DNA polymerase β gap-filling translesion DNA synthesis

Chemical Research in Toxicology

Volumn 25, Issue 12, 2012, Pages 2744-2754

  Chary, Parvathi ^a   Beard, William A ^b   Wilson, Samuel H ^b   Lloyd, R Stephen ^a  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

7,8 DIHYDRODIOL 9,10 EPOXIDE; ADENINE; BENZO[A]PYRENE; DINUCLEOTIDE; DNA BASE; DNA DIRECTED DNA POLYMERASE BETA; EPOXIDE; GUANINE; MUTANT PROTEIN; OLIGONUCLEOTIDE; POLYCYCLIC AROMATIC HYDROCARBON; RNA DIRECTED DNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; CARCINOGEN DNA INTERACTION; CONTROLLED STUDY; COVALENT BOND; DNA SYNTHESIS; DNA TEMPLATE; ENZYME INHIBITION; STEREOCHEMISTRY; STEREOSPECIFICITY; STRUCTURE ACTIVITY RELATION; TRANSLESION DNA SYNTHESIS; WILD TYPE;

7,8-DIHYDRO-7,8-DIHYDROXYBENZO(A)PYRENE 9,10-OXIDE; CATALYSIS; DNA; DNA ADDUCTS; DNA POLYMERASE BETA; DNA REPAIR; HIV REVERSE TRANSCRIPTASE;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84871233449     PISSN: 0893228X     EISSN: 15205010     Source Type: Journal    
DOI: 10.1021/tx300368f     Document Type: Article

References (34)

1. Beard, W. A. and Wilson, S. H. (2006) Structure and mechanism of DNA polymerase β Chem. Rev. 106, 361-382
2. Matsumoto, Y. and Kim, K. (1995) Excision of deoxyribose phosphate residues by DNA polymerase β during DNA repair Science 269, 699-702
3. Piersen, C. E., Prasad, R., Wilson, S. H., and Lloyd, R. S. (1996) Evidence for an imino intermediate in the DNA polymerase β deoxyribose phosphate excision reaction J. Biol. Chem. 271, 17811-17815 (Pubitemid 26250757)
4. Prasad, R., Beard, W. A., and Wilson, S. H. (1994) Studies of gapped DNA substrate binding by mammalian DNA polymerase β: Dependence on 5′-phosphate group J. Biol. Chem. 269, 18096-18101
5. Moon, A. F., Garcia-Diaz, M., Batra, V. K., Beard, W. A., Bebenek, K., Kunkel, T. A., Wilson, S. H., and Pedersen, L. C. (2007) The X family portrait: Structural insights into biological functions of X family polymerases DNA Repair 6, 1709-1725 (Pubitemid 350052723)
6. Canitrot, Y., Cazaux, C., Fréchet, M., Bouayadi, K., Lesca, C., Salles, B., and Hoffmann, J.-S. (1998) Overexpression of DNA polymerase β in cell results in a mutator phenotype and a decreased sensitivity to anticancer drugs Proc. Natl. Acad. Sci. U.S.A. 95, 12586-12590 (Pubitemid 28483808)
7. Servant, L., Cazaux, C., Bieth, A., Iwai, S., Hanaoka, F., and Hoffmann, J.-S. (2002) A role for DNA polymerase β in mutagenic UV lesion bypass J. Biol. Chem. 277, 50046-50053 (Pubitemid 36014457)
8. Batra, V. K., Shock, D. D., Prasad, R., Beard, W. A., Hou, E. W., Pedersen, L. C., Sayer, J. M., Yagi, H., Kumar, S., Jerina, D. M., and Wilson, S. H. (2006) Structure of DNA polymerase β with a benzo[ c ]phenanthrene diol epoxide-adducted template exhibits mutagenic features Proc. Natl. Acad. Sci. U.S.A. 103, 17231-17236 (Pubitemid 44788952)
9. Hoffmann, J. S., Pillaire, M. J., Garciaestefania, D., Lapalu, S., and Villani, G. (1996) In vitro bypass replication of the cisplatin-d(GpG) lesion by calf thymus DNA polymerase β and human immunodeficiency virus type I reverse transcriptase is highly mutagenic J. Biol. Chem. 271, 15386-15392 (Pubitemid 26225307)
10. Vaisman, A. and Chaney, S. G. (2000) The efficiency and fidelity of translesion synthesis past cisplatin and oxaliplatin GpG adducts by human DNA polymerase β J. Biol. Chem. 275, 13017-13025 (Pubitemid 30241462)
11. Efrati, E., Tocco, G., Eritja, R., Wilson, S. H., and Goodman, M. F. (1997) Abasic translesion synthesis by DNA polymerase β violates the "A-rule": Novel types of nucleotide incorporation by human DNA polymerase β at an abasic lesion in different sequence contexts J. Biol. Chem. 272, 2559-2569 (Pubitemid 27058550)
12. Efrati, E., Tocco, G., Eritja, R., Wilson, S. H., and Goodman, M. F. (1999) "Action-at-a-distance" mutagenesis: 8-Oxo-7,8-dihydro-2′- deoxyguanosine causes base substitution errors at neighboring template sites when copied by DNA polymerase β J. Biol. Chem. 274, 15920-15926
13. Osheroff, W. P., Beard, W. A., Yin, S., Wilson, S. H., and Kunkel, T. A. (2000) Minor groove interactions at the DNA polymerase β active site modulate single-base deletion error rates J. Biol. Chem. 275, 28033-28038
14. Batra, V. K., Beard, W. A., Shock, D. D., Pedersen, L. C., and Wilson, S. H. (2008) Structures of DNA polymerase β with active site mismatches suggest a transient abasic site intermediate during misincorporation Mol. Cell 30, 315-324 (Pubitemid 351615312)
15. Belousova, E. A., Maga, G., Fan, Y., Kubareva, E. A., Romanova, E. A., Lebedeva, N. A., Oretskaya, T. S., and Lavrik, O. I. (2010) DNA polymerases beta and lambda bypass thymine glycol in gapped DNA structures Biochemistry 49, 4695-4704
16. Maga, G., Crespan, E., Wimmer, U., van Loon, B., Amoroso, A., Mondello, C., Belgiovine, C., Ferrari, E., Locatelli, G., Villani, G., and Hubscher, U. (2008) Replication protein A and proliferating cell nuclear antigen coordinate DNA polymerase selection in 8-oxo-guanine repair Proc. Natl. Acad. Sci. U.S.A. 105, 20689-20694
17. Brown, W. C. and Romano, L. J. (1991) Effects of benzo[ a ]pyrene-DNA adducts on a reconstituted replication system Biochemistry 30, 1342-1350
18. Moore, P. D., Bose, K. K., Rabkin, S. D., and Strauss, B. S. (1981) Sites of termination of in vitro DNA synthesis on ultraviolet- and N-acetylaminofluorene-treated phi X174 templates by prokaryotic and eukaryotic DNA polymerases Proc. Natl. Acad. Sci. U.S.A. 78, 110-114 (Pubitemid 11131249)
19. Perlow, R. A., Kolbanovskii, A., Hingerty, B. E., Geacintov, N. E., Broyde, S., and Scicchitano, D. A. (2002) DNA adducts from a tumorigenic metabolite of benzo[a]pyrene block human RNA polymerase II elongation in a sequence- and stereochemistry-dependent manner J. Mol. Biol. 321, 29-47 (Pubitemid 34948467)
20. Jerina, D. M., Chadha, A., Cheh, A. M., Schurdak, M. E., Wood, A. W., and Sayer, J. M. (1991) Covalent bonding of bay-region diol epoxides to nucleic acids Adv. Exp. Med. Biol. 283, 533-553
21. Chary, P. and Lioyd, S. (1995) In vitro replication by prokaryotic and eukaryotic polymerases on DNA templates containing site-specific and stereospecific benzo [ a ]pyrene-7, 8-dihydrodiol-9, 10-epoxide adducts Nucleic Acids Res. 23, 1398-1405
22. Becerra, S. P., Kumar, A., Lewis, M. S., Widen, S. G., Abbotts, J., Karawya, E. M., Hughes, S. H., Shiloach, J., and Wilson, S. H. (1991) Protein-protein interactions of HIV-1 reverse transcriptase: Implication of central and C-terminal regions in subunit binding Biochemistry 30, 11707-11719
23. Beard, W. A., Osheroff, W. P., Prasad, R., Sawaya, M. R., Jaju, M., Wood, T. G., Kraut, J., Kunkel, T. A., and Wilson, S. H. (1996) Enzyme-DNA interactions required for efficient nucleotide incorporation and discrimination in human DNA polymerase β J. Biol. Chem. 271, 12141-12144 (Pubitemid 26160870)
24. Harris, C. M., Zhou, L., Strand, E. A., and Harris, T. M. (1991) New strategy for the synthesis of oligodeoxynucleotides bearing adducts at exocyclic amino sites of purine nucleosides J. Am. Chem. Soc. 113, 4328-4329
25. Kim, S. J., Stone, M. P., Harris, C. M., and Harris, T. M. (1992) A postoligomerization synthesis of oligodeoxynucleotides containing polycyclic aromatic hydrocarbon adducts at the N6 position of deoxyadenosine J. Am. Chem. Soc. 114, 5480-5481
26. Singhal, R. K. and Wilson, S. H. (1993) Short gap-filling synthesis by DNA polymerase β is processive J. Biol. Chem. 268, 15906-15911 (Pubitemid 23222095)
27. Osheroff, W. P., Beard, W. A., Wilson, S. H., and Kunkel, T. A. (1999) Base substitution specificity of DNA polymerase β depends on interactions in the DNA minor groove J. Biol. Chem. 274, 20749-20752
28. Miller, H., Prasad, R., Wilson, S. H., Johnson, F., and Grollman, A. P. (2000) 8-OxodGTP incorporation by DNA polymerase β is modified by active-site residue Asn279 Biochemistry 39, 1029-1033 (Pubitemid 30075330)
29. Sawaya, M. R., Prasad, P., Wilson, S. H., Kraut, J., and Pelletier, H. (1997) Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism Biochemistry 36, 11205-11215 (Pubitemid 27398440)
30. Prasad, R., Shock, D. D., Beard, W. A., and Wilson, S. H. (2010) Substrate channeling in mammalian base excision repair pathways: Passing the baton J. Biol. Chem. 285, 40479-40488
31. Freudenthal, B. D., Beard, W. A., and Wilson, S. H. Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure (Cambridge, MA, U. S.) 2012, in press.
32. Beard, W. A., Shock, D. D., Vande Berg, B. J., and Wilson, S. H. (2002) Efficiency of correct nucleotide insertion governs DNA polymerase fidelity J. Biol. Chem. 277, 47393-47398 (Pubitemid 36159254)
33. Beard, W. A. and Wilson, S. H. (2000) Structural design of a eukaryotic DNA repair polymerase: DNA polymerase β Mutat. Res. 460, 231-244 (Pubitemid 30628593)
34. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera: A visualization system for exploratory research and analysis J. Comput. Chem. 25, 1605-1612