Clostridium acetobutylicum 8-oxoguanine DNA glycosylase (Ogg) differs from eukaryotic Oggs with respect to opposite base discrimination

Biochemistry

Volumn 47, Issue 29, 2008, Pages 7626-7636

  Robey Bond, Susan M ^a   Barrantes Reynolds, Ramiro ^a   Bond, Jeffrey P ^a   Wallace, Susan S ^a   Bandaru, Viswanath ^a,b  

^a UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

^b Formulation Development Services   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDS; AMINES; AMINO ACIDS; BACTERIOLOGY; DNA; ESCHERICHIA COLI; FLOW INTERACTIONS; GENES; MAINTENANCE; NUCLEIC ACIDS; REPAIR;

8-OXOGUANINE; AMERICAN CHEMICAL SOCIETY (ACS); ARCHAEA; CLOSTRIDIUM ACETOBUTYLICUM; DNA GLYCOSYLASE; EUKARYOTIC ENZYMES; EVOLUTION (CO); FORMAMIDOPYRIMIDINE; FUNCTIONAL DIFFERENCES; IN-VITRO; KINETIC CONTROL; SELECTIVE PRESSURES; SINGLE STRANDED DNA (SS DNA);

ORGANIC ACIDS;

8 HYDROXYGUANINE; 8 OXOGUANINE DNA GLYCOSYLASE COMPLEX; BACTERIAL ENZYME; DNA FORMAMIDOPYRIMIDINE GLYCOSYLASE; DNA GLYCOSYLTRANSFERASE; SINGLE STRANDED DNA;

ARTICLE; CLOSTRIDIUM ACETOBUTYLICUM; DNA REPAIR; ENZYME KINETICS; ESCHERICHIA COLI; EUKARYOTE; EXCISION REPAIR; GENETIC VARIABILITY; NONHUMAN; OXIDATION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; QUALITATIVE ANALYSIS; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CLOSTRIDIUM ACETOBUTYLICUM; DNA GLYCOSYLASES; DNA-FORMAMIDOPYRIMIDINE GLYCOSYLASE; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PHYLOGENY; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); CLOSTRIDIA; CLOSTRIDIUM ACETOBUTYLICUM; ESCHERICHIA COLI; EUKARYOTA;

EID: 47649118611     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800162e     Document Type: Article

References (56)

1. Cathcart, R., Schwiers, E., Saul, R. L., and Ames, B. N. (1984) Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage. Proc. Natl. Acad. Sci. U.S.A. 81, 5633-5637.
2. Fraga, C. G., Shigenaga, M. K., Park, J. W., Degan, P., and Ames, B. N. (1990) Oxidative damage to DNA during aging: 8-hydroxy-2′-deoxyguanosine in rat organ DNA and urine. Proc. Natl. Acad. Sci. U.S.A. 87, 4533-4537.
3. Wallace, S. S. (1988) AP endonucleases and DNA glycosylases that recognize oxidative DNA damage. Environ. Mol. Mutagen. 12, 431-477.
4. Dizdaroglu, M., Nackerdien, Z., Chao, B. C., Gajewski, E., and Rao, G. (1991) Chemical nature of in vivo DNA base damage in hydrogen peroxide-treated mammalian cells. Arch. Biochem. Biophys. 285, 388-390.
5. Kuchino, Y., Mori, F., Kasai, H., Inoue, H., Iwai, S., Miura, K., Ohtsuka, E., and Nishimura, S. (1987) Misreading of DNA templates containing 8-hydroxydeoxyguanosine at the modified base and at adjacent residues. Nature 327, 77-79.
6. Wood, M. L., Dizdaroglu, M., Gajewski, E., and Essigmann, J. M. (1990) Mechanistic studies of ionizing radiation and oxidative mutagenesis: genetic effects of a single 8-hydroxyguanine (7-hydro-8-oxoguanine) residue inserted at a unique site in a viral genome. Biochemistry 29, 7024-7032.
7. van der Kemp, P. A., Thomas, D., Barbey, R., de Oliveira, R., and Boiteux, S. (1996) Cloning and expression in Escherichia coli of the OGG1 gene of Saccharomyces cerevisiae, which codes for a DNA glycosylase that excises 7,8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N- methylformamidopyrimidine. Proc. Natl. Acad. Sci. U.S.A. 93, 5197-5202.
8. Aburatani, H., Hippo, Y., Ishida, T., Takashima, R., Matsuba, C., Kodama, T., Takao, M., Yasui, A., Yamamoto, K., and Asano, M. (1997) Cloning and characterization of mammalian 8-hydroxyguanine-specific DNA glycosylase/ apurinic, apyrimidinic lyase, a functional mutM homologue. Cancer Res. 57, 2151-2156.
9. Arai, K., Morishita, K., Shinmura, K., Kohno, T., Kim, S. R., Nohmi, T., Taniwaki, M., Ohwada, S., and Yokota, J. (1997) Cloning of a human homolog of the yeast OGG1 gene that is involved in the repair of oxidative DNA damage. Oncogene 14, 2857-2861.
10. Rosenquist, T. A., Zharkov, D. O., and Grollman, A. P. (1997) Cloning and characterization of a mammalian 8-oxoguanine DNA glycosylase. Proc. Natl. Acad. Sci. U.S.A. 94, 7429-7434.
11. Bjoras, M., Luna, L., Johnsen, B., Hoff, E., Haug, T., Rognes, T., and Seeberg, E. (1997) Opposite base-dependent reactions of a human base excision repair enzyme on DNA containing 7,8-dihydro-8-oxoguanine and abasic sites. EMBO J. 16, 6314-6322.
12. Roldan-Arjona, T., Wei, Y. F., Carter, K. C., Klungland, A., Anselmino, C., Wang, R. P., Augustus, M., and Lindahl, T. (1997) Molecular cloning and functional expression of a human cDNA encoding the antimutator enzyme 8-hydroxyguanine-DNA glycosylase. Proc. Natl. Acad. Sci. U.S.A. 94, 8016-8020.
13. Nagashima, M., Sasaki, A., Morishita, K., Takenoshita, S., Nagamachi, Y., Kasai, H., and Yokota, J. (1997) Presence of human cellular protein(s) that specifically binds and cleaves 8-hydroxyguanine containing DNA. Mutat. Res. 383, 49-59.
14. Radicella, J. P., Dherin, C., Desmaze, C., Fox, M. S., and Boiteux, S. (1997) Cloning and characterization of hOGG1, a human homolog of the OGG1 gene of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 94, 8010-8015.
15. Klungland, A., Rosewell, I., Hollenbach, S., Larsen, E., Daly, G., Epe, B., Seeberg, E., Lindahl, T., and Barnes, D. E. (1999) Accumulation of premutagenic DNA lesions in mice defective in removal of oxidative base damage. Proc. Natl. Acad. Sci. U.S.A. 96, 13300-13305.
16. 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.
17. Lu, R., Nash, H. M., and Verdine, G. L. (1997) A mammalian DNA repair enzyme that excises oxidatively damaged guanines maps to a locus frequently lost in lung cancer. Curr. Biol. 7, 397-407.
18. Bjoras, M., Seeberg, E., Luna, L., Pearl, L. H., and Barrett, T. E. (2002) Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase. J. Mol. Biol. 317, 171-177.
19. Bruner, S. D., Norman, D. P., and Verdine, G. L. (2000) Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403, 859-866.
20. Radom, C. T., Banerjee, A., and Verdine, G. L. (2007) Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations. J. Biol. Chem. 282, 9182-9194.
21. Im, E. K., Hong, C. H., Back, J. H., Han, Y. S., and Chung, J. H. (2005) Functional identification of an 8-oxoguanine specific endonuclease from Thermotoga maritima. J. Biochem. Mol. Biol. 38, 676-682.
22. Gogos, A., and Clarke, N. D. (1999) Characterization of an 8-oxoguanine DNA glycosylase from Methanococcus jannaschii. J. Biol. Chem. 274, 30447-30450.
23. Chung, J. H., Suh, M. J., Park, Y. I., Tainer, J. A., and Han, Y. S. (2001) Repair activities of 8-oxoguanine DNA glycosylase from Archaeoglobus fulgidus, a hyperthermophilic archaeon. Mutat. Res. 486, 99-111.
24. Denver, D. R., Swenson, S. L., and Lynch, M. (2003) An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases. Mol. Biol. Evol. 20, 1603-1611.
25. Sartori, A. A., Lingaraju, G. M., Hunziker, P., Winkler, F. K., and Jiricny, J. (2004) Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases. Nucleic Acids Res. 32, 6531-6539.
26. Audebert, M., Radicella, J. P., and Dizdaroglu, M. (2000) Effect of single mutations in the OGG1 gene found in human tumors on the substrate specificity of the Ogg1 protein. Nucleic Acids Res. 28, 2672-2678.
27. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
28. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S. R., Griffiths-Jones, S., Howe, K. L., Marshall, M., and Sonnhammer, E. L. (2002) The Pfam protein families database. Nucleic Acids Res. 30, 276-280.
29. Marchler-Bauer, A., Anderson, J. B., Cherukuri, P. F., DeWeese-Scott, C., Geer, L. Y., Gwadz, M., He, S., Hurwitz, D. I., Jackson, J. D., Ke, Z., Lanczycki, C. J., Liebert, C. A., Liu, C., Lu, F., Marchler, G. H., Mullokandov, M., Shoemaker, B. A., Simonyan, V., Song, J. S., Thiessen, P. A., Yamashita, R. A., Yin, J. J., Zhang, D., and Bryant, S. H. (2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res. 33, D192-D196.
30. Marchler-Bauer, A., Anderson, J. B., Derbyshire, M. K., DeWeese-Scott, C., Gonzales, N. R., Gwadz, M., Hao, L., He, S., Hurwitz, D. I., Jackson, J. D., Ke, Z., Krylov, D., Lanczycki, C. J., Liebert, C. A., Liu, C., Lu, F., Lu, S., Marchler, G. H., Mullokandov, M., Song, J. S., Thanki, N., Yamashita, R. A., Yin, J. J., Zhang, D., and Bryant, S. H. (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 35, D237-D240.
31. Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217.
32. Katoh, K., Misawa, K., Kuma, K., and Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059-66.
33. Caffrey, D. R., Dana, P. H., Mathur, V., Ocano, M., Hong, E. J., Wang, Y. E., Somaroo, S., Caffrey, B. E., Potluri, S., and Huang, E. S. (2007) PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments. BMC Bioinf. 8, 381.
34. Clamp, M., Cuff, J., Searle, S. M., and Barton, G. J. (2004) The Jalview Java alignment editor. Bioinformatics 20, 426-427.
35. Galtier, N., Gouy, M., and Gautier, C. (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12, 543-548.
36. Saitou, N., and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
37. Felsenstein, J. (2005) Using the quantitative genetic threshold model for inferences between and within species. Philos. Trans. R. Soc. London, Ser. B 360, 1427-1434.
38. McGuffin, L. J., Bryson, K., and Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics 16, 404-405.
39. DeLano, W. L. (2002) The PyMOL molecular graphics system, DeLano Scientific, Palo Alto, CA.
40. Bandaru, V., Blaisdell, J. O., and Wallace, S. S. (2006) Oxidative DNA glycosylases: recipes from cloning to characterization. Methods Enzymol. 408, 15-33.
41. Dodson, M. L., Schrock, R. D., III, and Lloyd, R. S. (1993) Evidence for an imino intermediate in the T4 endonuclease V reaction. Biochemistry 32, 8284-8290.
42. R Development Core Team (2007) R Foundation for Statistical Computing, Vienna, Austria.
43. Setzer, R. W. (2007)odesolve: Solvers for Ordinary Differential Equations, R package version 5.0-18.
44. Cox, D. R. (2006) Principles of Statistical Inference, Cambridge University Press, Cambridge.
45. Wolf, M., Muller, T., Dandekar, T., and Pollack, J. D. (2004) Phytogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int. J. Syst. Evol. Microbiol. 54, 871-875.
46. Michaels, M. L., and Miller, J. H. (1992) 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.
47. Hill, J. W., and Evans, M. K. (2006) Dimerization and opposite base-dependent catalytic impairment of polymorphic S326C OGG1 glycosylase. Nucleic Acids Res. 34, 1620-1632.
48. Leipold, M. D., Workman, H., Muller, J. G., Burrows, C. J., and David, S. S. (2003) Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1, and yOGG2. Biochemistry 42, 11373-11381.
49. Fersht, A. (1985) Enzyme structure and mechanism, 2nd ed., W. H. Freeman, New York.
50. Zharkov, D. O., Rosenquist, T. A., Gerchman, S. E., and Grollman, A. P. (2000) Substrate specificity and reaction mechanism of murine 8-oxoguanine-DNA glycosylase. J. Biol. Chem. 275, 28607-28617.
51. Boiteux, S., O'Connor, T. R., Lederer, F., Gouyette, A., and Laval, J. (1990) Homogeneous Escherichia coli FPG protein. A DNA glycosylase which excises imidazole ring-opened purines and nicks DNA at apurinic/apyrimidinic sites. J. Biol. Chem. 265, 3916-3922.
52. Neto, J. B., Gentil, A., Cabral, R. E., and Sarasin, A. (1992) Mutation spectrum of heat-induced abasic sites on a single-stranded shuttle vector replicated in mammalian cells. J. Biol. Chem. 267, 19718-19723.
53. Kuznetsov, N. A., Koval, V. V., Nevinsky, G. A., Douglas, K. T., Zharkov, D. O., and Fedorova, O. S. (2007) Kinetic conformational analysis of human 8-oxoguanine-DNA glycosylase. J. Biol. Chem. 282, 1029-1038.
54. Eisen, J. A., and Hanawalt, P. C. (1999) A phylogenomic study of DNA repair genes, proteins, and processes. Mutat. Res. 435, 171-213.
55. Fromme, J. C., Bruner, S. D., Yang, W., Karplus, M., and Verdine, G. L. (2003) Product-assisted catalysis in base-excision DNA repair. Nat. Struct. Biol. 10, 204-211.
56. Sidorenko, V. S., Nevinsky, G. A., and Zharkov, D. O. (2007) Mechanism of interaction between human 8-oxoguanine-DNA glycosylase and AP endonuclease. DNA Repair (Amsterdam) 6, 317-328.