Repair of deaminated base damage by Schizosaccharomyces pombe thymine DNA glycosylase

DNA Repair

Volumn 7, Issue 12, 2008, Pages 1962-1972

  Dong, Liang ^a   Mi, Rongjuan ^a   Glass, Robert A ^a   Barry, John N ^a   Cao, Weiguo ^a  

^a CLEMSON UNIVERSITY   (United States)

Author keywords

Deamination; DNA damage; DNA repair; Fission yeast; Nitrosative stress; Thymine DNA glycosylase

Indexed keywords

DNA BASE; HYPOXANTHINE; OXANINE; THYMINE DNA GLYCOSYLASE; UNCLASSIFIED DRUG; URACIL; XANTHINE;

AMINO ACID SUBSTITUTION; ARTICLE; CHEMICAL STRUCTURE; CONTROLLED STUDY; DEAMINATION; DNA DAMAGE; DNA REPAIR; DOUBLE STRANDED DNA BREAK; ENZYME ACTIVITY; ENZYME BINDING; ENZYME KINETICS; ENZYME SPECIFICITY; EXCISION REPAIR; GENE SEQUENCE; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SCHIZOSACCHAROMYCES POMBE; SINGLE STRANDED DNA BREAK; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA DAMAGE; DNA REPAIR; DNA, FUNGAL; DNA, SINGLE-STRANDED; ELECTROPHORETIC MOBILITY SHIFT ASSAY; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PURINE NUCLEOSIDES; SCHIZOSACCHAROMYCES; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; THYMINE DNA GLYCOSYLASE; URACIL; XANTHINE;

EUKARYOTA; SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 55149093638     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2008.08.006     Document Type: Article

References (50)

1. Lindahl T. Instability and decay of the primary structure of DNA. Nature 362 (1993) 709-715
2. Spencer J.P., Whiteman M., Jenner A., and Halliwell B. Nitrite-induced deamination and hypochlorite-induced oxidation of DNA in intact human respiratory tract epithelial cells. Free Radic. Biol. Med. 28 (2000) 1039-1050
3. Burney S., Caulfield J.L., Niles J.C., Wishnok J.S., and Tannenbaum S.R. The chemistry of DNA damage from nitric oxide and peroxynitrite. Mutat. Res. 424 (1999) 37-49
4. Shapiro R. Damage to DNA caused by hydrolysis. In: Seeberg E., and Kleppe K. (Eds). Chromosome Damage and Repair (1981), Plenum Press, New York 3-18
5. Nguyen T., Brunson D., Crespi C.L., Penman B.W., Wishnok J.S., and Tannenbaum S.R. DNA damage and mutation in human cells exposed to nitric oxide in vitro. Proc. Natl. Acad. Sci. U.S.A. 89 (1992) 3030-3034
6. Dedon P.C., and Tannenbaum S.R. Reactive nitrogen species in the chemical biology of inflammation. Arch. Biochem. Biophys. 423 (2004) 12-22
7. Wink D.A., and Mitchell J.B. Chemical biology of nitric oxide: insights into regulatory, cytotoxic, and cytoprotective mechanisms of nitric oxide. Free Radic. Biol. Med. 25 (1998) 434-456
8. Suzuki T., Yamaoka R., Nishi M., Ide H., and Makino K. Isolation and characterization of a novel product, 2′-deoxyoxanosine, from 2′-deoxyguanosine, oligodeoxynucleotide and calf thymus DNA treated by nitrous-acid and nitric-oxide. J. Am. Chem. Soc. 118 (1996) 2515-2516
9. Suzuki T., Ide H., Yamada M., Endo N., Kanaori K., Tajima K., Morii T., and Makino K. Formation of 2′-deoxyoxanosine from 2′-deoxyguanosine and nitrous acid: mechanism and intermediates. Nucleic Acids Res. 28 (2000) 544-551
10. Vongchampa V., Dong M., Gingipalli L., and Dedon P. Stability of 2′-deoxyxanthosine in DNA. Nucleic Acids Res. 31 (2003) 1045-1051
11. Wuenschell G.E., O'Connor T.R., and Termini J. Stability, miscoding potential, and repair of 2′-deoxyxanthosine in DNA: implications for nitric oxide-induced mutagenesis. Biochemistry 42 (2003) 3608-3616
12. Suzuki T., Matsumura Y., Ide H., Kanaori K., Tajima K., and Makino K. Deglycosylation susceptibility and base-pairing stability of 2′-deoxyoxanosine in oligodeoxynucleotide. Biochemistry 36 (1997) 8013-8019
13. Dong M., Wang C., Deen W.M., and Dedon P.C. Absence of 2′-deoxyoxanosine and presence of abasic sites in DNA exposed to nitric oxide at controlled physiological concentrations. Chem. Res. Toxicol. 16 (2003) 1044-1055
14. Dong M., and Dedon P.C. Relatively small increases in the steady-state levels of nucleobase deamination products in DNA from human TK6 cells exposed to toxic levels of nitric oxide. Chem. Res. Toxicol. 19 (2006) 50-57
15. Caulfield J.L., Wishnok J.S., and Tannenbaum S.R. Nitric oxide-induced deamination of cytosine and guanine in deoxynucleosides and oligonucleotides. J. Biol. Chem. 273 (1998) 12689-12695
16. Duncan B.K., and Miller J.H. Mutagenic deamination of cytosine residues in DNA. Nature 287 (1980) 560-561
17. Coulondre C., Miller J.H., Farabaugh P.J., and Gilbert W. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274 (1978) 775-780
18. Kamiya H., Sakaguchi T., Murata N., Fujimuro M., Miura H., Ishikawa H., Shimizu M., Inoue H., Nishimura S., Matsukage A., Masutani C., Hanaoka F., and Ohtsuka E. In vitro replication study of modified bases in ras sequences. Chem. Pharm. Bull (Tokyo) 40 (1992) 2792-2795
19. Wink D.A., Kasprzak K.S., Maragos C.M., Elespuru R.K., Misra M., Dunams T.M., Cebula T.A., Koch W.H., Andrews A.W., Allen J.S., et al. DNA deaminating ability and genotoxicity of nitric oxide and its progenitors. Science 254 (1991) 1001-1003
20. Suzuki T., Yoshida M., Yamada M., Ide H., Kobayashi M., Kanaori K., Tajima K., and Makino K. Misincorporation of 2′-deoxyoxanosine 5′-triphosphate by DNA polymerases and its implication for mutagenesis. Biochemistry 37 (1998) 11592-11598
21. Hitchcock T.M., Dong L., Connor E.E., Meira L.B., Samson L.D., Wyatt M.D., and Cao W. Oxanine DNA glycosylase activity from mammalian alkyladenine glycosylase. J. Biol. Chem. 279 (2004) 38177-38183
22. Hitchcock T.M., Gao H., and Cao W. Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V. Nucleic Acids Res. 32 (2004) 4071-4080
23. Lindahl T., and Wood R.D. Quality control by DNA repair. Science 286 (1999) 1897-1905
24. David S.S., O'Shea V.L., and Kundu S. Base-excision repair of oxidative DNA damage. Nature 447 (2007) 941-950
25. Krokan H.E., Drablos F., and Slupphaug G. Uracil in DNA-occurrence, consequences and repair. Oncogene 21 (2002) 8935-8948
26. Pearl L.H. Structure and function in the uracil-DNA glycosylase superfamily. Mutat. Res. 460 (2000) 165-181
27. Cortazar D., Kunz C., Saito Y., Steinacher R., and Schar P. The enigmatic thymine DNA glycosylase. DNA Repair (Amst.) 6 (2007) 489-504
28. Hitomi K., Iwai S., and Tainer J.A. The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair. DNA Repair (Amst.) 6 (2007) 410-428
29. Wyatt M.D., Allan J.M., Lau A.Y., Ellenberger T.E., and Samson L.D. 3-Methyladenine DNA glycosylases: structure, function, and biological importance. Bioessays 21 (1999) 668-676
30. Saparbaev M., Mani J.C., and Laval J. Interactions of the human, rat, Saccharomyces cerevisiae and Escherichia coli 3-methyladenine-DNA glycosylases with DNA containing dIMP residues. Nucleic Acids Res. 28 (2000) 1332-1339
31. Dong M., Vongchampa V., Gingipalli L., Cloutier J.F., Kow Y.W., O'Connor T., and Dedon P.C. Development of enzymatic probes of oxidative and nitrosative DNA damage caused by reactive nitrogen species. Mutat. Res. 594 (2006) 120-134
32. Terato H., Masaoka A., Asagoshi K., Honsho A., Ohyama Y., Suzuki T., Yamada M., Makino K., Yamamoto K., and Ide H. Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid. Nucleic Acids Res. 30 (2002) 4975-4984
33. Nakano T., Katafuchi A., Shimizu R., Terato H., Suzuki T., Tauchi H., Makino K., Skorvaga M., Van Houten B., and Ide H. Repair activity of base and nucleotide excision repair enzymes for guanine lesions induced by nitrosative stress. Nucleic Acids Res. 33 (2005) 2181-2191
34. Dong L., Meira L.B., Hazra T.K., Samson L.D., and Cao W. Oxanine DNA glycosylase activities in mammalian systems. DNA Repair (Amst.) 7 (2008) 128-134
35. Hardeland U., Bentele M., Jiricny J., and Schar P. The versatile thymine DNA-glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs. Nucleic Acids Res. 31 (2003) 2261-2271
36. Gallinari P., and Jiricny J. A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature 383 (1996) 735-738
37. Saparbaev M., and 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
38. Ho S.N., Hunt H.D., Horton R.M., Pullen J.K., and Pease L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77 (1989) 51-59
39. Feng H., Klutz A.M., and Cao W. Active site plasticity of endonuclease V from Salmonella typhimurium. Biochemistry 44 (2005) 675-683
40. Kulikowska E., Kierdaszuk B., and Shugar D. Xanthine, xanthosine and its nucleotides: solution structures of neutral and ionic forms, and relevance to substrate properties in various enzyme systems and metabolic pathways. Acta Biochim. Pol. 51 (2004) 493-531
41. Poznanski J., Kierdaszuk B., and Shugar D. Structural properties of the neutral and monoanionic forms of xanthosine, highly relevant to their substrate properties with various enzyme systems. Nucleosides Nucleotides Nucleic Acids 22 (2003) 249-263
42. O'Neill R.J., Vorob'eva O.V., Shahbakhti H., Zmuda E., Bhagwat A.S., and Baldwin G.S. Mismatch uracil glycosylase from Escherichia coli: a general mismatch or a specific DNA glycosylase?. J. Biol. Chem. 278 (2003) 20526-20532
43. Saparbaev M., Langouet S., Privezentzev C.V., Guengerich F.P., Cai H., Elder R.H., and Laval J. 1,N(2)-Ethenoguanine, a mutagenic DNA adduct, is a primary substrate of Escherichia coli mismatch-specific uracil-DNA glycosylase and human alkylpurine-DNA-N-glycosylase. J. Biol. Chem. 277 (2002) 26987-26993
44. Sartori A.A., Fitz-Gibbon S., Yang H., Miller J.H., and Jiricny J. A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site. EMBO J. 21 (2002) 3182-3191
45. Feng H., Dong L., Klutz A.M., Aghaebrahim N., and Cao W. Defining amino acid residues involved in DNA-protein interactions and revelation of 3′-exonuclease activity in endonuclease V. Biochemistry 44 (2005) 11486-11495
46. Corfield P.W., Hunter W.N., Brown T., Robinson P., and Kennard O. Inosine adenine base pairs in a B-DNA duplex. Nucleic Acids Res. 15 (1987) 7935-7949
47. Parikh S.S., Putnam C.D., and Tainer J.A. Lessons learned from structural results on uracil-DNA glycosylase. Mutat. Res. 460 (2000) 183-199
48. Barrett T.E., Scharer O.D., Savva R., Brown T., Jiricny J., Verdine G.L., and Pearl L.H. Crystal structure of a thwarted mismatch glycosylase DNA repair complex. EMBO J. 18 (1999) 6599-6609
49. Hardeland U., Bentele M., Jiricny J., and Schar P. Separating substrate recognition from base hydrolysis in human thymine DNA glycosylase by mutational analysis. J. Biol. Chem. 275 (2000) 33449-33456
50. Steinacher R., and Schar P. Functionality of human thymine DNA glycosylase requires SUMO-regulated changes in protein conformation. Curr. Biol. 15 (2005) 616-623