Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis

Journal of Bacteriology

Volumn 184, Issue 20, 2002, Pages 5641-5653

  Sung, Huang Mo ^a   Yasbin, Ronald E ^a  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RECA PROTEIN;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL MUTATION; BACTERIUM CULTURE; CELL DIFFERENTIATION; ECOLOGY; GENOTYPE; MOLECULAR EVOLUTION; MUTAGENESIS; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; REGULATORY MECHANISM;

ADAPTATION, PHYSIOLOGICAL; AMINO ACIDS, ESSENTIAL; BACILLUS SUBTILIS; BACTERIAL PROTEINS; CULTURE MEDIA; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; MUTAGENESIS; TRANSCRIPTION FACTORS;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); POSIBACTERIA; PROKARYOTA;

EID: 0036785323     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.184.20.5641-5653.2002     Document Type: Article

References (83)

1. Ausubel, F., R. Brent, R. Kingston, J. Seidman, J. A. Smith, and K. Struhl. 2001. Current protocols in molecular biology, CD version. Wiley, New York, N.Y.
2. Berka, R. M., J. Hahn, M. Albano, I. Draskovic, M. Persuh, X. Cui, A. Sloma, W. Widner, and D. Dubnau. 2002. Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK. Mol. Microbiol. 43:1331-1345.
3. Bol, D., and R. E. Yasbin. 1990. Characterization of an inducible oxidative stress system in Bacillus subtilis. J. Bacteriol. 172:3503-3506.
4. Boylan, S. A., M. D. Thomas, and C. W. Price. 1991. Genetic method to identify regulons controlled by nonessential elements: isolation of a gene dependent on alternate transcription factor sigma B of Bacillus subtilis. J. Bacteriol. 173:7856-7866.
5. Bridges, B. A. 1997. Hypermutation under stress. Nature 387:557-558.
6. Bridges, B. A. 1998. The role of DNA damage in stationary phase ('adaptive') mutation. Mutat. Res. 408:1-9.
7. Bridges, B. A. 1993. Spontaneous mutation in stationary-phase Escherichia coli WP2 carrying various DNA repair alleles. Mutat. Res. 302:173-176.
8. Bull, H. J., G. J. McKenzie, P. J. Hastings, and S. M. Rosenberg. 2000. Evidence that stationary-phase hypermutation in the Escherichia coli chromosome is promoted by recombination. Genetics 154:1427-1437.
9. Bull, H. J., G. J. McKenzie, P. J. Hastings, and S. M. Rosenberg. 2000. Response to John Cairns: the contribution of transiently hypermutable cells to mutation in stationary phase. Genetics 156:925-926.
10. Cairns, J. 2000. The contribution of bacterial hypermutators to mutation in stationary phase. Genetics 156:923.
11. Cairns, J., and P. L. Foster. 1991. Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics 128:695-701.
12. Cairns, J., J. Overbaugh, and S. Miller. 1988. The origin of mutants. Nature 335:142-145.
13. Cheo, D. L., K. W. Bayles, and R. E. Yasbin. 1991. Cloning and characterization of DNA damage-inducible promoter regions from Bacillus subtilis. J. Bacteriol. 173:1696-1703.
14. Dubnau, D. 1991. Genetic competence in Bacillus subtilis. Microbiol. Rev. 55:395-424.
15. Foster, P. L. 1998. Adaptive mutation: has the unicorn landed? Genetics 148:1453-1459.
16. Foster, P. L. 1999. Mechanisms of stationary phase mutation: a decade of adaptive mutation. Annu. Rev. Genet. 33:57-88.
17. Foster, P. L. 1997. Nonadaptive mutations occur on the F′ episome during adaptive mutation conditions in Escherichia coli. J. Bacteriol. 179:1550-1554.
18. Foster, P. L., G. Gudmundsson, J. M. Trimarchi, H. Cai, and M. F. Goodman. 1995. Proofreading-defective DNA polymerase II increases adaptive mutation in Escherichia coli. Proc. Natl. Acad. Sci. USA 92:7951-7955.
19. Foster, P. L., and J. M. Trimarchi. 1994. Adaptive reversion of a frameshift mutation in Escherichia coli by simple base deletions in homopolymeric runs. Science 265:407-409.
20. Foster, P. L., and J. M. Trimarchi. 1995. Adaptive reversion of an episomal frameshift mutation in Escherichia coli requires conjugal functions but not actual conjugation. Proc. Natl. Acad. Sci. USA 92:5487-5490.
21. Foster, P. L., J. M. Trimarchi, and R. A. Maurer. 1996. Two enzymes, both of which process recombination intermediates, have opposite effects on adaptive mutation in Escherichia coli. Genetics 142:25-37.
22. H each contribute to survival of Bacillus subtilis under extreme growth conditions. J. Bacteriol. 180:3730-3733.
23. Galitski, T., and J. R. Roth. 1995. Evidence that F plasmid transfer replication underlies apparent adaptive mutation. Science 268:421-423.
24. + mutants of Escherichia coli MCS2. J. Bacteriol. 179:4620-4622.
25. Graham, J. B., and C. A. Istock. 1978. Genetic exchange in Bacillus subtilis in soil. Mol. Gen. Genet. 166:287-290.
26. Grossman, A. D. 1995. Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis. Annu. Rev. Genet. 29:477-508.
27. Guérout-Fleury, A. M., K. Shazand, N. Frandsen, and P. Stragier. 1995. Antibiotic-resistance cassettes for Bacillus subtilis. Gene 167:335-336.
28. Guillen, N., Y. Weinrauch, and D. A. Dubnau. 1989. Cloning and characterization of the regulatory Bacillus subtilis competence genes comA and comB. J. Bacteriol. 171:5354-5361.
29. Hadden, C., and E. W. Nester. 1968. Purification of competent cells in the Bacillus subtilis transformation system. J. Bacteriol. 95:876-885.
30. Hahn, J., A. Luttinger, and D. Dubnau. 1996. Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis. Mol. Microbiol. 21:763-775.
31. Hall, B. G. 1995. Genetics of selection-induced mutations: I. uvrA, uvrB, uvrC, and uvrD are selection-induced specific mutator loci. J. Mol. Evol. 40: 86-93.
32. Hall, B. G. 1997. On the specificity of adaptive mutations. Genetics 145:39-44.
33. Hall, B. G. 1990. Spontaneous point mutations that occur more often when advantageous than when neutral. Genetics 126:5-16.
34. Hamoen, L. W., A. F. Van Werkhoven, G. Venema, and D. Dubnau. 2000. The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 97:9246-9251.
35. Harris, R. S., H. J. Bull, and S. M. Rosenberg. 1997. A direct role for DNA polymerase III in adaptive reversion of a frameshift mutation in Escherichia coli. Mutat. Res. 375:19-24.
36. Harris, R. S., S. Longerich, and S. M. Rosenberg. 1994. Recombination in adaptive mutation. Science 264:258-260.
37. Harris, R. S., K. J. Ross, and S. M. Rosenberg. 1996. Opposing roles of the Holliday junction processing systems of Escherichia coli in recombination-dependent adaptive mutation. Genetics 142:681-691.
38. Hastings, P. J., H. J. Bull, J. R. Klump, and S. M. Rosenberg. 2000. Adaptive amplification: an inducible chromosomal instability mechanism. Cell 103: 723-731.
39. Hendrickson, H., E. S. Slechta, U. Bergthorsson, D. I. Andersson, and J. R. Roth. 2002. Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proc. Natl. Acad. Sci. USA 99:2164-2169.
40. Hengge-Aronis, R. 1993. Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in E. coli. Cell 72:165-168.
41. Hoch, J. A. 2000. Two-component and phosphorelay signal transduction. Curr. Opin. Microbiol. 3:165-170.
42. Innis, M. A., D. H. Gelfand, J. J. Sninsky, and T. J. White (ed.). 1990. PCR protocols: a guide to methods and applications. Academic Press, New York, N.Y.
43. Kasak, L., R. Horak, and M. Kivisaar. 1997. Promoter-creating mutations in Pseudomonas putida: a model system for the study of mutation in starving bacteria. Proc. Natl. Acad. Sci. USA 94:3134-3139.
44. Kroos, L., B. Zhang, H. Ichikawa, and Y. T. Yu. 1999. Control of sigma factor activity during Bacillus subtilis sporulation. Mol. Microbiol. 31:1285-1294.
45. Lea, D. E., and C. A. Coulson. 1949. The distribution of the numbers of mutants in bacterial populations. J. Genet. 49:264-285.
46. Lombardo, M. J., J, Torkelson, H. J. Bull, G. J. McKenzie, and S. M. Rosenberg, 1999. Mechanisms of genome-wide hypermutation in stationary phase. Ann. N. Y. Acad. Sci. 870:275-289.
47. Love, P. E., M. J. Lyle, and R. E. Yasbin. 1985. DNA damage inducible (din) loci are transcriptionally activated in competent Bacillus subtilis. Proc. Natl. Acad. Sci. USA 82:6201-6205.
48. Love, P. E., and R. E. Yasbin. 1984. Genetic characterization of the inducible "SOS-like" system of Bacillus subtilis. J. Bacteriol. 160:910-920.
49. Makinoshima, H., A. Nishimura, and A. Ishihama. 2002. Fractionation of Escherichia coli cell populations at different stages during growth transition to stationary phase. Mol. Microbiol. 43:269-279.
50. McKenzie, G. J., R. S. Harris, P. L. Lee, and S. M. Rosenberg. 2000. The SOS response regulates adaptive mutation. Proc. Natl. Acad. Sci. USA 97: 6646-6651.
51. McKenzie, G. J., P. L. Lee, M. J. Lombardo, P. J. Hastings, and S. M. Rosenberg. 2001. SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol. Cell 7:571-579.
52. McKenzie, G. J., and S. M. Rosenberg. 2001. Adaptive mutations, mutator-DNA polymerases and genetic change strategies of pathogens. Curr. Opin. Microbiol. 4:586-594.
53. McVeigh, R., and R. E. Yasbin. 1996. The smart phages of B. subtilis: type 4 SOS response. J. Bacteriol. 178:3399-3401.
54. Msadek, T. 1999. When the going gets tough: survival strategies and environmental signaling networks in Bacillus subtilis. Trends Microbiol. 7:201-207.
55. Ogura, M., H. Yamaguchi, K. Kobayashi, N. Ogasawara, Y. Fujita, and T. Tanaka. 2002. Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. J. Bacteriol. 184:2344-2351.
56. Ogura, M., H. Yamaguchi, K. Yoshida, Y. Fujita, and T. Tanaka. 2001. DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: an approach to comprehensive analysis of B. subtilis two-component regulatory systems. Nucleic Acids Res. 29:3804-3813.
57. Prival, M., and T. Cebula. 1996. Adaptive mutation and slow-growing revertants of an Escherichia coli lacZ amber mutant. Genetics 144:1337-1341.
58. Rosche, W. A., and P. L. Foster. 2000. Determining mutation rates in bacterial populations. Methods 20:4-17.
59. Rosenberg, S. M. 1997. Mutation for survival. Curr. Opin. Genet. Dev. 7:829-834.
60. Rosenberg, S. M., R. S. Harris, S. Longerich, and A. M. Galloway. 1996. Recombination-dependent mutation in non-dividing cells. Mutat. Res. 350: 69-76.
61. Rosenberg, S. M., R. S. Harris, and J. Torkelson. 1995. Molecular handles on adaptive mutation. Mol. Microbiol. 18:185-189.
62. Rosenberg, S. M., S. Longerich, P. Gee, and R. S. Harris. 1994. Adaptive mutation by deletions in small mononucleotide repeats. Science 265:405-407.
63. Rosenberg, S. M., C. Thulin, and R. S. Harris. 1998. Transient and heritable mutators in adaptive evolution in the lab and in nature. Genetics 148:1559-1566.
64. Rudner, R., A. Murray, and N. Huda. 1999. Is there a link between mutation rates and the stringent response in Bacillus subtilis? Ann. N. Y. Acad. Sci. 870:418-422.
65. Shapiro, J. A. 1984. Observations on the formation of clones containing araB-lacZ cistron fusions. Mol. Gen. Genet. 194:79-90.
66. Shapiro, J. A. 1998. Thinking about bacterial populations as multicellular organisms. Annu. Rev. Microbiol. 52:81-104.
67. Sonenshein, A. L., J. A. Hoch, and R. Losick (ed.). 1993. Bacillus subtilis and other gram-positive bacteria: physiology, biochemistry, and molecular genetics. American Society for Microbiology, Washington, D.C.
68. Spizizen, J. 1958. Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc. Natl. Acad. Sci. USA 44:1072-1078.
69. Steele, D. F., and S. Jinks-Robertson. 1992. An examination of adaptive reversion in Saccharomyces cerevisiae. Genetics 132:9-21.
70. Sullivan, M. A., R. E. Yasbin, and F. E. Young. 1984. New shuttle vectors for Bacillus subtilis and Escherichia coli. Gene 29:21-26.
71. Sung, H. M., and R. E. Yasbin. 2000. Transient growth requirement in Bacillus subtilis following the cessation of exponential growth. Appl. Environ. Microbiol. 66:1220-1222.
72. Tevethia, M. J., J. N. Baptist, and M. Mandel. 1974. Pleiotropic effects of suppressor mutations in Bacillus subtilis. J. Bacteriol. 119:961-975.
73. Torkelson, J., R. S. Harris, M. J. Lombardo, J. Nagendran, C. Thulin, and S. M. Rosenberg. 1997. Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-dependent adaptive mutation. EMBO J 16:3303-3311.
74. van Sinderen, D., A. Lutiinnger, L., Kong, D. Dubnau, G. Venema, and L. Hamoen. 1995. comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis. Mol. Microbiol. 15:455-462.
75. B-dependent general stress regulon confers multiple stress resistance in Bacillus subtilis. J. Bacteriol. 181:3942-3948.
76. von Borstel, R. C. 1978. Measuring spontaneous mutation rates in yeast. Methods Cell Biol. 20:1-24.
77. Wright, B. E. 2000. A biochemical mechanism for nonrandom mutations and evolution. J. Bacteriol. 182:2993-3001.
78. Yasbin, R. E., D. Cheo, and D. Bol. 1993. DNA repair systems, p. 529-537. In A. L. Sonenshein, R. Losick, and J. Hoch (ed.), Bacillus subtilis and other gram-positive organisms. American Society for Microbiology, Washington, D.C.
79. Yasbin, R. E., D. L. Cheo, and K. W. Bayles. 1992. Inducible DNA repair and differentiation in Bacillus subtilis: interactions between global regulons. Mol. Microbiol. 6:1263-1270.
80. Yasbin, R. E., P. I. Fields, and B. J. Andersen. 1980. Properties of Bacillus subtilis 168 derivatives freed of their natural prophages. Gene 12:155-159.
81. Yasbin, R. E., R. Miehl-Lester, and P. E. Love. 1987. Mutagenesis in Bacillus subtilis, p. 73-84. In M. Alacevic, D. Hranueli, and Z. Tomen (ed.), Genetics of industrial microorganisms. GIM-86, Split, Yugoslavia.
82. + gene of B. subtilis and its gene product: further characterization of this universal protein. Biochimie 73:245-250.
83. Yasbin, R. E., G. A. Wilson, and F. E. Young. 1973. Transformation and transfection in lysogenic strains of Bacillus subtilis 168. J. Bacteriol. 113:540-548.