Initiation of repair of A/G mismatches is modulated by sequence context

DNA Repair

Volumn 2, Issue 8, 2003, Pages 863-878

  Sanchez, Ana M ^a   Volk, David E ^b   Gorenstein, David G ^b   Lloyd, R Stephen ^a  

^a UNIVERSITY OF TEXAS MEDICAL BRANCH   (United States)

^b University of Texas Medical Branch School of Medicine   (United States)

Author keywords

DNA glycosylases; DNA repair; MutY

Indexed keywords

ADENINE NUCLEOTIDE; BACTERIAL ENZYME; DNA; DOUBLE STRANDED DNA;

ARTICLE; CHEMICAL BOND; CONFORMATIONAL TRANSITION; CORRELATION ANALYSIS; DNA CONFORMATION; DNA SEQUENCE; ENZYME GLYCOSYLATION; ENZYME KINETICS; ESCHERICHIA COLI; EXCISION REPAIR; MISMATCH REPAIR; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; THERMOSTABILITY;

ESCHERICHIA COLI; ZIZIPHUS MAURITIANA;

EID: 0142092698     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1568-7864(03)00067-3     Document Type: Article

References (67)

1. McCullough A.K., Dodson M.L., Lloyd R.S. Initiation of base excision repair: glycosylase mechanisms and structures. Annu. Rev. Biochem. 68:1999;255-285.
2. David R.S., Williams S.D. Chemistry of glycosylases and endonucleases involved in base-excision repair. Chem. Rev. 98:1998;1221-1262.
3. Modrich P., Lahue R. Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu. Rev. Biochem. 65:1996;101-133.
4. Lu A.L., Clark S., Modrich P. Methyl-directed repair of DNA base-pair mismatches in vitro. Proc. Natl. Acad. Sci. U.S.A. 80:1983;4639-4643.
5. Shibutani S., Takeshita M., Grollman A.P. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature. 349:1991;431-434.
6. Michaels M.L., Cruz C., Grollman A.P., Miller J.H. Evidence that MutY and MutM combine to prevent mutations by an oxidatively damaged form of guanine in DNA. Proc. Natl. Acad. Sci. U.S.A. 89:1992;7022-7025.
7. Michaels M.L., Tchou J., Grollman A.P., Miller J.H. A repair system for 8-oxo-7,8-dihydrodeoxyguanine. Biochemistry. 31:1992;10964-10968.
8. Au K.G., Cabrera M., Miller J.H., Modrich P. Escherichia coli mutY gene product is required for specific A:G - C:G mismatch correction. Proc. Natl. Acad. Sci. U.S.A. 85:1988;9163-9166.
9. Lu A.L., Chang D.Y. Repair of single base-pair transversion mismatches of Escherichia coli in vitro: correction of certain A/G mismatches is independent of dam methylation and host mutHLS gene functions. Genetics. 118:1988;593-600.
10. Radicella J.P., Clark E.A., Fox M.S. Some mismatch repair activities in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 85:1988;9674-9678.
11. Tsai-Wu J.J., Liu H.F., Lu A.L. Escherichia coli MutY protein has both N-glycosylase and apurinic/apyrimidinic endonuclease activities on A.C and A.G mispairs. Proc. Natl. Acad. Sci. U.S.A. 89:1992;8779-8783.
12. Michaels M.L., Pham L., Nghiem Y., Cruz C., Miller J.H. MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III. Nucleic Acids Res. 18:1990;3841-3845.
13. Manuel R.C., Czerwinski E.W., Lloyd R.S. Identification of the structural and functional domains of MutY, an Escherichia coli DNA mismatch repair enzyme. J. Biol. Chem. 271:1996;16218-16226.
14. Noll D.M., Gogos A., Granek J.A., Clarke N.D. The C-terminal domain of the adenine-DNA glycosylase MutY confers specificity for 8-oxoguanine.adenine mispairs and may have evolved from MutT, an 8-oxo-dGTPase. Biochemistry. 38:1999;6374-6379.
15. Li X., Lu A.L. Intact MutY and its catalytic domain differentially contact with A/8-oxoG-containing DNA. Nucleic Acids Res. 28:2000;4593-4603.
16. Li X., Wright P.M., Lu A.L. The C-terminal domain of MutY glycosylase determines the 7,8-dihydro-8-oxo-guanine specificity and is crucial for mutation avoidance. J. Biol. Chem. 275:2000;8448-8455.
17. Lu A.L., Tsai-Wu J.J., Cillo J. DNA determinants and substrate specificities of Escherichia coli MutY. J. Biol. Chem. 270:1995;23582-23588.
18. Lu A.L., Yuen D.S., Cillo J. Catalytic mechanism and DNA substrate recognition of Escherichia coli MutY protein. J. Biol. Chem. 271:1996;24138-24143.
19. Manuel R.C., Lloyd R.S. Cloning, overexpression, and biochemical characterization of the catalytic domain of MutY. Biochemistry. 36:1997;11140-11152.
20. Zharkov D.O., Gilboa R., Yagil I., Kycia J.H., Gerchman J.H., Shoham G., Grollman A.P. Role for lysine 142 in the excision of adenine from A:G mispairs by MutY DNA glycosylase of Escherichia coli. Biochemistry. 39:2000;14768-14778.
21. Williams S.D., David S.S. A single engineered point mutation in the adenine glycosylase MutY confers bifunctional glycosylase/AP lyase activity. Biochemistry. 39:2000;10098-11109.
22. Tchou J., Kasai H., Shibutani S., Chung M.H., Laval J., Grollman A.P., Nishimura S. 8-oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity. Proc. Natl. Acad. Sci. U.S.A. 88:1991;4690-4694.
23. Guan Y., Manuel R.C., Arvai A.S., Parikh S.S., Mol C.D., Miller J.H., Lloyd R.S., Tainer J.A. MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nat. Struct. Biol. 5:1998;1058-1064.
24. Volk D.E., House P.G., Thiviyanathan V., Luxon B.A., Zhang S., Lloyd R.S., Gorenstein D.G. Structural similarities between MutT and the C-terminal domain of MutY. Biochemistry. 39:2000;7331-7336.
25. House P.G., Volk D.E., Thiviyanathan V., Manuel R.C., Luxon B.A., Gorenstein D.G., Lloyd R.S. Potential double-flipping mechanism by E. coli MutY. Prog. Nucleic Acid Res. Mol. Biol. 68:2001;349-364.
26. Lu A.L., Chang D.Y. A novel nucleotide excision repair for the conversion of an A/G mismatch to C/G base pair in E. coli. Cell. 54:1988;805-812.
27. Plum G.E., Grollman A.P., Johnson F., Breslauer K.J. Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex. Biochemistry. 34:1995;16148-16160.
28. Cheng J.W., Chou S.H., Reid B.R. Base pairing geometry in GA mismatches depends entirely on the neighboring sequence. J. Mol. Biol. 228:1992;1037-1041.
29. Lane A., Martin S.R., Ebel S., Brown T. Solution conformation of a deoxynucleotide containing tandem G.A mismatched base pairs and 3′-overhanging ends in d(GTGAACTT)2. Biochemistry. 31:1992;12087-12095.
30. McAuley-Hecht K.E., Leonard G.A., Gibson N.J., Thomson J.B., Watson W.P., Hunter W.N., Brown T. Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs. Biochemistry. 33:1994;10266-10270.
31. Pope M.A., Porello S.L., David S.S. Escherichia coli apurinic- apyrimidinic endonucleases enhance the turnover of the adenine glycosylase MutY with G:A substrates. J. Biol. Chem. 277:2002;22605-22615.
32. syn base-pairs. J. Mol. Biol. 207:1989;455-457.
33. Smallcombe S.H., Patt S.L., Keifer P.A. WET solvent suppression and its applications to LC NMR and high-resolution NMR spectroscopy. J. Mag. Res. Series. A117:1995;295-303.
34. Smallcombe S.H. WET solvent suppression and its applications to LCNMR and high-resolution NMR spectroscopy. J. Magn. Reson. 117:1995;295-303.
35. Rance M. Improved techniques for homonuclear rotating-frame and isotropic mixing experiments. J. Magn. Reson. 74:1987;557-564.
36. S. Macura, W.M. Westler, J.L. Markley, Two Dimensional Exchange Spectroscopy of Proteins, Academic Press, San Diego, 1994.
37. T. Macke, D.A. Case, NAB 4.4, The Scripps Research Institute, San Diego, CA
38. D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheatham, W.S. Ross, C.L. Simmerling, T.A. Darden, K.M. Merz, R.V. Stanton, A.L. Chang, J.J. Vincent, M. Crowley, D.M. Ferguson, R.J. Radmer, G.L. Seibel, U.C. Singh, P.K. Weiner P.A. Kollman, AMBER, University of California, San Francisco, CA, 1997.
39. Darden T., York D., Pederson L. Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:1993;10089-10092.
40. R. Meadows, C.B. Post, B.A. Luxon, D.G. Gorenstein, MORASS, University of Texas Medical Branch, Galveston, TX, 1998.
41. Volk D.E., Rice J.S., Luxon B.A., Yeh H.J., Liang C., Xie G., Sayer J.M., Jerina D.M., Gorenstein D.G. NMR evidence for syn-anti interconversion of a trans opened (10R)-dA adduct of benzo[a]pyrene (7S,8R)-diol (9R,10S)-epoxide in a DNA duplex. Biochemistry. 39:2000;14040-14053.
42. W.S. Ross, CARNAL, University of California, San Francisco, CA, 1994.
43. Patel D.J., Kozlowski S.A., Ikuta S., Itakura K. Deoxyguanosine- deoxyadenosine pairing in the d(C-G-A-G-A-A-T-T-C-G-C-G) duplex: conformation and dynamics at and adjacent to the dG X dA mismatch site. Biochemistry. 23:1984;3207-3217.
44. Brown T., Hunter W.N., Kneale G., Kennard O. Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations. Proc. Natl. Acad. Sci. U.S.A. 83:1986;2402-2406.
45. Porello S.L., Leyes A.E., David S.S. Single-turnover and pre-steady-state kinetics of the reaction of the adenine glycosylase MutY with mismatch-containing DNA substrates. Biochemistry. 37:1998;14756-14764.
46. Wong I., Bernards A.S., Miller J.K., Wirz J.A. A dimeric mechanism for contextual target recognition by MutY glycosylase. J. Biol. Chem. 278:2003;2411-2418.
47. K. Wuthrich, NMR of Protein and Nucleic Acids, Wiley, New York, 1986.
48. Uesugi S., Ikehara M. C-13 Magnetic-resonance Spectra of 8-substituted purine nucleotides-characteristic shifts for syn conformation. J. Am. Chem. Soc. 99:1977;3250-3253.
49. Ikehara M., Uesugi S., Yoshida K. Conformation of purine nucleoside pyrophosphates as studied by circular dichroism. Biochemistry. 11:1972;830-836.
50. anti mismatch formation in DNA dodecamers at acidic pH: pH dependent conformational transition of G:A mispairs detected by proton NMR. J. Am. Chem. Soc. 110:1988;5178-5182.
51. Fazakerley G.V., Quignard E., Woisard A., Guschlbauer W., van der Marel G.A., van Boom J.H., Jones M., Radman M. Structures of mismatched base pairs in DNA and their recognition by the Escherichia coli mismatch repair system. EMBO J. 5:1986;3697-3703.
52. Slupphaug G., Mol C.D., Kavli B., Arvai A.S., Krokan H.E., Tainer J.A. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 384:1996;87-92.
53. Steitz T.A., Beese L., Freemont P.S., Friedman J.M., Sanderson M.R. Structural studies of Klenow fragment: an enzyme with two active sites. Cold Spring Harb. Symp. Quant. Biol. 52:1987;465-471.
54. Fersht A.R., Knill-Jones J.W., Tsui W.C. Kinetic basis of spontaneous mutation. Misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli. J. Mol. Biol. 156:1982;37-51.
55. Topal M.D., DiGuiseppi S.R., Sinha N.K. Molecular basis for substitution mutations. Effect of primer terminal and template residues on nucleotide selection by phage T4 DNA polymerase in vitro. J. Biol. Chem. 255:1980;11717-11724.
56. Eftedal I., Guddal P.H., Slupphaug G., Volden G., Krokan H.E. Consensus sequences for good and poor removal of uracil from double stranded DNA by uracil-DNA glycosylase. Nucleic Acids Res. 21:1993;2095-2101.
57. Brash D.E., Seetharam S., Kraemer K.H., Seidman M.M., Bredberg A. Photoproduct frequency is not the major determinant of UV base substitution hot spots or cold spots in human cells. Proc. Natl. Acad. Sci. U.S.A. 84:1987;3782-3786.
58. Haukanes B.I., Helland D.E., Kleppe K. Action of a mammalian AP-endonuclease on DNAs of defined sequences. Nucleic Acids Res. 17:1989;1493-1509.
59. Georgiadis P., Xu Y.Z., Swann P.F. Nitrosamine-induced cancer: O4-alkylthymine produces sites of DNA hyperflexibility. Biochemistry. 30:1991;11725-11732.
60. Li Y., Agrawal S. Oligonucleotides containing G.A pairs: effect of flanking sequences on structure and stability. Biochemistry. 34:1995;10056-10062.
61. Nikonowicz E.P., Meadows R.P., Fagan P., Gorenstein D.G. NMR structural refinement of a tandem G.A mismatched decamer d(CCAAGATTGG)2 via the hybrid matrix procedure. Biochemistry. 30:1991;1323-1334.
62. Brown T., Leonard G.A., Booth E.D., Kneale G. Influence of pH on the conformation and stability of mismatch base-pairs in DNA. J. Mol. Biol. 212:1990;437-440.
63. Greene K.L., Jones R.L., Li Y., Robinson H., Wang A.H., Zon G., Wilson W.D. Solution structure of a GA mismatch DNA sequence, d(CCATGAATGG)2, determined by 2D NMR and structural refinement methods. Biochemistry. 33:1994;1053-1062.
64. Kan L.S., Chandrasegaran S., Pulford S.M., Miller P.S. Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 80:1983;4263-4265.
65. Hunter W.N., Brown T., Kennard O. Structural features and hydration of d(C-G-C-G-A-A-T-T-A-G-C-G); a double helix containing two G.A mispairs. J. Biomol. Struct. Dyn. 4:1986;173-191.
66. Patel D.J., Kozlowski S.A., Ikuta S., Itakura K. Dynamics of DNA duplexes containing internal G.T, G.A, A.C, and T.C pairs: hydrogen exchange at and adjacent to mismatch sites. Fed. Proc. 43:1984;2663-2670.
67. Chuprina V.P., Poltev V.I. Possible conformations of double-helical polynucleotides containing incorrect base pairs. Nucleic Acids Res. 11:1983;5205-5222.