Identification and analysis of endogenous SUMO1 and SUMO2/3 targets in mammalian cells and tissues using monoclonal antibodies

Nature Protocols

Volumn 9, Issue 4, 2014, Pages 896-909

  Barysch, Sina V ^a   Dittner, Claudia ^a,b   Flotho, Annette ^a   Becker, Janina ^a   Melchior, Frauke ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MONOCLONAL ANTIBODY; SUMO 1 PROTEIN; SUMO 2 PROTEIN; SUMO 3 PROTEIN; SUMO PROTEIN; SUMO1 PROTEIN, HUMAN; SUMO2 PROTEIN, MOUSE; SUMO3 PROTEIN, MOUSE; UBIQUITIN;

ANIMAL CELL; ANIMAL TISSUE; ANTIBODY PRODUCTION; ARTICLE; BINDING AFFINITY; CLINICAL PROTOCOL; CONTROLLED STUDY; CYTOLYSIS; ELUTION; GENETIC MANIPULATION; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOPRECIPITATION; MALE; MAMMAL CELL; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN INTERACTION; PROTEIN TARGETING; SUMOYLATION; DENATURATION; DROSOPHILA MELANOGASTER; LIVER; PROTEIN ANALYSIS; VERTEBRATE; ANIMAL; METABOLISM; PROCEDURES;

ANIMALS; ANTIBODIES, MONOCLONAL; HUMANS; IMMUNOPRECIPITATION; LIVER; MICE; SMALL UBIQUITIN-RELATED MODIFIER PROTEINS; SUMO-1 PROTEIN; SUMOYLATION; UBIQUITINS;

EID: 84897139297     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.053     Document Type: Article

References (40)

1. Flotho, A. & Melchior, F. SUMOylation: a regulatory protein modification in health and disease. Annu. Rev. Biochem. 82, 357-385 (2013).
2. Jentsch, S. & Psakhye, I. Control of nuclear activities by substrate-selective and protein-group SUMOylation. Annu. Rev. Genet. 47, 167-186 (2013).
3. Gareau, J.R. & Lima, C.D. The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat. Rev. Mol. Cell Biol. 11, 861-871 (2010).
4. Cubenas-Potts, C. & Matunis, M.J. SUMO: a multifaceted modifier of chromatin structure and function. Dev. Cell 24, 1-12 (2013).
5. Hickey, C.M., Wilson, N.R. & Hochstrasser, M. Function and regulation of SUMO proteases. Nat. Rev. Mol. Cell Biol. 13, 755-766 (2012).
6. Hecker, C.M., Rabiller, M., Haglund, K., Bayer, P. & Dikic, I. Specification of SUMO1- and SUMO2-interacting motifs. J. Biol. Chem. 281, 16117-16127 (2006).
7. Song, J., Durrin, L.K., Wilkinson, T.A., Krontiris, T.G. & Chen, Y. Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc. Natl. Acad. Sci. USA 101, 14373-14378 (2004).
8. Song, J., Zhang, Z., Hu, W. & Chen, Y. Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation. J. Biol. Chem. 280, 40122-40129 (2005).
9. Watts, F.Z. Starting and stopping SUMOylation: What regulates the regulator? Chromosoma 122, 451-463 (2013).
10. Da Silva-Ferrada, E., Lopitz-Otsoa, F., Lang, V., Rodriguez, M.S. & Matthiesen, R. Strategies to identify recognition signals and targets of SUMOylation. Biochem. Res. Int. 2012, 875148 (2012).
11. Filosa, G., Barabino, S.M. & Bachi, A. Proteomics strategies to identify SUMO targets and acceptor sites: a survey of RNA-binding proteins SUMOylation. Neuromolecular. Med. 15, 661-676 (2013).
12. Desterro, J.M., Rodriguez, M.S. & Hay, R.T. SUMO-1 modification of I?Bα inhibits NF-?B activation. Mol. Cell 2, 233-239 (1998).
13. Mahajan, R., Gerace, L. & Melchior, F. Molecular characterization of the SUMO-1 modification of RanGAP1 and its role in nuclear envelope association. J. Cell Biol. 140, 259-270 (1998).
14. Rodriguez, M.S. et al. SUMO-1 modification activates the transcriptional response of p53. EMBO J. 18, 6455-6461 (1999).
15. Sternsdorf, T., Jensen, K., Reich, B. & Will, H. The nuclear dot protein sp100, characterization of domains necessary for dimerization, subcellular localization, and modification by small ubiquitin-like modifiers. J. Biol. Chem. 274, 12555-12566 (1999).
16. Pichler, A. et al. SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nat. Struct. Mol. Biol. 12, 264-269 (2005).
17. Rodriguez, M.S., Dargemont, C. & Hay, R.T. SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting. J. Biol. Chem. 276, 12654-12659 (2001).
18. Denison, C. et al. A proteomic strategy for gaining insights into protein SUMOylation in yeast. Mol. Cell Proteomics 4, 246-254 (2005).
19. Panse, V.G., Hardeland, U., Werner, T., Kuster, B. & Hurt, E. A proteome-wide approach identifies SUMOylated substrate proteins in yeast. J. Biol. Chem. 279, 41346-41351 (2004).
20. Zhou, W., Ryan, J.J. & Zhou, H. Global analyses of SUMOylated proteins in Saccharomyces cerevisiae. Induction of protein SUMOylation by cellular stresses. J. Biol. Chem. 279, 32262-32268 (2004).
21. Nie, M., Xie, Y., Loo, J.A. & Courey, A.J. Genetic and proteomic evidence for roles of Drosophila SUMO in cell cycle control, Ras signaling, and early pattern formation. PLoS ONE 4, e5905 (2009).
22. Kaminsky, R. et al. SUMO regulates the assembly and function of a cytoplasmic intermediate filament protein in C. elegans. Dev. Cell 17, 724-735 (2009).
23. Miller, M.J., Barrett-Wilt, G.A., Hua, Z. & Vierstra, R.D. Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis. Proc. Natl. Acad. Sci. USA 107, 16512-16517 (2010).
24. Tirard, M. et al. In vivo localization and identification of SUMOylated proteins in the brain of His6-HA-SUMO1 knock-in mice. Proc. Natl. Acad. Sci. USA 109, 21122-21127 (2012).
25. Vertegaal, A.C. et al. Distinct and overlapping sets of SUMO-1 and SUMO-2 target proteins revealed by quantitative proteomics. Mol. Cell Proteomics 5, 2298-2310 (2006).
26. Vertegaal, A.C. et al. A proteomic study of SUMO-2 target proteins. J. Biol. Chem. 279, 33791-33798 (2004).
27. Blomster, H.A. et al. Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites. Mol. Cell Proteomics 8, 1382-1390 (2009).
28. Galisson, F. et al. A novel proteomics approach to identify SUMOylated proteins and their modification sites in human cells. Mol. Cell Proteomics 10, M110 004796 (2011).
29. Matic, I. et al. In vivo identification of human small ubiquitin-like modifier polymerization sites by high-accuracy mass spectrometry and an in vitro-to-in vivo strategy. Mol. Cell Proteomics 7, 132-144 (2008).
30. Golebiowski, F. et al. System-wide changes to SUMO modifications in response to heat shock. Sci. Signal 2, ra24 (2009).
31. Golebiowski, F., Tatham, M.H., Nakamura, A. & Hay, R.T. High-stringency tandem affinity purification of proteins conjugated to ubiquitin-like moieties. Nat. Protoc. 5, 873-882 (2010).
32. Bruderer, R. et al. Purification and identification of endogenous polySUMO conjugates. EMBO Rep. 12, 142-148 (2011).
33. Matafora, V., D'Amato, A., Mori, S., Blasi, F. & Bachi, A. Proteomics analysis of nucleolar SUMO-1 target proteins upon proteasome inhibition. Mol. Cell Proteomics 8, 2243-2255 (2009).
34. Sarge, K.D. & Park-Sarge, O.K. Detection of proteins SUMOylated in vivo and in vitro. Methods Mol. Biol. 590, 265-277 (2009).
35. Becker, J. et al. Detecting endogenous SUMO targets in mammalian cells and tissues. Nat. Struct. Mol. Biol. 20, 525-531 (2013).
36. Matunis, M.J., Coutavas, E. & Blobel, G. A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex. J. Cell Biol. 135, 1457-1470 (1996).
37. Zhang, X.D. et al. SUMO-2/3 modification and binding regulate the association of CENP-E with kinetochores and progression through mitosis. Mol. Cell 29, 729-741 (2008).
38. Ong, S.E. & Mann, M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protoc. 1, 2650-2660 (2006).
39. Davis, J.M. Basic Cell Culture (Practical Approach Series) 2nd edn. (Oxford University Press, 2002).
40. Vlasak, J. & Ionescu, R. Fragmentation of monoclonal antibodies. MAbs 3, 253-263 (2011).