Nature 438, 679-684 (1 December 2005) | doi:10.1038/nature04187

Global analysis of protein phosphorylation in yeast

Jason Ptacek1,11, Geeta Devgan2,11, Gregory Michaud3,11, Heng Zhu2, Xiaowei Zhu2, Joseph Fasolo2, Hong Guo3, Ghil Jona2, Ashton Breitkreutz4, Richelle Sopko4, Rhonda R. McCartney5, Martin C. Schmidt5, Najma Rachidi6, Soo-Jung Lee7, Angie S. Mah8, Lihao Meng3, Michael J. R. Stark6, David F. Stern7, Claudio De Virgilio9, Mike Tyers4, Brenda Andrews4,10, Mark Gerstein1, Barry Schweitzer3, Paul F. Predki3 and Michael Snyder1,2

Protein phosphorylation is estimated to affect 30% of the proteome and is a major regulatory mechanism that controls many basic cellular processes1, 2, 3. Until recently, our biochemical understanding of protein phosphorylation on a global scale has been extremely limited; only one half of the yeast kinases have known in vivo substrates and the phosphorylating kinase is known for less than 160 phosphoproteins. Here we describe, with the use of proteome chip technology4, the in vitro substrates recognized by most yeast protein kinases5: we identified over 4,000 phosphorylation events involving 1,325 different proteins. These substrates represent a broad spectrum of different biochemical functions and cellular roles. Distinct sets of substrates were recognized by each protein kinase, including closely related kinases of the protein kinase A family and four cyclin-dependent kinases that vary only in their cyclin subunits. Although many substrates reside in the same cellular compartment or belong to the same functional category as their phosphorylating kinase, many others do not, indicating possible new roles for several kinases. Furthermore, integration of the phosphorylation results with protein–protein interaction6, 7, 8, 9, 10 and transcription factor binding data11, 12 revealed novel regulatory modules. Our phosphorylation results have been assembled into a first-generation phosphorylation map for yeast. Because many yeast proteins and pathways are conserved, these results will provide insights into the mechanisms and roles of protein phosphorylation in many eukaryotes.

  1. Department of Molecular Biophysics and Biochemistry, and
  2. Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
  3. Invitrogen Corporation, 1600 Faraday Avenue, Carlsbad, California 92008, USA
  4. Department of Medical Genetics and Microbiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M55 1A8, Canada
  5. Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
  6. Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
  7. Department of Pathology, Yale University School of Medicine, PO Box 208023, 310 Cedar Street BML 342, New Haven, Connecticut 06520-8023, USA
  8. Department of Biology, California Institute of Technology, Pasadena, California 91125, USA
  9. Department of Microbiology and Molecular Medicine, CMU, University of Geneva, 1211 Geneva, Switzerland
  10. Banting & Best Department of Medical Research, University of Toronto, Room 4285, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M55 1A8, Canada
  11. *These authors contributed equally to this work

Correspondence to: Michael Snyder1,2 Correspondence and requests for materials should be addressed to M.S. (Email: michael.snyder@yale.edu).

Received 21 June 2005; Accepted 1 September 2005


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