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Sci. Signal., 21 December 2010
Vol. 3, Issue 153, p. rs4
[DOI: 10.1126/scisignal.2001182]

RESEARCH RESOURCES

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

Bernd Bodenmiller1,2*{dagger}, Stefanie Wanka2,3*, Claudine Kraft4, Jörg Urban5, David Campbell6, Patrick G. Pedrioli4{ddagger}, Bertran Gerrits7§, Paola Picotti1, Henry Lam8, Olga Vitek9, Mi-Youn Brusniak6, Bernd Roschitzki7, Chao Zhang10, Kevan M. Shokat10, Ralph Schlapbach7, Alejandro Colman-Lerner11, Garry P. Nolan12, Alexey I. Nesvizhskii13, Matthias Peter4, Robbie Loewith5, Christian von Mering3, and Ruedi Aebersold1,6,14||

1 Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
2 Zurich PhD Program in Molecular Life Sciences, 8057 Zurich, Switzerland.
3 Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
4 Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland.
5 Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland.
6 Institute for Systems Biology, Seattle, WA 98103, USA.
7 Functional Genomics Center Zurich, University Zurich and ETH Zurich, 8057 Zurich, Switzerland.
8 Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
9 Departments of Statistics and Computer Science, Purdue University, West Lafayette, IN 47107, USA.
10 Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158–2280, USA.
11 Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, C1428EHA Buenos Aires, Argentina.
12 Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
13 Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
14 Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.

* These authors contributed equally to this work.

{dagger} Present address: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.

{ddagger} Present address: Scottish Institute for Cell Signalling, Sir James Black Centre, University of Dundee, Dundee, Scotland DD1 5EH, UK.

§ Present address: Novartis Institute for Biomedical Research, Novartis International AG, CH-4002 Basel, Switzerland.

Abstract: The phosphorylation and dephosphorylation of proteins by kinases and phosphatases constitute an essential regulatory network in eukaryotic cells. This network supports the flow of information from sensors through signaling systems to effector molecules and ultimately drives the phenotype and function of cells, tissues, and organisms. Dysregulation of this process has severe consequences and is one of the main factors in the emergence and progression of diseases, including cancer. Thus, major efforts have been invested in developing specific inhibitors that modulate the activity of individual kinases or phosphatases; however, it has been difficult to assess how such pharmacological interventions would affect the cellular signaling network as a whole. Here, we used label-free, quantitative phosphoproteomics in a systematically perturbed model organism (Saccharomyces cerevisiae) to determine the relationships between 97 kinases, 27 phosphatases, and more than 1000 phosphoproteins. We identified 8814 regulated phosphorylation events, describing the first system-wide protein phosphorylation network in vivo. Our results show that, at steady state, inactivation of most kinases and phosphatases affected large parts of the phosphorylation-modulated signal transduction machinery—and not only the immediate downstream targets. The observed cellular growth phenotype was often well maintained despite the perturbations, arguing for considerable robustness in the system. Our results serve to constrain future models of cellular signaling and reinforce the idea that simple linear representations of signaling pathways might be insufficient for drug development and for describing organismal homeostasis.

|| To whom correspondence should be addressed. E-mail: aebersold{at}imsb.biol.ethz.ch

Citation: B. Bodenmiller, S. Wanka, C. Kraft, J. Urban, D. Campbell, P. G. Pedrioli, B. Gerrits, P. Picotti, H. Lam, O. Vitek, M.-Y. Brusniak, B. Roschitzki, C. Zhang, K. M. Shokat, R. Schlapbach, A. Colman-Lerner, G. P. Nolan, A. I. Nesvizhskii, M. Peter, R. Loewith, C. von Mering, R. Aebersold, Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast. Sci. Signal. 3, rs4 (2010).

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