Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs

Mok, Janine; Kim, Philip M.; Lam, Hugo Y. K.; Piccirillo, Stacy; Zhou, Xiuqiong; Jeschke, Grace R.; Sheridan, Douglas L.; Parker, Sirlester A.; Desai, Ved; Jwa, Miri; Cameroni, Elisabetta; Niu, Hengyao; Good, Matthew; Remenyi, Attila; Ma, Jia-Lin Nianhan; Sheu, Yi-Jun; Sassi, Holly E.; Sopko, Richelle; Chan, Clarence S. M.; De Virgilio, Claudio; Hollingsworth, Nancy M.; Lim, Wendell A.; Stern, David F.; Stillman, Bruce; Andrews, Brenda J.; Gerstein, Mark B.; Snyder, Michael; Turk, Benjamin E.

doi:10.1126/scisignal.2000482

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Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs

Mok, Janine Department of Molecular, Cellular, and Developmental Biology, Yale University, USA - Stanford Genome Technology Center, Department of Biochemistry, Stanford University, USA
Kim, Philip M. Department of Molecular Biophysics and Biochemistry, Yale University, USA - Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
Lam, Hugo Y. K. Program in Computational Biology and Bioinformatics, Yale University, USA
Piccirillo, Stacy Department of Molecular, Cellular, and Developmental Biology, Yale University, USA
Zhou, Xiuqiong Department of Molecular, Cellular, and Developmental Biology, Yale University, USA
Jeschke, Grace R. Department of Pharmacology, Yale University School of Medicine, USA
Sheridan, Douglas L. Department of Pharmacology, Yale University School of Medicine, USA - Alexion Pharmaceuticals Inc., Cheshire, USA
Parker, Sirlester A. Department of Pharmacology, Yale University School of Medicine, USA
Desai, Ved Department of Pharmacology, Yale University School of Medicine, USA
Jwa, Miri Institute for Cellular and Molecular Biology, University of Texas, Austin, USA
Cameroni, Elisabetta Department of Medicine, Division of Biochemistry, University of Fribourg, Switzerland - Institute for Research in Biomedicine, Bellinzona, Switzerland
Niu, Hengyao Department of Biochemistry and Cell Biology, Stony Brook University, USA
Good, Matthew Department of Cellular and Molecular Pharmacology, University of California, San Francisco,USA
Remenyi, Attila Department of Cellular and Molecular Pharmacology, University of California, San Francisco,USA - Eötvös Loránd University, Department of Biochemistry, Budapest, Hungary
Ma, Jia-Lin Nianhan Department of Pathology, School of Medicine, Yale University, USA
Sheu, Yi-Jun Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
Sassi, Holly E. Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
Sopko, Richelle Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
Chan, Clarence S. M. Institute for Cellular and Molecular Biology, University of Texas, Austin, USA
De Virgilio, Claudio Department of Medicine, Division of Biochemistry, University of Fribourg, Switzerland
Hollingsworth, Nancy M. Department of Biochemistry and Cell Biology, Stony Brook University, USA
Lim, Wendell A. Eötvös Loránd University, Department of Biochemistry and Howard Hughes Medical Institute, Budapest, Hungary
Stern, David F. Department of Pathology, School of Medicine, Yale University, USA
Stillman, Bruce Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
Andrews, Brenda J. Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
Gerstein, Mark B. Department of Molecular Biophysics and Biochemistry, Yale University, USA - Program in Computational Biology and Bioinformatics, Yale University, USA
Snyder, Michael Department of Molecular, Cellular, and Developmental Biology, Yale University, USA - Department of Molecular Biophysics and Biochemistry, Yale University, USA - Department of Genetics, Stanford University, Palo Alto, USA
Turk, Benjamin E. Department of Pharmacology, Yale University School of Medicine, USA

16.02.2010

Published in:

Science Signaling. - 2010, vol. 3, no. 109, p. ra12

English Phosphorylation is a universal mechanism for regulating cell behavior in eukaryotes. Although protein kinases target short linear sequence motifs on their substrates, the rules for kinase substrate recognition are not completely understood. We used a rapid peptide screening approach to determine consensus phosphorylation site motifs targeted by 61 of the 122 kinases in Saccharomyces cerevisiae. By correlating these motifs with kinase primary sequence, we uncovered previously unappreciated rules for determining specificity within the kinase family, including a residue determining P–3 arginine specificity among members of the CMGC [CDK (cyclin-dependent kinase), MAPK (mitogen-activated protein kinase), GSK (glycogen synthase kinase), and CDK-like] group of kinases. Furthermore, computational scanning of the yeast proteome enabled the prediction of thousands of new kinase-substrate relationships. We experimentally verified several candidate substrates of the Prk1 family of kinases in vitro and in vivo and identified a protein substrate of the kinase Vhs1. Together, these results elucidate how kinase catalytic domains recognize their phosphorylation targets and suggest general avenues for the identification of previously unknown kinase substrates across eukaryotes.

Faculty

Faculté des sciences et de médecine

Department

Département de Biologie

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