Regulation of repair by the 26S proteasome

Journal of Biomedicine and Biotechnology

Volumn 2002, Issue 2, 2002, Pages 94-105

  Sweder, K ^a   Madura, K ^b  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

26S PROTEASOME; CHAPERONE; PROTEASOME; PROTEIN; PROTEIN RAD23; PROTEIN RAD4; UNCLASSIFIED DRUG; XERODERMA PIGMENTOSUM B PROTEIN;

COMPLEX FORMATION; DNA DAMAGE; DNA REPAIR; EXCISION REPAIR; GENETIC TRANSCRIPTION; HUMAN; NONHUMAN; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN PROCESSING; PROTEIN SYNTHESIS; REVIEW; RNA SYNTHESIS; ULTRAVIOLET RADIATION;

XERODERMA PIGMENTOSUM;

EID: 0041496232     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/S1110724302205033     Document Type: Review

References (76)

1. Guzder SN, Habraken Y, Sung P, Prakash L, Prakash S. Reconstitution of yeast nucleotide excision repair with purified Rad proteins, replication protein A, and transcription factor TFIIH. J Biol Chem. 1995;270(22):12973-12976.
2. Huang JC, Svoboda DL, Reardon JT, Sancar A. Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5′ and the 6th phosphodiester bond 3′ to the photodimer. Proc Natl Acad Sci USA. 1992;89(8):3664-3668.
3. Aboussekhra A, Biggerstaff M, Shivji MK, et al. Mammalian DNA nucleotide excision repair reconstituted with purified protein components. Cell. 1995;80(6):859-868.
4. Mu D, Park CH, Matsunaga T, Hsu DS, Reardon JT, Sancar A. Reconstitution of human DNA repair excision nuclease in a highly defined system. J Biol Chem. 1995;270(6):2415-2418.
5. Guzder SN, Bailly V, Sung P, Prakash L, Prakash S. Yeast DNA repair protein RAD23 promotes complex formation between transcription factor TFIIH and DNA damage recognition factor RAD14. J Biol Chem. 1995;270(15):8385-8388.
6. Guzder SN, Sung P, Prakash L, Prakash S. The DNA-dependent ATPase activity of yeast nucleotide excision repair factor 4 and its role in DNA damage recognition. J Biol Chem. 1998;273(11):6292-6296.
7. Eisen JA, Sweder KS, Hanawalt PC. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 1995;23(14):2715-2723.
8. Leadon SA, Lawrence DA. Strand-selective repair of DNA damage in the yeast GAL7 gene requires RNA polymerase II. J Biol Chem. 1992;267(32):23175- 23182.
9. Mellon I, Hanawalt PC. Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand. Nature. 1989;342(6245):95-98.
10. Bedoyan J, Gupta R, Thoma F, Smerdon MJ. Transcription, nucleosome stability, and DNA repair in a yeast minichromosome. J Biol Chem. 1992;267(9):5996-6005.
11. Sweder KS, Hanawalt PC. Preferential repair of cyclobutane pyrimidine dimers in the transcribed strand of a gene in yeast chromosomes and plasmids is dependent on transcription. Proc Natl Acad Sci USA. 1992;89(22):10696-10700.
12. Tijsterman M, Tasseron-de Jong JG, Verhage RA, Brouwer J. Defective Kin28, a subunit of yeast TFIIH, impairs transcription-coupled but not global genome nucleotide excision repair. Mutat Res. 1998;409(3):181-188.
13. Carreau M, Hunting D. Transcription-dependent and independent DNA excision repair pathways in human cells. Mutat Res. 1992;274(1):57-64.
14. Christians FC, Hanawalt PC. Inhibition of transcription and strand-specific DNA repair by α-amanitin in Chinese hamster ovary cells. Mutat Res. 1992;274(2):93-101.
15. Conconi A, Bespalov VA, Smerdon MJ. Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast. Proc Natl Acad Sci USA. 2002;99(2):649-654.
16. Troelstra C, Odijk H, de Wit J, et al. Molecular cloning of the human DNA excision repair gene ERCC-6. Mol Cell Biol. 1990;10(11):5806-5813.
17. Troelstra C, van Gool A, de Wit J, Vermeulen W, Bootsma D, Hoeijmakers JH. ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne's syndrome and preferential repair of active genes. Cell. 1992;71(6):939-953.
18. Huang ME, Chuat JC, Galibert F. A possible yeast homolog of human active-gene-repairing helicase ERCC6+. Biochem Biophys Res Commun. 1994;201(1):310-317.
19. van Gool AJ, Verhage R, Swagemakers SM, et al. RAD26, the functional S. cerevisiae homolog of the Cockayne syndrome B gene ERCC6. EMBO J. 1994;13(22):5361-5369.
20. Citterio E, Van den Boom V, Schnitzler G, et al. ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor. Mol Cell Biol. 2000;20(20):7643-7653.
21. Selby CP, Sancar A. Cockayne syndrome group B protein enhances elongation by RNA polymerase II. Proc Natl Acad Sci USA. 1997;94(21):11205-11209.
22. Kamiuchi S, Saijo M, Citterio E, de Jager M, Hoeijmakers JH, Tanaka K. Translocation of Cockayne syndrome group A protein to the nuclear matrix: possible relevance to transcription-coupled DNA repair. Proc Natl Acad Sci USA. 2002;99(1):201-206.
23. Dohmen RJ, Madura K, Bartel B, Varshavsky A. The N-end rule is mediated by the UBC2(RAD6) ubiquitin-conjugating enzyme. Proc Natl Acad Sci USA. 1991;88(16):7351-7355.
24. Hiyama H, Yokoi M, Masutani C, et al. Interaction of hHR23 with S5a. The ubiquitin-like domain of hHR23 mediates interaction with S5a subunit of 26S proteasome. J Biol Chem. 1999;274(39):28019-28025.
25. Hofmann RM, Pickart CM. Noncanonical MMS2-encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair. Cell. 1999;96(5):645-653.
26. Kumar S, Talis AL, Howley PM. Identification of HHR23A as a substrate for E6-associated protein-mediated ubiquitination. J Biol Chem. 1999;274(26):18785-18792.
27. Madura K, Prakash S, Prakash L. Expression of the Saccharomyces cerevisiae DNA repair gene RAD6 that encodes a ubiquitin conjugating enzyme, increases in response to DNA damage and in meiosis but remains constant during the mitotic cell cycle. Nucleic Acids Res. 1990;18(4):771-778.
28. Russell SJ, Reed SH, Huang W, Friedberg EC, Johnston SA. The 19S regulatory complex of the proteasome functions independently of proteolysis in nucleotide excision repair. Mol Cell. 1999;3(6):687-695.
29. Schauber C, Chen L, Tongaonkar P, et al. Rad23 links DNA repair to the ubiquitin/proteasome pathway. Nature. 1998;391(6668):715-718.
30. Spence J, Sadis S, Haas AL, Finley D. A ubiquitin mutant with specific defects in DNA repair and multiubiquitination. Mol Cell Biol. 1995;15(3):1265-1273.
31. van der Spek PJ, Smit EM, Beverloo HB, et al. Chromosomal localization of three repair genes: the xeroderma pigmentosum group C gene and two human homologs of yeast RAD23. Genomics. 1994;23(3):651-658.
32. Wang Z, Wei S, Reed SH, et al. The RAD7, RAD16, and RAD23 genes of Saccharomyces cerevisiae: requirement for transcription-independent nucleotide excision repair in vitro and interactions between the gene products. Mol Cell Biol. 1997;17(2):635-643.
33. Ramos PC, Hockendorff J, Johnson ES, Varshavsky A, Dohmen RJ. Ump1p is required for proper maturation of the 20S proteasome and becomes its substrate upon completion of the assembly. Cell. 1998;92(4):489-499.
34. Mieczkowski P, Dajewski W, Podlaska A, Skoneczna A, Ciesla Z, Sledziewska-Gojska E. Expression of UMP1 is inducible by DNA damage and required for resistance of S. cerevisiae cells to UV light. Curr Genet. 2000;38(2):53-59.
35. Ulrich HD, Jentsch S. Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair. EMBO J. 2000;19(13):3388-3397.
36. Ford JM, Hanawalt PC. Expression of wild-type p53 is required for efficient global genomic nucleotide excision repair in UV-irradiated human fibroblasts. J Biol Chem. 1997;272(44):28073-28080.
37. Ford JM, Baron EL, Hanawalt PC. Human fibroblasts expressing the human papillomavirus E6 gene are deficient in global genomic nucleotide excision repair and sensitive to ultraviolet irradiation. Cancer Res. 1998;58(4):599-603.
38. Wagenknecht B, Hermisson M, Eitel K, Weller M. Proteasome inhibitors induce p53/p21-independent apoptosis in human glioma cells. Cell Physiol Biochem. 1999;9(3):117-125.
39. Bregman DB, Halaban R, van Cool AJ, Henning KA, Friedberg EC, Warren SL. UV-induced ubiquitination of RNA polymerase II: a novel modification deficient in Cockayne syndrome cells. Proc Natl Acad Sci USA. 1996;93(21):11586-11590.
40. Ratner JN, Balasubramanian B, Corden J, Warren SL, Bregman DB. Ultraviolet radiation-induced ubiquitination and proteasomal degradation of the large subunit of RNA polymerase II. Implications for transcription-coupled DNA repair. J Biol Chem. 1998;273(9):5184-5189.
41. Lee KB, Wang D, Lippard SJ, Sharp PA. Transcription-coupled and DNA damage-dependent ubiquitination of RNA polymerase II in vitro. Proc Natl Acad Sci USA. 2002;99(7):4239-4244.
42. Huibregtse JM, Yang JC, Beaudenon SL. The large subunit of RNA polymerase II is a substrate of the Rsp5 ubiquitin-protein ligase. Proc Natl Acad Sci USA. 1997;94(8):3656-3661.
43. Beaudenon SL, Huacani MR, Wang G, McDonnell DP, Huibregtse JM. Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae. Mol Cell Biol. 1999;19(10):6972-6979.
44. Lommel L, Bucheli ME, Sweder KS. Transcription-coupled repair in yeast is independent from ubiquitylation of RNA pol II: implications for Cockayne's syndrome. Proc Natl Acad Sci USA. 2000;97(16):9088-9092.
45. Lommel L, Chen L, Madura K, Sweder K. The 26S proteasome negatively regulates the level of overall genomic nucleotide excision repair. Nucleic Acids Res. 2000;28(24):4839-4845.
46. Woudstra EC, Gilbert C, Fellows J, et al. A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage. Nature. 2002;415(6874):929-933.
47. Vu PK, Sakamoto KM. Ubiquitin-mediated proteolysis and human disease. Mol Genet Metab. 2000;71(1-2):261-266.
48. Hicke L. A new ticket for entry into budding vesicles-ubiquitin. Cell. 2001;106(5):527-530.
49. Varshavsky A. The ubiquitin system. Trends Biochem Sci. 1997;22(10):383-387.
50. Groll M, Bajorek M, Kohler A, et al. A gated channel into the proteasome core particle. Nat Struct Biol. 2000;7(11):1062-1067.
51. Hendil KB, Hartmann-Petersen R, Tanaka K. 26S proteasomes function as stable entities. J Mol Biol. 2002;315(4):627-636.
52. Enenkel C, Lehmann A, Kloetzel PM. Subcellular distribution of proteasomes implicates a major location of protein degradation in the nuclear envelope-ER network in yeast. EMBO J. 1998;17(21):6144-6154.
53. Enenkel C, Lehmann A, Kloetzel PM. GFP-labelling of 26S proteasomes in living yeast: insight into proteasomal functions at the nuclear envelope/rough ER. Mol Biol Rep. 1999;26(1-2):131-135.
54. Weeda G, Rossignol M, Fraser RA, et al. The XPB subunit of repair/transcription factor TFIIH directly interacts with SUG1, a subunit of the 26S proteasome and putative transcription factor. Nucleic Acids Res. 1997;25(12):2274-2283.
55. Yanagi S, Shimbara N, Tamura T. Tissue and cell distribution of a mammalian proteasomal ATPase, MSS1, and its complex formation with the basal transcription factors. Biochem Biophys Res Commun. 2000;279(2):568-573.
56. Watkins JF, Sung P, Prakash L, Prakash S. The Saccharomyces cerevisiae DNA repair gene RAD23 encodes a nuclear protein containing a ubiquitin-like domain required for biological function. Mol Cell Biol. 1993;13(12):7757-7765.
57. Mueller JP, Smerdon MJ. Rad23 is required for transcription-coupled repair and efficient overrall repair in Saccharomyces cerevisiae. Mol Cell Biol. 1996;16(5):2361-2368.
58. Jelinsky SA, Estep P, Church GM, Samson LD. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol. 2000;20(21):8157- 8167.
59. Mannhaupt G, Schnall R, Karpov V, Vetter I, Feldmann H. 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. 1999;450(1-2):27-34.
60. Swaffield JC, Bromberg JF, Johnston SA. Alterations in a yeast protein resembling HIV Tat-binding protein relieve requirement for an acidic activation domain in GAL4. Nature. 1992;357(6380):698-700.
61. Gonzalez F, Delahodde A, Kodadek T, Johnston SA. Recruitment of a 19S proteasome subcomplex to an activated promoter. Science. 2002;296(5567):548-550.
62. Lommel L, Ortolan T, Chen L, Madura K, Sweder K. Protcolysis of a nucleotide excision repair protein by the 26S proteasome. Curr Genet. 2002;2002.
63. Ng JMY. Mammalian RAD23 homologs: multifunctional proteins in DNA repair and development [Ph.D. thesis]. Rotterdamm, The Netherlands: Erasmus University. 2001.
64. Hwang BJ, Ford JM, Hanawalt PC, Chu G. Expression of the p48 xeroderma pigmentosum gene is p53-dependent and is involved in global genomic repair. Proc Natl Acad Sci USA. 1999;96(2):424-428.
65. Shiyanov P, Nag A, Raychaudhuri P. Cullin 4A associates with the UV-damaged DNA-binding protein DDB. J Biol Chern. 1999;274(50):35309-35312.
66. Nag A, Bondar T, Shiv S, Raychaudhuri P. The xeroderma pigmentosum group E gene product DDB2 is a specific target of cullin 4A in mammalian cells. Mol Cell Biol. 2001;21(20):6738-6747.
67. Chen X, Zhang Y, Douglas L, Zhou P. UV-damaged DNA-binding proteins are targets of CUL-4A-mediated ubiquitination and degradation. J Biol Chem. 2001;276(51):48175-48182.
68. Ortolan TG, Tongaonkar P, Lambertson D, Chen L, Schauber C, Madura K. The DNA repair protein Rad23 is a negative regulator of multi-ubiquitin chain assembly. Nat Cell Biol. 2000;2(9):601-608.
69. Bertolaet BL, Clarke DJ, Wolff M, et al. UBA domains of DNA damage-inducible proteins interact with ubiquitin. Nat Struct Biol. 2001;8(5):417-422.
70. Wilkinson CR, Seeger M, Hartmann-Petersen R, et al. Proteins containing the UBA domain are able to bind to multi-ubiquitin chains. Nat Cell Biol. 2001;3(10):939-943.
71. Anantharaman V, Koonin EV, Aravind L. Peptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are, respectively, active and inactivated enzymes sharing a common transglutaminase fold. Hum Mol Genet. 2001;10(16):1627-1630.
72. Kornitzer D, Raboy B, Kulka RG, Fink GR. Regulated degradation of the transcription factor Gcn4," EMBO J. 1994;13(24):6021-6030.
73. Meimoun A, Holtzman T, Weissman Z, et al. Degradation of the transcription factor Gcn4 requires the kinase Pho85 and the SCF(CDC4) ubiquitin-ligase complex. Mol Biol Cell. 2000;11(3):915-927.
74. Marbach I, Licht R, Frohnmeyer H, Engelberg D. Gcn2 mediates Gcn4 activation in response to glucose stimulation or UV radiation not via GCN4 translation. J Biol Chem. 2001;276(20):16944-16951.
75. Stitzel ML, Durso R, Reese JC. The proteasome regulates the UV-induced activation of the AP-1-like transcription factor Gcn4. Genes Dev. 2001;15(2):128-133.
76. Rockx DA, Mason R, van Hoffen A, et al. UV-induced inhibition of transcription involves repression of transcription initiation and phosphorylation of RNA polymerase II. Proc Natl Acad Sci USA. 2000;97(19):10503-10508.