Protein degradation and the stress response

Seminars in Cell and Developmental Biology

Volumn 23, Issue 5, 2012, Pages 515-522

  Flick, Karin ^a   Kaiser, Peter ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Stress sensors; Stress signaling; Ubiquitin ligases; Ubiquitin proteasome pathway

Indexed keywords

PROTEASOME; UBIQUITIN; UBIQUITIN PROTEASOME SYSTEM; UNCLASSIFIED DRUG;

AGING; ANEUPLOIDY; CELL STRESS; CELL TYPE; CELLULAR STRESS RESPONSE; CELLULAR STRESS SIGNAL; HEAT SHOCK; HUMAN; HYPOXIA; NEOPLASM; NEUROLOGIC DISEASE; NONHUMAN; PROTEIN DEGRADATION; PROTEIN MODIFICATION; REVIEW; SIGNAL TRANSDUCTION; UBIQUITINATION;

EUKARYOTA;

EID: 84863872261     PISSN: 10849521     EISSN: 10963634     Source Type: Journal    
DOI: 10.1016/j.semcdb.2012.01.019     Document Type: Review

References (86)

1. Buchberger A., Bukau B., Sommer T. Protein quality control in the cytosol and the endoplasmic reticulum: brothers in arms. Mol Cell 2010, 40:238-252.
2. Ciccia A., Elledge S.J. The DNA damage response: making it safe to play with knives. Mol Cell 2010, 40:179-204.
3. Kerscher O., Felberbaum R., Hochstrasser M. Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol 2006, 22:159-180.
4. Pickart C.M. Back to the future with ubiquitin. Cell 2004, 116:181-190.
5. Wilkinson K.D. Ubiquitination and deubiquitination: targeting of proteins for degradation by the proteasome. Semin Cell Dev Biol 2000, 11:141-148.
6. Ciechanover A., Orian A., Schwartz A.L. The ubiquitin-mediated proteolytic pathway: mode of action and clinical implications. J Cell Biochem Suppl 2000, 34:40-51.
7. Hershko A., Ciechanover A. The ubiquitin system. Annu Rev Biochem 1998, 67:425-479.
8. Tokunaga F., Sakata S., Saeki Y., Satomi Y., Kirisako T., Kamei K., et al. Involvement of linear polyubiquitylation of NEMO in NF-kappaB activation. Nat Cell Biol 2009, 11:123-132.
9. Rahighi S., Ikeda F., Kawasaki M., Akutsu M., Suzuki N., Kato R., et al. Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell 2009, 136:1098-1109.
10. Meierhofer D., Wang X., Huang L., Kaiser P. Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. J Proteome Res 2008, 7:4566-4576.
11. Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., et al. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol 2003, 21:921-926.
12. Li W., Bengtson M.H., Ulbrich A., Matsuda A., Reddy V.A., Orth A., et al. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling. PLoS One 2008, 3:e1487.
13. Ozkaynak E., Finley D., Solomon M.J., Varshavsky A. The yeast ubiquitin genes: a family of natural gene fusions. EMBO J 1987, 6:1429-1439.
14. Finley D., Ozkaynak E., Varshavsky A. The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses. Cell 1987, 48:1035-1046.
15. Fornace A.J., Alamo I., Hollander M.C., Lamoreaux E. Ubiquitin mRNA is a major stress-induced transcript in mammalian cells. Nucleic Acids Res 1989, 17:1215-1230.
16. Haas A.L., Bright P.M. The dynamics of ubiquitin pools within cultured human lung fibroblasts. J Biol Chem 1987, 262:345-351.
17. Hanna J., Leggett D.S., Finley D. Ubiquitin depletion as a key mediator of toxicity by translational inhibitors. Mol Cell Biol 2003, 23:9251-9261.
18. Crosas B., Hanna J., Kirkpatrick D.S., Zhang D.P., Tone Y., Hathaway N.A., et al. Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities. Cell 2006, 127:1401-1413.
19. Kimura Y., Yashiroda H., Kudo T., Koitabashi S., Murata S., Kakizuka A., et al. An inhibitor of a deubiquitinating enzyme regulates ubiquitin homeostasis. Cell 2009, 137:549-559.
20. Hanna J., Meides A., Zhang D.P., Finley D. A ubiquitin stress response induces altered proteasome composition. Cell 2007, 129:747-759.
21. Zhang D.D., Hannink M. Distinct cysteine residues in Keap1 are required for Keap1-dependent ubiquitination of Nrf2 and for stabilization of Nrf2 by chemopreventive agents and oxidative stress. Mol Cell Biol 2003, 23:8137-8151.
22. Zhang D.D., Lo S.C., Cross J.V., Templeton D.J., Hannink M. Keap1 is a redox-regulated substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex. Mol Cell Biol 2004, 24:10941-10953.
23. Kobayashi A., Kang M.I., Watai Y., Tong K.I., Shibata T., Uchida K., et al. Oxidative and electrophilic stresses activate Nrf2 through inhibition of ubiquitination activity of Keap1. Mol Cell Biol 2006, 26:221-229.
24. Yamamoto T., Suzuki T., Kobayashi A., Wakabayashi J., Maher J., Motohashi H., et al. Physiological significance of reactive cysteine residues of Keap1 in determining Nrf2 activity. Mol Cell Biol 2008, 28:2758-2770.
25. Kaiser P., Su N.Y., Yen J.L., Ouni I., Flick K. The yeast ubiquitin ligase SCF-Met30: connecting environmental and intracellular conditions to cell division. Cell Div 2006, 1:16.
26. Barbey R., Baudouin-Cornu P., Lee T.A., Rouillon A., Zarzov P., Tyers M., et al. Inducible dissociation of SCF(Met30) ubiquitin ligase mediates a rapid transcriptional response to cadmium. EMBO J 2005, 24:521-532.
27. Yen J.L., Su N.Y., Kaiser P. The yeast ubiquitin ligase SCFMet30 regulates heavy metal response. Mol Biol Cell 2005, 16:1872-1882.
28. Muckenthaler M.U., Galy B., Hentze M.W. Systemic iron homeostasis and the iron-responsive element/iron-regulatory protein (IRE/IRP) regulatory network. Annu Rev Nutr 2008, 28:197-213.
29. Vashisht A.A., Zumbrennen K.B., Huang X., Powers D.N., Durazo A., Sun D., et al. Control of iron homeostasis by an iron-regulated ubiquitin ligase. Science 2009, 326:718-721.
30. Stenkamp R.E. Dioxygen and hemerythrin. Chem Rev 1994, 94:715-726.
31. Marine J.C., Lozano G. Mdm2-mediated ubiquitylation: p53 and beyond. Cell Death Differ 2010, 17:93-102.
32. Perry M.E. The regulation of the p53-mediated stress response by MDM2 and MDM4. Cold Spring Harb Perspect Biol 2010, 2:a000968.
33. Courtois-Cox S., Jones S.L., Cichowski K. Many roads lead to oncogene-induced senescence. Oncogene 2008, 27:2801-2809.
34. Sherr C.J. Divorcing ARF and p53: an unsettled case. Nat Rev Cancer 2006, 6:663-673.
35. Lipton J.M., Ellis S.R. Diamond-Blackfan anemia: diagnosis, treatment, and molecular pathogenesis. Hematol Oncol Clin North Am 2009, 23:261-282.
36. Gilkes D.M., Chen L., Chen J. MDMX regulation of p53 response to ribosomal stress. EMBO J 2006, 25:5614-5625.
37. Shieh S.Y., Ikeda M., Taya Y., Prives C. DNA damage-induced phosphorylation of p53 alleviates inhibition by MDM2. Cell 1997, 91:325-334.
38. Meulmeester E., Maurice M.M., Boutell C., Teunisse A.F., Ovaa H., Abraham T.E., et al. Loss of HAUSP-mediated deubiquitination contributes to DNA damage-induced destabilization of Hdmx and Hdm2. Mol Cell 2005, 18:565-576.
39. Ulrich H.D., Walden H. Ubiquitin signalling in DNA replication and repair. Nat Rev Mol Cell Biol 2010, 11:479-489.
40. Huen M.S., Grant R., Manke I., Minn K., Yu X., Yaffe M.B., et al. RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly. Cell 2007, 131:901-914.
41. Kolas N.K., Chapman J.R., Nakada S., Ylanko J., Chahwan R., Sweeney F.D., et al. Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase. Science 2007, 318:1637-1640.
42. Mailand N., Bekker-Jensen S., Faustrup H., Melander F., Bartek J., Lukas C., et al. RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell 2007, 131:887-900.
43. Stewart G.S., Panier S., Townsend K., Al-Hakim A.K., Kolas N.K., Miller E.S., et al. The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell 2009, 136:420-434.
44. Doil C., Mailand N., Bekker-Jensen S., Menard P., Larsen D.H., Pepperkok R., et al. RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell 2009, 136:435-446.
45. Kim H., Chen J., Yu X. Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response. Science 2007, 316:1202-1205.
46. Liu Z., Wu J., Yu X. CCDC98 targets BRCA1 to DNA damage sites. Nat Struct Mol Biol 2007, 14:716-720.
47. Sobhian B., Shao G., Lilli D.R., Culhane A.C., Moreau L.A., Xia B., et al. RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science 2007, 316:1198-1202.
48. Wang B., Matsuoka S., Ballif B.A., Zhang D., Smogorzewska A., Gygi S.P., et al. Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response. Science 2007, 316:1194-1198.
49. Gfeller A., Liechti R., Farmer E.E. Arabidopsis jasmonate signaling pathway. Sci Signal 2010, 3:cm4.
50. Devoto A., Turner J.G. Regulation of jasmonate-mediated plant responses in arabidopsis. Ann Bot 2003, 92:329-337.
51. Chini A., Fonseca S., Fernandez G., Adie B., Chico J.M., Lorenzo O., et al. The JAZ family of repressors is the missing link in jasmonate signalling. Nature 2007, 448:666-671.
52. Thines B., Katsir L., Melotto M., Niu Y., Mandaokar A., Liu G., et al. JAZ repressor proteins are targets of the SCF(COI1) complex during jasmonate signalling. Nature 2007, 448:661-665.
53. Yan Y., Stolz S., Chetelat A., Reymond P., Pagni M., Dubugnon L., et al. A downstream mediator in the growth repression limb of the jasmonate pathway. Plant Cell 2007, 19:2470-2483.
54. Sheard L.B., Tan X., Mao H., Withers J., Ben-Nissan G., Hinds T.R., et al. Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor. Nature 2010, 468:400-405.
55. Santner A., Estelle M. The ubiquitin-proteasome system regulates plant hormone signaling. Plant J 2010, 61:1029-1040.
56. Itoh K., Mimura J., Yamamoto M. Discovery of the negative regulator of Nrf2, Keap1: a historical overview. Antioxid Redox Signal 2010, 13:1665-1678.
57. Kaelin W.G. Proline hydroxylation and gene expression. Annu Rev Biochem 2005, 74:115-128.
58. Flick K., Raasi S., Zhang H., Yen J.L., Kaiser P. A ubiquitin-interacting motif protects polyubiquitinated Met4 from degradation by the 26S proteasome. Nat Cell Biol 2006, 8:509-515.
59. Reed S.I. Ratchets and clocks: the cell cycle, ubiquitylation and protein turnover. Nat Rev Mol Cell Biol 2003, 4:855-864.
60. Skaar J.R., Pagano M. Control of cell growth by the SCF and APC/C ubiquitin ligases. Curr Opin Cell Biol 2009, 21:816-824.
61. Gutierrez G.J., Ronai Z. Ubiquitin and SUMO systems in the regulation of mitotic checkpoints. Trends Biochem Sci 2006, 31:324-332.
62. Bassermann F., Pagano M. Dissecting the role of ubiquitylation in the DNA damage response checkpoint in G2. Cell Death Differ 2010, 17:78-85.
63. Arndt V., Rogon C., Hohfeld J. To be, or not to be - molecular chaperones in protein degradation. Cell Mol Life Sci 2007, 64:2525-2541.
64. Sermeus A., Michiels C. Reciprocal influence of the p53 and the hypoxic pathways. Cell Death Dis 2011, 2:e164.
65. Wheeler G.L., Trotter E.W., Dawes I.W., Grant C.M. Coupling of the transcriptional regulation of glutathione biosynthesis to the availability of glutathione and methionine via the Met4 and Yap1 transcription factors. J Biol Chem 2003, 278:49920-49928.
66. Ouni I., Flick K., Kaiser P. A transcriptional activator is part of an SCF ubiquitin ligase to control degradation of its cofactors. Mol Cell 2010, 40:954-964.
67. Ouni I., Flick K., Kaiser P. Ubiquitin and transcription. The SCF/Met4 pathway, a (protein-) complex issue. Transcription 2011, 2:135-139.
68. Majmundar A.J., Wong W.J., Simon M.C. Hypoxia-inducible factors and the response to hypoxic stress. Mol Cell 2010, 40:294-309.
69. Petroski M.D., Deshaies R.J. Function and regulation of cullin-RING ubiquitin ligases. Nat Rev Mol Cell Biol 2005, 6:9-20.
70. Alexandru G., Graumann J., Smith G.T., Kolawa N.J., Fang R., Deshaies R.J. UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover. Cell 2008, 134:804-816.
71. Nakayama K., Qi J., Ronai Z. The ubiquitin ligase Siah2 and the hypoxia response. Mol Cancer Res 2009, 7:443-451.
72. Kaelin W.G. The von Hippel-Lindau tumour suppressor protein: O2 sensing and cancer. Nat Rev Cancer 2008, 8:865-873.
73. Richter K., Haslbeck M., Buchner J. The heat shock response: life on the verge of death. Mol Cell 2010, 40:253-266.
74. Anckar J., Sistonen L. Regulation of HSF1 function in the heat stress response: implications in aging and disease. Annu Rev Biochem 2011, 80:1089-1115.
75. Fang N.N., Ng A.H., Measday V., Mayor T. Hul5 HECT ubiquitin ligase plays a major role in the ubiquitylation and turnover of cytosolic misfolded proteins. Nat Cell Biol 2011, 13:1344-1352.
76. Koegl M., Hoppe T., Schlenker S., Ulrich H.D., Mayer T.U., Jentsch S. A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly. Cell 1999, 96:635-644.
77. Flick K., Kaiser P. Proteomic revelation: SUMO changes partners when the heat is on. Sci Signal 2009, 2:pe45.
78. Golebiowski F., Matic I., Tatham M.H., Cole C., Yin Y., Nakamura A., et al. System-wide changes to SUMO modifications in response to heat shock. Sci Signal 2009, 2:ra24.
79. Brunet Simioni M., De Thonel A., Hammann A., Joly A.L., Bossis G., Fourmaux E., et al. Heat shock protein 27 is involved in SUMO-2/3 modification of heat shock factor 1 and thereby modulates the transcription factor activity. Oncogene 2009, 28:3332-3344.
80. Sheltzer J.M., Amon A. The aneuploidy paradox: costs and benefits of an incorrect karyotype. Trends Genet 2011, 27:446-453.
81. Torres E.M., Dephoure N., Panneerselvam A., Tucker C.M., Whittaker C.A., Gygi S.P., et al. Identification of aneuploidy-tolerating mutations. Cell 2010, 143:71-83.
82. Hanna J., Hathaway N.A., Tone Y., Crosas B., Elsasser S., Kirkpatrick D.S., et al. Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell 2006, 127:99-111.
83. Hanahan D., Weinberg R.A. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674.
84. Jackson S.P., Bartek J. The DNA-damage response in human biology and disease. Nature 2009, 461:1071-1078.
85. Hoeijmakers J.H. DNA damage, aging, and cancer. N Engl J Med 2009, 361:1475-1485.
86. Rubinsztein D.C. The roles of intracellular protein-degradation pathways in neurodegeneration. Nature 2006, 443:780-786.