Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cellsA model, its experimental support and implications

Mutation Research - Reviews in Mutation Research

Volumn 437, Issue 1, 1999, Pages 11-20

  Lutsenko, Eugene ^a   Bhagwat, Ashok S ^a  

^a WAYNE STATE UNIVERSITY   (United States)

Author keywords

Cancer; DNA repair; Endogenous mutagen; Hydrolytic deamination; Mismatch correction; p53; Transition mutations

Indexed keywords

CYTOSINE; PROTEIN P53; THYMINE; URACIL DNA GLYCOSYLTRANSFERASE;

BASE MISPAIRING; CARCINOGENESIS; CELL GROWTH; DEAMINATION; DNA DAMAGE; DNA REPAIR; ESCHERICHIA COLI; HYDROLYSIS; METHYLATION; MODEL; MUTATION; MUTATION RATE; NONHUMAN; PRIORITY JOURNAL; REVERTANT; REVIEW;

ESCHERICHIA COLI;

EID: 0033166375     PISSN: 13835742     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1383-5742(99)00065-4     Document Type: Article

References (66)

1. Coulondre C., Miller J.H., Farabaugh P.J., Gilbert W. Molecular basis of substitution hot spots in Escherichia coli. Nature. 274:1978;775-780.
2. Marinus M.G., Morris N.R. Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12. J. Bacteriol. 114:1973;1143-1150.
3. Bigger C., Murray K., Murray N.E. Recognition sequence of a restriction enzyme. Nature New Biol. 244:1973;7-10.
4. Boyer H.W., Chow L.T., Dugaiczyk A., Hedgepeth J., Goodman H.M. DNA substrate site for the EcoRII restriction endonuclease and modification methylase. Nature New Biol. 244:1973;40-43.
5. Lieb M. Spontaneous mutation at a 5-methylcytosine hot spot is prevented by very short patch (VSP) mismatch repair. Genetics. 128:1991;23-27.
6. Wyszynski M., Gabbara S., Bhagwat A.S. Cytosine deaminations catalyzed by DNA cytosine methyltransferases are unlikely to be the major cause of mutational hot spots at sites of cytosine methylation in E. coli. Proc. Natl. Acad. Sci. U.S.A. 91:1994;1574-1578.
7. Cooper D.N., Youssoufian H. The CpG dinucleotide and human genetic disease. Hum. Genet. 78:1988;151-155.
8. Giannelli F., Green P.M., High K.A., Lozier J.N., Lillicrap D.P., Ludwig M., Olek K., Reitsma P.H., Goosens M., Yoshioka A., Sommer S., Brownlee G.G. Haemophilia B: database of point mutations and short additions and deletions. Nucleic Acids Res. 18:1990;4053-4059.
9. Jones P.A., Rideout W.A. III, Shen J.-C., Spruck C.H., Tsai Y.C. Methylation, mutation and cancer. BioEssays. 14:1992;33-36.
10. Koeberl D.D., Bottema C.D.K., Ketterling R.P., Bridge P.J., Lillicrap D.P., Sommer S.S. Mutations causing hemophilia B: direct estimate of the underlying rates of spontaneous germ-line transitions, transversions, and deletions in a human gene. Am. J. Hum. Genet. 47:1990;202-217.
11. Hirschhorn R., Tzall S., Ellenbogen A. Hot spot mutations in adenosine deaminase deficiency. Proc. Natl. Acad. Sci. U.S.A. 87:1990;6171-6175.
12. Kohler S.W., Provost G.S., Fieck A., Kretz P.L., Bullock W.O., Sorge J.A., Putman D.L., Short J.M. Spectra of spontaneous and mutagen-induced mutations in the lacI gene in transgenic mice. Proc. Natl. Acad. Sci. U.S.A. 88:1991;7958-7962.
13. Douglas G.R., Gingerich J.D., Gossen J.A., Bartlett S.A. Sequence spectra of spontaneous lacZ gene mutations in transgenic mouse somatic and germline tissues. Mutagenesis. 9:1994;451-458.
14. Zimmer D.M., Zhang X.B., Harbach P.R., Mayo J.K., Aaron C.S. Spontaneous and ethylnitrosourea-induced mutation fixation and molecular spectra at the lacI transgene in the Big Blue rat-2 embryo cell line. Environ. Mol. Mutagen. 28:1996;325-333.
15. Shen J.C., Creighton S., Jones P.A., Goodman M.F. A comparison of the fidelity of copying 5-methylcytosine and cytosine at a defined DNA template site. Nucleic Acids Res. 20:1992;5119-5125.
16. Lindahl T., Nyberg B. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry. 13:1974;3405-3410.
17. Ehrlich M., Norris K.F., Wang R.Y.-H., Kuo K.C., Gehrke C.W. DNA cytosine methylation and heat-induced deamination. Biosci. Rep. 6:1986;387-393.
18. Shapiro R., Klein R.S. The deamination of cytidine and cytosine by acidic buffer solutions. Mutagenic implications. Biochemistry. 5:1966;2358-2362.
19. Duncan B.K., Miller J.H. Mutagenic deamination of cytosine residues in DNA. Nature. 287:1980;560-561.
20. Lieb M. Specific mismatch correction in bacteriophage lambda crosses by very short patch repair. Mol. Gen. Genet. 191:1983;118-125.
21. Hennecke F., Kolmar H., Bründl K., Fritz H.-J. The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease. Nature. 353:1991;776-778.
22. Vairapandi M., Duker N.J. Enzymic removal of 5-methylcytosine from DNA by a human DNA-glycosylase. Nucleic Acids Res. 21:1993;5323-5327.
23. Shen J.-C., Rideout W.M. III, Jones P.A. High frequency mutagenesis by a DNA methyltransferase. Cell. 71:1992;1073-1080.
24. Yebra M.J., Bhagwat A.S. A cytosine methyltransferase converts 5-methylcytosine in DNA to thymine. Biochemistry. 34:1995;14752-14757.
25. Yang A.S., Shen J.-C., Zingg J.-M., Mi S., Jones P.A. HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair. Nucleic Acids Res. 23:1995;1380-1387.
26. Schmutte C., Yang A.S., Beart R.W., Jones P.A. Base excision repair of U:G mismatches at a mutational hot spot in the p53 gene is more efficient than base excision repair of T:G mismatches in extracts of human colon tumors. Cancer Res. 55:1995;3742-3746.
27. Denissenko M.F., Chen J.X., Tang M.S., Pfeifer G.P. Cytosine methylation determines hot spots of DNA damage in the human P53 gene. Proc. Natl. Acad. Sci. U.S.A. 94:1997;3893-3898.
28. Steinberg R.A. Enzymic removal of 5-methylcytosine from poly(dG-5-methyl-dC) by HeLa cell nuclear extracts is not by a DNA glycosylase. Nucleic Acids Res. 23:1995;1621-1624.
29. Vairapandi M., Duker N.J. Partial purification and characterization of human 5-methylcytosine-DNA glycosylase. Oncogene. 13:1996;933-938.
30. Sheluho D., Yebra M.J., Khariwala S.S., Bhagwat A.S. Lack of correlation between binding of methyltransferase to DNA duplexes containing mismatches and the promotion of C to T mutations. Mol. Gen. Genet. 255:1997;54-59.
31. Bandaru B., Gopal J., Bhagwat A.S. Overproduction of DNA cytosine methyltransferases causes methylation and C to T mutations at non-canonical sites. J. Biol. Chem. 271:1996;7851-7859.
32. Bandaru B., Wyszynski M., Bhagwat A.S. HpaII methyltransferase is mutagenic in Escherichia coli. J. Bacteriol. 177:1995;2950-2952.
33. A. Kornberg, T.A. Baker, DNA Replication, Freeman, New York, 1992, pp. 637-687.
34. Cooper S., Keasling J.D. Cycle-specific replication of chromosomal and F-plasmid origins. FEMS Microbiol. Lett. 163:1998;217-222.
35. Keasling J.D., Palsson B.O., Cooper S. Cell-cycle-specific F plasmid replication: regulation by cell size control of initiation. J. Bacteriol. 173:1991;2673-2680.
36. Kline B.C., Kogoma T., Tam J.E., Shields M.S. Requirement of the Escherichia coli DNAA gene product for plasmid F maintenance. J. Bacteriol. 168:1986;440-443.
37. Hansen E.B., Yarmolinsky M.B. Host participation in plasmid maintenance: dependence upon dnaA of replicons derived from P1 and F. Proc. Natl. Acad. Sci. U.S.A. 83:1986;4423-4427.
38. Henry M.F., Cronan J.E. Jr. A facile and reversible method to decrease the copy number of the ColE1-related cloning vectors commonly used in Escherichia coli. J. Bacteriol. 171:1989;5254-5261.
39. Nordstrom K., Austin S.J. Cell-cycle-specific initiation of replication. Mol. Microbiol. 10:1993;457-463.
40. Grindley N.D.F., Kelley W.S. Effects of different alleles of the E. coli K12 pol A gene on the replication of non-transferring plasmids. Mol. Gen. Genet. 143:1976;311-318.
41. Luria S.E., Delbrück M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics. 28:1943;491-511.
42. Shen J.-C., Rideout W.M. III, Jones P.A. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res. 22:1994;972-976.
43. Beletskii A., Bhagwat A.S. Transcription-induced mutations: increase in C to T mutations in the non-transcribed strand during transcription in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 93:1996;13919-13924.
44. Duncan B.K., Weiss B. Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli. J. Bacteriol. 151:1982;750-755.
45. Burgers P.M., Klein M.B. Selection by genetic transformation of a Saccharomyces cerevisiae mutant defective for the nuclear uracil-DNA-glycosylase. J. Bacteriol. 166:1986;905-913.
46. Gabbara S., Wyszynski M., Bhagwat A.S. A DNA repair process in Escherichia coli corrects U:G and T:G mismatches to C:G at sites of cytosine methylation. Mol. Gen. Genet. 243:1994;244-248.
47. Wiebauer K., Jiricny J. In vitro correction of G.T mispairs to G.C pairs in nuclear extracts from human cells. Nature. 339:1989;234-236.
48. Gallinari P., Jiricny J. A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature. 383:1996;735-738.
49. Macintyre G., Doiron K.M., Cupples C.G. The Vsr endonuclease of Escherichia coli: an efficient DNA repair enzyme and a potent mutagen. J. Bacteriol. 179:1997;6048-6052.
50. Tornaletti S., Pfeifer G.P. Complete and tissue-independent methylation of CpG sites in the p53 gene: implications for mutations in human cancers. Oncogene. 10:1995;1493-1499.
51. Frederico L.A., Kunkel T.A., Shaw B.R. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry. 29:1990;2532-2537.
52. Frederico L.A., Kunkel T.A., Shaw B.A. Cytosine deamination in mismatched base pairs. Biochemistry. 32:1993;6523-6530.
53. Krokan H., Wittwer C.U. Uracil DNA-glycosylase from HeLa cells: general properties, substrate specificity and effect of uracil analogs. Nucleic Acids Res. 9:1981;2599-2613.
54. Leblanc J.P., Martin B., Cadet J., Laval J. Uracil-DNA glycosylase. Purification and properties of uracil-DNA glycosylase from Micrococcus luteus. J. Biol. Chem. 257:1982;3477-3483.
55. Lieb M., Rehmat S. 5-Methylcytosine is not a mutation hot spot in nondividing Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 94:1997;940-945.
56. Dar M.E., Bhagwat A.S. Mechanism of expression of DNA repair gene vsr, an Escherichia coli gene that overlaps the DNA cytosine methylase gene, dcm. Mol. Microbiol. 9:1993;823-833.
57. Sohail A., Lieb M., Dar M., Bhagwat A.S. A gene required for very short patch repair in E. coli is adjacent to the DNA cytosine methylase gene. J. Bacteriol. 172:1990;4214-4221.
58. Doiron K.M., Viau S., Koutroumanis M., Cupples C.G. Overexpression of vsr in Escherichia coli is mutagenic. J. Bacteriol. 178:1996;4294-4296.
59. Saparbaev M., Laval J. 3,N4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase. Proc. Natl. Acad. Sci. U.S.A. 95:1998;8508-8513.
60. Hang B., Medina M., Fraenkel-Conrat H., Singer B. A 55-kDa protein isolated from human cells shows DNA glycosylase activity toward 3,N4-ethenocytosine and the G/T mismatch. Proc. Natl. Acad. Sci. U.S.A. 95:1998;13561-13566. in process citation.
61. Sibghat U., Gallinari P., Xu Y.Z., Goodman M.F., Bloom L.B., Jiricny J., Day R.S. III Base analog and neighboring base effects on substrate specificity of recombinant human G:T mismatch-specific thymine DNA-glycosylase. Biochemistry. 35:1996;12926-12932.
62. Waters T.R., Swann P.F. Kinetics of the action of thymine DNA glycosylase. J. Biol. Chem. 273:1998;20007-20014.
63. Martinez A., Kolter R. Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps. J. Bacteriol. 179:1997;5188-5194.
64. Ruiz-Rubio M., Yamamoto K., Bockrath R. An in vivo complex with DNA photolyase blocks UV mutagenesis targeted at a thymine-cytosine dimer in Escherichia coli. J. Bacteriol. 170:1988;5371-5374.
65. Lewis J.D., Meehan R.R., Henzel W.J., Maurer-Fogy I., Jeppesen P., Klein F., Bird A. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell. 69:1992;905-914.
66. Nan X., Campoy F.J., Bird A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell. 88:1997;471-481.