Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue.
Although protein ADP-ribosylation is involved in diverse biological processes, it has remained a challenge to identify ADP-ribose acceptor sites. Here, we present an experimental workflow for sensitive and unbiased analysis of endogenous ADP-ribosylation sites, capable of detecting more than 900 modification sites in mammalian cells and mouse liver. In cells, we demonstrate that Lys residues, besides Glu, Asp and Arg residues, are the dominant in vivo targets of ADP-ribosylation during oxidative stress. In normal liver tissue, we find Arg residues to be the predominant modification site. The cellular distribution and biological processes that involve ADP-ribosylated proteins are different in cultured cells and liver tissue, in the latter of which the majority of sites were found to be in cytosolic and mitochondrial protein networks primarily associated with metabolism. Collectively, we describe a robust methodology for the assessment of the role of ADP-ribosylation and ADP-ribosyltransferases in physiological and pathological states.
Faculty of Health Sciences, Department of Proteomics, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
Rita
R
Martello
Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland.|Molecular Life Science Program of the Life Science Graduate School, University of Zurich, Zurich CH-8057, Switzerland.
Mario
M
Leutert
Faculty of Health Sciences, Department of Proteomics, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
Stephanie
S
Jungmichel
Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland.|Molecular Life Science Program of the Life Science Graduate School, University of Zurich, Zurich CH-8057, Switzerland.
Vera
V
Bilan
Faculty of Health Sciences, Department of Proteomics, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
Sara C
http://orcid.org/0000-0001-6250-5467
SC
Larsen
Faculty of Health Sciences, Department of Proteomics, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
Clifford
C
Young
Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland.
Michael O
MO
Hottiger
Faculty of Health Sciences, Department of Proteomics, The Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
Michael L
ML
Nielsen
Cell Metab. 2011 Apr 6;13(4):461-8
21459330
Nature. 2011 Sep 04;477(7366):616-20
21892188
Mol Cell Biochem. 1994 Sep;138(1-2):221-6
7898467
FEBS Lett. 1987 Dec 10;225(1-2):48-52
2891567
Cells. 2015 Sep 25;4(4):569-95
26426055
Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):82-6
14676324
Nat Struct Mol Biol. 2013 Apr;20(4):508-14
23474712
ACS Chem Biol. 2013 Jul 19;8(7):1567-75
23631432
Cell Metab. 2012 Sep 5;16(3):290-5
22921416
J Proteome Res. 2015 Sep 4;14(9):4072-9
26211397
Mol Cell. 2001 Jun;7(6):1221-31
11430825
J Am Soc Mass Spectrom. 2005 Jun;16(6):880-2
15907703
Science. 2016 Jul 1;353(6294):45-50
27256882
Nucleic Acids Res. 2010 Oct;38(19):6350-62
20525793
Trends Biochem Sci. 2010 Apr;35(4):208-19
20106667
Nat Struct Mol Biol. 2013 Apr;20(4):502-7
23474714
Exp Cell Res. 2004 Jul 15;297(2):521-32
15212953
Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52
25352553
Mol Cell Proteomics. 2013 Dec;12(12):3444-52
24187339
Mol Cell. 2015 Jun 18;58(6):911-24
26091340
Mol Cell. 2012 Aug 10;47(3):444-56
22749529
Mol Cell. 2015 Jul 16;59(2):309-20
26166706
Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9
23203882
Nat Cell Biol. 2011 May;13(5):623-9
21478859
Nucleic Acids Res. 2012 Oct;40(18):9044-59
22810208
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18314-9
17116881
Mol Cell. 2016 Feb 4;61(3):474-85
26833088
Methods Mol Biol. 2011;780:3-34
21870251
FEBS Lett. 2011 Jun 6;585(11):1651-6
21443875
Mol Cell. 2013 Oct 24;52(2):272-85
24055347
Mol Cell Proteomics. 2002 May;1(5):376-86
12118079
Genes Dev. 2011 Mar 1;25(5):409-33
21363960
Nat Rev Cancer. 2010 Apr;10 (4):293-301
20200537
Mol Cell. 2011 Mar 4;41(5):497-9
21362545
Mol Cell. 2008 Oct 10;32(1):57-69
18851833
EMBO J. 2009 Sep 2;28(17):2601-15
19629035
Nat Rev Cancer. 2014 Jul;14 (7):502-9
24898058
Nat Commun. 2014 Jul 21;5:4426
25043379
Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):3948-53
15741271
Cell Commun Signal. 2013 Jan 19;11(1):5
23332125
J Biol Chem. 1996 May 3;271(18):10461-9
8631841
EMBO J. 2005 Jun 1;24(11):1911-20
15902274
Nat Biotechnol. 2008 Dec;26(12):1367-72
19029910
Science. 2012 May 11;336(6082):728-32
22582261
Nature. 2012 Mar 28;483(7391):570-5
22460902
Nat Cell Biol. 2012 Nov;14 (11):1223-30
23103912
Anal Chem. 2003 Feb 1;75(3):663-70
12585499
J Proteome Res. 2012 Jun 1;11(6):3487-97
22537090
Cell. 2010 Sep 17;142(6):943-53
20832105
J Proteome Res. 2010 Feb 5;9(2):761-76
19921851
Endocr Rev. 2010 Apr;31(2):194-223
20007326
Mol Cell Biol. 2004 Aug;24(16):7163-78
15282315
Int J Mass Spectrom. 2012 Feb 15;312:114-121
22563295
Mol Cell Proteomics. 2009 Mar;8(3):443-50
18952599
J Immunol. 2015 Sep 1;195(5):2057-66
26209623
J Biol Chem. 1981 Aug 10;256(15):7830-3
6267027
Nat Rev Drug Discov. 2013 Oct;12(10):725-7
24080684
Nature. 1986 Jul 24-30;322(6077):390-2
3736664
Sci Signal. 2010 Jan 12;3(104):ra3
20068231
Nucleic Acids Res. 2016 Sep 19;44(16):7630-45
27198223
Nucleic Acids Res. 2009 Jun;37(11):3723-38
19372272
Carcinogenesis. 2010 Dec;31(12 ):2058-65
20926829
J Am Chem Soc. 2009 Oct 14;131(40):14258-60
19764761
Nat Methods. 2013 Oct;10 (10 ):981-4
23955771
J Proteome Res. 2014 Aug 1;13(8):3510-22
24920161
Free Radic Biol Med. 2007 Jan 1;42(1):90-105
17157196
Cell. 2003 Jun 13;113(6):677-83
12809599
Nat Rev Microbiol. 2005 May;3(5):397-410
15821726
Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18475-80
20937877
Curr Opin Chem Biol. 2013 Feb;17(1):49-58
23298953