A new map to understand deubiquitination

Biochemical Society Transactions

Volumn 38, Issue 1, 2010, Pages 21-28

  Katz, Elijah J ^a   Isasa, Marta ^a   Crosas, Bernat ^a  

^a INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

Author keywords

Comparative proteomics; Cytokine; Deubiquitinating enzyme; Signalling; Ubiquitin proteasome system

Indexed keywords

BINDING PROTEIN; DEUBIQUITINATING ENZYME; JAMM PROTEIN; MACHADO JOSEPHIN DOMAIN PROTEIN; OVARIAN TUMOR PROTEASE; REGULATOR PROTEIN; UBIQUITIN SPECIFIC PROTEASE; UBIQUITIN THIOLESTERASE; UNCLASSIFIED DRUG;

APOPTOSIS; BIOGENESIS; CATABOLISM; CELLULAR DISTRIBUTION; CHROMATIN; DEUBIQUITINATION; DEVELOPMENT; DIFFERENTIATION; DNA DAMAGE; DNA REPAIR; HUMAN; MITOSIS; MORPHOGENESIS; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; RNA PROCESSING; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; TRANSLATION REGULATION;

ENDOPEPTIDASES; HUMANS; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; UBIQUITIN; UBIQUITIN THIOLESTERASE;

EID: 76449095082     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0380021     Document Type: Review

References (61)

1. Finley, D. (2009) Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu. Rev. Biochem. 78, 477-513
2. Xu, P., Duong, D.M., Seyfried, N.T., Cheng, D., Xie, Y., Robert, J., Rush, J., Hochstrasser, M., Finley, D. and Peng, J. (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137, 133-145
3. Nijman, S.M., Luna-Vargas, M.P., Velds, A., Brummelkamp, T.R., Dirac, A.M., Sixma, T.K. and Bernards, R. (2005) A genomic and functional inventory of deubiquitinating enzymes. Cell 123, 773-786
4. Komander, D., Clague, M.J. and Urbe', S. (2009) Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10, 550-563
5. Sowa, M.E., Bennett, E.J., Gygi, S.P. and Harper, J.W. (2009) Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389-403
6. Weber, B., Schaper, C., Wang, Y., Scholz, J. and Bein, B. (2009) Interaction of the ubiquitin carboxyl terminal esterase L1 with α2-adrenergic receptors inhibits agonist-mediated p44/42 MAP kinase activation. Cell. Signalling 21, 1513-1521
7. Trompouki, E., Hatzivassiliou, E., Tsichritzis, T., Farmer, H., Ashworth, A. and Mosialos, G. (2003) CYLD is a deubiquitinating enzyme that negatively regulates NF-?B activation by TNFR family members. Nature 424, 793-796
8. Gomez-Ferreria, M.A., Rath, U., Buster, D.W., Chanda, S.K., Caldwell, J.S., Rines, D.R. and Sharp, D.J. (2007) Human Cep192 is required for mitotic centrosome and spindle assembly. Curr. Biol. 17, 1960-1966
9. Enesa, K., Zakkar, M., Chaudhury, H., Luong le, A., Rawlinson, L., Mason, J.C., Haskard, D.O., Dean, J.L. and Evans, P.C. (2008) NF-κB suppression by the deubiquitinating enzyme Cezanne: a novel negative feedback loop in pro-inflammatory signaling. J. Biol. Chem. 283, 7036-7045
10. Jariel-Encontre, I., Bossis, G. and Piechaczyk, M. (2008) Ubiquitin-independent degradation of proteins by the proteasome. Biochem. Biophys. Acta 1786, 153-177
11. Buus, R., Faronato, M., Hammond, D.E., Urbé, S. and Clague, M.J. (2009) Deubiquitinase activities required for hepatocyte growth factor-induced scattering of epithelial cells. Curr. Biol. 19, 1463-1466
12. Stanisic, V., Malovannaya, A., Qin, J., Lonard, D.M. and O'Malley, B.W. (2009) OTU domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) deubiquitinates estrogen receptor (ER) α and affects ERα transcriptional activity. J. Biol. Chem. 284, 16135-16145
13. Sato, Y., Yoshikawa, A., Yamagata, A., Mimura, H., Yamashita, M., Ookata, K., Nureki, O., Iwai, K., Komada, M. and Fukai, S. (2008) Structural basis for specific cleavage of Lys63-linked polyubiquitin chains. Nature 455, 358-362
14. Boeddrich, A., Gaumer, S., Haacke, A., Tzvetkov, N., Albrecht, M., Evert, B.O., Müller, E.C., Lurz, R., Breuer, P., Schugardt, N. et al. (2006) An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis. EMBO J. 25, 1547-1558
15. Joo, H.Y., Zhai, L., Yang, C., Nie, S., Erdjument-Bromage, H., Tempst, P., Chang, C. and Wang, H. (2007) Regulation of cell cycle progression and gene expression by H2A deubiquitination. Nature 449, 1068-1072
16. Zhang, D., Zaugg, K., Mak, T.W. and Elledge, S.J. (2006) A role for the deubiquitinating enzyme USP28 in control of the DNA-damage response. Cell 126, 529-542
17. Popov, N., Wanzel, M., Madiredjo, M., Zhang, D., Beijersbergen, R., Bernards, R., Moll, R., Elledge, S.J. and Eilers, M. (2007) The ubiquitin-specific protease USP28 is required for MYC stability. Nat. Cell Biol. 9, 765-774
18. Stevenson, L.F., Sparks, A., Allende-Vega, N., Xirodimas, D.P., Lane, D.P. and Saville, M.K. (2007) The deubiquitinating enzyme USP2a regulates the p53 pathway by targeting Mdm2. EMBO J. 26, 976-986
19. Dayal, S., Sparks, A., Jacob, J., Allende-Vega, N., Lane, D.P. and Saville, M.K. (2009) Suppression of the deubiquitinating enzyme USP5 causes the accumulation of unanchored polyubiquitin and the activation of p53. J. Biol. Chem. 284, 5030-5041
20. Alwan, H.A. and van Leeuwen, J.E. (2007) UBPY-mediated epidermal growth factor receptor (EGFR) de-ubiquitination promotes EGFR degradation. J. Biol. Chem. 282, 1658-1669
21. Setsuie, R., Suzuki, M., Kabuta, T., Fujita, H., Miura, S., Ichihara, N., Yamada, D., Wang, Y.L., Ezaki, O., Suzuki, Y. and Wada, K. (2009) Ubiquitin C-terminal hydrolase-L3-knockout mice are resistant to diet-induced obesity and show increased activation of AMP-activated protein kinase in skeletal muscle. FASEB J. 23, 4148-4157
22. Ribarski, I., Lehavi, O., Yogev, L., Hauser, R., Bar-Shira Maymon, B., Botchan, A., Paz, G., Yavetz, H. and Kleiman, S.E. (2009) USP26 gene variations in fertile and infertile men. Hum. Reprod. 24, 477-484
23. Yan, M., Luo, J.K., Ritchie, K.J., Sakai, I., Takeuchi, K., Ren, R. and Zhang, D.E. (2007) Ubp43 regulates BCR-ABL leukemogenesis via the type 1 interferon receptor signaling. Blood 110, 305-312
24. Qiu, X.B., Ouyang, S.Y., Li, C.J., Miao, S., Wang, L. and Goldberg, A.L. (2006) hRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37. EMBO J. 25, 5742-5753
25. Borodovsky, A., Kessler, B.M., Casagrande, R., Overkleeft, H.S., Wilkinson, K.D. and Ploegh, H.L. (2001) A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J. 20, 5187-5196
26. Tsurumi, C., DeMartino, G.N., Slaughter, C.A., Shimbara, N. and Tanaka, K. (1995) cDNA cloning of p40, a regulatory subunit of the human 26S proteasome, and a homolog of the Mov-34 gene product. Biochem. Biophys. Res. Commun. 210, 600-608
27. Spataro, V., Toda, T., Craig, R., Seeger, M., Dubiel, W., Harris, A.L. and Norbury, C. (1997) Resistance to diverse drugs and ultraviolet light conferred by overexpression of a novel human 26 S proteasome subunit. J. Biol. Chem. 272, 30470-30475
28. Sharon, M., Taverner, T., Ambroggio, X.I., Deshaies, R.J. and Robinson, C.V. (2006) Structural organization of the 19S proteasome lid: insights from MS of intact complexes. PLoS Biol. 4, e267
29. Schwechheimer, C. (2004) The COP9 signalosome (CSN): an evolutionary conserved proteolysis regulator in eukaryotic development. Biochem. Biophys. Acta 1695, 45-54
30. Masutani, M., Sonenberg, N., Yokoyama, S. and Imataka, H. (2007) Reconstitution reveals the functional core of mammalian eIF3. EMBO J. 26, 3373-3383
31. Scheel, H. and Hofmann, K. (2005) Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes. BMC Bioinformatics 6, 71
32. Zhang, X.Y., Varthi, M., Sykes, S.M., Phillips, C., Warzecha, C., Zhu, W., Wyce, A., Thorne, A.W., Berger, S.L. and McMahon, S.B. (2008) The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progression. Mol. Cell 29, 102-111
33. Nicassio, F., Corrado, N., Vissers, J.H., Areces, L.B., Bergink, S., Marteijn, J.A., Geverts, B., Houtsmuller, A.B., Vermeulen, W., Di Fiore, P.P. and Citterio, E. (2007) Human USP3 is a chromatin modifier required for S phase progression and genome stability. Curr. Biol. 17, 1972-1977
34. van Leuken, R.J., Luna-Vargas, M.P., Sixma, T.K., Wolthuis, R.M. and Medema, R.H. (2008) Usp39 is essential for mitotic spindle checkpoint integrity and controls mRNA-levels of aurora B. Cell Cycle 7, 2710-2719
35. Wada, K. and Kamitani, T. (2006) UnpEL/Usp4 is ubiquitinated by Ro52 and deubiquitinated by itself. Biochem. Biophys. Res. Commun. 342, 253-258
36. Huang, X., Langelotz, C., Hetfeld-Pechoc, B.K., Schwenk, W. and Dubiel, W. (2009) The COP9 signalosome mediates β-catenin degradation by deneddylation and blocks adenomatous polyposis coli destruction via USP15. J. Mol. Biol. 391, 691-702
37. Wang, L., Bhattacharyya, N., Chelsea, D.M., Escobar, P.F. and Banerjee, S. (2004) A novel nuclear protein, MGC5306 interacts with DNA polymerase β and has a potential role in cellular phenotype. Cancer Res. 64, 7673-7677
38. Gorski, J.J., Pathak, S., Panov, K., Kasciukovic, T., Panova, T., Russell, J. and Zomerdijk, J.C. (2007) A novel TBP-associated factor of SL1 functions in RNA polymerase I transcription. EMBO J. 26, 1560-1568
39. Faus, H., Meyer, H.A., Huber, M., Bahr, I. and Haendler, B. (2005) The ubiquitin-specific protease USP10 modulates androgen receptor function. Mol. Cell. Endocrinol. 245, 138-146
40. Herrera-Vigenor, F., Hernández-García, R., Valadez-Sánchez, M., Vázquez-Prado, J. and Reyes-Cruz, G. (2006) AMSH regulates calcium-sensing receptor signaling through direct interactions. Biochem. Biophys. Res. Commun. 347, 924-930
41. Endo, A., Matsumoto, M., Inada, T., Yamamoto, A., Nakayama, K.I., Kitamura, N. and Komada, M. (2009) Nucleolar structure and function are regulated by the deubiquitylating enzyme USP36. J. Cell Sci. 122, 678-686
42. Jensen, D.E., Proctor, M., Marquis, S.T., Gardner, H.P., Ha, S.I., Chodosh, L.A., Ishov, A.M., Tommerup, N., Vissing, H., Sekido, Y. et al. (1998) BAP1: a novel ubiquitin hydrolase which binds to the BRCA1 RING finger and enhances BRCA1-mediated cell growth suppression. Oncogene 16, 1097-1112
43. Nijman, S.M., Huang, T.T., Dirac, A.M., Brummelkamp, T.R., Kerkhoven, R.M., D'Andrea, A.D. and Bernards, R. (2005) The deubiquitinating enzyme USP1 regulates the Fanconi anemia pathway. Mol. Cell 17, 331-339
44. Boudreau, H.E., Broustas, C.G., Gokhale, P.C., Kumar, D., Mewani, R.R., Rone, J.D., Haddad, B.R. and Kasid, U. (2007) Expression of BRCC3, a novel cell cycle regulated molecule, is associated with increased phospho-ERK and cell proliferation. Int. J. Mol. Med. 19, 29-39
45. Denuc, A., Bosch-Comas, A., Gonzàlez-Duarte, R. and Marfany, G. (2009) The UBA-UIM domains of the USP25 regulate the enzyme ubiquitination state and modulate substrate recognition. PLoS ONE 4, e5571
46. Uchiyama, K., Jokitalo, E., Kano, F., Murata, M., Zhang, X., Canas, B., Newman, R., Rabouille, C., Pappin, D., Freemont, P. and Kondo, H. (2002) VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo. J. Cell Biol. 159, 855-866
47. Wertz, I.E., O'Rourke, K.M., Zhou, H., Eby, M., Aravind, L., Seshagiri, S., Wu, P., Wiesmann, C., Baker, R., Boone, D.L. et al. (2004) De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling. Nature 430, 694-699
48. Stegmeier, F., Rape, M., Draviam, V.M., Nalepa, G., Sowa, M.E., Ang, X.L., McDonald, 3rd, E.R., Li, M.Z., Hannon, G.J., Sorger, P.K. et al. (2007) Anaphase initiation is regulated by antagonistic ubiquitination and deubiquitination activities. Nature 446, 876-881
49. Kayagaki, N., Phung, Q., Chan, S., Chaudhari, R., Quan, C., O'Rourke, K.M., Eby, M., Pietras, E., Cheng, G., Bazan, J.F. et al. (2007) DUBA: a deubiquitinase that regulates type I interferon production. Science 318, 1628-1632
50. Li, M., Chen, D., Shiloh, A., Luo, J., Nikolaev, A.Y., Qin, J. and Gu, W. (2002) Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416, 648-653
51. Antrobus, R. and Boutell, C. (2008) Identification of a novel higher molecular weight isoform of USP7/HAUSP that interacts with the Herpes simplex virus type-1 immediate early protein ICP0. Virus Res. 137, 64-71
52. Yamaguchi, T., Kimura, J., Miki, Y. and Yoshida, K. (2007) The deubiquitinating enzyme USP11 controls an IκB kinase α (IKKα)-p53 signaling pathway in response to tumor necrosis factor α (TNFα). J. Biol. Chem. 282, 33943-33948
53. Schoenfeld, A.R., Apgar, S., Dolios, G., Wang, R. and Aaronson, S.A. (2004) BRCA2 is ubiquitinated in vivo and interacts with USP11, a deubiquitinating enzyme that exhibits prosurvival function in the cellular response to DNA damage. Mol. Cell. Biol. 24, 7444-7455
54. Lin, C.H., Chang, H.S. and Yu, W.C. (2008) USP11 stabilizes HPV-16E7 and further modulates the E7 biological activity. J. Biol. Chem. 283, 15681-15688
55. 2 adrenergic receptor recycling and resensitization, EMBO J. 28, 1684-1696
56. Gao, T., Furnari, F. and Newton, A.C. (2005) PHLPP: a phosphatase that directly dephosphorylates Akt, promotes apoptosis, and suppresses tumor growth. Mol. Cell 18, 13-24
57. Cohn, M.A., Kowal, P., Yang, K., Haas, W., Huang, T.T., Gygi, S.P. and D'Andrea, A.D. (2007) A UAF1-containing multisubunit protein complex regulates the Fanconi anemia pathway. Mol. Cell 28, 786-797
58. Cohn, M.A., Kee, Y., Haas, W., Gygi, S.P. and D'Andrea, A.D. (2009) UAF1 is a subunit of multiple deubiquitinating enzyme complexes. J. Biol. Chem. 284, 5343-5351
59. Li, X., Liu, J. and Gao, T. (2009) β-TrCP-mediated ubiquitination and degradation of PHLPP1 is negatively regulated by Akt. Mol. Cell. Biol. 29, 6192-6205
60. Wong, R.W., Blobel, G. and Coutavas, E. (2006) Rae1 interaction with NuMA is required for bipolar spindle formation. Proc. Natl. Acad. Sci. U.S.A. 103, 19783-19787
61. Yoon, Y.M., Baek, K.H., Jeong, S.J., Shin, H.J., Ha, G.H., Jeon, A.H., Hwang, S.G., Chun, J.S. and Lee, C.W. (2004) WD repeat-containing mitotic checkpoint proteins act as transcriptional repressors during interphase. FEBS Lett. 575, 23-29