The 3′-5′ proofreading exonuclease of archaeal family-B DNA polymerase hinders the copying of template strand deaminated bases

Nucleic Acids Research

Volumn 37, Issue 22, 2009, Pages 7603-7611

  Russell, Henry J ^a   Richardson, Tomas T ^a   Emptage, Kieran ^a   Connolly, Bernard A ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA; EXONUCLEASE; HYPOXANTHINE; URACIL; ARCHAEAL PROTEIN; DNA DIRECTED DNA POLYMERASE; EXODEOXYRIBONUCLEASE; PFU DNA POLYMERASE; PRIMER DNA;

ARTICLE; BASE MISPAIRING; CONTROLLED STUDY; DNA BINDING; DNA FLANKING REGION; DNA STRAND; DNA SYNTHESIS INHIBITION; DNA TEMPLATE; ENZYMATIC DEGRADATION; ENZYME ACTIVITY; ENZYME INHIBITION; NONHUMAN; PRIORITY JOURNAL; PYROCOCCUS FURIOSUS; CHEMISTRY; DEAMINATION; ENZYMOLOGY; METABOLISM;

ARCHAEA; PYROCOCCUS FURIOSUS;

ARCHAEAL PROTEINS; DEAMINATION; DNA PRIMERS; DNA-DIRECTED DNA POLYMERASE; EXODEOXYRIBONUCLEASES; HYPOXANTHINE; PYROCOCCUS FURIOSUS; TEMPLATES, GENETIC; URACIL;

EID: 75649109233     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp800     Document Type: Article

References (31)

1. Joyce, C.M. (1989) How DNA travels between the separate polymerase and 30-50 exonuclease sites of DNA polymerase I (Klenow fragment). J. Biol. Chem., 264, 10858-10866.
2. Kunkel, T.A. (1992) DNA replication fidelity. J. Biol. Chem., 267, 18251-18254.
3. Johnson, K.A. (1993) Conformational coupling in DNA polymerase fidelity. Annu. Rev. Biochem., 62, 685-713.
4. Joyce, C.M. and Steitz, T.A. (1994) Function and structure relationships in DNA polymerases. Annu. Rev. Biochem., 63, 777-822.
5. Benkovic, S.J., Valentine, A.M. and Salinas, S. (2001) Replisome-mediated DNA replication. Annu. Rev. Biochem., 70, 181-208.
6. Joyce, C.M. and Benkovic, S.J. (2004) DNA polymerase fidelity: kinetics, structure, and checkpoints. Biochemistry, 43, 14317-14324.
7. Lundberg, K.S., Shoemaker, D.D., Adams, M.W.W., Short, J.M., Sorge, J.A. and Mathur, E.J. (1991) High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene, 101, 1-6.
8. Cline, J., Braman, J.C. and Hogrefe, H.H. (1996) PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res., 24, 3546-3551.
9. Hopfner, K.-P., Eichinger, A., Engh, R.A., Laue, F., Ankenbauer, W., Huber, R. and Angerer, B. (1999) Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius. Proc. Natl Acad. Sci. USA, 96, 3600-3605.
10. Greagg, M.A., Fogg, M.J., Panayotou, G., Evans, S.J., Connolly, B.A. and Pearl, L.H. (1999) A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil. Proc. Natl Acad. Sci. USA, 96, 9045-9050.
11. Fogg, M.J., Pearl, L.H. and Connolly, B.A. (2002) Structural basis for uracil recognition by archaeal family B DNA polymerases. Nat. Struct. Biol., 9, 922-927.
12. Shuttleworth, G., Fogg, M.J., Kurpiewski, M.R., Jen-Jacobson, L. and Connolly, B.A. (2004) Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea. J. Mol. Biol., 337, 621-634.
13. Firbank, S.J., Wardle, J., Heslop, P., Lewis, R.J. and Connolly, B.A. (2008) Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography. J. Mol. Biol., 381, 529-539.
14. Connolly, B.A. (2009) Recognition of deaminated bases by archaeal family-B polymerases. Biochem. Soc. Trans., 37, 65-68.
15. Gill, S., O'Neill, R., Lewis, R.J. and Connolly, B.A. (2007) Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases. J. Mol. Biol., 372, 855-863.
16. Gruz, P., Shimizu, M., Pisani, F.M., DeFelice, M., Kanke, Y. and Nohmi, T. (2003) Processing of DNA lesions by archaeal DNA polymerases from Sulfolobus solfataricus. Nucleic Acids Res., 31, 4024-4030.
17. Franklin, M.C., Wang, J. and Steitz, T.A. (2001) Structure of the replicating complex of a Pol alpha family DNA polymerase. Cell, 105, 657-666.
18. Shamoo, Y. and Steitz, T.A. (1999) Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell, 99, 155-166. Nucleic Acids Research, 2009, Vol. 37, No. 22 7611.
19. Emptage, K., O'Neill, R., Solovyova, A. and Connolly, B.A. (2008) Interplay between DNA polymerase and proliferating cell nuclear antigen switches off base excision repair of uracil and hypoxanthine during replication in archaea. J. Mol. Biol., 383, 762-771.
20. Evans, S.J., Fogg, M.J., Mamone, A., Davis, M., Pearl, L.H. and Connolly, B.A. (2000) Improving dideoxynucleotide-triphosphate utilisation by the hyper-thermophilic DNA polymerase from Pyrococcus furiosus. Nucleic Acids Res., 28, 1059-1066.
21. Donlin, M.J., Patel, S.S. and Johnson, K.A. (1991) Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction. Biochemistry, 30, 538-546.
22. Khare, V. and Eckert, K.A. (2001) The 30-50 exonuclease of T4 DNA polymerase removes premutagenic alkyl mispairs and contributes to futile cycling at 06 methylguanine lesions. J. Biol. Chem., 276, 24286-24292.
23. Khare, V. and Eckert, K.A. (2002) The proofreading 30-50 exonuclease activity of DNA polymerases: a kinetic barrier to translesion DNA synthesis. Mutation Res., 510, 45-54.
24. Schwartz, H., Shavitt, O. and Livneh, Z. (1988) The role of exonucleolytic processing and polymerase-DNA association in vitro: significance for SOS targeted mutagenesis. J. Biol. Chem., 263, 18277-18285.
25. Garg, P., Stith, C.M., Sabouri, N., Johansson, E. and Burgers, P.M.J. (2004) Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication. Genes Dev., 18, 2764-2773.
26. Wardle, J., Burgers, P.M.J., Cann, I.K.O., Darley, K., Heslop, P., Johansson, E., Lin, L., McGlynn, P., Sanvoisin, J., Stith, C.M. et al. (2008) Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya. Nucleic Acids Res., 36, 705-711.
27. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature, 286, 709-715.
28. Lindahl, T. and Nyberg, B. (1974) Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry, 13, 3405-3410.
29. Schroeder, G.K. and Wolfenden, R. (2007) Rates of spontaneous disintegration of DNA and the rate enhancements produced by DNA glycosylases and deaminases. Biochemistry, 46, 13638-13647.
30. Baynton, K. and Fuchs, R.P.P. (2000) Lesions in DNA: hurdles for polymerases. Trends Biochem. Sci., 25, 74-79.
31. Cox, M.M. (2001) Recombinational DNA repair of damaged replication forks in Escherichia coli: questions. Annu. Rev. Genet., 35, 53-82.