Investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry.
BACKGROUND
Poly(ADP-ribose) polymerases (PARPs) catalyze the formation of poly(ADP-ribose) (pADPr), a post-translational modification involved in several important biological processes, namely surveillance of genome integrity, cell cycle progression, initiation of the DNA damage response, apoptosis, and regulation of transcription. Poly(ADP-ribose) glycohydrolase (PARG), on the other hand, catabolizes pADPr and thereby accounts for the transient nature of poly(ADP-ribosyl)ation. Our investigation of the interactomes of PARP-1, PARP-2, and PARG by affinity-purification mass spectrometry (AP-MS) aimed, on the one hand, to confirm current knowledge on these interactomes and, on the other hand, to discover new protein partners which could offer insights into PARPs and PARG functions.


RESULTS
PARP-1, PARP-2, and PARG were immunoprecipitated from human cells, and pulled-down proteins were separated by gel electrophoresis prior to in-gel trypsin digestion. Peptides were identified by tandem mass spectrometry. Our AP-MS experiments resulted in the identifications of 179 interactions, 139 of which are novel interactions. Gene Ontology analysis of the identified protein interactors points to five biological processes in which PARP-1, PARP-2 and PARG may be involved: RNA metabolism for PARP-1, PARP-2 and PARG; DNA repair and apoptosis for PARP-1 and PARP-2; and glycolysis and cell cycle for PARP-1.


CONCLUSIONS
This study reveals several novel protein partners for PARP-1, PARP-2 and PARG. It provides a global view of the interactomes of these proteins as well as a roadmap to establish the systems biology of poly(ADP-ribose) metabolism.
Isabelle
Maxim
M
Axe cancer, CHUQ Research Center, Faculty of Medicine, Laval University, 2705 Boulevard Laurier, Québec, Canada, G1V 4G2. guy.poirier@crchul.ulaval.ca.
Moreel
Xavier
X
Gagné
Jean-Philippe
JP
Rouleau
Michèle
M
Ethier
Chantal
C
Gagné
Pierre
P
Hendzel
Michael J
MJ
Poirier
Guy G
GG
J Biol Chem. 2002 Jul 26;277(30):26921-6
12011073
Ann N Y Acad Sci. 2008 Dec;1147:233-41
19076445
Anal Chem. 2002 Oct 15;74(20):5383-92
12403597
Nat Cell Biol. 2001 Sep;3(9):839-43
11533664
Comput Appl Biosci. 1993 Apr;9(2):161-7
8481818
Biochem Cell Biol. 2006 Oct;84(5):703-12
17167533
Int J Cancer. 2007 Mar 15;120(6):1192-7
17163414
FEBS Lett. 2002 Mar 13;514(2-3):122-8
11943137
J Biol Chem. 2002 Jun 21;277(25):23028-36
11948190
Mol Cell Biochem. 1999 Mar;193(1-2):53-60
10331638
J Biol Chem. 2008 Jul 18;283(29):19991-8
18495665
Nat Rev Cancer. 2010 Apr;10(4):293-301
20200537
Cell. 2006 Dec 29;127(7):1389-400
17190602
Oncogene. 2004 Sep 23;23(44):7322-9
15286704
Biochem J. 2005 Dec 15;392(Pt 3):499-509
16117724
DNA Repair (Amst). 2003 Sep 18;2(9):955-69
12967653
Nucleic Acids Res. 2008 Jan;36(Database issue):D440-4
17984083
DNA Repair (Amst). 2009 Mar 1;8(3):286-97
19144573
Cancer Cell. 2008 Sep 9;14(3):250-62
18772114
Circulation. 2002 Jun 18;105(24):2899-904
12070120
Dev Biol. 2009 Jul 15;331(2):326-38
19463809
Nature. 2004 Dec 2;432(7017):645-9
15577915
J Biochem. 1999 Oct;126(4):748-55
10502684
J Biol Chem. 1998 Nov 13;273(46):30069-72
9804757
Cancer Res. 2003 Sep 15;63(18):6008-15
14522929
Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17699-704
15591342
Bioinformatics. 2006 Nov 15;22(22):2830-2
16877754
J Biol Chem. 1998 Jun 5;273(23):14461-7
9603959
Front Biosci (Landmark Ed). 2009 Jan 01;14:1116-28
19273119
Mol Biol Cell. 2008 Jun;19(6):2534-43
18367544
RNA. 2002 Apr;8(4):426-39
11991638
Nat Genet. 2000 May;25(1):25-9
10802651
J Am Soc Nephrol. 2009 Jan;20(1):95-103
19056868
Front Biosci. 2008 Jan 01;13:3046-82
17981777
Biochim Biophys Acta. 2008 Sep;1786(1):49-59
18544349
J Biol Chem. 2001 Sep 7;276(36):33375-83
11443112
EMBO J. 2009 Mar 4;28(5):556-67
19165146
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18314-9
17116881
Nature. 2006 Mar 30;440(7084):637-43
16554755
Biochem Cell Biol. 2005 Jun;83(3):354-64
15959561
Mol Cell. 2008 Oct 10;32(1):57-69
18851833
J Biol Chem. 1997 Jan 17;272(3):1769-76
8999859
Mol Cell. 2004 Jun 18;14(6):801-11
15200957
Nat Methods. 2007 Oct;4(10):787-97
17901868
Curr Opin Genet Dev. 2006 Jun;16(3):270-5
16647847
Genome Res. 2003 Nov;13(11):2498-504
14597658
Nat Rev Mol Cell Biol. 2007 Aug;8(8):645-54
17593931
Nature. 2006 Mar 30;440(7084):631-6
16429126
Chromosoma. 2006 Oct;115(5):343-54
16575476
EMBO J. 2001 Oct 1;20(19):5491-502
11574481
EMBO J. 2003 May 1;22(9):2255-63
12727891
Proteomics. 2001 Nov;1(11):1390-404
11922599
Oncogene. 2008 May 29;27(24):3371-83
18223694
Bioinformatics. 2005 Aug 15;21(16):3448-9
15972284
Nucleic Acids Res. 2008 Dec;36(22):6959-76
18981049
Genes Dev. 2005 Jul 1;19(13):1512-7
15998806
J Biol Chem. 1999 Jun 18;274(25):17860-8
10364231
Mol Cell Biol. 2003 Aug;23(16):5919-27
12897160
Proteomics. 2008 May;8(9):1744-9
18442176
Mol Cell Biochem. 1999 Mar;193(1-2):5-11
10331631
Anal Chem. 2003 Sep 1;75(17):4646-58
14632076
Br Med Bull. 2009;89:23-40
19208614
Cell Mol Life Sci. 2005 Apr;62(7-8):739-50
15868399
Proteomics. 2010 Mar;10(6):1265-9
20077414
Nature. 2007 Dec 13;450(7172):991-1000
18075578
Int J Biochem Cell Biol. 1999 Jan;31(1):139-49
10216949
Biochemistry. 2000 Jun 27;39(25):7559-69
10858306
J Biol Chem. 2008 Jul 4;283(27):19095-111
18469000
J Cereb Blood Flow Metab. 2007 Feb;27(2):304-15
16736046
Mol Cell Biol. 1999 Jun;19(6):4390-404
10330179
Biochimie. 1995;77(5):364-7
8527490
PLoS Genet. 2009 Feb;5(2):e1000387
19229318
Nucleic Acids Res. 2000 Oct 15;28(20):3887-96
11024167
Cancer Res. 1995 Feb 15;55(4):868-73
7850801
Nucleic Acids Res. 2009 Jun;37(11):3501-13
19346337
Biochem Biophys Res Commun. 2003 Sep 5;308(4):809-13
12927790
Curr Protoc Protein Sci. 2001 May;Chapter 16:Unit 16.10
18429128
J Biol Chem. 2007 Oct 26;282(43):31289-301
17823127
Nat Rev Genet. 2009 Sep;10(9):617-27
19687803