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

Volumn 198, Issue 2 JAN, 1997, Pages 115-126

  Narumi, Issay ^a   Cherdchu, Korbkit ^a   Kitayama, Shigeru ^b   Watanabe, Hiroshi ^a  

^a TAKASAKI ADVANCED RADIATION RESEARCH INSTITUTE   (Japan)

^b INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

Author keywords

Cosmid library; DNA repair; Excinuclease; Insertion sequence; Nucleotide excision; Sequence homology; Transformation

Indexed keywords

MITOMYCIN C; REPETITIVE DNA; RESOLVASE; ADENOSINE TRIPHOSPHATASE; BACTERIAL DNA; BACTERIAL PROTEIN; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; MITOMYCIN; UVRA PROTEIN, E COLI;

AMINO ACID SEQUENCE; ANTIBIOTIC SENSITIVITY; ARTICLE; COSMID; DEINOCOCCUS RADIODURANS; DNA DAMAGE; DNA REPAIR; GENE INSERTION SEQUENCE; GENE MUTATION; IONIZING RADIATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; XANTHOMONAS; BACTERIAL GENE; GENE DELETION; GENETICS; GRAM POSITIVE COCCI; MOLECULAR CLONING; MOLECULAR GENETICS; MUTATION; RESTRICTION MAPPING; SEQUENCE ALIGNMENT; TRANSPOSON;

ADENOSINE TRIPHOSPHATASES; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; CLONING, MOLECULAR; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; DNA-BINDING PROTEINS; ESCHERICHIA COLI PROTEINS; GENES, BACTERIAL; GRAM-POSITIVE COCCI; MITOMYCIN; MOLECULAR SEQUENCE DATA; MUTATION; RESTRICTION MAPPING; SEQUENCE ALIGNMENT; SEQUENCE DELETION; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0030613729     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/s0378-1119(97)00301-6     Document Type: Article

References (45)

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.
2. Al-Bakri, G.H., Mackay, M.W., Whittaker, P.A., Moseley, B.E.B., 1985. Cloning of the DNA repair genes mtcA, mtcB, uvsC, uvsD, uvsE and the leuB gene from Deinococcus radiodurans. Gene 33, 305-311.
3. Anderson, A.W., Nordan, H.C., Cain, R.F., Parrish, G., Duggan, D., 1956. Studies on a radio-resistance micrococcus. I. Isolation, morphology, cultural characteristics, and resistance to gamma radiation. Food Technol. 10, 575-758.
4. Berg, J.M., 1986. Potential metal-binding domains in nucleic acid binding proteins. Science 232, 485-487.
5. Claassen, L.A., Grossman, L., 1991. Deletion mutagenesis of the Escherichia coli UvrA protein localizes domains for DNA binding, damage recognition, and protein-protein interactions. J. Biol. Chem. 266, 11388-11394.
6. de la Morena, M., Hendrixson, D.R., St Geme III, J.W., 1996. Isolation and characterization of the Haemophilus Influenzae uvrA gene. Gene 177, 23-28.
7. Doolittle, R.F., Johnson, M.S., Husain, I., Van Houten, B., Thomas, D.C., Sancar, A., 1986. Domainal evolution of a prokaryotic DNA repair protein and its relationship to active-transport proteins. Nature 323, 451-453.
8. Driedger, A.A., Grayston, M.J., 1970. Rapid lysis of cell walls of Micrococcus radiodurans with lysozyme: effects of butanol pretreatment on DNA. Can. J. Microbiol. 16, 889-893.
9. Grossman, L., Thiagalingam, S., 1993. Nucleotide excision repair, a tracking mechanism in search of damage. J. Biol. Chem. 268, 16871-16874.
10. Harsojo, A., Kitayama, S., Matsuyama, A., 1981. Genome multiplicity and radiation resistance in Micrococcus radiodurans. J. Biochem. 90, 877-880.
11. Hensel, R., Demharter, W., Kandler, O., Kroppenstedt, R.M., Stackebrandt, E., Chemotaxonomic and molecular-genetic studies of the genus Thermus: evidence for a phylogenetic relationship of Thermus aquaticus and Thermus ruber to the genus Deinococcus. 1986. Int. J. Syst. Bacteriol. 36, 444-453.
12. Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B.C., Herrmann, R., 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucl. Acids Res. 24, 4420-4449.
13. Husain, I., Van Houten, B., Thomas, D.C., Sancar, A., 1986. Sequences of Escherichia coli uvrA gene and protein reveal two potential ATP binding sites. J. Biol. Chem. 261, 4895-4901.
14. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., Kimura, T., Hosouchi, T., Matsuno, A., Muraki, A., Nakazaki, N., Naruo, K., Okumura, S., Shimpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M., Tabata, S., Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PPC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. 1996. DNA Res. 3, 109-136.
15. Karlin, S., Weinstock, G.M., Brendel, V., 1995. Bacterial classifications derived from RecA protein sequence comparisons. J. Bacteriol. 177, 6881-6893.
16. Kikuchi, M., Kitayama, S., Sjarief, S.H., Watanabe, H., 1994. Plasmids in several strains of Deinococcus radiodurans. Radiat. Res. 139, 123-125.
17. Kitayama, S., Asaka, S., Totsuka, K., 1983. DNA double-strand breakage and removal of cross-links in Deinococcus radiodurans. J. Bacteriol. 155, 1200-1207.
18. Kitayama, S., Matsuyama, A., 1975. Loss of characteristic radiation resistance by mutation of Micrococcus radiodurans. Mutat. Res. 29, 327-332.
19. Klaer, R., Kühn, S., Tillmann, E., Fritz, H.-J., Starlinger, P., 1981. The sequence of IS4. Mol. Gen. Genet. 181, 169-175.
20. Koyama, Y., Furukawa, K., Cloning and sequencing analysis of tryptophan synthetase genes of an extreme thermophile, Thermus thermophilus HB27: plasmid transfer from replica-plated Escherichia coli recombinant colonies to competent T. thermophilus cells. 1990. J. Bacteriol. 172, 3490-3495.
21. Liu, C.-C., Wang, H.-R., Chou, H.-C., Chang, W.-T., Tu, J., 1992. Analysis of the genes and gene products of Xanthomonas transposable element ISXc5 and ISXc4. Gene 120, 99-103.
22. Moseley, B.E.B., 1967. The isolation and some properties of radiation sensitive mutants of Micrococcus radiodurans. J. Gen. Microbiol. 49, 293-300.
23. Moseley, B.E.B., 1983. Photobiology and radiobiology of Micrococcus (Deinococcus) radiodurans. Photochem. Photobiol. Rev. 7, 223-274.
24. Moseley, B.E.B., Copland, H.J.R., 1978. 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. 160, 331-337.
25. Moseley, B.E.B., Evans, D.M., 1983. Isolation of 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. 192, 2437-2445.
26. Mozhaev, V.V., Martinek, K., 1984. Structure-stability relationships in proteins: new approaches to stabilizing enzymes. Enzyme Microb. Technol. 6, 50-59.
27. Murray, R.G.E. and Brooks, B.W. (1986) Deinococcus. In Sneath, P.H.A., Mair, N.S., Sharpe, M.E., Holt, J.G. (Eds.), Bergey's Manual of Systematic Bacteriology, Vol. 2. Williams and Wilkins, Baltimore, MD, pp. 1035-1043.
28. Nakamura, T., Yoshioka, I., Takahashi, M., Toh, H., Izui, K., 1995. Cloning and sequencing analysis of the gene for phosphoenolpyruvate carboxylase from an extreme thermophile Thermus sp.. J. Biochem. 118, 319-324.
29. Narumi, I., Nakayama, N., Nakamoto, S., Kihara, H., 1995. Bacillus stearothermophilus plasmid pSTK1 replicon is functional in Escherichia coli. Biotechnol. Lett. 17, 475-480.
30. Narumi, I., Watanabe, H., 1996. Sequence analysis of L-lactate dehydrogenase-encoding gene of Deinococcus radiodurans, a suitable mesophilic counterpart for Thermus. Gene 172, 117-119.
31. Navaratnam, S., Myles, G.M., Strange, R.W., Sancar, A., 1989. Evidence from extended X-ray absorption fine structure and site-directed mutagenesis for zinc fingers in UvrA protein of Escherichia coli. J. Biol. Chem. 264, 16067-16071.
32. Philipp, W.J., Poulet, S., Eiglmeier, K., Pascopella, L., Balasubramanian, V., Heym, B., Bergh, S., Bloom, B.R., Jacobs, W.R., , JrCole, S.T., 1996. An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae. Proc. Natl. Acad. Sci. USA 93, 3132-3137.
33. Rezsöhazy, R., Hallet, B., Deicour, J., Mahillon, J., 1993. The IS4 family of insertion sequences: evidence for a conserved transposase motif. Mol. Microbiol. 9, 1283-1295.
34. Saito, H., Miura, K., 1963. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim. Biophys. Acta. 72, 619-629.
35. Sambrook, J., Fritsch, E.F., Maniatis, T., 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
36. Shiota, S., Nakayama, H., 1989. Micrococcus luteus homolog of the Escherichia coli uvrA gene: identification of a mutation in the UV-sensitive mutant DB7. Mol. Gen. Genet. 217, 332-340.
37. Singleton Jr, R., Amelunxen, R., 1973. Proteins from thermophilic microorganisms. Bacteriol. Rev. 37, 320-342.
38. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22, 4673-4680.
39. Tu, J., Wang, H.-R., Chang, S.-F., Charng, Y.-C., Lurz, R., Dobrinski, B., Wu, W.-C., 1989. Transposable elements of Xanthomonas campestris pv. citri originating from indigenous plasmids. Mol. Gen. Genet. 217, 505-510.
40. Visse, R., de Ruijter, M., Ubbink, M., Brandsma, J.A., van de Putte, P., 1993. The first zinc-binding domain of UvrA is not essential for UvrABC-mediated DNA excision repair. Mutat. Res. 294, 263-274.
41. Walker, J.E., Saraste, M., Runswick, M.J., Gay, N.J., 1982. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1, 945-951.
42. Wang, J., Grossman, L., 1993. Mutations in the helix-turn-helix motif of the Escherichia coli UvrA protein eliminate its specificity for UV-damaged DNA. J. Biol. Chem. 268, 5323-5331.
43. Wang, J., Mueller, K.L., Grossman, L., 1994. A mutational study of the C-terminal zinc-finger motif of the Escherichia coli UvrA protein. J. Biol. Chem. 269, 10771-10775.
44. Weisburg, W.G., Giovannoni, S.J., Woese, C.R., 1989. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. System. Appl. Microbiol. 11, 128-134.
45. Yamamoto, N., Kato, R., Kuramitsu, S., 1996. Cloning, sequencing and expression of the uvrA gene from an extremely thermophilic bacterium, Thermus thermophilus HB8. Gene 171, 103-106.