title: Proteomics strategies to identify SUMO targets and acceptor sites: a survey of RNA-binding proteins SUMOylation.
abstract: SUMOylation is a protein posttranslational modification that participates in the regulation of numerous biological processes within the cells. Small ubiquitin-like modifier (SUMO) proteins are members of the ubiquitin-like protein family and, similarly to ubiquitin, are covalently linked to a lysine residue on a target protein via a multi-enzymatic cascade. To assess the specific mechanism triggered by SUMOylation, the identification of SUMO protein substrates and of the precise acceptor site to which SUMO is bound is of critical relevance. Despite hundreds of mammalian proteins have been described as targets of SUMOylation, the identification of the precise acceptor sites still represents an important analytical challenge because of the relatively low stoichiometry in vivo and the highly dynamic nature of this modification. Moreover, mass spectrometry-based identification of SUMOylated sites is hampered by the large peptide remnant of SUMO proteins that are left on the modified lysine residue upon tryptic digestion. The present review provides a survey of the strategies that have been exploited in order to enrich, purify and identify SUMOylation substrates and acceptor sites in human cells on a large-scale format. The success of the presented strategies helped to unravel the numerous activities of this modification, as it was shown by the exemplary case of the RNA-binding protein family, whose SUMOylation is here reviewed.
authors: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
authors: Giuseppe
authors: G
authors: Filosa
authors: Silvia M L
authors: SM
authors: Barabino
authors: Angela
authors: A
authors: Bachi
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line; D002466:Cell Nucleolus / Q000378:metabolism; D016384:Consensus Sequence; D003546:Cysteine Endopeptidases / Q000378:metabolism; D006801:Humans; D008322:Mammals / Q000378:metabolism; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D009410:Nerve Degeneration; D009419:Nerve Tissue Proteins / Q000378:metabolism*; D040901:Proteomics; D016601:RNA-Binding Proteins / Q000378:metabolism*; D025841:Small Ubiquitin-Related Modifier Proteins / Q000302:isolation & purification / Q000378:metabolism*; D013379:Substrate Specificity; D058207:Sumoylation / Q000502:physiology*; D043743:Ubiquitin-Protein Ligase Complexes / Q000378:metabolism
chemical_list: D009419:Nerve Tissue Proteins; D016601:RNA-Binding Proteins; D025841:Small Ubiquitin-Related Modifier Proteins; D043743:Ubiquitin-Protein Ligase Complexes; D003546:Cysteine Endopeptidases
references: J Biol Chem. 2001 Jun 15;276(24):21664-9
references: 11259410
references: J Biol Chem. 2000 Mar 3;275(9):6252-8
references: 10692421
references: Annu Rev Biochem. 2002;71:375-403
references: 12045101
references: Curr Opin Neurobiol. 2011 Dec;21(6):904-19
references: 21813273
references: Adv Exp Med Biol. 2010;693:54-66
references: 21189685
references: J Biol Chem. 2005 Nov 18;280(46):38153-9
references: 16144832
references: Mol Cell Proteomics. 2009 Dec;8(12):2664-75
references: 19721078
references: Nat Rev Mol Cell Biol. 2007 Dec;8(12):947-56
references: 18000527
references: J Cell Biol. 2012 Apr 16;197(2):179-87
references: 22508508
references: Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14018-23
references: 14612560
references: Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16119-24
references: 20805487
references: Sci Signal. 2009 May 26;2(72):ra24
references: 19471022
references: Nature. 2008 Apr 10;452(7188):709-11
references: 18401402
references: EMBO J. 2002 Mar 15;21(6):1456-64
references: 11889051
references: Annu Rev Biochem. 2004;73:355-82
references: 15189146
references: Nat Rev Genet. 2013 Jan;14(1):35-48
references: 23207911
references: Nat Rev Mol Cell Biol. 2004 Sep;5(9):699-711
references: 15340378
references: Bioessays. 2004 Jun;26(6):629-38
references: 15170860
references: EMBO J. 2002 Jun 3;21(11):2682-91
references: 12032081
references: BMC Bioinformatics. 2008 Jan 08;9:8
references: 18179724
references: Mol Cancer Res. 2002 Nov;1(1):48-55
references: 12496368
references: Cell. 2000 Jun 23;101(7):753-62
references: 10892746
references: Nat Methods. 2006 Jul;3(7):533-9
references: 16791211
references: Rapid Commun Mass Spectrom. 2013 Jan 15;27(1):127-34
references: 23239325
references: Nat Biotechnol. 2010 Aug;28(8):868-73
references: 20639865
references: Mol Cell Proteomics. 2009 Jun;8(6):1382-90
references: 19240082
references: DNA Repair (Amst). 2009 Apr 5;8(4):491-8
references: 19213614
references: Annu Rev Cell Dev Biol. 2005;21:105-31
references: 16212489
references: Nature. 2007 May 17;447(7142):321-5
references: 17486098
references: Mol Cell Proteomics. 2005 Oct;4(10):1626-36
references: 16020427
references: J Biol Chem. 2004 Jun 25;279(26):27233-8
references: 15123604
references: Cell. 2005 Apr 8;121(1):37-47
references: 15820677
references: Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14373-8
references: 15388847
references: Nat Rev Neurosci. 2009 Aug;10(8):597-609
references: 19584893
references: Mol Cell Proteomics. 2011 Feb;10(2):M110.004796
references: 21098080
references: J Biol Chem. 1999 Apr 9;274(15):10618-24
references: 10187858
references: J Biol Chem. 1999 Apr 30;274(18):12555-66
references: 10212234
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D261-70
references: 22135298
references: Mol Cell Biol. 1988 May;8(5):2159-65
references: 2455217
references: Mol Cell. 2006 Nov 3;24(3):341-54
references: 17081986
references: Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1805-10
references: 17261810
references: Nucleus. 2011 Jan-Feb;2(1):30-7
references: 21647297
references: Mol Biol Cell. 2005 Nov;16(11):5115-26
references: 16120648
references: J Biol Chem. 1997 Oct 24;272(43):26799-802
references: 9341106
references: EMBO J. 2012 Dec 12;31(24):4502-10
references: 23232809
references: Mol Cell Biol. 2004 May;24(9):3623-32
references: 15082759
references: Mol Cell. 2010 Aug 27;39(4):618-31
references: 20797632
references: Cell Cycle. 2002 Jul-Aug;1(4):245-9
references: 12429940
references: EMBO Rep. 2011 Feb;12(2):142-8
references: 21252943
references: EMBO J. 1998 Jan 2;17(1):61-70
references: 9427741
references: EMBO J. 2006 Nov 1;25(21):5083-93
references: 17036045
references: J Cell Biol. 1998 Jan 26;140(2):259-70
references: 9442102
references: Mol Cell Proteomics. 2011 Oct;10(10):M111.013284
references: 21890473
references: Chembiochem. 2011 Jan 24;12(2):224-34
references: 21243711
references: Nat Struct Mol Biol. 2008 Jun;15(6):626-33
references: 18488044
references: J Biol Chem. 2006 Jun 9;281(23):16117-27
references: 16524884
references: J Biol Chem. 2000 Nov 17;275(46):36316-23
references: 10961991
references: J Cell Biol. 2006 May 8;173(3):319-25
references: 16682524
references: Biochem Res Int. 2012;2012:875148
references: 22811915
references: Nat Genet. 2004 Aug;36(8):837-41
references: 15247916
references: Mol Cell. 2008 Aug 8;31(3):371-82
references: 18691969
references: Mol Cell. 2010 Aug 27;39(4):641-52
references: 20797634
references: Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):21122-7
references: 23213215
references: Mol Cell Proteomics. 2008 Nov;7(11):2107-22
references: 18565875
references: J Mass Spectrom. 2012 May;47(5):644-54
references: 22576878
references: Mol Cell Proteomics. 2009 Oct;8(10):2243-55
references: 19596686
references: J Biol Chem. 2004 May 14;279(20):20999-1002
references: 15016812
references: Nat Rev Mol Cell Biol. 2003 Sep;4(9):690-9
references: 14506472
references: FASEB J. 2009 Nov;23(11):3917-27
references: 19638400
references: Cell. 2011 Dec 23;147(7):1601-14
references: 22196734
references: Oncogene. 2010 Feb 18;29(7):1017-30
references: 19946338
references: Proc Natl Acad Sci U S A. 2005 May 24;102(21):7689-94
references: 15897463
references: BMC Cell Biol. 2004 Jan 22;5:5
references: 14736338
references: EMBO J. 2010 Apr 7;29(7):1235-47
references: 20186123
references: Hum Mutat. 2013 Jun;34(6):812-26
references: 23559573
references: Mol Cell Proteomics. 2006 Dec;5(12):2298-310
references: 17000644
references: Nat Protoc. 2009;4(9):1363-71
references: 19730420
references: Mol Cell Proteomics. 2002 May;1(5):376-86
references: 12118079
references: Biochemistry. 2010 Jan 12;49(1):1-10
references: 19995069
references: J Biol Chem. 2004 Aug 6;279(32):33791-8
references: 15175327
references: EMBO Rep. 2008 Mar;9(3):273-9
references: 18259216
references: Mol Cell Proteomics. 2013 Sep;12(9):2536-50
references: 23750026
references: Nature. 2008 Jul 3;454(7200):56-61
references: 18548003
references: Nat Protoc. 2010 May;5(5):873-82
references: 20431533
references: J Biol Chem. 2010 Jun 18;285(25):19324-9
references: 20388717
references: Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12913-8
references: 17646655
references: Nucleic Acids Res. 2002 May 15;30(10):2251-60
references: 12000845
references: Mol Cell. 1998 Aug;2(2):233-9
references: 9734360
references: Genes Cells. 2011 Jun;16(6):652-69
references: 21554500
references: RNA Biol. 2013 Jan;10(1):44-55
references: 22995827
references: Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):45-50
references: 16371476
references: FEBS Lett. 1997 Nov 17;417(3):297-300
references: 9409737
references: EMBO J. 2011 Mar 16;30(6):1067-78
references: 21326211
references: Nature. 2009 Dec 17;462(7275):886-90
references: 20016594
references: Cell Death Differ. 2006 Jan;13(1):96-108
references: 15976810
references: Trends Biochem Sci. 2007 Jun;32(6):286-95
references: 17499995
references: J Struct Biol. 2008 Aug;163(2):137-46
references: 18571432
references: Nat Struct Mol Biol. 2013 Apr;20(4):525-31
references: 23503365
references: Eur J Biochem. 1994 Aug 15;224(1):109-14
references: 8076630
references: Mol Cell. 2009 Feb 13;33(3):400-9
references: 19217413
references: Cell. 2005 Dec 16;123(6):1065-78
references: 16360036
references: Mol Cell Proteomics. 2005 Jan;4(1):56-72
references: 15576338
references: FEBS Lett. 2008 Jun 18;582(14):1977-86
references: 18342629
references: Nat Biotechnol. 1999 Oct;17(10):1030-2
references: 10504710
references: Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11370-5
references: 20534433
references: Biochem J. 2010 May 13;428(2):133-45
references: 20462400
references: Mol Cell Proteomics. 2010 Apr;9(4):705-18
references: 20047951
references: Oncogene. 2006 Aug 17;25(36):4955-64
references: 16568089
references: Methods Mol Biol. 2012;832:93-110
references: 22350878