DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?

Molecular Microbiology

Volumn 29, Issue 6, 1998, Pages 1331-1339

  Mizrahi, Valerie ^a,b   Andersen, Susan J ^a  

^a NATIONAL HEALTH LABORATORY SERVICE   (South Africa)

^b UNIVERSITY OF THE WITWATERSRAND   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATING AGENT; BACTERIAL DNA; REACTIVE OXYGEN METABOLITE;

ARTICLE; BACTERIAL MUTATION; BACTERIUM COMPETENCE; BASE MISPAIRING; DNA ALKYLATION; DNA REPAIR; ESCHERICHIA COLI; EXCISION REPAIR; GENETIC RECOMBINATION; GENETIC STABILITY; GENETIC VARIABILITY; GENOME; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATIVE STRESS; PRIORITY JOURNAL; R FACTOR;

DATABASES, FACTUAL; DNA DAMAGE; DNA REPAIR; DRUG RESISTANCE, MICROBIAL; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME, BACTERIAL; MUTAGENESIS; MYCOBACTERIUM TUBERCULOSIS; RECOMBINATION, GENETIC; SOS RESPONSE (GENETICS);

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; UNCULTURED ACTINOMYCETE; UNIDENTIFIED BACTERIOPHAGE; ZIZIPHUS MAURITIANA;

EID: 0031692027     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1998.01038.x     Document Type: Article

References (73)

1. Altschul, S.F., and Gish, W. (1996) Local alignment statistics. Methods Enzymol 266: 460-480.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
3. Bairoch, A., Bucher, P., and Hofmann, K. (1997) The PROSITE database, its status in 1997. Nucleic Acids Res 25: 217-221.
4. Bridges, B.A. (1997) Hypermutation under stress. Nature 387: 557-558.
5. Bridges, B.A., Sekiguchi, M., and Tajiri, T. (1996) Effect of mutY and mutM/fpg-1 mutations on starvation-associated mutation in Escherichia coli: implications for the role of 7,8-dihydro-8-oxoguanine. Mol Gen Genet 251: 352-357.
6. Bridges, B.A., and Timms, A.R. (1997) Mutation in Escherichia coli under starvation conditions: a new pathway leading to small deletions in strains defective in mismatch correction. EMBO J 16: 3349-3356.
7. Cole, S.T., and Telenti, A. (1995) Drug resistance in Mycobacterium tuberculosis. Eur Respir J 20 (Suppl.): 701S-713S.
8. Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
9. Colston, M.J., and Davis, E.O. (1994) Homologous recombination, DNA repair, and mycobacterial recA genes. In: Tuberculosis. Pathogenesis, Protection and Control. Bloom, B.R. (ed.). Washington, DC: American Society for Microbiology Press. pp. 217-226.
10. Colston, M.J., Davis, E.O., Movahedzadeh, F., Papavinasasundaram, K.G., Thomas, N., Jenner, P., and Bachrach, G. (1998) The mycobacterial response to DNA damage and intracellular stress. Keystone Symposium on TB: Molecular Mechanisms and Immunologic Aspects. Abstract Y1: 007.
11. Cox, E.C. (1976) Bacterial mutator genes and the control of spontaneous mutation. Annu Rev Genet 10: 135-156.
12. David, H.L., and Newman, C.M. (1971) Some observations on the genetics of isoniazid resistance in the tubercle bacilli. Am Rev Respir Dis 104: 508-515.
13. Davis, E.O., Sedgwick., S.G., and Colston, M.J. (1991) Novel structure of the recA locus of Mycobacterium tuberculosis implies processing of the gene product. J Bacteriol 173: 5653-5662.
14. Davis, E.O., Jenner, P.J., Brooks, P.C., Colston, M.J., and Sedgwick, S.G. (1992) Protein splicing in the maturation of M. tuberculosis RecA protein: a mechanism for tolerating a novel class of intervening sequence. Cell 71: 201-210.
15. Demple, B. (1991) Regulation of bacterial oxidative stress genes. Annu Rev Genet 25: 315-337.
16. Demple, B., and Harrison, L. (1994) Repair of oxidative damage to DNA: enzymology and biology. Annu Rev Biochem 63: 915-948.
17. Dullaghan, E.M., and Davis, E.O. (1998) Sequence requirements for Mycobacterium tuberculosis LexA binding. Keystone Symposium on TB: Molecular Mechanisms and Immunologic Aspects. Abstract Y1: 412.
18. Durbach, S.I., Andersen, S.J., and Mizrahi, V. (1997) SOS induction in mycobacteria: analysis of the DNA-binding activity of a LexA-like repressor and its role in DNA damage induction of the recA gene from Mycobacterium smegmatis. Mol Microbiol 26: 643-653.
19. Fajardo-Cavazos, P., Salazar, C., and Nicholson, W.L. (1993) Molecular cloning and characterization of the Bacillus subtilis spore photoproduct photolyase (spl) gene, which is involved in repair of UV-irradiation-induced DNA damage during spore germination. J Bacteriol 175: 1735-1744.
20. Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., Fleischmann, R.D., et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
21. Friedberg, E.C., Walker, G.C., and Siede, W. (1995) DNA Repair and Mutagenesis. Washington, DC: American Society for Microbiology Press.
22. Frothingham, R., and Meeker-O'Connell, W.A. (1998) Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144: 1189-1196.
23. Gordhan, B.G., De Meyer, A.R., Andersen, S.J., and Mizrahi, V. (1996) Construction by homologous recombination and phenotypic characterisation of a DNA polymerase domain polA mutant of Mycobacterium smegmatis. Gene 178: 125-130.
24. Grilley, M., Welsh, K.M., Su, S.S., and Modrich, P. (1989) Isolation and characterization of the Escherichia coli mutL gene product. J Biol Chem 264: 1000-1004.
25. Groenen, P.M., Bunschoten, A.E., van Soolingen, D., and van Embden, J.D. (1993) Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol 10: 1057-1065.
26. Huang, J.C., Hsu, D.S., Kazantsev, A., and Sancar, A. (1994) Substrate spectrum of human excinuclease: repair of abasic sites, methylated bases, mismatches, and bulky adducts. Proc Natl Acad Sci USA 91: 12213-12217.
27. Huberts, P., and Mizrahi, V. (1995) Cloning and sequence analysis of the gene encoding the DNA polymerase I from Mycobacterium tuberculosis. Gene 164: 133-136.
28. Jacobs, K.L., and Grogan, D.W. (1997) Rates of spontaneous mutation in an archaeon from geothermal environments. J Bacteriol 179: 3298-3303.
29. Kapur, V., Whittam, T.S., and Musser, J.M. (1994) Is Mycobacterium tuberculosis 15,000 years old? J Infect Dis 170: 1348-1349.
30. Klenk, H.P., Clayton, R.A., Tomb, J.F., White, O., Nelson, K.E., Ketchum, K.A., et al. (1997) The complete genome sequence of the hyperthermophilic, sulfate-reducing archaeon Archaeoglobus fulgidus. Nature 390: 364-370.
31. Koonin, E.V., and Galperin, M.Y. (1997) Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr Opin Genet Dev 7: 757-763.
32. Koonin, E.V., Mushegian, A.R., and Bork, P. (1996) Non-orthologous gene displacement. Trends Genet 12: 334-336.
33. Koonin, E.V., Mushegian, A.R., Galperin, M.Y., and Walker, D.R. (1997) Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol Microbiol 25: 619-637.
34. Kowalczykowski, S.C., Dixon, D.A., Eggleston, A.K., Lauder, S.D., and Rehrauer, W.M. (1994) Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58: 401-465.
35. Kumar, R.A., Vaze, M.B., Chandra, N.R., Vijayan, M., and Muniyappa, K. (1996) Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis. Biochemistry 35: 1793-1802.
36. LeClerc, J.E., Li, B., Payne, W.L., and Cebula, T.A. (1996) High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274: 1208-1211.
37. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature 362: 709-715.
38. S (KatF) in bacterial global regulation. Annu Rev Microbiol 48: 53-80.
39. McFadden, J. (1996) Recombination in mycobacteria. Mol Microbiol 21: 205-211.
40. Magdalena, J., Vachee, A., Supply, P., and Locht, C. (1998) Identification of a new DNA region specific for members of Mycobacterium tuberculosis complex. J Clin Microbiol 36: 937-943.
41. Martinez, A., and Kolter, R. (1997) Protection of DNA during oxidative stress by the non-specific DNA-bindmg protein Dps. J Bacteriol 179: 5188-5194.
42. Matic, I., Taddei, F., and Radman, M. (1996) Genetic barriers among bacteria. Trends Microbiol 4: 69-72.
43. Mellon, I., and Champe, G.N. (1996) Products of DNA mismatch repair genes mutS and mutL are required for transcription-coupled nucleotide-excision repair of the lactose operon in Escherichia coli. Proc Natl Acad Sci USA 93: 1292-1297.
44. Michaels, M.L., and Miller, J.H. (1992) The GO system protects organisms from the mutagenic effects of the spontaneous lesion, 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J Bacteriol 174: 6321-6325.
45. Mizrahi, V., and Huberts, P. (1996) Deoxy- and dideoxynucleotide discrimination and identification of critical 5′ nuclease domain residues of the DNA polymerase I from Mycobacterium tuberculosis. Nucleic Acids Res 24: 4845-4852.
46. Modrich, P., and Lahue, R. (1996) Mismatch repair in replication fidelity, genetic recombination and cancer biology. Annu Rev Biochem 65: 101-133.
47. Movahedzadeh, F., Colston, M.J., and Davis, E.O. (1997) Characterization of Mycobacterium tuberculosis LexA: recognition of a Cheo (Bacillus-type SOS) box. Microbiology 143: 929-936.
48. Papavinasasundaram, K.G., Movahedzadeh, F., Keer, J.T., Stoker, N.G., Colston, M.J., and Davis, E.O. (1997) Mycobacterial recA is cotranscribed with a potential regulatory gene called recX. Mol Microbiol 24: 141-153.
49. Parrish, N.M., Dick, J.D., and Bishai, W.R. (1998) Mechanisms of latency in Mycobacterium tuberculosis. Trends Microbiol 6: 107-112.
50. Parsons, L.M., Driscoll, J.R., Taber, H.W., and Salfinger, M. (1997) Drug resistance in tuberculosis. Infect Dis Clin N Am 11: 905-928.
51. Parsons, L.M., Jankowski, C.S., and Derbyshire, K.M. (1998) Conjugal transfer of chromosomal DNA in Mycobacterium smegmatis. Mol Microbiol 28: 571-582.
52. Poterszman, A., Lamour, V., Egly, J.M., Moras, D., Thierry, J.C., and Poch, O. (1997) A eukaryotic XPB/ERCC3-like helicase in Mycobacterium leprae? Trends Biochem Sci 2: 418-419.
53. Poulet, S., and Cole, S.T. (1995a) Repeated DNA sequences in mycobacteria. Arch Microbiol 163: 79-86.
54. Poulet, S., and Cole, S.T. (1995b) Characterization of the highly abundant polymorphic GC-rich-repetitive sequence (PGRS) present in Mycobacterium tuberculosis. Arch Microbiol 163: 87-95.
55. Riesenfeld, C., Everett, M., Piddock, L.J., and Hall, B.G. (1997) Adaptive mutations produce resistance to ciprofloxacin. Antimicrob Agents Chemother 41: 2059-2060.
56. Rosenberg, S.M. (1997) Mutation for survival. Curr Opin Genet Dev 7: 829-834.
57. Sancar, A. (1994) Mechanisms of DNA excision repair. Science 266: 1954-1956.
58. 6-alkylguanine-DNA alkyltranferase deficient cells. Carcinogenesis 18: 1561-1567.
59. Scorpio, A., Lindholm-Levy, P., Heifets, L., Gilman, R., Siddiqi, S., Cynamon, M., and Zhang, Y. (1997) Characterization of pncA mutations in pyrazinamide-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 41: 540-543.
60. Seeberg, E., Eide, L., and Bjoras, M. (1995) The base excision repair pathway. Trends Biochem Sci 20: 391-397.
61. Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J.J., Aldredge, T., et al. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol 179: 7135-7155.
62. Smith, R.F., Wiese, B.A., Wojzynski., M.K., Davison, D.B., and Worley, K.C. (1996) BCM Search Launcher: an integrated interface to molecular biology database search and analysis services available on the World Wide Web. Genome Res 6: 454-462.
63. Sreevatsan, S., Pan, X., Stockbauer, K.E., Connell, N.D., Kreiswirth, B.N., Whittam, T.S., and Musser, J.M. (1997) Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionary recent global dissemination. Proc Natl Acad Sci USA 94: 9869-9874.
64. Supply, P., Magdalena, J., Himpens, S., and Locht, C. (1997) Identification of novel intergenic repetitive units in a mycobacterial two-component system operon. Mol Microbiol 26: 991-1003.
65. Taddei, F., Matic, I., Godelle, B., and Radman, M. (1997) To be a mutator, or how pathogenic and commensal bacteria can evolve rapidly. Trends Microbiol 5: 427-428.
66. Taverna, P., and Sedgwick, B. (1996) Generation of an endogenous DNA-methylating agent by nitrosation in Escherichia coli. J Bacteriol 178: 5105-5111.
67. Tseng, Y.C., Hung, J.L., and Wang, T.C. (1994) Involvement of RecF pathway recombination genes in postreplication repair in UV-irradiated Escherichia coli cells. Mutat Res 315: 1-9.
68. van Soolingen, D., de Haas, P.E., Hermans, P.W., Groenen, P.M., and van Embden, J.D. (1993) Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J Clin Microbiol 31: 1987-95.
69. Villarroya, M., Pérez-Roger, I., Macián, F., and Armengod, M.E. (1998) Stationary phase induction of dnaN and recF, two genes of Escherichia coli involved in DNA replication and repair. EMBO J 17: 1829-1837.
70. Wootton, J.C., and Federhen, S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266: 554-571.
71. Worley, K.C., Wiese, B.A., and Smith, R.F. (1995) BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res 5: 173-184.
72. Young, D.B. (1997) TB research; entering the post-genomic era. Mol Med Today 3: 6-7.
73. Zhang, Y., and Young, D. (1994) Strain variation in the katG region of Mycobacterium tuberculosis. Mol Microbiol 14: 301-308.