title: Proteomic and phosphoproteomic analyses of yeast reveal the global cellular response to sphingolipid depletion.
abstract: Sphingolipids are essential components of eukaryotic cells with important functions in membrane biology and cellular signaling. Their levels are tightly controlled and coordinated with the abundance of other membrane lipids. How sphingolipid homeostasis is achieved is not yet well understood. Studies performed primarily in yeast showed that the phosphorylation states of several enzymes and regulators of sphingolipid synthesis are important, although a global understanding for such regulation is lacking. Here, we used high-resolution MS-based proteomics and phosphoproteomics to analyze the cellular response to sphingolipid synthesis inhibition. Our dataset reveals that changes in protein phosphorylation, rather than protein abundance, dominate the response to blocking sphingolipid synthesis. We identified Ypk signaling as a pathway likely to be activated under these conditions, and we identified potential Ypk1 target proteins. Our data provide a rich resource for on-going mechanistic studies of key elements of the cellular response to the depletion of sphingolipid levels and the maintenance of sphingolipid homeostasis. All MS data have been deposited in the ProteomeXchange with identifier PXD003854 (http://proteomecentral.proteomexchange.org/dataset/PXD003854).
authors.affiliation: Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.|Department of Cell Biology, Harvard Medical School, Boston, MA, USA.|Molecular Membrane Biology Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Fröhlich
authors.affiliation: Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.|Department of Cell Biology, Harvard Medical School, Boston, MA, USA.|Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
authors.forename: Daniel K
authors.initials: DK
authors.lastname: Olson
authors.affiliation: Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.|Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
authors.forename: Romain
authors.initials: R
authors.lastname: Christiano
authors.affiliation: Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.|Department of Cell Biology, Harvard Medical School, Boston, MA, USA.|Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Robert V
authors.initials: RV
authors.lastname: Farese
authors.affiliation: Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA. twalther@hsph.harvard.edu.|Department of Cell Biology, Harvard Medical School, Boston, MA, USA. twalther@hsph.harvard.edu.|Broad Institute of MIT and Harvard, Cambridge, MA, USA. twalther@hsph.harvard.edu.|Howard Hughes Medical Institute, Boston, MA, USA. twalther@hsph.harvard.edu.
authors.forename: Tobias C
authors.initials: TC
authors.lastname: Walther
mesh_terms: D006706:Homeostasis / Q000235:genetics; D010766:Phosphorylation; D017346:Protein Serine-Threonine Kinases / Q000235:genetics* / Q000378:metabolism; D021381:Protein Transport / Q000235:genetics; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction; D013107:Sphingolipids / Q000235:genetics* / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D013107:Sphingolipids; D017346:Protein Serine-Threonine Kinases; C000621797:YPK1 protein, S cerevisiae
keywords: Cell biology; Mass spectrometry; Myriocin; Phosphorylation; SILAC; Saccharomyces cerevisiae; Sphingolipid metabolism