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Global analysis of protein expression in yeast

Nature volume 425, pages 737–741 (2003)Cite this article

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.

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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.

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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.

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Authors and Affiliations

  1. Howard Hughes Medical Institute, University of California–San Francisco, San Francisco, California, 94143-2240, USA

    Sina Ghaemmaghami, Won-Ki Huh, Kiowa Bower, Russell W. Howson, Archana Belle, Noah Dephoure, Erin K. O'Shea & Jonathan S. Weissman

  2. Departments of Cellular & Molecular Pharmacology, University of California–San Francisco, San Francisco, California, 94143-2240, USA

    Sina Ghaemmaghami, Kiowa Bower & Jonathan S. Weissman

  3. Biochemistry & Biophysics, University of California–San Francisco, San Francisco, California, 94143-2240, USA

    Won-Ki Huh, Russell W. Howson, Archana Belle, Noah Dephoure & Erin K. O'Shea

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  1. Sina Ghaemmaghami
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Correspondence to Jonathan S. Weissman.

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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

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