Identification of high excision capacity for 5-hydroxymethyluracil mispaired with guanine in DNA of Escherichia coli MutM, Nei and Nth DNA glycosylases

Nucleic Acids Research

Volumn 31, Issue 4, 2003, Pages 1191-1196

  Hori, Masaki ^c   Yonei, Shuji ^c   Sugiyama, Hiroshi ^a   Kino, Katsuhito ^a   Yamamoto, Kazuo ^b   Zhang, Qiu Mei ^c  

^a TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^b TOHOKU UNIVERSITY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLURACIL; 5 METHYLCYTOSINE; ADENINE; BACTERIAL DNA; DNA; DNA GLYCOSYLTRANSFERASE; GUANINE; METHYL GROUP; OLIGONUCLEOTIDE; THYMINE; URACIL DERIVATIVE;

BASE MISPAIRING; BASE PAIRING; CONTROLLED STUDY; DEAMINATION; ENZYME ACTIVITY; ESCHERICHIA COLI; EXCISION REPAIR; GENE CONVERSION; IN VITRO STUDY; INCUBATION TIME; MAMMAL CELL; NONHUMAN; OXIDATION; PRIORITY JOURNAL; PURIFICATION; REVIEW; YEAST;

BASE PAIR MISMATCH; BASE SEQUENCE; DEOXYRIBONUCLEASE (PYRIMIDINE DIMER); DNA GLYCOSYLASES; DNA REPAIR; DNA-FORMAMIDOPYRIMIDINE GLYCOSYLASE; ENDODEOXYRIBONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GUANINE; N-GLYCOSYL HYDROLASES; OLIGONUCLEOTIDES; PENTOXYL; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; MAMMALIA; NEGIBACTERIA;

EID: 0037440695     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg223     Document Type: Review

References (50)

1. Wallace,S.S. (1997) Oxidative damage to DNA and its repair. In Scandalios,J.G. (ed.), Oxidative Stress and the Molecular Biology of Antioxidant Defenses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 49-90.
2. Cadet,J., Delatour,T., Douki,T., Gasparutto,D., Pouget,J.-P., Ravanat,J.-L. and Sauvaigo,S. (1999) Hydroxyl radicals and DNA base damage. Mutat. Res., 424, 9-21.
3. Marnett,L.J. (2000) Oxyradicals and DNA damage. Carcinogenesis, 21, 361-370.
4. Ames,B.N., Shigenaga,M. and Hagen,T.M. (1993) Oxidants, antioxidants, diseases and the degenerative of aging. Proc. Natl Acad Sci. USA, 90, 7915-7922.
5. Warner,H.R. (1994) Superoxide dismutase, aging and degenerative disease. Free Radic. Biol. Med., 17, 249-258.
6. Beckman,K.B. and Ames,B.N. (1998) The free radical theory of aging matures. Physiol. Rev., 78, 547-581.
7. Demple,B. and Harrison,L. (1994) Repair of oxidative damage to DNA: enzymology and biology. Annu. Rev. Biochem., 63, 915-948.
8. David,S.S. and Williams,S.D. (1998) Chemistry of glycosylase and endonuclease involved in base-excision repair. Chem. Rev., 98, 1221-1261.
9. Mol,C.D., Parikh,S.S., Putnam,C.D., Lo,T.P. and Tainer,J.A. (1999) DNA repair mechanisms for the recognition and removal of damaged bases. Annu. Rev. Biophys. Biomol. Struct., 28, 101-128.
10. Tofigh,S. and Frenkel,K. (1989) Effect of metals on nucleoside hydroperoxide, a product of ionizing radiation in DNA. Free Radic. Biol. Med, 7, 131-143.
11. Zhang,Q.-M., Sugiyama,H., Miyabe,I., Matsuda,S., Saito,I. and Yonei,S. (1997) Replication of DNA templates containing 5-formyluracil, a major oxidative lesion of thymine in DNA. Nucleic Acids Res., 25, 3969-3973.
12. Miyabe,I., Zhang,Q.-M., Sugiyama,H., Kino,K. and Yonei,S. (2001) Mutagenic effects of 5-formyluracil on a plasmid vector during replication in Escherichia coli. Int. J. Radiat. Biol., 77, 53-58.
13. Klungland,A., Paulsen,R., Rolseth,V., Yamada,Y., Ueno,Y., Wiik,P., Matsuda,A., Seeberg,E. and Bjelland,S. (2001) 5-formyluracil and its nucleoside derivatives confer toxicity and mutagenicity to mammalian cells by interfering with normal RNA and DNA metabolism. Toxicol. Lett., 119, 71-78.
14. Bjelland,S., Birkeland,N.K., Benneche,T., Volden,G. and Seeberg,E. (1994) DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the AlkA enzyme in Escherichia coli. J. Biol. Chem., 269, 30489-30495.
15. Zhang,Q.-M., Miyabe,I., Matsumoto,Y., Kino,K., Sugiyama.H. and Yonei,S. (2000) Identification of repair enzymes for 5-formyluracil in DNA. Nth, Nei, and MutM proteins of Escherichia coli. J. Biol. Chem., 275, 35471-35477.
16. Miyabe,I., Zhang,Q.-M., Kino,K., Sugiyama,H., Takao,M., Yasui,A. and Yonei,S. (2002) Identification of 5-formyluracil DNA glycosylase activity of human hNTH1 protein. Nucleic Acids Res., 30, 3443-3448.
17. Zhang,Q.-M. (2001) Role of the Escherichia coli and human DNA glycosylases that remove 5-formyluracil from DNA in the prevention of mutations. J. Radiat. Res., 42, 11-19.
18. Frenkel,K., Cummings,A., Solomon,J., Cadet,J. and Teebor,G.W. (1985) Quantitative determination of the 5-(hydroxymethyl)uracil moiety in the DNA of gamma-irradiated cells. Biochemistry, 24, 4527-4533.
19. Teebor,G.W., Boorstein,R.J. and Cadet,J. (1988) The repairability ofoxidative free radical mediated damage to DNA: a review. Int. J. Radiat. Biol., 54, 131-150.
20. Levy,D.D. and Teebor,G.W. (1991) Site directed substitution of 5-hydroxymethyluracil for thymine in replicating phi X-174am3 DNA via synthesis of 5-hydroxymethyl-2′-deoxyuridine-5′-triphosphate. Nucleic Acids Res., 19, 3337-3343.
21. Zhang,Q.-M., Sugiyama,H., Miyabe,I., Matsuda,S., Kino,K., Saito,I. and Yonei,S. (1999) Replication in vitro and cleavage by restriction endonuclease of 5-formyluracil- and 5-hydroxymethyluracil-containing oligonucleotides. Int. J. Radiat. Biol., 75, 59-65.
22. Vilpo,J.A. and Vilpo,L.M. (1995) Restriction, methylation and ligation of 5-hydroxymethyluracil-containing DNA. Mutat. Res., 316, 123-131.
23. Hollstein,M.C., Brooks,P., Linn,S. and Ames,B.N. (1984) Hydroxymethyluracil DNA glycosylase in mammalian cells. Proc. Natl Acad. Sci. USA, 81, 4003-4007.
24. Boorstein,R.J., Chiu,L.-N. and Teebor,G.W. (1992) A mammalian cell line deficient in activity of the DNA repair enzyme 5-hydroxymethyluracil-DNA glycosylase is resistant to the toxic effects of the thymidine analog 5-hydroxymethyl-2′-deoxyuridine. Mol. Cell. Biol. 12, 5536-5540.
25. Friedberg,E.C., Ganesan,A.K. and Minton,K. (1975) N-glycosidase activity in extracts of Bacillus subtilis and its inhibition after infection with bacteriophage PBS2. J. Virol., 16, 315-321.
26. Boorstein,R.J., Levy,D.D. and Teebor,G.W. (1987) 5-hydroxymethyluracil-DNA glycosylase activity is a differentiated function of mammalian cells. Mutat. Res., 183, 257-263.
27. Rusmintratip,V. and Sowers,L.C. (2000) An unexpectedly high excision capacity for mispaired 5-hydroxymethyluracil in human cell extracts. Proc. Natl Acad. Sci. USA, 97, 14183-14187.
28. Cannon-Carlson,S.V., Gokhale,H. and Teebor,G.W. (1989) Purification and characterization of 5-hydroxymethyluracil-DNA glycosylase from calf thymus. Its possible role in the maintenance of methylated cytosine residues. J. Biol. Chem., 264, 13306-13312.
29. Sugiyama,H., Matsuda,S., Kino,K., Zhang,Q.-M., Yonei,S. and Saito,I. (1996) New synthetic method of 5-formyluracil-containing oligonucleotides and their melting behavior. Tetrahedron Lett., 37, 9067-9070.
30. Matsumoto,Y., Zhang,Q.-M., Takao,M., Yasui,A. and Yonei,S. (2001) Escherichia coli Nth and human hNTH1 DNA glycosylases are involved in removal of 8-oxoguanine from 8-oxoguanine/guanine mispairs in DNA. Nucleic Acids Res., 29, 1975-1981.
31. McCullough,A.K., Dodson,M.L. and Lloyd,R.S. (1999) Initiation of base excision repair: glycosylase mechanisms and structures. Annu. Rev. Biochem., 68, 255-285.
32. Nash,H.M., Bruner,S.D., Scharer,O.D., Kawate,T., Addona,T.A., Spooner,E., Lane,W.S. and Verdine,G.L. (1996) Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA-repair protein superfamily. Curr. Biol., 6, 968-980.
33. Rabow,L.E. and Kow,Y.W. (1997) Mechanism of action of base release by Escherichia coli Fpg protein: role of lysine 155 in catalysis. Biochemistry, 36, 5084-5096.
34. Kallen,R.G., Simon,M. and Marmur,J. (1962) The occurrence of a new pyrimidine base replacing thymine in a bacteriophage DNA: 5-hydroxymethyl uracil. J. Mol. Biol., 5, 248-250.
35. Mellac,S., Fazakerley,G.V. and Sowers,L.C. (1993) Structures of base pairs with 5-(hydroxymethyl)-2′-deoxyuridine in DNA determined by NMR spectroscopy. Biochemistry, 32, 7779-7786.
36. Herrala,A.M. and Vilpo,J.A. (1989) Template-primer activity of 5-(hydroxymethyl)uracil-containing DNA for prokaryotic and eukaryotic DNA and RNA polymerases. Biochemistry, 28, 8274-8277.
37. Marinus,M.G. (1973) Location of DNA methylation genes on the Escherichia coli K-12 genetic map. Mol. Gen. Genet., 127, 47-55.
38. Hanck,T., Schmidt,S. and Fritz,H.J. (1993) Sequence-specific and mechanism-based crosslinking of Dcm DNA cytosine-C5 methyltransferase of E. coli K-12 to synthetic oligonucleotide containing 5-fluoro-2′-deoxycytidine. Nucleic Acids Res., 21, 303-309.
39. Coulondre,C., Miller,J.H., Farabauge,P.J. and Gilbert,W. (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature, 274, 775-780.
40. Lieb,M. (1991) Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair. Genetics, 128, 23-27.
41. Lieb,M. and Bhagwat,A.S. (1996) Very short patch repair: reducing the cost of cytosine methylation. Mol. Microbiol., 20, 467-473.
42. Eisen,J.A. and Hanawalt,P.C. (1999) A phylogenomic study of DNA repair genes, proteins and processes. Mutat. Res., 435, 171-213.
43. Aravind,L., Walker,D.R. and Koonin,E.V. (2000) Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res., 27, 1223-1242.
44. Ikeda,S., Biswas,T., Roy,R., Izumi,T., Boldogh,I., Kurosky,A., Sarker,A.H., Seki,S. and Mitra,S. (1998) Purification and characterization of human NTH1, a homolog of Escherichia coli endonuclease III. J. Biol. Chem., 273, 21585-21593.
45. Dizdaroglu,M., Bauche,C., Rodriguez,H. and Laval,J. (2000) Novel substrates of Escherichia coli Nth protein and its kinetics for excision of modified bases from DNA damaged by free radicals. Biochemistry, 39, 5586-5592.
46. Spruck,C.H.,II, Rideout,W.M.,III and Jones,P.A. (1993) DNA methylation and cancer. In Jost,J.P. and Saluz,H.P. (eds), DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, Switzerland, pp. 487-509.
47. Jones,P.A., Rideout,W.M.,III, Shen,J.-C., Spruck,C.H. and Tsai,Y.C. (1992) Methylation, mutation and cancer. BioEssays, 14, 33-36.
48. Laird,P.W. and Jaenisch,R. (1994) DNA methylation and cancer. Hum. Mol. Genet., 3, 1487-1495.
49. Baker,D., Liu,P., Burdzy,A. and Sowers,L.C. (2002) Characterization of the substrate specificity of a human 5-hydroxymethyluracil glycosylase activity. Chem. Res. Toxicol., 15, 33-39.
50. Boorstein,R.J., Cummings,A.,Jr, Marenstein,D.R., Chan,M.K., Ma,Y., Nuebert,T.A., Brown,S.M. and Teebor,G.W. (2001) Definitive identification of mammalian 5-hydroxymethyluracil DNA N-glycosylase activity as SMUG1. J. Biol. Chem., 276, 41991-41997.