Proteomic snapshot of the EGF-induced ubiquitin network.
The activity, localization and fate of many cellular proteins are regulated through ubiquitination, a process whereby one or more ubiquitin (Ub) monomers or chains are covalently attached to target proteins. While Ub-conjugated and Ub-associated proteomes have been described, we lack a high-resolution picture of the dynamics of ubiquitination in response to signaling. In this study, we describe the epidermal growth factor (EGF)-regulated Ubiproteome, as obtained by two complementary purification strategies coupled to quantitative proteomics. Our results unveil the complex impact of growth factor signaling on Ub-based intracellular networks to levels that extend well beyond what might have been expected. In addition to endocytic proteins, the EGF-regulated Ubiproteome includes a large number of signaling proteins, ubiquitinating and deubiquitinating enzymes, transporters and proteins involved in translation and transcription. The Ub-based signaling network appears to intersect both housekeeping and regulatory circuitries of cellular physiology. Finally, as proof of principle of the biological relevance of the EGF-Ubiproteome, we demonstrated that EphA2 is a novel, downstream ubiquitinated target of epidermal growth factor receptor (EGFR), critically involved in EGFR biological responses.
IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.
Elisabetta
E
Argenzio
Tanja
T
Bange
Barbara
B
Oldrini
Fabrizio
F
Bianchi
Raghunath
R
Peesari
Sara
S
Mari
Pier Paolo
PP
Di Fiore
Matthias
M
Mann
Simona
S
Polo
D000818:Animals; D015153:Blotting, Western; D002460:Cell Line; D016000:Cluster Analysis; D004815:Epidermal Growth Factor / Q000737:chemistry / Q000378:metabolism*; D006367:HeLa Cells; D006801:Humans; D013058:Mass Spectrometry; D051379:Mice; D008856:Microscopy, Fluorescence; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D036104:Receptor, EphA2 / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods*; D025801:Ubiquitin / Q000737:chemistry / Q000378:metabolism*
D020543:Proteome; D025801:Ubiquitin; D004815:Epidermal Growth Factor; D036104:Receptor, EphA2
Electrophoresis. 1999 Dec;20(18):3551-67
10612281
Ann N Y Acad Sci. 2003 Apr;986:497-503
12763870
J Biol Chem. 2003 Oct 31;278(44):43169-77
12907674
Cell. 2007 Aug 24;130(4):651-62
17719543
Mol Cell Proteomics. 2005 Dec;4(12):2010-21
16249172
Mol Cell. 1999 Dec;4(6):1029-40
10635327
Nat Cell Biol. 2006 Nov;8(11):1246-54
17013377
Mol Syst Biol. 2007;3:151
18059446
Cancer Cell. 2008 May;13(5):375-6
18455118
Mol Cell. 2009 Feb 13;33(3):275-86
19217402
Cell. 1989 Oct 6;59(1):33-43
2790960
Nat Cell Biol. 2003 May;5(5):461-6
12717448
Mol Interv. 2007 Jun;7(3):157-67
17609522
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
16381927
Nat Protoc. 2006;1(6):2650-60
17406521
Trends Cell Biol. 2010 Apr;20(4):196-204
20138522
Nat Rev Mol Cell Biol. 2005 Dec;6(12):907-18
16227975
Mol Cell. 2006 Mar 17;21(6):737-48
16543144
Nat Rev Mol Cell Biol. 2008 Sep;9(9):679-90
18698327
Nat Rev Mol Cell Biol. 2005 Aug;6(8):610-21
16064137
Cell. 2008 Aug 22;134(4):668-78
18724939
Nat Rev Mol Cell Biol. 2006 Jun;7(6):391-403
16723975
Nat Biotechnol. 2008 Dec;26(12):1367-72
19029910
Science. 2009 Aug 14;325(5942):834-40
19608861
J Biol Chem. 2004 Jul 2;279(27):28017-27
15117950
Cancer Cell. 2008 May;13(5):385-93
18455122
Biochim Biophys Acta. 2004 Nov 29;1695(1-3):189-207
15571815
Nat Rev Mol Cell Biol. 2006 Jul;7(7):473-83
16829979
Cell. 2009 Feb 6;136(3):521-34
19203585
Cell. 2006 Mar 24;124(6):1183-95
16499958
Mol Biol Cell. 1994 May;5(5):539-47
7919536
Nat Rev Neurosci. 2007 Dec;8(12):935-47
17987031
Mol Cell Proteomics. 2009 Feb;8(2):226-31
18815124
Exp Cell Res. 2009 May 15;315(9):1610-8
19007773
Nucleic Acids Res. 2008 Jan;36(Database issue):D240-4
17962309
J Proteome Res. 2010 May 7;9(5):2734-42
20222723
Cell Div. 2007 Mar 13;2:11
17355622
Traffic. 2009 Apr;10(4):349-63
19183301
Biochem J. 2006 Nov 1;399(3):361-72
17034365
Science. 2007 Jan 12;315(5809):201-5
17218518
Mol Cell. 2007 Dec 14;28(5):730-8
18082598
Nature. 2002 Mar 28;416(6879):451-5
11919637
Mol Cancer Res. 2002 Nov;1(1):79-87
12496371
Bioinformatics. 2007 Dec 1;23(23):3251-3
17644558
Mol Cell Proteomics. 2006 Apr;5(4):737-48
16432255
Mol Cell. 2006 Dec 8;24(5):701-711
17157253
Nat Biotechnol. 2004 Sep;22(9):1139-45
15314609
Biochem Biophys Res Commun. 2002 Aug 9;296(1):214-20
12147253
FEBS J. 2009 Jun;276(12):3199-210
19438715
J Proteome Res. 2008 Oct;7(10):4566-76
18781797
Cell. 2008 Apr 4;133(1):38-52
18394988