title: Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
abstract: Cells respond to environmental stimuli via specialized signaling pathways. Concurrent stimuli trigger multiple pathways that integrate information, predominantly via protein phosphorylation. Budding yeast responds to NaCl and pheromone via two mitogen-activated protein kinase cascades, the high osmolarity, and the mating pathways, respectively. To investigate signal integration between these pathways, we quantified the time-resolved phosphorylation site dynamics after pathway co-stimulation. Using shotgun mass spectrometry, we quantified 2,536 phosphopeptides across 36 conditions. Our data indicate that NaCl and pheromone affect phosphorylation events within both pathways, which thus affect each other at more levels than anticipated, allowing for information exchange and signal integration. We observed a pheromone-induced down-regulation of Hog1 phosphorylation due to Gpd1, Ste20, Ptp2, Pbs2, and Ptc1. Distinct Ste20 and Pbs2 phosphosites responded differently to the two stimuli, suggesting these proteins as key mediators of the information exchange. A set of logic models was then used to assess the role of measured phosphopeptides in the crosstalk. Our results show that the integration of the response to different stimuli requires complex interconnections between signaling pathways.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland.
authors.forename: Stefania
authors.initials: S
authors.lastname: Vaga
authors.affiliation: European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Cambridge, UK.
authors.forename: Marti
authors.initials: M
authors.lastname: Bernardo-Faura
authors.affiliation: European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Cambridge, UK.
authors.forename: Thomas
authors.initials: T
authors.lastname: Cokelaer
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland.
authors.forename: Alessio
authors.initials: A
authors.lastname: Maiolica
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Barnes
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland.
authors.forename: Ludovic C
authors.initials: LC
authors.lastname: Gillet
authors.affiliation: Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.
authors.forename: Björn
authors.initials: B
authors.lastname: Hegemann
authors.affiliation: Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.
authors.forename: Frank
authors.initials: F
authors.lastname: van Drogen
authors.affiliation: Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.
authors.forename: Hoda
authors.initials: H
authors.lastname: Sharifian
authors.affiliation: Department of Biology, Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany.
authors.forename: Edda
authors.initials: E
authors.lastname: Klipp
authors.affiliation: Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.
authors.forename: Matthias
authors.initials: M
authors.lastname: Peter
authors.affiliation: European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Cambridge, UK.
authors.forename: Julio
authors.initials: J
authors.lastname: Saez-Rodriguez
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology ETH Zürich, Zürich, Switzerland Faculty of Science, University of Zurich, Zurich, Switzerland aebersold@imsb.biol.ethz.ch.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D015536:Down-Regulation; D020928:Mitogen-Activated Protein Kinases / Q000235:genetics / Q000378:metabolism; D008962:Models, Theoretical; D009994:Osmolar Concentration; D010675:Pheromones / Q000378:metabolism*; D010766:Phosphorylation; D020543:Proteome / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D012965:Sodium Chloride / Q000378:metabolism
chemical_list: D010675:Pheromones; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D012965:Sodium Chloride; C075580:FUS3 protein, S cerevisiae; C088589:HOG1 protein, S cerevisiae; D020928:Mitogen-Activated Protein Kinases
keywords: HOG pathway; cell signaling network; crosstalk; pheromone pathway; phosphoproteomics