Protein complexes in nucleotide excision repair

Mutation Research - DNA Repair

Volumn 435, Issue 1, 1999, Pages 23-33

  Araújo, Sofia J ^a   Wood, Richard D ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

DNA; Nucleotide excision repair; Protein complexes

Indexed keywords

DNA; NUCLEOTIDE;

ANIMAL CELL; DNA DAMAGE; EXCISION REPAIR; HUMAN; HUMAN CELL; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; SHORT SURVEY; ULTRAVIOLET RADIATION; XERODERMA PIGMENTOSUM;

EID: 0040241960     PISSN: 09218777     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0921-8777(99)00042-7     Document Type: Article

References (83)

1. E.C. Friedberg, G.C. Walker, W. Siede, DNA repair and mutagenesis. ASM Press, Washington DC, 1995, 247.
2. de Laat W.L., Jaspers N.G.J., Hoeijmakers J.H.J. Molecular mechanism of nucleotide excision repair. Genes Dev. 13:1999;768-785.
3. J.E. Cleaver, K.H. Kraemer, Xeroderma pigmentosum and Cockayne syndrome, in: C.R. Scriver et al. (Eds.), The Metabolic and Molecular Bases of Inherited Disease, McGraw-Hill, New York, 1995, pp. 4393-4419.
4. Masutani C., Kusumoto R., Yamada A., Dohmae N., Yokoi M., Yuasa M., Araki M., Iwai S., Takio K., Hanaoka F. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase? Nature. 399:1999;700-704.
5. Aboussekhra A., Biggerstaff M., Shivji M.K.K., Vilpo J.A., Moncollin V., Podust V.N., Protic' M., Hübscher U., Egly J.-M., Wood R.D. Mammalian DNA nucleotide excision repair reconstituted with purified protein components. Cell. 80:1995;859-868.
6. Guzder S.N., 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. 270:1995;12973-12976.
7. Mu D., Park C.H., Matsunaga T., Hsu D.S., Reardon J.T., Sancar A. Reconstitution of human DNA-repair excision nuclease in a highly defined system. J. Biol. Chem. 270:1995;2415-2418.
8. Mu D., Hsu D.S., Sancar A. Reaction-mechanism of human DNA-repair excision nuclease. J. Biol. Chem. 271:1996;8285-8294.
9. Wood R.D. DNA damage recognition during nucleotide excision repair in mammalian cells. Biochimie. 81:1999;39-44.
10. Sugasawa K., Ng J.M.Y., Masutani C., van der Spek I.S., van der Spek P.J., Eker A.P.M., Hanaoka F., Bootsma D., Hoeijmakers J.H.J. Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Mol. Cell. 2:1998;223-232.
11. Wakasugi M., Sancar A. Order of assembly of human DNA repair excision nuclease. J. Biol. Chem. 274:1999;18759-18768.
12. Hanawalt P., Mellon I. Stranded in an active gene. Curr. Biol. 3:1993;67-69.
13. Donahue B.A., Yin S., Taylor J.-S., Reines D., Hanawalt P.C. Transcript cleavage by RNA polymerase II arrested by a ciclobutane pyrimidine dimer in the DNA template. Proc. Natl. Acad. Sci. U.S.A. 91:1994;8502-8506.
14. Selby C.P., Drapkin R., Reinberg D., Sancar A. RNA-polymerase-II stalled at a thymine dimer - footprint and effect on excision-repair. Nucleic Acids Res. 25:1997;787-793.
15. Mu D., Sancar A. Model for XPC independent transcription-coupled repair of pyrimidine dimers in humans. J. Biol. Chem. 272:1997;7570-7573.
16. Evans E., Fellows J., Coffer A., Wood R.D. Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein. EMBO J. 16:1997;625-638.
17. Evans E., Moggs J.G., Hwang J.R., Egly J.-M., Wood R.D. Mechanism of open complex and dual incision formation by human nucleotide excision repair factors. EMBO J. 16:1997;6559-6573.
18. Wakasugi M., Reardon J.T., Sancar A. The non-catalytic function of XPG protein during dual incision in human nucleotide excision repair. J. Biol. Chem. 272:1997;16030-16034.
19. Wakasugi M., Sancar A. Assembly, subunit composition, and footprint of human DNA-repair excision nuclease. Proc. Natl. Acad. Sci. U.S.A. 95:1998;6669-6674.
20. Constantinou A., Gunz D., Evans E., Lalle P., Bates P.A., Wood R.D., Clarkson S.G. Conserved residues of human XPG protein important for nuclease activity and function in nucleotide excision repair. J. Biol. Chem. 274:1999;5637-5648.
21. O'Donovan A., Davies A.A., Moggs J.G., West S.C., Wood R.D. XPG endonuclease makes the 3′ incision in human DNA nucleotide excision repair. Nature. 371:1994;432-435.
22. Matsunaga T., Mu D., Park C.H., Reardon J.T., Sancar A. Human DNA-repair excision nuclease - analysis of the roles of the subunits involved in dual incisions by using anti-XPG and anti-ERCC1 antibodies. J. Biol. Chem. 270:1995;20862-20869.
23. Sijbers A.M., de Laat W.L., Ariza R.R., Biggerstaff M., Wei Y.-F., Moggs J.G., Carter K.C., Shell B.K., Evans E., de Jong M.C., Rademakers S., de Rooij J., Jaspers N.G.J., Hoeijmakers J.H.J., Wood R.D. Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease. Cell. 86:1996;811-822.
24. Moggs J.G., Yarema K.J., Essigmann J.M., Wood R.D. Analysis of incision sites produced by human cell extracts and purified proteins during nucleotide excision repair of a 1,3-intrastrand d(GpTpG)-cisplatin adduct. J. Biol. Chem. 271:1996;7177-7186.
25. Shivji M.K.K., Podust V.N., Hübscher U., Wood R.D. Nucleotide excision repair DNA synthesis by DNA polymerase ε in the presence of PCNA, RFC and RPA. Biochemistry. 34:1995;5011-5017.
26. Wood R., Shivji M. Which DNA polymerases are used for DNA repair in eukaryotes? Carcinogenesis. 18:1997;605-610.
27. Nocentini S. Rejoining kinetics of DNA single- and double-strand breaks in normal and DNA ligase deficient cells after exposure to ultraviolet C and gamma radiation: an evaluation of ligating activities involved in different DNA repair processes. Radiat. Res. 151:1999;423-432.
28. Svejstrup J.Q., Wang Z., Feaver W.J., Wu X., Bushnell D.A., Donahue T.F., Friedberg E.C., Kornberg R.D. Different forms of TFIIH for transcription and DNA repair: holo-TFIIH and a nucleotide excision repairosome. Cell. 80:1995;21-28.
29. Guzder S.N., Sung P., Prakash L., Prakash S. Nucleotide excision repair in yeast is mediated by sequential assembly of repair factors and not by a pre-assembled repairosome. J. Biol. Chem. 271:1996;8903-8910.
30. Wang Z.G., Wei S.G., Reed S.H., Wu X.H., Svejstrup J.Q., Feaver W.J., Kornberg R.D., Friedberg E.C. 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. 17:1997;635-643.
31. Guzder S.N., Sung P., Prakash L., Prakash S. Yeast Rad7-Rad16 complex, specific for the nucleotide excision-repair of the nontranscribed DNA strand, is an ATP dependent DNA damage sensor. J. Biol. Chem. 272:1997;21665-21668.
32. Verhage R., Zeeman A., Degroot N., Gleig F., Bang D., van de Putte P., Brouwer J. The RAD7 and RAD16 genes, which are essential for pyrimidine dimer removal from the silent mating-type loci, are also required for repair of the nontranscribed strand of an active gene in Saccharomyces cerevisiae. Mol. Cell. Biol. 14:1994;6135-6142.
33. Reed S.H., You Z.Y., Friedberg E.C. The yeast RAD7 and RAD16 genes are required for postincision events during nucleotide excision repair. J. Biol. Chem. 273:1998;29481-29488.
34. Guzder S.N., 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. 273:1998;6292-6296.
35. Watkins J.F., 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. 13:1993;7757-7765.
36. Schauber C., Chen L., Tongaonkar P., Vega I., Lambertson D., Potts W., Madura K. Rad23 links DNA-repair to the ubiquitin/proteasome pathway. Nature. 391:1998;715-718.
37. Mueller J.P., Smerdon M.J. Rad23 is required for transcription-coupled repair and efficient overall repair in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:1996;2361-2368.
38. Guzder S.N., Sung P., Prakash L., Prakash S. Affinity of yeast nucleotide excision repair factor 2, consisting of the Rad4 and Rad23 proteins, for ultraviolet damaged DNA. J. Biol. Chem. 273:1998;31541-31546.
39. Jansen L.E.T., Verhage R.A., Brouwer J.A. Preferential binding of yeast Rad4-Rad23 complex to damaged DNA. J. Biol. Chem. 273:1998;33111-33114.
40. Bardwell A.J., Bardwell L., Iyer N., Svejstrup J.Q., Feaver W.J., Kornberg R.D., Friedberg E.C. Yeast nucleotide excision repair proteins Rad2 and Rad4 interact with RNA polymerase II basal transcription factor b (TFIIH). Mol. Cell. Biol. 14:1994;3569-3576.
41. Guzder S.N., 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. 270:1995;8385-8388.
42. Rodriguez K., Talamantez J., Huang W., Reed S.H., Wang Z., Chen L., Feaver W.J., Friedberg E.C., Tomkinson A.E. Affinity purification and partial characterization of a yeast multiprotein complex for nucleotide excision repair using histidine-tagged Rad14 protein. J. Biol. Chem. 273:1998;34180-34189.
43. Feaver W.J., Svejstrup J.Q., Bardwell L., Bardwell A.J., Buratowski S., Gulyas K.D., Donahue T.F., Friedberg E.C., Kornberg R.D. Dual roles of a multiprotein complex from Saccharomyces cerevisiae in transcription and DNA repair. Cell. 75:1993;1379-1387.
44. Habraken Y., Sung P., Prakash L., Prakash S. Structure-specific nuclease activity in yeast nucleotide excision-repair protein Rad2. J. Biol. Chem. 270:1995;30194-30198.
45. Bardwell A.J., Bardwell L., Tomkinson A.E., Friedberg E.C. Specific cleavage of model recombination and repair intermediates by the yeast Rad1-Rad10 DNA endonuclease. Science. 265:1994;2082-2085.
46. Park C.H., Mu D., Reardon J.T., Sancar A. The general transcription-repair factor TFIIH is recruited to the excision repair complex by the XPA protein independent of the TFIIE transcription factor. J. Biol. Chem. 270:1995;4896-4902.
47. Nocentini S., Coin F., Saijo M., Tanaka K., Egly J.M. DNA damage recognition by XPA protein promotes efficient recruitment of transcription factor IIH. J. Biol. Chem. 272:1997;22991-22994.
48. Drapkin R., Reardon J.T., Ansari A., Huang J.C., Zawel L., Ahn K.J., Sancar A., Reinberg D. Dual role of TFIIH in DNA excision-repair and in transcription by RNA-polymerase-II. Nature. 368:1994;769-772.
49. van der Spek P.J., Eker A., Rademakers S., Visser C., Sugasawa K., Masutani C., Hanaoka F., Bootsma D., Hoeijmakers J.H.J. XPC and human homologs of Rad23 - intracellular-localization and relationship to other nucleotide excision repair complexes. Nucleic Acids Res. 24:1996;2551-2559.
50. Iyer N., Reagan M.S., Wu K.J., Canagarajah B., Friedberg E.C. Interactions involving the human RNA polymerase II transcription/nucleotide excision repair complex TFIIH, the nucleotide excision repair protein XPG, and Cockayne syndrome group B (CSB) protein. Biochemistry. 35:1996;2157-2167.
51. He Z., Henricksen L.A., Wold M.S., Ingles C.J. RPA involvement in the damage recognition and incision steps of nucleotide excision repair. Nature. 374:1995;566-569.
52. de Laat W.L., Appeldoorn E., Sugasawa K., Weterings E., Jaspers N.G.J., Hoeijmakers J.H.J. DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes Dev. 12:1998;2598-2609.
53. Li L., Elledge S.J., Peterson C.A., Bales E.S., Legerski R.J. Specific association between the human DNA repair proteins XPA and ERCC1. Proc. Natl. Acad. Sci. U.S.A. 91:1994;5012-5016.
54. Li L., Peterson C.A., Lu X.Y., Legerski R.J. Mutations in XPA that prevent association with ERCC1 are defective in nucleotide excision-repair. Mol. Cell. Biol. 15:1995;1993-1998.
55. Park C.H., Sancar A. Formation of a ternary complex by human XPA, ERCC1, and ERCC4 (XPF) excision-repair proteins. Proc. Natl. Acad. Sci. U.S.A. 91:1994;5017-5021.
56. Matsuda T., Saijo M., Kuraoka I., Kobayashi T., Nakatsu Y., Nagai A., Enjoji T., Masutani C., Sugasawa K., Hanaoka F., Yasui A., Tanaka K. DNA repair protein XPA binds replication protein A (RPA). J. Biol. Chem. 270:1995;4152-4157.
57. Bessho T., Sancar A., Thompson L.H., Thelen M.P. Reconstitution of human excision nuclease with recombinant XPF-ERCC1 complex. J. Biol. Chem. 272:1997;3833-3837.
58. Saijo M., Kuraoka I., Masutani C., Hanaoka F., Tanaka K. Sequential binding of DNA-repair proteins RPA and ERCC1 to XPA in vitro. Nucleic Acids Res. 24:1996;4719-4724.
59. Walther A.P., Gomes X.V., Lao Y., Lee C.G., Wold M.S. Replication protein A interactions with DNA. 1. Functions of the DNA binding and zinc-finger domains of the 70 kDa subunit. Biochemistry. 38:1999;3963-3973.
60. Maldonado E., Shiekhattar R., Sheldon M., Cho H., Drapkin R., Rickert P., Lees E., Anderson C.W., Linn S., Reinberg D. A human RNA polymerase II complex associated with SRB and DNA repair proteins. Nature. 381:1996;86-89.
61. He Z.G., Ingles C.J. Isolation of human complexes proficient in nucleotide excision repair. Nucleic Acids Res. 25:1997;1136-1141.
62. Shivji M.K.K., Kenny M.K., Wood R.D. Proliferating cell nuclear antigen is required for DNA excision repair. Cell. 69:1992;367-374.
63. Habraken Y., Sung P., Prakash S., Prakash L. Transcription factor TFIIH and DNA endonuclease Rad2 constitute yeast nucleotide excision repair factor 3 - implications for nucleotide excision repair and Cockayne syndrome. Proc. Natl. Acad. Sci. U.S.A. 93:1996;10718-10722.
64. Winkler G.S., Vermeulen W., Coin F., Egly J.M., Hoeijmakers J.H.J., Weeda G. Affinity purification of human DNA repair transcription factor TFIIH using epitope-tagged xeroderma pigmentosum B protein. J. Biol. Chem. 273:1998;1092-1098.
65. Weeda G., Rossignol M., Fraser R.A., Winkler G.S., Vermeulen W., van t'Veer L.J., Ma L., Hoeijmakers J.H.J., Egly J.M. 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. 25:1997;2274-2283.
66. Russell S.J., Reed S.H., Huang W., Friedberg E.C., Johnston S.A. The 19S regulatory complex of the proteasome functions independently of proteolysis in nucleotide excision repair. Mol. Cell. 3:1999;687-695.
67. Houtsmuller A.B., Rademakers S., Hoogstraten N.A.L., Hoogstraten D., Hoeijmakers J.H.J., Vermeulen W. Action of DNA repair endonuclease ERCC1/XPF in living cells. Science. 284:1999;958-961.
68. Mu D., Wakasugi M., Hsu D.S., Sancar A. Characterization of reaction intermediates of human excision-repair nuclease. J. Biol. Chem. 272:1997;28971-28979.
69. Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell. 92:1998;291-294.
70. Staley J.P., Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. 92:1998;315-326.
71. Baker T.A. Polymerases and the replisome: machines within machines. Cell. 92:1998;295-305.
72. Ossipow V., Tassan J.-P., Nigg E.A., Schibler U. A mammalian RNA polymerase II holoenzyme containing all components required for promoter-specific transcription initiation. Cell. 83:1995;137-146.
73. Myer V.E., Young R.A. RNA polymerase II holoenzymes and subcomplexes. J. Biol. Chem. 273:1998;27757-27760.
74. Jordan P., Cunha C., Carmo-Fonseca M. The cdk7-cyclin H-MAT1 complex associated with TFIIH is localized in coiled bodies. Mol. Biol. Cell. 8:1997;1207-1217.
75. Hozak P., Hassan A.B., Jackson D.A., Cook P.R. Visualization of replication factories attached to a nucleoskeleton. Cell. 73:1993;361-373.
76. Iborra F.J., Pombo A., Jackson D.A., Cook P.R. Active RNA polymerases are localized within discrete transcription factories in human nuclei. J. Cell Sci. 109:1996;1427-1436.
77. Cook P.R. The organization of replication and transcription. Science. 284:1999;1790-1795.
78. Jackson D.A., Balajee A.S., Mullenders L., Cook P.R. Sites in human nuclei where DNA damaged by ultraviolet light is repaired - visualization and localization relative to the nucleoskeleton. J. Cell Sci. 107:1994;1745-1752.
79. Jackson D.A., Hassan A.B., Errington R.J., Cook P.R. Sites in human nuclei where damage-induced by ultraviolet light is repaired - localization relative to transcription sites and concentrations of proliferating cell nuclear antigen and the tumor suppressor protein, p53. J. Cell Sci. 107:1994;1753-1760.
80. Koehler D.R., Hanawalt P.C. Recruitment of damaged DNA to the nuclear matrix in hamster cells following ultraviolet-irradiation. Nucleic Acids Res. 24:1996;2877-2884.
81. Stigger E., Drissi R., Lee S. Functional-analysis of human replication protein-A in nucleotide excision-repair. J. Biol. Chem. 273:1998;9337-9343.
82. Li L., Lu X.Y., Peterson C.A., Legerski R.J. An interaction between the DNA repair factor XPA and replication protein A appears essential for nucleotide excision repair. Mol. Cell. Biol. 15:1995;5396-5402.
83. Lee S.H., Kim D.K., Drissi R. Human xeroderma pigmentosum group A protein interacts with human replication protein A and inhibits DNA replication. J. Biol. Chem. 270:1995;21800-21805.