Abstract
The 2004 Nobel Prize in chemistry for the discovery of protein ubiquitination has led to the recognition of cellular proteolysis as a central area of research in biology. Eukaryotic proteins targeted for degradation by this pathway are first ‘tagged’ by multimers of a protein known as ubiquitin and are later proteolyzed by a giant enzyme known as the proteasome. This article recounts the key observations that led to the discovery of ubiquitin-proteasome system (UPS). In addition, different aspects of proteasome biology are highlighted. Finally, some key roles of the UPS in different areas of biology and the use of inhibitors of this pathway as possible drug targets are discussed.
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Abbreviations
- AAA-ATPase:
-
ATPases associated with various cellular activities-ATPase
- BrAAP:
-
branched chain amino acids preferring
- CSN:
-
COP9 signalosome
- ER:
-
endoplasmic reticulum
- HECT:
-
homologous to E6-AP carboxyl terminus
- IFN:
-
interferon
- MHC:
-
major histocompatibility complex
- NTN:
-
N-terminal nucleophile
- PA:
-
proteasome activator
- PAC:
-
proteasome assembling chaperone
- PAN:
-
proteasome-activating nucleotidase
- PI:
-
proteasome inhibitor
- POMP:
-
proteasome maturing protein
- RING:
-
really interesting new gene
- Rpn:
-
regulatory particle non-ATPase
- Rpt:
-
regulatory particle tripleA-ATPase
- SCF:
-
Skp-Cullin-F box
- SNAAP:
-
small neutral amino acids preferring
- UBH:
-
ubiquitin hydrolase
- UBP:
-
ubiqutin processing
- UMP1:
-
ubiquitin mediated proteolysis-1
- UPS:
-
ubiquitin-proteasome system
References
Adams J 2003 Potential for proteasome inhibition in the treatment of cancer;Drug Discovery Today 8 307–315
Adrain C, Creagh E M, Cullen S P and Martin S J 2004 Caspasedependent inactivation of proteasome function during programmed cell death inDrosophila and man;J. Biol. Chem. 279 36923–36930
Apcher G S, Heink S, Zantopf D, Kloetzel P M, Schmid H P, Mayer R J and Kruger E 2003 Human immunodeficiency virus-1 Tat protein interacts with distinct proteasomal alpha and beta subunits;FEBSLett. 553 200–204
Arendt C S and Hochstrasser M 1999 Eukaryotic 20S proteasome catalytic subunit propeptides prevent active site inactivation by N-terminal acetylation and promote particle assembly;EMBO J. 18 3575–3585
Arrigo A P, Tanaka K, Goldberg A L and Welch W J 1988 Identity of the 19S ‘prosome’ particle with the large multifunctional protease complex of mammalian cells (the proteasome);Nature (London) 331 192–204
Arthur J S, Elce J S, Hegadorn C, Williams K and Greer P A 2000 Disruption of the murine calpain small subunit gene, Capn4: calpain is essential for embryonic development but not for cell growth and division;Mol. Cell. Biol. 20 4474–4481.
Barton L F, Cruz M, Rangwala R, Deepe G S Jr and Monaco J J 2002 Regulation of immunoproteasome subunit expressionin vivo following pathogenic fungal infection;J. Immunol. 169 3046–3052
Barton L F, Runnels H A, Schell T D, Cho Y, Gibbons R, Tevethia S S, Deepe G S Jr and Monaco J J 2004 Immune defects in 28-kDa proteasome activator gamma-deficient mice;J. Immunol. 172 3948–3954.
Benaroudj N and Goldberg A L 2000 PAN, the proteasome-activating nucleotidase from archaebacteria, is a protein-unfolding molecular chaperone;Nat. Cell. Biol. 2 833–839
Benaroudj N, Zwickl P, Seemuller E, Baumeister W and Goldberg A L 2003 ATP hydrolysis by the proteasome regulatory complex PAN serves multiple functions in protein degradation;Mol. Cell 11 69–78
Berndt C, Bech-Otschir D, Dubiel W and Seeger M 2002 Ubiquitin System: JAMMing in the Name of the Lid;Curr. Biol. 12 R815-R817
Brown M S, Ye J, Rawson R B and Goldstein J L 2000 Regulated intramembrane proteolysis: a control mechanism conserved from bacteria to humans;Cell 100 391–398
Burri L, Hockendorff J, Boehm U, Klamp T, Dohmen R J and Levy F 2000 Identification and characterization of a mammalian protein interacting with 20S proteasome precursors;Proc. Natl. Acad. Sci. USA 97 10348–10353
Cardozo T and Pagano M 2004 The SCF ubiquitin ligase: insights into a molecular machine;Nat. Rev. Mol. Cell. Biol. 5 739–751
Chu-Ping M, Slaughter C A and Demartino G N 1992 Purification and characterization of a protein inhibitor of the 20S proteasome (macropain);Biochem. Biophys. Acta 1119 303–311
Chandu D and Nandi D 2002 From proteins to peptides to amino acids: comparative genomics of enzymes involved in downstream events during cytosolic protein degradation;Appl. Genom. Proteom. 4 235–252
Chandu D and Nandi D 2004 Comparative genomics and functional roles of the ATP-dependent proteases Lon and Clp during cytosolic protein degradation;Res. Microbiol. 155 710–719
Chen P and Hochstrasser M 1996 Autocatalytic subunit processing couples active site formation in the 20S proteasome to completion of assembly;Cell 86 961–972
Ciechanover A, Hod Y and Hershko A 1978 A heat-stable polypeptide component of an ATP-dependent proteolytic system from reticulocytes;Biochem. Biophys. Res. Commun. 81 1100–1105
Ciechanover A, Finley D and Varshavsky A 1984 Ubiquitin dependence of selective protein degradation demonstrated in the mammalian cell cycle mutant ts85;Cell 37 57–66
Ciechanover A and Ben-Saadon R 2004 N-terminal ubiquitination: more protein substrates join in;Trends Cell Biol. 14 103–106
Ciechanover A and Iwai K 2004 The ubiquitin system: from basic mechanisms to the patient bed;IUBMB Life 56 193–201
Cuervo A M, Palmer A, Rivett A J and Knecht E 1995 Degradation of proteasomes by lysosomes in rat liver;Eur. J. Biochem. 227 792–800
Dahlmann B, Kopp F, Kuehn L, Niedel B, Pfeifer G, Hegerl R and Baumeister W 1989 The multicatalytic proteinase (prosome) is ubiquitous from eukaryotes to archaebacteria;FEBS Lett. 251 125–131
Darwin K H, Ehrt S, Gutierrez-Ramos J C, Weich N and Nathan C F 2003 The proteasome ofMycobacterium tuberculosis is required for resistance to nitric oxide;Science 302 1963–1966
Darwin K H, Lin G, Chen Z, Li H and Nathan C F 2005 Characterization of aMycobacterium tuberculosis proteasomal ATPase homologue;Mol. Microbiol. 55 561–571
De M, Jayarapu K, Elenich L, Monaco J J, Colbert R A and Griffin T A 2003 Beta 2 subunit propeptides influence cooperative proteasome assembly;J. Biol. Chem. 278 6153–6159
Dick T P, Ruppert T, Groettrup M, Kloetzel P M, Kuehn L, Koszinowski U H, Stevanovic S, Schild H and Rammensee H G 1996 Coordinated dual cleavages induced by the proteasome regulator PA28 lead to dominant MHC ligands;Cell 86 253–262
Etlinger J D and Goldberg A L 1977 A soluble ATP-dependent proteolytic system responsible for the degradation of abnormal proteins in reticulocytes;Proc. Natl. Acad. Sci. USA. 74 54–58
Enenkel C, Lehmann A and Kloetzel P M 1998 Subcellular distribution of proteasomes implicates a major location of protein degradation in the nuclear envelope-ER network in yeast;EMBOJ. 17 6144–6154
Elsasser S and Finley D 2005 Delivery of ubiquitinated substrates to protein-unfolding machines;Nat. CellBiol. 7 742–749
Fabunmi R P, Wigley W C, Thomas P J and DeMartino G N 2000 Activity and regulation of the centrosome-associated proteasome;J. Biol. Chem. 275 409–413
Fehling H J, Swat W, Laplace C, Kuhn R, Rajewsky K, Muller U and von Boehmer H 1994 MHC class I expression in mice lacking the proteasome subunit LMP-7;Science 265 1234–1237
Fenteany G, Standaert R F, Lane W S, Choi S, Corey E J and Schreiber S L 1995 Inhibition of proteasome activities and subunit-specific amino-terminal threonine modification by lactacystin;Science 268 726–731
Finley D, Ciechanover A and Varshavsky A 1984 Thermolability of ubiquitin-activating enzyme from the mammalian cell cycle mutant ts85;Cell 37 43–55
Förster A, Whitby F G and Hill C P 2003 The pore of activated 20S proteasomes has an ordered 7-fold symmetric conformation;EMBOJ. 22 4356–4364
Förster A, Masters E I, Whitby F G, Robinson H and Hill C P 2005 The 1.9 Å structure of aproteasome-11S activator complex and implications forproteasome-PAN/PA700 interactions;Mol. Cell 18 589–599
Frentzel S, Pesold-Hurt B, Seelig A and Kloetzel P M 1994 20 S proteasomes are assembled via distinct precursor complexes. Processing of LMP2 and LMP7 proproteins takes place in 13–16 S preproteasome complexes;J. Mol. Biol. 236 975–981
Gaczynska M, Osmulski P A, Gao Y, Post M J and Simons M 2003 Proline and arginine-rich peptides constitute a novel class of allosteric inhibitors of proteasome activity;Biochemistry 42 8663–8670.
Gao Y, Lecker S, Post M J, Hietaranta A J, Li J, Volk R, Li M, Sato K, Saluja A K, Steer M L, Goldberg A L and Simons M 2000 Inhibition of ubiquitin-proteasome pathway-mediated I kappa B alpha degradation by a naturally occurring antibacterial peptide;J. Clin. Invest. 106 439–448.
Glickman M H, Rubin D M, Fried V A and Finley D 1998 The regulatory particle of theSaccharomyces cerevisiae proteasome;Mol. Cell. Biol. 18 3149–3162
Goldstein J L 2004 Towering science: an ounce of creativity is worth a ton of impact;Nat. Med. 10 1015–1016
Griffin T A, Nandi D, Cruz M, Fehling H J, Kaer L V, Monaco J J and Colbert R A 1998 Immunoproteasome assembly: cooperative incorporation of interferon gamma (IFN-gamma)-inducible subunits;J. Exp. Med. 187 97–104
Griffin T A, Slack J P, McCluskey T S, Monaco J J and Colbert R A 2000 Identification of proteassemblin, a mammalian homologue of the yeast protein, Ump1p, that is required for normal proteasome assembly;Mol. Cell. Biol. Res. Commun. 3 212–217
Groll M, Ditzel L, Lowe J, Stock D, Bochtler M, Bartunik H D and Huber R 1997 Structure of 20S Proteasome from yeast at 2.4Å resolution;Nature (London) 386 463–470
Groll M, Heinemeyer W, Jager S, Ullrich T, Bochtler M, Wolf D H and Huber R 1999 The catalytic sites of 20S proteasomes and their role in subunit maturation: a mutational and crystallographic study;Proc. Natl. Acad. Sci. USA 96 10976–10983
Groll M, Kim K B, Kairies N, Huber R and Crews C M 2000 Crystal structure of epoxomicin: 20S proteasome reveals a molecular bassifor selectivity of alpha ‘beta’ —epoxyketone proteasome inhibitors;J. Am. Chem. Soc. 122 1237–1238
Groll M and Huber R 2004 Inhibitors of the eukaryotic 20S proteasome core particle: a structural approach;Biochim. Biophys. Acta 1695 33–44
Grune T, Jung T, Merker K and Davies K J 2004 Decreased proteolysis caused by protein aggregates, inclusion bodies, plaques, lipofuscin, ceroid, and ‘aggresomes’ during oxidative stress, aging, and disease;Int. J. Biochem. Cell. Biol. 36 2519–2530
Grziwa A, Maack S, Puhler G, Wiegand G, Baumeister W and Jaenicke R 1994 Dissociation and reconstitution of the Thermoplasma proteasome;Eur. J. Biochem. 223 1061–1067
Guo G G, Gu M and Etlinger J D 1994 240-kDa proteasome inhibitor (CF-2) is identical to delta-aminolevulinic acid dehydratase;J. Biol. Chem. 269 12399–12402
Harbers K, Muller U, Grams A, Li E, Jaenisch R and Franz T 1996 Provirus integration into a gene encoding a ubiquitin-conjugating enzyme results in a placental defect and embryonic lethality;Proc. Natl. Acad. Sci. USA 93 12412–12417
Harris J L, Alper P B, Li J, Rechsteiner M and Backes B J 2001 Substrate specificity of the human proteasome;Chem. Biol. 8 1131–1141
Heink S, Ludwig D, Kloetzel P and Kruger E 2005 IFNγ-induced immune adaptation of the proteasome system is an accelerated and transient response;Proc. Natl. Acad. Sci. USA. 102 9241–9246
Hendil K B, Khan S and Tanaka K 1998 Simultaneous binding of PA28 and PA700 activators to 20S proteasomes;Biochem. J. 332 749–754
Hershko A, Ciechanover A and Rose I A 1979 Resolution of the ATP-dependent proteolytic system from reticulocytes: a component that interacts with ATP;Proc. Natl. Acad. Sci. USA 76 3107–3110
Hershko A, Ciechanover A, Heller H, Haas A L and Rose I A 1980 Proposed role of ATP in protein breakdown: conjugation of protein with multiple chains of the polypeptide of ATP-dependent proteolysis;Proc. Natl. Acad. Sci. USA 77 1783–1786
Hershko A, Ciechanover A and Rose I A 1981 Identification of the active amino acid residue of the polypeptide of ATP-dependent protein breakdown;J. Biol. Chem. 256 1525–1528
Hershko A, Eytan E, Ciechanover A and Haas A L 1982 Immunochemical analysis of the turnover of ubiquitin-protein conjugates in intact cells. Relationship to the breakdown of abnormal proteins;J. Biol. Chem. 257 13964–13970
Hershko A, Heller H, Elias S and Ciechanover A 1983 Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown;J. Biol. Chem 258 8206–8214
Hershko A, Helen H, Eytane and Ressy 1986 The Protein substrate binding site of the Ubiquitin-Protein ligase system;J. Biol. Chem. 261 11982–11989
Hershko A, Ganoth D, Sudakin V, Dahan A, Cohen L H, Luca F C, Ruderman J V and Eytan E 1994 Components of a system that ligates cyclin to ubiquitin and their regulation by the protein kinase cdc2;J. Biol. Chem. 269 4940–4946
Heinemeyer W, Fischer M, Krimmer T, Stachon U and Wolf D H 1997 The active sites of the eukaryotic 20 S proteasome and their involvement in subunit precursor processing;J. Biol. Chem. 272 25200–25209
Hicke L 2001 Protein regulation by monoubiquitin;Nat. Rev. Mol. Cell. Biol. 2 195–201
Hirano Y, Hendil K B, Yashiroda H, Iemura S, Nagane R, Hioki Y, Natsume T, Tanaka K and Murata S 2005 A heterodimeric complex that promotes the assembly of mammalian 20S proteasomes;Nature (London) 437 1381–1385
Hoffman L, Pratt G and Rechsteiner M 1992 Multiple forms of the 20 S multicatalytic and the 26 S ubiquitin/ATP-dependent proteases from rabbit reticulocyte lysate;J. Biol. Chem. 267 22362–22368
Hoppe T 2005 Multiubiquitylation by E4 enzymes: ‘one size’ doesn't fit all;Trends Biochem. Sci. 30 183–187
Hough R, Pratt G and Rechsteiner M 1986 Ubiquitin-lysozyme conjugates. Identification and characterization of an ATP-dependent protease from rabbit reticulocyte lysates;j. Biol. Chem. 261 2400–2408
Hu Z, Zhang Z, Doo E, Coux O, Goldberg A L and Liang T J 1999 Hepatitis B virus X protein is both a substrate and a potential inhibitor of the proteasome complex;J. Virol. 73 7231–7240
Jager S, Groll M, Huber R, Wolf D H and Heinemeyer W 1999 Proteasome beta-type subunits: unequal roles of propeptides in core particle maturation and a hierarchy of active site function;J. Mol. Biol. 291 997–1013
Johnston J A, Ward C L and Kopito R R 1998 Aggresomes: a cellular response to misfolded proteins;J. Cell. Biol. 143 1883–1898
Karin M and Ben-Neriah Y 2000 Phosphorylation meets ubiquitination: the control of NF-[kappa]B activity;Annu. Rev. Immunol. 18 621–663
Khan S, van den Broek M, Schwarz K, de Giuli R, Diener P A and Groettrup M 2001 Immunoproteasomes largely replace constitutive proteasomes during an antiviral and antibacterial immune response in the liver;J. Immunol. 167 6859–6868
Kim J H, Park K C, Jung S S, Bang O and Chung C H 2003 Deubiquitinating enzymes as cellular regulators;J. Biochem. 134 9–18
Kingsbury D J, Griffin T A and Colbert R A 2000 Novel propeptide function in 20 S proteasome assembly influences beta subunit composition;J. Biol. Chem. 275 24156–24162
Kishino T, Lalande M and Wagstaff J. 1997 UBE3A/E6-AP mutations cause Angelman syndrome;Nat. Genet. 15 70–73
Kisselev A F, Akopian T N and Goldberg A L 1998 Range of sizes of peptide products generated during degradation of different proteins by archaeal proteasomes;J. Biol. Chem. 273, 1982–1989
Kisselev A F, Akopian T N, Woo K M and Goldberg A L 1999 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
Kisselev A F, Songyang Z and Goldberg A L 2000 Why does threonine, and not serine, function as the active site nucleophile in proteasomes?;J. Biol. Chem. 275 14831–14837
Kloetzel P M 2004 The proteasome and MHC class I antigen processing;Biochim. Biophys. Acta 1695 225–233
Knipfer N and Shrader T E 1997 Inactivation of the 20S proteasome inMycobacterium smegmatis;Mol. Microbiol. 25 375–383
Knowlton J R, Johnston S C, Whitby F G, Realini C, Zhang Z, Rechsteiner M and Hill C P 1997 Structure of the proteasome activator REGalpha (PA28alpha);Nature (London) 390 639–643
Koegl M, Hoppe T, Schlenker S, Ulrich H D, Mayer T U and Jentsch S 1999 A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly;Cell 96 635–644
Kostova Z and Wolf D H 2003 For whom the bell tolls: protein quality control of the endoplasmic reticulum and the ubiquitin-proteasome connection;EMBOJ. 22 2309–2317
Kruger E, Kloetzel P M and Enenkel C 2001 20S proteasome biogenesis;Biochimie 83 289–293
Leggett D S, Hanna J, Borodovsky A, Crosas B, Schmidt M, Baker R T, Walz T, Ploegh H and Finley D 2002 Multiple associated proteins regulate proteasome structure and function;Mol. Cell. 10 495–507
Li J, Gao X, Joss L and Rechsteiner M 2000 The proteasome activator 11 S REG or PA28: chimeras implicate carboxyl-terminal sequences in oligomerization and proteasome binding but not in the activation of specific proteasome catalytic subunits;J. Mol. Biol. 299 641–654
Liu C W, Corboy M J, DeMartino G N and Thomas P J 2003 Endoproteolytic Activity of the Proteasome;Science 299 408–411
Lowe J, Stock D, Jap B, Zwick P, Baumeister W and Huber R 1995 Crystal structure of the 20S Proteasome from the ArchaeonT. acidophilum at 3.4Å resolution;Science 268 533–539
Lupas A, Zwickl P and Baumeister W 1994 Proteasome sequences in eubacteria;Trends Biochem. Sci. 19 533–534
Lykke-Andersen K, Schaefer L, Menon S, Deng X W, Miller J B and Wei N 2003 Disruption of the COP9 signalosome Csn2 subunit in mice causes deficient cell proliferation, accumulation of p53 and cyclin E, and early embryonic death;Mol. Cell Biol. 23 6790–6797
Matsumoto M, Yada M, Hatakeyama S, Ishimoto H, Tanimura T, Tsuji S, Kakizuka A, Kitagawa M and Nakayama K I 2004 Molecular clearance of ataxin-3 is regulated by a mammalian E4;EMBOJ. 23 659–669
McCutchen-Maloney S L, Matsuda K, Shimbara N, Binns D D, Tanaka K, Slaughter C A and DeMartino G N 2000 cDNA cloning, expression, and functional characterization of PI31, a prolinerich inhibitor of the proteasome;J. Biol. Chem. 275 18557–18565
McDonough H and Patterson C 2003 CHIP: a link between the chaperone and proteasome systems;Cell Stress Chaperones 8 303–308
Meiners S, Heyken D, Weller A, Ludwig A, Stangl K, Kloetzel P M and Kruger E 2003 Inhibition of proteasome activity induces concerted expression of proteasome genes andde novo formation of mammalian proteasomes;J. Biol. Chem. 278 21517–21525
Meng L, Mohan R, Kwok B H, Elofsson M, Sin N and Crews C M 1999 Epoxomicin, a potent and selective proteasome inhibitor, exhibits in vivo antiinflammatory activity;Proc. Natl. Acad. Sci. USA 96 10403–10408
Monaco J J and McDevitt H O 1984 H-2-linked low-molecular weight polypeptide antigens assemble into an unusual macromolecular complex;Nature (London) 309 797–799
Murata S, Kawahara H, Tohma S, Yamamoto K, Kasahara M, Nabeshima Y, Tanaka K and Chiba T 1999 Growth retardation in mice lacking the proteasome activator PA28gamma;J. Biol. Chem. 274 38211–38215
Murata S, Udono H, Tanahashi N, Hamada N, Watanabe K, Adachi K, Yamano T, Yui K, Kobayashi N, Kasahara M, Tanaka K and Chiba T 2001 Immunoproteasome assembly and antigen presentation in mice lacking both PA28alpha and PA28beta;EMBO J. 20 5898–5907
Murray A W 2004 Recycling the cell cycle: cyclins revisited;Cell 116 221–234
Nandi D, Woodward E, Ginsburg D B and Monaco J J 1997 Intermediates in the formation of mouse 20S proteasomes: implications for the assembly of precursor beta subunits;EMBO J. 16 5363–5375
Nandi D, Marusina K and Monaco J J 1998 How do endogenous proteins become peptides and reach the endoplasmic reticulum;Curr. Top. Microbiol. Immunol. 232 15–47
Niedermann G, Grimm R, Geier E, Maurer M, Realini C, Gartmann C, Soll J, Omura S, Rechsteiner M C, Baumeister W and Eichmann K 1997 Potential immunocompetence of proteolytic fragments produced by proteasomes before evolution of the vertebrate immune system;J. Exp. Med. 186 209–220
Park Y, Hwang Y P, Lee J S, Seo S H, Yoon S K and Yoon J B 2005 Proteasomal ATPase-associated factor 1 negatively regulates proteasome activity by interacting with proteasomal ATPases;Mol. Cell. Biol. 25 3842–3853
Pickart C M 2001 Mechanisms underlying ubiquitination;Annu. Rev. Biochem. 70 503–533
Pickart C M and Cohen R E 2004 Proteasomes and their kin: proteases in the machine age;Nat. Rev. Mol. Cell. Biol. 5 177–187
Ping M C, Willy P J, Slaughter C A and DeMartino G N 1993 PA28, an activator of the 20 S proteasome, is inactivated by proteolytic modification at its carboxyl terminus;J. Biol. Chem. 268 22514–22519
Rajkumar S V, Richardson P G, Hideshima T and Anderson K C 2005 Proteasome inhibition as a novel therapeutic target in human cancer;J. Clin. Oncol. 23 630–639
Ramos P C, Hockendorff J, Johnson E S, Varshavsky A and Dohmen R J 1998 Ump1p is required for proper maturation of the 20S proteasome and becomes its substrate upon completion of the assembly;Cell 92 489–499
Rao H, Uhlmann F, Nasmyth K and Varshavsky A 2001 Degradation of a cohesin subunit by the N-end rule pathway is essential for chromosome stability;Nature (London) 410 955–959
Rechsteiner M and Hill C P 2005 Mobilizing the proteolytic machine: cell biological roles of proteasome activators and inhibitors;Trends Cell. Biol. 15 7–33
Reits E A, Benham A M, Plougastel B, Neefjes J and Trowsdale J 1997 Dynamics of proteasome distribution in living cells;EMBO J. 16 6087–6094
Richard I, Roudaut C, Marchand S, Baghdiguian S, Herasse M, Stockholm D, Ono Y, Suel L, Bourg N, Sorimachi H, Lefranc G, Fardeau M, Sebille A and Beckmann J S 2000 Loss of calpain 3 proteolytic activity leads to muscular dystrophy and to apoptosis-associated IkappaBalpha/nuclear factor kappaB pathway perturbation in mice;J. Cell. Biol. 151 1583–1590
Rock K L, Gramm C, Rothstein L, Clark K, Stein R, Dick L, Hwang D and Goldberg A L 1994 Inhibitors of the proteasome block the degradation of most cell proteins and the generation of peptides presented on MHC class I molecules;Cell 78 761–771
Ruepp A, Eckerskorn C, Bogyo M and Baumeister W 1998 Proteasome function is dispensable under normal but not under heat shock conditions inThermoplasma acidophilum;FEBS Lett. 425 87–90
Sassetti C M, Boyd D H and Rubin E J 2003 Genes required for mycobacterial growth defined by high density mutagenesis;Mol. Microbiol. 48 77–84
Schauber C, Chen L, Tongaonkar P, Vega I, Lambertson D, Potts W and Madura K 1998 Rad23 links DNA repair to the ubiquitin/proteasome pathway;Nature (London) 391 715–718
Schmid H P, Akhayat O, Martins De Sa C, Puvion F, Koehler K and Scherrer K 1984 The prosome: an ubiquitous morphologically distinct RNP particle associated with repressed mRNPs and containing specific ScRNA and a characteristic set of proteins;EMBO J. 3 29–34
Schwechheimer C 2004 The COP9 signalosome (CSN): an evolutionary conserved proteolysis regulator in eukaryotic development;Biochim. Biophys. Acta 1695 45–54
Seemuller E, Lupas A, Stock D, Lowe J, Huber R and Baumeister W 1995 Proteasome fromThermoplasma acidophilum: a threonine protease;Science 268 579–582
Semple C A, Riken Ger Group and GSL Members 2003 The comparative proteomics of ubiquitination in mouse;Genome Res. 13 1389–1394
Soza A, Knuehl C, Groettrup M, Henklein P, Tanaka K and Kloetzel P M 1997 Expression and subcellular localization of mouse 20S proteasome activator complex PA28;FEBS Lett. 413 27–34
Staub O, Gautschi I, Ishikawa T, Breitschopf K, Ciechanover A, Schild L and Rotin D 1997 Regulation of stability and function of the epithelial Na+ channel (ENaC) by ubiquitination;EMBO J. 16 6325–6336
Sun X M, Butterworth M, MacFarlane M, Dubiel W, Ciechanover A and Cohen G M 2004 Caspase activation inhibits proteasome function during apoptosis;Mol. Cell. 14 81–93
Tanaka K, Ii K, Ichihara A, Waxman L and Goldberg A L 1986 A high molecular weight protease in the cytosol of rat liver. I. Purification, enzymological properties, and tissue distribution;J. Biol. Chem. 261 15197–15203
Tanaka K, Yoshimura T and Ichihara A 1989 Role of substrate in reversible activation of proteasomes (multi-protease complexes) by sodium dodecyl sulfate;J. Biochem. (Tokyo) 106 495–500
Turk V, Turk B and Turk D 2001 Lysosomal cysteine proteases: facts and opportunities;EMBO. J. 20 4629–4633
Unno M, Mizushima T, Morimoto Y, Tomisugi Y, Tanaka K, Yasuoka N and Tsukihara T 2002 The structure of the mammalian 20S proteasome at 2.75 Å resolution;Structure (Camb). 10 609–618
Ustrell V, Hoffman L, Pratt G and Rechsteiner M 2002 PA200, a nuclear proteasome activator involved in DNA repair;EMBO J. 21 3516–3525
Van Kaer L, Ashton-Rickardt P G, Eichelberger M, Gaczynska M, Nagashima K, Rock K L, Goldberg A L, Doherty P C and Tonegawa S 1994 Altered peptidase and viral-specific T cell response in LMP2 mutant mice;Immunity 1 533–541
Varshavsky A 2005 Regulated protein degradation;Trends Biochem Sci. 30 283–286
Vassilev L T, Vu B T, Graves B, Carvajal D, Podlaski F, Filipovic Z, Kong N, Kammlott U, Lukacs C, Klein C, Fotouhi N and Liu E A 2004In vivo activation of the p53 pathway by small-molecule antagonists of MDM2;Science 303 844–848
Velichutina I, Connerly P L, Arendt C S, Li X and Hochstrasser M 2004 Plasticity in eucaryotic 20S proteasome ring assembly revealed by a subunit deletion in yeast;EMBO J. 23 500–510
Verma R, Chen S, Feldman R, Schieltz D, Yates J, Dohmen J and Deshaies R J 2000 Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes;Mol. Biol. Cell. 11 3425–3439
Verma R, Aravind L, Oania R, McDonald W H, Yates J R 3rd, Koonin E V and Deshaies R J 2002 Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome;Science 298 611–615
Voges D, Zwickl P and Baumeister W 1999 The 26S proteasome: a molecular machine designed for controlled proteolysis;Annu. Rev. Biochem. 68 1015–10168
Wang H R, Kania M, Baumeister W and Nederlof P M 1997 Import of human and Thermoplasma 20S proteasomes into nuclei of HeLA cells requires functional NLS sequences;Eur. J. Cell. Biol. 73 105–113
Ward C L, Omura S and Kopito R R 1995 Degradation of CFTR by the ubiquitin-proteasome pathway;Cell 83 121–127
Weissman A M 2001 Themes and variations on ubiquitylation;Nat. Rev. Mol. Cell. Biol. 2 169–178
Whitby F G, Masters E I, Kramer L, Knowlton J R, Yao Y, Wang C C and Hill C P 2000 Structural basis for the activation of 20S proteasomes by 11S regulators;Nature (London) 408 115–120
Wigley W C, Fabunmi R P, Lee M G, Marino C R, Muallem S, DeMartino G N and Thomas P J 1999 Dynamic association of proteasomal machinery with the centrosome;J. Cell. Biol. 145 481–490
Wilk S and Orlowski M 1983 Evidence that pituitary cation-sensitive neutral endopeptidase is a multicatalytic protease complex;J. Neurochem. 40 842–849
Wilkinson K D, Urban M K and Haas A L 1980 Ubiquitin is the ATP-dependent proteolysis factor I of rabbit reticulocytes;J. Biol. Chem. 255 7529–7532
Wilkinson C R, Wallace M, Morphew M, Perry P, Allshire R, Javerzat J P, McIntosh J R and Gordon C 1998 Localization of the 26S proteasome during mitosis and meiosis in fission yeast;EMBO. J. 17 6465–6476
Witt E, Zantopf D, Schmidt M, Kraft R, Kloetzel P M and Kruger E 2000 Characterisation of the newly identified human Ump1 homologue POMP and analysis of LMP7 (β5i) incorporation into 20S proteasomes;J. Mol. Biol. 30 1–9
Wojcik C and DeMartino G N 2003 Intracellular localization of proteasomes;Int. J. Biochem. Cell. Biol. 35 579–589
Yao T and Cohen R E2002 A cryptic protease couples deubiquitination and degradation by the proteasome;Nature (London) 419 403–407
Yen H C, Gordon C and Chang E C 2003Schizosaccharomyces pombe Int6 and Ras homologs regulate cell division and mitotic fidelity via the proteasome;Cell 112 207–217
Zaiss D M, Standera S, Holzhutter H, Kloetzel P and Sijts A J 1999 The proteasome inhibitor PI31 competes with PA28 for binding to 20S proteasomes;FEBSLett. 457 333–338
Zaiss D M, Standera S, Kloetzel P M and Sijts A J 2002 PI31 is a modulator of proteasome formation and antigen processing;Proc. Natl. Acad. Sci. USA 99 14344–14349
Zhang Z, Clawson A and Rechsteiner M 1998a The proteasome activator 11 S regulator or PA28. Contribution By both alpha and beta subunits to proteasome activation;J. Biol. Chem. 273 30660–30668
Zhang Z, Clawson A, Realini C, Jensen C C, Knowlton J R, Hill C P and Rechsteiner M 1998b Identification of an activation region in the proteasome activator REGalpha;Proc. Natl. Acad. Sci. USA 95 2807–2811
Zwickl P, Kleinz J and Baumeister W 1994 Critical elements in proteasome assembly;Nat. Struct. Biol. 1 765–770
Zwickl P, Ng D, Woo K M, Klenk H P and Goldberg A L 1999 An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26 S proteasome, activates protein breakdown by 20 S proteasomes;J. Biol. Chem. 274 26008–26016
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Nandi, D., Tahiliani, P., Kumar, A. et al. The ubiquitin-proteasome system. J. Biosci. 31, 137–155 (2006). https://doi.org/10.1007/BF02705243
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DOI: https://doi.org/10.1007/BF02705243