title: Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.
abstract: Phosphorylation of proteins is a key posttranslational modification in cellular signaling, regulating many aspects of cellular responses. We used a quantitative, integrated, phosphoproteomics approach to characterize the cellular responses of the yeast Saccharomyces cerevisiae to the fatty acid oleic acid, a molecule with broad human health implications and a potent inducer of peroxisomes. A combination of cryolysis and urea solubilization was used to minimize the opportunity for reorientation of the phosphoproteome, and hydrophilic interaction liquid chromatography and IMAC chemistries were used to fractionate and enrich for phosphopeptides. Using these approaches, numerous phosphorylated peptides specific to oleate-induced and glucose-repressed conditions were identified and mapped to known signaling pathways. These include several transcription factors, two of which, Pip2p and Cst6p, must be phosphorylated for the normal transcriptional response of fatty acid-responsive loci encoding peroxisomal proteins. The phosphoproteome data were integrated with results from genome-wide assays studying the effects of signaling molecule deletions and known protein-protein interactions to generate a putative fatty acid-responsive signaling network. In this network, the most highly connected nodes are those with the largest effects on cellular responses to oleic acid. These properties are consistent with a scale-free topology, demonstrating that scale-free properties are conserved in condition-specific networks.
authors.affiliation: Institute for Systems Biology, Seattle, Washington 98103, USA.
authors.forename: Ramsey A
authors.initials: RA
authors.lastname: Saleem
authors.forename: Richard S
authors.initials: RS
authors.lastname: Rogers
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Ratushny
authors.forename: David J
authors.initials: DJ
authors.lastname: Dilworth
authors.forename: Paul T
authors.initials: PT
authors.lastname: Shannon
authors.forename: David
authors.initials: D
authors.lastname: Shteynberg
authors.forename: Yakun
authors.initials: Y
authors.lastname: Wan
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
authors.forename: Richard A
authors.initials: RA
authors.lastname: Rachubinski
authors.forename: John D
authors.initials: JD
authors.lastname: Aitchison
mesh_terms: D013058:Mass Spectrometry; D020411:Oligonucleotide Array Sequence Analysis; D020675:Peroxisomes; D010750:Phosphoproteins / Q000378:metabolism*; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D015398:Signal Transduction
chemical_list: D010750:Phosphoproteins
references.citation: Biochim Biophys Acta. 2006 Dec;1763(12):1392-402
references.pmid: 16949166
references.citation: Electrophoresis. 1999 Dec;20(18):3551-67
references.pmid: 10612281
references.citation: BMC Biotechnol. 2004 Apr 16;4:7
references.pmid: 15090068
references.citation: Mol Cell Proteomics. 2005 Mar;4(3):310-27
references.pmid: 15665377
references.citation: Mol Syst Biol. 2007;3:115
references.pmid: 17551510
references.citation: Biophys J. 2008 Oct;95(8):3715-23
references.pmid: 18621837
references.citation: Trends Biochem Sci. 2000 Dec;25(12):596-601
references.pmid: 11116185
references.citation: Nat Biotechnol. 2006 Oct;24(10):1285-92
references.pmid: 16964243
references.citation: Mol Cell Proteomics. 2005 Jul;4(7):873-86
references.pmid: 15858219
references.citation: Cell. 2000 Oct 13;103(2):193-200
references.pmid: 11057893
references.citation: Nat Biotechnol. 2005 Nov;23(11):1391-8
references.pmid: 16273072
references.citation: Mol Syst Biol. 2005;1:2005.0017
references.pmid: 16729052
references.citation: Nat Biotechnol. 2001 Apr;19(4):375-8
references.pmid: 11283598
references.citation: Cell. 2007 Jan 26;128(2):225-31
references.pmid: 17254958
references.citation: Nucleic Acids Res. 1998 Jan 1;26(1):73-9
references.pmid: 9399804
references.citation: J Am Soc Mass Spectrom. 2010 Aug;21(8):1417-22
references.pmid: 20451407
references.citation: J Proteome Res. 2008 Mar;7(3):1088-97
references.pmid: 18257517
references.citation: Anal Chem. 2002 Oct 15;74(20):5383-92
references.pmid: 12403597
references.citation: Proteome Sci. 2006 Jul 19;4:15
references.pmid: 16854217
references.citation: Bioinformatics. 2006 Nov 15;22(22):2830-2
references.pmid: 16877754
references.citation: Nat Rev Genet. 2004 Feb;5(2):101-13
references.pmid: 14735121
references.citation: BMC Bioinformatics. 2007 Nov 19;8:456
references.pmid: 18021453
references.citation: Nat Protoc. 2008;3(10):1630-8
references.pmid: 18833199
references.citation: Nat Biotechnol. 2007 Mar;25(3):285-6
references.pmid: 17344875
references.citation: Nat Immunol. 2009 Apr;10(4):437-43
references.pmid: 19270711
references.citation: Mol Cell Biol. 2009 May;29(9):2346-58
references.pmid: 19273605
references.citation: J Proteome Res. 2009 Feb;8(2):887-99
references.pmid: 19072539
references.citation: Mol Cell Proteomics. 2008 May;7(5):971-80
references.pmid: 18212344
references.citation: Bioinformatics. 2008 Sep 15;24(18):2110-1
references.pmid: 18635572
references.citation: J Cell Biol. 2004 Dec 20;167(6):1099-112
references.pmid: 15596542
references.citation: Curr Opin Cell Biol. 2009 Feb;21(1):119-26
references.pmid: 19188056
references.citation: Nat Biotechnol. 2008 Dec;26(12):1339-40
references.pmid: 19060867
references.citation: Mol Cell Biol. 2000 Jun;20(12):4340-9
references.pmid: 10825197
references.citation: Mol Cell Proteomics. 2008 Jul;7(7):1389-96
references.pmid: 18407956
references.citation: Nat Biotechnol. 2002 Mar;20(3):301-5
references.pmid: 11875433
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):11-6
references.pmid: 11125038
references.citation: Proteomics. 2010 Mar;10(6):1150-9
references.pmid: 20101611
references.citation: Mol Syst Biol. 2006;2:2006.0009
references.pmid: 16738555
references.citation: Biochim Biophys Acta. 2006 Dec;1763(12):1541-51
references.pmid: 17050007
references.citation: Mol Cell Proteomics. 2002 May;1(5):376-86
references.pmid: 12118079
references.citation: Cell. 2006 Nov 3;127(3):635-48
references.pmid: 17081983
references.citation: Bioinformatics. 2004 Jun 12;20(9):1466-7
references.pmid: 14976030
references.citation: Anal Chem. 2003 Sep 1;75(17):4646-58
references.pmid: 14632076
references.citation: Proteomics. 2008 Nov;8(21):4453-65
references.pmid: 18972525
references.citation: Nature. 2001 May 3;411(6833):41-2
references.pmid: 11333967
references.citation: J Cell Biol. 2008 Apr 21;181(2):281-92
references.pmid: 18426976
references.citation: J Cell Biol. 2002 Jul 22;158(2):259-71
references.pmid: 12135984
references.citation: Nat Biotechnol. 2007 May;25(5):566-8
references.pmid: 17450129
references.citation: Mol Biol Cell. 2002 Aug;13(8):2783-94
references.pmid: 12181346
references.citation: Anal Chem. 2004 Jul 15;76(14):3935-43
references.pmid: 15253627
references.citation: Nat Biotechnol. 2004 Sep;22(9):1139-45
references.pmid: 15314609
references.citation: J Biol Chem. 2008 Apr 18;283(16):10264-75
references.pmid: 18285336
references.citation: Anal Chem. 2003 Dec 1;75(23):6648-57
references.pmid: 14640741
references.citation: Nat Methods. 2005 Aug;2(8):591-8
references.pmid: 16094384