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.

  • Article
  • Published:

Global analysis of protein localization in budding yeast

Nature volume 425, pages 686–691 (2003)Cite this article

Abstract

A fundamental goal of cell biology is to define the functions of proteins in the context of compartments that organize them in the cellular environment. Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories, and provide localization information for 70% of previously unlocalized proteins. Analysis of this high-resolution, high-coverage localization data set in the context of transcriptional, genetic, and protein–protein interaction data helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Microscopic analysis of yeast strains expressing GFP-tagged proteins.
Figure 2: Subcellular localization of yeast proteins.
Figure 3: Correlation between transcriptional co-regulation and subcellular localization.
Figure 4: Relationship between genetic and physical interactions and subcellular localization.

Similar content being viewed by others

References

  1. Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563–567 (1996)

    Article  CAS  Google Scholar 

  2. Velculescu, V. E. et al. Characterization of the yeast transcriptome. Cell 88, 243–251 (1997)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Martzen, M. R. et al. A biochemical genomics approach for identifying genes by the activity of their products. Science 286, 1153–1155 (1999)

    Article  CAS  Google Scholar 

  5. Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 293, 2101–2105 (2001)

    Article  CAS  Google Scholar 

  6. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 (2000)

    Article  CAS  Google Scholar 

  7. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001)

    Article  CAS  Google Scholar 

  8. 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 

  9. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002)

    Article  CAS  Google Scholar 

  10. Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002)

    Article  CAS  Google Scholar 

  11. Ross-Macdonald, P. et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402, 413–418 (1999)

    Article  CAS  Google Scholar 

  12. 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 

  13. Tong, A. H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364–2368 (2001)

    Article  CAS  Google Scholar 

  14. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002)

    Article  CAS  Google Scholar 

  15. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737–741 (2003)

    Article  CAS  Google Scholar 

  16. Kumar, A. et al. Subcellular localization of the yeast proteome. Genes Dev. 16, 707–719 (2002)

    Article  CAS  Google Scholar 

  17. Tsien, R. Y. The green fluorescent protein. Annu. Rev. Biochem. 67, 509–544 (1998)

    Article  CAS  Google Scholar 

  18. Dolinski, K. et al. Saccharomyces Genome Database 〈http://www-genome.stanford.edu/Saccharomyces〉 (2003).

  19. 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 

  20. Campbell, R. E. et al. A monomeric red fluorescent protein. Proc. Natl Acad. Sci. USA 99, 7877–7882 (2002)

    Article  CAS  Google Scholar 

  21. 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 

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

    Article  CAS  Google Scholar 

  23. Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148, 635–651 (2000)

    Article  CAS  Google Scholar 

  24. Wigge, P. A. et al. Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. J. Cell Biol. 141, 967–977 (1998)

    Article  CAS  Google Scholar 

  25. Bhattacharya, S., Chen, L., Broach, J. R. & Powers, S. Ras membrane targeting is essential for glucose signaling but not for viability in yeast. Proc. Natl Acad. Sci. USA 92, 2984–2988 (1995)

    Article  CAS  Google Scholar 

  26. van Berkel, M. A., Caro, L. H., Montijn, R. C. & Klis, F. M. Glucosylation of chimeric proteins in the cell wall of Saccharomyces cerevisiae. FEBS Lett. 349, 135–138 (1994)

    Article  CAS  Google Scholar 

  27. Gould, S. J. et al. Peroxisomal protein import is conserved between yeast, plants, insects and mammals. EMBO J. 9, 85–90 (1990)

    Article  CAS  Google Scholar 

  28. Pelham, H. R., Hardwick, K. G. & Lewis, M. J. Sorting of soluble ER proteins in yeast. EMBO J. 7, 1757–1762 (1988)

    Article  CAS  Google Scholar 

  29. Taylor, S. W., Fahy, E. & Ghosh, S. S. Global organellar proteomics. Trends Biotechnol. 21, 82–88 (2003)

    Article  CAS  Google Scholar 

  30. Shou, W. et al. Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex. Cell 97, 233–244 (1999)

    Article  CAS  Google Scholar 

  31. Visintin, R., Hwang, E. S. & Amon, A. Cfi1 prevents premature exit from mitosis by anchoring Cdc14 phosphatase in the nucleolus. Nature 398, 818–823 (1999)

    Article  CAS  Google Scholar 

  32. San-Segundo, P. A. & Roeder, G. S. Pch2 links chromatin silencing to meiotic checkpoint control. Cell 97, 313–324 (1999)

    Article  CAS  Google Scholar 

  33. Rabitsch, K. P. et al. Kinetochore recruitment of two nucleolar proteins is required for homolog segregation in meiosis I. Dev. Cell 4, 535–548 (2003)

    Article  CAS  Google Scholar 

  34. Andersen, J. S. et al. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12, 1–11 (2002)

    Article  Google Scholar 

  35. Hodges, P. E. et al. Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. Nucleic Acids Res. 30, 137–141 (2002)

    Article  CAS  Google Scholar 

  36. DeRisi, J. L., Iyer, V. R. & Brown, P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680–686 (1997)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  39. Drawid, A., Jansen, R. & Gerstein, M. Genome-wide analysis relating expression level with protein subcellular localization. Trends Genet. 16, 426–430 (2000)

    Article  CAS  Google Scholar 

  40. 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 

  41. Koc, E. C. et al. The large subunit of the mammalian mitochondrial ribosome. J. Biol. Chem. 276, 43958–43969 (2001)

    Article  CAS  Google Scholar 

  42. von Mering, C. et al. Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417, 399–403 (2002)

    Article  CAS  Google Scholar 

  43. Breitkreutz, B.-J., Stark, C. & Tyers, M. The GRID: the General Repository for Interaction Datasets. Genome Biol. 4, R23 (2003)

    Article  Google Scholar 

  44. Madden, K. & Snyder, M. Cell polarity and morphogenesis in budding yeast. Annu. Rev. Microbiol. 52, 687–744 (1998)

    Article  CAS  Google Scholar 

  45. Trilla, J. A., Duran, A. & Roncero, C. Chs7p, a new protein involved in the control of protein export from the endoplasmic reticulum that is specifically engaged in the regulation of chitin synthesis in Saccharomyces cerevisiae. J. Cell Biol. 145, 1153–1163 (1999)

    Article  CAS  Google Scholar 

  46. DeMarini, D. J. et al. A septin-based hierarchy of proteins required for localized deposition of chitin in the Saccharomyces cerevisiae cell wall. J. Cell Biol. 139, 75–93 (1997)

    Article  CAS  Google Scholar 

  47. Cope, M. J., Yang, S., Shang, C. & Drubin, D. G. Novel protein kinases Ark1p and Prk1p associate with and regulate the cortical actin cytoskeleton in budding yeast. J. Cell Biol. 144, 1203–1218 (1999)

    Article  CAS  Google Scholar 

  48. Breitkreutz, B.-J., Stark, C. & Tyers, M. Osprey: a network visualization system. Genome Biol. 4, R22 (2003)

    Article  Google Scholar 

Download references

Acknowledgements

We thank F. Lam for designing the original relational data model and for assistance with database organization; M. Springer for sharing microscopy expertise; J. Newman for assistance with FACS analysis; N. Barkai, S. Ghaemmaghami and K. Bower for discussions and sharing results; R. Tsien for providing the pRSET–mRFP1 plasmid; M. Levin for assistance with preparation of RFP-tagged strains; R. Marion for contributing GFP-tagged strains of CAK1, PHO4, RTS2, SET1 and STP4; A. DePace for preparing the illustration in Fig. 4c; D. Ahern, F. Sanchez, A. Belle and M. Liku for primer synthesis and other technical assistance; and S. Emr and members of the O'Shea and Weissman laboratories for critical discussion of the work. This work was supported by the Howard Hughes Medical Institute and the David and Lucile Packard Foundation (J.S.W. and E.K.O.). J.V.F. is the recipient of a Ruth L. Kirschstein National Research Service Award. The database and strain collection information is accessible at http://yeastgfp.ucsf.edu.Authors' contributions Strain construction and analysis was performed by W.-K.H. and J.V.F., bioinformatics analysis and database management by L.C.G., with additional database management by A.S.C., and oligonucleotide primer design by R.W.H.

Author information

Author notes

  1. Won-Ki Huh and James V. Falvo: These authors contributed equally to this work

Authors and Affiliations

  1. Howard Hughes Medical Institute, University of California–San Francisco, Department of Biochemistry and Biophysics, 600 16th Street, San Francisco, California, 94143-2240, USA

    Won-Ki Huh, James V. Falvo, Luke C. Gerke, Adam S. Carroll, Russell W. Howson, Jonathan S. Weissman & Erin K. O'Shea

  2. Department of Cellular and Molecular Pharmacology, 600 16th Street, San Francisco, California, 94143-2240, USA

    Jonathan S. Weissman

Authors
  1. Won-Ki Huh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. James V. Falvo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Luke C. Gerke
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Adam S. Carroll
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Russell W. Howson
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jonathan S. Weissman
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Erin K. O'Shea
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Erin K. O'Shea.

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

Huh, WK., Falvo, J., Gerke, L. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003). https://doi.org/10.1038/nature02026

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature02026

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

Advanced 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