼15, and â¼2.5 mM, respectively (primary sources)."

Uri M

content, metabolites, energy currency of the cell

13663

115841

Fraction of intracellular buffering capacity that is contributed by the side-chains and free amino- and carboxy-termini of amino acids and proteins

Budding yeast Saccharomyces cerevisiae

24901537

[93] Roos A, Boron WF. Intracellular pH. Physiol Rev. 1981 Apr61(2):296-434 DOI: 10.1152/physrev.1981.61.2.296 [94] Poznanski J, Szczesny P, RuszczyÅska K, Zielenkiewicz P, Paczek L. Proteins contribute insignificantly to the intrinsic buffering capacity of yeast cytoplasm. iochem Biophys Res Commun. 2013 Jan 11 430(2):741-4. doi: 10.1016/j.bbrc.2012.11.079

7012859, 23206695

Primary source [94] abstract: "Using data from both high-throughput experiments and in vitro laboratory experiments, [investigators] tested this concept [that a large portion of and possibly most of the cell's intrinsic (i.e., passive non-bicarbonate) buffering effect was attributed to proteins]. [They] assessed the buffering capacity of the yeast proteome using protein abundance data and compared it to [their] own titration of yeast cytoplasm."

P.6665 left column 2nd paragraph: "As a rule of thumb, the pH of the cytoplasm is 7.2 (ref 91), and it is critical to maintain this value for any given organism (ref 92). Phosphate or bicarbonate ions and other weak acids and bases within the cell provide the intracellular buffering capacity, to which the side-chains and free amino- and carboxy-termini of amino acids and proteins contribute less than 1% (primary sources)."

Uri M

pH buffer, hydrogen ion buffer, acidity, polypeptide

13664

115844

Range of pH in which unfolding of ordered proteins is common

Budding yeast Saccharomyces cerevisiae

unitless

24901537

[100] Fink AL, Calciano LJ, Goto Y, Kurotsu T, Palleros DR. Classification of acid denaturation of proteins: intermediates and unfolded states. Biochemistry. 1994 Oct 18 33(41):12504-11

7918473

Primary source [100] abstract: "A systematic investigation of the effect of acid on the denaturation of some 20 monomeric proteins indicates that several different types of conformational behavior occur, depending on the protein, the acid, the presence of salts or denaturant, and the temperature. Three major types of effects were observed. Type I proteins, when titrated with HCl in the absence of salts, show two transitions, initially unfolding in the vicinity of pH 3-4 and then refolding to a molten globule-like conformation, the A state, at lower pH."

P.6665 left column 4th paragraph: "How do changes in intracellular pH affect disordered proteins? Ordered proteins are sensitive to pH, and unfolding is common at pH values <3 (primary source)."

Uri M

pH buffer,hydrogen ion buffer,acidity,polypeptide

13961

117020

Definition of one microStern (µS), a unit to measure mitotic crossovers

Budding yeast Saccharomyces cerevisiae

1.00E-06

crossovers/division

Rosen DM, Younkin EM, Miller SD, Casper AM. Fragile site instability in Saccharomyces cerevisiae causes loss of heterozygosity by mitotic crossovers and break-induced replication. PLoS Genet. 2013 9(9):e1003817. doi: 10.1371/journal.pgen.1003817 p.8 right column 4th paragraph

24068975

[28] St Charles J, Petes TD. High-resolution mapping of spontaneous mitotic recombination hotspots on the 1.1 Mb arm of yeast chromosome IV. PLoS Genet. 2013 Apr9(4):e1003434. doi: 10.1371/journal.pgen.1003434

23593029

Primary source abstract: "[Investigators] mapped about 140 spontaneous reciprocal crossovers on the right arm of the yeast chromosome IV using single-nucleotide-polymorphism (SNP) microarrays. [Their] mapping and subsequent experiments demonstrate that inverted repeats of Ty retrotransposable elements are mitotic recombination hotspots."

P.8 right column 4th paragraph: "St Charles and Petes [primary source] defined the microStern (µS) as a unit to measure mitotic crossovers, with 10^â6 crossovers/division equal to one microStern, and they estimated the entire yeast genome has a mitotic genetic map length of 620 µS. The portion of chromosome III [investigators] evaluated accounts for 1.3% of the physical yeast genome, therefore [they] expect a genetic map length of 8 µS."

Uri M

mitosis,chromosome,dna

13963

117022

Fraction of the transcriptome (including many essential genes), that is expressed at less than 2 copies per cell

Budding yeast Saccharomyces cerevisiae

Zenklusen D, Larson DR, Singer RH. Single-RNA counting reveals alternative modes of gene expression in yeast.Nat Struct Mol Biol. 2008 Dec15(12):1263-71. p.1263 left column bottom paragraph

19011635

[12] Holstege FC et al., Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998 Nov 25 95(5):717-28

9845373

Primary source abstract: "Genome-wide expression analysis was used to identify genes whose expression depends on the functions of key components of the transcription initiation machinery in yeast."

P.1263 left column bottom paragraph: "High-throughput analyses in yeast showed that protein variation for most genes is low [ref 11]. However, in the yeast Saccharomyces cerevisiae, most mRNAs are present in low abundance: 80% of the transcriptome, including many essential genes, are expressed at less than two copies per cell [primary source]."

Uri M

ribonucleic acid, transcription, mrna, transcript

14222

117288

Nucleosomes per yeast cell

Budding yeast Saccharomyces cerevisiae

57,000 - 60,000

nucleosomes per cell

Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome Elisa Oberbeckmann, Michael Wolff, Nils Krietenstein, Mark Heron, Jessica L Ellins, Andrea Schmid, Stefan Krebs, Helmut Blum, Ulrich Gerland, and Philipp Korber Genome Res. gr.253419.119Published in Advance November 6, 2019, doi:10.1101/gr.253419.119

31694866

https://www.ncbi.nlm.nih.gov/pubmed/31694866

Matan Lotem