Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.
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.
Saleem
Ramsey A
RA
Institute for Systems Biology, Seattle, Washington 98103, USA.
Rogers
Richard S
RS
Ratushny
Alexander V
AV
Dilworth
David J
DJ
Shannon
Paul T
PT
Shteynberg
David
D
Wan
Yakun
Y
Moritz
Robert L
RL
Nesvizhskii
Alexey I
AI
Rachubinski
Richard A
RA
Aitchison
John D
JD
D013058:Mass Spectrometry; D020411:Oligonucleotide Array Sequence Analysis; D020675:Peroxisomes; D010750:Phosphoproteins / Q000378:metabolism*; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D015398:Signal Transduction
D010750:Phosphoproteins
Biochim Biophys Acta. 2006 Dec;1763(12):1392-402
16949166
Electrophoresis. 1999 Dec;20(18):3551-67
10612281
BMC Biotechnol. 2004 Apr 16;4:7
15090068
Mol Cell Proteomics. 2005 Mar;4(3):310-27
15665377
Mol Syst Biol. 2007;3:115
17551510
Biophys J. 2008 Oct;95(8):3715-23
18621837
Trends Biochem Sci. 2000 Dec;25(12):596-601
11116185
Nat Biotechnol. 2006 Oct;24(10):1285-92
16964243
Mol Cell Proteomics. 2005 Jul;4(7):873-86
15858219
Cell. 2000 Oct 13;103(2):193-200
11057893
Nat Biotechnol. 2005 Nov;23(11):1391-8
16273072
Mol Syst Biol. 2005;1:2005.0017
16729052
Nat Biotechnol. 2001 Apr;19(4):375-8
11283598
Cell. 2007 Jan 26;128(2):225-31
17254958
Nucleic Acids Res. 1998 Jan 1;26(1):73-9
9399804
J Am Soc Mass Spectrom. 2010 Aug;21(8):1417-22
20451407
J Proteome Res. 2008 Mar;7(3):1088-97
18257517
Anal Chem. 2002 Oct 15;74(20):5383-92
12403597
Proteome Sci. 2006 Jul 19;4:15
16854217
Bioinformatics. 2006 Nov 15;22(22):2830-2
16877754
Nat Rev Genet. 2004 Feb;5(2):101-13
14735121
BMC Bioinformatics. 2007 Nov 19;8:456
18021453
Nat Protoc. 2008;3(10):1630-8
18833199
Nat Biotechnol. 2007 Mar;25(3):285-6
17344875
Nat Immunol. 2009 Apr;10(4):437-43
19270711
Mol Cell Biol. 2009 May;29(9):2346-58
19273605
J Proteome Res. 2009 Feb;8(2):887-99
19072539
Mol Cell Proteomics. 2008 May;7(5):971-80
18212344
Bioinformatics. 2008 Sep 15;24(18):2110-1
18635572
J Cell Biol. 2004 Dec 20;167(6):1099-112
15596542
Curr Opin Cell Biol. 2009 Feb;21(1):119-26
19188056
Nat Biotechnol. 2008 Dec;26(12):1339-40
19060867
Mol Cell Biol. 2000 Jun;20(12):4340-9
10825197
Mol Cell Proteomics. 2008 Jul;7(7):1389-96
18407956
Nat Biotechnol. 2002 Mar;20(3):301-5
11875433
Nucleic Acids Res. 2001 Jan 1;29(1):11-6
11125038
Proteomics. 2010 Mar;10(6):1150-9
20101611
Mol Syst Biol. 2006;2:2006.0009
16738555
Biochim Biophys Acta. 2006 Dec;1763(12):1541-51
17050007
Mol Cell Proteomics. 2002 May;1(5):376-86
12118079
Cell. 2006 Nov 3;127(3):635-48
17081983
Bioinformatics. 2004 Jun 12;20(9):1466-7
14976030
Anal Chem. 2003 Sep 1;75(17):4646-58
14632076
Proteomics. 2008 Nov;8(21):4453-65
18972525
Nature. 2001 May 3;411(6833):41-2
11333967
J Cell Biol. 2008 Apr 21;181(2):281-92
18426976
J Cell Biol. 2002 Jul 22;158(2):259-71
12135984
Nat Biotechnol. 2007 May;25(5):566-8
17450129
Mol Biol Cell. 2002 Aug;13(8):2783-94
12181346
Anal Chem. 2004 Jul 15;76(14):3935-43
15253627
Nat Biotechnol. 2004 Sep;22(9):1139-45
15314609
J Biol Chem. 2008 Apr 18;283(16):10264-75
18285336
Anal Chem. 2003 Dec 1;75(23):6648-57
14640741
Nat Methods. 2005 Aug;2(8):591-8
16094384