The limited strand-separating activity of the UvrAB protein complex and its role in the recognition of DNA damage

EMBO Journal

Volumn 16, Issue 4, 1997, Pages 889-895

  Gordienko, Irina ^a   Rupp, W Dean ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Damage recognition; DNA repair; Helicase; Nucleotide excision repair; UvrAB complex

Indexed keywords

DNA; HELICASE; N (2 FLUORENYL)ACETAMIDE; OLIGONUCLEOTIDE; SINGLE STRANDED DNA;

ARTICLE; CONTROLLED STUDY; DNA DAMAGE; DNA STRAND; ESCHERICHIA COLI; EXCISION REPAIR; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

2-ACETYLAMINOFLUORENE; ADENOSINE TRIPHOSPHATASES; BACTERIAL PROTEINS; DNA ADDUCTS; DNA DAMAGE; DNA HELICASES; DNA REPAIR; DNA, CIRCULAR; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; ESCHERICHIA COLI PROTEINS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES;

EID: 0031039924     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.4.889     Document Type: Article

References (45)

1. Bertrand-Burggraf, E., Selby, C.P., Hearst, J.E. and Sancar, A. (1991) Identification of the different intermediates in the interaction of (A)BC excinuclease with its substrates by DNase I footprinting on two uniquely modified oligonucleotides. J. Mol. Biol., 219, 27-36.
2. Bianchi, M., Riboli, B. and Magni, G. (1985) E.coli RecA protein possesses a strand separating activity on short duplex DNA. EMBO J., 4, 3025-3030.
3. Boyce, R.P. and Howard-Flanders, P. (1964) Genetic control of DNA breakdown and repair in E.coli K-12 treated with mitomycin C or ultraviolet light. Z. Vererbungsl., 95, 345-350.
4. Caron, P.R. and Grossman, L. (1988) Involvement of a cryptic ATPase activity of UvrB and its proteolysis product, UvrB* in DNA repair. Nucleic Acids Res., 16, 10891-10902.
5. Cormack, B. (1994) Mutagenesis of cloned DNA. In Ausubel, F.M. (ed.), Current Protocols in Molecular Biology. John Wiley & Sons, Inc., pp. 8.1.1-8.1.6.
6. Friedberg, E.C. (1994) Closing remarks. Ann. N.Y. Acad. Sci., 726, 367-373.
7. Friedberg, E.C., Walker, G.C. and Siede, W. (1995) DNA Repair and Mutagenesis. ASM Press, Washington, DC.
8. Fuchs, R.P. and Seeberg, E. (1984) pBR322 plasmid DNA modified with 2-acetylaminofluorene derivatives: transforming activity and in vitro strand cleavage by the Escherichia coli UvrABC endonuclease. EMBO J., 3, 757-760.
9. Gordienko, I. and Rupp, W.D. (1997) UvrAB activity at a damaged DNA site: is unpaired DNA present? EMBO J., 16, 880-888.
10. Hanawalt, P.C. and Haynes, R.H. (1965) Repair replication of DNA in bacteria: irrelevance of chemical nature of base defect. Biochem. Biophys. Res. Commun., 19, 462-467.
11. Hansson, J., Munn, M., Rupp, W.D., Kahn, R. and Wood, R.D. (1989) Localization of DNA repair synthesis by human cell extracts to a short region at the site of a lesion. J. Biol. Chem., 264, 21788-21792.
12. Harosh, I., Naumovski, L. and Friedberg, E.C. (1989) Purification and characterization of Rad3 ATPase/DNA helicase from Saccharomyces cerevisiae. J. Biol. Chem., 264, 20532-20539.
13. Hsu, D.S., Kim, S.-T., Sun, Q. and Sancar, A. (1995) Structure and function of the UvrB protein. J. Biol. Chem., 270, 8319-8327.
14. Kacinski, B.M. and Rupp, W.D. (1981) E.coli UvrB protein binds to DNA in the presence of UvrA protein. Nature, 294, 480-481.
15. Kodadek, T. and Gamper, H. (1988) Efficient synthesis of a supercoiled M13 DNA molecule containing a site specifically placed psoralen adduct and its use as a substrate for DNA replication. Biochemistry, 27, 3210-3215.
16. Koo, H.S., Claassen, L., Grossman, L. and Liu, L.F. (1991) ATP-dependent partitioning of the DNA template into supercoiled domains by Escherichia coli UvrAB. Proc. Natl Acad. Sci. USA, 88, 1212-1216.
17. Kriek, E., Miller, J.A., Juhl, U. and Miller, E.C. (1967) 8-(N-2-fluorenylacetamido) guanosine, an arylamidation reaction product of guanosine and the carcinogen N-acetoxy-N-2-fluorenylacetamide in neutral solution. Biochemistry, 6, 177-182.
18. Matson, S.W. (1991) DNA helicases of Escherichia coli. Prog. Nucleic Acid Res. Mol. Biol., 40, 289-326.
19. Matson, S.W. and Kaiser-Rogers, K.A. (1990) DNA helicases. Annu. Rev. Biochem., 59, 289-329.
20. Mazur, S.J. and Grossman, L. (1991) Dimerization of Escherichia coli UvrA and its binding to undamaged and ultraviolet light damaged DNA. Biochemistry, 30, 4432-4443.
21. Moolenaar, G.F., Visse, R., Ortiz-Buysse, M., Goosen, N. and van de Putte, P. (1994) Helicase motifs V and VI of the Escherichia coli UvrB protein of the UvrABC endonuclease are essential for the formation of the preincision complex. J. Mol. Biol., 40, 294-307.
22. Morris, C.F., Hama-Inaba, H., Mace, D., Sinha, N.K. and Alberts, B. (1979) Purification of the gene 43, 44, 45 and 62 proteins of the bacteriophage T4 DNA replication apparatus. J. Biol. Chem., 254, 6787-6796.
23. Munn, M.M. and Rupp, W.D. (1991) Interaction of the UvrABC endonuclease with DNA containing a psoralen monoadduct or crosslink. Differential effects of superhelical density and comparison of preincision complexes. J. Biol. Chem., 266, 24748-24756.
24. Naegeli, H., Bardwell, L. and Friedberg, E.C. (1992) The DNA helicase and adenosine triphosphatase activities of yeast Rad3 protein are inhibited by DNA damage. A potential mechanism for damage-specific recognition. J. Biol. Chem., 267, 392-398.
25. Naegeli, H., Bardwell, L. and Friedberg, E.C. (1993) Inhibition of Rad3 DNA helicase activity by DNA adducts and abasic sites: implications for the role of a DNA helicase in damage-specific incision of DNA. Biochemistry, 32, 613-621.
26. Nossal, N.G. (1979) DNA replication with bacteriophage T4 proteins. Purification of the proteins encoded by T4 genes 41, 45, 44 and 62 using a complementation assay. J. Biol. Chem., 254, 6026-6031.
27. Oh, E.Y. and Grossman, L. (1987) Helicase properties of the Escherichia coli UvrAB protein complex. Proc. Natl Acad. Sci. USA, 84, 3638-3642.
28. Oh, E.Y. and Grossman, L. (1989) Characterization of the helicase activity of the Escherichia coli UvrAB protein complex. J. Biol. Chem., 264, 1336-1343.
29. Orren, D.K., Selby, C.P., Hearst, J.E. and Sancar, A. (1992) Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I. J. Biol. Chem., 267, 780-788.
30. Rush, J., Lin, T.-C., Quinones, M., Spicer, E.K., Douglas, I., Williams, K.R. and Konigsberg, W.H. (1989) The 44P subunit of the T4 DNA polymerase accessory protein complex catalyzes ATP hydrolysis. J. Biol. Chem., 264, 10943-10953.
31. Sancar, A. and Rupp, W.D. (1983) A novel repair enzyme: UvrABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region. Cell, 33, 249-260.
32. Sancar, A., Franklin, K.A., Sancar, G.B. and Tang, M.S. (1985) Repair of psoralen and acetylamino-fluorene DNA adduct by UvrABC excinuclease. J. Mol. Biol., 184, 725-734.
33. Seeberg, E. and Fuchs, R.P. (1990) Acetylaminofluorene bound to different guanines of the sequence -GGCGCC-is excised with different efficiencies by the UvrABC excision nuclease in a pattern not correlated to the potency of mutation induction. Proc. Natl Acad. Sci. USA, 87, 191-194.
34. Seeberg, E. and Steinum, A.-L. (1982) Purification and properties of the UvrA protein from Escherichia coli. Proc. Natl Acad. Sci. USA, 79, 988-992.
35. Seeley, T.W. and Grossman, L. (1990) The role of Escherichia coli UvrB in nucleotide excision repair. J. Biol. Chem., 265, 7158-7165.
36. Shi, Q., Thresher, R., Sancar, A. and Griffith, J. (1992) Electron microscopic study of (A)BC excinuclease. DNA is sharply bent in the UvrB-DNA complex. J. Mol. Biol., 226, 425-432.
37. Sung, P., Prakash, L., Matson, S.W. and Prakash, S. (1987) RAD3 protein of Saccharomyces cerevisiae is a DNA helicase. Proc. Natl Acad. Sci. USA, 84, 8951-8955.
38. Thiagalingam, S. and Grossman, L. (1993) The multiple roles for ATP in the Escherichia coli UvrABC endonuclease-catalyzed incision reaction. J. Biol. Chem., 268, 18382-18389.
39. Van Houten, B., Gamper, H., Sancar, A. and Hearst, J.E. (1987) DNase I footprint of ABC excinuclease. J. Biol. Chem., 262, 13180-13187.
40. Visse, R., de Ruijter, M., Moolenaar, G.F. and van de Putte, P. (1992) Analysis of UvrABC endonuclease reaction intermediates on cisplatin-damaged DNA using mobility shift gel electrophoresis. J. Biol. Chem., 267, 6736-6742.
41. Visse, R., King, A., Moolenaar, G.F., Goosen, N. and van de Putte, P. (1994) Protein-DNA interactions and alterations in the DNA structure upon UvrB-DNA preincision complex formation during nucleotide excision repair in Escherichia coli. Biochemistry, 33, 9881-9888.
42. Yancey-Wrona, J.E., Wood, E.R., George, J.W., Smith, K.R. and Matson, S.W. (1992) Escherichia coli Rep protein and helicase IV. Distributive single-stranded DNA dependent ATPases that catalyze a limited unwinding reaction in vitro. Eur. J. Biochem., 207, 479-485.
43. Yeung, A.T., Mattes, W.B., Oh, E.Y. and Grossman, L. (1983) Enzymatic properties of purified Escherichia coli UvrABC proteins. Proc. Natl Acad. Sci. USA, 80, 6157-6161.
44. Yeung, A.T., Mattes, W.B. and Grossman, L. (1986a) Protein complexes formed during the incision reaction catalyzed by the Escherichia coli UvrABC endonuclease. Nucleic Acids Res., 14, 2567-2582.
45. Yeung, A.T., Mattes, W.B., Oh, E.Y., Yoakum, G.H. and Grossman, L. (1986b) The purification of the Escherichia coli UvrABC incision system. Nucleic Acids Res., 14, 8535-8556.