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

Bernd Bodenmiller, Stefanie Wanka, Claudine Kraft, Joerg Urban, David Campbell, Patrick G. Pedrioli, Bertran Gerrits, Paola Picotti, Henry Lam, Olga Vitek, Mi-Youn Brusniak, Bernd Roschitzki, Chao Zhang, Kevan M. Shokat, Ralph Schlapbach, Alejandro Colman-Lerner, Garry P. Nolan, Alexey I. Nesvizhskii, Matthias Peter, Robbie LoewithChristian von Mering, Ruedi Aebersold

    Research output: Contribution to journalArticlepeer-review

    267 Citations (Scopus)


    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.

    Original languageEnglish
    Article numberrs4
    Pages (from-to)-
    Number of pages8
    JournalScience Signaling
    Issue number153
    Publication statusPublished - 2010


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