Functional Organization of the S. cerevisiae Phosphorylation Network

Dorothea Fiedler, Hannes Braberg, Monika Mehta, Gal Chechik, Gerard Cagney, Paromita Mukherjee, Andrea C. Silva, Michael Shales, Sean R. Collins, Sake van Wageningen, Patrick Kemmeren, Frank C.P. Holstege, Jonathan S. Weissman, Michael Christopher Keogh, Daphne Koller, Kevan M. Shokat, Nevan J. Krogan

Research output: Contribution to journalArticlepeer-review

215 Scopus citations

Abstract

Reversible protein phosphorylation is a signaling mechanism involved in all cellular processes. To create a systems view of the signaling apparatus in budding yeast, we generated an epistatic miniarray profile (E-MAP) comprised of 100,000 pairwise, quantitative genetic interactions, including virtually all protein and small-molecule kinases and phosphatases as well as key cellular regulators. Quantitative genetic interaction mapping reveals factors working in compensatory pathways (negative genetic interactions) or those operating in linear pathways (positive genetic interactions). We found an enrichment of positive genetic interactions between kinases, phosphatases, and their substrates. In addition, we assembled a higher-order map from sets of three genes that display strong interactions with one another: triplets enriched for functional connectivity. The resulting network view provides insights into signaling pathway regulation and reveals a link between the cell-cycle kinase, Cak1, the Fus3 MAP kinase, and a pathway that regulates chromatin integrity during transcription by RNA polymerase II.

Original languageEnglish
Pages (from-to)952-963
Number of pages12
JournalCell
Volume136
Issue number5
DOIs
StatePublished - 6 Mar 2009
Externally publishedYes

Bibliographical note

Funding Information:
The authors thank A. Roguev, C. Kaplan, C.J. Ingles, P. Aguilar, T. Walther, J.H. Morris, and members of the Krogan, Shokat, and Keogh labs for advice and comments. We also thank W.A. Lim for discussion on MAP kinase cascades. We are grateful to A. Chan, E. Cheng, Y. Nijati, and Li Jieying for technical assistance. We thank F. Winston and S. Buratowski for providing yeast strains and B. Strahl, S. Hahn, and D. Morgan for sharing unpublished data. The work was supported by an Ernst Schering Postdoctoral Fellowship (D.F.), the Biophysics Graduate Group at UCSF (H.B.), the National Science Foundation (G.C. and D.K.), the New York Speakers Fund for Biomedical Research (M.-C.K.), the Howard Hughes Medical Institute (K.M.S.), the NIH (N.J.K. and K.M.S.), and Sandler Family Funding (N.J.K.).

Keywords

  • SIGNALING

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