Cellular maintenance of nuclear protein homeostasis

Cellular and Molecular Life Sciences

Volumn 71, Issue 10, 2014, Pages 1865-1879

  Gallagher, Pamela S ^a   Oeser, Michelle L ^a,b   Abraham, Ayelet Chen ^c   Kaganovich, Daniel ^c   Gardner, Richard G ^a,b  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Aggregation; Aggresome; Chaperone; Inclusion; JUNQ; Misfolded protein; Nucleus; Proteasome; Ubiquitin; Ubiquitin protein ligase; Unfolded protein response

Indexed keywords

CELL PROTEIN; CHAPERONE; NUCLEAR PROTEIN; PROTEASOME; UBIQUITIN; UBIQUITIN PROTEIN LIGASE;

BIOACCUMULATION; CELL NUCLEUS; CELL STRESS; CELLULAR DISTRIBUTION; HUMAN; NONHUMAN; PROTEIN AGGREGATION; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN HOMEOSTASIS; PROTEIN LOCALIZATION; PROTEIN MISFOLDING; PROTEIN QUALITY CONTROL; REVIEW; SIGNAL TRANSDUCTION; SUMOYLATION;

CELL NUCLEUS; HOMEOSTASIS; HUMANS; MOLECULAR CHAPERONES; NUCLEAR PROTEINS; PROTEASOME ENDOPEPTIDASE COMPLEX; SIGNAL TRANSDUCTION; SUMOYLATION; UBIQUITIN; UBIQUITIN-PROTEIN LIGASES;

EID: 84900329183     PISSN: 1420682X     EISSN: 14209071     Source Type: Journal    
DOI: 10.1007/s00018-013-1530-y     Document Type: Review

References (163)

1. Balch WE, Morimoto RI, Dillin A, Kelly JW (2008) Adapting proteostasis for disease intervention. Science 319:916-919
2. Wang SS, Wu JW, Yamamoto S, Liu HS (2008) Diseases of protein aggregation and the hunt for potential pharmacological agents. Biotechnol J 3:165-192
3. Kikis EA, Gidalevitz T, Morimoto RI (2010) Protein homeostasis in models of aging and age-related conformational disease. Adv Exp Med Biol 694:138-159
4. Taylor RC, Dillin A (2011) Aging as an event of proteostasis collapse. Cold Spring Harb Perspect Biol 3:a004440
5. Voisine C, Pedersen JS, Morimoto RI (2010) Chaperone networks: tipping the balance in protein folding diseases. Neurobiol Dis 40:12-20
6. Chen B, Retzlaff M, Roos T, Frydman J (2011) Cellular strategies of protein quality control. Cold Spring Harb Perspect Biol 3:a004374
7. Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475:324-332
8. Fredrickson EK, Gardner RG (2012) Selective destruction of abnormal proteins by ubiquitin-mediated protein quality control degradation. Semin Cell Dev Biol 23:530-537
9. Sridhar S, Botbol Y, Macian F, Cuervo AM (2012) Autophagy and disease: always two sides to a problem. J Pathol 226:255-273
10. Arndt V, Rogon C, Hohfeld J (2007) To be, or not to be-molecular chaperones in protein degradation. Cell Mol Life Sci 64:2525-2541
11. Wickner S, Maurizi MR, Gottesman S (1999) Posttranslational quality control: folding, refolding, and degrading proteins. Science 286:1888-1893
12. Gardner BM, Pincus D, Gotthardt K, Gallagher CM, Walter P (2013) Endoplasmic reticulum stress sensing in the unfolded protein response. Cold Spring Harb Perspect Biol 5:a013169
13. Haynes CM, Fiorese CJ, Lin YF (2013) Evaluating and responding to mitochondrial dysfunction: the mitochondrial unfolded-protein response and beyond. Trends Cell Biol 23:311-318
14. Woulfe J (2008) Nuclear bodies in neurodegenerative disease. Biochim Biophys Acta 1783:2195-2206
15. Ross CA (2002) Polyglutamine pathogenesis: emergence of unifying mechanisms for Huntington's disease and related disorders. Neuron 35:819-822
16. Amiel J, Trochet D, Clement-Ziza M, Munnich A, Lyonnet S (2004) Polyalanine expansions in human. Hum Mol Genet 13 Spec No 2: R235-R243
17. David A, Dolan BP, Hickman HD, Knowlton JJ, Clavarino G, Pierre P, Bennink JR, Yewdell JW (2012) Nuclear translation visualized by ribosome-bound nascent chain puromycylation. J Cell Biol 197:45-57
18. Iborra FJ, Jackson DA, Cook PR (2001) Coupled transcription and translation within nuclei of mammalian cells. Science 293:1139-1142
19. Iborra FJ, Escargueil AE, Kwek KY, Akoulitchev A, Cook PR (2004) Molecular cross-talk between the transcription, translation, and nonsense-mediated decay machineries. J Cell Sci 117:899-906
20. Iborra FJ, Jackson DA, Cook PR (2004) The case for nuclear translation. J Cell Sci 117:5713-5720
21. Dahlberg JE, Lund E, Goodwin EB (2003) Nuclear translation: what is the evidence? RNA 9:1-8
22. Pederson T (2013) The persistent plausibility of protein synthesis in the nucleus: process, palimpsest or pitfall? Curr Opin Cell Biol 25:520-521
23. Nathanson L, Xia T, Deutscher MP (2003) Nuclear protein synthesis: a re-evaluation. RNA 9:9-13
24. Dahlberg J, Lund E (2012) Nuclear translation or nuclear peptidyl transferase? Nucleus 3:320-321
25. Grossman E, Medalia O, Zwerger M (2012) Functional architecture of the nuclear pore complex. Annu Rev Biophys 41:557-584
26. Pante N, Kann M (2002) Nuclear pore complex is able to transport macromolecules with diameters of about 39 nm. Mol Biol Cell 13:425-434
27. Dudek J, Rehling P, van der Laan M (2013) Mitochondrial protein import: common principles and physiological networks. Biochim Biophys Acta 1833:274-285
28. Johnson N, Powis K, High S (2012) Post-translational translocation into the endoplasmic reticulum. Biochim Biophys Acta 1833:2403-2409
29. Guerriero CJ, Weiberth KF, Brodsky JL (2013) Hsp70 targets a cytoplasmic quality control substrate to the San1p ubiquitin ligase. J Biol Chem 288:18506-18520
30. Heck JW, Cheung SK, Hampton RY (2010) Cytoplasmic protein quality control degradation mediated by parallel actions of the E3 ubiquitin ligases Ubr1 and San1. Proc Natl Acad Sci USA 107:1106-1111
31. Park SH, Kukushkin Y, Gupta R, Chen T, Konagai A, Hipp MS, Hayer-Hartl M, Hartl FU (2013) PolyQ proteins interfere with nuclear degradation of cytosolic proteins by sequestering the Sis1p chaperone. Cell 154:134-145
32. Prasad R, Kawaguchi S, Ng DT (2010) A nucleus-based quality control mechanism for cytosolic proteins. Mol Biol Cell 21:2117-2127
33. Prasad R, Kawaguchi S, Ng DT (2012) Biosynthetic mode can determine the mechanism of protein quality control. Biochem Biophys Res Commun 425:689-695
34. Summers DW, Wolfe KJ, Ren HY, Cyr DM (2013) The Type II Hsp40 Sis1 cooperates with Hsp70 and the E3 ligase Ubr1 to promote degradation of terminally misfolded cytosolic protein. PLoS ONE 8:e52099
35. Wojcik C, DeMartino GN (2003) Intracellular localization of proteasomes. Int J Biochem Cell Biol 35:579-589
36. D'Angelo MA, Raices M, Panowski SH, Hetzer MW (2009) Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. Cell 136:284-295
37. Arrasate M, Finkbeiner S (2012) Protein aggregates in Huntington's disease. Exp Neurol 238:1-11
38. DiFiglia M, Sapp E, Chase K, Schwarz C, Meloni A, Young C, Martin E, Vonsattel JP, Carraway R, Reeves SA et al (1995) Huntingtin is a cytoplasmic protein associated with vesicles in human and rat brain neurons. Neuron 14:1075-1081
39. DiFiglia M, Sapp E, Chase KO, Davies SW, Bates GP, Vonsattel JP, Aronin N (1997) Aggregation of huntingtin in neuronal intranuclear inclusions and dystrophic neurites in brain. Science 277:1990-1993
40. Peters MF, Nucifora FC Jr, Kushi J, Seaman HC, Cooper JK, Herring WJ, Dawson VL, Dawson TM, Ross CA (1999) Nuclear targeting of mutant Huntingtin increases toxicity. Mol Cell Neurosci 14:121-128
41. Schilling G, Savonenko AV, Klevytska A, Morton JL, Tucker SM, Poirier M, Gale A, Chan N, Gonzales V, Slunt HH, Coonfield ML, Jenkins NA, Copeland NG, Ross CA, Borchelt DR (2004) Nuclear-targeting of mutant huntingtin fragments produces Huntington's disease-like phenotypes in transgenic mice. Hum Mol Genet 13:1599-1610
42. Shen Y, Peterson AS (2009) Atrophins' emerging roles in development and neurodegenerative disease. Cell Mol Life Sci 66:437-446
43. Katsuno M, Tanaka F, Adachi H, Banno H, Suzuki K, Watanabe H, Sobue G (2012) Pathogenesis and therapy of spinal and bulbar muscular atrophy (SBMA). Prog Neurobiol 99:246-256
44. Brais B (2009) Oculopharyngeal muscular dystrophy: a polyalanine myopathy. Curr Neurol Neurosci Rep 9:76-82
45. Guigas G, Kalla C, Weiss M (2007) The degree of macromolecular crowding in the cytoplasm and nucleoplasm of mammalian cells is conserved. FEBS Lett 581:5094-5098
46. Guigas G, Kalla C, Weiss M (2007) Probing the nanoscale viscoelasticity of intracellular fluids in living cells. Biophys J 93:316-323
47. Clapier CR, Cairns BR (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem 78:273-304
48. Lempiainen H, Shore D (2009) Growth control and ribosome biogenesis. Curr Opin Cell Biol 21:855-863
49. Morris GE (2008) The Cajal body. Biochim Biophys Acta 1783:2108-2115
50. Lallemand-Breitenbach V, de The H (2010) PML nuclear bodies. Cold Spring Harb Perspect Biol 2:a000661
51. Dittmer TA, Misteli T (2011) The lamin protein family. Genome Biol 12:222
52. Schreiber KH, Kennedy BK (2013) When lamins go bad: nuclear structure and disease. Cell 152:1365-1375
53. Ehrlich ME (2012) Huntington's disease and the striatal medium spiny neuron: cell-autonomous and non-cell-autonomous mechanisms of disease. Neurotherapeutics 9:270-284
54. Desplats PA, Kass KE, Gilmartin T, Stanwood GD, Woodward EL, Head SR, Sutcliffe JG, Thomas EA (2006) Selective deficits in the expression of striatal-enriched mRNAs in Huntington's disease. J Neurochem 96:743-757
55. Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Ulrich Hartl F (2013) Molecular chaperone functions in protein folding and proteostasis. Annu Rev Biochem 82:323-355
56. Kriegenburg F, Ellgaard L, Hartmann-Petersen R (2012) Molecular chaperones in targeting misfolded proteins for ubiquitin-dependent degradation. FEBS J 279:532-542
57. Kodiha M, Chu A, Lazrak O, Stochaj U (2005) Stress inhibits nucleocytoplasmic shuttling of heat shock protein hsc70. Am J Physiol Cell Physiol 289:C1034-C1041
58. Welch WJ, Feramisco JR (1984) Nuclear and nucleolar localization of the 72,000-dalton heat shock protein in heat-shocked mammalian cells. J Biol Chem 259:4501-4513
59. Velazquez JM, Lindquist S (1984) hsp70: nuclear concentration during environmental stress and cytoplasmic storage during recovery. Cell 36:655-662
60. Pelham HR (1984) Hsp70 accelerates the recovery of nucleolar morphology after heat shock. EMBO J 3:3095-3100
61. Lamian V, Small GM, Feldherr CM (1996) Evidence for the existence of a novel mechanism for the nuclear import of Hsc70. Exp Cell Res 228:84-91
62. Kose S, Furuta M, Imamoto N (2012) Hikeshi, a nuclear import carrier for Hsp70s, protects cells from heat shock-induced nuclear damage. Cell 149:578-589
63. Imamoto N, Kose S (2012) Heat-shock stress activates a novel nuclear import pathway mediated by Hikeshi. Nucleus 3:422-428
64. Quan X, Rassadi R, Rabie B, Matusiewicz N, Stochaj U (2004) Regulated nuclear accumulation of the yeast hsp70 Ssa4p in ethanol-stressed cells is mediated by the N-terminal domain, requires the nuclear carrier Nmd5p and protein kinase C. FASEB J 18:899-901
65. Quan X, Tsoulos P, Kuritzky A, Zhang R, Stochaj U (2006) The carrier Msn5p/Kap142p promotes nuclear export of the hsp70 Ssa4p and relocates in response to stress. Mol Microbiol 62:592-609
66. Chughtai ZS, Rassadi R, Matusiewicz N, Stochaj U (2001) Starvation promotes nuclear accumulation of the hsp70 Ssa4p in yeast cells. J Biol Chem 276:20261-20266
67. Kawai R, Fujita K, Iwahashi H, Komatsu Y (1999) Direct evidence for the intracellular localization of Hsp104 in Saccharomyces cerevisiae by immunoelectron microscopy. Cell Stress Chaperones 4:46-53
68. Tkach JM, Glover JR (2008) Nucleocytoplasmic trafficking of the molecular chaperone Hsp104 in unstressed and heat-shocked cells. Traffic 9:39-56
69. Parsell DA, Kowal AS, Singer MA, Lindquist S (1994) Protein disaggregation mediated by heat-shock protein Hsp104. Nature 372:475-478
70. Willsie JK, Clegg JS (2002) Small heat shock protein p26 associates with nuclear lamins and HSP70 in nuclei and nuclear matrix fractions from stressed cells. J Cell Biochem 84:601-614
71. Rossi JM, Lindquist S (1989) The intracellular location of yeast heat-shock protein 26 varies with metabolism. J Cell Biol 108:425-439
72. Kodiha M, Chu A, Matusiewicz N, Stochaj U (2004) Multiple mechanisms promote the inhibition of classical nuclear import upon exposure to severe oxidative stress. Cell Death Differ 11:862-874
73. Czubryt MP, Austria JA, Pierce GN (2000) Hydrogen peroxide inhibition of nuclear protein import is mediated by the mitogen-activated protein kinase, ERK2. J Cell Biol 148:7-16
74. Miyamoto Y, Saiwaki T, Yamashita J, Yasuda Y, Kotera I, Shibata S, Shigeta M, Hiraoka Y, Haraguchi T, Yoneda Y (2004) Cellular stresses induce the nuclear accumulation of importin alpha and cause a conventional nuclear import block. J Cell Biol 165:617-623
75. Furuta M, Kose S, Koike M, Shimi T, Hiraoka Y, Yoneda Y, Haraguchi T, Imamoto N (2004) Heat-shock induced nuclear retention and recycling inhibition of importin alpha. Genes Cells 9:429-441
76. Kodiha M, Tran D, Qian C, Morogan A, Presley JF, Brown CM, Stochaj U (2008) Oxidative stress mislocalizes and retains transport factor importin-alpha and nucleoporins Nup153 and Nup88 in nuclei where they generate high molecular mass complexes. Biochim Biophys Acta 1783:405-418
77. Yasuda Y, Miyamoto Y, Saiwaki T, Yoneda Y (2006) Mechanism of the stress-induced collapse of the Ran distribution. Exp Cell Res 312:512-520
78. Kelley JB, Paschal BM (2007) Hyperosmotic stress signaling to the nucleus disrupts the Ran gradient and the production of RanGTP. Mol Biol Cell 18:4365-4376
79. Crampton N, Kodiha M, Shrivastava S, Umar R, Stochaj U (2009) Oxidative stress inhibits nuclear protein export by multiple mechanisms that target FG nucleoporins and Crm1. Mol Biol Cell 20:5106-5116
80. Waelter S, Boeddrich A, Lurz R, Scherzinger E, Lueder G, Lehrach H, Wanker EE (2001) Accumulation of mutant huntingtin fragments in aggresome-like inclusion bodies as a result of insufficient protein degradation. Mol Biol Cell 12:1393-1407
81. Abel A, Walcott J, Woods J, Duda J, Merry DE (2001) Expression of expanded repeat androgen receptor produces neurologic disease in transgenic mice. Hum Mol Genet 10:107-116
82. Jana NR, Tanaka M, Wang G, Nukina N (2000) Polyglutamine length-dependent interaction of Hsp40 and Hsp70 family chaperones with truncated N-terminal huntingtin: their role in suppression of aggregation and cellular toxicity. Hum Mol Genet 9:2009-2018
83. Bailey CK, Andriola IF, Kampinga HH, Merry DE (2002) Molecular chaperones enhance the degradation of expanded polyglutamine repeat androgen receptor in a cellular model of spinal and bulbar muscular atrophy. Hum Mol Genet 11:515-523
84. Adachi H, Katsuno M, Minamiyama M, Sang C, Pagoulatos G, Angelidis C, Kusakabe M, Yoshiki A, Kobayashi Y, Doyu M, Sobue G (2003) Heat shock protein 70 chaperone overexpression ameliorates phenotypes of the spinal and bulbar muscular atrophy transgenic mouse model by reducing nuclear-localized mutant androgen receptor protein. J Neurosci 23:2203-2211
85. Ishihara K, Yamagishi N, Saito Y, Adachi H, Kobayashi Y, Sobue G, Ohtsuka K, Hatayama T (2003) Hsp105alpha suppresses the aggregation of truncated androgen receptor with expanded CAG repeats and cell toxicity. J Biol Chem 278:25143-25150
86. Latouche M, Fragner P, Martin E, El Hachimi KH, Zander C, Sittler A, Ruberg M, Brice A, Stevanin G (2006) Polyglutamine and polyalanine expansions in ataxin7 result in different types of aggregation and levels of toxicity. Mol Cell Neurosci 31:438-445
87. Janer A, Martin E, Muriel MP, Latouche M, Fujigasaki H, Ruberg M, Brice A, Trottier Y, Sittler A (2006) PML clastosomes prevent nuclear accumulation of mutant ataxin-7 and other polyglutamine proteins. J Cell Biol 174:65-76
88. Seidel K, Meister M, Dugbartey GJ, Zijlstra MP, Vinet J, Brunt ER, van Leeuwen FW, Rub U, Kampinga HH, den Dunnen WF (2012) Cellular protein quality control and the evolution of aggregates in spinocerebellar ataxia type 3 (SCA3). Neuropathol Appl Neurobiol 38:548-558
89. Bao YP, Cook LJ, O'Donovan D, Uyama E, Rubinsztein DC (2002) Mammalian, yeast, bacterial, and chemical chaperones reduce aggregate formation and death in a cell model of oculopharyngeal muscular dystrophy. J Biol Chem 277:12263-12269
90. Corbeil-Girard LP, Klein AF, Sasseville AM, Lavoie H, Dicaire MJ, Saint-Denis A, Page M, Duranceau A, Codere F, Bouchard JP, Karpati G, Rouleau GA, Massie B, Langelier Y, Brais B (2005) PABPN1 overexpression leads to upregulation of genes encoding nuclear proteins that are sequestered in oculopharyngeal muscular dystrophy nuclear inclusions. Neurobiol Dis 18:551-567
91. Chartier A, Benoit B, Simonelig M (2006) A Drosophila model of oculopharyngeal muscular dystrophy reveals intrinsic toxicity of PABPN1. EMBO J 25:2253-2262
92. Tavanez JP, Bengoechea R, Berciano MT, Lafarga M, Carmo-Fonseca M, Enguita FJ (2009) Hsp70 chaperones and type I PRMTs are sequestered at intranuclear inclusions caused by polyalanine expansions in PABPN1. PLoS ONE 4:e6418
93. Fu L, Gao YS, Tousson A, Shah A, Chen TL, Vertel BM, Sztul E (2005) Nuclear aggresomes form by fusion of PML-associated aggregates. Mol Biol Cell 16:4905-4917
94. Fu L, Gao YS, Sztul E (2005) Transcriptional repression and cell death induced by nuclear aggregates of non-polyglutamine protein. Neurobiol Dis 20:656-665
95. Moran DM, Shen H, Maki CG (2009) Puromycin-based vectors promote a ROS-dependent recruitment of PML to nuclear inclusions enriched with HSP70 and Proteasomes. BMC Cell Biol 10:32
96. Ciechanover A (2012) Intracellular protein degradation: from a vague idea through the lysosome and the ubiquitin-proteasome system and onto human diseases and drug targeting. Neurodegener Dis 10:7-22
97. Finley D, Ulrich HD, Sommer T, Kaiser P (2012) The ubiquitin-proteasome system of Saccharomyces cerevisiae. Genetics 192:319-360
98. Dasgupta A, Ramsey KL, Smith JS, Auble DT (2004) Sir antagonist 1 (San1) is a ubiquitin ligase. J Biol Chem 279:26830-26838
99. Gardner RG, Nelson ZW, Gottschling DE (2005) Degradation-mediated protein quality control in the nucleus. Cell 120:803-815
100. Evans DR, Brewster NK, Xu Q, Rowley A, Altheim BA, Johnston GC, Singer RA (1998) The yeast protein complex containing cdc68 and pob3 mediates core-promoter repression through the cdc68 N-terminal domain. Genetics 150:1393-1405
101. Estruch F, Peiro-Chova L, Gomez-Navarro N, Durban J, Hodge C, Del Olmo M, Cole CN (2009) A genetic screen in Saccharomyces cerevisiae identifies new genes that interact with me67-5, a temperature-sensitive allele of the gene encoding the mRNA export receptor. Mol Genet Genomics 281:125-134
102. Lewis MJ, Pelham HR (2009) Inefficient quality control of thermosensitive proteins on the plasma membrane. PLoS ONE 4:e5038
103. Rosenbaum JC, Fredrickson EK, Oeser ML, Garrett-Engele CM, Locke MN, Richardson LA, Nelson ZW, Hetrick ED, Milac TI, Gottschling DE, Gardner RG (2011) Disorder targets misorder in nuclear quality control degradation: a disordered ubiquitin ligase directly recognizes its misfolded substrates. Mol Cell 41:93-106
104. Fredrickson EK, Gallagher PS, Clowes Candadai SV, Gardner RG (2013) Substrate recognition in nuclear protein quality control degradation is governed by exposed hydrophobicity that correlates with aggregation and insolubility. J Biol Chem 288:6130-6139
105. Fredrickson EK, Rosenbaum JC, Locke MN, Milac TI, Gardner RG (2011) Exposed hydrophobicity is a key determinant of nuclear quality control degradation. Mol Biol Cell 22:2384-2395
106. Fredrickson EK, Clowes Candadai SV, Tam CH, Gardner RG (2013) Means of self-preservation: how an intrinsically disordered ubiquitin-protein ligase averts self-destruction. Mol Biol Cell 24:1041-1052
107. Matsuo Y, Kishimoto H, Tanae K, Kitamura K, Katayama S, Kawamukai M (2011) Nuclear protein quality is regulated by the ubiquitin-proteasome system through the activity of Ubc4 and San1 in fission yeast. J Biol Chem 286:13775-13790
108. Iwata A, Nagashima Y, Matsumoto L, Suzuki T, Yamanaka T, Date H, Deoka K, Nukina N, Tsuji S (2009) Intra-nuclear degradation of polyglutamine aggregates by the ubiquitin proteasome system. J Biol Chem 284:9796-9803
109. Mishra A, Dikshit P, Purkayastha S, Sharma J, Nukina N, Jana NR (2008) E6-AP promotes misfolded polyglutamine proteins for proteasomal degradation and suppresses polyglutamine protein aggregation and toxicity. J Biol Chem 283:7648-7656
110. Tasaki T, Sriram SM, Park KS, Kwon YT (2012) The N-end rule pathway. Annu Rev Biochem 81:261-289
111. Sultana R, Theodoraki MA, Caplan AJ (2012) UBR1 promotes protein kinase quality control and sensitizes cells to Hsp90 inhibition. Exp Cell Res 318:53-60
112. Bartel B, Wunning I, Varshavsky A (1990) The recognition component of the N-end rule pathway. EMBO J 9:3179-3189
113. Xia Z, Webster A, Du F, Piatkov K, Ghislain M, Varshavsky A (2008) Substrate-binding sites of UBR1, the ubiquitin ligase of the N-end rule pathway. J Biol Chem 283:24011-24028
114. Varshavsky A (2011) The N-end rule pathway and regulation by proteolysis. Protein Sci 20:1298-1345
115. Shemorry A, Hwang CS, Varshavsky A (2013) Control of protein quality and stoichiometries by N-terminal acetylation and the N-end rule pathway. Mol Cell 50:540-551
116. Hwang CS, Shemorry A, Varshavsky A (2010) N-terminal acetylation of cellular proteins creates specific degradation signals. Science 327:973-977
117. Piatkov KI, Brower CS, Varshavsky A (2012) The N-end rule pathway counteracts cell death by destroying proapoptotic protein fragments. Proc Natl Acad Sci USA 109:E1839-E1847
118. Piatkov KI, Colnaghi L, Bekes M, Varshavsky A, Huang TT (2012) The auto-generated fragment of the Usp1 deubiquitylase is a physiological substrate of the N-end rule pathway. Mol Cell 48:926-933
119. Rao H, Uhlmann F, Nasmyth K, Varshavsky A (2001) Degradation of a cohesin subunit by the N-end rule pathway is essential for chromosome stability. Nature 410:955-959
120. Brower CS, Piatkov KI, Varshavsky A (2013) Neurodegeneration-associated protein fragments as short-lived substrates of the N-end rule pathway. Mol Cell 50:161-171
121. Eisele F, Wolf DH (2008) Degradation of misfolded protein in the cytoplasm is mediated by the ubiquitin ligase Ubr1. FEBS Lett 582:4143-4146
122. Kitamura K, Taki M, Tanaka N, Yamashita I (2011) Fission yeast Ubr1 ubiquitin ligase influences the oxidative stress response via degradation of active Pap1 bZIP transcription factor in the nucleus. Mol Microbiol 80:739-755
123. Swanson R, Locher M, Hochstrasser M (2001) A conserved ubiquitin ligase of the nuclear envelope/endoplasmic reticulum that functions in both ER-associated and Matalpha2 repressor degradation. Genes Dev 15:2660-2674
124. Huyer G, Piluek WF, Fansler Z, Kreft SG, Hochstrasser M, Brodsky JL, Michaelis S (2004) Distinct machinery is required in Saccharomyces cerevisiae for the endoplasmic reticulum-associated degradation of a multispanning membrane protein and a soluble luminal protein. J Biol Chem 279:38369-38378
125. Carvalho P, Goder V, Rapoport TA (2006) Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins. Cell 126:361-373
126. Ravid T, Kreft SG, Hochstrasser M (2006) Membrane and soluble substrates of the Doa10 ubiquitin ligase are degraded by distinct pathways. EMBO J 25:533-543
127. English AR, Voeltz GK (2013) Endoplasmic reticulum structure and interconnections with other organelles. Cold Spring Harb Perspect Biol 5:a013227
128. Deng M, Hochstrasser M (2006) Spatially regulated ubiquitin ligation by an ER/nuclear membrane ligase. Nature 443:827-831
129. Alfassy OS, Cohen I, Reiss Y, Tirosh B, Ravid T (2013) Placing a disrupted degradation motif at the C terminus of proteasome substrates attenuates degradation without impairing ubiquitylation. J Biol Chem 288:12645-12653
130. Furth N, Gertman O, Shiber A, Alfassy OS, Cohen I, Rosenberg MM, Doron NK, Friedler A, Ravid T (2011) Exposure of bipartite hydrophobic signal triggers nuclear quality control of Ndc10 at the endoplasmic reticulum/nuclear envelope. Mol Biol Cell 22:4726-4739
131. Kreft SG, Wang L, Hochstrasser M (2006) Membrane topology of the yeast endoplasmic reticulum-localized ubiquitin ligase Doa10 and comparison with its human ortholog TEB4 (MARCH-VI). J Biol Chem 281:4646-4653
132. Castro PH, Tavares RM, Bejarano ER, Azevedo H (2012) SUMO, a heavyweight player in plant abiotic stress responses. Cell Mol Life Sci 69:3269-3283
133. Tempe D, Piechaczyk M, Bossis G (2008) SUMO under stress. Biochem Soc Trans 36:874-878
134. Miller MJ, Scalf M, Rytz TC, Hubler SL, Smith LM, Vierstra RD (2013) Quantitative proteomics reveals factors regulating RNA biology as dynamic targets of stress-induced SUMOylation in Arabidopsis. Mol Cell Proteomics 12:449-463
135. Miller MJ, Barrett-Wilt GA, Hua Z, Vierstra RD (2010) Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis. Proc Natl Acad Sci USA 107:16512-16517
136. Golebiowski F, Matic I, Tatham MH, Cole C, Yin Y, Nakamura A, Cox J, Barton GJ, Mann M, Hay RT (2009) System-wide changes to SUMO modifications in response to heat shock. Sci Signal 2: ra24
137. Zhou W, Ryan JJ, Zhou H (2004) Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J Biol Chem 279:32262-32268
138. Uzunova K, Gottsche K, Miteva M, Weisshaar SR, Glanemann C, Schnellhardt M, Niessen M, Scheel H, Hofmann K, Johnson ES, Praefcke GJ, Dohmen RJ (2007) Ubiquitin-dependent proteolytic control of SUMO conjugates. J Biol Chem 282:34167-34175
139. Tatham MH, Matic I, Mann M, Hay RT (2011) Comparative proteomic analysis identifies a role for SUMO in protein quality control. Sci Signal 4: rs4
140. Marblestone JG, Edavettal SC, Lim Y, Lim P, Zuo X, Butt TR (2006) Comparison of SUMO fusion technology with traditional gene fusion systems: enhanced expression and solubility with SUMO. Protein Sci 15:182-189
141. Malakhov MP, Mattern MR, Malakhova OA, Drinker M, Weeks SD, Butt TR (2004) SUMO fusions and SUMO-specific protease for efficient expression and purification of proteins. J Struct Funct Genomics 5:75-86
142. Krumova P, Weishaupt JH (2013) Sumoylation in neurodegenerative diseases. Cell Mol Life Sci 70:2123-2138
143. Goedert M, Spillantini MG, Del Tredici K, Braak H (2013) 100 years of Lewy pathology. Nat Rev Neurol 9:13-24
144. Krumova P, Meulmeester E, Garrido M, Tirard M, Hsiao HH, Bossis G, Urlaub H, Zweckstetter M, Kugler S, Melchior F, Bahr M, Weishaupt JH (2011) Sumoylation inhibits alpha-synuclein aggregation and toxicity. J Cell Biol 194:49-60
145. Ryu J, Cho S, Park BC, Lee do H (2010) Oxidative stress-enhanced SUMOylation and aggregation of ataxin-1: implication of JNK pathway. Biochem Biophys Res Commun 393:280-285
146. Steffan JS, Agrawal N, Pallos J, Rockabrand E, Trotman LC, Slepko N, Illes K, Lukacsovich T, Zhu YZ, Cattaneo E, Pandolfi PP, Thompson LM, Marsh JL (2004) SUMO modification of Huntingtin and Huntington's disease pathology. Science 304:100-104
147. Mittler R, Finka A, Goloubinoff P (2012) How do plants feel the heat? Trends Biochem Sci 37:118-125
148. Morano KA, Grant CM, Moye-Rowley WS (2012) The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics 190:1157-1195
149. Morimoto RI (2011) The heat shock response: systems biology of proteotoxic stress in aging and disease. Cold Spring Harb Symp Quant Biol 76:91-99
150. Goldberg AL (2003) Protein degradation and protection against misfolded or damaged proteins. Nature 426:895-899
151. Caughey B, Lansbury PT (2003) Protofibrils, pores, fibrils, and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. Annu Rev Neurosci 26:267-298
152. Escusa-Toret S, Vonk WI, Frydman J (2013) Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness during stress. Nat Cell Biol 15:1231-1243
153. Kaganovich D, Kopito R, Frydman J (2008) Misfolded proteins partition between two distinct quality control compartments. Nature 454:1088-1095
154. Malinovska L, Kroschwald S, Munder MC, Richter D, Alberti S (2012) Molecular chaperones and stress-inducible protein-sorting factors coordinate the spatiotemporal distribution of protein aggregates. Mol Biol Cell 23:3041-3056
155. Spokoini R, Moldavski O, Nahmias Y, England JL, Schuldiner M, Kaganovich D (2012) Confinement to organelle-associated inclusion structures mediates asymmetric inheritance of aggregated protein in budding yeast. Cell Rep 2:738-747
156. Tyedmers J, Treusch S, Dong J, McCaffery JM, Bevis B, Lindquist S (2010) Prion induction involves an ancient system for the sequestration of aggregated proteins and heritable changes in prion fragmentation. Proc Natl Acad Sci USA 107:8633-8638
157. Johnston JA, Ward CL, Kopito RR (1998) Aggresomes: a cellular response to misfolded proteins. J Cell Biol 143:1883-1898
158. Weisberg SJ, Lyakhovetsky R, Werdiger AC, Gitler AD, Soen Y, Kaganovich D (2012) Compartmentalization of superoxide dismutase 1 (SOD1G93A) aggregates determines their toxicity. Proc Natl Acad Sci USA 109:15811-15816
159. Zhang X, Qian SB (2011) Chaperone-mediated hierarchical control in targeting misfolded proteins to aggresomes. Mol Biol Cell 22:3277-3288
160. Zaarur N, Meriin AB, Gabai VL, Sherman MY (2008) Triggering aggresome formation. Dissecting aggresome-targeting and aggregation signals in synphilin 1. J Biol Chem 283:27575-27584
161. Garcia-Mata R, Bebok Z, Sorscher EJ, Sztul ES (1999) Characterization and dynamics of aggresome formation by a cytosolic GFP-chimera. J Cell Biol 146:1239-1254
162. Wigley WC, Fabunmi RP, Lee MG, Marino CR, Muallem S, DeMartino GN, Thomas PJ (1999) Dynamic association of proteasomal machinery with the centrosome. J Cell Biol 145:481-490
163. Latonen L, Moore HM, Bai B, Jaamaa S, Laiho M (2011) Proteasome inhibitors induce nucleolar aggregation of proteasome target proteins and polyadenylated RNA by altering ubiquitin availability. Oncogene 30:790-805