Putting it all together: intrinsic and extrinsic mechanisms governing proteasome biogenesis

Lauren A. Howell, Robert J. Tomko Jr., Andrew R. Kusmierczyk

PDF(5711 KB)
PDF(5711 KB)
Front. Biol. ›› 2017, Vol. 12 ›› Issue (1) : 19-48. DOI: 10.1007/s11515-017-1439-1
REVIEW
REVIEW

Putting it all together: intrinsic and extrinsic mechanisms governing proteasome biogenesis

Author information +
History +

Abstract

BACKGROUND: The 26S proteasome is at the heart of the ubiquitin-proteasome system, which is the key cellular pathway for the regulated degradation of proteins and enforcement of protein quality control. The 26S proteasome is an unusually large and complicated protease comprising a 28-subunit core particle (CP) capped by one or two 19-subunit regulatory particles (RP). Multiple activities within the RP process incoming ubiquitinated substrates for eventual degradation by the barrel-shaped CP. The large size and elaborate architecture of the proteasome have made it an exceptional model for understanding mechanistic themes in macromolecular assembly.

OBJECTIVE: In the present work, we highlight the most recent mechanistic insights into proteasome assembly, with particular emphasis on intrinsic and extrinsic factors regulating proteasome biogenesis. We also describe new and exciting questions arising about how proteasome assembly is regulated and deregulated in normal and diseased cells.

METHODS: A comprehensive literature search using the PubMed search engine was performed, and key findings yielding mechanistic insight into proteasome assembly were included in this review.

RESULTS: Key recent studies have revealed that proteasome biogenesis is dependent upon intrinsic features of the subunits themselves as well as extrinsic factors, many of which function as dedicated chaperones.

CONCLUSION: Cells rely on a diverse set of mechanistic strategies to ensure the rapid, efficient, and faithful assembly of proteasomes from their cognate subunits. Importantly, physiological as well as pathological changes to proteasome assembly are emerging as exciting paradigms to alter protein degradation in vivo.

Keywords

proteasome assembly / assembly chaperones / ubiquitin-proteasome system / proteolysis / macromolecular complex

Cite this article

Download citation ▾
Lauren A. Howell, Robert J. Tomko Jr., Andrew R. Kusmierczyk. Putting it all together: intrinsic and extrinsic mechanisms governing proteasome biogenesis. Front. Biol., 2017, 12(1): 19‒48 https://doi.org/10.1007/s11515-017-1439-1

References

[1]
Agarwal A K, Xing C, DeMartino G N, Mizrachi D, Hernandez M D, Sousa A B, Martínez de Villarreal L, dos Santos H G, Garg A (2010). PSMB8 encoding the beta5i proteasome subunit is mutated in joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy syndrome. Am J Hum Genet, 87(6): 866–872
CrossRef Google scholar
[2]
Akahane T, Sahara K, Yashiroda H, Tanaka K, Murata S (2013). Involvement of Bag6 and the TRC pathway in proteasome assembly. Nat Commun, 4: 2234
CrossRef Google scholar
[3]
Arendt C S, Hochstrasser M (1997). Identification of the yeast 20S proteasome catalytic centers and subunit interactions required for active-site formation. Proc Natl Acad Sci USA, 94(14): 7156–7161
CrossRef Google scholar
[4]
Arendt C S, Hochstrasser M (1999). Eukaryotic 20S proteasome catalytic subunit propeptides prevent active site inactivation by N-terminal acetylation and promote particle assembly. EMBO J, 18(13): 3575–3585
CrossRef Google scholar
[5]
Arima K, Kinoshita A, Mishima H, Kanazawa N, Kaneko T, Mizushima T, Ichinose K, Nakamura H, Tsujino A, Kawakami A, Matsunaka M, Kasagi S, Kawano S, Kumagai S, Ohmura K, Mimori T, Hirano M, Ueno S, Tanaka K, Tanaka M, Toyoshima I, Sugino H, Yamakawa A, Tanaka K, Niikawa N, Furukawa F, Murata S, Eguchi K, Ida H, Yoshiura K (2011). Proteasome assembly defect due to a proteasome subunit beta type 8 (PSMB8) mutation causes the autoinflammatory disorder, Nakajo-Nishimura syndrome. Proc Natl Acad Sci USA, 108(36): 14914–14919
CrossRef Google scholar
[6]
Asano S, Fukuda Y, Beck F, Aufderheide A, Forster F, Danev R, Baumeister W (2015). Proteasomes. A molecular census of 26S proteasomes in intact neurons. Science, 347(6220): 439–442
CrossRef Google scholar
[7]
Aufderheide A, Beck F, Stengel F, Hartwig M, Schweitzer A, Pfeifer G, Goldberg A L, Sakata E, Baumeister W, Förster F (2015). Structural characterization of the interaction of Ubp6 with the 26S proteasome. Proc Natl Acad Sci USA, 112(28): 8626–8631
CrossRef Google scholar
[8]
Bader M, Benjamin S, Wapinski O L, Smith D M, Goldberg A L, Steller H (2011). A conserved f box regulatory complex controls proteasome activity in Drosophila. Cell, 145(3): 371–382
CrossRef Google scholar
[9]
Bai M, Zhao X, Sahara K, Ohte Y, Hirano Y, Kaneko T, Yashiroda H, Murata S (2014). Assembly mechanisms of specialized core particles of the proteasome. Biomolecules, 4(3): 662–677
CrossRef Google scholar
[10]
Barrault M B, Richet N, Godard C, Murciano B, Le Tallec B, Rousseau E, Legrand P, Charbonnier J B, Le Du M H, Guerois R, Ochsenbein F, Peyroche A (2012). Dual functions of the Hsm3 protein in chaperoning and scaffolding regulatory particle subunits during the proteasome assembly. Proc Natl Acad Sci USA, 109(17): E1001–E1010
CrossRef Google scholar
[11]
Barthelme D, Chen J Z, Grabenstatter J, Baker T A, Sauer R T (2014). Architecture and assembly of the archaeal Cdc48•20S proteasome. Proc Natl Acad Sci USA, 111(17): E1687–E1694
CrossRef Google scholar
[12]
Barthelme D, Jauregui R, Sauer RT (2015). An ALS disease mutation in Cdc48/p97 impairs 20S proteasome binding and proteolytic communication. Protein Sci, 24:1521–1527
[13]
Barthelme D, Sauer R T (2012a). Identification of the Cdc48•20S proteasome as an ancient AAA+ proteolytic machine. Science, 337(6096): 843–846
CrossRef Google scholar
[14]
Barthelme D, Sauer RT (2012b). Identification of the Cdc48•20S proteasome as an ancient AAA+ proteolytic machine. Science, 337(6096): 843–846
[15]
Barthelme D, Sauer R T (2013). Bipartite determinants mediate an evolutionarily conserved interaction between Cdc48 and the 20S peptidase. Proc Natl Acad Sci USA, 110(9): 3327–3332
CrossRef Google scholar
[16]
Bashore C, Dambacher C M, Goodall E A, Matyskiela M E, Lander G C, Martin A (2015). Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome. Nat Struct Mol Biol, 22(9): 712–719
CrossRef Google scholar
[17]
Basler M, Kirk C J, Groettrup M (2013). The immunoproteasome in antigen processing and other immunological functions. Curr Opin Immunol, 25(1): 74–80
CrossRef Google scholar
[18]
Beck F, Unverdorben P, Bohn S, Schweitzer A, Pfeifer G, Sakata E, Nickell S, Plitzko J M, Villa E, Baumeister W, Forster F (2012). Near-atomic resolution structural model of the yeast 26S proteasome. Proc Natl Acad Sci USA, 109(37): 14870–14875
CrossRef Google scholar
[19]
Beckwith R, Estrin E, Worden E J, Martin A (2013). Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase. Nat Struct Mol Biol, 20(10): 1164–1172
CrossRef Google scholar
[20]
Benaroudj N, Goldberg A L (2000). PAN, the proteasome-activating nucleotidase from archaebacteria, is a protein-unfolding molecular chaperone. Nat Cell Biol, 2(11): 833–839
CrossRef Google scholar
[21]
Braun B C, Glickman M, Kraft R, Dahlmann B, Kloetzel P M, Finley D, Schmidt M (1999). The base of the proteasome regulatory particle exhibits chaperone-like activity. Nat Cell Biol, 1(4): 221–226
CrossRef Google scholar
[22]
Burri L, Hockendorff J, Boehm U, Klamp T, Dohmen R J, Levy F (2000). Identification and characterization of a mammalian protein interacting with 20S proteasome precursors. Proc Natl Acad Sci USA, 97(19): 10348–10353
CrossRef Google scholar
[23]
Cascio P (2014). PA28alphabeta: the enigmatic magic ring of the proteasome? Biomolecules, 4(2): 566–584
CrossRef Google scholar
[24]
Chen P, Hochstrasser M (1996). Autocatalytic subunit processing couples active site formation in the 20S proteasome to completion of assembly. Cell, 86(6): 961–972
CrossRef Google scholar
[25]
Chu-Ping M, Slaughter C A, DeMartino G N (1992). Purification and characterization of a protein inhibitor of the 20S proteasome (macropain). Biochim Biophys Acta, 1119(3): 303–311
CrossRef Google scholar
[26]
Cohen-Kaplan V, Livneh I, Avni N, Fabre B, Ziv T, Kwon Y T, Ciechanover A (2016). p62- and ubiquitin-dependent stress-induced autophagy of the mammalian 26S proteasome. Proc Natl Acad Sci USA, 113(47): E7490–E7499
CrossRef Google scholar
[27]
Colot H V, Park G, Turner G E, Ringelberg C, Crew C M, Litvinkova L, Weiss R L, Borkovich K A, Dunlap J C (2006). A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci USA, 103(27): 10352–10357
CrossRef Google scholar
[28]
da Fonseca P C, He J, Morris E P (2012). Molecular Model of the Human 26S Proteasome. Mol Cell, 46(1): 54–66
CrossRef Google scholar
[29]
Dahlqvist J, Klar J, Tiwari N, Schuster J, Törmä H, Badhai J, Pujol R, van Steensel M A M, Brinkhuizen T, Gijezen L, Chaves A, Tadini G, Vahlquist A, Dahl N (2010). A single-nucleotide deletion in the POMP 5′ UTR causes a transcriptional switch and altered epidermal proteasome distribution in KLICK genodermatosis. Am J Hum Genet, 86(4): 596–603
CrossRef Google scholar
[30]
Dambacher C M, Worden E J, Herzik M A, Martin A, Lander G C (2016). Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition. eLife, 5: e13027
CrossRef Google scholar
[31]
Dange T, Smith D, Noy T, Rommel P C, Jurzitza L, Cordero R J B, Legendre A, Finley D, Goldberg A L, Schmidt M (2011). Blm10 protein promotes proteasomal substrate turnover by an active gating mechanism. J Biol Chem, 286(50): 42830–42839
CrossRef Google scholar
[32]
De M, Jayarapu K, Elenich L, Monaco J J, Colbert R A, Griffin T A (2003). Beta 2 subunit propeptides influence cooperative proteasome assembly. J Biol Chem, 278(8): 6153–6159
CrossRef Google scholar
[33]
De La Mota-Peynado A, Lee S Y, Pierce B M, Wani P, Singh C R, Roelofs J (2013). The proteasome-associated protein Ecm29 inhibits proteasomal ATPase activity and in vivo protein degradation by the proteasome. J Biol Chem, 288(41): 29467–29481
CrossRef Google scholar
[34]
DeMartino G N, Proske R J, Moomaw C R, Strong A A, Song X, Hisamatsu H, Tanaka K, Slaughter C A (1996). Identification, purification, and characterization of a PA700-dependent activator of the proteasome. J Biol Chem, 271(6): 3112–3118
CrossRef Google scholar
[35]
Ding W X, Ni H M, Gao W, Yoshimori T, Stolz D B, Ron D, Yin X M (2007). Linking of autophagy to ubiquitin-proteasome system is important for the regulation of endoplasmic reticulum stress and cell viability. Am J Pathol, 171(2): 513–524
CrossRef Google scholar
[36]
Driscoll J, Brown M G, Finley D, Monaco J J (1993). MHC-linked LMP gene products specifically alter peptidase activities of the proteasome. Nature, 365(6443): 262–264
CrossRef Google scholar
[37]
Enenkel C, Lehmann A, Kloetzel P M (1998). Subcellular distribution of proteasomes implicates a major location of protein degradation in the nuclear envelope-ER network in yeast. EMBO J, 17(21): 6144–6154
CrossRef Google scholar
[38]
Estrin E, Lopez-Blanco J R, Chacon P, Martin A (2013). Formation of an Intricate Helical Bundle Dictates the Assembly of the 26S Proteasome Lid. Structure, 21(9): 1624–1635
CrossRef Google scholar
[39]
Fehlker M, Wendler P, Lehmann A, Enenkel C (2003). Blm3 is part of nascent proteasomes and is involved in a late stage of nuclear proteasome assembly. EMBO Rep, 4(10): 959–963
CrossRef Google scholar
[40]
Finley D (2009). Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem, 78(1): 477–513
CrossRef Google scholar
[41]
Forouzan D, Ammelburg M, Hobel C F, Stroh L J, Sessler N, Martin J, Lupas A N (2012). The archaeal proteasome is regulated by a network of AAA ATPases. J Biol Chem, 287(46): 39254–39262
CrossRef Google scholar
[42]
Forster A, Masters E I, Whitby F G, Robinson H, Hill C P (2005). The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Mol Cell, 18(5): 589–599
CrossRef Google scholar
[43]
Fort P, Kajava A V, Delsuc F, Coux O (2015). Evolution of proteasome regulators in eukaryotes. Genome Biol Evol, 7(5): 1363–1379
CrossRef Google scholar
[44]
Frentzel S, Pesold-Hurt B, Seelig A, 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(4): 975–981
CrossRef Google scholar
[45]
Fricke B, Heink S, Steffen J, Kloetzel P M, Kruger E (2007). The proteasome maturation protein POMP facilitates major steps of 20S proteasome formation at the endoplasmic reticulum. EMBO Rep, 8(12): 1170–1175
CrossRef Google scholar
[46]
Fukunaga K, Kudo T, Toh-e A, Tanaka K, Saeki Y (2010). Dissection of the assembly pathway of the proteasome lid in Saccharomyces cerevisiae. Biochem Biophys Res Commun, 396(4): 1048–1053
CrossRef Google scholar
[47]
Funakoshi M, Tomko R J Jr, Kobayashi H, Hochstrasser M (2009). Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base. Cell, 137(5): 887–899
CrossRef Google scholar
[48]
Gaczynska M, Rock K L, Goldberg A L (1993). Gamma-interferon and expression of MHC genes regulate peptide hydrolysis by proteasomes. Nature, 365(6443): 264–267
CrossRef Google scholar
[49]
Gerards W L, Enzlin J, Häner M, Hendriks I LA M, Aebi U , Bloemendal H, Boelens W (1997). The human alpha-type proteasomal subunit HsC8 forms a double ringlike structure, but does not assemble into proteasome-like particles with the beta-type subunits HsDelta or HsBPROS26. J Biol Chem, 272(15): 10080–10086
CrossRef Google scholar
[50]
Gerards W L, de Jong W W, Bloemendal H, Boelens W (1998). The human proteasomal subunit HsC8 induces ring formation of other alpha-type subunits. J Mol Biol, 275(1): 113–121
CrossRef Google scholar
[51]
Ghaemmaghami S, Huh W K, Bower K, Howson R W, Belle A, Dephoure N, O’Shea E K, Weissman J S (2003). Global analysis of protein expression in yeast. Nature, 425(6959): 737–741
CrossRef Google scholar
[52]
Gille C, Goede A, Schlöetelburg C, Preißner R, Kloetzel P M, Göbel U B, Frömmel C (2003). A comprehensive view on proteasomal sequences: implications for the evolution of the proteasome. J Mol Biol, 326(5): 1437–1448
CrossRef Google scholar
[53]
Gillette T G, Kumar B, Thompson D, Slaughter C A, DeMartino G N (2008). Differential roles of the COOH termini of AAA subunits of PA700 (19 S regulator) in asymmetric assembly and activation of the 26 S proteasome. J Biol Chem, 283(46): 31813–31822
CrossRef Google scholar
[54]
Gomes A V (2013). Genetics of proteasome diseases. Scientifica (Cairo), 2013: 637629
CrossRef Google scholar
[55]
Gragnoli C, Cronsell J (2007). PSMD9 gene variants within NIDDM2 may rarely contribute to type 2 diabetes. J Cell Physiol, 212(3): 568–571
CrossRef Google scholar
[56]
Griffin T A, Nandi D, Cruz M, Fehling H J, Kaer L V, Monaco J J, Colbert R A (1998). Immunoproteasome assembly: cooperative incorporation of interferon gamma (IFN-gamma)-inducible subunits. J Exp Med, 187(1): 97–104
CrossRef Google scholar
[57]
Griffin T A, Slack J P, McCluskey T S, Monaco J J, 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(4): 212–217
CrossRef Google scholar
[58]
Groettrup M, Standera S, Stohwasser R, Kloetzel P M (1997). The subunits MECL-1 and LMP2 are mutually required for incorporation into the 20S proteasome. Proc Natl Acad Sci USA, 94(17): 8970–8975
CrossRef Google scholar
[59]
Groll M, Brandstetter H, Bartunik H, Bourenkow G, Huber R (2003). Investigations on the maturation and regulation of archaebacterial proteasomes. J Mol Biol, 327(1): 75–83
CrossRef Google scholar
[60]
Groll M, Ditzel L, Löwe J, Stock D, Bochtler M, Bartunik H D, Huber R (1997). Structure of 20S proteasome from yeast at 2.4 A resolution. Nature, 386(6624): 463–471
CrossRef Google scholar
[61]
Groll M, Glickman M H, Finley D, Bajorek M, Köhler A, Moroder L, Rubin D M, Huber R (2000). A gated channel into the proteasome core particle. Nat Struct Biol, 7(11): 1062–1067
CrossRef Google scholar
[62]
Groll M, Heinemeyer W, Jager S, Ullrich T, Bochtler M, Wolf D H, 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(20): 10976–10983
CrossRef Google scholar
[63]
Haarer B, Aggeli D, Viggiano S, Burke D J, Amberg D C (2011). Novel interactions between actin and the proteasome revealed by complex haploinsufficiency. PLoS Genet, 7(9): e1002288
CrossRef Google scholar
[64]
Hanssum A, Zhong Z, Rousseau A, Krzyzosiak A, Sigurdardottir A, Bertolotti A (2014). An inducible chaperone adapts proteasome assembly to stress. Mol Cell, 55(4): 566–577
CrossRef Google scholar
[65]
Hatanaka A, Chen B, Sun J Q, Mano Y, Funakoshi M, Kobayashi H, Ju Y, Mizutani T, Shinmyozu K, Nakayama J, Miyamoto K, Uchida H, Oki M (2011). Fub1p, a novel protein isolated by boundary screening, binds the proteasome complex. Genes Genet Syst, 86(5): 305–314
CrossRef Google scholar
[66]
Heinemeyer W, Fischer M, Krimmer T, Stachon U, Wolf D H (1997). The active sites of the eukaryotic 20 S proteasome and their involvement in subunit precursor processing. J Biol Chem, 272(40): 25200–25209
CrossRef Google scholar
[67]
Heink S, Ludwig D, Kloetzel P M, Kruger E (2005). IFN-gamma-induced immune adaptation of the proteasome system is an accelerated and transient response. Proc Natl Acad Sci USA, 102(26): 9241–9246
CrossRef Google scholar
[68]
Hirano Y, Hayashi H, Iemura S, Hendil K B, Niwa S, Kishimoto T, Kasahara M, Natsume T, Tanaka K, Murata S (2006). Cooperation of multiple chaperones required for the assembly of mammalian 20S proteasomes. Mol Cell, 24(6): 977–984
CrossRef Google scholar
[69]
Hirano Y, Hendil K B, Yashiroda H, Iemura S, Nagane R, Hioki Y, Natsume T, Tanaka K, Murata S (2005). A heterodimeric complex that promotes the assembly of mammalian 20S proteasomes. Nature, 437(7063): 1381–1385
CrossRef Google scholar
[70]
Hirano Y, Kaneko T, Okamoto K, Bai M, Yashiroda H, Furuyama K, Kato K, Tanaka K, Murata S (2008). Dissecting beta-ring assembly pathway of the mammalian 20S proteasome. EMBO J, 27(16): 2204–2213
CrossRef Google scholar
[71]
Hoang B, Benavides A, Shi Y, Frost P, Lichtenstein A (2009). Effect of autophagy on multiple myeloma cell viability. Mol Cancer Ther, 8(7): 1974–1984
CrossRef Google scholar
[72]
Hoefer M M, Boneberg E M, Grotegut S, Kusch J, Illges H (2006). Possible tetramerisation of the proteasome maturation factor POMP/proteassemblin/hUmp1 and its subcellular localisation. Int J Biol Macromol, 38(3-5): 259–267
CrossRef Google scholar
[73]
Huang X, Luan B, Wu J, Shi Y (2016). An atomic structure of the human 26S proteasome. Nat Struct Mol Biol, 23(9): 778–785
CrossRef Google scholar
[74]
Huber E M, Heinemeyer W, Li X, Arendt C S, Hochstrasser M, Groll M (2016). A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome. Nat Commun, 7: 10900
CrossRef Google scholar
[75]
Huh W K, Falvo J V, Gerke L C, Carroll A S, Howson R W, Weissman J S, O’Shea E K (2003). Global analysis of protein localization in budding yeast. Nature, 425(6959): 686–691
CrossRef Google scholar
[76]
Ishii K, Noda M, Yagi H, Thammaporn R, Seetaha S, Satoh T, Kato K, Uchiyama S (2015). Disassembly of the self-assembled, double-ring structure of proteasome alpha7 homo-tetradecamer by alpha6. Sci Rep, 5: 18167
CrossRef Google scholar
[77]
Isono E, Nishihara K, Saeki Y, Yashiroda H, Kamata N, Ge L, Ueda T, Kikuchi Y, Tanaka K, Nakano A, Toh-e A (2007). The assembly pathway of the 19S regulatory particle of the yeast 26S proteasome. Mol Biol Cell, 18(2): 569–580
CrossRef Google scholar
[78]
Iwata A, Riley B E, Johnston J A, Kopito R R (2005). HDAC6 and microtubules are required for autophagic degradation of aggregated huntingtin. J Biol Chem, 280(48): 40282–40292
CrossRef Google scholar
[79]
Jager S, Groll M, Huber R, Wolf D H, 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(4): 997–1013
CrossRef Google scholar
[80]
Ju D, Xie Y (2004). Proteasomal degradation of RPN4 via two distinct mechanisms, ubiquitin-dependent and-independent. J Biol Chem, 279(23): 23851–23854
CrossRef Google scholar
[81]
Kaganovich D, Kopito R, Frydman J (2008). Misfolded proteins partition between two distinct quality control compartments. Nature, 454(7208): 1088–1095
CrossRef Google scholar
[82]
Kaneko T, Hamazaki J, Iemura S, Sasaki K, Furuyama K, Natsume T, Tanaka K, Murata S (2009). Assembly pathway of the Mammalian proteasome base subcomplex is mediated by multiple specific chaperones. Cell, 137(5): 914–925
CrossRef Google scholar
[83]
Kim D U, Hayles J, Kim D, Wood V, Park H O, Won M, Yoo H S, Duhig T, Nam M, Palmer G, Han S, Jeffery L, Baek S T, Lee H, Shim Y S, Lee M, Kim L, Heo K S, Noh E J, Lee A R, Jang Y J, Chung K S, Choi S J, Park J Y, Park Y, Kim H M, Park S K, Park H J, Kang E J, Kim H B, Kang H S, Park H M, Kim K, Song K, Song K B, Nurse P, Hoe K L (2010a). Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol, 28(6): 617–623
CrossRef Google scholar
[84]
Kim S, Saeki Y, Fukunaga K, Suzuki A, Takagi K, Yamane T, Tanaka K, Mizushima T, Kato K (2010b). Crystal structure of yeast rpn14, a chaperone of the 19 S regulatory particle of the proteasome. J Biol Chem, 285(20): 15159–15166
CrossRef Google scholar
[85]
Kim Y C, Snoberger A, Schupp J, Smith D M (2015). ATP binding to neighbouring subunits and intersubunit allosteric coupling underlie proteasomal ATPase function. Nat Commun, 6(8520):1
[86]
Kingsbury D J, Griffin T A, Colbert R A (2000). Novel propeptide function in 20 S proteasome assembly influences beta subunit composition. J Biol Chem, 275(31): 24156–24162
CrossRef Google scholar
[87]
Kleijnen M F, Roelofs J, Park S, Hathaway N A, Glickman M, King R W, Finley D (2007). Stability of the proteasome can be regulated allosterically through engagement of its proteolytic active sites. Nat Struct Mol Biol, 14(12): 1180–1188
CrossRef Google scholar
[88]
Kloetzel P M (2004). Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII. Nat Immunol, 5(7): 661–669
CrossRef Google scholar
[89]
Kock M, Nunes M M, Hemann M, Kube S, Jürgen Dohmen R, Herzog F, Ramos P C, Wendler P (2015). Proteasome assembly from 15S precursors involves major conformational changes and recycling of the Pba1-Pba2 chaperone. Nat Commun, 6: 6123
CrossRef Google scholar
[90]
Koizumi S, Irie T, Hirayama S, Sakurai Y, Yashiroda H, Naguro I, Ichijo H, Hamazaki J, Murata S (2016). The aspartyl protease DDI2 activates Nrf1 to compensate for proteasome dysfunction. eLife, 5: e18357
[91]
Kragelund B B, Schenstrom S M, Rebula C A, Panse V G, Hartmann-Petersen R (2016). DSS1/Sem1, a multifunctional and intrinsically disordered protein. Trends Biochem Sci, 41(5): 446–459
CrossRef Google scholar
[92]
Kriegenburg F, Seeger M, Saeki Y, Tanaka K, Lauridsen A M B, Hartmann-Petersen R, Hendil K B (2008). Mammalian 26S proteasomes remain intact during protein degradation. Cell, 135(2): 355–365
CrossRef Google scholar
[93]
Kulak N A, Pichler G, Paron I, Nagaraj N, Mann M (2014). Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods, 11(3): 319–324
CrossRef Google scholar
[94]
Kusmierczyk A R, Hochstrasser M (2008). Some assembly required: dedicated chaperones in eukaryotic proteasome biogenesis. Biol Chem, 389(9): 1143–1151
CrossRef Google scholar
[95]
Kusmierczyk A R, Kunjappu M J, Funakoshi M, Hochstrasser M (2008). A multimeric assembly factor controls the formation of alternative 20S proteasomes. Nat Struct Mol Biol, 15(3): 237–244
CrossRef Google scholar
[96]
Kusmierczyk A R, Kunjappu M J, Kim R Y, Hochstrasser M (2011). A conserved 20S proteasome assembly factor requires a C-terminal HbYX motif for proteasomal precursor binding. Nat Struct Mol Biol, 18(5): 622–629
CrossRef Google scholar
[97]
Kwon Y D, Nagy I, Adams P D, Baumeister W, Jap B K (2004a). Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. J Mol Biol, 335(1): 233–245
CrossRef Google scholar
[98]
Kwon Y D, Nagy I, Adams P D, Baumeister W, Jap B K (2004b). Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. J Mol Biol, 335(1): 233–245
CrossRef Google scholar
[99]
Lander G C, Estrin E, Matyskiela M E, Bashore C, Nogales E, Martin A (2012). Complete subunit architecture of the proteasome regulatory particle. Nature, 482: 186–191
[100]
Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W (2012). Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA, 109(5): 1380–1387
CrossRef Google scholar
[101]
Le Tallec B, Barrault M B, Courbeyrette R, Guerois R, Marsolier-Kergoat M C, Peyroche A (2007). 20S proteasome assembly is orchestrated by two distinct pairs of chaperones in yeast and in mammals. Mol Cell, 27(4): 660–674
CrossRef Google scholar
[102]
Le Tallec B, Barrault M B, Guerois R, Carre T, Peyroche A (2009). Hsm3/S5b participates in the assembly pathway of the 19S regulatory particle of the proteasome. Mol Cell, 33(3): 389–399
CrossRef Google scholar
[103]
Lee S C, Shaw B D (2007). A novel interaction between N-myristoylation and the 26S proteasome during cell morphogenesis. Mol Microbiol, 63(4): 1039–1053
CrossRef Google scholar
[104]
Lee S Y, De la Mota-Peynado A, Roelofs J (2011). Loss of Rpt5 protein interactions with the core particle and Nas2 protein causes the formation of faulty proteasomes that are inhibited by Ecm29 protein. J Biol Chem, 286(42): 36641–36651
CrossRef Google scholar
[105]
Leggett D S, Hanna J, Borodovsky A, Crosas B, Schmidt M, Baker R T, Walz T, Ploegh H, Finley D (2002). Multiple associated proteins regulate proteasome structure and function. Mol Cell, 10(3): 495–507
CrossRef Google scholar
[106]
Lehmann A, Janek K, Braun B, Kloetzel P M, Enenkel C (2002). 20 S proteasomes are imported as precursor complexes into the nucleus of yeast. J Mol Biol, 317(3): 401–413
CrossRef Google scholar
[107]
Lehmann A, Niewienda A, Jechow K, Janek K, Enenkel C (2010). Ecm29 fulfils quality control functions in proteasome assembly. Mol Cell, 38(6): 879–888
CrossRef Google scholar
[108]
Lehrbach N J, Ruvkun G (2016). Proteasome dysfunction triggers activation of SKN-1A/Nrf1 by the aspartic protease DDI-1. eLife, 5: e17721
[109]
Lek M, Karczewski K J, Minikel E V, Samocha K E, Banks E, Fennell T, O’Donnell-Luria A H, Ware J S, Hill A J, Cummings B B, Tukiainen T, Birnbaum D P, Kosmicki J A, Duncan L E, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper D N, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki M I, Moonshine A L, Natarajan P, Orozco L, Peloso G M, Poplin R, Rivas M A, Ruano-Rubio V, Rose S A, Ruderfer D M, Shakir K, Stenson P D, Stevens C, Thomas B P, Tiao G, Tusie-Luna M T, Weisburd B, Won H H, Yu D, Altshuler D M, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez J C, Gabriel S B, Getz G, Glatt S J, Hultman C M, Kathiresan S, Laakso M, McCarroll S, McCarthy M I, McGovern D, McPherson R, Neale B M, Palotie A, Purcell S M, Saleheen D, Scharf J M, Sklar P, Sullivan P F, Tuomilehto J, Tsuang M T, Watkins H C, Wilson J G, Daly M J, MacArthur D G (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616): 285–291
CrossRef Google scholar
[110]
Li D, Dong Q, Tao Q, Gu J, Cui Y, Jiang X, Yuan J, Li W, Xu R, Jin Y, Li P, Weaver D T, Ma Q, Liu X, Cao C (2015). c-Abl regulates proteasome abundance by controlling the ubiquitin-proteasomal degradation of PSMA7 subunit. Cell Reports, 10(4): 484–496
CrossRef Google scholar
[111]
Li J, Zou C, Bai Y, Wazer D E, Band V, Gao Q (2006). DSS1 is required for the stability of BRCA2. Oncogene, 25(8): 1186–1194
CrossRef Google scholar
[112]
Li X, Kusmierczyk A R, Wong P, Emili A, Hochstrasser M (2007). beta-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint. EMBO J, 26(9): 2339–2349
CrossRef Google scholar
[113]
Li X, Li Y, Arendt C S, Hochstrasser M (2016). Distinct elements in the proteasomal beta5 subunit propeptide required for autocatalytic processing and proteasome assembly. J Biol Chem, 291(4): 1991–2003
CrossRef Google scholar
[114]
Li X, Thompson D, Kumar B, DeMartino G N (2014). Molecular and cellular roles of PI31 (PSMF1) protein in regulation of proteasome function. J Biol Chem, 289(25): 17392–17405
CrossRef Google scholar
[115]
Liu J, Yuan X, Liu J, Tian L, Quan J, Liu J, Chen X, Wang Y, Shi Z, Zhang J (2012). Validation of the association between PSMA6 -8 C/G polymorphism and type 2 diabetes mellitus in Chinese Dongxiang and Han populations. Diabetes Res Clin Pract, 98(2): 295–301
CrossRef Google scholar
[116]
Lowe J, Stock D, Jap B, Zwickl P, Baumeister W, Huber R (1995). Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. Science, 268(5210): 533–539
CrossRef Google scholar
[117]
Luan B, Huang X, Wu J, Mei Z, Wang Y, Xue X, Yan C, Wang J, Finley D J, Shi Y, Wang F (2016). Structure of an endogenous yeast 26S proteasome reveals two major conformational states. Proc Natl Acad Sci USA, 113(10): 2642–2647
CrossRef Google scholar
[118]
Mannhaupt G, Schnall R, Karpov V, Vetter I, Feldmann H (1999). 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(1-2): 27–34
CrossRef Google scholar
[119]
Mao I, Liu J, Li X, Luo H (2008). REGgamma, a proteasome activator and beyond? Cellular and molecular life sciences. Cell Mol Life Sci, 65: 3971–3980
CrossRef Google scholar
[120]
Marques A J, Glanemann C, Ramos P C, Dohmen R J (2007). The C-terminal extension of the beta7 subunit and activator complexes stabilize nascent 20 S proteasomes and promote their maturation. J Biol Chem, 282(48): 34869–34876
CrossRef Google scholar
[121]
Marshall R S, Li F, Gemperline D C, Book A J, Vierstra R D (2015). Autophagic degradation of the 26S proteasome is mediated by the dual ATG8/ubiquitin receptor RPN10 in Arabidopsis. Mol Cell, 58(6): 1053–1066
CrossRef Google scholar
[122]
Marshall R S, McLoughlin F, Vierstra R D (2016). Autophagic turnover of inactive 26S Proteasomes in yeast is directed by the ubiquitin receptor Cue5 and the Hsp42 chaperone. Cell Reports, 16(6): 1717–1732
CrossRef Google scholar
[123]
Matyskiela M E, Lander G C, Martin A (2013). Conformational switching of the 26S proteasome enables substrate degradation. Nat Struct Mol Biol, 20(7): 781–788
CrossRef Google scholar
[124]
Mayr J, Seemuller E, Muller S A, Engel A, Baumeister W (1998a). Late events in the assembly of 20S proteasomes. J Struct Biol, 124(2-3): 179–188
CrossRef Google scholar
[125]
Mayr J, Seemuller E, Muller S A, Engel A, Baumeister W (1998b). Late events in the assembly of 20S proteasomes. J Struct Biol, 124(2-3): 179–188
CrossRef Google scholar
[126]
Mayr J, Wang H R, Nederlof P, Baumeister W (1999). The import pathway of human and Thermoplasma 20S proteasomes into HeLa cell nuclei is different from that of classical NLS-bearing proteins. Biol Chem, 380(10): 1183–1192
CrossRef Google scholar
[127]
Meiners S, Heyken D, Weller A, Ludwig A, Stangl K, Kloetzel P M, Kruger E (2003). Inhibition of proteasome activity induces concerted expression of proteasome genes and de novo formation of Mammalian proteasomes. J Biol Chem, 278(24): 21517–21525
CrossRef Google scholar
[128]
Murata S, Sasaki K, Kishimoto T, Niwa S, Hayashi H, Takahama Y, Tanaka K (2007). Regulation of CD8+ T cell development by thymus-specific proteasomes. Science, 316(5829): 1349–1353
CrossRef Google scholar
[129]
Nakamura Y, Umehara T, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S (2007). Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome. Biochem Biophys Res Commun, 359(3): 503–509
CrossRef Google scholar
[130]
Nandi D, Woodward E, Ginsburg D B, Monaco J J (1997). Intermediates in the formation of mouse 20S proteasomes: implications for the assembly of precursor beta subunits. EMBO J, 16(17): 5363–5375
CrossRef Google scholar
[131]
Nederlof P M, Wang H R, Baumeister W (1995). Nuclear localization signals of human and Thermoplasma proteasomal alpha subunits are functional in vitro. Proc Natl Acad Sci USA, 92(26): 12060–12064
CrossRef Google scholar
[132]
Pack C G, Yukii H, Toh-e A, Kudo T, Tsuchiya H, Kaiho A, Sakata E, Murata S, Yokosawa H, Sako Y, Baumeister W, Tanaka K, Saeki Y (2014). Quantitative live-cell imaging reveals spatio-temporal dynamics and cytoplasmic assembly of the 26S proteasome. Nat Commun, 5: 3396
CrossRef Google scholar
[133]
Padmanabhan A, Vuong S A, Hochstrasser M (2016). Assembly of an evolutionarily conserved alternative proteasome isoform in human cells. Cell Reports, 14(12): 2962–2974
CrossRef Google scholar
[134]
Pandey U B, Nie Z, Batlevi Y, McCray B A, Ritson G P, Nedelsky N B, Schwartz S L, DiProspero N A, Knight M A, Schuldiner O, Padmanabhan R, Hild M, Berry D L, Garza D, Hubbert C C, Yao T P, Baehrecke E H, Taylor J P (2007). HDAC6 rescues neurodegeneration and provides an essential link between autophagy and the UPS. Nature, 447(7146): 859–863
CrossRef Google scholar
[135]
Panfair D, Ramamurthy A, Kusmierczyk A R (2015). Alpha-ring independent assembly of the 20S proteasome. Sci Rep, 5: 13130
CrossRef Google scholar
[136]
Paraskevopoulos K, Kriegenburg F, Tatham M H, Rösner H I, Medina B, Larsen I B, Brandstrup R, Hardwick K G, Hay R T, Kragelund B B, Hartmann-Petersen R, Gordon C (2014). Dss1 is a 26S proteasome ubiquitin receptor. Mol Cell, 56(3): 453–461
CrossRef Google scholar
[137]
Park S, Kim W, Tian G, Gygi S P, Finley D (2011). Structural defects in the regulatory particle-core particle interface of the proteasome induce a novel proteasome stress response. J Biol Chem, 286(42): 36652–36666
CrossRef Google scholar
[138]
Park S, Li X, Kim H M, Singh C R, Tian G, Hoyt M A, Lovell S, Battaile K P, Zolkiewski M, Coffino P, Roelofs J, Cheng Y, Finley D (2013). Reconfiguration of the proteasome during chaperone-mediated assembly. Nature, 497(7450): 512–516
CrossRef Google scholar
[139]
Park S, Roelofs J, Kim W, Robert J, Schmidt M, Gygi S P, Finley D (2009). Hexameric assembly of the proteasomal ATPases is templated through their C termini. Nature, 459(7248): 866–870
CrossRef Google scholar
[140]
Pathare G R, Nagy I, Sledz P, Anderson D J, Zhou H J, Pardon E, Steyaert J, Forster F, Bracher A, Baumeister W (2014). Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11. Proc Natl Acad Sci USA, 111(8): 2984–2989
CrossRef Google scholar
[141]
Peters L Z, Karmon O, David-Kadoch G, Hazan R, Yu T, Glickman M H, Ben-Aroya S (2015). The protein quality control machinery regulates its misassembled proteasome subunits. PLoS Genet, 11(4): e1005178
CrossRef Google scholar
[142]
Radhakrishnan S K, den Besten W, Deshaies R J (2014). p97-dependent retrotranslocation and proteolytic processing govern formation of active Nrf1 upon proteasome inhibition. eLife, 3: e01856
CrossRef Google scholar
[143]
Radhakrishnan S K, Lee C S, Young P, Beskow A, Chan J Y, Deshaies R J (2010). Transcription factor Nrf1 mediates the proteasome recovery pathway after proteasome inhibition in mammalian cells. Mol Cell, 38(1): 17–28
CrossRef Google scholar
[144]
Ramos P C, Hockendorff J, Johnson E S, Varshavsky A, 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(4): 489–499
CrossRef Google scholar
[145]
Ramos P C, Marques A J, London M K, Dohmen R J (2004). Role of C-terminal extensions of subunits beta2 and beta7 in assembly and activity of eukaryotic proteasomes. J Biol Chem, 279(14): 14323–14330
CrossRef Google scholar
[146]
Reits E A, Benham A M, Plougastel B, Neefjes J, Trowsdale J (1997). Dynamics of proteasome distribution in living cells. EMBO J, 16(20): 6087–6094
CrossRef Google scholar
[147]
Roelofs J, Park S, Haas W, Tian G, McAllister F E, Huo Y, Lee B H, Zhang F, Shi Y, Gygi S P, Finley D (2009). Chaperone-mediated pathway of proteasome regulatory particle assembly. Nature, 459(7248): 861–865
CrossRef Google scholar
[148]
Russell S J, Steger K A, Johnston S A (1999). Subcellular localization, stoichiometry, and protein levels of 26 S proteasome subunits in yeast. J Biol Chem, 274(31): 21943–21952
CrossRef Google scholar
[149]
Sa-Moura B, Simões A M, Fraga J, Fernandes H, Abreu I A, Botelho H M, Gomes C M, Marques A J, Dohmen R J, Ramos P C, Macedo-Ribeiro S (2013). Biochemical and biophysical characterization of recombinant yeast proteasome maturation factor ump1. Comput Struct Biotechnol J, 7(8): e201304006
CrossRef Google scholar
[150]
Sadre-Bazzaz K, Whitby F G, Robinson H, Formosa T, Hill C P (2010). Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening. Mol Cell, 37(5): 728–735
CrossRef Google scholar
[151]
Saeki Y, Toh E A, Kudo T, Kawamura H, Tanaka K (2009). Multiple proteasome-interacting proteins assist the assembly of the yeast 19S regulatory particle. Cell, 137(5): 900–913
CrossRef Google scholar
[152]
Sakata E, Stengel F, Fukunaga K, Zhou M, Saeki Y, Förster F, Baumeister W, Tanaka K, Robinson C V (2011). The catalytic activity of Ubp6 enhances maturation of the proteasomal regulatory particle. Mol Cell, 42(5): 637–649
CrossRef Google scholar
[153]
Satoh T, Saeki Y, Hiromoto T, Wang Y H, Uekusa Y, Yagi H, Yoshihara H, Yagi-Utsumi M, Mizushima T, Tanaka K, Kato K (2014). Structural basis for proteasome formation controlled by an assembly chaperone nas2. Structure, 22(5): 731–743
CrossRef Google scholar
[154]
Savulescu A F, Shorer H, Kleifeld O, Cohen I, Gruber R, Glickman M H, Harel A (2011). Nuclear import of an intact preassembled proteasome particle. Mol Biol Cell, 22(6): 880–891
CrossRef Google scholar
[155]
Schmidt M, Haas W, Crosas B, Santamaria P G, Gygi S P, Walz T, Finley D (2005). The HEAT repeat protein Blm10 regulates the yeast proteasome by capping the core particle. Nat Struct Mol Biol, 12(4): 294–303
CrossRef Google scholar
[156]
Schmidtke G, Kraft R, Kostka S, Henklein P, Frömmel C, Löwe J, Huber R, Kloetzel P M, Schmidt M (1996). Analysis of mammalian 20S proteasome biogenesis: the maturation of beta-subunits is an ordered two-step mechanism involving autocatalysis. EMBO J, 15: 6887–6898
[157]
Schmidtke G, Schmidt M, Kloetzel P M (1997). Maturation of mammalian 20 S proteasome: purification and characterization of 13 S and 16 S proteasome precursor complexes. J Mol Biol, 268(1): 95–106
CrossRef Google scholar
[158]
Schweitzer A, Aufderheide A, Rudack T, Beck F, Pfeifer G, Plitzko J M, Sakata E, Schulten K, Förster F, Baumeister W (2016). Structure of the human 26S proteasome at a resolution of 3.9 A. Proc Natl Acad Sci USA, 113(28): 7816–7821
CrossRef Google scholar
[159]
Sha Z, Goldberg A L (2014). Proteasome-mediated processing of Nrf1 is essential for coordinate induction of all proteasome subunits and p97. Curr Biol, 24(14): 1573–1583
CrossRef Google scholar
[160]
Sharon M, Taverner T, Ambroggio X I, Deshaies R J, Robinson C V (2006). Structural organization of the 19S proteasome lid: insights from MS of intact complexes. PLoS Biol, 4(8): e267
CrossRef Google scholar
[161]
Sharon M, Witt S, Glasmacher E, Baumeister W, Robinson C V (2007). Mass spectrometry reveals the missing links in the assembly pathway of the bacterial 20 S proteasome. J Biol Chem, 282(25): 18448–18457
CrossRef Google scholar
[162]
Shi Y, Chen X, Elsasser S, Stocks B B, Tian G, Lee B H, Shi Y, Zhang N, de Poot S A H, Tuebing F, Sun S, Vannoy J, Tarasov S G, Engen J R, Finley D, Walters K J (2016). Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Science
CrossRef Google scholar
[163]
Shirozu R, Yashiroda H, Murata S (2015). Identification of minimum Rpn4-responsive elements in genes related to proteasome functions. FEBS Lett, 589(8): 933–940
CrossRef Google scholar
[164]
Singh C R, Lovell S, Mehzabeen N, Chowdhury W Q, Geanes E S, Battaile K P, Roelofs J (2014). 1.15 A resolution structure of the proteasome-assembly chaperone Nas2 PDZ domain. Acta Crystallogr F Struct Biol Commun, 70(4): 418–423
CrossRef Google scholar
[165]
Sledz P, Unverdorben P, Beck F, Pfeifer G, Schweitzer A, Forster F, Baumeister W (2013). Structure of the 26S proteasome with ATP-gammaS bound provides insights into the mechanism of nucleotide-dependent substrate translocation. Proc Natl Acad Sci USA, 110(18): 7264–7269
CrossRef Google scholar
[166]
Smith D M, Chang S C, Park S, Finley D, Cheng Y, Goldberg A L (2007). Docking of the proteasomal ATPases’ carboxyl termini in the 20S proteasome’s alpha ring opens the gate for substrate entry. Mol Cell, 27(5): 731–744
CrossRef Google scholar
[167]
Sokolova V, Li F, Polovin G, Park S (2015). Proteasome activation is mediated via a functional switch of the Rpt6 C-terminal tail following chaperone-dependent assembly. Sci Rep, 5: 14909
CrossRef Google scholar
[168]
Stadtmueller B M, Hill C P (2011). Proteasome activators. Mol Cell, 41(1): 8–19
CrossRef Google scholar
[169]
Stadtmueller B M, Kish-Trier E, Ferrell K, Petersen C N, Robinson H, Myszka D G, Eckert D M, Formosa T, Hill C P (2012). Structure of a proteasome Pba1-Pba2 complex: implications for proteasome assembly, activation, and biological function. J Biol Chem, 287(44): 37371–37382
CrossRef Google scholar
[170]
Takagi K, Kim S, Yukii H, Ueno M, Morishita R, Endo Y, Kato K, Tanaka K, Saeki Y, Mizushima T (2012). Structural basis for specific recognition of Rpt1p, an ATPase subunit of 26S proteasome, by proteasome-dedicated chaperone Hsm3p. J Biol Chem, 287(15): 12172–12182
CrossRef Google scholar
[171]
Takagi K, Saeki Y, Yashiroda H, Yagi H, Kaiho A, Murata S, Yamane T, Tanaka K, Mizushima T, Kato K (2014). Pba3-Pba4 heterodimer acts as a molecular matchmaker in proteasome alpha-ring formation. Biochem Biophys Res Commun, 450(2): 1110–1114
CrossRef Google scholar
[172]
Takeuchi J, Tamura T (2004). Recombinant ATPases of the yeast 26S proteasome activate protein degradation by the 20S proteasome. FEBS Lett, 565(1-3): 39–42
CrossRef Google scholar
[173]
Tanaka K, Yoshimura T, Tamura T, Fujiwara T, Kumatori A, Ichihara A (1990). Possible mechanism of nuclear translocation of proteasomes. FEBS Lett, 271(1-2): 41–46
CrossRef Google scholar
[174]
Thompson D, Hakala K, DeMartino G N (2009). Subcomplexes of PA700, the 19S regulator of the 26 S proteasome, reveal relative roles of AAA subunits in 26 S proteasome assembly and activation and ATPase activity. J Biol Chem, 284(37): 24891–24903
CrossRef Google scholar
[175]
Tian G, Park S, Lee M J, Huck B, McAllister F, Hill C P, Gygi S P, Finley D (2011). An asymmetric interface between the regulatory and core particles of the proteasome. Nat Struct Mol Biol, 18(11): 1259–1267
CrossRef Google scholar
[176]
Tomko R J Jr, Funakoshi M, Schneider K, Wang J, Hochstrasser M (2010). Heterohexameric ring arrangement of the eukaryotic proteasomal ATPases: implications for proteasome structure and assembly. Mol Cell, 38(3): 393–403
CrossRef Google scholar
[177]
Tomko R J Jr, Hochstrasser M (2011). Incorporation of the Rpn12 subunit couples completion of proteasome regulatory particle lid assembly to lid-base joining. Mol Cell, 44(6): 907–917
CrossRef Google scholar
[178]
Tomko R J Jr, Hochstrasser M (2013). Molecular architecture and assembly of the eukaryotic proteasome. Annu Rev Biochem, 82(1): 415–445
CrossRef Google scholar
[179]
Tomko R J Jr, Hochstrasser M (2014). The intrinsically disordered Sem1 protein functions as a molecular tether during proteasome lid biogenesis. Mol Cell, 53(3): 433–443
CrossRef Google scholar
[180]
Tomko R J Jr, Taylor D W, Chen Z A, Wang H W, Rappsilber J, Hochstrasser M (2015). A Single alpha helix drives extensive remodeling of the proteasome lid and completion of regulatory particle assembly. Cell, 163(2): 432–444
CrossRef Google scholar
[181]
Uekusa Y, Okawa K, Yagi-Utsumi M, Serve O, Nakagawa Y, Mizushima T, Yagi H, Saeki Y, Tanaka K, Kato K (2014). Backbone (1)H, (1)(3)C and (1)(5)N assignments of yeast Ump1, an intrinsically disordered protein that functions as a proteasome assembly chaperone. Biomol NMR Assign, 8(2): 383–386
CrossRef Google scholar
[182]
Unno M, Mizushima T, Morimoto Y, Tomisugi Y, Tanaka K, Yasuoka N, Tsukihara T (2002). The structure of the mammalian 20S proteasome at 2.75 A resolution. Structure, 10(5): 609–618
CrossRef Google scholar
[183]
Unverdorben P, Beck F, led P, Schweitzer A, Pfeifer G, Plitzko J M, Baumeister W, Forster F (2014). Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome. Proc Natl Acad Sci USA, 111(15): 5544–5549
CrossRef Google scholar
[184]
Ustrell V, Hoffman L, Pratt G, Rechsteiner M (2002). PA200, a nuclear proteasome activator involved in DNA repair. EMBO J, 21(13): 3516–3525
CrossRef Google scholar
[185]
Velichutina I, Connerly P L, Arendt C S, Li X, Hochstrasser M (2004). Plasticity in eucaryotic 20S proteasome ring assembly revealed by a subunit deletion in yeast. EMBO J, 23(3): 500–510
CrossRef Google scholar
[186]
Verma R, (2002). Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science, 298(5593): 611–615
CrossRef Google scholar
[187]
Volker C, Lupas A N (2002). Molecular evolution of proteasomes. Curr Top Microbiol Immunol, 268: 1–22
CrossRef Google scholar
[188]
Waite K A, De-La Mota-Peynado A, Vontz G, Roelofs J (2016). Starvation induces proteasome autophagy with different pathways for core and regulatory particles. J Biol Chem, 291(7): 3239–3253
CrossRef Google scholar
[189]
Wang H R, Kania M, Baumeister W, 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
[190]
Wang W, Chan J Y (2006). Nrf1 is targeted to the endoplasmic reticulum membrane by an N-terminal transmembrane domain. Inhibition of nuclear translocation and transacting function. J Biol Chem, 281(28): 19676–19687
CrossRef Google scholar
[191]
Wani P S, Rowland M A, Ondracek A, Deeds E J, Roelofs J (2015). Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association. Nat Commun, 6: 6384
CrossRef Google scholar
[192]
Wani P S, Suppahia A, Capalla X, Ondracek A, Roelofs J (2016). Phosphorylation of the C-terminal tail of proteasome subunit alpha7 is required for binding of the proteasome quality control factor Ecm29. Sci Rep, 6: 27873
CrossRef Google scholar
[193]
Weberruss M H, Savulescu A F, Jando J, Bissinger T, Harel A, Glickman M H, Enenkel C (2013). Blm10 facilitates nuclear import of proteasome core particles. EMBO J, 32(20): 2697–2707
CrossRef Google scholar
[194]
Wei S J, Williams J G, Dang H, Darden T A, Betz B L, Humble M M, Chang F M, Trempus C S, Johnson K, Cannon R E, Tennant R W (2008). Identification of a specific motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. J Mol Biol, 383(3): 693–712
CrossRef Google scholar
[195]
Welk V, Coux O, Kleene V, Abeza C, Trümbach D, Eickelberg O, Meiners S (2016). Inhibition of proteasome activity induces formation of alternative proteasome complexes. J Biol Chem, 291(25): 13147–13159
CrossRef Google scholar
[196]
Wendler P, Lehmann A, Janek K, Baumgart S, Enenkel C (2004). The bipartite nuclear localization sequence of Rpn2 is required for nuclear import of proteasomal base complexes via karyopherin alphabeta and proteasome functions. J Biol Chem, 279(36): 37751–37762
CrossRef Google scholar
[197]
Whitby F G, Masters E I, Kramer L, Knowlton J R, Yao Y, Wang C C, Hill C P (2000). Structural basis for the activation of 20S proteasomes by 11S regulators. Nature, 408(6808): 115–120
CrossRef Google scholar
[198]
Witt E, Zantopf D, Schmidt M, Kraft R, Kloetzel P M, Kruger E (2000). Characterisation of the newly identified human Ump1 homologue POMP and analysis of LMP7(beta 5i) incorporation into 20 S proteasomes. J Mol Biol, 301(1): 1–9
CrossRef Google scholar
[199]
Wollenberg K, Swaffield J C (2001). Evolution of proteasomal ATPases. Mol Biol Evol, 18(6): 962–974
CrossRef Google scholar
[200]
Worden E J, Padovani C, Martin A (2014). Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat Struct Mol Biol, 21(3): 220–227
CrossRef Google scholar
[201]
Xie Y, Varshavsky A (2001). RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit. Proc Natl Acad Sci USA, 98(6): 3056–3061
CrossRef Google scholar
[202]
Yao T, Cohen R E (2002). A cryptic protease couples deubiquitination and degradation by the proteasome. Nature, 419(6905): 403–407
CrossRef Google scholar
[203]
Yao Y, Toth C R, Huang L, Wong M L, Dias P, Burlingame A L, Coffino P, Wang C C (1999). alpha5 subunit in Trypanosoma brucei proteasome can self-assemble to form a cylinder of four stacked heptamer rings. Biochem J, 344(Pt 2): 349–358
[204]
Yashiroda H, Mizushima T, Okamoto K, Kameyama T, Hayashi H, Kishimoto T, Niwa S, Kasahara M, Kurimoto E, Sakata E, Takagi K, Suzuki A, Hirano Y, Murata S, Kato K, Yamane T, Tanaka K (2008). Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes. Nat Struct Mol Biol, 15(3): 228–236
CrossRef Google scholar
[205]
Yashiroda H, Toda Y, Otsu S, Takagi K, Mizushima T, Murata S (2015). N-terminal alpha7 deletion of the proteasome 20S core particle substitutes for yeast PI31 function. Mol Cell Biol, 35(1): 141–152
CrossRef Google scholar
[206]
Yu Y, Smith D M, Kim H M, Rodriguez V, Goldberg A L, Cheng Y (2010). Interactions of PAN’s C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions. EMBO J, 29(3): 692–702
CrossRef Google scholar
[207]
Yu Z, Livnat-Levanon N, Kleifeld O, Mansour W, Nakasone M A, Castaneda C A, Dixon E K, Fushman D, Reis N, Pick E, Glickman M H (2015). Base-CP proteasome can serve as a platform for stepwise lid formation. Biosci Rep, 35(3): e00194
CrossRef Google scholar
[208]
Zaiss D M, Standera S, Kloetzel P M, Sijts A J (2002). PI31 is a modulator of proteasome formation and antigen processing. Proc Natl Acad Sci USA, 99(22): 14344–14349
CrossRef Google scholar
[209]
Zhang F, Hu M, Tian G, Zhang P, Finley D, Jeffrey P D, Shi Y (2009). Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol Cell, 34(4): 473–484
CrossRef Google scholar
[210]
Zhang Y, Lucocq J M, Yamamoto M, Hayes J D (2007). The NHB1 (N-terminal homology box 1) sequence in transcription factor Nrf1 is required to anchor it to the endoplasmic reticulum and also to enable its asparagine-glycosylation. Biochem J, 408(2): 161–172
CrossRef Google scholar
[211]
Zhu K, Dunner K Jr, McConkey D J (2010). Proteasome inhibitors activate autophagy as a cytoprotective response in human prostate cancer cells. Oncogene, 29(3): 451–462
CrossRef Google scholar
[212]
Zuhl F, Seemuller E, Golbik R, Baumeister W (1997). Dissecting the assembly pathway of the 20S proteasome. FEBS Lett, 418(1-2): 189–194
CrossRef Google scholar
[213]
Zwickl P, Kleinz J, Baumeister W (1994). Critical elements in proteasome assembly. Nat Struct Biol, 1(11): 765–770
CrossRef Google scholar
[214]
Zwickl P, Ng D, Woo K M, Klenk H P, Goldberg A L (1999). An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26S proteasome, activates protein breakdown by 20 S proteasomes. J Biol Chem, 274(37): 26008–26014
CrossRef Google scholar

Acknowledgements

The authors apologize to their colleagues whose work could not be discussed due to space limitations. This work was supported in part by start-up funds from the Florida State University College of Medicine (R.J.T.Jr.) and by a Research Support Funds Grant from Indiana University-Purdue University Indianapolis (A.R.K.).

Compliance with ethics guidelines

Lauren A. Howell, Robert J. Tomko Jr. and Andrew R. Kusmierczyk declare that they have no conflict of interest. This article does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

2017 Higher Education Press and Springer-Verlag Berlin Heidelberg
PDF(5711 KB)

Accesses

Citations

Detail

Sections
Recommended

/