title: Phosphoproteomic analysis identifies proteins involved in transcription-coupled mRNA decay as targets of Snf1 signaling.
abstract: Stresses, such as glucose depletion, activate Snf1, the Saccharomyces cerevisiae ortholog of adenosine monophosphate-activated protein kinase (AMPK), enabling adaptive cellular responses. In addition to affecting transcription, Snf1 may also promote mRNA stability in a gene-specific manner. To understand Snf1-mediated signaling, we used quantitative mass spectrometry to identify proteins that were phosphorylated in a Snf1-dependent manner. We identified 210 Snf1-dependent phosphopeptides in 145 proteins. Thirteen of these proteins are involved in mRNA metabolism. Of these, we found that Ccr4 (the major cytoplasmic deadenylase), Dhh1 (an RNA helicase), and Xrn1 (an exoribonuclease) were required for the glucose-induced decay of Snf1-dependent mRNAs that were activated by glucose depletion. Unexpectedly, deletion of XRN1 reduced the accumulation of Snf1-dependent transcripts that were synthesized during glucose depletion. Deletion of SNF1 rescued the synthetic lethality of simultaneous deletion of XRN1 and REG1, which encodes a regulatory subunit of a phosphatase that inhibits Snf1. Mutation of three Snf1-dependent phosphorylation sites in Xrn1 reduced glucose-induced mRNA decay. Thus, Xrn1 is required for Snf1-dependent mRNA homeostasis in response to nutrient availability.
authors.affiliation: Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA.
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Braun
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8057 Zurich, Switzerland.
authors.forename: Stefania
authors.initials: S
authors.lastname: Vaga
authors.affiliation: Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA.
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Dombek
authors.affiliation: Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA.
authors.forename: Fang
authors.initials: F
authors.lastname: Fang
authors.affiliation: Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA.
authors.forename: Salvator
authors.initials: S
authors.lastname: Palmisano
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8057 Zurich, Switzerland. Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195-7350, USA. ety@uw.edu.
authors.forename: Elton T
authors.initials: ET
authors.lastname: Young
mesh_terms: D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism*; D054645:Protein Phosphatase 1 / Q000235:genetics / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics; D020871:RNA Stability / Q000502:physiology*; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D010750:Phosphoproteins; D012331:RNA, Fungal; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; C071570:SNF1-related protein kinases; D017346:Protein Serine-Threonine Kinases; D005095:Exoribonucleases; C068398:XRN1 protein, S cerevisiae; D054645:Protein Phosphatase 1; C070829:REG1 protein, S cerevisiae