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Volume 155, Issue 9

DNA polymerase X from implicated in bacterial tolerance to DNA damage is characterized as a short patch base excision repair polymerase Free

Abstract

The R1 genome encodes an X-family DNA repair polymerase homologous to eukaryotic DNA polymerase . The recombinant deinococcal polymerase X (PolX) purified from transgenic showed deoxynucleotidyltransferase activity. Unlike the Klenow fragment of , this enzyme showed short patch DNA synthesis activity on heteropolymeric DNA substrate. The recombinant enzyme showed 5′-deoxyribose phosphate (5′-dRP) lyase activity and base excision repair function with the help of externally supplied glycosylase and AP endonuclease functions. A disruption mutant of expressing 5′-dRP lyase and a truncated polymerase domain was comparatively less sensitive to -radiation than a deletion mutant. Both mutants showed higher sensitivity to hydrogen peroxide. Excision repair mutants of expressing this polymerase showed functional complementation of UV sensitivity. These results suggest the involvement of deinococcal polymerase X in DNA-damage tolerance of , possibly by contributing to DNA double-strand break repair and base excision repair.

  • Received:
  • Accepted:
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Keyword(s): AP, apurinic/apyrimidinic , BER, base excision repair , dRP, deoxyribose phosphate , MMC, mitomycin C , NER, nucleotide excision repair , PHP, polymerase and histidinol phosphatase , PolX, polymerase X , Polβ, polymerase β , T/P, template/primer and UDG, uracil DNA glycosylase
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2009-09-01
2024-04-19
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References

  1. Agostini H. J., Carroll J. D., Minton K. W. 1996; Identification and characterization of uvrA, a DNA repair gene of Deinococcus radiodurans . J Bacteriol 178:6759–6765
     [Google Scholar]
  2. Aravind L., Koonin E. V. 1999; DNA polymerase β like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res 27:1609–1618
     [Google Scholar]
  3. Arrage A. A., Phelps T. J., Benoit R. E., White D. C. 1993; Survival of subsurface microorganisms exposed to UV radiation and hydrogen peroxide. Appl Environ Microbiol 59:3545–3550
     [Google Scholar]
  4. Baños B., Lázaro J. M., Villar L., Salas M., de Vega M. 2008; Characterization of a Bacillus subtilis 64 kDa DNA polymerase X potentially involved in DNA repair. J Mol Biol 384:1019–1028
     [Google Scholar]
  5. Battista J. R. 2000; Radiation resistance: the fragments that remain. Curr Biol 10:R204–R205
     [Google Scholar]
  6. Battista J. R., Park M. J., McLemore A. E. 2001; Inactivation of two homologous proteins presumed to be involved in the desiccation tolerance of plants sensitizes Deinococcus radiodurans R1 to desiccation. Cryobiology 43:133–139
     [Google Scholar]
  7. Bjelland S., Bjøras M., Seeberg E. 1993; Excision of 3-methylguanine from alkylated DNA by 3-methyladenine DNA glycosylase I of Escherichia coli . Nucleic Acids Res 21:2045–2049
     [Google Scholar]
  8. Bjelland S., Birkeland N. K., Benneche T., Volden G., Seeberg E. 1994; DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the AlkA enzyme in Escherichia coli . J Biol Chem 269:30489–30495
     [Google Scholar]
  9. Blasius M., Shevelev I., Jolivet E., Sommer S., Hübscher U. 2006; DNA polymerase X from Deinococcus radiodurans possesses a structure-modulated 3′→5′ exonuclease activity involved in radioresistance. Mol Microbiol 60:165–176
     [Google Scholar]
  10. Blasius M., Sommer S., Hubscher U. 2008; Deinococcus radiodurans: what belongs to the survival kit?. Crit Rev Biochem Mol Biol 43:221–238
     [Google Scholar]
  11. Bonacossa de Almeida C., Costa G., Sommer S., Bailone A. 2002; Quantification of RecA protein in Deinococcus radiodurans reveals involvement of RecA, but not LexA, in its regulation. Mol Genet Genomics 268:28–41
     [Google Scholar]
  12. Daly M. J., Minton K. W. 1996; An alternative pathway of recombination of chromosomal fragments precedes recA-dependent recombination in the radioresistant bacterium Deinococcus radiodurans . J Bacteriol 178:4461–4471
     [Google Scholar]
  13. de Laat W. L., Jaspers N. G., Hoeijmakers J. H. 1999; Molecular mechanism of nucleotide excision repair. Genes Dev 13:768–785
     [Google Scholar]
  14. Dianova I. I., Sleeth K. M., Allinson S. L., Parsons J. L., Breslin C., Caldecott K. W., Dianov G. L. 2004; XRCC-1-DNA polymerase β interaction is required for efficient base excision repair. Nucleic Acids Res 32:2550–2555
     [Google Scholar]
  15. Evans D. M., Moseley B. E. 1983; Roles of the uvsC, uvsD, uvsE, and mtcA genes in the two pyrimidine dimer excision repair pathways of Deinococcus radiodurans . J Bacteriol 156:576–583
     [Google Scholar]
  16. Friedberg E. C., Bardwell A. J., Bardwell L., Feaver W. J., Kornberg R. D., Svejstrup J. Q., Tomkinson A. E., Wang Z. 1995; Nucleotide excision repair in the yeast Saccharomyces cerevisiae: its relationship to specialized mitotic recombination and RNA polymerase II basal transcription. Philos Trans R Soc Lond B Biol Sci 347:63–68
     [Google Scholar]
  17. Grzesiuk E., Gozdek A., Tudek B. 2001; Contribution of E. coli AlkA, TagA glycosylases and UvrABC-excinuclease in MMS mutagenesis. Mutat Res 480:48177–84
     [Google Scholar]
  18. Heinz K., Marx A. 2007; Lesion bypass activity of DNA polymerase A from the extremely radioresistant organism Deinococcus radiodurans . J Biol Chem 282:10908–10914
     [Google Scholar]
  19. Holmes J. Jr, Clark S., Modrich P. 1990; Strand-specific mismatch correction in nuclear extracts of human and Drosophila melanogaster cell lines. Proc Natl Acad Sci U S A 87:5837–5841
     [Google Scholar]
  20. Keller K. L., Overbeck-Carrick T. L., Beck D. J. 2001; Survival and induction of SOS in Escherichia coli treated with cisplatin, UV-irradiation, or mitomycin C are dependent on the functions of the RecBC and RecFOR pathways of homologous recombination. Mutat Res 486:21–29
     [Google Scholar]
  21. Khairnar N. P., Kamble V. A., Mangoli S. H., Apte S. K., Misra H. S. 2007; Involvement of a periplasmic protein kinase in DNA strand break repair and homologous recombination in Escherichia coli . Mol Microbiol 65:294–304
     [Google Scholar]
  22. Khairnar N. P., Kamble V. A., Misra H. S. 2008; RecBC enzyme overproduction affects UV and gamma radiation survival of Deinococcus radiodurans . DNA Repair (Amst 7:40–47
     [Google Scholar]
  23. Kota S., Misra H. S. 2006; PprA: a protein implicated in radioresistance of Deinococcus radiodurans stimulates catalase activity in Escherichia coli . Appl Microbiol Biotechnol 72:790–796
     [Google Scholar]
  24. Kubota Y., Nash R. A., Klungland A., Schar P., Bames D. E., Lindahl T. 1996; Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase β and the XRCC-1 protein. EMBO J 15:6662–6670
     [Google Scholar]
  25. Lahue R. S., Au K., Modrich G. P. 1989; DNA mismatch correction in a defined system. Science 245:160–164
     [Google Scholar]
  26. Lecointe F., Shevelev I. V., Bailone A., Sommer S., Hubscher U. 2004; Involvement of an X family DNA polymerase in double stranded break repair in the radioresistant bacterium Deinococcus radiodurans . Mol Microbiol 53:1721–1730
     [Google Scholar]
  27. Leulliot N., Cladière L., Lecointe F., Durand D., Hübscher U., van Tilbeurgh H. 2009; The X-family DNA polymerase from Deinococcus radiodurans adopts a non-standard extended conformation. J Biol Chem 284:11992–11999
     [Google Scholar]
  28. Lieb M. 1987; Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites. J Bacteriol 169:5241–5246
     [Google Scholar]
  29. Makarova K. S., Aravind L., Wolf Y. I., Tatusov R. L., Minton K. W., Koonin E. V., Daly M. J. 2001; Genome of extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspectives of comparative genomics. Microbiol Mol Biol Rev 65:44–79
     [Google Scholar]
  30. Markillie L. M., Varnum S. M., Hradechy P., Wong K. K. 1999; Targeted mutagenesis by duplication insertion in the radioresistant bacterium Deinococcus radiodurans: radiation sensitivities of catalase ( katA) and superoxide dismutase ( sodA) mutants. J Bacteriol 181:666–669
     [Google Scholar]
  31. Meima R., Rothfuss H. M., Gewin L., Lidstrom M. E. 2001; Promoter cloning in the radioresistant bacterium Deinococcus radiodurans . J Bacteriol 183:3169–3175
     [Google Scholar]
  32. Misra H. S., Pandey P. K., Modak M. J., Vinayak R., Pandey V. N. 1998; Polyamide nucleic acid-DNA chimera lacking the phosphate backbone are novel primers for polymerase reaction catalyzed by DNA polymerases. Biochemistry 37:1917–1925
     [Google Scholar]
  33. Misra H. S., Khairnar N. P., Kota S., Srivastava S., Joshi V. P., Apte S. K. 2006; An exonuclease I sensitive DNA repair pathway in Deinococcus radiodurans: a major determinant of radiation resistance. Mol Microbiol 59:1308–1316
     [Google Scholar]
  34. Moore M. H., Gulbis J. M., Dodson E. J., Demple B., Moody P. C. 1994; Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli . EMBO J 13:1495–1501
     [Google Scholar]
  35. Narumi I., Cherdchu K., Kitayama S., Watanabe H. 1997; The Deinococcus radiodurans uvrA gene: identification of mutation sites in two mitomycin-sensitive strains and the first discovery of insertion sequence element from deinobacteria. Gene 198:115–126
     [Google Scholar]
  36. Narumi I., Satoh K., Kikuchi M., Funayama T., Yanagisawa T., Kobayashi Y., Watanabe H., Yamamoto K. 2001; The LexA protein from Deinococcus radiodurans is not involved in RecA induction following gamma irradiation. J Bacteriol 183:6951–6956
     [Google Scholar]
  37. O'Brien P. J., Ellenberger T. 2004; The Escherichia coli 3-methyladenine DNA glycosylase AlkA has a remarkably versatile active site. J Biol Chem 279:26876–26884
     [Google Scholar]
  38. Parikh S. S., Mol C. D., Hosfield D. J., Tainer J. A. 1999; Envisioning the molecular choreography of DNA base excision repair. Curr Opin Struct Biol 9:37–47
     [Google Scholar]
  39. Prasad R., Bebenek K., Hou E., Shock D. D., Beard W. A., Woodgate R., Kunkel T. A., Wilson S. H. 2003; Localization of the deoxyribose phosphate lyase active site in human DNA polymerase iota by controlled proteolysis. J Biol Chem 278:29649–29654
     [Google Scholar]
  40. Sambrook J., Russell D. W. 2001 Molecular Cloning: a Laboratory Manual , 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  41. Satoh K., Ohba H., Sghaier H., Narumi I. 2006; Down-regulation of radioresistance by LexA2 in Deinococcus radiodurans . Microbiology 152:3217–3226
     [Google Scholar]
  42. Schafer M., Schmitz C., Facius R., Horneck G., Milow B., Funken K.-H., Ortner J. 2000; Systematic study of parameters influencing the action of Rose Bengal with visible light on bacterial cells: comparison between biological effect and singlet-oxygen production. Photochem Photobiol 71:514–523
     [Google Scholar]
  43. Seeberg E., Eide I., Bjoras M. 1995; The base excision repair pathways. Trends Biochem Sci 20:391–397
     [Google Scholar]
  44. Servant L., Cazaux C., Bieth A., Iwai S., Hanaoka F., Hoffmann J. S. 2002; A role for DNA polymerase β in mutagenic UV lesion bypass. J Biol Chem 277:50046–50053
     [Google Scholar]
  45. Sheng D., Zheng Z., Tian B., Shen B., Hua Y. 2004; LexA analog (dra0074) is a regulatory protein that is irrelevant to recA induction. J Biochem 136:787–793
     [Google Scholar]
  46. Shinohara A., Ogawa T. 1995; Homologous recombination and the roles of double-strand breaks. Trends Biochem Sci 20:387–391
     [Google Scholar]
  47. Tudek B., Van Zeeland A. A., Kusmierek J. T., Laval J. 1998; Activity of Escherichia coli DNA-glycosylase on DNA damaged by methylating and ethylating agents and influence of 3-substituted adenine derivatives. Mutat Res 407:169–176
     [Google Scholar]
  48. White O., Eisen J. A., Heildelberg J. F., Hickey E. K., Peterson J. D., Dodson R. J., Haft D. H., Gwinn M. L., Nelson W. C. other authors 1999; Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286:1571–1577
     [Google Scholar]
  49. Wiebauer K., Jiricny J. 1990; Mismatch-specific thymine DNA glycosylase and DNA polymerase β mediate the correction of G.T mispairs in nuclear extracts from human cells. Proc Natl Acad Sci U S A 87:5842–5845
     [Google Scholar]
  50. Yamada M., Nunoshiba T., Shimizu M., Gruz P., Kamiya H., Harashima H., Nohmi T. 2006; Involvement of Y-family DNA polymerase in mutagenesis caused by oxidized nucleotides in Escherichia coli . J Bacteriol 188:4992–4995
     [Google Scholar]
  51. Yoshida S., Cavalieri L. F. 1971; Multiple molecular species of Escherichia coli DNA polymerase. Proc Natl Acad Sci U S A 68:200–204
     [Google Scholar]
  52. Zahradka K., Slade D., Bailone A., Sommer S., Averbeck D., Petranovic M., Lindner A. B., Radman M. 2006; Reassembly of shattered chromosomes in Deinococcus radiodurans . Nature 443:569–573
     [Google Scholar]
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DNA polymerase X from Deinococcus radiodurans implicated in bacterial tolerance to DNA damage is characterized as a short patch base excision repair polymerase
Microbiology 155, 3005 (2009); https://doi.org/10.1099/mic.0.029223-0
/content/journal/micro/10.1099/mic.0.029223-0
/content/journal/micro/10.1099/mic.0.029223-0
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