Exploring proteasome complexes by proteomic approaches

Proteomics

Volumn 7, Issue 7, 2007, Pages 1047-1058

  Drews, Oliver ^a   Zong, Chenggong ^a   Ping, Peipei ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Cardiovascular Research Laboratories   (United States)

Author keywords

Mass spectrometry; Proteasome; Protein complexes; Two dimensional electrophoresis

Indexed keywords

CELL PROTEIN; PROTEASOME; PROTEIN SUBUNIT; PROTEOME; UBIQUITIN;

AFFINITY CHROMATOGRAPHY; APOPTOSIS; CELL CYCLE; CELLULAR DISTRIBUTION; CONFOCAL MICROSCOPY; ELECTRON MICROSCOPY; ENZYME LOCALIZATION; ENZYME PURIFICATION; ENZYME STRUCTURE; ENZYME SUBUNIT; HUMAN; IMMUNE RESPONSE; IMMUNOBLOTTING; IMMUNOFLUORESCENCE TEST; IMMUNOHISTOCHEMISTRY; IMMUNOPRECIPITATION; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; MASS SPECTROMETRY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEOMICS; REVIEW; STRUCTURE ANALYSIS; TWO DIMENSIONAL ELECTROPHORESIS; WESTERN BLOTTING;

ANIMALS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; MASS SPECTROMETRY; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEINS; PROTEOMICS; UBIQUITIN;

EID: 34247522791     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200600574     Document Type: Review

References (147)

1. Yoshimura, T., Kameyama, K., Takagi, T., Ikai, A. et al., J. Struct. Biol. 1993, 111, 200-211.
2. Tanaka, K., Ii, K., Ichihara, A., Waxman, L., Goldberg, A. L., J. Biol. Chem. 1986, 261, 15197-15203.
3. Hough, R., Pratt, G., Rechsteiner, M., J. Biol. Chem. 1987, 262, 8303-8313.
4. Waxman, L., Fagan, J. M., Goldberg, A. L., J. Biol. Chem. 1987, 262, 2451-2457.
5. Ganoth, D., Leshinsky, E., Eytan, E., Hershko, A., J. Biol. Chem. 1988, 263, 12412-12419.
6. Peters, J. M., Cejka, Z., Harris, J. R., Kleinschmidt, J. A., Baumeister, W., J. Mol. Biol. 1993, 234, 932-937.
7. Ikai, A., Nishigai, M., Tanaka, K., Ichihara, A., FEBS Lett. 1991, 292, 21-24.
8. Hegerl, R., Pfeifer, G., Puhler, G., Dahlmann, B., Baumeister, W., FEBS Lett. 1991, 283, 117-121.
9. Puhler, G., Weinkauf, S., Bachmann, L., Muller, S. et al., Embo. J. 1992, 11, 1607-1616.
10. Gray, C. W., Slaughter, C. A., DeMartino, G. N., J. Mol. Biol. 1994, 236, 7-15.
11. Lowe, J., Stock, D., Jap, B., Zwickl, P. et al., Science 1995, 268, 533-539.
12. Heinemeyer, W., Kleinschmidt, J. A., Saidowsky, J., Escher, C., Wolf, D. H., Embo. J. 1991, 10, 555-562.
13. Aki, M., Shimbara, N., Takashina, M., Akiyama, K. et al., J. Biochem. Tokyo 1994, 115, 257-269.
14. Gaczynska, M., Rock, K. L., Goldberg, A. L., Nature 1993, 365, 264-267.
15. Driscoll, J., Brown, M. G., Finley, D., Monaco, J. J., Nature 1993, 365, 262-264.
16. Akiyama, K., Kagawa, S., Tamura, T., Shimbara, N. et al., FEBS Lett. 1994, 343, 85-88.
17. Akiyama, K., Yokota, K., Kagawa, S., Shimbara, N et al., Science 1994, 265, 1231-1234.
18. Hisamatsu, H., Shimbara, N., Saito, Y., Kristensen, P. et al., J. Exp. Med. 1996, 183, 1807-1816.
19. Coux, O., Nothwang, H. G., Silva Pereira, I., Recillas Targa, F. et al., Mol. Gen. Genet. 1994, 245, 769-780.
20. Seemuller, E., Lupas, A., Stock, D., Lowe, J. et al., Science 1995, 268, 579-582.
21. Fenteany, G., Standaert, R. F., Lane, W. S., Choi, S. et al., Science 1995, 268, 726-731.
22. Orlowski, M., Biochemistry 1990, 29, 10289-10297.
23. Rivett, A. J., J. Biol. Chem. 1989, 264, 12215-12219.
24. Rivett, A. J., Biochem. J. 1993, 291 (Pt 1), 1-10.
25. Dahlmann, B., Becher, B., Sobek, A., Ehlers, C. et al., Enzyme Protein 1993, 47, 274-284.
26. Orino, E., Tanaka, K., Tamura, T., Sone, S. et al., FEBS Lett. 1991, 284, 206-210.
27. Peters, J. M., Franke, W. W., Kleinschmidt, J. A., J. Biol. Chem. 1994, 269, 7709-7718.
28. Schmidt, M., Hanna, J., Elsasser, S., Finley, D., Biol. Chem. 2005, 386, 725-737.
29. Glickman, M. H., Rubin, D. M., Fried, V. A., Finley, D., Mol. Cell. Biol. 1998, 18, 3149-3162.
30. Hartmann-Petersen, R., Tanaka, K., Hendil, K. B., Arch. Biochem. Biophys. 2001, 386, 89-94.
31. Verma, R., Chen, S., Feldman, R., Schieltz, D. et al., Mol. Biol. Cell 2000, 11, 3425-3439.
32. Sone, T., Saeki, Y., Toh-e, A., Yokosawa, H., J. Biol. Chem. 2004, 279, 28807-28816.
33. Lam, Y. A., Lawson, T. G., Velayutham, M., Zweier, J. L., Pickart, C. M., Nature 2002, 416, 763-767.
34. Elsasser, S., Finley, D., Nat. Cell Biol. 2005, 7, 742-749.
35. Verma, R., Aravind, L., Oania, R., McDonald, W. H. et al., Science 2002, 298, 611-615.
36. Whitby, F. G., Masters, E. I., Kramer, L., Knowlton, J. R., et al., Nature 2000, 408, 115-120.
37. Sijts, A., Sun, Y., Janek, K., Kral, S., et al., Mol. Immunol. 2002, 39, 165-169.
38. Realini, C., Jensen, C. C., Zhang, Z., Johnston, S. C. et al., J. Biol. Chem. 1997, 272, 25483-25492.
39. Barton, L. F., Runnels, H. A., Schell, T. D., Cho, Y. et al., J. Immunol. 2004, 172, 3948-3954.
40. Schmidt, M., Haas, W., Crosas, B., Santamaria, P. G. et al., Nat. Struct. Mol. Biol. 2005, 12, 294-303.
41. Cascio, P., Call, M., Petre, B. M., Walz, T., Goldberg, A. L., Embo. J. 2002, 21, 2636-2645.
42. Gomes, A. V., Zong, C., Edmondson, R., Li, X., et al., Circ Res 2006, 99, 362-371.
43. Claverol, S., Burlet-Schiltz, O., Girbal-Neuhauser, E., Gairin, J. E., Monsarrat, B., Mol. Cell Proteomics 2002, 1, 567-578.
44. Schmidt, F., Dahlmann, B., Janek, K., Kloss, A. et al., Proteomics 2006, 6, 4622-4632.
45. Castano, J. G., Mahillo, E., Arizti, P., Arribas, J., Biochemistry 1996, 35, 3782-3789.
46. Leggett, D. S., Glickman, M. H., Finley, D., Methods Mol. Biol. 2005, 301, 57-70.
47. Feng, Y., Longo, D. L., Ferris, D. K., Cell Growth Differ. 2001, 12, 29-37.
48. Patel, S. D., Monaco, J. J., McDevitt, H. O., Proc. Natl. Acad. Sci. USA 1994, 91, 296-300.
49. Yang, Y., Fruh, K., Ahn, K., Peterson, P. A., J. Biol. Chem. 1995, 270, 27687-27694.
50. Rivett, A. J., J. Biol. Chem. 1985, 260, 12600-12606.
51. Groll, M., Ditzel, L., Lowe, J., Stock, D. et al., Nature 1997, 386, 463-471.
52. Dahlmann, B., Ruppert, T., Kuehn, L., Merforth, S., Kloetzel, P. M., J. Mol. Biol. 2000, 303, 643-653.
53. Leggett, D. S., Hanna, J., Borodovsky, A., Crosas, B. et al., Mol. Cell 2002, 10, 495-507.
54. Gorbea, C., Goellner, G. M., Teter, K., Holmes, R. K., Rechsteiner, M., J. Biol. Chem. 2004, 279, 54849-54861.
55. Hoffman, L., Pratt, G., Rechsteiner, M., J Biol Chem 1992, 267, 22362-22368.
56. Ugai, S., Tamura, T., Tanahashi, N., Takai, S. et al., J. Biochem. Tokyo 1993, 113, 754-768.
57. Glickman, M. H., Ciechanover, A., Physiol. Rev. 2002, 82, 373-428.
58. Ustrell, V., Hoffman, L., Pratt, G., Rechsteiner, M., Embo. J. 2002, 21, 3516-3525.
59. Wang, H. R., Kania, M., Baumeister, W., Nederlof, P. M., Eur. J. Cell Biol. 1997, 73, 105-113.
60. Wendler, P., Lehmann, A., Janek, K., Baumgart, S., Enenkel, C., J. Biol. Chem. 2004, 279, 37751-37762.
61. Benedict, C. M., Clawson, G. A., Biochemistry 1996, 35, 11612-11621.
62. Knuehl, C., Seelig, A., Brecht, B., Henklein, P., Kloetzel, P. M., Exp. Cell Res. 1996, 225, 67-74.
63. Moriishi, K., Okabayashi, T., Nakai, K., Moriya, K. et al., J. Virol. 2003, 77, 10237-10249.
64. Brooks, P., Fuertes, G., Murray, R. Z., Bose, S. et al., Biochem. J. 2000, 346 Pt 1, 155-161.
65. Foucrier, J., Grand, M. C., De Conto, F., Bassaglia, Y. et al., J. Cell Sci. 1999, 112 (Pt 7), 989-1001.
66. Mengual, E., Arizti, P., Rodrigo, J., Gimenez-Amaya, J. M., Castano, J. G., J. Neurosci. 1996, 16, 6331-6341.
67. Reits, E. A., Benham, A. M., Plougastel, B., Neefjes, J., Trowsdale, J., Embo. J. 1997, 16, 6087-6094.
68. Adori, C., Kovacs, G. G., Low, P., Molnar, K. et al., Neurobiol. Dis. 2005, 19, 427-435.
69. Girao, H., Pereira, P., Taylor, A., Shang, F., Invest. Ophthalmol. Vis. Sci. 2005, 46, 1386-1392.
70. Palmer, A., Mason, G. G., Paramio, J. M., Knecht, E., Rivett, A. J., Eur. J. Cell. Biol. 1994, 64, 163-175.
71. Kuckelkorn, U., Knuehl, C., Boes-Fabian, B., Drung, I., Kloetzel, P. M., Biol. Chem. 2000, 381, 1017-1023.
72. Fabunmi, R. P., Wigley, W. C., Thomas, P. J., DeMartino, G. N., J. Biol. Chem. 2000, 275, 409-413.
73. Palmer, A., Rivett, A. J., Thomson, S., Hendil, K. B. et al., Biochem. J. 1996, 316 (Pt 2), 401-407.
74. Hendil, K. B., Kristensen, P., Uerkvitz, W., Biochem. J. 1995, 305 (Pt 1), 245-252.
75. Froment, C., Uttenweiler-Joseph, S., Bousquet-Dubouch, M. P., Matondo, M. et al., Proteomics 2005, 5, 2351-2363.
76. Kuckelkorn, U., Ruppert, T., Strehl, B., Jungblut, P. R. et al., J. Exp. Med. 2002, 195, 983-990.
77. Nandi, D., Woodward, E., Ginsburg, D., Monaco, J., EMBO J. 1997, 16, 5363-5375.
78. Griffin, T. A., Nandi, D., Cruz, M., Fehling, H. J. et al., J. Exp. Med. 1998, 187, 97-104.
79. Groettrup, M., Standera, S., Stohwasser, R., Kloetzel, P. M., Proc. Natl. Acad. Sci. USA 1997, 94, 8970-8975.
80. Kingsbury, D. J., Griffin, T. A., Colbert, R. A., J. Biol. Chem. 2000, 275, 24156-24162.
81. De, M., Jayarapu, K., Elenich, L., Monaco, J. J. et al., J. Biol. Chem. 2003, 278, 6153-6159.
82. Schmidtke, G., Schmidt, M., Kloetzel, P., J. MOL. Biol. 1997, 268, 95-106.
83. Griffin, T. A., Slack, J. P., McCluskey, T. S., Monaco, J. J., Colbert, R. A., Mol. Cell Biol. Res. Commun. 2000, 3, 212-217.
84. Jayarapu, K., Griffin, T. A., Biochem. Biophys. Res. Commun. 2004, 314, 523-528.
85. Hirano, Y., Hendil, K., Yashiroda, H., Iemura, S. et al., Nature 2005, 437, 1381-1385.
86. Yang, P., Fu, H., Walker, J., Papa, C. M. et al., J. Biol. Chem. 2004, 279, 6401-6413.
87. Shibahara, T., Kawasaki, H., Hirano, H., Eur. J. Biochem. 2002, 269, 1474-1483.
88. Dubiel, W., Pratt, G., Ferrell, K., Rechsteiner, M., J. Biol. Chem. 1992, 267, 22369-22377.
89. Ludemann, R., Lerea, K. M., Etlinger, J. D., J. Biol. Chem. 1993, 268, 17413-17417.
90. Bose, S., Stratford, F. L., Broadfoot, K. I., Mason, G. G., Rivett, A. J., Biochem. J. 2004, 378, 177-184.
91. Mason, G. G., Hendil, K. B., Rivett, A. J., Eur. J. Biochem. 1996, 238, 453-462.
92. Satoh, K., Sasajima, H., Nyoumura, K. I., Yokosawa, H., Sawada, H., Biochemistry 2001, 40, 314-319.
93. Zong, C., Gomes, A. V., Drews, O., Li, X., et al., Circ Res 2006, 99, 372-380.
94. Bardag-Gorce, F., Venkatesh, R., Li, J., French, B. A., French, S. W. Life Sci. 2004, 75, 585-597.
95. Tokumoto, M., Horiguchi, R., Nagahama, Y., Ishikawa, K., Tokumoto, T.Eur. J. Biochem. 2000, 267, 97-103.
96. Horiguchi, R., Yoshikuni, M., Tokumoto, M., Nagahama, Y., Tokumoto, T.Cell. Signal. 2005, 17, 205-215.
97. Rivett, A. J., Bose, S., Brooks, P., Broadfoot, K. I., Biochimie 2001, 83, 363-366.
98. Kimura, Y., Takaoka, M., Tanaka, S., Sassa, H. et al., J. Biol. Chem. 2000, 275, 4635-4639.
99. Chondrogianni, N., Stratford, F. L., Trougakos, I. P., Friguet, B. et al., J. Biol. Chem. 2003, 278, 28026-28037.
100. Horiguchi, R., Dohra, H., Tokumoto, T., Proteomics 2006, 6, 4195-4202.
101. Bulteau, A. L., Lundberg, K. C., Humphries, K. M., Sadek, H. A. et al., J. Biol. Chem. 2001, 276, 30057-30063.
102. Aebersold, R., Mann, M.Nature 2003, 422, 198-207.
103. Loo, J. A., Berhane, B., Kaddis, C. S., Wooding, K. M. et al., J. Am. Soc. Spectrom. Mass 2005, 16, 998-1008.
104. Huang, L., Burlingame, A. L.Methods Enzymol. 2005, 405, 187-236.
105. Medalia, N., Sharon, M., Martinez-Arias, R., Mihalache, O. et al., J. of Struct. Biol. 2006, 156, 84-92.
106. Sharon, M., Taverner, T., Ambroggio, X. I., Deshaies, R. J., Robinson, C. V., PLoS Biol. 2006, 4, e267.
107. Kisselev, A. F., Akopian, T. N., Goldberg, A. L., J. Biol. Chem. 1998, 273, 1982-1989.
108. Kisselev, A. F., Akopian, T. N., Woo, K. M., Goldberg, A. L., J. Biol. Chem. 1999, 274, 3363-3371.
109. Palombella, V. J., Rando, O. J., Goldberg, A. L., Maniatis, T.Cell 1994, 78, 773-785.
110. Emmerich, N. P., Nussbaum, A. K., Stevanovic, S., Priemer, M. et al., J. Biol. Chem. 2000, 275, 21140-21148.
111. Morel, S., Levy, F., Burlet-Schiltz, O., Brasseur, F. et al., Immunity 2000, 12, 107-117.
112. Dick, T. P., Nussbaum, A. K., Deeg, M., Heinemeyer, W. et al., J. Biol. Chem. 1998, 273, 25637-25646.
113. Schwarz, K., de Giuli, R., Schmidtke, G., Kostka, S. et al., J. Immunol. 2000, 164, 6147-6157.
114. Groettrup, M., Ruppert, T., Kuehn, L., Seeger, M. et al., J. Biol. Chem. 1995, 270, 23808-23815.
115. Zaiss, D. M., Standera, S., Kloetzel, P. M., Sijts, A. J., Proc. Natl. Acad. Sci. USA 2002, 99, 14344-14349.
116. Miconnet, I., Servis, C., Cerottini, J. C., Romero, P., Levy, F.J. Biol. Chem. 2000, 275, 26892-26897.
117. Shimbara, N., Ogawa, K., Hidaka, Y., Nakajima, H. et al., J. Biol. Chem. 1998, 273, 23062-23071.
118. Dick, L. R., Aldrich, C., Jameson, S. C., Moomaw, C. R. et al., J. Immunol. 1994, 152, 3884-3894.
119. Weissman, A. M.Nat. Rev. Mol. Cell Biol. 2001, 2, 169-178.
120. Laub, M., Steppuhn, J. A., Bluggel, M., Immler, D. et al., Eur. J. Biochem. 1998, 255, 422-431.
121. Warren, M. R., Parker, C. E., Mocanu, V., Klapper, D., Borchers, C. H., Rapid Commun. Spectrom. Mass 2005, 19, 429-437.
122. Marotti, L. A., Jr., Newitt, R., Wang, Y., Aebersold, R., Dohlman, H. G., Biochemistry 2002, 41, 5067-5074.
123. Cooper, H. J., Heath, J. K., Jaffray, E., Hay, R. T. et al., Anal. Chem. 2004, 76, 6982-6988.
124. Wang, D., Cotter, R. J.Anal. Chem. 2005, 77, 1458-1466.
125. Hitchcock, A. L., Auld, K., Gygi, S. P., Silver, P. A. Proc. Natl. Acad. Sci. USA 2003, 100, 12735-12740.
126. Kirkpatrick, D. S., Weldon, S. F., Tsaprailis, G., Liebler, D. C., Gandolfi, A. J., Proteomics 2005, 5, 2104-2111.
127. Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C. et al., Nat. Biotechnol. 2003, 21, 921-926.
128. Vasilescu, J., Smith, J. C., Ethier, M., Figeys, D., J. Proteome Res. 2005, 4, 2192-2200.
129. Mayor, T., Deshaies, R. J., Methods Enzymol. 2005, 399, 385-392.
130. Mayor, T., Lipford, J. R., Graumann, J., Smith, G. T., Deshaies, R. J., Mol. Cell. Proteomics 2005, 4, 741-751.
131. Peters, J. M., Harris, J. R., Kleinschmidt, J. A., Eur. J. Cell. Biol. 1991, 56, 422-432.
132. Babbitt, S. E., Kiss, A., Deffenbaugh, A. E., Chang, Y. H. et al., Cell 2005, 121, 553-565.
133. Unno, M., Mizushima, T., Morimoto, Y., Tomisugi, Y. et al., Structure (Camb) 2002, 10, 609-618.
134. Stock, D., Ditzel, L., Baumeister, W., Huber, R., Lowe, J., Cold Spring Harb. Symp. Quant. Biol. 1995, 60, 525-532.
135. Groll, M., Koguchi, Y., Huber, R., Kohno, J., J. Mol. Biol. 2001, 311, 543-548.
136. Forster, A., Whitby, F. G., Hill, C. P., Embo. J. 2003, 22, 4356-4364.
137. Ortega, J., Heymann, J. B., Kajava, A. V., Ustrell, V. et al., J. Mol. Biol. 2005, 346, 1221-1227.
138. Rivett, A. J., Palmer, A., Knecht, E., J. Histochem. Cytochem. 1992, 40, 1165-1172.
139. Adori, C., Low, P., Moszkovkin, G., Bagdy, G. et al., J. Histochem. Cytochem. 2006, 54, 263-267.
140. Soza, A., Knuehl, C., Groettrup, M., Henklein, P. et al., FEBS Lett. 1997, 413, 27-34.
141. Wigley, W. C., Fabunmi, R. P., Lee, M. G., Marino, C. R. et al., J. Cell Biol. 1999, 145, 481-490.
142. Baz, A., Henry, L., Chateau, M. T., Scherrer, K., Bureau, J. P., Leuk. Res. 1997, 21, 1061-1070.
143. Low, P., Hastings, R. A., Dawson, S. P., Sass, M. et al., Cell Death Differ. 2000, 7, 1210-1217.
144. Yanagawa, Y., Hasezawa, S., Kumagai, F., Oka, M. et al., Plant Cell Physiol. 2002, 43, 604-613.
145. Enenkel, C., Lehmann, A., Kloetzel, P. M., Mol. Biol. Rep. 1999, 26, 131-135.
146. Enenkel, C., Lehmann, A., Kloetzel, P. M., Embo. J. 1998, 17, 6144-6154.
147. Wilkinson, C. R., Wallace, M., Morphew, M., Perry, P. et al., Embo. J. 1998, 17, 6465-6476.