title: Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.
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.
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Bernd
authors.initials: B
authors.lastname: Bodenmiller
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wanka
authors.forename: Claudine
authors.initials: C
authors.lastname: Kraft
authors.forename: Jörg
authors.initials: J
authors.lastname: Urban
authors.forename: David
authors.initials: D
authors.lastname: Campbell
authors.forename: Patrick G
authors.initials: PG
authors.lastname: Pedrioli
authors.forename: Bertran
authors.initials: B
authors.lastname: Gerrits
authors.forename: Paola
authors.initials: P
authors.lastname: Picotti
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.forename: Olga
authors.initials: O
authors.lastname: Vitek
authors.forename: Mi-Youn
authors.initials: MY
authors.lastname: Brusniak
authors.forename: Bernd
authors.initials: B
authors.lastname: Roschitzki
authors.forename: Chao
authors.initials: C
authors.lastname: Zhang
authors.forename: Kevan M
authors.initials: KM
authors.lastname: Shokat
authors.forename: Ralph
authors.initials: R
authors.lastname: Schlapbach
authors.forename: Alejandro
authors.initials: A
authors.lastname: Colman-Lerner
authors.forename: Garry P
authors.initials: GP
authors.lastname: Nolan
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
authors.forename: Matthias
authors.initials: M
authors.lastname: Peter
authors.forename: Robbie
authors.initials: R
authors.lastname: Loewith
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D001499:Bayes Theorem; D002853:Chromatography, Liquid; D017353:Gene Deletion; D053858:Metabolic Networks and Pathways / Q000502:physiology*; D008954:Models, Biological; D010750:Phosphoproteins / Q000378:metabolism*; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics / Q000378:metabolism*; D010766:Phosphorylation; D010770:Phosphotransferases / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae; D015398:Signal Transduction / Q000502:physiology*; D013045:Species Specificity; D053719:Tandem Mass Spectrometry
chemical_list: D010750:Phosphoproteins; D010770:Phosphotransferases; D010744:Phosphoric Monoester Hydrolases