Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Global analysis of protein expression in yeast

Abstract

The availability of complete genomic sequences and technologies that allow comprehensive analysis of global expression profiles of messenger RNA1,2,3 have greatly expanded our ability to monitor the internal state of a cell. Yet biological systems ultimately need to be explained in terms of the activity, regulation and modification of proteins—and the ubiquitous occurrence of post-transcriptional regulation makes mRNA an imperfect proxy for such information. To facilitate global protein analyses, we 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, we obtain a census of proteins expressed during log-phase growth and measurements of their absolute levels. We find that about 80% of the proteome is expressed during normal growth conditions, and, using additional sequence information, we systematically identify misannotated genes. The abundance of proteins ranges from fewer than 50 to more than 106 molecules per cell. Many of these molecules, including essential proteins and most transcription factors, are present at levels that are not readily detectable by other proteomic techniques nor predictable by mRNA levels or codon bias measurements.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Tagging and detection of the yeast proteome.
Figure 2: Analysis of proteins expressed during log-phase growth.
Figure 3: Functional categorization of proteins expressed during log-phase growth in rich medium.
Figure 4: Abundance distribution of the yeast proteome.

References

  1. Lashkari, D. A. et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl Acad. Sci. USA 94, 13057–13062 (1997)

    Article  CAS  Google Scholar 

  2. Collins, F. S., Green, E. D., Guttmacher, A. E. & Guyer, M. S. A vision for the future of genomics research. Nature 422, 835–847 (2003)

    Article  CAS  Google Scholar 

  3. Lockhart, D. J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675–1680 (1996)

    Article  CAS  Google Scholar 

  4. Longtine, M. S. et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14, 953–961 (1998)

    Article  CAS  Google Scholar 

  5. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030–1032 (1999)

    Article  CAS  Google Scholar 

  6. Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002)

    Article  CAS  Google Scholar 

  7. Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999)

    Article  CAS  Google Scholar 

  8. Schwob, E., Bohm, T., Mendenhall, M. D. & Nasmyth, K. The B-type cyclin kinase inhibitor p40SIC1 controls the G1 to S transition in S. cerevisiae. Cell 79, 233–244 (1994)

    Article  CAS  Google Scholar 

  9. Grandin, N. & Reed, S. I. Differential function and expression of Saccharomyces cerevisiae B-type cyclins in mitosis and meiosis. Mol. Cell. Biol. 13, 2113–2125 (1993)

    Article  CAS  Google Scholar 

  10. Huh, W.-K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003)

    Article  CAS  Google Scholar 

  11. Harrison, P. M., Kumar, A., Lang, N., Snyder, M. & Gerstein, M. A question of size: The eukaryotic proteome and the problems in defining it. Nucleic Acids Res. 30, 1083–1090 (2002)

    Article  CAS  Google Scholar 

  12. Goffeau, A. Four years of post-genomic life with 6,000 yeast genes. FEBS Lett. 480, 37–41 (2000)

    Article  CAS  Google Scholar 

  13. Das, S. et al. Biology's new Rosetta stone. Nature 385, 29–30 (1997)

    Article  CAS  Google Scholar 

  14. Kowalczuk, M., Mackiewicz, P., Gierlik, A., Dudek, M. R. & Cebrat, S. Total number of coding open reading frames in the yeast genome. Yeast 15, 1031–1034 (1999)

    Article  CAS  Google Scholar 

  15. Zhang, C. T. & Wang, J. Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve. Nucleic Acids Res. 28, 2804–2814 (2000)

    Article  CAS  Google Scholar 

  16. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003)

    Article  CAS  Google Scholar 

  17. Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71–76 (2003)

    Article  CAS  Google Scholar 

  18. Ihmels, J. et al. Revealing modular organization in the yeast transcriptional network. Nature Genet. 31, 370–377 (2002)

    Article  CAS  Google Scholar 

  19. Bergmann, S., Ihmels, J. & Barkai, N. Iterative signature algorithm for the analysis of large-scale gene expression data. Phys. Rev. E 67, 031902 (2003)

    Article  Google Scholar 

  20. Gygi, S. P., Rochon, Y., Franza, B. R. & Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720–1730 (1999)

    Article  CAS  Google Scholar 

  21. Futcher, B., Latter, G. I., Monardo, P., McLaughlin, C. S. & Garrels, J. I. A sampling of the yeast proteome. Mol. Cell. Biol. 19, 7357–7368 (1999)

    Article  CAS  Google Scholar 

  22. Washburn, M. P. et al. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 100, 3107–3112 (2003)

    Article  CAS  Google Scholar 

  23. Washburn, M. P., Wolters, D. & Yates, J. R. III Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19, 242–247 (2001)

    Article  CAS  Google Scholar 

  24. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003)

    Article  CAS  Google Scholar 

  25. Holstege, F. C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717–728 (1998)

    Article  CAS  Google Scholar 

  26. Wang, Y. et al. Precision and functional specificity in mRNA decay. Proc. Natl Acad. Sci. USA 99, 5860–5865 (2002)

    Article  CAS  Google Scholar 

  27. Sharp, P. M. & Li, W. H. The codon Adaptation Index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281–1295 (1987)

    Article  CAS  Google Scholar 

  28. Grantham, R., Gautier, C. & Gouy, M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 8, 1893–1912 (1980)

    Article  CAS  Google Scholar 

  29. Spellman, P. T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273–3297 (1998)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank A. Carroll and F. Sanchez for technical assistance; J. Falvo, L. Gerke, J. Newman and members of the Weissman and O'Shea laboratories for discussions; and N. Barkai for providing data before publication. This work was supported by the Howard Hughes Medical Institute and the David and Lucile Packard Foundation. S.G. is a recipient of the Ruth L. Kirschstein National Research Service Award.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jonathan S. Weissman.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ghaemmaghami, S., Huh, WK., Bower, K. et al. Global analysis of protein expression in yeast. Nature 425, 737–741 (2003). https://doi.org/10.1038/nature02046

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature02046

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing