Understanding Cullin-RING E3 Biology Through Proteomics-based Substrate Identification

Overview

Journal Mol Cell Proteomics

Specialties Biochemistry
Cell Biology
Molecular Biology

Date 2012 Sep 11

PMID 22962057

Citations 44

Authors

J Wade Harper

Meng-Kwang Marcus Tan

Affiliations

Soon will be listed here.

Abstract

Protein turnover through the ubiquitin-proteasome pathway controls numerous developmental decisions and biochemical processes in eukaryotes. Central to protein ubiquitylation are ubiquitin ligases, which provide specificity in targeted ubiquitylation. With more than 600 ubiquitin ligases encoded by the human genome, many of which remain to be studied, considerable effort is being placed on the development of methods for identifying substrates of specific ubiquitin ligases. In this review, we describe proteomic technologies for the identification of ubiquitin ligase targets, with a particular focus on members of the cullin-RING E3 class of ubiquitin ligases, which use F-box proteins as substrate specific adaptor proteins. Various proteomic methods are described and are compared with genetic approaches that are available. The continued development of such methods is likely to have a substantial impact on the ubiquitin-proteasome field.

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References

Jin L, Pahuja K, Wickliffe K, Gorur A, Baumgartel C, Schekman R . Ubiquitin-dependent regulation of COPII coat size and function. Nature. 2012; 482(7386):495-500. PMC: 3292188. DOI: 10.1038/nature10822. View

Liao H, Liu X, Blank J, Bouck D, Bernard H, Garcia K . Quantitative proteomic analysis of cellular protein modulation upon inhibition of the NEDD8-activating enzyme by MLN4924. Mol Cell Proteomics. 2011; 10(11):M111.009183. PMC: 3226404. DOI: 10.1074/mcp.M111.009183. View

Winston J, Strack P, Chu C, Elledge S, Harper J . The SCFbeta-TRCP-ubiquitin ligase complex associates specifically with phosphorylated destruction motifs in IkappaBalpha and beta-catenin and stimulates IkappaBalpha ubiquitination in vitro. Genes Dev. 1999; 13(3):270-83. PMC: 316433. DOI: 10.1101/gad.13.3.270. View

Sarikas A, Hartmann T, Pan Z . The cullin protein family. Genome Biol. 2011; 12(4):220. PMC: 3218854. DOI: 10.1186/gb-2011-12-4-220. View

Soucy T, Smith P, Milhollen M, Berger A, Gavin J, Adhikari S . An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature. 2009; 458(7239):732-6. DOI: 10.1038/nature07884. View

Welcker M, Clurman B . FBW7 ubiquitin ligase: a tumour suppressor at the crossroads of cell division, growth and differentiation. Nat Rev Cancer. 2007; 8(2):83-93. DOI: 10.1038/nrc2290. View

Huber C, Dias-Santagata D, Glaser A, OSullivan J, Brauner R, Wu K . Identification of mutations in CUL7 in 3-M syndrome. Nat Genet. 2005; 37(10):1119-24. DOI: 10.1038/ng1628. View

Feldman R, Correll C, Kaplan K, Deshaies R . A complex of Cdc4p, Skp1p, and Cdc53p/cullin catalyzes ubiquitination of the phosphorylated CDK inhibitor Sic1p. Cell. 1997; 91(2):221-30. DOI: 10.1016/s0092-8674(00)80404-3. View

Hjerpe R, Thomas Y, Chen J, Zemla A, Curran S, Shpiro N . Changes in the ratio of free NEDD8 to ubiquitin triggers NEDDylation by ubiquitin enzymes. Biochem J. 2011; 441(3):927-36. PMC: 3280039. DOI: 10.1042/BJ20111671. View

10.

Persaud A, Alberts P, Amsen E, Xiong X, Wasmuth J, Saadon Z . Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays. Mol Syst Biol. 2009; 5:333. PMC: 2824488. DOI: 10.1038/msb.2009.85. View

11.

Willems A, Goh T, Taylor L, Chernushevich I, Shevchenko A, Tyers M . SCF ubiquitin protein ligases and phosphorylation-dependent proteolysis. Philos Trans R Soc Lond B Biol Sci. 1999; 354(1389):1533-50. PMC: 1692661. DOI: 10.1098/rstb.1999.0497. View

12.

Yen H, Elledge S . Identification of SCF ubiquitin ligase substrates by global protein stability profiling. Science. 2008; 322(5903):923-9. DOI: 10.1126/science.1160462. View

13.

Dorrello N, Peschiaroli A, Guardavaccaro D, Colburn N, Sherman N, Pagano M . S6K1- and betaTRCP-mediated degradation of PDCD4 promotes protein translation and cell growth. Science. 2006; 314(5798):467-71. DOI: 10.1126/science.1130276. View

14.

Cardozo T, Pagano M . The SCF ubiquitin ligase: insights into a molecular machine. Nat Rev Mol Cell Biol. 2004; 5(9):739-51. DOI: 10.1038/nrm1471. View

15.

Xu G, Paige J, Jaffrey S . Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat Biotechnol. 2010; 28(8):868-73. PMC: 2946519. DOI: 10.1038/nbt.1654. View

16.

Behrends C, Harper J . Constructing and decoding unconventional ubiquitin chains. Nat Struct Mol Biol. 2011; 18(5):520-8. DOI: 10.1038/nsmb.2066. View

17.

Duan S, Skaar J, Kuchay S, Toschi A, Kanarek N, Ben-Neriah Y . mTOR generates an auto-amplification loop by triggering the βTrCP- and CK1α-dependent degradation of DEPTOR. Mol Cell. 2011; 44(2):317-24. PMC: 3212871. DOI: 10.1016/j.molcel.2011.09.005. View

18.

Ang X, Seeburg D, Sheng M, Harper J . Regulation of postsynaptic RapGAP SPAR by Polo-like kinase 2 and the SCFbeta-TRCP ubiquitin ligase in hippocampal neurons. J Biol Chem. 2008; 283(43):29424-32. PMC: 2570879. DOI: 10.1074/jbc.M802475200. View

19.

Mailand N, Bekker-Jensen S, Bartek J, Lukas J . Destruction of Claspin by SCFbetaTrCP restrains Chk1 activation and facilitates recovery from genotoxic stress. Mol Cell. 2006; 23(3):307-18. DOI: 10.1016/j.molcel.2006.06.016. View

20.

Harper J, Burton J, Solomon M . The anaphase-promoting complex: it's not just for mitosis any more. Genes Dev. 2002; 16(17):2179-206. DOI: 10.1101/gad.1013102. View