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Global analysis of protein localization in budding yeast

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.

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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.

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Correspondence to Erin K. O'Shea.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Figure 1 (PDF 332 kb)

Supplementary Figure 2 (PDF 238 kb)

Supplementary Figure 3 (PDF 349 kb)

Supplementary Figure 4 (PDF 245 kb)

Supplementary Methods, Figure Legends and Tables (DOC 174 kb)

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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.

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