Studies on the base excision repair (BER) complex in Pyrococcus furiosus

Biochemical Society Transactions

Volumn 37, Issue 1, 2009, Pages 79-82

  Kiyonari, Shinichi ^a,b   Tahara, Saki ^a   Uchimura, Maiko ^a   Shirai, Tsuyoshi ^b,c   Ishino, Sonoko ^a,b   Ishino, Yoshizumi ^a,b  

^a KYUSHU UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c NAGAHAMA INSTITUTE OF BIO SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Apurinic apyrimidinic endonuclease (AP endonuclease); Base excision repair (BER); Hyperthermophilic archaeon; Proliferating cell nuclear antigen interacting protein (PIP); Pyrococcus furiosus; Uracil DNA glycosylase

Indexed keywords

CYCLINE; DNA (APURINIC OR APYRIMIDINIC SITE) LYASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; URACIL DNA GLYCOSIDASE;

ANTIBODY COMBINING SITE; ANTIGEN STRUCTURE; ARTICLE; BACTERIAL GENOME; DNA REPLICATION; DNA STRUCTURE; EXCISION REPAIR; GENE IDENTIFICATION; MOLECULAR MODEL; NONHUMAN; OPEN READING FRAME; OPERON; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PYROCOCCUS FURIOSUS; STRUCTURE ANALYSIS; CHEMISTRY; DNA REPAIR; ENZYMOLOGY; METABOLISM; PROTEIN BINDING; REVIEW;

ARCHAEA; PYROCOCCUS FURIOSUS;

DNA REPAIR; PROLIFERATING CELL NUCLEAR ANTIGEN; PROTEIN BINDING; PYROCOCCUS FURIOSUS; URACIL-DNA GLYCOSIDASE;

EID: 59749103010     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0370079     Document Type: Article

References (32)

1. Moldovan, G.L., Pfander, B. and Jentsch, S. (2007) PCNA, the maestro of the replication fork. Cell 129, 665-679
2. Warbrick, W. (2000) The puzzle of PCNA's many partners. BioEssays 22, 997-1006
3. Haracska, L., Johnson, R.E., Unk, I., Phillips, B., Hurwitz, J., Prakash, L. and Prakash, S. (2001) Physical and functional interactions of human DNA polymerase n with PCNA. Mol. Cell. Biol. 21, 7199-7206
4. Gomes, X.V. and Burgers, P.M. (2000) Two modes of FEN1 binding to PCNA regulated by DNA. EMBO J. 19, 3811-3821
5. Levin, D.S., McKenna, A.E., Motycka, T.A., Matsumoto, Y. and Tomkinson, A.E. (2000) Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair. Curr. Biol. 10, 919-922
6. Tori, K., Kimizu, M., Ishino, S. and Ishino, Y. (2007) DNA polymerases BI and D from the hyperthermophilic archaeon Pyrococcus furiosus both bind to proliferating cell nuclear antigen with their C-terminal PIP-box motifs. J. Bacteriol. 189, 5652-5657
7. Matsumiya, S., Ishino, S., Ishino, Y. and Morikawa, K. (2002) Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus. Genes Cells 7, 911-922
8. Fujikane, R., Shinagawa, H. and Ishino, Y. (2006) The archaeal Hjm helicase has recQ-like functions, and may be involved in repair of stalled replication fork. Genes Cells 11, 99-110
9. Kiyonari, S., Takayama, K., Nishida, H. and Ishino, Y. (2006) Identification of a novel binding motif in Pyrococcus furiosus DNA ligase for the functional interaction with proliferating cell nuclear antigen. J. Biol. Chem. 281, 28023-28032
10. Nishida, H., Kiyonari, S., Ishino, Y. and Morikawa, K. (2006) The closed structure of an archaeal DNA ligase from Pyrococcus furiosus. J. Mol. Biol. 360, 956-967
11. Berti, P.J. and McCann, J.A.B. (2006) Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transfer. Chem. Rev. 106, 506-555
12. Yang, H., Chiang, J.H., Fitz-Gibbon, S., Lebel, M., Sartori, A.A., Jiricny, J., Slupska, M.M. and Miller, J.H. (2002) Direct interaction between uracil-DNA glycosylase and a proliferating cell nuclear antigen homolog in the crenarchaeon Pyrobaculum aerophilum. J. Biol. Chem. 277, 22271-22278
13. Dionne, I. and Bell, S.D. (2005) Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins. Biochem. J. 387, 859-863
14. Kiyonari, S., Uchimura, M., Shirai, T. and Ishino, Y. (2008) Physical and functional interactions between uracil-DNA glycosylase and proliferating cell nuclear antigen from the euryarchaeon Pyrococcus furiosus. J. Biol. Chem. 283, 24185-24193
15. Kiyonari, S., Kamigochi, T. and Ishino, Y. (2007) A single amino acid substitution in the DNA-binding domain of Aeropyrum pernix DNA ligase impairs its interaction with proliferating cell nuclear antigen. Extremophiles 11, 675-684
16. Kosaka, H., Hoseki, J, Nakagawa, N., Kuramitsu, S. and Masui, R. (2007) Crystal structure of family 5 uracil-DNA glycosylase bound to DNA. J. Mol. Biol. 373, 839-850
17. Otterlei, M., Warbrick, E., Nagelhus, T.A., Haug, T., Slupphaug, G., Akbari, M., Aas, P.A., Steinsbekk, K., Bakke, O. and Krokan, H.E. (1999) Post-replicative base excision repair in replication foci. EMBO J. 18, 3834-3844
18. Akbari, M., Otterlei, M., Peña-Diaz, J., Aas, P.A., Kavli, B., Liabakk, N.B., Hagen, L., Imai, K., Durandy, A., Slupphaug, G. and Krokan, H.E. (2004) Repair of U/G and U/A in DNA by UNG2-associated repair complexes takes place predominantly by short-patch repair both in proliferating and growth-arrested cells. Nucleic Acids Res. 32, 5486-5498
19. Parlanti, E., Locatelli, G., Maga, G. and Dogliotti, E. (2007) Human base excision repair complex is physically associated to DNA replication and cell cycle regulatory proteins. Nucleic Acids Res. 35, 1569-1577
20. Friedberg, E.C., Walker, G.C., Siede, W., Wood, R.D., Schultz, R.A. and Ellenberger, T. (2006) Base excision repair. In DNA Repair and Mutagenesis, 2nd edn, pp. 169-226, ASM Press, Washington, DC
21. Miertzschke, M. and Greiner-Stoffele, T. (2003) The xthA gene product of Archaeoglobus fulgidus is an unspecific DNase. Eur. J. Biochem. 270, 1838-1849
22. Pfeifer, S. and Greiner-Stoffele, T. (2005) A recombinant exonuclease III homologue of the thermophilic archaeon Methanothermobacter thermautotrophicus. DNA Repair 4, 433-444
23. Kaneda, K., Ohishi, K., Sekiguchi, J. and Shida, T. (2006) Characterization of the AP endonucleases from Thermoplasma volcanium and Lactobacillus plantarum: contributions of two important tryptophan residues to AP site recognition. Biosci. Biotechnol. Biochem. 70, 2213-2221
24. Back, J.H., Chung, J.H., Park, Y.I., Kim, K.-S. and Han, Y.S. (2003) Endonuclease IV enhances base excision repair of endonuclease III from Methanobacterium thermoautotrophicum. DNA Repair 2, 455-470
25. Sartori, A.A. and Jiricny, J. (2003) Enzymology of base excision repair in the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Biol. Chem. 278, 24563-24576
26. Lindahl, T. and Nyberg, B. (1974) Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 13, 3405-3410
27. Georgescu, R.E., Kim, S.-S., Yurieva, O., Kuriyan, J., Kong, X.-P. and O'Donnell, M. (2008) Structure of a sliding clamp on DNA. Cell 132, 43-54
28. Lasken, R.S., Schugter, D.M. and Rashtchian, A. (1996) Archaebacterial DNA polymerases tightly bind uracil-containing DNA. J. Biol. Chem. 271, 17692-17696
29. 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. U.S.A. 96, 9045-9050
30. 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
31. Hogrefe, H.H., Hansen, C.J., Scott, B.R. and Nielson, K.B. (2002) Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation. Proc. Natl. Acad. Sci. U.S.A. 99, 596-601
32. Connolly, B.A., Fogg, M.J., Shuttleworth, G. and Wilson, B.T. (2003) Uracil recognition by archaeal family B DNA polymerases. Biochem. Soc. Trans. 31, 699-702