Base-excision repair of oxidative DNA damage (original) (raw)

• Lindahl, T. Instability and decay of the primary structure of DNA. Nature 362, 709–715 (1993).
  ADS CAS PubMed Google Scholar
• Friedberg, E. C. DNA damage and repair. Nature 421, 436–440 (2003).
  ADS PubMed Google Scholar
• Pfeifer, G. P. et al. Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancers. Oncogene 21, 7435–7451 (2002).
  CAS PubMed Google Scholar
• Friedberg, E. C. Inroads into base excision repair II. The discovery of the DNA glycosylases. DNA Repair (Amst.) 3, 1531–1536 (2004).
  CAS Google Scholar
• David, S. S. & Williams, S. D. Chemistry of glycosylases and endonucleases involved in base-excision repair. Chem. Rev. 98, 1221–1261 (1998).
  CAS PubMed Google Scholar
• Fromme, J. C. & Verdine, G. L. Base excision repair. Adv. Protein Chem. 69, 1–41 (2004).
  CAS PubMed Google Scholar
• Barnes, D. E. & Lindahl, T. Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Annu. Rev. Genet. 38, 445–476 (2004).
  CAS PubMed Google Scholar
• Sung, J.-S. & Demple, B. Roles of base excision repair subpathways in correcting oxidized abasic sites in DNA. FEBS J. 273, 1620–1629 (2006).
  CAS PubMed Google Scholar
• Klaunig, J. E. & Kamendulis, L. M. The role of oxidative stress in carcinogenesis. Annu. Rev. Pharmacol. Toxicol. 44, 239–267 (2004).
  CAS PubMed Google Scholar
• Neeley, W. L. & Essigmann, J. M. Mechanisms of formation, genotoxicity, and mutation of guanine oxidation products. Chem. Res. Toxicol. 19, 491–505 (2006).
  CAS PubMed Google Scholar
• Burrows, C. M. & Muller, J. Oxidative nucleobase modifications leading to strand scission. Chem. Rev. 98, 1109–1152 (1998).
  CAS PubMed Google Scholar
• Shibutani, S., Takeshita, M. & Grollman, A. P. Insertion of specific bases during DNA synthesis past the oxidation damaged base 8-oxodG. Nature 349, 431–434 (1991).
  ADS CAS PubMed Google Scholar
• Hsu, G. W., Ober, M., Carell, T. & Beese, L. S. Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature 431, 217–221 (2004).
  ADS CAS PubMed Google Scholar
• Michaels, M. L. & Miller, J. H. The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J. Bacteriol. 174, 6321–6325 (1992).
  CAS PubMed PubMed Central Google Scholar
• Krahn, J. M., Beard, W. A., Miller, H., Grollman, A. P. & Wilson, S. H. Structure of DNA polymerase β with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure 11, 121–127 (2003).
  CAS PubMed Google Scholar
• Gedik, C. M. & Collins, A. Establishing the background level of base oxidation in human lymphocyte DNA: results on an interlaboratory validation study. FASEB J. 19, 82–84 (2005).
  CAS PubMed Google Scholar
• Parikh, S. S., Putnam, C. D. & Tainer, J. A. Lessons learned from structural results on uracil-DNA glycosylase. Mutat. Res. 460, 183–199 (2000).
  CAS PubMed Google Scholar
• Stivers, J. T. Site-specific DNA damage recognition by enzyme-induced base flipping. Prog. Nucleic Acid Res. Mol. Biol. 77, 37–65 (2004).
  CAS PubMed Google Scholar
• Fromme, J. C., Banerjee, A. & Verdine, G. L. DNA glycosylase recognition and catalysis. Curr. Opin. Struct. Biol. 14, 43–49 (2004).
  CAS PubMed Google Scholar
• Huffman, J. L., Sundheim, O. & Tainer, J. A. DNA base damage recognition and removal: new twists and grooves. Mutat. Res. 577, 55–76 (2005).
  CAS PubMed Google Scholar
• Hitomi, K., Iwai, S. & Tainer, J. A. The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal and repair. DNA Repair (Amst.) 6, 410–428 (2007).
  CAS Google Scholar
• Bruner, S. D., Norman, D. P. & Verdine, G. L. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403, 859–866 (2000).
  ADS CAS PubMed Google Scholar
• Banerjee, A., Yang, W., Karplus, M. & Verdine, G. L. Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434, 612–618 (2005).
  ADS CAS PubMed Google Scholar
• Radom, C. T., Banerjee, A. & Verdine, G. L. Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations. J. Biol. Chem. 282, 9182–9194 (2007).
  CAS PubMed Google Scholar
• Banerjee, A. & Verdine, G. L. A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex. Proc. Natl Acad. Sci. USA 103, 15020–15025 (2006).
  ADS CAS PubMed PubMed Central Google Scholar
• Banerjee, A., Santos, W. L. & Verdine, G. L. Structure of a DNA glycosylase searching for DNA lesions. Science 311, 1153–1157 (2006).
  ADS CAS PubMed Google Scholar
• Fromme, J. C. & Verdine, G. L. DNA lesion recognition by the bacterial repair enzyme MutM. J. Biol. Chem. 278, 51543–51548 (2003).
  CAS PubMed Google Scholar
• Blainey, P. C., van Oijen, A. M., Banerjee, A., Verdine, G. L. & Xie, X. S. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl Acad. Sci. USA 103, 5752–5757 (2006).
  ADS CAS PubMed PubMed Central Google Scholar
• Jiang, Y. L. et al. Recognition of an unnatural difluorophenyl nucleotide by uracil DNA glycosylase. Biochemistry 43, 15429–15438 (2004).
  CAS PubMed Google Scholar
• Noll, D. M., Gogos, A., Granek, J. A. & Clarke, N. D. The C-terminal domain of the adenine-DNA glycosylase MutY confers specificity of 8-oxoguanine–adenine mispairs and may have evolved from MutT, an 8-oxo-dGTPase. Biochemistry 38, 6374–6379 (1999).
  CAS PubMed Google Scholar
• Chmiel, N. H., Golinelli, M.-P., Francis, A. W. & David, S. S. Efficient recognition of substrates and substrate analogs by the adenine glycosylase MutY requires the C-terminal domain. Nucleic Acids Res. 29, 553–564 (2001).
  CAS PubMed PubMed Central Google Scholar
• Fromme, J. C., Banerjee, A., Huang, S. J. & Verdine, G. L. Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature 427, 652–656 (2004).
  ADS CAS PubMed Google Scholar
• Wiederholdt, C. J., Delaney, M. O., Pope, M. A., David, S. S. & Greenberg, M. M. Repair of DNA containing FapydG and its C-nucleoside analogue by formamidopyrimidine DNA glycosylase and MutY. Biochemistry 42, 9755–9760 (2003).
  Google Scholar
• Bernards, A. S., Miller, J. K., Bao, K. K. & Wong, I. Flipping duplex DNA inside out: a double base-flipping reaction mechanism by Escherichia coli MutY adenine glycosylase. J. Biol. Chem. 277, 20960–20964 (2002).
  CAS PubMed Google Scholar
• Al-Tassan, N. et al. Inherited variants of MYH associated with somatic G:C to T:A mutations in colorectal tumors. Nature Genet. 30, 227–232 (2002).
  CAS PubMed Google Scholar
• Fearnhead, N. S., Britton, M. P. & Bodmer, W. F. The ABC of APC. Hum. Mol. Genet. 10, 721–733 (2001).
  CAS PubMed Google Scholar
• Chmiel, N. H., Livingston, A. L. & David, S. S. Insight into the functional consequences of inherited variants of the hMYH adenine glycosylase associated with colorectal cancer: complementation assays with hMYH variants and pre-steady-state kinetics of the corresponding mutated E. coli enzymes. J. Mol. Biol. 327, 431–443 (2003).
  CAS PubMed Google Scholar
• Sampson, J. R., Jones, S., Dolwani, S. & Cheadle, J. P. MutYH (MYH) and colorectal cancer. Biochem. Soc. Trans. 33, 679–683 (2005).
  CAS PubMed Google Scholar
• Cheadle, J. P. & Sampson, J. R. MUTYH-associated polyposis — from defect in base excision repair to clinical genetic testing. DNA Repair (Amst.) 6, 274–279 (2007).
  CAS Google Scholar
• Livingston, A. L., Kundu, S., Henderson-Pozzi, M., Anderson, D. W. & David, S. S. Insight into the roles of tyrosine 82 and glycine 253 in the Escherichia coli adenine glycosylase MutY. Biochemistry 44, 14179–14190 (2005).
  CAS PubMed Google Scholar
• Pope, M. A., Chmiel, N. H. & David, S. S. Insight into the functional consequences of hMYH variants associated with colorectal cancer: distinct differences in the adenine glycosylase activity and the response to AP endonuclease of Y150C and G365D murine MYH. DNA Repair (Amst.) 4, 315–325 (2005).
  CAS Google Scholar
• Tominaga, Y. et al. MUTYH prevents OGG1 or APEX1 from inappropriately processing its substrate or reaction product with its C-terminal domain. Nucleic Acids Res. 32, 3198–3211 (2004).
  CAS PubMed PubMed Central Google Scholar
• Wooden, S. H., Bassett, H. M., Wood, T. G. & McCullough, A. K. Identification of critical residues required for the mutation avoidance function of human MutY (hMYH) and implications in colorectal cancer. Cancer Lett. 205, 89–95 (2004).
  CAS PubMed Google Scholar
• Hirano, S. et al. Mutator phenotype of MutYH-null mouse embryonic stem cells. J. Biol. Chem. 278, 38121–38124 (2003).
  CAS PubMed Google Scholar
• Lipton, L. et al. Carcinogenesis in MYH-associated polyposis follows a distinct genetic pathway. Cancer Res. 63, 7595–7599 (2003).
  CAS PubMed Google Scholar
• Xie, Y. et al. Deficiencies in mouse Myh and Ogg1 results in tumor predisposition and G to T mutations in codon 12 of the K-ras oncogene in lung tumors. Cancer Res. 64, 3096–3102 (2004).
  CAS PubMed Google Scholar
• Russo, M. T. et al. Accumulation of the oxidative base lesion 8-hydroxyguanine in DNA of tumor-prone mice defective in both the Myh and Ogg1 DNA glycosylase. Cancer Res. 64, 4411–4414 (2004).
  CAS PubMed Google Scholar
• Sieber, O. M. et al. Myh deficiency enhances intestinal tumorigenesis in multiple intestinal neoplasia (_Apc_Min/+) mice. Cancer Res. 64, 8876–8881 (2004).
  CAS PubMed Google Scholar
• Sampson, J. R. et al. MYH polyposis: a new autosomal recessive form of familial adenomatous polyposis demanding reappraisal of genetic risk and family management. Lancet 362, 39–41 (2003).
  CAS PubMed Google Scholar
• Chow, E., Thirlwell, C., Macrae, F. & Lipton, L. Colorectal cancer and inherited mutations in base-excision repair. Lancet Oncol. 5, 600–606 (2004).
  CAS PubMed Google Scholar
• Lipton, L. & Tomlinson, I. The multiple colorectal adenoma phenotype and MYH, a excision repair gene. Clin. Gastroenterol. Hepatol. 2, 633–638 (2004).
  CAS PubMed Google Scholar
• Tenesa, A. et al. Association of MutYH and colorectal cancer. Br. J. Cancer 95, 239–242 (2006).
  CAS PubMed PubMed Central Google Scholar
• Lipton, L. & Tomlinson, I. The genetics of FAP and FAP-like syndromes. Fam. Cancer 5, 221–226 (2006).
  CAS PubMed Google Scholar
• Farrington, S. M. et al. Germline susceptibility to colorectal cancer due to base-excision repair gene defects. Am. J. Hum. Genet. 77, 112–119 (2005).
  CAS PubMed PubMed Central Google Scholar
• Fleischmann, C. et al. Comprehensive analysis of the contribution of germline MYH variation of early-onset colorectal cancer. Int. J. Cancer 109, 554–558 (2004).
  CAS PubMed Google Scholar
• Strate, L. L. & Syngal, S. Hereditary colorectal cancer syndromes. Cancer Causes Control 16, 201–213 (2005).
  PubMed Google Scholar
• Jo, W. S. & Chung, D. C. Genetics of hereditary colorectal cancer. Semin. Oncol. 32, 11–23 (2005).
  CAS PubMed Google Scholar
• Bodmer, W. F. Cancer genetics: colorectal cancer as a model. J. Hum. Genet. 51, 391–396 (2006).
  CAS PubMed PubMed Central Google Scholar
• Kinzler, K. W. & Vogelstein, B. Lessons from hereditary colorectal cancer. Cell 87, 159–170 (1996).
  CAS PubMed Google Scholar
• Soreide, K., Janssen, E. A. M., Soiland, H., Korner, H. & Baak, J. P. Microsatellite instability in colorectal cancer. Br. J. Surg. 93, 395–406 (2006).
  CAS PubMed Google Scholar
• Lindor, N. M. et al. Recommendations for the care of individuals with an inherited predisposition to Lynch syndrome. JAMA 296, 1507–1517 (2006).
  CAS PubMed Google Scholar
• Venesio, T. et al. High frequency of MYH gene mutations in a subset of patients with familial adenomatous polyposis. Gastroenterology 126, 1681–1685 (2004).
  CAS PubMed Google Scholar
• Leite, J. S. et al. Is prophylactic colectomy indicated in patients with MYH-associated polyposis? Colorectal Dis. 7, 327–331 (2005).
  CAS PubMed Google Scholar
• Bai, H. et al. Functional characterization of two human MutY homolog (hMYH) missense mutations (R227W and V232F) that lie within the putative hMSH6 binding domain and are associated with hMYH polyposis. Nucleic Acids Res. 33, 597–604 (2005).
  CAS PubMed PubMed Central Google Scholar
• Bai, H. et al. Functional characterization of human MutY homolog (hMYH) missense mutation (R231L) that is linked with hMYH-associated polyposis. Cancer Lett. 250, 74–81 (2007).
  CAS PubMed Google Scholar
• Alhopuro, P. et al. A novel functionally deficient MYH variant in individuals with colorectal adenomatous polyposis. Hum. Mutat. 26, 393 (2005).
  PubMed Google Scholar
• Klunglund, A. et al. Accumulation of premutagenic DNA lesions in mice defective in removal of oxidative base damage. Proc. Natl Acad. Sci. USA 96, 13300–13305 (1999).
  ADS Google Scholar
• Osterod, M. et al. A global DNA repair mechanism involving Cockayne syndrome B (CSB) gene product can prevent the in vivo accumulation of endogenous oxidative DNA base damage. Oncogene 21, 8232–8239 (2002).
  CAS PubMed Google Scholar
• Osterod, M. et al. Age-related and tissue-specific accumulation of oxidative DNA base damage in 7,8-dihydro-8-oxoguanine-DNA glycosylase (Ogg1) deficient mice. Carcinogenesis 22, 1459–1463 (2001).
  CAS PubMed Google Scholar
• Sunesen, M., Stevnsner, T., Brosh, R. M., Dianov, G. L. & Bohr, V. A. Global genome repair of 8-oxoG in hamster cells requires a functional CSB gene product. Oncogene 21, 3571–3578 (2002).
  CAS PubMed Google Scholar
• Cadet, J., Decarroz, C., Wang, S. Y. & Midden, W. R. Mechanisms and products of photosensitized degradation of nucleic acids and related model compounds. Isr. J. Chem. 1983, 420–429 (1983).
  Google Scholar
• Ravanat, J. L. & Cadet, J. Reaction of singlet oxygen with 2'-deoxyguanosine and DNA. Isolation and characterization of the main oxidation products. Chem. Res. Toxicol. 8, 379–388 (1995).
  CAS PubMed Google Scholar
• Ravanat, J. L., Berger, M., Bernard, F., Langlois, R. & Ouellet, R. Phthalocyanine and naphthalocyanine photosensitized oxidation of 2'-deoxyguanosine: distinct type I and type II products. Photochem. Photobiol. 55, 809–814 (1992).
  CAS Google Scholar
• Luo, W., Muller, J. G., Rachlin, E. M. & Burrows, C. J. Characterization of spiroiminodihydantoin as a product of one-electron oxidation of 8-oxo-7,8-dihydroguanosine. Org. Lett. 2, 613–616 (2000).
  CAS PubMed Google Scholar
• Niles, J. C., Wishnok, J. S. & Tannenbaum, S. R. Spiroiminodihydantoin is the major product of the 8-oxo-7,8-dihydroguanosine reaction with peroxynitrite in the presence of thiols and guanosine photooxidation by methylene blue. Org. Lett. 3, 963–966 (2001).
  CAS PubMed Google Scholar
• Adam, W. et al. Spiroiminodihydantoin is a major product in the photooxidation of 2'-deoxyguanosine by the triplet states and oxyl radicals generated from hydroxyacetophenone photolysis and dioxetane thermolysis. Org. Lett. 4, 537–540 (2002).
  CAS PubMed Google Scholar
• Burrows, C. J. et al. Structure and potential mutagenicity of new hydantoin products from guanosine and 8-oxo-7,8-dihydroguanosine oxidation by transition metals. Environ. Health Perspect. 110, 713–717 (2002).
  CAS PubMed PubMed Central Google Scholar
• Luo, W., Muller, J. G., Rachlin, E. M. & Burrows, C. J. Characterization of hydantoin products from one-electron oxidation of 8-oxo-7,8-dihydroguanosine in a nucleoside model. Chem. Res. Toxicol. 14, 927–938 (2001).
  CAS PubMed Google Scholar
• Kornyushyna, O., Berges, A. M., Muller, J. G. & Burrows, C. J. In vitro nucleotide misinsertion opposite the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin and DNA synthesis past the lesions using Escherichia coli DNA polymerase I (Klenow fragment). Biochemistry 41, 15304–15314 (2002).
  CAS PubMed Google Scholar
• Kornyushyna, O. & Burrows, C. J. Effect of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin on proofreading by Escherichia coli DNA polymerase I (Klenow fragment) in different sequence contexts. Biochemistry 42, 13008–13018 (2003).
  CAS PubMed Google Scholar
• Henderson, P. T. et al. The hydantoin lesions from oxidation of 7,8-dihydro-8-oxoguanine are potent sources of replication errors in vivo. Biochemistry 42, 9257–9262 (2003).
  CAS PubMed Google Scholar
• Delaney, S., Neeley, W. L., Delaney, J. C. & Essigmann, J. M. The substrate specificity of MutY for hyperoxidized guanine lesions in vivo. Biochemistry, 46, 1448–1455 (2007).
  CAS PubMed Google Scholar
• Leipold, M. D., Muller, J. G., Burrows, C. J. & David, S. S. Removal of hydantoin products of 8-oxoguanine oxidation by the Escherichia coli DNA repair enzyme, Fpg. Biochemistry 39, 14984–14992 (2000).
  CAS PubMed Google Scholar
• Leipold, M. D., Workman, H., Muller, J. G., Burrows, C. J. & David, S. S. Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1 and yOGG2. Biochemistry 42, 11373–11381 (2003).
  CAS PubMed Google Scholar
• Hazra, T. K. et al. Repair of hydantoins, one electron oxidation product of 8-oxoguanine, by DNA glycosylases of Escherichia coli. Nucleic Acids Res. 29, 1967–1974 (2001).
  CAS PubMed PubMed Central Google Scholar
• Wallace, S. S., Bandaru, V., Kathe, S. D. & Bond, J. P. The enigma of endonuclease VIII. DNA Repair (Amst.) 2, 441–453 (2003).
  CAS Google Scholar
• Hailer, M. K., Slade, P. G., Martin, B. D. & Sugden, K. D. Nei-deficient Escherichia coli are sensitive to chromate and accumulate the oxidized guanine lesion spiroiminodihydantoin. Chem. Res. Toxicol. 18, 1378–1383 (2005).
  CAS PubMed PubMed Central Google Scholar
• Bandaru, V., Sunkara, S., Wallace, S. S. & Bond, J. P. A novel human DNA glycosylase that removes oxidative DNA damage and is homologous to Escherichia coli endonuclease VIII. DNA Repair (Amst.) 1, 517–529 (2002).
  CAS Google Scholar
• Hazra, T. K. et al. Identification and characterization of a human DNA glycosylase for repair of modified oxidatively damaged DNA. Proc. Natl Acad. Sci. USA 99, 3523–3528 (2002).
  ADS CAS PubMed PubMed Central Google Scholar
• Hazra, T. K. et al. Identification of a novel human DNA glycosylase for repair of cytosine-derived lesions. J. Biol. Chem. 277, 30417–30420 (2002).
  CAS PubMed Google Scholar
• Morland, I. et al. Human DNA glycosylases of the bacterial Fpg/MutM superfamily: an alternative pathway for the repair of 8-oxoguanine and other oxidation products in DNA. Nucleic Acids Res. 30, 4926–4936 (2002).
  CAS PubMed PubMed Central Google Scholar
• Doublie, S., Bandaru, V., Bond, J. P. & Wallace, S. S. The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity. Proc. Natl Acad. Sci. USA 101, 10284–10289 (2004).
  ADS CAS PubMed PubMed Central Google Scholar
• Dou, H., Mitra, S. & Hazra, T. K. Repair of oxidized bases in DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2. J. Biol. Chem. 278, 49679–49684 (2003).
  CAS PubMed Google Scholar
• Hailer, K. M., Slade, P. G., Martin, B. D., Rosenquist, T. A. & Sugden, K. D. Recognition of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin in DNA by the base excision repair glycosylases NEIL1 and NEIL2. DNA Repair (Amst.) 4, 41–50 (2005).
  CAS Google Scholar
• Das, A., Hazra, T. K., Boldogh, I., Mitra, S. & Bhakat, K. K. Induction of the human oxidized base-specific DNA glycosylase NEIL1 by reactive oxygen species. J. Biol. Chem. 280, 35272–35280 (2005).
  CAS PubMed Google Scholar
• Rosenquist, T. A. et al. The novel DNA glycosylase, NEIL1, protects mammalian cells from radiation-mediated cell death. DNA Repair (Amst.) 2, 581–591 (2003).
  CAS Google Scholar
• Shinmura, K. et al. Inactivating mutations of the human base excision repair gene NEIL1 in gastric cancer. Carcinogenesis 25, 2311–2317 (2004).
  CAS PubMed Google Scholar
• Vartanian, V. et al. The metabolic syndrome resulting from a knockout of the NEIL1 DNA glycosylase. Proc. Natl Acad. Sci. USA 103, 1864–1869 (2006).
  ADS CAS PubMed PubMed Central Google Scholar
• Guan, Y. et al. MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nature Struct. Biol. 5, 1058–1064 (1998).
  CAS PubMed Google Scholar
• Lukianova, O. L. & David, S. S. A role for iron–sulfur clusters in DNA repair. Curr. Opin. Chem. Biol. 9, 145–151 (2005).
  CAS PubMed Google Scholar