The regulation of proteasome degradation by multi-ubiquitin chain binding proteins

FEBS Letters

Volumn 579, Issue 15, 2005, Pages 3224-3230

  Miller, Jayne ^a   Gordon, Colin ^a  

^a WESTERN GENERAL HOSPITAL   (United Kingdom)

Author keywords

Proteasome; UBA; Ubiquitin; UBL; UBX; UIM

Indexed keywords

BINDING PROTEIN; CARRIER PROTEIN; PROTEASOME; UBIQUITIN;

AMINO TERMINAL SEQUENCE; ENZYME DEGRADATION; ENZYME REGULATION; ENZYME SUBSTRATE; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN TRANSPORT; SHORT SURVEY; UBIQUITINATION;

ANIMALS; HUMANS; MOLECULAR CHAPERONES; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN BINDING; UBIQUITIN;

EID: 20444399163     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.03.042     Document Type: Short Survey

References (71)

1. D. Voges, P. Zwickl, and W. Baumeister The 26S proteasome: a molecular machine designed for controlled proteolysis Annu. Rev. Biochem. 68 1999 1015 1068
2. M. Koegl, T. Hoppe, S. Schlenker, H.D. Ulrich, T.U. Mayer, and S. Jentsch A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly Cell 96 1999 635 644
3. L. Hicke Protein regulation by monoubiquitin Nat. Rev. Mol. Cell Biol. 2 2001 195 201
4. A.M. Weissman Themes and variations on ubiquitylation Nat. Rev. Mol. Cell Biol. 2 2001 169 178
5. P. Zwickl, D. Voges, and W. Baumeister The proteasome: a macromolecular assembly designed for controlled proteolysis Philos. Trans. R. Soc. Lond. B: Biol. Sci. 354 1999 1501 1511
6. J.S. Thrower, L. Hoffman, M. Rechsteiner, and C.M. Pickart Recognition of the polyubiquitin proteolytic signal EMBO J. 19 2000 94 102
7. M. Groll, L. Ditzel, J. Lowe, D. Stock, M. Bochtler, H.D. Bartunik, and R. Huber Structure of 20S proteasome from yeast at 2.4 Å resolution Nature 386 1997 463 471
8. M. Unno, T. Mizushima, Y. Morimoto, Y. Tomisugi, K. Tanaka, N. Yasuoka, and T. Tsukihara The structure of the mammalian 20S proteasome at 2.75 A resolution Structure (Cambridge) 10 2002 609 618
9. A. Kohler, P. Cascio, D.S. Leggett, K.M. Woo, A.L. Goldberg, and D. Finley The axial channel of the proteasome core particle is gated by the Rpt2 ATPase and controls both substrate entry and product release Mol. Cell 7 2001 1143 1152
10. M. Groll, M. Bajorek, A. Kohler, L. Moroder, D.M. Rubin, R. Huber, M.H. Glickman, and D. Finley A gated channel into the proteasome core particle Nat. Struct. Biol. 7 2000 1062 1067
11. C. Realini, W. Dubiel, G. Pratt, K. Ferrell, and M. Rechsteiner Molecular cloning and expression of a gamma-interferon-inducible activator of the multicatalytic protease J. Biol. Chem. 269 1994 20727 20732
12. S. Lyapina, G. Cope, A. Shevchenko, G. Serino, T. Tsuge, C. Zhou, D.A. Wolf, N. Wei, A. Shevchenko, and R.J. Deshaies Promotion of NEDD-CUL1 conjugate cleavage by COP9 signalosome Science 292 2001 1382 1385
13. R. Groisman, J. Polanowska, I. Kuraoka, J. Sawada, M. Saijo, R. Drapkin, A.F. Kisselev, K. Tanaka, and Y. Nakatani The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage Cell 113 2003 357 367
14. C. Zhou, S. Wee, E. Rhee, M. Naumann, W. Dubiel, and D.A. Wolf Fission yeast COP9/signalosome suppresses cullin activity through recruitment of the deubiquitylating enzyme Ubp12p Mol. Cell 11 2003 927 938
15. N. Tanahashi, Y. Murakami, Y. Minami, N. Shimbara, K.B. Hendil, and K. Tanaka Hybrid proteasomes. Induction by interferon-gamma and contribution to ATP-dependent proteolysis J. Biol. Chem. 275 2000 14336 14345
16. P. Cascio, M. Call, B.M. Petre, T. Walz, and A.L. Goldberg Properties of the hybrid form of the 26S proteasome containing both 19S and PA28 complexes EMBO J. 21 2002 2636 2645
17. M.H. Glickman, D.M. Rubin, H. Fu, C.N. Larsen, O. Coux, I. Wefes, G. Pfeifer, Z. Cjeka, R. Vierstra, W. Baumeister, V. Fried, and D. Finley Functional analysis of the proteasome regulatory particle Mol. Biol. Rep. 26 1999 21 28
18. W. Baumeister, J. Walz, F. Zuhl, and E. Seemuller The proteasome: paradigm of a self-compartmentalizing protease Cell 92 1998 367 380
19. B.C. Braun, M. Glickman, R. Kraft, B. Dahlmann, P.M. Kloetzel, D. Finley, and M. Schmidt The base of the proteasome regulatory particle exhibits chaperone-like activity Nat. Cell Biol. 1 1999 221 226
20. T. Rinaldi, C. Ricci, D. Porro, M. Bolotin-Fukuhara, and L. Frontali A mutation in a novel yeast proteasomal gene, RPN11/MPR1, produces a cell cycle arrest, overreplication of nuclear and mitochondrial DNA, and an altered mitochondrial morphology Mol. Biol. Cell 9 1998 2917 2931
21. M. Penney, C. Wilkinson, M. Wallace, J.P. Javerzat, K. Ferrell, M. Seeger, W. Dubiel, S. McKay, R. Allshire, and C. Gordon The Pad1+ gene encodes a subunit of the 26 S proteasome in fission yeast J. Biol. Chem. 273 1998 23938 23945
22. T. Yao, and R.E. Cohen A cryptic protease couples deubiquitination and degradation by the proteasome Nature 419 2002 403 407
23. Q. Deveraux, V. Ustrell, C. Pickart, and M. Rechsteiner A 26 S protease subunit that binds ubiquitin conjugates J. Biol. Chem. 269 1994 7059 7061
24. C.R. Wilkinson, K. Ferrell, M. Penney, M. Wallace, W. Dubiel, and C. Gordon Analysis of a gene encoding Rpn10 of the fission yeast proteasome reveals that the polyubiquitin-binding site of this subunit is essential when Rpn12/Mts3 activity is compromised J. Biol. Chem. 275 2000 15182 15192
25. Y.A. Lam, T.G. Lawson, M. Velayutham, J.L. Zweier, and C.M. Pickart A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal Nature 416 2002 763 767
26. R.D. Fisher, B. Wang, S.L. Alam, D.S. Higginson, H. Robinson, W.I. Sundquist, and C.P. Hill Structure and ubiquitin binding of the ubiquitin-interacting motif J. Biol. Chem. 278 2003 28976 28984
27. H. Fu, S. Sadis, D.M. Rubin, M. Glickman, S. van Nocker, D. Finley, and R.D. Vierstra Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26 S proteasome subunit Mcb1 J. Biol. Chem. 273 1998 1970 1981
28. S. van Nocker, S. Sadis, D.M. Rubin, M. Glickman, H. Fu, O. Coux, I. Wefes, D. Finley, and R.D. Vierstra The multiubiquitin-chain-binding protein Mcb1 is a component of the 26S proteasome in Saccharomyces cerevisiae and plays a nonessential, substrate-specific role in protein turnover Mol. Cell Biol. 16 1996 6020 6028
29. R. Verma, R. Oania, J. Graumann, and R.J. Deshaies Multiubiquitin chain receptors define a layer of substrate selectivity in the ubiquitin-proteasome system Cell 118 2004 99 110
30. T. Mayor, J. Russell Lipford, J. Graumann, G.T. Smith, and R.J. Deshaies Analysis of poly-ubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets Mol. Cell Proteomics 2005
31. K. Hofmann, and P. Bucher The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway Trends Biochem. Sci. 21 1996 172 173
32. T. Dieckmann, E.S. Withers-Ward, M.A. Jarosinski, C.F. Liu, I.S. Chen, and J. Feigon Structure of a human DNA repair protein UBA domain that interacts with HIV-1 Vpr Nat. Struct. Biol. 5 1998 1042 1047
33. B.L. Bertolaet, D.J. Clarke, M. Wolff, M.H. Watson, M. Henze, G. Divita, and S.I. Reed UBA domains of DNA damage-inducible proteins interact with ubiquitin Nat. Struct. Biol. 8 2001 417 422
34. B.L. Bertolaet, D.J. Clarke, M. Wolff, M.H. Watson, M. Henze, G. Divita, and S.I. Reed UBA domains mediate protein-protein interactions between two DNA damage-inducible proteins J. Mol. Biol. 313 2001 955 963
35. R. Hartmann-Petersen, C.A. Semple, C.P. Ponting, K.B. Hendil, and C. Gordon UBA domain containing proteins in fission yeast Int. J. Biochem. Cell Biol. 35 2003 629 636
36. T.D. Mueller, and J. Feigon Structural determinants for the binding of ubiquitin-like domains to the proteasome EMBO J. 22 2003 4634 4645
37. C.R. Wilkinson, M. Seeger, R. Hartmann-Petersen, M. Stone, M. Wallace, C. Semple, and C. Gordon Proteins containing the UBA domain are able to bind to multi-ubiquitin chains Nat. Cell Biol. 3 2001 939 943
38. M. Funakoshi, T. Sasaki, T. Nishimoto, and H. Kobayashi Budding yeast Dsk2p is a polyubiquitin-binding protein that can interact with the proteasome Proc. Natl. Acad. Sci. USA 99 2002 745 750
39. H. Rao, and A. Sastry Recognition of specific ubiquitin conjugates is important for the proteolytic functions of the ubiquitin-associated domain proteins Dsk2 and Rad23 J. Biol. Chem. 277 2002 11691 11695
40. S. Raasi, I. Orlov, K.G. Fleming, and C.M. Pickart Binding of polyubiquitin chains to ubiquitin-associated (UBA) domains of HHR23A J. Mol. Biol. 341 2004 1367 1379
41. C. Schauber, L. Chen, P. Tongaonkar, I. Vega, D. Lambertson, W. Potts, and K. Madura Rad23 links DNA repair to the ubiquitin/proteasome pathway Nature 391 1998 715 718
42. M.F. Kleijnen, A.H. Shih, P. Zhou, S. Kumar, R.E. Soccio, N.L. Kedersha, G. Gill, and P.M. Howley The hPLIC proteins may provide a link between the ubiquitination machinery and the proteasome Mol. Cell 6 2000 409 419
43. Y. Saeki, T. Sone, A. Toh-e, and H. Yokosawa Identification of ubiquitin-like protein-binding subunits of the 26S proteasome Biochem. Biophys. Res. Commun. 296 2002 813 819
44. D. Lambertson, L. Chen, and K. Madura Pleiotropic defects caused by loss of the proteasome-interacting factors Rad23 and Rpn10 of Saccharomyces cerevisiae Genetics 153 1999 69 79
45. Y. Saeki, A. Saitoh, A. Toh-e, and H. Yokosawa Ubiquitin-like proteins and Rpn10 play cooperative roles in ubiquitin-dependent proteolysis Biochem. Biophys. Res. Commun. 293 2002 986 992
46. R. Hartmann-Petersen, M. Seeger, and C. Gordon Transferring substrates to the 26S proteasome Trends Biochem. Sci. 28 2003 26 31
47. C. Brignone, K.E. Bradley, A.F. Kisselev, and S.R. Grossman A post-ubiquitination role for MDM2 and hHR23A in the p53 degradation pathway Oncogene 23 2004 4121 4129
48. S. Elsasser, R.R. Gali, M. Schwickart, C.N. Larsen, D.S. Leggett, B. Muller, M.T. Feng, F. Tubing, G.A. Dittmar, and D. Finley Proteasome subunit Rpn1 binds ubiquitin-like protein domains Nat. Cell Biol. 4 2002 725 730
49. M. Seeger, R. Hartmann-Petersen, C.R. Wilkinson, M. Wallace, I. Samejima, M.S. Taylor, and C. Gordon Interaction of the anaphase-promoting complex/cyclosome and proteasome protein complexes with multiubiquitin chain-binding proteins J. Biol. Chem. 278 2003 16791 16796
50. H. Hiyama, M. Yokoi, C. Masutani, K. Sugasawa, T. Maekawa, K. Tanaka, J.H. Hoeijmakers, and F. Hanaoka Interaction of hHR23 with S5a. The ubiquitin-like domain of hHR23 mediates interaction with S5a subunit of 26 S proteasome J. Biol. Chem. 274 1999 28019 28025
51. K.J. Walters, M.F. Kleijnen, A.M. Goh, G. Wagner, and P.M. Howley Structural studies of the interaction between ubiquitin family proteins and proteasome subunit S5a Biochemistry 41 2002 1767 1777
52. S. Raasi, and C.M. Pickart Rad23 ubiquitin-associated domains (UBA) inhibit 26 S proteasome-catalyzed proteolysis by sequestering lysine 48-linked polyubiquitin chains J. Biol. Chem. 278 2003 8951 8959
53. P.G. Woodman p97, a protein coping with multiple identities J. Cell Sci. 116 2003 4283 4290
54. M. Rape, T. Hoppe, I. Gorr, M. Kalocay, H. Richly, and S. Jentsch Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone Cell 107 2001 667 677
55. H.H. Meyer, Y. Wang, and G. Warren Direct binding of ubiquitin conjugates by the mammalian p97 adaptor complexes, p47 and Ufd1-Npl4 EMBO J. 21 2002 5645 5652
56. R. Hartmann-Petersen, M. Wallace, K. Hofmann, G. Koch, A.H. Johnsen, K.B. Hendil, and C. Gordon The Ubx2 and Ubx3 cofactors direct Cdc48 activity to proteolytic and nonproteolytic ubiquitin-dependent processes Curr. Biol. 14 2004 824 828
57. C. Schuberth, H. Richly, S. Rumpf, and A. Buchberger Shp1 and Ubx2 are adaptors of Cdc48 involved in ubiquitin-dependent protein degradation EMBO Rep. 5 2004 818 824
58. H. Richly, M. Rape, S. Braun, S. Rumpf, C. Hoege, and S. Jentsch A series of ubiquitin binding factors connects CDC48/p97 to substrate multiubiquitylation and proteasomal targeting Cell 120 2005 73 84
59. J.C. Young, V.R. Agashe, K. Siegers, and F.U. Hartl Pathways of chaperone-mediated protein folding in the cytosol Nat. Rev. Mol. Cell Biol. 5 2004 781 791
60. C. Esser, S. Alberti, and J. Hohfeld Cooperation of molecular chaperones with the ubiquitin/proteasome system Biochim. Biophys. Acta 1695 2004 171 188
61. J. Luders, J. Demand, and J. Hohfeld The ubiquitin-related BAG-1 provides a link between the molecular chaperones Hsc70/Hsp70 and the proteasome J. Biol. Chem. 275 2000 4613 4617
62. M. Lassle, G.L. Blatch, V. Kundra, T. Takatori, and B.R. Zetter Stress-inducible, murine protein mSTI1. Characterization of binding domains for heat shock proteins and in vitro phosphorylation by different kinases J. Biol. Chem. 272 1997 1876 1884
63. F.J. Kaye, S. Modi, I. Ivanovska, E.V. Koonin, K. Thress, A. Kubo, S. Kornbluth, and M.D. Rose A family of ubiquitin-like proteins binds the ATPase domain of Hsp70-like Stch FEBS Lett. 467 2000 348 355
64. H. McDonough, and C. Patterson CHIP: a link between the chaperone and proteasome systems Cell Stress. Chaperones 8 2003 303 308
65. E. Sakata, Y. Yamaguchi, E. Kurimoto, J. Kikuchi, S. Yokoyama, S. Yamada, H. Kawahara, H. Yokosawa, N. Hattori, Y. Mizuno, K. Tanaka, and K. Kato Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain EMBO Rep. 4 2003 301 306
66. T. Kitada, S. Asakawa, N. Hattori, H. Matsumine, Y. Yamamura, S. Minoshima, M. Yokochi, Y. Mizuno, and N. Shimizu Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism Nature 392 1998 605 608
67. R. Verma, S. Chen, R. Feldman, D. Schieltz, J. Yates, J. Dohmen, and R.J. Deshaies Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes Mol. Biol. Cell 11 2000 3425 3439
68. R.K. Vadlamudi, I. Joung, J.L. Strominger, and J. Shin p62, a phosphotyrosine-independent ligand of the SH2 domain of p56lck, belongs to a new class of ubiquitin-binding proteins J. Biol. Chem. 271 1996 20235 20237
69. M.L. Seibenhener, J.R. Babu, T. Geetha, H.C. Wong, N.R. Krishna, and M.W. Wooten Sequestosome 1/p62 is a polyubiquitin chain binding protein involved in ubiquitin proteasome degradation Mol. Cell. Biol. 24 2004 8055 8068
70. R. Layfield, B. Ciani, S.H. Ralston, L.J. Hocking, P.W. Sheppard, M.S. Searle, and J.R. Cavey Structural and functional studies of mutations affecting the UBA domain of SQSTM1 (p62) which cause Paget's disease of bone Biochem. Soc. Trans. 32 2004 728 730
71. Y. Hirano, S. Yoshinaga, K. Ogura, M. Yokochi, Y. Noda, H. Sumimoto, and F. Inagaki Solution structure of atypical protein kinase C PB1 domain and its mode of interaction with ZIP/p62 and MEK5 J. Biol. Chem. 279 2004 31883 31890