What is the total number of protein molecules per cell volume? A call to rethink some published values

Abstract

Novel methods such as mass‐spectrometry enable a view of the proteomes of cells in unprecedented detail. Recently, these efforts have culminated in quantitative measurements of the number of copies per cell for most expressed proteins in organisms ranging from bacteria to mammalian cells. Here, we estimate the expected total number of proteins per unit of cell volume using known parameters related to the composition of cells such as the fraction of cell mass that is protein, and the average protein length. Using simple arguments, we estimate a range of 2–4 million proteins per cubic micron (i.e. 1 fL) in bacteria, yeast, and mammalian cells. Interestingly, we find that measured values that are reported for fission yeast and mammalian cells are often about 3–10 times lower. We discuss this apparent discrepancy and how to use the estimate as benchmark to recalibrate proteome‐wide quantitative censuses or to revisit assumptions about cell composition.

Shown for reading. Its publisher allows quoting it, not republishing it.

References 37

1. 1.

   Sapan CV, Lundblad RL, Price NC. Colorimetric protein assay techniques. Biotechnol Appl Biochem. 1999;29:99-108.

   Not in our library

2. 2.

   Aitken A, Learmonth M. Protein determination by UV absorption. Notes. 2002;205:3-6.

   Not in our library

3. 3.

   Pedersen S, Bloch PL, Reeh S, Neidhardt FC. Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates. Cell. 1978;14:179-90.

   Not in our library10.1016/0092-8674(78)90312-4

4. 4.

   Cox J, Mann M. Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem. 2011;80:273-99.

   Not in our library10.1146/annurev-biochem-061308-093216

5. 5.

   Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422:198-207.

   Not in our library10.1038/nature01511

6. 6.

   Kühner S, Van Noort V, Betts MJ, Leo-Macias A, et al. Proteome organization in a genome-reduced bacterium. Science (New York, NY). 2009;326:1235-40.

   Not in our library10.1126/science.1176343

7. 7.

   Schmidt A, Beck M, Malmström J, Lam H, et al. Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Mol Syst Biol. 2011;7:510.

   Not in our library10.1038/msb.2011.37

8. 8.
   Protein abundance profiling of the Escherichia coli cytosol · 2008

   No notice
9. 9.
   Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells · 2012

   No notice
10. 10.

    Schwanhäusser B, Busse D, Li N, Dittmar G, et al. Global quantification of mammalian gene expression control. Nature. 2011;473:337-42.

    Not in our library10.1038/nature10098

11. 11.

    Beck M, Schmidt A, Malmstroem J, Claassen M, et al. The quantitative proteome of a human cell line. Mol Syst Biol. 2011;7:549.

    Not in our library10.1038/msb.2011.82

12. 12.

    Nagaraj N, Wisniewski JR, Geiger T, Cox J, et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol. 2011;7:548.

    Not in our library10.1038/msb.2011.81

13. 13.

    Geiger T, Wehner A, Schaab C, Cox J, et al. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics. 2012;11:M111.014050.

    Not in our library10.1074/mcp.m111.014050

14. 14.

    Geiger T, Velic A, Macek B, Lundberg E, et al. Initial quantitative proteomic map of twenty-eight mouse tissues using the SILAC mouse. Mol Cell Proteomics. 2013;12:1709-22.

    Not in our library10.1074/mcp.m112.024919

15. 15.

    Eldar A, Elowitz MB. Functional roles for noise in genetic circuits. Nature. 2010;467:167-73.

    Not in our library10.1038/nature09326

16. 16.

    Phillips R, Milo R. A feeling for the numbers in biology. Proc Natl Acad Sci USA. 2009;106:21465-71.

    Not in our library10.1073/pnas.0907732106

17. 17.

    Schwanhäusser B, Busse D, Li N, Dittmar G, et al. Corrigendum: global quantification of mammalian gene expression control. Nature. 2013;495:126-7.

    Not in our library10.1038/nature11848

18. 18.

    Arike L, Valgepea K, Peil L, Nahku R, et al. Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. J Proteomics. 2012;75:5437-48.

    Not in our library10.1016/j.jprot.2012.06.020

19. 19.

    Finka A, Goloubinoff P. Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis. Cell Stress Chaperones. 2013;18:591-605.

    Not in our library10.1007/s12192-013-0413-3

20. 20.

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

    Not in our library10.1016/s0022-5193(05)80266-8

21. 21.

    Milo R, Jorgensen P, Moran U, Weber G, et al. BioNumbers—the database of key numbers in molecular and cell biology. Nucl Acids Res. 2010;38:D750–-53.

    Not in our library10.1093/nar/gkp889

22. 22.

    Brocchieri L, Karlin S. Protein length in eukaryotic and prokaryotic proteomes. Nucl Acids Res. 2005;33:3390-400.

    Not in our library10.1093/nar/gki615

23. 23.

    Zhang J. Protein-length distributions for the three domains of life. Trends Genet. 2000;16:107-9.

    Not in our library10.1016/s0168-9525(99)01922-8

24. 24.

    Zimmerman SB, Trach SO. Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J Mol Biol. 1991;222:599-620.

    Not in our library10.1016/0022-2836(91)90499-v

25. 25.

    Ellis RJ. Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr Opin Struct Biol. 2001;11:114-9.

    Not in our library10.1016/s0959-440x(00)00172-x

26. 26.

    Wang Z, Shen W, Kotler DP, Heshka S, et al. Total body protein: a new cellular level mass and distribution prediction model. Am J Clin Nutr. 2003;78:979-84.

    Not in our library10.1093/ajcn/78.5.979

27. 27.

    Dennis PP, Bremer H. Macromolecular composition during steady-state growth of Escherichia coli B-r. J Bacteriol. 1974;119:270-81.

    Not in our library10.1128/jb.119.1.270-281.1974

28. 28.

    Inoyye S, Takeishi K, Lee N, DeMartini M, et al. Lipoprotein from the outer membrane of Escherichia coli: purification, paracrystallization, and some properties of its free form. J Bacteriol. 1976;127:555-63.

    Not in our library10.1128/jb.127.1.555-563.1976

29. 29.

    Luciani AM, Rosi A, Matarrese P, Arancia G, et al. Changes in cell volume and internal sodium concentration in HeLa cells during exponential growth and following lonidamine treatment. Eur J Cell Biol. 2001;80:187-95.

    Not in our library10.1078/0171-9335-00102

30. 30.

    Lu P, Vogel C, Wang R, Yao X, et al. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007;25:117-24.

    Not in our library10.1038/nbt1270

31. 31.

    Ghaemmaghami S, Huh W-K, Bower K, Howson RW, et al. Global analysis of protein expression in yeast. Nature. 2003;425:737-41.

    Not in our library10.1038/nature02046

32. 32.

    Taniguchi Y, Choi PJ, Li G, Chen H, et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science. 2010;329:533-8.

    Not in our library10.1126/science.1188308

33. 33.

    Maass S, Sievers S, Zühlke D, Kuzinski J, et al. Efficient, global-scale quantification of absolute protein amounts by integration of targeted mass spectrometry and two-dimensional gel-based proteomics. Anal Chem. 2011;83:2677-84.

    Not in our library10.1021/ac1031836

34. 34.

    Futcher B, Latter GI, Monardo P, McLaughlin CS, et al. A sampling of the yeast proteome. Mol Cell Biol. 1999;19:7357-68.

    Not in our library10.1128/mcb.19.11.7357

35. 35.
    A quantitative estimation of the global translational activity in logarithmically growing yeast cells · 2008

    No notice
36. 36.

    Maier T, Schmidt A, Güell M, Kühner S, et al. Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Sys Biol. 2011;7:511.

    Not in our library10.1038/msb.2011.38

37. 37.

    Beck M, Malmström JA, Lange V, Schmidt A, et al. Visual proteomics of the human pathogen Leptospira interrogans. Nat Methods. 2009;6:817-23.

    Not in our library10.1038/nmeth.1390

Cited by papers we hold 22

• Pre-clinical safety and efficacy evaluation of Helicobacter Pylori neutrophil-activating protein (NAP)-armed CAR-T cells targeting B cell lymphomas · 2025
  Not checked
• High-throughput determination of dry mass of single bacterial cells by ultrathin membrane resonators · 2022
  Not checked
• Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. · 2022
  Not checked
• Advances and Trends in Omics Technology Development · 2022
  No notice
• A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation · 2021
  Not checked
• Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2 · 2021
  No notice
• From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions · 2021
  Corrected
• RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs · 2020
  No notice
• Metabolic profiling of cancer cells reveals genome-wide crosstalk between transcriptional regulators and metabolism · 2019
  No notice
• Essential metabolism for a minimal cell · 2019
  No notice
• Central dogma rates and the trade-off between precision and economy in gene expression · 2019
  No notice
• Complex‐centric proteome profiling by SEC‐SWATH‐MS · 2019
  No notice
• Intrinsically Disordered Regions Can Contribute Promiscuous Interactions to RNP Granule Assembly · 2018
  Not checked
• DNA-induced liquid phase condensation of cGAS activates innate immune signaling · 2018
  No notice
• Assessing species biomass contributions in microbial communities via metaproteomics · 2017
  No notice
• A thiol probe for measuring unfolded protein load and proteostasis in cells · 2017
  No notice
• Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding · 2017
  No notice
• Gene‐specific correlation of RNA and protein levels in human cells and tissues · 2016
  No notice
• Coiled‐coils: The long and short of it · 2016
  No notice
• The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization · 2016
  No notice

and 2 more

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.