Novel DNA Polymerases and Novel Genotoxicity Assays

Genes and Environment

Volumn 29, Issue 3, 2007, Pages 75-88

  Nohmi, Takehiko ^a  

^a NATIONAL INSTITUTE OF HEALTH SCIENCES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 67650979138     PISSN: 18807046     EISSN: 18807062     Source Type: Journal    
DOI: 10.3123/jemsge.29.75     Document Type: Article

References (95)

1. Maskarinec G, Noh JJ. The effect of migration on cancer incidence among Japanese in Hawaii. Ethn Dis. 2004; 14:431-9.
2. Takahashi Y, Miyaki K, Nakayama T. Analysis of news of the Japanese asbestos panic: a supposedly resolved issue that turned out to be a time bomb. J Public Health (Oxf). 2007; 29: 62-9.
3. Furuya S, Natori Y, Ikeda R. Asbestos in Japan. Int J Occup Environ Health. 2003; 9: 260.
4. Morinaga K, Kishimoto T, Sakatani M, Akira M, Yokoyama K, Sera Y. Asbestos-related lung cancer and mesothelioma in Japan. Ind Health. 2001; 39: 65-74.
5. Hei TK, Xu A, Huang SX, Zhao Y. Mechanism of fiber carcinogenesis: from reactive radical species to silencing of the beta igH3 gene. Inhal Toxicol. 2006; 18: 985-90.
6. Bofietta P. Human cancer from environmental pollutants: the epidemiological evidence. Mutat Res. 2006; 608: 157-62.
7. Xu A, Smilenov LB, He P, Masumura K, Nohmi T, Yu Z, et al. New insight into intrachromosomal deletions induced by chrysotile in the gpt delta transgenic mutation assay. Environ Health Perspect. 2007; 115: 87-92.
8. Dopp E, Schifimann D. Analysis of chromosomal alterations induced by asbestos and ceramic fibers. Toxicol Lett. 1998; 96-97: 155-62.
9. Topinka J, Loli P, Georgiadis P, Dusinska M, Hurbankova M, Kovacikova Z, et al. Mutagenesis by asbestos in the lung of lambda-lacI transgenic rats. Mutat Res. 2004; 553: 67-78.
10. Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993; 362: 709-15.
11. Nohmi T. Environmental stress and lesion-bypass DNA polymerases. Annu Rev Microbiol. 2006; 60: 231-53.
12. Josephy PD, Gruz P, Nohmi T. Recent advances in the construction of bacterial genotoxicity assays. Mutat Res. 1997; 386: 1-23.
13. Nohmi T, Masumura K. Molecular nature of in-trachromosomal deletions and base substitutions induced by environmental mutagens. Environ Mol Mutagen. 2005; 45: 150-61.
14. Kornberg A, Baker TA. DNA Replication, Second Edition. New York: W.H. Freeman and company, 1992.
15. Ito J, Braithwaite DK. Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res. 1991; 19: 4045-57.
16. Friedberg EC. Sufiering in silence: the tolerance of DNA damage. Nat Rev Mol Cell Biol. 2005; 6: 943-53.
17. Friedberg EC, Gerlach VL. Novel DNA polymerases ofier clues to the molecular basis of mutagenesis. Cell. 1999; 98: 413-6.
18. Ohmori H, Friedberg EC, Fuchs RP, Goodman MF, Hanaoka F, Hinkle D, et al. The Y-family of DNA poly-merases. Mol Cell. 2001; 8: 7-8.
19. Ling H, Boudsocq F, Woodgate R, Yang W. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell. 2001; 107: 91-102.
20. Burgers PM, Koonin EV, Bruford E, Blanco L, Burtis KC, Christman MF, et al. Eukaryotic DNA polymerases: proposal for a revised nomenclature. J Biol Chem. 2001; 276: 43487-90.
21. Prakash S, Johnson RE, Prakash L. Eukaryotic transle-sion synthesis DNA polymerases: specificity of structure and function. Annu Rev Biochem. 2005; 74: 317-53.
22. Maron DM, Ames BN. Revised methods for the Salmonella mutagenicity test. Mutat Res. 1983; 113: 173-215.
23. Nohmi T, Hakura A, Nakai Y, Watanabe M, Murayama SY, Sofuni T. Salmonella typhimurium has two homologous but difierent umuDC operons: cloning of a new umuDC-like operon (samAB) present in a 60-megadalton cryptic plasmid of S. typhimurium. J Bacteriol. 1991; 173: 1051-63.
24. Kokubo K, Yamada M, Kanke Y, Nohmi T. Roles of replicative and specialized DNA polymerases in frameshift mutagenesis: mutability of Salmonella typhimurium strains lacking one or all of SOS-inducible DNA polymerases to 26 chemicals. DNA Repair (Amst). 2005; 4: 1160-71.
25. Indiani C, McInerney P, Georgescu R, Goodman MF, ODonnell M. A sliding-clamp toolbelt binds high-and low-fidelity DNA polymerases simultaneously. Mol Cell. 2005; 19: 805-15.
26. Friedberg EC, Lehmann AR, Fuchs RP. Trading places: how do DNA polymerases switch during translesion DNA synthesis? Mol Cell. 2005; 18: 499-505.
27. Matsui K, Yamada M, Imai M, Yamamoto K, Nohmi T. Specificity of replicative and SOS-inducible DNA poly-merases in frameshift mutagenesis: mutability of Salmonella typhimurium strains overexpressing SOS-in-ducible DNA polymerases to 30 chemical mutagens. DNA Repair (Amst). 2006; 5: 465-78.
28. Warbrick E. The puzzle of PCNAs many partners. Bioessays. 2000; 22: 997-1006.
29. Stelter P, Ulrich HD. Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature. 2003; 425: 188-91.
30. Watanabe K, Tateishi S, Kawasuji M, Tsurimoto T, Inoue H, Yamaizumi M. Rad18 guides poleta to replication stalling sites through physical interaction and PCNA monoubiquitination. EMBO J. 2004; 23: 3886-96.
31. Kannouche PL, Wing J, Lehmann AR. Interaction of human DNA polymerase eta with monoubiquitinated PCNA: a possible mechanism for the polymerase switch in response to DNA damage. Mol Cell. 2004; 14: 491-500.
32. Masutani C, Kusumoto R, Yamada A, Dohmae N, Yokoi M, Yuasa M, et al. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta. Nature. 1999; 399: 700-4.
33. Johnson RE, Kondratick CM, Prakash S, Prakash L. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science. 1999; 285: 263-5.
34. Bienko M, Green CM, Crosetto N, Rudolf F, Zapart G, Coull B, et al. Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science. 2005; 310: 1821-4.
35. Lehmann AR. New functions for Y family polymerases. Mol Cell. 2006; 24: 493-5.
36. Kawamoto T, Araki K, Sonoda E, Yamashita YM, Harada K, Kikuchi K, et al. Dual roles for DNA poly-merase h in homologous DNA recombination and translesion DNA synthesis. Mol Cell. 2005; 20: 793-9.
37. McIlwraith MJ, Vaisman A, Liu Y, Fanning E, Woodgate R, West SC. Human DNA polymerase h promotes DNA synthesis from strand invasion intermediates of homologous recombination. Mol Cell. 2005; 20:783-92.
38. Mayorov VI, Rogozin IB, Adkison LR, Gearhart PJ. DNA polymerase h contributes to strand bias of mutations of A versus T in immunoglobulin genes. J Immunol. 2005; 174: 7781-6.
39. Shimizu M, Gruz P, Kamiya H, Kim SR, Pisani FM, Masutani C, et al. Erroneous incorporation of oxidized DNA precursors by Y-family DNA polymerases. EMBO Rep. 2003; 4: 269-73.
40. Shimizu M, Gruz P, Kamiya H, Masutani C, Xu Y, Usui Y, et al. Efficient and erroneous incorporation of oxidized DNA precursors by human DNA polymerase eta. Biochemistry. 2007; 46: 5515-22.
41. Yamada M, Nunoshiba T, Shimizu M, Gruz P, Kamiya H, Harashima H, et al. Involvement of Y-family DNA polymerases in mutagenesis caused by oxidized nucleo-tides in Escherichia coli. J Bacteriol. 2006; 188: 4992-5.
42. Sekiguchi M, Tsuzuki T. Oxidative nucleotide damage: consequences and prevention. Oncogene. 2002; 21: 8895-904.
43. Godoy VG, Jarosz DF, Walker FL, Simmons LA, Walker GC. Y-family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression. EMBO J. 2006; 25: 868-79.
44. Tokiwa H, Ohnishi Y. Mutagenicity and carcinogenicity of nitroarenes and their sources in the environment. Crit Rev Toxicol. 1986; 17: 23-60.
45. Nagao M, Ochiai M, Ushijima T, Watanabe M, Sugimura T, Nakagama H. Genetic determinant and environmental carcinogens. Mutat Res. 1998; 402: 85-91.
46. Sugimura T, Wakabayashi K, Ohgaki H, Takayama S, Nagao M, Esumi H. Heterocyclic amines produced in cooked food: unavoidable xenobiotics. Princess Takamatsu Symp. 1990; 21: 279-88.
47. Watanabe M, Ishidate M, Jr., Nohmi T. Sensitive method for the detection of mutagenic nitroarenes and aromatic amines: new derivatives of Salmonella typhimurium tester strains possessing elevated O-acetyltransferase levels. Mutat Res. 1990; 234: 337-48.
48. Watanabe M, Ishidate M, Jr., Nohmi T. A sensitive method for the detection of mutagenic nitroarenes: construction of nitroreductase-overproducing derivatives of Salmonella typhimurium strains TA98 and TA100. Mutat Res. 1989; 216: 211-20.
49. Watanabe M, Nohmi T, Ishidate M, Jr. New tester strains of Salmonella typhimurium highly sensitive to mutagenic nitroarenes. Biochem Biophys Res Commun. 1987; 147: 974-9.
50. Yamada M, Hakura A, Sofuni T, Nohmi T. New method for gene disruption in Salmonella typhimurium: construction and characterization of an ada-deletion derivative of Salmonella typhimurium TA1535. J Bacteriol. 1993; 175: 5539-47.
51. Yamada M, Sedgwick B, Sofuni T, Nohmi T. Construction and characterization of mutants of Salmonella typhimurium deficient in DNA repair of O6-methylgua-nine. J Bacteriol. 1995; 177: 1511-9.
52. Sedgwick B. Repairing DNA-methylation damage. Nat Rev Mol Cell Biol. 2004; 5: 148-57.
53. Yamada M, Matsui K, Sofuni T, Nohmi T. New tester strains of Salmonella typhimurium lacking O6-methyl-guanine DNA methyltransferases and highly sensitive to mutagenic alkylating agents. Mutat Res. 1997; 381: 15-24.
54. Kushida H, Fujita K, Suzuki A, Yamada M, Nohmi T, Kamataki T. Development of a Salmonella tester strain sensitive to promutagenic N-nitrosamines: expression of recombinant CYP2A6 and human NADPH-cytochrome P450 reductase in S. typhimurium YG7108. Mutat Res. 2000; 471: 135-43.
55. Kushida H, Fujita K, Suzuki A, Yamada M, Endo T, Nohmi T, et al. Metabolic activation of N-alkylnitrosa-mines in genetically engineered Salmonella typhimurium expressing CYP2E1 or CYP2A6 together with human NADPH-cytochrome P450 reductase. Carcinogenesis. 2000; 21: 1227-32.
56. Suzuki M, Matsui K, Yamada M, Kasai H, Sofuni T, Nohmi T. Construction of mutants of Salmonella typhimurium deficient in 8-hydroxyguanine DNA glycosylase and their sensitivities to oxidative mutagens and nitro compounds. Mutat Res. 1997; 393: 233-46.
57. Nohmi T, Kim SR, Yamada M. Modulation of oxidative mutagenesis and carcinogenesis by polymorphic forms of human DNA repair enzymes. Mutat Res. 2005; 591: 60-73.
58. Kasai H. Chemistry-based studies on oxidative DNA damage: formation, repair, and mutagenesis. Free Radic Biol Med. 2002; 33: 450-6.
59. Michaels ML, Miller JH. The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J Bacteriol. 1992; 174: 6321-5.
60. Kim SR, Kokubo K, Matsui K, Yamada N, Kanke Y, Fukuoka M, et al. Light-dependent mutagenesis by benzo[a]pyrene is mediated via oxidative DNA damage. Environ Mol Mutagen. 2005; 46: 141-9.
61. Kohno T, Shinmura K, Tosaka M, Tani M, Kim SR, Sugimura H, et al. Genetic polymorphisms and alternative splicing of the hOGG1 gene, that is involved in the repair of 8-hydroxyguanine in damaged DNA. Oncogene. 1998; 16: 3219-25.
62. Goldsmith M, Sarov-Blat L, Livneh Z. Plasmid-encoded MucB protein is a DNA polymerase (pol RI) specialized for lesion bypass in the presence of MucA, RecA, and SSB. Proc Natl Acad Sci USA. 2000; 97: 11227-31.
63. Heddle JA, Dean S, Nohmi T, Boerrigter M, Casciano D, Douglas GR, et al. In vivo transgenic mutation assays. Environ Mol Mutagen. 2000; 35: 253-9.
64. Nohmi T, Suzuki T, Masumura K. Recent advances in the protocols of transgenic mouse mutation assays. Mutat Res. 2000; 455: 191-215.
65. Nohmi T, Masumura K. gpt delta transgenic mouse: a novel approach for molecular dissection of deletion mutations in vivo. Adv Biophys. 2004; 38: 97-121.
66. Nohmi T, Suzuki M, Masumura K, Yamada M, Matsui K, Ueda O, et al. Spi- selection: An efficient method to detect gamma-ray-induced deletions in transgenic mice. Environ Mol Mutagen. 1999; 34: 9-15.
67. Masumura K, Matsui M, Katoh M, Horiya N, Ueda O, Tanabe H, et al. Spectra of gpt mutations in ethyl-nitrosourea-treated and untreated transgenic mice. Environ Mol Mutagen. 1999; 34: 1-8.
68. Ikeda H, Shimizu H, Ukita T, Kumagai M. A novel assay for illegitimate recombination in Escherichia coli: stimulation of lambda bio transducing phage formation by ultra-violet light and its independence from RecA function. Adv Biophys. 1995; 31: 197-208.
69. Nohmi T, Katoh M, Suzuki H, Matsui M, Yamada M, Watanabe M, et al. A new transgenic mouse mutagenesis test system using Spi” and 6-thioguanine selections. Environ Mol Mutagen. 1996; 28: 465-70.
70. Horiguchi M, Masumura K, Ikehata H, Ono T, Kanke Y, Sofuni T, et al. UVB-induced gpt mutations in the skin of gpt delta transgenic mice. Environ Mol Mutagen. 1999; 34: 72-9.
71. Masumura K, Kuniya K, Kurobe T, Fukuoka M, Yatagai F, Nohmi T. Heavy-ion-induced mutations in the gpt delta transgenic mouse: comparison of mutation spectra induced by heavy-ion, X-ray, and gamma-ray radiation. Environ Mol Mutagen. 2002; 40: 207-15.
72. Takeiri A, Mishima M, Tanaka K, Shioda A, Ueda O, Suzuki H, et al. Molecular characterization of mitomycin C-induced large deletions and tandem-base substitutions in the bone marrow of gpt delta transgenic mice. Chem Res Toxicol. 2003; 16: 171-9.
73. Masumura K, Matsui K, Yamada M, Horiguchi M, Ishida K, Watanabe M, et al. Mutagenicity of 2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine (PhIP) in the new gpt delta transgenic mouse. Cancer Lett. 1999; 143: 241-4.
74. Masumura K, Totsuka Y, Wakabayashi K, Nohmi T. Potent genotoxicity of aminophenylnorharman, formed from non-mutagenic norharman and aniline, in the liver of gpt delta transgenic mouse. Carcinogenesis. 2003; 24: 1985-93.
75. Masumura K, Horiguchi M, Nishikawa A, Umemura T, Kanki K, Kanke Y, et al. Low dose genotoxicity of 2-amino-3, 8-dimethylimidazo[4,5-.] quinoxaline (MeIQx) in gpt delta transgenic mice. Mutat Res. 2003; 541: 91-102.
76. Ikeda M, Masumura K, Sakamoto Y, Wang B, Nenoi M, Sakuma K, et al. Combined genotoxic effects of radiation and a tobacco-specific nitrosamine in the lung of gpt delta transgenic mice. Mutat Res. 2007; 626: 15-25.
77. Horiguchi M, Masumura KI, Ikehata H, Ono T, Kanke Y, Nohmi T. Molecular nature of ultraviolet B light-induced deletions in the murine epidermis. Cancer Res. 2001; 61: 3913-8.
78. Masumura K, Matsui K, Yamada M, Horiguchi M, Ishida K, Watanabe M, et al. Characterization of mutations induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine in the colon of gpt delta transgenic mouse: novel G:C deletions beside runs of identical bases. Carcinogenesis. 2000; 21: 2049-56.
79. Lakin ND, Jackson SP. Regulation of p53 in response to DNA damage. Oncogene. 1999; 18: 7644-55.
80. Yatagai F, Kurobe T, Nohmi T, Masumura K, Tsukada T, Yamaguchi H, et al. Heavy-ion-induced mutations in the gpt delta transgenic mouse: effect of p53 gene knockout. Environ Mol Mutagen. 2002; 40: 216-25.
81. Gatti RA, Becker-Catania S, Chun HH, Sun X, Mitui M, Lai CH, et al. The pathogenesis of ataxia-telangiectasia. Learning from a Rosetta Stone. Clin Rev Allergy Immunol. 2001; 20: 87-108.
82. Furuno-Fukushi I, Masumura K, Furuse T, Noda Y, Takahagi M, Saito T, et al. Effect of Atm disruption on spontaneously arising and radiation-induced deletion mutations in mouse liver. Radiat Res. 2003; 160: 549-58.
83. Yoshihara K, Hashida T, Yoshihara H, Tanaka Y, Ohgushi H. Enzyme-bound early product of purified poly(ADP-ribose) polymerase. Biochem Biophys Res Commun. 1977; 78: 1281-8.
84. Adolph KW, Song MK. Decrease in ADP-ribosylation of HeLa non-histone proteins from interphase to metaphase. Biochemistry. 1985; 24: 345-52.
85. Wesierska-Gadek J, Schmid G, Cerni C. ADP-ribosyla-tion of wild-type p53 in vitro: binding of p53 protein to specific p53 consensus sequence prevents its modification. Biochem Biophys Res Commun. 1996; 224: 96-102.
86. Shibata A, Kamada N, Masumura K, Nohmi T, Kobayashi S, Teraoka H, et al. Parp-1 deficiency causes an increase of deletion mutations and insertionsrearrangements in vivo after treatment with an alkylating agent. Oncogene. 2005; 24: 1328-37.
87. Takeiri A, Mishima M, Tanaka K, Shioda A, Harada A, Watanabe K, et al. A newly established GDL1 cell line from gpt delta mice well reflects the in vivo mutation spectra induced by mitomycin C. Mutat Res. 2006; 609: 102-15.
88. Ohkumo T, Kondo Y, Yokoi M, Tsukamoto T, Yamada A, Sugimoto T, et al. UV-B radiation induces epithelial tumors in mice lacking DNA polymerase eta and mesen-chymal tumors in mice deficient for DNA polymerase iota. Mol Cell Biol. 2006; 26: 7696-706.
89. Lin Q, Clark AB, McCulloch SD, Yuan T, Bronson RT, Kunkel TA, et al. Increased susceptibility to UV-induced skin carcinogenesis in polymerase eta-deficient mice. Cancer Res. 2006; 66: 87-94.
90. Friedberg EC, Meira LB. Database of mouse strains carrying targeted mutations in genes affecting biological responses to DNA damage Version 7. DNA Repair (Amst). 2006; 5: 189-209.
91. Kamataki T. Genetic polymorphism of CYP2A6 and tobacco-related cancer risk: from the establishment of genetically engineering Salmonella to large scale epidemiology. Genes and Environ. 2006; 28: 77-83.
92. Hengstler JG, Bogdanffy MS, Bolt HM, Oesch F. Challenging dogma: thresholds for genotoxic carcinogens? The case of vinyl acetate. Annu Rev Pharmacol Toxicol. 2003; 43: 485-520.
93. Fukushima S, Kinoshita A, Puatanachokchai R, Kushida M, Wanibuchi H, Morimura K. Hormesis and dose-response-mediated mechanisms in carcinogenesis: evidence for a threshold in carcinogenicity of non-genotoxic carcinogens. Carcinogenesis. 2005; 26: 1835-45.
94. Hagiwara Y, Watanabe M, Oda Y, Sofuni T, Nohmi T. Specificity and sensitivity of Salmonella typhimurium YG1041 and YG1042 strains possessing elevated levels of both nitroreductase and acetyltransferase activity. Mutat Res. 1993; 291: 171-80.
95. Yamada M, Matsui K, Nohmi T. Development of a bacterial hyper-sensitive tester strain for specific detection of the genotoxicity of polycyclic aromatic hydrocarbons. Genes and Environ. 2007; 28: 23-30.