Skip to main content
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1996 Dec;178(23):6759–6765. doi: 10.1128/jb.178.23.6759-6765.1996

Identification and characterization of uvrA, a DNA repair gene of Deinococcus radiodurans.

H J Agostini 1, J D Carroll 1, K W Minton 1
PMCID: PMC178572  PMID: 8955293

Abstract

Deinococcus radiodurans is extraordinarily resistant to DNA damage, because of its unusually efficient DNA repair processes. The mtcA+ and mtcB+ genes of D. radiodurans, both implicated in excision repair, have been cloned and sequenced, showing that they are a single gene, highly homologous to the uvrA+ genes of other bacteria. The Escherichia coli uvrA+ gene was expressed in mtcA and mtcB strains, and it produced a high degree of complementation of the repair defect in these strains, suggesting that the UvrA protein of D. radiodurans is necessary but not sufficient to produce extreme DNA damage resistance. Upstream of the uvrA+ gene are two large open reading frames, both of which are directionally divergent from the uvrA+ gene. Evidence is presented that the proximal of these open reading frames may be irrB+.

Full Text

The Full Text of this article is available as a PDF (363.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Al-Bakri G. H., Mackay M. W., Whittaker P. A., Moseley B. E. Cloning of the DNA repair genes mtcA, mtcB, uvsC, uvsD, uvsE and the leuB gene from Deinococcus radiodurans. Gene. 1985;33(3):305–311. doi: 10.1016/0378-1119(85)90238-0. [DOI] [PubMed] [Google Scholar]
  2. Berg J. M. Potential metal-binding domains in nucleic acid binding proteins. Science. 1986 Apr 25;232(4749):485–487. doi: 10.1126/science.2421409. [DOI] [PubMed] [Google Scholar]
  3. Carroll J. D., Daly M. J., Minton K. W. Expression of recA in Deinococcus radiodurans. J Bacteriol. 1996 Jan;178(1):130–135. doi: 10.1128/jb.178.1.130-135.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Claassen L. A., Grossman L. Deletion mutagenesis of the Escherichia coli UvrA protein localizes domains for DNA binding, damage recognition, and protein-protein interactions. J Biol Chem. 1991 Jun 15;266(17):11388–11394. [PubMed] [Google Scholar]
  5. Daly M. J., Ouyang L., Fuchs P., Minton K. W. In vivo damage and recA-dependent repair of plasmid and chromosomal DNA in the radiation-resistant bacterium Deinococcus radiodurans. J Bacteriol. 1994 Jun;176(12):3508–3517. doi: 10.1128/jb.176.12.3508-3517.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. De Vries J., Genschel J., Urbanke C., Thole H., Wackernagel W. The single-stranded-DNA-binding proteins (SSB) of Proteus mirabilis and Serratia marcescens. Eur J Biochem. 1994 Sep 1;224(2):613–622. doi: 10.1111/j.1432-1033.1994.00613.x. [DOI] [PubMed] [Google Scholar]
  7. Dubnau D., Cirigliano C. Fate of transforming deoxyribonucleic acid after uptake by competent Bacillus subtilis: size and distribution of the integrated donor segments. J Bacteriol. 1972 Aug;111(2):488–494. doi: 10.1128/jb.111.2.488-494.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Evans D. M., Moseley B. E. Deinococcus radiodurans UV endonuclease beta DNA incisions do not generate photoreversible thymine residues. Mutat Res. 1988 Mar-Apr;207(3-4):117–119. doi: 10.1016/0165-7992(88)90074-7. [DOI] [PubMed] [Google Scholar]
  9. Evans D. M., Moseley B. E. Identification and initial characterisation of a pyrimidine dimer UV endonuclease (UV endonuclease beta) from Deinococcus radiodurans; a DNA-repair enzyme that requires manganese ions. Mutat Res. 1985 May;145(3):119–128. doi: 10.1016/0167-8817(85)90018-5. [DOI] [PubMed] [Google Scholar]
  10. Evans D. M., Moseley B. E. Roles of the uvsC, uvsD, uvsE, and mtcA genes in the two pyrimidine dimer excision repair pathways of Deinococcus radiodurans. J Bacteriol. 1983 Nov;156(2):576–583. doi: 10.1128/jb.156.2.576-583.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Grossman L., Thiagalingam S. Nucleotide excision repair, a tracking mechanism in search of damage. J Biol Chem. 1993 Aug 15;268(23):16871–16874. [PubMed] [Google Scholar]
  12. Gurney T., Jr, Fox M. S. Physical and genetic hybrids formed in bacterial transformation. J Mol Biol. 1968 Feb 28;32(1):83–100. doi: 10.1016/0022-2836(68)90147-2. [DOI] [PubMed] [Google Scholar]
  13. Gutman P. D., Carroll J. D., Masters C. I., Minton K. W. Sequencing, targeted mutagenesis and expression of a recA gene required for the extreme radioresistance of Deinococcus radiodurans. Gene. 1994 Apr 8;141(1):31–37. doi: 10.1016/0378-1119(94)90124-4. [DOI] [PubMed] [Google Scholar]
  14. Gutman P. D., Fuchs P., Minton K. W. Restoration of the DNA damage resistance of Deinococcus radiodurans DNA polymerase mutants by Escherichia coli DNA polymerase I and Klenow fragment. Mutat Res. 1994 Jan;314(1):87–97. doi: 10.1016/0921-8777(94)90064-7. [DOI] [PubMed] [Google Scholar]
  15. Gutman P. D., Yao H. L., Minton K. W. Partial complementation of the UV sensitivity of Deinococcus radiodurans excision repair mutants by the cloned denV gene of bacteriophage T4. Mutat Res. 1991 May;254(3):207–215. doi: 10.1016/0921-8777(91)90058-w. [DOI] [PubMed] [Google Scholar]
  16. Hansen M. T. Four proteins synthesized in response to deoxyribonucleic acid damage in Micrococcus radiodurans. J Bacteriol. 1980 Jan;141(1):81–86. doi: 10.1128/jb.141.1.81-86.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Husain I., Van Houten B., Thomas D. C., Sancar A. Sequences of Escherichia coli uvrA gene and protein reveal two potential ATP binding sites. J Biol Chem. 1986 Apr 15;261(11):4895–4901. [PubMed] [Google Scholar]
  18. Jannière L., Niaudet B., Pierre E., Ehrlich S. D. Stable gene amplification in the chromosome of Bacillus subtilis. Gene. 1985;40(1):47–55. doi: 10.1016/0378-1119(85)90023-x. [DOI] [PubMed] [Google Scholar]
  19. Jarosik G. P., Hansen E. J. Cloning and sequencing of the Haemophilus influenzae ssb gene encoding single-strand DNA-binding protein. Gene. 1994 Aug 19;146(1):101–103. doi: 10.1016/0378-1119(94)90841-9. [DOI] [PubMed] [Google Scholar]
  20. Kitayama S., Asaka S., Totsuka K. DNA double-strand breakage and removal of cross-links in Deinococcus radiodurans. J Bacteriol. 1983 Sep;155(3):1200–1207. doi: 10.1128/jb.155.3.1200-1207.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kovalsky O. I., Grossman L. The use of monoclonal antibodies for studying intermediates in DNA repair by the Escherichia coli Uvr(A)BC endonuclease. J Biol Chem. 1994 Nov 4;269(44):27421–27426. [PubMed] [Google Scholar]
  22. Lennon E., Minton K. W. Gene fusions with lacZ by duplication insertion in the radioresistant bacterium Deinococcus radiodurans. J Bacteriol. 1990 Jun;172(6):2955–2961. doi: 10.1128/jb.172.6.2955-2961.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Masters C. I., Smith M. D., Gutman P. D., Minton K. W. Heterozygosity and instability of amplified chromosomal insertions in the radioresistant bacterium Deinococcus radiodurans. J Bacteriol. 1991 Oct;173(19):6110–6117. doi: 10.1128/jb.173.19.6110-6117.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Mattimore V., Udupa K. S., Berne G. A., Battista J. R. Genetic characterization of forty ionizing radiation-sensitive strains of Deinococcus radiodurans: linkage information from transformation. J Bacteriol. 1995 Sep;177(18):5232–5237. doi: 10.1128/jb.177.18.5232-5237.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Minton K. W. DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans. Mol Microbiol. 1994 Jul;13(1):9–15. doi: 10.1111/j.1365-2958.1994.tb00397.x. [DOI] [PubMed] [Google Scholar]
  26. Moseley B. E., Copland H. F. Four mutants of Micrococcus radiodurans defective in the ability to repair DNA damaged by mitomycin-C, two of which have wild-type resistance to ultraviolet radiation. Mol Gen Genet. 1978 Apr 17;160(3):331–337. doi: 10.1007/BF00332977. [DOI] [PubMed] [Google Scholar]
  27. Moseley B. E., Evans D. M. Isolation and properties of strains of Micrococcus (Deinococcus) radiodurans unable to excise ultraviolet light-induced pyrimidine dimers from DNA: evidence for two excision pathways. J Gen Microbiol. 1983 Aug;129(8):2437–2445. doi: 10.1099/00221287-129-8-2437. [DOI] [PubMed] [Google Scholar]
  28. Navaratnam S., Myles G. M., Strange R. W., Sancar A. Evidence from extended X-ray absorption fine structure and site-specific mutagenesis for zinc fingers in UvrA protein of Escherichia coli. J Biol Chem. 1989 Sep 25;264(27):16067–16071. [PubMed] [Google Scholar]
  29. Novick R. P., Clowes R. C., Cohen S. N., Curtiss R., 3rd, Datta N., Falkow S. Uniform nomenclature for bacterial plasmids: a proposal. Bacteriol Rev. 1976 Mar;40(1):168–189. doi: 10.1128/br.40.1.168-189.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ogasawara N., Nakai S., Yoshikawa H. Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin. DNA Res. 1994;1(1):1–14. doi: 10.1093/dnares/1.1.1. [DOI] [PubMed] [Google Scholar]
  31. Peterson B. C., Rownd R. H. Homologous sequences other than insertion elements can serve as recombination sites in plasmid drug resistance gene amplification. J Bacteriol. 1983 Oct;156(1):177–185. doi: 10.1128/jb.156.1.177-185.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Sancar A., Tang M. S. Nucleotide excision repair. Photochem Photobiol. 1993 May;57(5):905–921. doi: 10.1111/j.1751-1097.1993.tb09233.x. [DOI] [PubMed] [Google Scholar]
  33. Sancar A., Williams K. R., Chase J. W., Rupp W. D. Sequences of the ssb gene and protein. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4274–4278. doi: 10.1073/pnas.78.7.4274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Shiota S., Nakayama H. Micrococcus luteus homolog of the Escherichia coli uvrA gene: identification of a mutation in the UV-sensitive mutant DB7. Mol Gen Genet. 1989 Jun;217(2-3):332–340. doi: 10.1007/BF02464901. [DOI] [PubMed] [Google Scholar]
  35. Smith M. D., Abrahamson R., Minton K. W. Shuttle plasmids constructed by the transformation of an Escherichia coli cloning vector into two Deinococcus radiodurans plasmids. Plasmid. 1989 Sep;22(2):132–142. doi: 10.1016/0147-619x(89)90022-x. [DOI] [PubMed] [Google Scholar]
  36. Smith M. D., Lennon E., McNeil L. B., Minton K. W. Duplication insertion of drug resistance determinants in the radioresistant bacterium Deinococcus radiodurans. J Bacteriol. 1988 May;170(5):2126–2135. doi: 10.1128/jb.170.5.2126-2135.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Smith M. D., Masters C. I., Lennon E., McNeil L. B., Minton K. W. Gene expression in Deinococcus radiodurans. Gene. 1991 Feb 1;98(1):45–52. doi: 10.1016/0378-1119(91)90102-h. [DOI] [PubMed] [Google Scholar]
  38. Sweet D. M., Moseley B. E. The resistance of Micrococcus radiodurans to killing and mutation by agents which damage DNA. Mutat Res. 1976 Feb;34(2):175–186. doi: 10.1016/0027-5107(76)90122-6. [DOI] [PubMed] [Google Scholar]
  39. Tempest P. R., Moseley B. E. Defective excision repair in a mutant of Micrococcus radiodurans hypermutable by some monofunctional alkylating agents. Mol Gen Genet. 1980;179(1):191–199. doi: 10.1007/BF00268463. [DOI] [PubMed] [Google Scholar]
  40. Thiagalingam S., Grossman L. Both ATPase sites of Escherichia coli UvrA have functional roles in nucleotide excision repair. J Biol Chem. 1991 Jun 15;266(17):11395–11403. [PubMed] [Google Scholar]
  41. Udupa K. S., O'Cain P. A., Mattimore V., Battista J. R. Novel ionizing radiation-sensitive mutants of Deinococcus radiodurans. J Bacteriol. 1994 Dec;176(24):7439–7446. doi: 10.1128/jb.176.24.7439-7446.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Visse R., de Ruijter M., Ubbink M., Brandsma J. A., van de Putte P. The first zinc-binding domain of UvrA is not essential for UvrABC-mediated DNA excision repair. Mutat Res. 1993 Oct;294(3):263–274. doi: 10.1016/0921-8777(93)90009-6. [DOI] [PubMed] [Google Scholar]
  43. Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1(8):945–951. doi: 10.1002/j.1460-2075.1982.tb01276.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wang J., Grossman L. Mutations in the helix-turn-helix motif of the Escherichia coli UvrA protein eliminate its specificity for UV-damaged DNA. J Biol Chem. 1993 Mar 5;268(7):5323–5331. [PubMed] [Google Scholar]
  45. Wang J., Mueller K. L., Grossman L. A mutational study of the C-terminal zinc-finger motif of the Escherichia coli UvrA protein. J Biol Chem. 1994 Apr 8;269(14):10771–10775. [PubMed] [Google Scholar]
  46. Zhu Y., Oliveira S. C., Splitter G. A. Isolation of Brucella abortus ssb and uvrA genes from a genomic library by use of lymphocytes as probes. Infect Immun. 1993 Dec;61(12):5339–5344. doi: 10.1128/iai.61.12.5339-5344.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. de Vries J., Wackernagel W. Cloning and sequencing of the Proteus mirabilis gene for a single-stranded DNA-binding protein (SSB) and complementation of Escherichia coli ssb point and deletion mutations. Microbiology. 1994 Apr;140(Pt 4):889–895. doi: 10.1099/00221287-140-4-889. [DOI] [PubMed] [Google Scholar]
  48. de Vries J., Wackernagel W. Cloning and sequencing of the Serratia marcescens gene encoding a single-stranded DNA-binding protein (SSB) and its promoter region. Gene. 1993 May 15;127(1):39–45. doi: 10.1016/0378-1119(93)90614-9. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES