title: Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.
abstract: The target of rapamycin complex 1 (TORC1) is an essential multiprotein complex conserved from yeast to humans. Under favorable growth conditions, and in the absence of the macrolide rapamycin, TORC1 is active, and influences virtually all aspects of cell growth. Although two direct effectors of yeast TORC1 have been reported (Tap42, a regulator of PP2A phosphatases and Sch9, an AGC family kinase), the signaling pathways that couple TORC1 to its distal effectors were not well understood. To elucidate these pathways we developed and employed a quantitative, label-free mass spectrometry approach. Analyses of the rapamycin-sensitive phosphoproteomes in various genetic backgrounds revealed both documented and novel TORC1 effectors and allowed us to partition phosphorylation events between Tap42 and Sch9. Follow-up detailed characterization shows that Sch9 regulates RNA polymerases I and III, the latter via Maf1, in addition to translation initiation and the expression of ribosomal protein and ribosome biogenesis genes. This demonstrates that Sch9 is a master regulator of protein synthesis.
authors.affiliation: Department of Molecular Biology, University of Geneva, Geneva, Switzerland.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Huber
authors.forename: Bernd
authors.initials: B
authors.lastname: Bodenmiller
authors.forename: Aino
authors.initials: A
authors.lastname: Uotila
authors.forename: Michael
authors.initials: M
authors.lastname: Stahl
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wanka
authors.forename: Bertran
authors.initials: B
authors.lastname: Gerrits
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Robbie
authors.initials: R
authors.lastname: Loewith
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000378:metabolism; D000935:Antifungal Agents / Q000494:pharmacology; D003513:Cycloheximide / Q000494:pharmacology; D010766:Phosphorylation / Q000187:drug effects; D011485:Protein Binding; D014176:Protein Biosynthesis / Q000502:physiology*; D017346:Protein Serine-Threonine Kinases / Q000378:metabolism*; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology; D021381:Protein Transport; D020543:Proteome / Q000187:drug effects; D012318:RNA Polymerase I / Q000378:metabolism; D012320:RNA Polymerase III / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000378:metabolism / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D015398:Signal Transduction; D020123:Sirolimus / Q000494:pharmacology; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D000935:Antifungal Agents; C104954:MAF1 protein, S cerevisiae; D011500:Protein Synthesis Inhibitors; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; C100984:TAP42 protein, S cerevisiae; D014157:Transcription Factors; D003513:Cycloheximide; D017346:Protein Serine-Threonine Kinases; C530964:SCH9 protein, S cerevisiae; D012318:RNA Polymerase I; D012320:RNA Polymerase III; D020123:Sirolimus
references.citation: J Cell Biol. 2000 Sep 18;150(6):1507-13
references.pmid: 10995454
references.citation: J Biol Chem. 2005 Feb 25;280(8):6455-62
references.pmid: 15590667
references.citation: Mol Biol Cell. 2004 Feb;15(2):946-56
references.pmid: 14595104
references.citation: Cell. 2002 Jul 26;110(2):163-75
references.pmid: 12150925
references.citation: Yeast. 1997 Dec;13(16):1505-18
references.pmid: 9509571
references.citation: Mol Biol Cell. 2001 Dec;12(12):4103-13
references.pmid: 11739804
references.citation: Cell. 2006 Nov 3;127(3):635-48
references.pmid: 17081983
references.citation: Cell. 2006 Feb 10;124(3):471-84
references.pmid: 16469695
references.citation: Mol Cell Proteomics. 2008 Nov;7(11):2138-50
references.pmid: 18511481
references.citation: EMBO J. 1999 May 17;18(10):2782-92
references.pmid: 10329624
references.citation: Curr Biol. 2002 Mar 5;12(5):389-95
references.pmid: 11882290
references.citation: Science. 2005 Nov 18;310(5751):1193-6
references.pmid: 16293764
references.citation: Nat Biotechnol. 2001 Apr;19(4):375-8
references.pmid: 11283598
references.citation: Genes Dev. 2003 Apr 1;17(7):859-72
references.pmid: 12654728
references.citation: Biochem Biophys Res Commun. 1998 Oct 20;251(2):520-6
references.pmid: 9792806
references.citation: J Biol Chem. 2009 May 8;284(19):12604-8
references.pmid: 19299514
references.citation: Genome Res. 2009 Apr;19(4):556-66
references.pmid: 19158363
references.citation: Nucleic Acids Res. 2002 Feb 1;30(3):643-8
references.pmid: 11809875
references.citation: Mol Syst Biol. 2007;3:139
references.pmid: 17940529
references.citation: Mol Cell. 2006 Jun 9;22(5):623-32
references.pmid: 16762835
references.citation: Mol Cell Biol. 2004 Apr;24(7):2779-88
references.pmid: 15024067
references.citation: Proteomics. 2007 Oct;7(19):3470-80
references.pmid: 17726677
references.citation: Mol Cell. 2006 Jun 9;22(5):633-44
references.pmid: 16762836
references.citation: BMC Bioinformatics. 2008 Dec 16;9:542
references.pmid: 19087345
references.citation: Nature. 1999 Dec 9;402(6762):689-92
references.pmid: 10604478
references.citation: FEMS Yeast Res. 2006 Jan;6(1):112-9
references.pmid: 16423076
references.citation: Oncogene. 2006 Oct 16;25(48):6392-415
references.pmid: 17041625
references.citation: Cell. 2008 Apr 4;133(1):78-89
references.pmid: 18394991
references.citation: Biochem J. 2003 Jun 1;372(Pt 2):555-66
references.pmid: 12611592
references.citation: J Mol Biol. 2001 Jun 29;310(1):1-26
references.pmid: 11419933
references.citation: Trends Biochem Sci. 2007 Feb;32(2):51-3
references.pmid: 17174096
references.citation: Mol Cell. 2007 Jun 8;26(5):663-74
references.pmid: 17560372
references.citation: Cell. 2008 Apr 18;133(2):292-302
references.pmid: 18423200
references.citation: Nat Methods. 2007 Mar;4(3):231-7
references.pmid: 17293869
references.citation: Science. 2006 Apr 14;312(5771):212-7
references.pmid: 16614208
references.citation: Mol Cell Biol. 1998 Aug;18(8):4463-70
references.pmid: 9671456
references.citation: EMBO J. 1998 Dec 1;17(23):6924-31
references.pmid: 9843498
references.citation: J Biol Chem. 2008 Jul 11;283(28):19184-91
references.pmid: 18456653
references.citation: Mol Microbiol. 2008 Jul;69(1):277-85
references.pmid: 18513215
references.citation: J Biol Chem. 2007 Sep 7;282(36):26623-8
references.pmid: 17616518
references.citation: Curr Opin Cell Biol. 2008 Dec;20(6):678-87
references.pmid: 18930818
references.citation: Genes Dev. 1989 Sep;3(9):1336-48
references.pmid: 2558053
references.citation: Oncogene. 2006 Oct 16;25(48):6384-91
references.pmid: 17041624
references.citation: Genes Dev. 1996 Aug 1;10(15):1904-16
references.pmid: 8756348
references.citation: PLoS Genet. 2008 Jan;4(1):e13
references.pmid: 18225956
references.citation: Prog Nucleic Acid Res Mol Biol. 2004;77:323-53
references.pmid: 15196897
references.citation: Genes Dev. 2006 Aug 1;20(15):2030-40
references.pmid: 16882981
references.citation: Gene. 1997 Feb 7;185(2):291-6
references.pmid: 9055829
references.citation: Mol Cell. 2008 Dec 26;32(6):878-87
references.pmid: 19111667
references.citation: Nat Biotechnol. 2007 Mar;25(3):345-52
references.pmid: 17322870
references.citation: Genes Dev. 2004 Oct 15;18(20):2491-505
references.pmid: 15466158
references.citation: Annu Rev Genet. 1999;33:261-311
references.pmid: 10690410
references.citation: Mol Biol Cell. 2008 Jul;19(7):2708-17
references.pmid: 18417610
references.citation: Mol Cell Biol. 2005 Aug;25(16):6899-911
references.pmid: 16055704
references.citation: Mol Cell. 2009 Mar 27;33(6):704-16
references.pmid: 19328065
references.citation: Trends Biochem Sci. 1999 Nov;24(11):437-40
references.pmid: 10542411
references.citation: Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15044-9
references.pmid: 17005718
references.citation: Eukaryot Cell. 2004 Oct;3(5):1261-71
references.pmid: 15470255
references.citation: Proc Natl Acad Sci U S A. 1999 May 11;96(10):5440-5
references.pmid: 10318902
references.citation: Anal Chem. 2004 Jul 15;76(14):3935-43
references.pmid: 15253627
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D655-8
references.pmid: 16381952
references.citation: Mol Cell. 2002 Dec;10(6):1489-94
references.pmid: 12504022
references.citation: Mol Cell. 2003 Jun;11(6):1467-78
references.pmid: 12820961
references.citation: Mol Cell Biol. 2008 Jun;28(12):4204-14
references.pmid: 18391023
references.citation: J Proteome Res. 2008 Jan;7(1):51-61
references.pmid: 18173218