Proteasomes: Perspectives from the archaea

Frontiers in Bioscience

Volumn 9, Issue , 2004, Pages 1743-1758

  Maupin Furlow, Julie A ^a   Gil, Malgorzata A ^a   Karadzic, Ivanka M ^a   Kirkland, Phillip A ^a   Reuter, Christopher J ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

AAA family; Archaea; ATPases; Chaperone; Protease; Proteasome; Protein quality control; Review

Indexed keywords

GAMMA INTERFERON; PEPTIDE; PROTEASOME; PROTEIN SUBUNIT; ARCHAEAL PROTEIN; CYSTEINE PROTEINASE; MULTIENZYME COMPLEX;

ACTINOMYCETES; AMINO TERMINAL SEQUENCE; ARCHAEBACTERIUM; CAENORHABDITIS ELEGANS; CHANNEL GATING; EUKARYOTE; GENOME; GENOMICS; GRAM POSITIVE BACTERIUM; HALOFERAX VOLCANII; HYDROLYSIS; NONHUMAN; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN STRUCTURE; QUALITY CONTROL; REVIEW; X RAY DIFFRACTION; YEAST; CHEMISTRY; ENERGY METABOLISM; ENZYMOLOGY; METABOLISM; PHYSIOLOGY;

ACTINOBACTERIA (CLASS); ARCHAEA; BACTERIA (MICROORGANISMS); CAENORHABDITIS; CAENORHABDITIS ELEGANS; EUKARYOTA; HALOFERAX; HALOFERAX VOLCANII; POSIBACTERIA;

ARCHAEA; ARCHAEAL PROTEINS; CYSTEINE ENDOPEPTIDASES; ENERGY METABOLISM; MULTIENZYME COMPLEXES; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN SUBUNITS;

EID: 2442658184     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/1363     Document Type: Review

References (186)

1. Volker, C. & A. N. Lupas: Molecular evolution of proteasomes. Curr Top Microbiol Immunol 268, 1-22 (2002)
2. Kostova, Z. & D. H. Wolf: For whom the bell tolls: protein quality control of the endoplasmic reticulum and the ubiquitin-proteasome connection. EMBO J 22, 2309-2317 (2003)
3. Dahlmann, B., F. Kopp, L. Kuehn, B. Niedel, G. Pfeifer, R. Hegerl, & W. Baumeister: The multicatalytic proteinase (prosome) is ubiquitous from eukaryotes to archaebacteria. FEBS Lett 251, 125-131 (1989)
4. De Mot, R., I. Nagy, J. Walz, & W. Baumeister: Proteasomes and other self-compartmentalizing proteases in prokaryotes. Trends Microbiol 7, 88-92 (1999)
5. Lupas, A., J. M. Flanagan, T. Tamura, & W. Baumeister: Self-compartmentalizing proteases. Trends Biochem Sci 22, 399-404 (1997)
6. Lipford, J. R. & R. J. Deshaies: Diverse roles for ubiquitin-dependent proteolysis in transcriptional activation. Nat Cell Biol 5, 845-850 (2003)
7. Muratani, M. & W. P. Tansey: How the ubiquitin-proteasome system controls transcription. Nat Rev Mol Cell Biol 4, 192-201 (2003)
8. Dunand-Sauthier, I., C. Walker, C. Wilkinson, C. Gordon, R. Crane, C. Norbury, & T. Humphrey: Sum1, a component of the fission yeast eIF3 translation initiation complex, is rapidly relocalized during environmental stress and interacts with components of the 26S proteasome. Mol Biol Cell 13, 1626-1640 (2002)
9. Russell, S. J., S. H. Reed, W. Huang, E. C. Friedberg, & S. A. Johnston: The 19S regulatory complex of the proteasome functions independently of proteolysis in nucleotide excision repair. Mol Cell 3, 687-695 (1999)
10. Gillette, T. G., W. Huang, S. J. Russell, S. H. Reed, S. A. Johnston, & E. C. Friedberg: The 19S complex of the proteasome regulates nucleotide excision repair in yeast. Genes Dev 15, 1528-1539 (2001)
11. Ferdous, A., F. Gonzalez, L. Sun, T. Kodadek, & S. A. Johnston: The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II. Mol Cell 7, 981-991 (2001)
12. Gonzalez, F., A. Delahodde, T. Kodadek, & S. A. Johnston: Recruitment of a 19S proteasome subcomplex to an activated promoter. Science 296, 548-550 (2002)
13. Nishiyama, A., K. Tachibana, Y. Igarashi, H. Yasuda, N. Tanahashi, K. Tanaka, K. Ohsumi, & T. Kishimoto: A nonproteolytic function of the proteasome is required for the dissociation of cdc2 and cyclin B at the end of M phase. Genes Dev 14, 2344-2357 (2000)
14. Knipfer, N. & T. E. Shrader: Inactivation of the 20S proteasome in Mycobacterium smegmatis. Mol Microbiol 25, 375-383 (1997)
15. Darwin, K. H., S. Ehrt, J. C. Gutierrez-Ramos, N. Weich, & C. F. Nathan: The proteasome of Mycobacterium tuberculosis is required for resistance to nitric oxide. Science 302, 1963-1966 (2003)
16. Baliga, N. S., M. Pan, Y. A. Goo, E. C. Yi, D. R. Goodlett, K. Dimitrov, P. Shannon, R. Aebersold, W. V. Ng, & L. Hood: Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci USA 99, 14913-14918 (2002)
17. Löwe, J., D. Stock, B. Jap, P. Zwickl, W. Baumeister, & R. Huber: Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268, 533-539 (1995)
18. Groll, M., H. Brandstetter, H. Bartunik, G. Bourenkow, & R. Huber: Investigations on the maturation and regulation of archaebacterial proteasomes. J Mol Biol 327, 75-83 (2003)
19. Groll, M., L. Ditzel, J. Löwe, D. Stock, M. Bochtler, H. D. Bartunik, & R. Huber: Structure of 20S proteasome from yeast at 2.4 Å resolution. Nature 386, 463-471 (1997)
20. Unno, M., T. Mizushima, Y. Morimoto, Y. Tomisugi, K. Tanaka, N. Yasuoka, & T. Tsukihara: The structure of the mammalian 20S proteasome at 2.75 Å resolution. Structure (Camb) 10, 609-618 (2002)
21. Coux, O., H. G. Nothwang, I. S. Pereira, F. R. Targa, F. Bey, & K. Scherrer: Phylogenic relationships of the amino acid sequences of prosome (proteasome, MCP) subunits. Mol Gen Genet 245, 769-780 (1994)
22. Grziwa, A., W. Baumeister, B. Dahlmann, & F. Kopp: Localization of subunits in proteasomes from Thermoplasma acidophilum by immunoelectron microscopy. FEBS Lett 290, 186-190 (1991)
23. Seemüller, E., A. Lupas, D. Stock, J. Löwe, R. Huber, & W. Baumeister: Proteasome from Thermoplasma acidophilum: a threonine protease. Science 268, 579-582 (1995)
24. Groll, M., M. Bajorek, A. Kohler, L. Moroder, D. M. Rubin, R. Huber, M. H. Glickman, & D. Finley: A gated channel into the proteasome core particle. Nat Struct Biol 7, 1062-1067 (2000)
25. Kohler, A., M. Bajorek, M. Groll, L. Moroder, D. M. Rubin, R. Huber, M. H. Glickman, & D. Finley: The substrate translocation channel of the proteasome. Biochimie 83, 325-332 (2001)
26. Kohler, A., P. Cascio, D. S. Leggett, K. M. Woo, A. L. Goldberg, & 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, 1143-1152 (2001)
27. Benaroudj, N., P. Zwickl, E. Seemuller, W. Baumeister, & A. L. Goldberg: ATP hydrolysis by the proteasome regulatory complex PAN serves multiple functions in protein degradation. Mol Cell 11, 69-78 (2003)
28. Zühl, F., T. Tamura, I. Dolenc, Z. Cejka, I. Nagy, R. De Mot, & W. Baumeister: Subunit topology of the Rhodococcus proteasome. FEBS Lett 400, 83-90 (1997)
29. Kaczowka, S. J. & J. A. Maupin-Furlow: Subunit topology of two 20S proteasomes from Haloferax volcanii. J Bacteriol 185, 165-174 (2003)
30. Mayr, J., E. Seemüller, S. A. Muller, A. Engel, & W. Baumeister: Late events in the assembly of 20S proteasomes. J Struct Biol 124, 179-188 (1998)
31. Puhler, G., F. Pitzer, P. Zwickl, & W. Baumeister: Proteasomes: Multisubunit proteinases common to Thermoplasma and eukaryotes. System Appl Microbiol 16, 734-741 (1994)
32. Gille, C., A. Goede, C. Schloetelburg, R. Preissner, P. M. Kloetzel, U. B. Gobel, & C. Frommel: A comprehensive view on proteasomal sequences: implications for the evolution of the proteasome. J Mol Biol 326, 1437-1448 (2003)
33. Van den Eynde, B. J. & S. Morel: Differential processing of class-I-restricted epitopes by the standard proteasome and the immunoproteasome. Curr Opin Immunol 13, 147-153 (2001)
34. Ma, J., E. Katz, & J. M. Belote: Expression of proteasome subunit isoforms during spermatogenesis in Drosophila melanogaster. Insect Mol Biol 11, 627-639 (2001)
35. Fu, H., J. H. Doelling, C. S. Arendt, M. Hochstrasser, & R. D. Vierstra: Molecular organization of the 20S proteasome gene family from Arabidopsis thaliana. Genetics 149, 677-692 (1998)
36. Yang, P., H. Fu, J. Walker, C. M. Papa, J. Smalle, Y. M. Ju, & R. D. Vierstra: Purification of the Arabidopsis 26S proteasome: Biochemical and molecular analyses revealed the presence of multiple isoforms. J Biol Chem in press, (2003)
37. Claverol, S., O. Burlet-Schiltz, E. Girbal-Neuhauser, J. E. Gairin, & B. Monsarrat: Mapping and structural dissection of human 20 S proteasome using proteomic approaches. Mol Cell Proteomics 1, 567-578 (2002)
38. Wilson, H. L., H. C. Aldrich, & J. A. Maupin-Furlow: Halophilic 20S proteasomes of the archaeon Haloferax volcanii: purification, characterization, and gene sequence analysis. J Bacteriol 181, 5814-5824 (1999)
39. Brannigan, J. A., G. Dodson, H. J. Duggleby, P. C. E. Moody, J. L. Smith, D. R. Tomchick, & A. G. Murzin: A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature 378, 416-419 (1995)
40. Zwickl, P., E. Seemuller, B. Kapelari, & W. Baumeister: The proteasome: a supramolecular assembly designed for controlled proteolysis. Adv Protein Chem 59, 187-222 (2001)
41. Kisselev, A. F., Z. Songyang, & A. L. Goldberg: Why does threonine, and not serine, function as the active site nucleophile in proteasomes? J Biol Chem 275, 14831-14837 (2000)
42. Maupin-Furlow, J. A., H. C. Aldrich, & J. G. Ferry: Biochemical characterization of the 20S proteasome from the methanoarchaeon Methanosarcina thermophila. J Bacteriol 180, 1480-1487 (1998)
43. Kisselev, A. F., T. N. Akopian, & A. L. Goldberg: Range of sizes of peptide products generated during degradation of different proteins by archaeal proteasomes. J Biol Chem 273, 1982-1989 (1998)
44. Kisselev, A. F., T. N. Akopian, K. M. Woo, & A. L. Goldberg: The sizes of peptides generated from protein by mammalian 26 and 20 S proteasomes. Implications for understanding the degradative mechanism and antigen presentation. J Biol Chem 274, 3363-3371 (1999)
45. Nussbaum, A. K., T. P. Dick, W. Keilholz, M. Schirle, S. Stevanovic, K. Dietz, W. Heinemeyer, M. Groll, D. H. Wolf, R. Huber: Cleavage motifs of the yeast 20S proteasome β subunits deduced from digests of enolase 1. Proc Natl Acad Sci USA 95, 12504-12509 (1998)
46. Emmerich, N. P., A. K. Nussbaum, S. Stevanovic, M. Priemer, R. E. Toes, H. G. Rammensee, & H. Schild: The human 26S and 20S proteasomes generate overlapping but different sets of peptide fragments from a model protein substrate. J Biol Chem 275, 21140-21148 (2000)
47. Akopian, T. N., A. F. Kisselev, & A. L. Goldberg: Processive degradation of proteins and other catalytic properties of the proteasome from Thermoplasma acidophilum. J Biol Chem 272, 1791-1798 (1997)
48. Lee, C., M. P. Schwartz, S. Prakash, M. Iwakura, & A. Matouschek: ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal. Mol Cell 7, 627-637 (2001)
49. Cardozo, C. & C. Michaud: Proteasome-mediated degradation of tau proteins occurs independently of the chymotrypsin-like activity by a nonprocessive pathway. Arch Biochem Biophys 408, 103-110 (2002)
50. Liu, C. W., M. J. Corboy, G. N. DeMartino, & P. J. Thomas: Endoproteolytic activity of the proteasome. Science 299, 408-411 (2003)
51. Lee, C., S. Prakash, & A. Matouschek: Concurrent translocation of multiple polypeptide chains through the proteasomal degradation channel. J Biol Chem 277, 34760-34765 (2002)
52. Dick, T. P., A. K. Nussbaum, M. Deeg, W. Heinemeyer, M. Groll, M. Schirle, W. Keilholz, S. Stevanovic, D. H. Wolf, R. Huber: Contribution of proteasomal β-subunits to the cleavage of peptide substrates analyzed with yeast mutants. J Biol Chem 273, 25637-25646 (1998)
53. Schmidtke, G., S. Emch, M. Groettrup, & H. G. Holzhutter: Evidence for the existence of a non-catalytic modifier site of peptide hydrolysis by the 20S proteasome. J Biol Chem 275, 22056-22063 (2000)
54. Schmidtke, G., H.-G. Holzhutter, M. Bogyo, N. Kairies, M. Groll, R. de Giuli, S. Emch, & M. Groettrup: How an inhibitor of the HIV-I protease modulates proteasome activity. J Biol Chem 274, 35734-35740 (1999)
55. Andre, P., M. Groettrup, P. Klenerman, R. de Giuli, B. L. Booth, Jr., V. Cerundolo, M. Bonneville, F. Jotereau, R. M. Zinkernagel, & V. Lotteau: An inhibitor of HIV-1 protease modulates proteasome activity, antigen presentation, and T cell responses. Proc Natl Acad Sci USA 95, 13120-13124 (1998)
56. Kisselev, A. F., D. Kaganovich, & A. L. Goldberg: Binding of hydrophobic peptides to several non-catalytic sites promotes peptide hydrolysis by all active sites of 20S proteasomes. Evidence for peptide-induced channel opening in the α-rings. J Biol Chem 111, 22260-22270 (2002)
57. Osmulski, P. A. & M. Gaczynska: Nanoenzymology of the 20S proteasome: proteasomal actions are controlled by the allosteric transition. Biochemistry 41, 7047-7053 (2002)
58. + superfamily ATPases: common structure-diverse function. Genes Cells 6, 575-597 (2001)
59. + proteins and substrate recognition, it all depends on their partner in crime. FEBS Lett 529, 6-10 (2002)
60. Lupas, A. N. & J. Martin: AAA proteins. Curr Opin Struct Biol 12, 746-753 (2002)
61. Finley, D., K. Tanaka, C. Mann, H. Feldmann, M. Hochstrasser, R. Vierstra, S. Johnston, R. Hampton, J. Haber, J. Mccusker: Unified nomenclature for subunits of the Saccharomyces cerevisiae proteasome regulatory particle. Trends Biochem Sci 23, 244-245 (1998)
62. Glickman, M. H., D. M. Rubin, O. Coux, I. Wefes, G. Pfeifer, Z. Cjeka, W. Baumeister, V. A. Fried, & D. Finley: A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3. Cell 94, 615-623 (1998)
63. Coux, O., K. Tanaka, & A. L. Goldberg: Structure and functions of the 20S and 26S proteasomes. Annu Rev Biochem 65, 801-847 (1996)
64. Hendil, K. B., S. Khan, & K. Tanaka: Simultaneous binding of PA28 and PA700 activators to 20S proteasomes. Biochem J 332, 749-754 (1998)
65. Fu, H., P. A. Girod, J. H. Doelling, S. van Nocker, M. Hochstrasser, D. Finley, & R. D. Vierstra: Structure and functional analysis of the 26S proteasome subunits from plants. Mol Biol Rep 26, 137-146 (1999)
66. Shibahara, T., H. Kawasaki, & H. Hirano: Identification of the 19S regulatory particle subunits from the rice 26S proteasome. Eur J Biochem 269, 1474-1483 (2002)
67. Zou, C. B., J. Nakajima-Shimada, T. Nara, & T. Aoki: Cloning and functional expression of Rpn1, a regulatory-particle non-ATPase subunit 1, of proteasome from Trypanosoma cruzi. Mol Biochem Parasitol 110, 323-331 (2000)
68. Shibahara, T., H. Kawasaki, & H. Hirano: Mass spectrometric analysis of expression of ATPase subunits encoded by duplicated genes in the 19S regulatory particle of rice 26S proteasome. Arch Biochem Biophys 421, 34-41 (2004)
69. Wei, N. & X. W. Deng: The cop9 signalosome. Annu Rev Cell Dev Biol 19, 261-286 (2003)
70. Eckardt, N. A.: Characterization of the last subunit of the Arabidopsis COP9 signalosome. Plant Cell 15, 580-581 (2003)
71. Zwickl, P., D. Ng, K. M. Woo, H.-P. Klenk, & A. L. Goldberg: An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26S proteasome, activates protein breakdown by 20S proteasomes. J Biol Chem 274, 26008-26014 (1999)
72. Wilson, H. L., M. S. Ou, H. C. Aldrich, & J. A. Maupin-Furlow: Biochemical and physical properties of the Methanococcus jannaschii 20S proteasome and PAN, a homolog of the ATPase (Rpt) subunits of the eucaryal 26S proteasome. J Bacteriol 182, 1680-1692 (2000)
73. Benaroudj, N. & A. L. Goldberg: PAN, the proteasome-activating nucleotidase from archaebacteria, is a protein-unfolding molecular chaperone. Nat Cell Biol 2, 833-839 (2000)
74. Baliga, N. S., Y. A. Goo, W. V. Ng, L. Hood, C. J. Daniels, & S. DasSarma: Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol 36, 1184-1185 (2000)
75. Navon, A. & A. L. Goldberg: Proteins are unfolded on the surface of the ATPase ring before transport into the proteasome. Mol Cell 8, 1339-1349 (2001)
76. Maytal-Kivity, V., N. Reis, K. Hofmann, & M. H. Glickman: MPN+, a putative catalytic motif found in a subset of MPN domain proteins from eukaryotes and prokaryotes, is critical for Rpn11 function. BMC Biochem 3, 28 (2002)
77. Verma, R., L. Aravind, R. Oania, W. H. McDonald, J. R. Yates, E. V. Koonin & R. J. Deshaies: Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611-615 (2002)
78. Tran, H. J., M. D. Allen, J. Lowe, & M. Bycroft: Structure of the Jab1/MPN domain and its implications for proteasome function. Biochemistry 42, 11460-11465 (2003)
79. Fröhlich, K. U., H. W. Fries, J. M. Peters, & D. Mecke: The ATPase activity of purified CDC48p from Saccharomyces cerevisiae shows complex dependence on ATP-, ADP-, and NADH-concentrations and is completely inhibited by NEM. Biochim Biophys Acta 1253, 25-32 (1995)
80. Rockel, B., J. Walz, R. Hegerl, J. Peters, D. Typke, & W. Baumeister: Structure of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum as studied by electron tomography. FEBS Lett 451, 27-32 (1999)
81. Golbik, R., A. N. Lupas, K. K. Koretke, W. Baumeister, & J. Peters: The Janus face of the archaeal Cdc48/p97 homologue VAT: protein folding versus unfolding. Biol Chem 380, 1049-1062 (1999)
82. Rabinovich, E., A. Kerem, K.-U. Frohlich, N. Diamant, & S. Bar-Nun: AAA-ATPase p97/Cdc48p, a cytosolic chaperone required for endoplasmic reticulum-associated protein degradation. Mol Cell Biol 22, 626-634 (2002)
83. Bays, N. W. & R. Y. Hampton: Cdc48-Ufd1-Np14: stuck in the middle with Ub. Curr Biol 12, R366-R371 (2002)
84. Flierman, D., Y. Ye, M. Dai, V. Chau, & T. A. Rapoport: Polyubiquitin serves as a recognition signal, rather than a ratcheting molecule, during retrotranslocation of proteins across the endoplasmic reticulum membrane. J Biol Chem 278, 34774-34782 (2003)
85. Hill, C. P., E. I. Masters, & F. G. Whitby: The 11S regulators of 20S proteasome activity. Curr Top Microbiol Immunol 268, 73-89 (2002)
86. Guo, G. G., M. Gu, & J. D. Etlinger: 240-kDa proteasome inhibitor (CF-2) is identical to δ-aminolevulinic acid dehydratase. J Biol Chem 269, 12399-12402 (1994)
87. Gregori, L., J. F. Hainfeld, M. N. Simon, & D. Goldgaber: Binding of amyloid β-protein to the 20 S proteasome. J Biol Chem 272, 58-62 (1997)
88. McCutchen-Maloney, S. L., K. Matsuda, N. Shimbara, D. D. Binns, K. Tanaka, C. A. Slaughter, & G. N. DeMartino: cDNA cloning, expression, and functional characterization of PI31, a proline-rich inhibitor of the proteasome. J Biol Chem 275, 18557-18565 (2000)
89. Tsubuki, S., Y. Saito, & S. Kawashima: Purification and characterization of an endogenous inhibitor specific to the Z-Leu-Leu-Leu-MCA degrading activity in proteasome and its identification as heat-shock protein 90. FEBS Lett 344, 229-233 (1994)
90. Ehlers, C., F. Kopp, & B. Dahlmann: Screening for molecules interacting with proteasomes in Thermoplasma acidophilum. Biol Chem 378, 249-253 (1997)
91. Whitby, F. G., E. I. Masters, L. Kramer, J. R. Knowlton, Y. Yao, C. C. Wang, & C. P. Hill: Structural basis for the activation of 20S proteasomes by 11S regulators. Nature 408, 115-120 (2000)
92. Stohwasser, R., U. Salzmann, J. Giesebrecht, P. M. Kloetzel, & H. G. Holzhutter: Kinetic evidences for facilitation of peptide channelling by the proteasome activator PA28. Eur J Biochem 267, 6221-6230 (2000)
93. Bochtler, M., C. Hartmann, H. K. Song, G. P. Bourenkov, H. D. Bartunik, & R. Huber: The structures of HsIU and the ATP-dependent protease HsIU-HsIV. Nature 403, 800-805 (2000)
94. Wang, J., J. J. Song, M. C. Franklin, S. Kamtekar, Y. J. Im, S. H. Rho, I. S. Seong, C. S. Lee, C. H. Chung, & S. H. Eom: Crystal structures of the Hs1VU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism. Structure (Camb) 9, 177-184 (2001)
95. Bochtler, M., H. K. Song, C. Hartmann, R. Ramachandran, & R. Huber: The quaternary arrangement of Hs1U and Hs1V in a cocrystal: a response to Wang, Yale. J Struct Biol 135, 281-293 (2001)
96. + chaperone, ClpA. J Biol Chem 277, 46753-46762 (2002)
97. Guo, F., M. R. Maurizi, L. Esser, & D. Xia: Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease. J Biol Chem 277, 46743-46752 (2002)
98. Kim, D. Y. & K. K. Kim: Crystal structure of ClpX molecular chaperone from Helicobacter pylori. J Biol Chem 278, 50664-50670 (2003)
99. Krzywda, S., A. M. Brzozowski, C. Verma, K. Karata, T. Ogura, & A. J. Wilkinson: The crystal structure of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli at 1.5 Å resolution. Structure (Camb) 10, 1073-1083 (2002)
100. Pickart, C. M.: Mechanisms underlying ubiquitination. Annu Rev Biochem 70, 503-533 (2001)
101. Hershko, A. & A. Ciechanover: The ubiquitin system. Annu Rev Biochem 67, 425-480 (1998)
102. Lam, Y. A., T. G. Lawson, M. Velayutham, J. L. Zweier, & C. M. Pickart: A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal. Nature 416, 763-767 (2002)
103. Fu, H., S. Sadis, D. M. Rubin, M. Glickman, S. van Nocker, D. Finley, & R. D. Vierstra: Multiubiquitin chain binding and protein degradation are mediated by distinct domains within the 26S proteasome subunit Mcb1. J Biol Chem 273, 1970-1981 (1998)
104. Schwartz, D. C. & M. Hochstrasser: A superfamily of protein tags: ubiquitin, SUMO and related modifiers. Trends Biochem Sci 28, 321-328 (2003)
105. Saeki, Y., T. Sone, H. Yokosawa, & H. Yokosawa: Identification of ubiquitin-like protein-binding subunits of the 26S proteasome. Biochem Biophys Res Commun 296, 813-819 (2002)
106. Wilkinson, C. R., M. Seeger, R. Hartmann-Petersen, M. Stone, M. Wallace, C. Semple, & C. Gordon: Proteins containing the UBA domain are able to bind to multi-ubiquitin chains. Nat Cell Biol 3, 939-943 (2001)
107. Elsasser, S., R. R. Gali, M. Schwickart, C. N. Larsen, D. S. Leggett, B. Muller, M. T. Feng, F. Tubing, G. A. Dittmar, & D. Finley: Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat Cell Biol 4, 725-730 (2002)
108. Dai, R. M. & C. C. Li: Valosin-containing protein is a multi-ubiquitin chain-targeting factor required in ubiquitin-proteasome degradation. Nat Cell Biol 3, 740-744 (2001)
109. Song, C., Q. Wang, & C. C. Li: ATPase activity of p97-VCP: D2 mediates the major enzyme activity and D1 contributes to the heat-induced activity. J Biol Chem 278, 3648-3655 (2003)
110. Orlowski, M. & S. Wilk: Ubiquitin-independent proteolytic functions of the proteasome. Arch Biochem Biophys 415, 1-5 (2003)
111. Zwickl, P., W. Baumeister, & A. Steven: Disassembly lines: the proteasome and related ATPase-assisted proteases. Curr Opin Struct Biol 10, 242-250 (2000)
112. Neher, S. B., R. T. Sauer, & T. A. Baker: Distinct peptide signals in the UmuD and UmuD′ subunits of UmuD/D′ mediate tethering and substrate processing by the ClpXP protease. Proc Natkl Acad Sci USA 100, 13219-13224 (2003)
113. Wah, D. A., I. Levchenko, T. A. Baker, & R. T. Sauer: Characterization of a specificity factor for an AAA+ ATPase. Assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer. Chem Biol 9, 1237-1245 (2002)
114. S by the proteolytic targeting factor RssB and ClpX. EMBO J 22, 4111-4120 (2003)
115. Zwickl, P. & W. Baumeister: AAA-ATPases at the crossroads of protein life and death. Nat Cell Biol 1, E97-8 (1999)
116. Braun, B. C., M. Glickman, R. Kraft, B. Dahlmann, P. M. Kloetzel, D. Finley, & M. Schmidt: The base of the proteasome regulatory particle exhibits chaperone-like activity. Nat Cell Biol 1, 221-226 (1999)
117. Horwich, A. L., E. U. Weber-Ban, & D. Finley: Chaperone rings in protein folding and degradation. Proc Natl Acad Sci USA 96, 11033-11040 (1999)
118. Osmulski, P. A. & M. Gaczynska: Atomic force microscopy reveals two conformations of the 20S proteasome from fission yeast. J Biol Chem 275, 13171-13174 (2000)
119. Forster, A., F. G. Whitby, & C. P. Hill: The pore of activated 20S proteasomes has an ordered 7-fold symmetric conformation. EMBO J 22, 4356-4364 (2003)
120. Walz, J., A. Erdmann, M. Kania, D. Typke, A. J. Koster, & W. Baumeister: 26S proteasome structure revealed by three-dimensional electron microscopy. J Struct Biol 121, 19-29 (1998)
121. Fleming, J. A., E. S. Lightcap, S. Sadis, V. Thoroddsen, C. E. Bulawa, & R. K. Blackman: Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341. Proc Natl Acad Sci USA 99, 1461-1466 (2002)
122. Meiners, S., D. Heyken, A. Weller, A. Ludwig, K. Stangl, P.-M. Kloetzel, & E. Kruger: Inhibition of proteasome activity induces concerted expression of proteasome genes and de novo formation of mammalian proteasomes. J Biol Chem 278, 21517-21525 (2003)
123. Wojcik, C. & G. N. DeMartino: Analysis of Drosophila 26S proteasome using RNA interference. J Biol Chem 277, 6188-6197 (2002)
124. Rock, K. L., I. A. York, T. Saric, & A. L. Goldberg: Protein degradation and the generation of MHC class I-presented peptides. Adv Immunol 80, 1-70 (2002)
125. Shimbara, N., E. Orino, S. Sone, T. Ogura, M. Takashina, M. Shono, T. Tamura, H. Yasuda, K. Tanaka, & A. Ichihara: Regulation of gene expression of proteasomes (multi-protease complexes) during growth and differentiation of human hematopoietic cells. J Biol Chem 267, 18100-18109 (1992)
126. Pal, J. K., C. Martins de Sa, & K. Scherrer: Differential synthesis and cytolocalization of prosomes in chick embryos during development. Int J Dev Biol 38, 525-534 (1994)
127. Dawson, S. P., J. E. Arnold, N. J. Mayer, S. E. Reynolds, M. A. Billett, C. Gordon, L. Colleaux, P. M. Kloetzel, K. Tanaka, & R. J. Mayer: Developmental changes of the 26 S proteasome in abdominal intersegmental muscles of Manduca sexta during programmed cell death. J Biol Chem 270, 1850-1858 (1995)
128. Haass, C. & P.-M. Kloetzel: The Drosophila proteasome undergoes changes in its subunit pattern during development. Exp Cell Res 180, 243-252 (1989)
129. Peng, Z., J. M. Staub, G. Serino, S. F. Kwok, J. Kurepa, B. D. Bruce, R. D. Vierstra, N. Wei, & X. W. Deng: The cellular level of PR500, a protein complex related to the 19S regulatory particle of the proteasome, is regulated in response to stresses in plants. Mol Biol Cell 12, 383-392 (2001)
130. Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, & P. O. Brown: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11, 4241-4257 (2000)
131. Fujimuro, M., H. Takada, Y. Saeki, A. Toh-e, K. Tanaka, & H. Yokosawa: Growth-dependent change of the 26S proteasome in budding yeast. Biochem Biophys Res Commun 251, 818-823 (1998)
132. Finley, D., E. Özkaynak, & A. Varshavsky: The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses. Cell 48, 1035-1046 (1987)
133. Mannhaupt, G., R. Schnall, V. Karpov, I. Vetter, & H. Feldmann: Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett 450, 27-34 (1999)
134. Xie, Y. & A. Varshavsky: RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: A negative feedback circuit. Proc Natl Acad Sci USA 98, 3056-3061 (2001)
135. van Nocker, S., S. Sadis, D. M. Rubin, M. Glickman, H. Fu, O. Coux, I. Wefes, D. Finley, & 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, 6020-6028 (1996)
136. Haracska, L. & A. Udvardy: Mapping the ubiquitin-binding domains in the p54 regulatory complex subunit of the Drosophila 26S protease. FEBS Lett 412, 331-336 (1997)
137. Arendt, C. S. & M. Hochstrasser: Eukaryotic 20S proteasome catalytic subunit propeptides prevent active site inactivation by N-terminal acetylation and promote particle assembly. EMBO 718, 3575-3585 (1999)
138. α-acetylation and proteolytic activity of the yeast 20 S proteasome. J Biol Chem 275, 4635-4639 (2000)
139. Kimura, Y., Y. Saeki, H. Yokosawa, B. Polevoda, F. Sherman, & H. Hirano: N-Terminal modifications of the 19S regulatory particle subunits of the yeast proteasome. Arch Biochem Biophys 409, 341-348 (2003)
140. Ferrell, K., C. R. Wilkinson, W. Dubiel, & C. Gordon: Regulatory subunit interactions of the 26S proteasome, a complex problem. Trends Biochem Sci 25, 83-88 (2000)
141. Iwafune, Y., H. Kawasaki, & H. Hirano: Electrophoretic analysis of phosphorylation of the yeast 20S proteasome. Electrophoresis 23, 329-338 (2002)
142. Rivett, A. J., S. Bose, P. Brooks, & K. I. Broadfoot: Regulation of proteasome complexes by γ-interferon and phosphorylation. Biochimie 83, 363-366 (2001)
143. Egerton, M., O. R. Ashe, D. Chen, B. J. Druker, W. H. Burgess, & L. E. Samelson: VCP, the mammalian homolog of cdc48, is tyrosine phosphorylated in response to T cell antigen receptor activation. EMBO J 11, 3533-3540 (1992)
144. Satoh, K., H. Sasajima, K. Nyoumura, H. Yokosawa, & H. Sawada: Assembly of the 26S proteasome is regulated by phosphorylation of the p45/Rpt6 ATPase subunit. Biochemistry 40, 314-319 (2001)
145. Zwickl, P., F. Lottspeich, B. Dahlmann, & W. Baumeister: Cloning and sequencing of the gene encoding the large (α-) subunit of the proteasome from Thermoplasma acidophilum. FEBS Lett 278, 217-221 (1991)
146. Maupin-Furlow, J. A. & J. G. Ferry: A proteasome from the methanogenic archaeon Methanosarcina thermophila. J Biol Chem 270, 28617-28622 (1995)
147. Shockley, K. R., D. E. Ward, S. R. Chhabra, S. B. Conners, C. I. Montero, & R. M. Kelly: Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus. Appl Environ Microbiol 69, 2365-2371 (2003)
148. Ruepp, A., C. Eckerskorn, M. Bogyo, & W. Baumeister: Proteasome function is dispensable under normal but not under heat shock conditions in Thermoplasma acidophilum. FEBS Lett 425, 87-90 (1998)
149. Ramos, P. C., J. Hockendorff, E. S. Johnson, A. Varshavsky, & R. J. Dohmen: Ump1p is required for proper maturation of the 20S proteasome and becomes its substrate upon completion of the assembly. Cell 92, 489-499 (1998)
150. Lehmann, A., K. Janek, B. Braun, P. M. Kloetzel, & C. Enenkel: 20 S proteasomes are imported as precursor complexes into the nucleus of yeast. J Mol Biol 317, 401-413 (2002)
151. Tone, Y. & A. Toh-e: Nob1p is required for biogenesis of the 26S proteasome and degraded upon its maturation in Saccharomyces cerevisiae. Genes Dev 16, 3142-3157 (2002)
152. Tone, Y., N. Tanahashi, K. Tanaka, M. Fujimuro, H. Yokosawa, & A. Toh-e: Nob1p, a new essential protein, associates with the 26S proteasome of growing Saccharomyces cerevisiae cells. Gene 243, 37-45 (2000)
153. Bajorek, M., D. Finley, & M. H. Glickman: Proteasome disassembly and downregulation is correlated with viability during stationary phase. Curr Biol 13, 1140-1144 (2003)
154. Liu, C, L. Millen, T. B. Roman, H. Xiong, H. F. Gilbert, R. Noiva, G. N. DeMartino, & P. J. Thomas: Conformational remodeling of proteasomal substrates by PA700, the 19 S regulatory complex of the 26 S proteasome. J Biol Chem 277, 26815-26820 (2002)
155. Flynn, J. M., S. B. Neher, Y. I. Kim, R. T. Sauer, & T. A. Baker: Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol Cell 11, 671-683 (2003)
156. Weichart, D., N. Querfurth, M. Dreger, & R. Hengge-Aronis: Global role for ClpP-containing proteases in stationary-phase adaptation of Escherichia coli. J Bacteriol 185, 115-125 (2003)
157. W- controlled pbpE gene, resulting in filamentous growth of Bacillus subtilis. J Bacteriol 185, 973-982 (2003)
158. Peng, J., D. Schwartz, J. E. Elias, C. C. Thoreen, D. Cheng, G. Marsischky, J. Roelofs, D. Finley, & S. P. Gygi: A proteomics approach to understanding protein ubiquitination. Nat Biotechnol 21, 921-926 (2003)
159. Verma, R., S. Chen, R. Feldman, D. Schieltz, J. Yates, J. Dohmen, & R. J. Deshaies: Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol Biol Cell 11, 3425-3439 (2000)
160. Leggett, D. S., J. Hanna, A. Borodovsky, B. Crosas, M. Schmidt, R. T. Baker, T. Walz, H. Ploegh, & D. Finley: Multiple associated proteins regulate proteasome structure and function. Mol Cell 10, 495-507 (2002)
161. Klenk, H.-P., R. A. Clayton, J. F. Tomb, O. White, K. E. Nelson, K. A. Ketchum, R. J. Dodson, M. Gwinn, E. K. Hickey, J. D. Peterson: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364-370 (1997)
162. Ng, W. V., S. P. Kennedy, G. G. Mahairas, B. Berquist, M. Pan, H. D. Shukla, S. R. Lasky, N. S. Baliga, V. Thorsson, J. Sbrogna: Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci USA 97, 12176-12181 (2000)
163. Bult, C. J., O. White, G. J. Olsen, L. Zhou, D. Fleischmann, G. G. Sutton, J. A. Blake, M. FitzGerald, R. A. Clayton, J. D. Gocayne: Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073 (1996)
164. Slesarev, A. I., K. V. Mezhevaya, K. S. Makarova, N. N. Polushin, O. V. Shcherbinina, V. V. Shakhova, G. I. Belova, L. Aravind, D. A. Natale, I. B. Rogozin: The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci USA 99, 4644-4649 (2002)
165. Galagan, J. E., C. Nusbaum, A. Roy, M. G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor: The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12, 532-542 (2002)
166. Deppenmeier, U., A. Johann, T. Hartsch, R. Merkl, R. A. Schmitz, R. Martinez-Arias, A. Henne, A. Wiezer, S. Baumer, C. Jacobi: The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4, 453-461 (2002)
167. Smith, D. R., L. A. Doucette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert: Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: functional analysis and comparative genomics. J Bacteriol 179, 7135-7155 (1997)
168. Cohen, G. N., V. Barbe, D. Flament, M. Galperin, R. Heilig, O. Lecompte, O. Poch, D. Prieur, J. Querellou, R. Ripp: An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol 47, 1495-1512 (2003)
169. Robb, F. T., D. L. Maeder, J. R. Brown, J. DiRuggiero, M. D. Stump, R. K. Yeh, R. B. Weiss, & D. M. Dunn: Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. Methods Enzymol 330, 134-57, 134-157 (2001)
170. Kawarabayasi, Y., M. Sawada, H. Horikawa, Y. Haidawa, Y. Hino, S. Yamamoto, M. Sekine, S. Baba, H. Kosugi, A. Hosoyama: Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res 5, 147-155 (1998)
171. Jeon, S. J., S. Fujiwara, M. Takagi, & T. Imanaka: Pk-cdcA encodes a CDC48/VCP homolog in the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1: transcriptional and enzymatic characterization. Mol Gen Genet 262, 559-567 (1999)
172. Zwickl, P., A. Grziwa, G. Pühler, B. Dahlmann, F. Lottspeich, & W. Baumeister: Primary structure of the Thermoplasma proteasome and its implications for the structure, function, and evolution of the multicatalytic proteinase. Biochemistry 31, 964-972 (1992)
173. Ruepp, A., W. Graml, M. L. Santos-Martinez, K. K. Koretke, C. Volker, H. W. Mewes, D. Frishman, S. Stocker, A. N. Lupas, & W. Baumeister: The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407, 508-513 (2000)
174. Kawashima, T., N. Amano, H. Koike, S. Makino, S. Higuchi, Y. Kawashima-Ohya, K. Watanabe, M. Yamazaki, K. Kanehori, T. Kawamoto: Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc Natl Acad Sci USA 97, 14257-14262 (2000)
175. Kawarabayasi, Y., Y. Hino, H. Horikawa, S. Yamazaki, Y. Haikawa, K. Jin-no, M. Takahashi, M. Sekine, S. Baba, A. Ankai: Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res 6, 83-52 (1999)
176. Fitz-Gibbon, S. T., H. Ladner, U. J. Kim, K. O. Stetter, M. I. Simon, & J. H. Miller: Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci USA 99, 984-989 (2002)
177. She, Q., R. K. Singh, F. Confalonieri, Y. Zivanovic, G. Allard, M. J. Awayez, C. C. Chan-Weiher, I. G. Clausen, B. A. Curtis, A. De Moors: The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci USA (2001)
178. Kawarabayasi, Y., Y. Hino, H. Horikawa, K. Jin-no, M. Takahashi, M. Sekine, S. Baba, A. Ankai, H. Kosugi, A. Hosoyama: Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res 8, 123-140 (2001)
179. Waters, E., M. J. Hohn, I. Ahel, D. E. Graham, M. D. Adams, M. Barnstead, K. Y. Beeson, L. Bibbs, R. Bolanos, M. Keller: The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci USA 100, 12984-12988 (2003)
180. Franzetti, B., G. Schoehn, J. F. Hernandez, M. Jaquinod, R. W. Ruigrok, & G. Zaccai: Tetrahedral aminopeptidase: a novel large protease complex from archaea. EMBO J 21, 2132-2138 (2002)
181. Du, X., I. G. Choi, R. Kim, W. Wang, J. Jancarik, H. Yokota, & S. H. Kim: Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-Å resolution. Proc Natl Acad Sci USA 97, 14079-14084 (2000)
182. Fukui, T., T. Eguchi, H. Atomi, & T. Imanaka: A membrane-bound archaeal Lon protease displays ATP-independent proteolytic activity towards unfolded proteins and ATP-dependent activity for folded proteins. J Bacteriol 184, 3689-3698 (2002)
183. Shimohata, N., S. Chiba, N. Saikawa, K. Ito, & Y. Akiyama: The Cpx stress response system of Escherichia coli senses plasma membrane proteins and controls HtpX, a membrane protease with a cytosolic active site. Genes Cells 1, 653-662 (2002)
184. Clausen, T., C. Southan, & M. Ehrmann: The HtrA family of proteases: implications for protein composition and cell fate. Mol Cell 10, 443-455 (2002)
185. Arnold, I. & T. Langer: Membrane protein degradation by AAA proteases in mitochondria. Biochim Biophys Acta 1592, 89-96 (2002)
186. Macario, A. J., M. Lange, B. K. Ahring, & E. C. de Macario: Stress genes and proteins in the archaea. Microbiol Mol Biol Rev 63, 923-967 (1999)