Bacterial stationary-state mutagenesis and mammalian tumorigenesis as stress-induced cellular adaptations and the role of epigenetics

Current Genomics

Volumn 7, Issue 8, 2006, Pages 481-496

  Karpinets, T V ^a,b   Greenwood, D J ^c   Pogribny, I P ^d   Samatova, N F ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

^c UNIVERSITY OF WARWICK   (United Kingdom)

^d NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

Author keywords

Adaptive mutagenesis; Bacteria; Cancer; Epigenetic alterations; Histone like proteins; Stress

Indexed keywords

DNA POLYMERASE;

ADAPTIVE BEHAVIOR; APOPTOSIS; BACTERIAL CELL; CARCINOGENESIS; CELL AGING; CELL CYCLE REGULATION; CELL DIVISION; CELL FUNCTION; CELL POPULATION; CELL PROLIFERATION; CELL STRESS; CELL SURVIVAL; CELL TRANSFORMATION; DNA REPAIR; DNA SEQUENCE; EPIGENETICS; GENE MUTATION; MAMMAL CELL; MULTIGENE FAMILY; MUTAGENESIS; NONHUMAN; PHENOTYPE; REVIEW; SIGNAL TRANSDUCTION; STEADY STATE;

BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 33846054066     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920206779315764     Document Type: Review

References (143)

1. Hall, B.G. Adaptive mutagenesis: a process that generates almost exclusively beneficial mutations. Genetica 1998, 102-103: 109-125.
2. Janion, C. A new look at adaptive mutations in bacteria. Acta Biochim. Pol. 2001, 47: 451-457.
3. Karpinets, T.V., Foy, B.D. Tumorigenesis: the adaptation of mammalian cells to sustained stress environment by epigenetic alterations and succeeding matched mutations. Carcinogenesis 2005, 26: 1323-1334.
4. Tenaillon, O., Denamur E., Matic, I. Evolutionary significance of stress-induced mutagenesis in bacteria. Trends Microbiol. 2004, 12: 264-270.
5. Finkel, S.E. Long-term survival during stationary phase: evolution and the GASP phenotype. Nat. Rev. Microbiol. 2006, 4: 113-120.
6. Denamur, E., Matic I. Evolution of mutation rates in bacteria. Mol. Microbiol. 2006 60: 820-827.
7. Nephew, K.P., Huang T.H. Epigenetic gene silencing in cancer initiation and progression. Cancer Lett., 2003, 190: 125-133.
8. Esteller, M. Aberrant DNA methylation as a cancer-inducing mechanism. Annu. Rev. Pharmacol. Toxicol, 2005, 45: 629-656.
9. Cheung, P., Lau, P. Epigenetic regulation by historic methylation and histone variants. Mol. Endocrinol. 2005, 19: 563-573.
10. Mattick, J.S., Makunin, I.V. Small regulatory RNAs in mammals. Hum. Mol. Genet. 2005, 14: R121-132.
11. Talbert, P.B., Henikoff, S. Spreading of silent chromatin: inaction at a distance. Nat. Rev. Genet. 2006, 7: 793-803.
12. Wion, D., Casadesus, J. N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. Nat. Rev. Microbiol. 2006, 4: 183-192.
13. Yin, J. C. P., Krebs, M. P., Reznikoff, W. S. Effect of dam methylation on Tn5 transposition. J. Mol. Biol. 1988, 199: 35-45.
14. Rasmussen, L.J., Lobner-Olesen, A., Marinus, M.G. Growth-rate-dependent transcription initiation from the dam P2 promoter. Gene 1995, 157: 213-215.
15. Low, D.A., Weyand, N.J., Mahan, M.J. Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect. Immun. 2001, 69: 7197-7204.
16. Schofield, M.J., Hsieh, P. DNA mismatch repair: molecular mechanisms and biological function. Annu. Rev. Microbiol. 2003, 57: 579-608.
17. Lobner-Olesen, A., Skovgaard, O., Marinus, M.G. Dam methylation: coordinating cellular processes. Curr. Opin. Microbiol. 2005, 8: 154-160.
18. Stephens, C., Reisenauer, A., Wright, R., Shapiro, L. A cell cycle-regulated bacterial DNA methyltransferase is essential for viability. Proc. Natl. Acad. Sci. USA, 1997, 93: 1210-1214.
19. Kahng, L.S., Shapiro, L. The CcrM DNA methyltransferase of Agrobacterium tumefaciens is essential, and its activity is cell cycle regulated. J. Bacteriol. 2001, 183: 3065-3075.
20. Kossykh, V.G., Lloyd, R.S. A DNA adenine methyltransferase of Escherichia coli that is cell cycle regulated and essential for viability. J. Bacteriol. 2004, 186: 6340.
21. Shanado, Y., Kato, J., Ikeda, H. Escherichia coli HU protein suppresses DNA-gyrase-mediated illegitimate recombination and SOS induction. Genes Cells 1998, 3: 511-520.
22. Kobryn, K., Lavoie, B.D., Chaconas, G. Z. Supercoiling-dependent site-specific binding of HU to naked Mu DNA. J. Mol. Biol. 1999, 289: 777-784.
23. Balandina, A., Claret, L., Hengge-Aronis, R., Rouviere-Yaniv, J. The Escherichia coli histone-like protein HU regulates rpoS translation. Mol. Microbiol. 2001, 39: 1069-1079.
24. Dorman, C.J., Deighan, P. Regulation of gene expression by histone-like proteins in bacteria. Curr. Opin. Genet. Dev. 2003, 13: 179-184.
25. Sagi, D., Friedman, N., Vorgias, C., Oppenheim, A.B., Stavans, J. Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes. J. Mol. Biol. 2004, 341: 419-428.
26. Swinger, K.K., Rice, P.A. IHF and HU: flexible architects of bent DNA. Curr. Opin. Struct. Biol. 2004, 14: 28-35.
27. Yamashino, T., Ueguchi, C., Mizuno, T. Quantitative control of the stationary phase-specific sigma factor, sigma S, in Escherichia coli: involvement of the nucleoid protein H-NS. EMBO J. 1995, 14: 594-602;
28. Atlung, T., Ingmer, H. H-NS: a modulator of environmentally regulated gene expression. Mol. Microbiol. 1997, 24: 7-17.
29. Palchaudhuri, S., Tominna, B., Leon, M.A. H-NS regulates DNA repair in Shigella. J. Bacteriol. 1998, 180: 5260-5262.
30. Ali Azam, T., Iwata, A., Nishimura, A., Ueda, S., Ishihama, A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol. 1999, 181: 6361-6370.
31. Hommais, F., Krin, E., Laurent-Winter, C., Soutourina, O., Malpertuy, A., Le Caer, J.P., Danchin, A., Bertin, P. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol. Microbiol. 2001, 40: 20-36.
32. Schroder, O., Wagner, R. The bacterial regulatory protein H-NS-a versatile modulator of nucleic acid structures. Biol. Chem. 2002, 383: 945-960.
33. Rimsky, S. Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. Curr. Opin. Microbiol. 2004, 7: 109-114.
34. Nishino, K., Yamaguchi, A. Role of histone-like protein H-NS in multidrug resistance of Escherichia coli. J. Bacteriol. 2004, 186: 1423-1429.
35. Dame, R.T., Luijsterburg, M.S., Krin, E., Bertin, P.N., Wagner, R., Wuite G.J. DNA bridging: a property shared among H-NS-like proteins. J. Bacteriol. 2005, 187: 1845-1848.
36. Opel, M.L., Aeling, K,A., Holmes, W.M., Johnson, R.C., Benham, C.J., Hatfield, G.W. Z. Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism. Mol. Microbiol. 2004, 53: 665-674.
37. Luijsterburg, M.S., Noom, M.C., Wuite, G.J., Dame, R.T. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective. J. Struct. Biol. 2006, 156: 262-272.
38. Hirsch, M., Elliott, T. Fis regulates transcriptional induction of RpoS in Salmonella enterica. J. Bacteriol. 2005, 187: 1568-1580.
39. Pul, U., Wurm, R., Lux, B., Meltzer, M. Menzel, A., Wagner. R. LRP and H-NS - cooperative partners for transcription regulation at Escherichia coli rRNA promoters. Mol. Microbiol. 2005, 58: 864-876.
40. Skoko, D,, Yan, J,, Johnson, R.C., Marko, J.F. Low-force DNA condensation and discontinuous high-force decondensation reveal a loop-stabilizing function of the protein Fis. Phys. Rev. Lett. 2005, 95: 208101.
41. Nair, S., Finkel, S.E. Dps protects cells against multiple stresses during stationary phase. J. Bacteriol. 2004, 186: 4192-4198.
42. Frenkiel-Krispin, D., Ben-Avraham, I., Englander, J., Shimoni, E., Wolf, S.G., Minsky, A. Nucleoid restructuring in stationary-state bacteria. Mol. Microbiol. 2004, 51: 395-405.
43. Su, M., Cavallo, S., Stefanini, S., Chiancone, E., Chasteen, N.D. The so-called Listeria innocua ferritin is a Dps protein. Iron incorporation, detoxification, and DNA protection properties. Biochemistry 2005, 44: 5572-5578.
44. Murtin, C., Engelhorn, M., Geiselmann, J., Boccard, F. A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell J. Mol. Biol. 1998, 284, 949-961
45. Ilves, H., Horak, R., Teras, R., Kivisaar, M. IHF is the limiting host factor in transposition of Pseudomonas putida transposon Tn4652 in stationary phase. Mol. Microbiol. 2004, 51: 1773-1785.
46. Landgraf, J. R., Wu, J., Calvo, J. M. Effects of nutrition and growth rate on Lrp levels in Escherichia coli. J. Bacteriol 1997, 178, 6930-6936.
47. Tani, T.H., Khodursky, A., Blumenthal, R.M., Brown, P.O., Matthews, R.G. Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 2002, 99: 13471-13476.
48. Brinkman, A.B., Ettema, T.J., de Vos, W.M., van der Oost, J. The Lrp family of transcriptional regulators. Mol. Microbiol. 2003, 48: 287-294.
49. Hernday, A., Braaten, B., Low, D. The intricate workings of a bacterial epigenetic switch. Adv. Exp. Med. Biol. 2004, 547: 83-89.
50. Weber, H., Polen, T., Heuveling, J., Wendisch, V.F., Hengge, R. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J. Bacteriol. 2005, 187: 1591-1603.
51. Masse, E., Majdalani, N., Gottesman, S. Regulatory roles for small RNAs in bacteria, Curr. Opin. Microbiol. 2003, 6: 120-124.
52. Repoila, F., Majdalani, N., Gottesman, S. Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Mol. Microbiol. 2003, 48: 855-861.
53. Gottesman, S. The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol. 2004, 58: 303-328.
54. Majdalani, N., Vanderpool, C.K., Gottesman, S. Bacterial small RNA regulators. Crit. Rev. Biochem. Mol. Biol. 2005, 40: 93-113.
55. van der Woude, M., Hale, W.B., Low, D.A. Formation of DNA methylation patterns: nonmethylated GATC sequences in gut and pap operons. J. Bacteriol. 1998, 180: 5913-5920.
56. Travers, A., Muskhelishvili G. Bacterial chromatin. Curr. Opin. Genet. Dev. 2005 15: 507-514.
57. Wang, H., Noordewier, M., Benham, C.J. Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters. Genome Res. 2004, 14: 1575-1584.
58. Altuvia, S. Regulatory small RNAs: the key to coordinating global regulatory circuits. J. Bacteriol. 2004, 186: 6679-6680.
59. Kasak, L., Horak, R., Kivisaar M. Promoter-creating mutations in Pseudomonas putida: a model system for the study of mutation in starving bacteria. Proc. Natl. Acad. Sci. USA 1997, 94: 3134-3139
60. Sung, H.M., Yasbin, R.E. Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis. J. Bacteriol. 2002, 84: 5641-53.
61. Bjedov, I., Tenaillon, O., Gerard, B., Souza, V., Denamur, E., Radman, M., Taddei, F., Matic, I. Stress-induced mutagenesis in bacteria, Science 2003, 300: 1404-1409.
62. Rosenberg, S. M., Hastings, P.J. Adaptive Point Mutation and Adaptive Amplification Pathways in the Escherichia coli Lac System: Stress Responses Producing Genetic Change J. Bacteriol. 2004, 186: 4838-4843.
63. Hersh, M.N., Ponder, R.G., Hastings, P.J., Rosenberg, S.M. Adaptive mutation and amplification in Escherichia coli: two pathways of genome adaptation under stress. Res. Microbiol. 2004, 155: 352-359.
64. Roth, J.R., Andersson, D.I. Amplification-mutagenesis-how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation. Res. Microbiol. 2004, 155: 342-51.
65. Torkelson, J., Harris, R.S., Lombardo, M.J., Nagendran, J., Thulin, C., Rosenberg, S.M. Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-dependent adaptive mutation. EMBO J. 1997, 16: 3303-3311.
66. Lombardo, M. J., Torkelson, J., Bull, H.J., McKenzie, G.J., Rosenberg, S.M. Mechanisms of genome-wide hypermutation in stationary phase. Ann. N. Y. Acad. Sci. 1999, 870: 275-289.
67. Bridges, B. A. Hypermutation under stress. Nature 1997, 387: 557-558.
68. Lewis, K. Programmed death in bacteria. Microbiol. Mol. Biol. Rev. 2000, 64: 503-14.
69. Gerdes, K., Christensen, S.K., Lobner-Olesen, A. Prokaryotic toxin-antitoxin stress response loci. Nat. Rev. Microbiol. 2005, 3: 371-382.
70. Saumaa, S., Tarassova, K., Tark, M., Tover, A., Tegova, R., Kivisaar, M. Involvement of DNA mismatch repair in stationary-phase mutagenesis during prolonged starvation of Pseudomonas putida. DNA Repair (Amst). 2006, 5: 505-514.
71. Karpinets, T.V., Foy, B.D. Model of the developing tumorigenic phenotype in mammalian cells and the role of sustained stress. J. Theoret. Biol. 2004, 227: 253-264.
72. Ben-Porath, I., Weinberg, R.A. When cells get stressed: an integrative view of cellular senescence. J. Clin. Invest. 2004, 113: 8-13.
73. Ben-Porath, I., Weinberg, R.A. The signals and pathways activating cellular senescence. Int. J. Biochem. Cell. Biol. 2005, 37: 961-976.
74. Nystrom, T. Conditional senescence in bacteria: death of the immortals. Mol. Microbiol. 2003, 48: 17-23.
75. Hamoen, L. W., Venema, G., Kuipers, O.P. Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology 2003, 149: 9-17.
76. Tortosa, P., Dubnau, D. Competence for transformation: a matter of taste. Curr. Opin. Microbiol. 1999, 2: 588-592.
77. Gerdes, K., Christensen, S.K., Lobner-Olesen, A. Prokaryotic toxin-antitoxin stress response loci. Nat. Rev. Microbiol. 2005, 3: 371-82.
78. Shah, D., Zhang, Z., Khodursky, A., Kaldalu, N., Kurg, K., Lewis, K. Persisters: a distinct physiological state of E. coli. BMC Microbiol. 2006, 6: 53.
79. Bihani, T., Mason, D.X., Jackson, T.J., Chen, S.C., Boettner, B., Lin, A.W. Differential oncogenic Ras signaling and senescence in tumor cells. Cell Cycle 2004, 3: 1201-1207.
80. Murray, H.D., Schneider, D.A., Gourse, R.L. Control of rRNA expression by small molecules is dynamic and nonredundant. Mol. Cell. 2003, 12: 125-34.
81. Scott, J.M., Haldenwang, W.G. Obg, an essential GTP binding protein of Bacillus subtilis, is necessary for stress activation of transcription factor sigma(B). J. Bacteriol 1999, 181: 4653-4660.
82. Nystrom, T. Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Mol. Microbiol. 2004, 54: 855-862.
83. Magnusson, L.U., Farewell, A., Nystrom, T. ppGpp: a global regulator in Escherichia coli. Trends Microbiol. 2005, 13: 236-242.
84. Wout, P., Pu, K., Sullivan, S.M., Reese, V., Zhou, S., Lin, B., Maddock, J.R. The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase. J. Bacteriol. 2004, 186: 5249-5257.
85. Lerner, C.G., Inouye, M. Pleiotropic changes resulting from depletion of Era, an essential GTP-binding protein in Escherichia coli. Mol. Microbiol. 1991, 5: 951-957.
86. Britton, R.A., Powell, B.S., Dasgupta, S., Sun, Q., Margolin, W., Lupski, J.R., Court, D.L. Cell cycle arrest in Era GTPase mutants: a potential growth rate-regulated checkpoint in Escherichia coli. Mol. Microbiol. 1998, 30: 739-750;
87. Foti, J.J., Schienda, J., Sutera, V.A. Jr., Lovett, S.T. A bacterial G protein-mediated response to replication arrest. Mol. Cell. 2005, 17: 549-560.
88. Michel, B. Obg/CtgA, a signaling protein that controls replication, translation, and morphological development? Dev. Cell 2005, 8: 300-301.
89. Boeneman, K., Crooke, E. Chromosomal replication and the cell membrane. Curr. Opin. Microbiol. 2005, 8: 143-148.
90. Messer, W. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol. Rev. 2002, 26: 355-74.
91. Ichihashi, N., Kurokawa, K., Matsuo, M., Kaito, C., Sekimizu, K. Inhibitory effects of basic or neutral phospholipids on acidic phospholipid-mediated dissociation of adenine nucleotide bound to DnaA protein, the initiator of chromosomal DNA replication, J. Biol. Chem. 2003, 278: 28778-28786.
92. Yuk, H.G., Marshall, D.L. Effect of trisodium, phosphate adaptation on changes in membrane lipid composition, verotoxin secretion, and acid resistance of Escherichia coli O157: H7 in simulated gastric fluid. Int. J. Food Microbiol. 2006, 106: 39-44.
93. Wold, S., Crooke, E., Skarstad, K. The Escherichia coli Fis protein prevents initiation of DNA replication from oriC in vitro. Nucleic Acids Res. 1997, 24: 3527-3532.
94. Ryan, V.T., Grimwade, J.E., Camara, J.E., Crooke, E., Leonard, AC. Escherichia coli prereplication complex assembly is regulated by dynamic interplay among Fis, IHF and DnaA. Mol. Microbiol. 2004, 51: 1347-1359.
95. Ninnemann, O., Koch, C., Kahmann, R. The E. coli fis promoter is subject to stringent control and autoregulation. EMBO J. 1992, 11: 13-20.
96. Aizenman, E., Engelberg-Kulka, H., Glaser, G. An Escherichia coli chromosomal "addiction module" regulated by guanosine 3′,5′-bispyrophosphate: a model for programmed bacterial cell death. Proc. Natl. Acad. Sci. USA 1997, 93: 6059-6063.
97. Hazan, R., Sat, B., Engelberg-Kulka, H. Escherichia coli mazEF-Mediated Cell Death Is Triggered by Various Stressful Conditions, J. Bacteriol. 2004, 186: 3663-3669.
98. Harris, R.S., Feng, G., Ross, K.J., Sidhu, R., Thulin, C., Longerich, S., Szigety, S.K., Winkler, M.E., Rosenberg, S.M. Mismatch repair protein MutL becomes limiting during stationary-phase mutation. Genes Dev. 1997, 11: 2426-37.
99. Bridges, B.A., Timms A. Effect of endogenous carotenoids and defective RpoS sigma factor on spontaneous mutation under starvation conditions in Escherichia coli: evidence for the possible involvement of singlet oxygen. Mutat.. Res. 1998, 403: 21-28.
100. Harris, R.S., Feng, G., Ross, K.J., Sidhu, R., Thulin, C., Longerich, S., Szigety, S.K., Hastings, P.J., Winkler, M.E., Rosenberg, S.M. Mismatch repair is diminished during stationary-phase mutation. Mutat. Res. 1999, 437: 51-60.
101. Pedraza-Reyes, M., Yasbin, R.E. Contribution of the mismatch DNA repair system to the generation of stationary-phase-induced mutants of Bacillus subtilis. J. Bacteriol. 2004, 186: 6485-6491.
102. Ponder, R.G., Fonville, N.C., and Rosenberg, S.M. Switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol. Cell 2005, 19: 791-804.
103. Eichenbaum, Z., Livneh, Z. UV light induces IS10 transposition in Escherichia coli. Genetics 1998, 149: 1173-1181.
104. Ilves, H., Horak, R., Kivisaar, M. Involvement of sigma [S] in starvation-induced transposition of Pseudomonas putida transposon Tn4652. J. Bacteriol. 2001, 183: 5445-5448.
105. Ghanekar, K., McBride, A., Dellagostin, O., Thorne, S., Mooney, R., McFadden, J. Stimulation of transposition of the Mycobacterium tuberculosis insertion sequence IS6110 by exposure to a microaerobic environment. Mol. Microbiol. 1999, 33: 982-993.
106. Jock, S., Jacob, T., Kim, W.S., Hildebrand, M., Vosberg, H.P., Geider, K. Instability of short-sequence DNA repeats of pear pathogenic Erwinia strains from Japan and Erwinia amylovora fruit tree and raspberry strains. Mol. Genet. Genomics 2003, 268: 739-49.
107. Jackson, A.L., Chen, R., Loeb, L.A. Induction of microsatellite instability by oxidative DNA damage. Proc. Natl. Acad. Sci. USA 1998, 95: 12468-12473.
108. Jackson, A.L., Loeb, L.A. Microsatellite instability induced by hydrogen peroxide in Escherichia coli. Mutat. Res. 2000, 447: 187-198.
109. Yamamura, E., Nunoshiba, T., Nohmi, T., Yamamoto, K. Hydrogen peroxide-induced microsatellite instability in the Escherichia coli K-12 endogenous tonB gene. Biochem. Biophys. Res. Commun. 2003, 306: 570-576.
110. Rocha, E.P., Matic, I., Taddei, F. Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions? Nucleic Acids Res. 2002, 30: 1886-1894.
111. Ilves, H., Horak, R., Kivisaar M. Involvement of sigmaS in Starvation-Induced Transposition of Pseudomonas putida Transposon Tn4652 J. Bacteriol. 2001, 183: 5445-5448.
112. Liu, D., Crellin, P., Chalmers, R. Cyclic changes in the affinity of protein-DNA interactions drive the progression and regulate the outcome of the Tn10 transposition reaction. Nucleic Acids Res. 2005. 33: 1982-1992.
113. Mahillon, J., Chandler, M. Insertion sequences. Microbiol. Mol. Biol. Rev. 1998, 62: 725-774.
114. Roberts, D., Hoopes, B C., McClure, W. R., Kleckner, N. IS10 transposition is regulated by DNA adenine methylation. Cell 1985, 43: 117-130.
115. Yin, J. C. P., Krebs, M. P., Reznikoff, W. S. Effect of dam methylation on Tn5 transposition. J. Mol. Biol. 1988, 199: 35-45.
116. Shcherbakova, P,V., Fijalkowska, I.J. Translesion synthesis DNA polymerases and control of genome stability. Front Biosci. 2006, 11: 2496-2517.
117. Nohmi, T. Environmental stress and lesion-bypass DNA polymerases. Annu. Rev. Microbiol. 2006,60: 231-53.
118. Avkin, S., Sevilyam, Z., Toubem, L., Geacintovm, N., Chaneym, S.G., Orenm, M., Livneh, Z. p53 and p21 regulate error-prone DNA repair to yield a lower mutation load. Mol. Cell 2006, 22: 407-413
119. Roos, W.P., Kaina, B. DNA damage-induced cell death by apoptosis. Trends. Mol. Med. 2006, 12: 440-450.
120. Metzgar, D., Wills, C. Evidence for the adaptive evolution of mutation rates. Cell 2000, 101: 581-584.
121. McKenzie, G.J., Rosenberg, S.M.. Adaptive mutations, mutator DNA polymerases and genetic change strategies of pathogens. Curr. Opin. Microbiol. 2001, 4: 586-594.
122. Loewe, L.L., Textor, V., Scherer, S. High Deleterious Genomic Mutation Rate in Stationary Phase of Escherichia coli. Science 2003, 302: 1558-1560.
123. Faure, D., Frederick, R., Wloch, D., Portier, P., Blot, M., Adams, J. Genomic Changes Arising in Long-Term Stab Cultures of Escherichia coli. J. Bacteriol. 2004, 186: 6437-6442.
124. Naas, T., Blot, M., Fitch, W. M., Arber, W. Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol. Biol. Evol. 1995, 12: 198-207.
125. Zinser, E. R., Schneider, D., Blot, M., Kolter, R. Bacterial evolution through the selective loss of beneficial genes: trade-offs in expression involving two loci. Genetics 2003, 164: 1271-1277.
126. Zinser, E. R., Kolter, R. Prolonged stationary-phase incubation selects for lrp mutation in Escherichia coli K-12. J. Bacteriol. 2000, 182: 4361-4365
127. Hamoen, L. W., Venema, G., Kuipers, O.P. Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology 2003, 149: 9-17.
128. Boles, B.R., Thoendel, M., Singh, P.K. Self-generated diversity produces "insurance effects" in biofilm communities. Proc. Natl. Acad. Sci. USA 2004, 101: 16630-16635.
129. Bachman, M.A., Swanson, M.S. Genetic evidence that Legionella pneumophila RpoS modulates expression of the transmission phenotype in both the exponential phase and the stationary phase. Infect. Immun. 2004, 72: 2468-2476.
130. Lombardo, M.J., Aponyi, I. and Rosenberg, S.M. General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli. Genetics 2004, 166: 669-680.
131. Madan. R., Kolter, R., Mahadevan, S. Mutations that activate the silent bgl operon of Escherichia coli confer a growth advantage in stationary phase. J. Bacteriol. 2005, 187: 7912-7917.
132. Tompkins, J.D., Nelson, J. L., Hazel, J.C., Leugers, S.L., Stumpf, J.D., Foster, P.L. Error-prone polymerase, DNA polymerase IV, is responsible for transient hypermutation during adaptive mutation in Escherichia coli. J. Bacteriol. 2003, 185: 3469-3472.
133. Sung, H.M., Yeamans, G., Ross, C.A., Yasbin, R.E. Roles of YqjH and YqjW, homologs of the Escherichia coli UmuC/DinB or Y superfamily of DNA polymerases, in stationary-phase mutagenesis and UV-induced mutagenesis of Bacillus subtilis. J. Bacteriol. 2003, 185: 2153-2160.
134. Goodman, M. F. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 2000, 71: 17-50.
135. Perez-Capilla, T., Baquero, M.R., Gomez-Gomez, J.M., Ionel, A., Martin, S., Blazquez, J. SOS-independent induction of dinB transcription by β-lactam-mediated inhibition of cell wall synthesis in Escherichia coli, J. Bacteriol. 2005, 187: 1515-1518.
136. Nohmi, T. Environmental stress and lesion-bypass DNA polymerases. Annu. Rev. Microbiol. 2006, 60: 231-53.
137. Camps, M., Loeb, L.A. When pol I goes into high gear: processive DNA synthesis by pol I in the cell. Cell Cycle 2004,3: 116-118.
138. Banach-Orlowska, M., Fijalkowska, I.J., Schaaper, R.M., Jonczyk, P. DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli. Mol. Microbiol. 2005, 58: 61-70.
139. Layton, J.C., Foster, P.L. Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli. Mol. Microbiol. 2003, 50: 549-61.
140. Yeiser, B., Pepper, E. D., Goodman, M. F., Finkel, S.E. SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness. Proc. Natl. Acad. Sci. USA 2002, 99: 8737-8741.
141. Tegova, R., Tover, A., Tarassova, K., Tark, M., Kivisaar, M. Involvement of error-prone DNA polymerase IV in stationary-phase mutagenesis in Pseudomonas putida. J. Bacteriol. 2004, 186: 2735-2744.
142. Saint-Ruf C., Matic I. Environmental tuning of mutation rates. Environment. Microbiol. 2006, 8: 193-199.
143. Cirz, R.T., Romesberg, F.E. Induction and inhibition of ciprofloxacin resistance-conferring mutations in hypermutator bacteria. Antimicrob. Agents Chemother. 2006 50: 220-225.