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Chapter 13 : The DNA Damage Response

Author: Susan T. Lovett1
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Affiliations: 1: Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110
Content Type: Monograph
Publication Year: 2011

Category: Microbial Genetics and Molecular Biology

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Abstract:

This chapter reviews the current knowledge about the mechanism of the LexA/RecA regulated response and its output in , stressing newly emerging areas such as regulation of RecA filament formation and management of specialized DNA repair polymerases. It also talks about the SOS response in other bacterial species and its implications for the evolution and treatment of bacterial pathogens, and further discusses the more poorly understood LexA/ RecA-independent damage response in several model organisms and a potentially larger network of the response to DNA damage. ATP binding, but not hydrolysis, is required for DNA binding; DNA binding greatly stimulates ATP hydrolysis, which in turn promotes RecA’s release from DNA. The current widespread use of fluoroquinolone antibiotics, which, as topoisomerase II poisons, are potent SOS inducers, has potentially serious clinical consequences and influence on evolution of pathogens. In , , and there is increasing evidence of LexA/RecA independent modes of DNA damage response, including genes involved in DNA replication and repair. The majority of DNA damage inducible genes are not controlled by LexA or RecA . The DNA damage response has important implications for the evolution and treatment of bacterial pathogens because of its ability to promote genetic change through mutation and induction of mobile genetic elements, potentially induced by the very agents used to treat bacterial infections.

Citation: Lovett S. 2011. The DNA Damage Response, p 205-228. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch13
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The DNA Damage Response
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Citation: Lovett S. 2011. The DNA Damage Response, p 205-228. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch13
/content/10.1128/9781555816841.ch13.ch13fig01
Figure 1.
Basic mechanics of the SOS response. In the repressed state, LexA binds to multiple genes, including itself, RecA, and other genes involved in DNA repair and cell division inhibition (the “output”), repressing transcription. When ssDNA accumulates, RecA forms a filament (“the signal”) that cleaves and inactivates LexA, turning on the output genes. Note that the increase of LexA expression will drive back repression quickly in the absence of “signal.”
10.1128/9781555816841/f0206-01_thmb.gif
10.1128/9781555816841/f0206-01.gif
Image of Figure 1.
Figure 1.

Basic mechanics of the SOS response. In the repressed state, LexA binds to multiple genes, including itself, RecA, and other genes involved in DNA repair and cell division inhibition (the “output”), repressing transcription. When ssDNA accumulates, RecA forms a filament (“the signal”) that cleaves and inactivates LexA, turning on the output genes. Note that the increase of LexA expression will drive back repression quickly in the absence of “signal.”

Citation: Lovett S. 2011. The DNA Damage Response, p 205-228. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch13
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Figure 2.
RecA loading pathways. Single-strand DNA that accumulates during blocks to replication or after UV irradiation becomes bound by SSB. The RecFOR proteins promote removal of SSB and replacement with a RecA filament. Double-strand breaks, such as those produced by ionizing radiation or topoisomerase poisons, are resected by RecBCD exonuclease, which loads RecA onto the emergent single-strand. Note that some gaps may be converted to breaks.
10.1128/9781555816841/f0208-01_thmb.gif
10.1128/9781555816841/f0208-01.gif
Image of Figure 2.
Figure 2.

RecA loading pathways. Single-strand DNA that accumulates during blocks to replication or after UV irradiation becomes bound by SSB. The RecFOR proteins promote removal of SSB and replacement with a RecA filament. Double-strand breaks, such as those produced by ionizing radiation or topoisomerase poisons, are resected by RecBCD exonuclease, which loads RecA onto the emergent single-strand. Note that some gaps may be converted to breaks.

Citation: Lovett S. 2011. The DNA Damage Response, p 205-228. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch13
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Figure 3.
Circuitry of the SOS response. LexA represses itself, RecA, and several other genes that modulate the RecA:ssDNA filament (“RecA*”), including DinI (a positive regulator of RecA filament) and RecX and UvrD (negative regulators of the RecA filament). RecA* inhibits LexA by promoting its cleavage.
10.1128/9781555816841/f0209-01_thmb.gif
10.1128/9781555816841/f0209-01.gif
Image of Figure 3.
Figure 3.

Circuitry of the SOS response. LexA represses itself, RecA, and several other genes that modulate the RecA:ssDNA filament (“RecA*”), including DinI (a positive regulator of RecA filament) and RecX and UvrD (negative regulators of the RecA filament). RecA* inhibits LexA by promoting its cleavage.

Citation: Lovett S. 2011. The DNA Damage Response, p 205-228. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch13
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Figure 4.
Polymerase switching during translesion DNA synthesis. The beta clamp (dark donut shape) binds the replicative DNA polymerase III core (dark oval) during normal processive DNA synthesis. A second translesion polymerase (light gray oval) is bound in reserve on the beta clamp “tool belt.” Upon encounter of a template lesion (black hexagon), polymerase III will stall. The translesion polymerase is then engaged with the primer terminus, which promotes brief, distributive synthesis past the lesion. (Polymerase III core may or may not be released from the clamp on this step, although the latter is shown here.) Because of the limited processivity of the translesion polymerase, polymerase III is reengaged to continue DNA replication shortly after bypass.
10.1128/9781555816841/f0215-01_thmb.gif
10.1128/9781555816841/f0215-01.gif
Image of Figure 4.
Figure 4.

Polymerase switching during translesion DNA synthesis. The beta clamp (dark donut shape) binds the replicative DNA polymerase III core (dark oval) during normal processive DNA synthesis. A second translesion polymerase (light gray oval) is bound in reserve on the beta clamp “tool belt.” Upon encounter of a template lesion (black hexagon), polymerase III will stall. The translesion polymerase is then engaged with the primer terminus, which promotes brief, distributive synthesis past the lesion. (Polymerase III core may or may not be released from the clamp on this step, although the latter is shown here.) Because of the limited processivity of the translesion polymerase, polymerase III is reengaged to continue DNA replication shortly after bypass.

Citation: Lovett S. 2011. The DNA Damage Response, p 205-228. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch13
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References

/content/book/10.1128/9781555816841.ch13
1. Abella,, M., I. Erill,, M. Jara,, G. Mazón,, S. Campoy, and J. Barbé. 2004. Widespread distribution of a lexA -regulated DNA damage-inducible multiple gene cassette in the Proteobacteria phylum. Mol. Microbiol. 54: 212– 222.
2. Acheson, D. W., and, A. Donohue-Rolfe. 1989. Cancer-associated hemolytic uremic syndrome: a possible role of mitomycin in relation to Shiga-like toxins. J. Clin. Oncol. 7: 1943.
3. Adams, D. W., and, J. Errington. 2009. Bacterial cell division: assembly, maintenance and disassembly of the Z ring. Nat. Rev. Microbiol. 7: 642– 653.
4. Aertsen, A., and, C. W. Michiels. 2005. Mrr instigates the SOS response after high pressure stress in Escherichia coli. Mol. Microbiol. 58: 1381– 1391.
5. Althorpe,, N. J.,, P. M. Chilley,, A. T. Thomas,, W. J. Brammar, and, B. M. Wilkins. 1999. Transient transcriptional activation of the Incl1 plasmid anti-restriction gene ( ardA) and SOS inhibition gene ( psiB) early in conjugating recipient bacteria. Mol. Microbiol. 31: 133– 142.
6. Anderson, D. G., and, S. C. Kowalczykowski. 1997. The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chi-regulated manner. Cell 90: 77– 86.
7. Arthur, H. M., and, R. G. Lloyd. 1980. Hyper-recombination in uvrD mutants of Escherichia coli K-12. Mol. Gen. Genet. 180: 185– 191.
8. Au,, N., E. Kuester-Schoeck,, V. Mandava,, L. E. Bothwell,, S. P. Canny,, K. Chachu,, S. A. Colavito,, S. N. Fuller,, E. S. Groban,, L. A. Hensley,, T. C. O’Brien,, A. Shah,, J. T. Tierney,, L. L. Tomm,, T. M. O’Gara,, A. I. Goranov,, A. D. Grossman, and, C. M. Lovett. 2005. Genetic composition of the Bacillus subtilis SOS system. J. Bacteriol. 187: 7655– 7666.
9. Bagdasarian,, M., A. Bailone,, M. M. Bagdasarian,, P. A. Manning,, R. Lurz,, K. N. Timmis, and, R. Devoret. 1986. An inhibitor of SOS induction, specified by a plasmid locus in Escherichia coli. Proc. Natl. Acad. Sci. USA 83: 5723– 5726.
10. Baitin, D. M.,, M. C. Gruenig, and, M. M. Cox. 2008. SSB antagonizes RecX-RecA interaction. J. Biol. Chem. 283: 14198– 14204.
11. Banach-Orlowska, M.,, I. J. Fijalkowska,, R. M. Schaaper, and, P. Jonczyk. 2005. DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli. Mol. Microbiol. 58: 61– 70.
12. Beaber, J. W.,, B. Hochhut, and, M. K. Waldor. 2004. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427: 72– 74.
13. Becskei, A., and, L. Serrano. 2000. Engineering stability in gene networks by autoregulation. Nature 405: 590– 593.
14. Bell, C. E. 2005. Structure and mechanism of Escherichia coli RecA ATPase. Mol. Microbiol. 58: 358– 366.
15. Berg, O. G. 1988. Selection of DNA binding sites by regulatory proteins: the LexA protein and the arginine repressor use different strategies for functional specificity. Nucleic Acids Res. 16: 5089– 5105.
16. Bi, E., and, J. Lutkenhaus. 1990. Analysis of ftsZ mutations that confer resistance to the cell division inhibitor SulA (SfiA). J. Bacteriol. 172: 5602– 5609.
17. Bianco, P. R.,, R. B. Tracy, and, S. C. Kowalczykowski. 1998. DNA strand exchange proteins: a biochemical and physical comparison. Front. Biosci. 3:D 570– 603.
18. Bierne, H.,, M. Seigneur,, S. D. Ehrlich, and, B. Michel. 1997. uvrD mutations enhance tandem repeat deletion in the Escherichia coli chromosome via SOS induction of the RecF recombination pathway. Mol. Microbiol. 26: 557– 567.
19. Blasius,, M., S. Sommer, and, U. Hübscher. 2008. Deinococcus radiodurans: what belongs to the survival kit Crit. Rev. Biochem. Mol. Biol. 43: 221– 238.
20. Bonacossa de Almeida,, C., G. Coste,, S. Sommer, and, A. Bailone. 2002. Quantification of RecA protein in Deinococcus radiodurans reveals involvement of RecA, but not LexA, in its regulation. Mol. Genet. Genomics 268: 28– 41.
21. Bonner, C. A.,, S. Hays,, K. McEntee, and, M. F. Goodman. 1990. DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 87: 7663– 7667.
22. Bonner,, C. A.,, S. K. Randall,, C. Rayssiguier,, M. Radman,, R. Eritja,, B. E. Kaplan,, K. McEntee, and, M. F. Goodman. 1988. Purification and characterization of an inducible Escherichia coli DNA polymerase capable of insertion and bypass at abasic lesions in DNA. J. Biol. Chem. 263: 18946– 18952.
23. Boshoff,, H. I.,, M. B. Reed,, C. E. Barry, and, V. Mizrahi. 2003. DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis. Cell 113: 183– 193.
24. Bougdour,, A., C. Cunning,, P. J. Baptiste,, T. Elliott, and, S. Gottesman. 2008. Multiple pathways for regulation of sigmaS (RpoS) stability in Escherichia coli via the action of multiple anti-adaptors. Mol. Microbiol. 68: 298– 313.
25. Breña-Valle, M., and, J. Serment-Guerrero. 1998. SOS induction by gamma-radiation in Escherichia coli strains defective in repair and/or recombination mechanisms. Mutagenesis 13: 637– 641.
26. Brooks, P. C.,, F. Movahedzadeh, and, E. O. Davis. 2001. Identification of some DNA damage-inducible genes of Mycobacterium tuberculosis: apparent lack of correlation with LexA binding. J. Bacteriol. 183: 4459– 4467.
27. Brotcorne-Lannoye, A., and, G. Maenhaut-Michel. 1986. Role of RecA protein in untargeted UV mutagenesis of bacteriophage lambda: evidence for the requirement for the dinB gene. Proc. Natl. Acad. Sci. USA 83: 3904– 3908.
28. Bunting,, K. A. and, L. H. Pearl. 2003. Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the betaclamp. EMBO J. 22: 5883– 5892.
29. Burckhardt, S. E.,, R. Woodgate,, R. H. Scheuermann and, H. Echols. 1988. UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proc. Natl. Acad. Sci. USA 85: 1811– 1815.
30. Burdett,, V., C. Baitinger,, M. Viswanathan,, S. T. Lovett and, P. Modrich. 2001. In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair. Proc. Natl. Acad. Sci. USA 98: 6765– 6770.
31. Butala,, M., D. Zgur-Bertok, and, S. J. Busby. 2009. The bacterial LexA transcriptional repressor. Cell Mol. Life Sci. 66: 82– 93.
32. Cai,, H., H. Yu,, K. McEntee,, T. A. Kunkel, and, M. F. Goodman. 1995. Purification and properties of wild-type and exonuclease-deficient DNA polymerase II from Escherichia coli. J. Biol. Chem. 270: 15327– 15335.
33. Camara,, J. E.,, A. M. Breier,, T. Brendler,, S. Austin,, N. R. Cozzarelli, and, E. Crooke. 2005. Hda inactivation of DnaA is the predominant mechanism preventing hyperinitiation of Escherichia coli DNA replication. EMBO Rep. 6: 736– 741.
34. Camas, F. M.,, J. Blázquez, and, J. F. Poyatos. 2006. Autogenous and nonautogenous control of response in a genetic network. Proc. Natl. Acad. Sci. USA 103: 12718– 12723.
35. Centore, R. C.,, M. C. Leeson, and, S. J. Sandler. 2009. UvrD303, a hyperhelicase mutant that antagonizes RecA-dependent SOS expression by a mechanism that depends on its C terminus. J. Bacteriol. 191: 1429– 1438.
36. Centore, R. C., and, S. J. Sandler. 2007. UvrD limits the number and intensities of RecA-green fluorescent protein structures in Escherichia coli K-12. J. Bacteriol. 189: 2915– 2920.
37. Chaudhury, A. M., and, G. R. Smith. 1985. Role of Escherichia coli RecBC enzyme in SOS induction. Mol. Gen. Genet. 201: 525– 528.
38. Chen,, Z., H. Yang, and, N. Pavletich. 2008. Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures. Nature 453: 489– 494.
39. Chiancone, E.,, P. Ceci,, A. Ilari,, F. Ribacchi, and, S. Stefanini. 2004. Iron and proteins for iron storage and detoxification. Biometals 17: 197– 202.
40. Cirz,, R. T.,, J. K. Chin,, D. R. Andes,, V. de Crécy-Lagard,, W. A. Craig, and, F. E. Romesberg. 2005. Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol. 3: e176.
41. Cordell, S. C.,, E. J. Robinson, and, J. Lowe. 2003. Crystal structure of the SOS cell division inhibitor SulA and in complex with FtsZ. Proc. Natl. Acad. Sci. USA 100: 7889– 7894.
42. Courcelle,, J., A. Khodursky,, B. Peter,, P. O. Brown, and, P. C. Hanawalt. 2001. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics 158: 41– 64.
43. Courcelle,, J.,, J. R. Donaldson,, K. H. Chow, and, C. T. Courcelle. 2003. DNA damage-induced replication fork regression and processing in Escherichia coli. Science 299: 1064– 1067.
44. Cox, M. M. 2007. Regulation of bacterial RecA protein function. Crit. Rev. Biochem. Mol. Biol. 42: 41– 63.
45. Cox, M. M., and, J. R. Battista. 2005. Deinococcus radiodurans— the consummate survivor. Nat. Rev. Microbiol. 3: 882– 892.
46. Cox,, M. M.,, M. F. Goodman,, K. N. Kreuzer,, D. J. Sherratt,, S. J. Sandler, and, K. J. Marians. 2000. The importance of repairing stalled replication forks. Nature 404: 37– 41.
47. Cromie, G. A., and, D. R. Leach. 2001. Recombinational repair of chromosomal DNA double-strand breaks generated by a restriction endonuclease. Mol. Microbiol. 41: 873– 883.
48. Curti, E.,, J. P. McDonald,, S. Mead, and, R. Woodgate. 2009. DNA polymerase switching: effects on spontaneous mutagenesis in Escherichia coli. Mol. Microbiol. 71: 315– 331.
49. Dajkovic,, A., A. Mukherjee, and, J. Lutkenhaus. 2008. Investigation of regulation of FtsZ assembly by SulA and development of a model for FtsZ polymerization. J. Bacteriol. 190: 2513– 2526.
50. Dalrymple,, B. P.,, K. Kongsuwan,, G. Wijffels,, N. E. Dixon, and, P. A. Jennings. 2001. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc. Natl. Acad. Sci. USA 98: 11627– 11632.
51. Darmon,, E.,, M. A. Lopez-Vernaza,, A. C. Helness,, A. Borking,, E. Wilson,, Z. Thacker,, L. Wardrope, and, D. R. Leach. 2007. SbcCD regulation and localization in Escherichia coli. J. Bacteriol. 189: 6686– 6694.
52. Davis,, E. O.,, B. Springer,, K. K. Gopaul,, K. G. Papavinasasundaram,, P. Sander, and, E. C. Böttger. 2002a. DNA damage induction of recA in Mycobacterium tuberculosis independently of RecA and LexA. Mol. Microbiol. 46: 791– 800.
53. Davis, E. O.,, E. M. Dullaghan, and, L. Rand. 2002b. Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. J. Bacteriol. 184: 3287– 3295.
54. De Anda,, J.,, A. R. Poteete, and, R. T. Sauer. 1983. P22 c 2 repressor. Domain structure and function. J. Biol. Chem. 258: 10536– 10542.
55. De Mot,, R., G. Schoofs, and, J. Vanderleyden. 1994. A putative regulatory gene downstream of recA is conserved in gram-negative and gram-positive bacteria. Nucleic Acids Res. 22: 1313– 1314.
56. Delmas, S., and, I. Matic. 2006. Interplay between replication and recombination in Escherichia coli: impact of the alternative DNA polymerases. Proc. Natl. Acad. Sci. USA 103: 4564– 4569.
57. Demple,, B., A. Johnson, and, D. Fung. 1986. Exonuclease III and endonuclease IV remove 3′ blocks from DNA synthesis primers in H2O2–damaged Escherichia coli. Proc. Natl. Acad. Sci. USA 83: 7731– 7735.
58. Dillingham, M. S., and, S. C. Kowalczykowski. 2008. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol. Mol. Biol. Rev. 72: 642– 671., Table of Contents.
59. Dos Vultos, T.,, O. Mestre,, T. Tonjum, and, B. Gicquel. 2009. DNA repair in Mycobacterium tuberculosis revisited. FEMS Microbiol. Rev. 33: 471– 487.
60. Drees,, J. C.,, S. L. Lusetti,, S. Chitteni-Pattu,, R. B. Inman, and, M. M. Cox. 2004a. A RecA filament capping mechanism for RecX protein. Mol. Cell 15: 789– 798.
61. Drees, J. C.,, S. L. Lusetti, and, M. M. Cox. 2004b. Inhibition of RecA protein by the Escherichia coli RecX protein: modulation by the RecA C terminus and filament functional state. J. Biol. Chem. 279: 52991– 52997.
62. Dri, A. M., and, P. L. Moreau. 1994. Control of the LexA regulon by pH: evidence for a reversible inactivation of the LexA repressor during the growth cycle of Escherichia coli. Mol. Microbiol. 12: 621– 629.
63. Drlica, K., and, X. Zhao. 1997. DNA gyrase, topoisomerase IV, and the 4–quinolones. Microbiol. Mol. Biol. Rev. 61: 377– 392.
64. Duzen, J. M.,, G. C. Walker, and, M. D. Sutton. 2004. Identification of specific amino acid residues in the E. Coli beta processivity clamp involved in interactions with DNA polymerase III, UmuD and UmuD’. DNA Repair (Amst.) 3: 301– 312.
65. Dwyer, D. J.,, M. A. Kohanski, and, J. J. Collins. 2009. Role of reactive oxygen species in antibiotic action and resistance. Curr. Opin. Microbiol. 12: 482– 489.
66. Earl,, A. M.,, M. M. Mohundro,, I. S. Mian, and, J. R. Battista. 2002. The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression. J. Bacteriol. 184: 6216– 6224.
67. Eguchi,, Y., T. Ogawa, and, H. Ogawa. 1988. Cleavage of bacteriophage phi 80 CI repressor by RecA protein. J. Mol. Biol. 202: 565– 573.
68. Eisenstark, A.,, M. J. Calcutt,, M. Becker-Hapak, and, A. Ivanova. 1996. Role of Escherichia coli rpoS and associated genes in defense against oxidative damage. Free Radic. Biol. Med. 21: 975– 993.
69. Erill,, I., S. Campoy, and, J. Barbé. 2007. Aeons of distress: an evolutionary perspective on the bacterial SOS response. FEMS Microbiol. Rev. 31: 637– 656.
70. Feinstein, S. I., and, K. B. Low. 1986. Hyper-recombining recipient strains in bacterial conjugation. Genetics 113: 13– 33.
71. Fernandez De Henestrosa,, A. R.,, T. Ogi,, S. Aoyagi,, D. Chafin,, J. J. Hayes,, H. Ohmori, and, R. Woodgate. 2000. Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. 35: 1560– 1572.
72. Finch, P. W.,, P. Chambers, and, P. T. Emmerson. 1985. Identification of the Escherichia coli recN gene product as a major SOS protein. J. Bacteriol. 164: 653– 658.
73. 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.
74. Frank,, E. G.,, N. Cheng,, C. C. Do,, M. E. Cerritelli,, I. Bruck,, M. F. Goodman,, E. H. Egelman,, R. Woodgate, and, A. C. Steven. 2000. Visualization of two binding sites for the Escherichia coli UmuD’(2)C complex (DNA pol V) on RecA-ssDNA filaments. J. Mol. Biol. 297: 585– 597.
75. Friedberg,, E. C.,, G. C. Walker,, W. Siede,, R. D. Wood,, R. A. Schultz, and, T. Ellenberger. 2005. DNA Repair and Mutagenesis. ASM Press, Washington, DC.
76. Friedman, N.,, S. Vardi,, M. Ronen,, U. Alon, and, J. Stavans. 2005. Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. PLoS Biol. 3: e238.
77. Fuchs, R. P.,, S. Fujii, and, J. Wagner. 2004. Properties and functions of Escherichia coli: Pol IV and Pol V. Adv. Protein Chem. 69: 229– 264.
78. Fujii, S., and, R. P. Fuchs. 2004. Defining the position of the switches between replicative and bypass DNA polymerases. EMBO J. 23: 4342– 4352.
79. Galhardo,, R. S.,, R. P. Rocha,, M. V. Marques, and, C. F. Menck. 2005. An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus. Nucleic Acids Res. 33: 2603– 2614.
80. Galkin,, V. E.,, X. Yu,, J. Bielnicki,, D. Ndjonka,, C. E. Bell, and, E. H. Egelman. 2009. Cleavage of bacteriophage lambda c I repressor involves the RecA C-terminal domain. J. Mol. Biol. 385: 779– 787.
81. Galletto, R., and, S. C. Kowalczykowski. 2007. RecA. Curr. Biol. 17:R 395– 397.
82. Gamulin,, V., H. Cetkovic, and, I. Ahel. 2004. Identification of a promoter motif regulating the major DNA damage response mechanism of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 238: 57– 63.
83. Gayda, R. C.,, L. T. Yamamoto, and, A. Markovitz. 1976. Secondsite mutations in capR ( lon) strains of Escherichia coli K-12 that prevent radiation sensitivity and allow bacteriophage lambda to lysogenize. J. Bacteriol. 127: 1208– 1216.
84. Gefter,, M. L.,, I. J. Molineux,, T. Kornberg, and, H. G. Khorana. 1972. Deoxyribonucleic acid synthesis in cell-free extracts. 3. Catalytic properties of deoxyribonucleic acid polymerase II. J. Biol. Chem. 247: 3321– 3326.
85. George,, J., M. Castellazzi, and, G. Buttin. 1975. Prophage induction and cell division in E. coli. III. Mutations sfiA and sfiB restore division in tif and lon strains and permit the expression of mutator properties of tif. Mol. Gen. Genet. 140: 309– 332.
86. Golub,, E., A. Bailone, and, R. Devoret. 1988. A gene encoding an SOS inhibitor is present in different conjugative plasmids. J. Bacteriol. 170: 4392– 4394.
87. Gon,, S., J. Camara,, H. Klungsøyr,, E. Crooke,, K. Skarstad, and, J. Beckwith. 2006. A novel regulatory mechanism couples deoxyribonucleotide synthesis and DNA replication in Escherichia coli. EMBO J. 25: 1137– 1147.
88. Goodman, M. F. 2002. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71: 17– 50.
89. Goosen, N., and, G. F. Moolenaar. 2008. Repair of UV damage in bacteria. DNA Repair (Amst.) 7: 353– 379.
90. Goranov, A. I.,, E. Kuester-Schoeck,, J. D. Wang, and, A. D. Grossman. 2006. Characterization of the global transcriptional responses to different types of DNA damage and disruption of replication in Bacillus subtilis. J. Bacteriol. 188: 5595– 5605.
91. Goranov,, A. I.,, L. Katz,, A. M. Breier,, C. B. Burge, and, A. D. Grossman. 2005. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc. Natl. Acad. Sci. USA 102: 12932– 12937.
92. Gudas, L. J., and, D. W. Mount. 1977. Identification of the recA ( tif) gene product of Escherichia coli. Proc. Natl. Acad. Sci. USA 74: 5280– 5284.
93. Guerin,, E., G. Cambray,, N. Sanchez-Alberola,, S. Campoy,, I. Erill,, S. Da Re,, B. Gonzalez-Zorn,, J. Barbé,, M. C. Ploy, and, D. Mazel. 2009. The SOS response controls integron recombination. Science 324: 1034.
94. Han,, E. S.,, D. L. Cooper,, N. S. Persky,, V. A. Sutera,, R. D. Whitaker,, M. L. Montello, and, S. T. Lovett. 2006. RecJ exonuclease: substrates, products and interaction with SSB. Nucleic Acids Res. 34: 1084– 1091.
95. Handa, N.,, A. Ichige,, K. Kusano, and, I. Kobayashi. 2000. Cellular responses to postsegregational killing by restriction-modification genes. J. Bacteriol. 182: 2218– 2229.
96. Harmon, F. G.,, W. M. Rehrauer, and, S. C. Kowalczykowski. 1996. Interaction of Escherichia coli RecA protein with LexA repressor. II. Inhibition of DNA strand exchange by the uncleavable LexA S119A repressor argues that recombination and SOS induction are competitive processes. J. Biol. Chem. 271: 23874– 23883.
97. Heltzel,, J. M.,, S. K. Scouten Ponticelli,, L. H. Sanders,, J. M. Duzen,, V. Cody,, J. Pace,, E. H. Snell, and, M. D. Sutton. 2009. Sliding clamp-DNA interactions are required for viability and contribute to DNA polymerase management in Escherichia coli. J. Mol. Biol. 387: 74– 91.
98. Hersh,, M. N.,, L. D. Morales,, K. J. Ross, and, S. M. Rosenberg. 2006. Single-strand-specific exonucleases prevent frameshift mutagenesis by suppressing SOS induction and the action of DinB/DNA polymerase IV in growing cells. J. Bacteriol. 188: 2336– 2342.
99. Higashitani, N.,, A. Higashitani,, A. Roth, and, K. Horiuchi. 1992. SOS induction in Escherichia coli by infection with mutant filamentous phage that are defective in initiation of complementarystrand DNA synthesis. J. Bacteriol. 174: 1612– 1618.
100. Hirano, T. 2005. SMC proteins and chromosome mechanics: from bacteria to humans. Philos. Trans. R. Soc. Lond. B 360: 507– 514.
101. Hishida,, T.,, Y. W. Han,, T. Shibata,, Y. Kubota,, Y. Ishino,, H. Iwasaki, and, H. Shinagawa. 2004. Role of the Escherichia coli RecQ DNA helicase in SOS signaling and genome stabilization at stalled replication forks. Genes Dev. 18: 1886– 1897.
102. Hobbs, M. D.,, A. Sakai, and, M. M. Cox. 2007. SSB protein limits RecOR binding onto single-stranded DNA. J. Biol. Chem. 282: 11058– 11067.
103. Hong,, J.,, J. M. Ahn,, B. C. Kim, and, M. B. Gu. 2009. Construction of a functional network for common DNA damage responses in Escherichia coli. Genomics 93: 514– 524.
104. Howard-Flanders,, P., E. Simson, and, L. Theriot. 1964. A locus that controls filament formation and sensitivity to radiation in Escherichia coli K-12. Genetics 49: 237– 246.
105. Hua,, Y., I. Narumi,, G. Gao,, B. Tian,, K. Satoh,, S. Kitayama, and, B. Shen. 2003. PprI: a general switch responsible for extreme radioresistance of Deinococcus radiodurans. Biochem. Biophys. Res. Commun. 306: 354– 360.
106. Huisman,, O., R. D’Ari, and, S. Gottesman. 1984. Cell-division control in Escherichia coli: specific induction of the SOS function SfiA protein is sufficient to block septation. Proc. Natl. Acad. Sci. USA 81: 4490– 4494.
107. Indiani, C.,, L. D. Langston,, O. Yurieva,, M. F. Goodman, and, M. O’Donnell. 2009. Translesion DNA polymerases remodel the replisome and alter the speed of the replicative helicase. Proc. Natl. Acad. Sci. USA 106: 6031– 6038.
108. Indiani, C.,, P. McInerney,, R. Georgescu,, M. F. Goodman, and, M. O’Donnell. 2005. A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously. Mol. Cell 19: 805– 815.
109. Iwasaki, H.,, A. Nakata,, G. C. Walker, and, H. Shinagawa. 1990. The Escherichia coli polB gene, which encodes DNA polymerase II, is regulated by the SOS system. J. Bacteriol. 172: 6268– 6273.
110. Janion, C. 2008. Inducible SOS response system of DNA repair and mutagenesis in Escherichia coli. Int. J. Biol. Sci. 4: 338– 344.
111. Jarosz,, D. F.,, P. J. Beuning,, S. E. Cohen, and, G. C. Walker. 2007. Y-family DNA polymerases in Escherichia coli. Trends Microbiol. 15: 70– 77.
112. Jarosz,, D. F.,, V. G. Godoy,, J. C. Delaney,, J. M. Essigmann, and, G. C. Walker. 2006. A single amino acid governs enhanced activity of DinB DNA polymerases on damaged templates. Nature 439: 225– 228.
113. Johnson, B. F., and, J. Greenberg. 1975. Mapping of sul, the suppressor of lon in Escherichia coli. J. Bacteriol. 122: 570– 574.
114. Joo,, C.,, S. A. McKinney,, M. Nakamura,, I. Rasnik,, S. Myong, and, T. Ha. 2006. Real-time observation of RecA filament dynamics with single monomer resolution. Cell 126: 515– 527.
115. Kaasch,, M., J. Kaasch, and, A. Quiñones. 1989. Expression of the dnaN and dnaQ genes of Escherichia coli is inducible by mitomycin C. Mol. Gen. Genet. 219: 187– 192.
116. Kantake,, N.,, M. V. Madiraju,, T. Sugiyama, and, S. C. Kowalczykowski. 2002. Escherichia coli RecO protein anneals ssDNA complexed with its cognate ssDNA-binding protein: A common step in genetic recombination. Proc. Natl. Acad. Sci. USA 99: 15327– 15332.
117. Katayama,, T., K. Fujimitsu, and, T. Ogawa. 2001. Multiple pathways regulating DnaA function in Escherichia coli: distinct roles for DnaA titration by the datA locus and the regulatory inactivation of DnaA. Biochimie 83: 13– 17.
118. Kato, T., and, Y. Shinoura. 1977. Isolation and characterization of mutants of Escherichia coli deficient in induction of mutations by ultraviolet light. Mol. Gen. Genet. 156: 121– 131.
119. Keller, K. L.,, T. L. Overbeck-Carrick, and, D. J. Beck. 2001. Survival and induction of SOS in Escherichia coli treated with cisplatin, UV-irradiation, or mitomycin C are dependent on the function of the RecBC and RecFOR pathways of homologous recombination. Mutat. Res. 486: 21– 29.
120. Kelley, W. L. 2006. Lex marks the spot: the virulent side of SOS and a closer look at the LexA regulon. Mol. Microbiol. 62: 1228– 1238.
121. Kenyon, C. J., and, G. C. Walker. 1980. DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. Proc. Natl. Acad. Sci. USA 77: 2819– 2823.
122. Khil, P. P., and, R. D. Camerini-Otero. 2002. Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44: 89– 105.
123. Kidane,, D., H. Sanchez,, J. C. Alonso, and, P. L. Graumann. 2004. Visualization of DNA double-strand break repair in live bacteria reveals dynamic recruitment of Bacillus subtilis RecF, RecO and RecN proteins to distinct sites on the nucleoids. Mol. Microbiol. 52: 1627– 1639.
124. Kim,, S. R.,, G. Maenhaut-Michel,, M. Yamada,, Y. Yamamoto,, K. Matsui,, T. Sofuni,, T. Nohmi, and, H. Ohmori. 1997. Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA. Proc. Natl. Acad. Sci. USA 94: 13792– 13797.
125. Kim,, S. R.,, K. Matsui,, M. Yamada,, P. Gruz, and, T. Nohmi. 2001. Roles of chromosomal and episomal dinB genes encoding DNA pol IV in targeted and untargeted mutagenesis in Escherichia coli. Mol. Genet. Genomics 266: 207– 215.
126. Kimmitt, P. T.,, C. R. Harwood, and, M. R. Barer. 2000. Toxin gene expression by shiga toxin-producing Escherichia coli: the role of antibiotics and the bacterial SOS response. Emerg. Infect. Dis. 6: 458– 465.
127. Kitagawa,, Y., E. Akaboshi,, H. Shinagawa,, T. Horii,, H. Ogawa, and, T. Kato. 1985. Structural analysis of the umu operon required for inducible mutagenesis in Escherichia coli. Proc. Natl. Acad. Sci. USA 82: 4336– 4340.
128. Kleinsteuber, S., and, A. Quiñones. 1995. Expression of the dnaB gene of Escherichia coli is inducible by replication-blocking DNA damage in a recA-independent manner. Mol. Gen. Genet. 248: 695– 702.
129. Kohanski,, M. A.,, D. J. Dwyer,, B. Hayete,, C. A. Lawrence, and, J. J. Collins. 2007. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130: 797– 810.
130. Kornberg, T., and, M. L. Gefter. 1971. Purification and DNA synthesis in cell-free extracts: properties of DNA polymerase II. Proc. Natl. Acad. Sci. USA 68: 761– 764.
131. Kosa,, J. L.,, Z. Z. Zdraveski,, S. Currier,, M. G. Marinus, and, J. M. Essigmann. 2004. RecN and RecG are required for Escherichia coli survival of Bleomycin-induced damage. Mutat. Res. 554: 149– 157.
132. Kowalczykowski, S. C.,, J. Clow,, R. Somani, and, A. Varghese. 1987. Effects of the Escherichia coli SSB protein on the binding of Escherichia coli RecA protein to single-stranded DNA. Demonstration of competitive binding and the lack of a specific protein-protein interaction. J. Mol. Biol. 193: 81– 95.
133. Kuban,, W., M. Banach-Orlowska,, M. Bialoskorska,, A. Lipowska,, R. M. Schaaper,, P. Jonczyk, and, I. J. Fijalkowska. 2005. Mutator phenotype resulting from DNA polymerase IV overproduction in Escherichia coli: preferential mutagenesis on the lagging strand. J. Bacteriol. 187: 6862– 6866.
134. Kuban,, W., M. Banach-Orlowska,, R. M. Schaaper,, P. Jonczyk, and, I. J. Fijalkowska. 2006. Role of DNA polymerase IV in Escherichia coli SOS mutator activity. J. Bacteriol. 188: 7977– 7980.
135. Layton, J. C., and, P. L. Foster. 2003. Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli. Mol. Microbiol. 50: 549– 561.
136. Lee,, B. I.,, K. H. Kim,, S. J. Park,, S. H. Eom,, H. K. Song, and, S. W. Suh. 2004. Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair. EMBO J. 23: 2029– 2038.
137. Leiros, I.,, J. Timmins,, D. R. Hall, and, S. McSweeney. 2005. Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans. EMBO J. 24: 906– 918.
138. Lestini, R., and, B. Michel. 2007. UvrD controls the access of recombination proteins to blocked replication forks. EMBO J. 26: 3804– 3814.
139. Lestini, R., and, B. Michel. 2008. UvrD and UvrD252 counteract RecQ, RecJ and RecFOR in the rep mutant. J. Bacteriol. 190: 5995– 6001.
140. Lewin, C. S., and, S. G. Amyes. 1991. The role of the SOS response in bacteria exposed to zidovudine or trimethoprim. J. Med. Microbiol. 34: 329– 332.
141. Lewis,, L. K.,, G. R. Harlow,, L. A. Gregg-Jolly, and, D. W. Mount. 1994. Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli. J. Mol. Biol. 241: 507– 523.
142. Lewis, L. K., and, D. W. Mount. 1992. Interaction of LexA repressor with the asymmetric dinG operator and complete nucleotide sequence of the gene. J. Bacteriol. 174: 5110– 5116.
143. Lin, L. L., and, J. W. Little. 1988. Isolation and characterization of noncleavable (Ind-) mutants of the LexA repressor of Escherichia coli K-12. J. Bacteriol. 170: 2163– 2173.
144. Ling, H.,, F. Boudsocq,, R. Woodgate, and, W. Yang. 2001. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107: 91– 102.
145. Little, J. W. 1984. Autodigestion of lexA and phage lambda repressors. Proc. Natl. Acad. Sci. USA 81: 1375– 1379.
146. Little,, J. W.,, S. H. Edmiston,, L. Z. Pacelli, and, D. W. Mount. 1980. Cleavage of the Escherichia coli lexA protein by the recA protease. Proc. Natl. Acad. Sci. USA 77: 3225– 3229.
147. Long, J. E.,, N. Renzette, and, S. J. Sandler. 2009. Suppression of constitutive SOS expression by recA4162 (I298V) and recA4164 (L126V) requires UvrD and RecX in Escherichia coli K-12. Mol. Microbiol. 73: 226– 239.
148. Lovett, S. T. 2006. Replication arrest-stimulated recombination: Dependence on the RecA paralog, RadA/Sms and translesion polymerase, DinB. DNA Repair (Amst.) 5: 1421– 1427.
149. Lovett, S. T., and, R. D. Kolodner. 1989. Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the recJ gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 86: 2627– 2631.
150. Lu,, H., G. Gao,, G. Xu,, L. Fan,, L. Yin,, B. Shen, and, Y. Hua. 2009. Deinococcus radiodurans PprI switches on DNA damage response and cellular survival networks after radiation damage. Mol. Cell Proteomics 8: 481– 494.
151. Luisi-DeLuca, C., and, R. Kolodner. 1994. Purification and characterization of the Escherichia coli RecO protein. Renaturation of complementary single-stranded DNA molecules catalyzed by the RecO protein. J. Mol. Biol. 236: 124– 138.
152. Luo,, Y.,, R. A. Pfuetzner,, S. Mosimann,, M. Paetzel,, E. A. Frey,, M. Cherney,, B. Kim,, J. W. Little, and, N. C. Strynadka. 2001. Crystal structure of LexA: a conformational switch for regulation of self-cleavage. Cell 106: 585– 594.
153. Lusetti,, S. L.,, J. C. Drees,, E. A. Stohl,, H. S. Seifert, and, M. M. Cox. 2004a. The DinI and RecX proteins are competing modulators of RecA function. J. Biol. Chem. 279: 55073– 55079.
154. Lusetti,, S. L.,, M. D. Hobbs,, E. A. Stohl,, S. Chitteni-Pattu,, R. B. Inman,, H. S. Seifert, and, M. M. Cox. 2006. The RecF protein antagonizes RecX function via direct interaction. Mol. Cell 21: 41– 50.
155. Lusetti,, S. L.,, O. N. Voloshin,, R. B. Inman,, R. D. Camerini-Otero, and, M. M. Cox. 2004b. The DinI protein stabilizes RecA protein filaments. J. Biol. Chem. 279: 30037– 30046.
156. Lutkenhaus, J. F. 1983. Coupling of DNA replication and cell division: sulB is an allele of ftsZ. J. Bacteriol. 154: 1339– 1346.
157. Magner,, D. B.,, M. D. Blankschien,, J. A. Lee,, J. M. Pennington,, J. R. Lupski, and, S. M. Rosenberg. 2007. RecQ promotes toxic recombination in cells lacking recombination intermediateremoval proteins. Mol. Cell 26: 273– 286.
158. Maiques,, E., C. Ubeda,, S. Campoy,, N. Salvador,, I. Lasa,, R. P. Novick,, J. Barbé, and, J. R. Penadés. 2006. beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus. J. Bacteriol. 188: 2726– 2729.
159. Maor-Shoshani, A., and, Z. Livneh. 2002. Analysis of the stimulation of DNA polymerase V of Escherichia coli by processivity proteins. Biochemistry 41: 14438– 14446.
160. Maor-Shoshani, A.,, N. B. Reuven,, G. Tomer, and, Z. Livneh. 2000. Highly mutagenic replication by DNA polymerase V (UmuC) provides a mechanistic basis for SOS untargeted mutagenesis. Proc. Natl. Acad. Sci. USA 97: 565– 570.
161. Maul,, R. W.,, S. K. Ponticelli,, J. M. Duzen, and, M. D. Sutton. 2007. Differential binding of Escherichia coli DNA polymerases to the beta-sliding clamp. Mol. Microbiol. 65: 811– 827.
162. McCool,, J. D.,, E. Long,, J. F. Petrosino,, H. A. Sandler,, S. M. Rosenberg, and, S. J. Sandler. 2004. Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence. Mol. Microbiol. 53: 1343– 1357.
163. McEntee, K. 1977. Protein X is the product of the recA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 74: 5275– 5279.
164. McGrew, D. A., and, K. L. Knight. 2003. Molecular design and functional organization of the RecA protein. Crit. Rev. Biochem. Mol. Biol. 38: 385– 432.
165. 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.
166. 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.
167. Meddows,, T. R.,, A. P. Savory,, J. I. Grove,, T. Moore, and, R. G. Lloyd. 2005. RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks. Mol. Microbiol. 57: 97– 110.
168. Merrikh,, H.,, A. E. Ferrazzoli,, A. Bougdour,, A. Olivier-Mason, and, S. T. Lovett. 2009. A DNA damage response in Escherichia coli involving the alternative sigma factor, RpoS. Proc. Natl. Acad. Sci. USA 106: 611– 616.
169. Messer, W., and, C. Weigel. 1997. DnaA initiator—also a transcription factor. Mol. Microbiol. 24: 1– 6.
170. Miller,, C.,, L. E. Thomsen,, C. Gaggero,, R. Mosseri,, H. Ingmer, and, S. N. Cohen. 2004. SOS response induction by beta-lactams and bacterial defense against antibiotic lethality. Science 305: 1629– 1631.
171. Miller,, M. C.,, J. B. Resnick,, B. T. Smith, and, C. M. Lovett. 1996. The bacillus subtilis dinR gene codes for the analogue of Escherichia coli LexA. Purification and characterization of the DinR protein. J. Biol. Chem. 271: 33502– 33508.
172. Mizusawa, S., and, S. Gottesman. 1983. Protein degradation in Escherichia coli: the lon gene controls the stability of sulA protein. Proc. Natl. Acad. Sci. USA 80: 358– 362.
173. Moolenaar, G. F.,, S. van Rossum-Fikkert,, M. van Kesteren, and, N. Goosen. 2002. Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair. Proc. Natl. Acad. Sci. USA 99: 1467– 1472.
174. Moreau, P. L. 1988. Overproduction of single-stranded-DNA-binding protein specifically inhibits recombination of UV irradiated bacteriophage DNA in Escherichia coli. J. Bacteriol. 170: 2493– 2500.
175. Morimatsu, K., and, S. C. Kowalczykowski. 2003. RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair. Mol. Cell 11: 1337– 1347.
176. Moser,, M. J.,, W. R. Holley,, A. Chatterjee, and, I. S. Mian. 1997. The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. Nucleic Acids Res. 25: 5110– 5118.
177. Mukherjee,, A., C. Cao, and, J. Lutkenhaus. 1998. Inhibition of FtsZ polymerization by SulA, an inhibitor of septation in Escherichia coli. Proc. Natl. Acad. Sci. USA 95: 2885– 2890.
178. Mulvey, M. R., and, P. C. Loewen. 1989. Nucleotide sequence of katF of Escherichia coli suggests KatF protein is a novel sigma transcription factor. Nucleic Acids Res. 17: 9979– 9991.
179. Nagashima,, K., Y. Kubota,, T. Shibata,, C. Sakaguchi,, H. Shinagawa, and, T. Hishida. 2006. Degradation of Escherichia coli RecN aggregates by ClpXP protease and its implications for DNA damage tolerance. J. Biol. Chem. 281: 30941– 30946.
180. Napolitano,, R., R. Janel-Bintz,, J. Wagner, and, R. P. Fuchs. 2000. All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. EMBO J. 19: 6259– 6265.
181. Narumi,, I., K. Satoh,, M. Kikuchi,, T. Funayama,, T. Yanagisawa,, Y. Kobayashi,, H. Watanabe, and, K. Yamamoto. 2001. The LexA protein from Deinococcus radiodurans is not involved in RecA induction following gamma irradiation. J. Bacteriol. 183: 6951– 6956.
182. Narumi,, I., K. Satoh,, S. Cui,, T. Funayama,, S. Kitayama, and, H. Watanabe. 2004. PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation. Mol. Microbiol. 54: 278– 285.
183. Neher,, S. B.,, J. Villén,, E. C. Oakes,, C. E. Bakalarski,, R. T. Sauer,, S. P. Gygi, and, T. A. Baker. 2006. Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon. Mol. Cell 22: 193– 204.
184. Newmark,, K. G.,, E. K. O’Reilly,, J. R. Pohlhaus, and, K. N. Kreuzer. 2005. Genetic analysis of the requirements for SOS induction by nalidixic acid in Escherichia coli. Gene 356: 69– 76.
185. Nohmi, T. 2006. Environmental stress and lesion-bypass DNA polymerases. Annu. Rev. Microbiol. 60: 231– 253.
186. Nohmi,, T.,, J. R. Battista,, L. A. Dodson, and, G. C. Walker. 1988. RecA-mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. Proc. Natl. Acad. Sci. USA 85: 1816– 1820.
187. Noirot-Gros,, M. F.,, M. Velten,, M. Yoshimura,, S. McGovern,, T. Morimoto,, S. D. Ehrlich,, N. Ogasawara,, P. Polard, and, P. Noirot. 2006. Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 103: 2368– 2373.
188. Novick, R. P. 2003. Mobile genetic elements and bacterial toxinoses: the superantigen-encoding pathogenicity islands of Staphylococcus aureus. Plasmid 49: 93– 105.
189. Ohmori,, H.,, E. C. Friedberg,, R. P. Fuchs,, M. F. Goodman,, F. Hanaoka,, D. Hinkle,, T. A. Kunkel,, C. W. Lawrence,, Z. Livneh,, T. Nohmi,, L. Prakash,, S. Prakash,, T. Todo,, G. C. Walker,, Z. Wang, and, R. Woodgate. 2001. The Y-family of DNA polymerases. Mol. Cell 8: 7– 8.
190. Onnis-Hayden,, A., H. Weng,, M. He,, S. Hansen,, V. Ilyin,, K. Lewis, and, A. Z. Guc. 2009. Prokaryotic real-time gene expression profiling for toxicity assessment. Environ. Sci. Technol. 43: 4574– 4581.
191. Opperman,, T., S. Murli,, B. T. Smith, and, G. C. Walker. 1999. A model for a umuDC-dependent prokaryotic DNA damage checkpoint. Proc. Natl. Acad. Sci. USA 96: 9218– 9223.
192. O’Reilly, E. K., and, K. N. Kreuzer. 2004. Isolation of SOS constitutive mutants of Escherichia coli. J. Bacteriol. 186: 7149– 7160.
193. Ossanna, N., and, D. W. Mount. 1989. Mutations in uvrD induce the SOS response in Escherichia coli. J. Bacteriol. 171: 303– 307.
194. Pagès, V., and, R. P. Fuchs. 2002. How DNA lesions are turned into mutations within cells? Oncogene 21: 8957– 8966.
195. Pagès,, V., N. Koffel-Schwartz, and, R. P. Fuchs. 2003. recX, a new SOS gene that is co-transcribed with the recA gene in Escherichia coli. DNA Repair (Amst.) 2: 273– 284.
196. Papavinasasundaram,, K. G.,, F. Movahedzadeh,, J. T. Keer,, N. G. Stoker,, M. J. Colston, and, E. O. Davis. 1997. Mycobacterial recA is cotranscribed with a potential regulatory gene called recX. Mol. Microbiol. 24: 141– 153.
197. Pennington, J. M., and, S. M. Rosenberg. 2007. Spontaneous DNA breakage in single living Escherichia coli cells. Nat. Genet. 39: 797– 802.
198. Persky, N. S., and, S. T. Lovett. 2008. Mechanisms of recombination: lessons from E. coli. Crit. Rev. Biochem. Mol. Biol. 43: 347– 370.
199. Picksley, S. M.,, P. V. Attfield, and, R. G. Lloyd. 1984. Repair of DNA double-strand breaks in Escherichia coli K12 requires a functional recN product. Mol. Gen. Genet. 195: 267– 274.
200. Ponder, R. G.,, N. C. Fonville, and, S. M. Rosenberg. 2005. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol. Cell 19: 791– 804.
201. Qiu, Z., and, M. F. Goodman. 1997. The Escherichia coli polB locus is identical to dinA, the structural gene for DNA polymerase II. Characterization of Pol II purified from a polB mutant. J. Biol. Chem. 272: 8611– 8617.
202. Quillardet, P.,, M. A. Rouffaud, and, P. Bouige. 2003. DNA array analysis of gene expression in response to UV irradiation in Escherichia coli. Res. Microbiol. 154: 559– 572.
203. Quiñones, A.,, W. R. Jüterbock, and, W. Messer. 1991. Expression of the dnaA gene of Escherichia coli is inducible by DNA damage. Mol. Gen. Genet. 227: 9– 16.
204. Quinones,, M.,, H. H. Kimsey, and, M. K. Waldor. 2005. LexA cleavage is required for CTX prophage induction. Mol. Cell 17: 291– 300.
205. Radman, M. 1975. SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci. 5A: 355– 367.
206. Ragone, S.,, J. D. Maman,, N. Furnham, and, L. Pellegrini. 2008. Structural basis for inhibition of homologous recombination by the RecX protein. EMBO J. 27: 2259– 2269.
207. Rand,, L., J. Hinds,, B. Springer,, P. Sander,, R. S. Buxton, and, E. O. Davis. 2003. The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA. Mol. Microbiol. 50: 1031– 1042.
208. Rangarajan,, S., G. Gudmundsson,, Z. Qiu,, P. L. Foster, and, M. F. Goodman. 1997. Escherichia coli DNA polymerase II catalyzes chromosomal and episomal DNA synthesis in vivo. Proc. Natl. Acad. Sci. USA 94: 946– 951.
209. Rangarajan, S., R. Woodgate, and, M. F. Goodman. 1999. A phenotype for enigmatic DNA polymerase II: a pivotal role for pol II in replication restart in UV-irradiated Escherichia coli. Proc. Natl. Acad. Sci. USA 96: 9224– 9229.
210. Rangarajan, S., R. Woodgate, and, M. F. Goodman. 2002. Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins. Mol. Microbiol. 43: 617– 628.
211. Register, J. C., and, J. Griffith. 1985. The direction of RecA protein assembly onto single strand DNA is the same as the direction of strand assimilation during strand exchange. J. Biol. Chem. 260: 12308– 12312.
212. Rehrauer,, W. M.,, P. E. Lavery,, E. L. Palmer,, R. N. Singh, and, S. C. Kowalczykowski. 1996. Interaction of Escherichia coli RecA protein with LexA repressor. I. LexA repressor cleavage is competitive with binding of a secondary DNA molecule. J. Biol. Chem. 271: 23865– 23873.
213. Ren,, B., X. Duan, and, H. Ding. 2009. Redox control of the DNA damage-inducible protein DinG helicase activity via its ironsulfur cluster. J. Biol. Chem. 284: 4829– 4835.
214. Renzette, N., N. Gumlaw, and, S. J. Sandler. 2007. DinI and RecX modulate RecA-DNA structures in Escherichia coli K-12. Mol. Microbiol. 63: 103– 115.
215. Reuven,, N. B.,, G. Arad,, A. Maor-Shoshani, and, Z. Livneh. 1999. The mutagenesis protein UmuC is a DNA polymerase activated by UmuD’, RecA, and SSB and is specialized for translesion replication. J. Biol. Chem. 274: 31763– 31766.
216. Roberts, J. W.,, C. W. Roberts, and, N. L. Craig. 1978. Escherichia coli recA gene product inactivates phage lambda repressor. Proc. Natl. Acad. Sci. USA 75: 4714– 4718.
217. Ronen, M.,, R. Rosenberg,, B. I. Shraiman, and, U. Alon. 2002. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. USA 99: 10555– 10560.
218. SaiSree,, L., M. Reddy, and, J. Gowrishankar. 2000. lon incompatibility associated with mutations causing SOS induction: null uvrD alleles induce an SOS response in Escherichia coli. J. Bacteriol. 182: 3151– 3157.
219. Sakai, A., and, M. M. Cox. 2009. RecFOR and RecOR as distinct RecA loading pathways. J. Biol. Chem. 284: 3264– 3272.
220. Salles, B., and, C. Paoletti. 1983. Control of UV induction of recA protein. Proc. Natl. Acad. Sci. USA 80: 65– 69.
221. Sancar, A. 1996. DNA excision repair. Annu. Rev. Biochem. 65: 43– 81.
222. Sanders,, L. H.,, A. Rockel,, H. Lu,, D. J. Wozniak, and, M. D. Sutton. 2006. Role of Pseudomonas aeruginosa dinB-encoded DNA polymerase IV in mutagenesis. J. Bacteriol. 188: 8573– 8585.
223. Sandler, S. J., and, A. J. Clark. 1994. RecOR suppression of recF mutant phenotypes in Escherichia coli K-12. J. Bacteriol. 176: 3661– 3672.
224. Sano, Y. 1993. Role of the recA-related gene adjacent to the recA gene in Pseudomonas aeruginosa. J. Bacteriol. 175: 2451– 2454.
225. Sargentini, N. J., and, K. C. Smith. 1986. Quantitation of the involvement of the recA, recB, recC, recF, recJ, recN, lexA, radA, radB, uvrD, and umuC genes in the repair of X-ray-induced DNA double-strand breaks in Escherichia coli. Radiat. Res. 107: 58– 72.
226. Sassanfar, M., and, J. W. Roberts. 1990. Nature of the SOS-inducing signal in Escherichia coli. The involvement of DNA replication. J. Mol. Biol. 212: 79– 96.
227. Satoh, K.,, H. Ohba,, H. Sghaier, and, I. Narumi. 2006. Downregulation of radioresistance by LexA2 in Deinococcus radiodurans. Microbiology 152: 3217– 3226.
228. Schlacher,, K.,, M. M. Cox,, R. Woodgate, and, M. F. Goodman. 2006. RecA acts in trans to allow replication of damaged DNA by DNA polymerase V. Nature 442: 883– 887.
229. Schuldiner,, S., V. Agmon,, J. Brandsma,, A. Cohen,, E. Friedman, and, E. Padan. 1986. Induction of SOS functions by alkaline intracellular pH in Escherichia coli. J. Bacteriol. 168: 936– 939.
230. Selva,, L., D. Viana,, G. Regev-Yochay,, K. Trzcinski,, J. M. Corpa,, I. Lasa,, R. P. Novick, and, J. R. Penadés. 2009. Killing niche competitors by remote-control bacteriophage induction. Proc. Natl. Acad. Sci. USA 106: 1234– 1238.
231. Sheng, D.,, J. Jao,, M. Li,, P. Xu, and, J. Zhang. 2009. RecX is involved in the switch between DNA damage response and normal metabolism in D. Radiodurans. J. Biochem. 146: 337– 342.
232. Sheng,, D., R. Liu,, Z. Xu,, P. Singh,, B. Shen, and, Y. Hua. 2005. Dual negative regulatory mechanisms of RecX on RecA functions in radiation resistance, DNA recombination and consequent genome instability in Deinococcus radiodurans. DNA Repair (Amst.) 4: 671– 678.
233. Sheng, D.,, Z. Zheng,, B. Tian,, B. Shen, and, Y. Hua. 2004. LexA analog (dra0074) is a regulatory protein that is irrelevant to recA induction. J. Biochem. 136: 787– 793.
234. Shimoni, Y.,, S. Altuvia,, H. Margalit, and, O. Biham. 2009. Stochastic analysis of the SOS response in Escherichia coli. PLoS ONE 4: e5363.
235. Shinagawa, H.,, H. Iwasaki,, Y. Ishino, and, A. Nakata. 1991. SOSinducible DNA polymerase II of E coli is homologous to replicative DNA polymerase of eukaryotes. Biochimie 73: 433– 435.
236. Shinagawa, H.,, H. Iwasaki,, T. Kato, and, A. Nakata. 1988. RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis. Proc. Natl. Acad. Sci. USA 85: 1806– 1810.
237. Simmons,, L. A.,, J. J. Foti,, S. E. Cohen, and, G. C. Walker. 2008, July 25. Chapter 5.4.3, The SOS regulatory network. In R. Curtiss III et al. (ed.), EcoSal— Escherichia coli and Salmonella: cellular and molecular biology. ASM Press, Washington, DC. http://www.ecosal.org.
238. Simmons,, L. A.,, A. I. Goranov,, H. Kobayashi,, B. W. Davies,, D. S. Yuan,, A. D. Grossman, and, G. C. Walker. 2009. Comparison of responses to double-strand breaks between Escherichia coli and Bacillus subtilis reveals different requirements for SOS induction. J. Bacteriol. 191: 1152– 1161.
239. Slilaty, S. N., and, J. W. Little. 1987. Lysine-156 and serine-119 are required for LexA repressor cleavage: a possible mechanism. Proc. Natl. Acad. Sci. USA 84: 3987– 3991.
240. Slupska,, M. M.,, J. H. Chiang,, W. M. Luther,, J. L. Stewart,, L. Amii,, A. Conrad, and, J. H. Miller. 2000. Genes involved in the determination of the rate of inversions at short inverted repeats. Genes Cells 5: 425– 437.
241. Sousa,, F. J.,, L. M. Lima,, A. B. Pacheco,, C. L. Oliveira,, I. Torriani,, D. F. Almeida,, D. Foguel,, J. L. Silva, and, R. Mohana-Borges. 2006. Tetramerization of the LexA repressor in solution: implications for gene regulation of the E. Coli SOS system at acidic pH. J. Mol. Biol. 359: 1059– 1074.
242. Spies,, M., I. Amitani,, R. J. Baskin, and, S. C. Kowalczykowski. 2007. RecBCD enzyme switches lead motor subunits in response to chi recognition. Cell 131: 694– 705.
243. Spies,, M.,, P. R. Bianco,, M. S. Dillingham,, N. Handa,, R. J. Baskin, and, S. C. Kowalczykowski. 2003. A molecular throttle: the recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell 114: 647– 654.
244. Spies, M., and, S. C. Kowalczykowski. 2006. The RecA binding locus of RecBCD is a general domain for recruitment of DNA strand exchange proteins. Mol. Cell 21: 573– 580.
245. Stohl,, E. A.,, J. P. Brockman,, K. L. Burkle,, K. Morimatsu,, S. C. Kowalczykowski, and, H. S. Seifert. 2003. Escherichia coli RecX inhibits RecA recombinase and coprotease activities in vitro and in vivo. J. Biol. Chem. 278: 2278– 2285.
246. Stohl, E. A., and, H. S. Seifert. 2001. The recX gene potentiates homologous recombination in Neisseria gonorrhoeae. Mol. Microbiol. 40: 1301– 1310.
247. Sugino,, A.,, C. L. Peebles,, K. N. Kreuzer, and, N. R. Cozzarelli. 1977. Mechanism of action of nalidixic acid: purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme. Proc. Natl. Acad. Sci. USA 74: 4767– 4771.
248. Sukchawalit, R.,, P. Vattanaviboon,, S. Utamapongchai,, G. Vaughn, and, S. Mongkolsuk. 2001. Characterization of Xanthomonas oryzae pv. oryzae recX, a gene that is required for high-level expression of recA. FEMS Microbiol. Lett. 205: 83– 89.
249. Sutton, M. D., and, G. C. Walker. 2001. umuDC-mediated cold sensitivity is a manifestation of functions of the UmuD(2)C complex involved in a DNA damage checkpoint control. J. Bacteriol. 183: 1215– 1224.
250. Tang,, M., P. Pham,, X. Shen,, J. S. Taylor,, M. O’Donnell,, R. Woodgate, and, M. F. Goodman. 2000. Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature 404: 1014– 1018.
251. Tang,, M., X. Shen,, E. G. Frank,, M. O’Donnell,, R. Woodgate, and, M. F. Goodman. 1999. UmuD’(2)C is an error-prone DNA polymerase, Escherichia coli pol V. Proc. Natl. Acad. Sci. USA 96: 8919– 8924.
252. Tessman, I., and, M. A. Kennedy. 1994. DNA polymerase II of Escherichia coli in the bypass of abasic sites in vivo. Genetics 136: 439– 448.
253. Ubeda,, C., E. Maiques,, E. Knecht,, I. Lasa,, R. P. Novick, and, J. R. Penadés. 2005. Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci. Mol. Microbiol. 56: 836– 844.
254. Uchida,, K., A. Furukohri,, Y. Shinozaki,, T. Mori,, D. Ogawara,, S. Kanaya,, T. Nohmi,, H. Maki, and, M. Akiyama. 2008. Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal. Mol. Microbiol. 70: 608– 622.
255. Umezu,, K.,, N. W. Chi, and, R. D. Kolodner. 1993. Biochemical interaction of the Escherichia coli RecF, RecO, and RecR proteins with RecA protein and single-stranded DNA binding protein. Proc. Natl. Acad. Sci. USA 90: 3875– 3879.
256. Umezu, K., and, R. D. Kolodner. 1994. Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein. J. Biol. Chem. 269: 30005– 30013.
257. Umezu,, K., K. Nakayama, and, H. Nakayama. 1990. Escherichia coli RecQ protein is a DNA helicase. Proc. Natl. Acad. Sci. USA 87: 5363– 5367.
258. Van Dyk, T. K.,, E. J. DeRose, and, G. E. Gonye. 2001. LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains. J. Bacteriol. 183: 5496– 5505.
259. Van Houten,, B.,, J. A. Eisen, and, P. C. Hanawalt. 2002. A cut above: discovery of an alternative excision repair pathway in bacteria. Proc. Natl. Acad. Sci. USA 99: 2581– 2583.
260. VanLoock,, M. S.,, X. Yu,, S. Yang,, V. E. Galkin,, H. Huang,, S. S. Rajan,, W. F. Anderson,, E. A. Stohl,, H. S. Seifert, and, E. H. Egelman. 2003. Complexes of RecA with LexA and RecX differentiate between active and inactive RecA nucleoprotein filaments. J. Mol. Biol. 333: 345– 354.
261. Veaute,, X., S. Delmas,, M. Selva,, J. Jeusset,, E. Le Cam,, I. Matic,, F. Fabre, and, M. A. Petit. 2005. UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli. EMBO J. 24: 180– 189.
262. Venkatesh,, R., N. Ganesh,, N. Guhan,, M. S. Reddy,, T. Chandrasekhar, and, K. Muniyappa. 2002. RecX protein abrogates ATP hydrolysis and strand exchange promoted by RecA: insights into negative regulation of homologous recombination. Proc. Natl. Acad. Sci. USA 99: 12091– 12096.
263. Vierling, S.,, T. Weber,, W. Wohlleben, and, G. Muth. 2000. Transcriptional and mutational analyses of the Streptomyces lividans recX gene and its interference with RecA activity. J. Bacteriol. 182: 4005– 4011.
264. Viguera,, E., M. Petranovic,, D. Zahradka,, K. Germain,, D. S. Ehrlich, and, B. Michel. 2003. Lethality of bypass polymerases in Escherichia coli cells with a defective clamp loader complex of DNA polymerase III. Mol. Microbiol. 50: 193– 204.
265. Volkert, M. R., and, M. A. Hartke. 1984. Suppression of Escherichia coli recF mutations by recA-linked srfA mutations. J. Bacteriol. 157: 498– 506.
266. Voloshin,, O. N.,, B. E. Ramirez,, A. Bax, and, R. D. Camerini-Otero. 2001. A model for the abrogation of the SOS response by an SOS protein: a negatively charged helix in DinI mimics DNA in its interaction with RecA. Genes Dev. 15: 415– 427.
267. Voloshin, O. N.,, F. Vanevski,, P. P. Khil, and, R. D. Camerini-Otero. 2003. Characterization of the DNA damage-inducible helicase DinG from Escherichia coli. J. Biol. Chem. 278: 28284– 28293.
268. Voloshin, O. N., and, R. D. Camerini-Otero. 2007. The DinG protein from Escherichia coli is a structure-specific helicase. J. Biol. Chem. 282: 18437– 18447.
269. Wade,, J. T.,, N. B. Reppas,, G. M. Church, and, K. Struhl. 2005. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 19: 2619– 2630.
270. Wagner,, J., P. Gruz,, S. R. Kim,, M. Yamada,, K. Matsui,, R. P. Fuchs, and, T. Nohmi. 1999. The dinB gene encodes a novel E. Coli DNA polymerase, DNA pol IV, involved in mutagenesis. Mol. Cell 4: 281– 286.
271. Wagner, J., and, T. Nohmi. 2000. Escherichia coli DNA polymerase IV mutator activity: genetic requirements and mutational specificity. J. Bacteriol. 182: 4587– 4595.
272. Wagner,, P. L.,, J. Livny,, M. N. Neely,, D. W. Acheson,, D. I. Friedman, and, M. K. Waldor. 2002. Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli. Mol. Microbiol. 44: 957– 970.
273. Waldor, M. K., and, D. I. Friedman. 2005. Phage regulatory circuits and virulence gene expression. Curr. Opin. Microbiol. 8: 459– 465.
274. Walker, G. C. 1984. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol. Rev. 48: 60– 93.
275. Wang,, L., G. Xu,, H. Chen,, Y. Zhao,, N. Xu,, B. Tian, and, Y. Hua. 2008. DrRRA: a novel response regulator essential for the extreme radioresistance of Deinococcus radiodurans. Mol. Microbiol. 67: 1211– 1222.
276. Webb, B. L.,, M. M. Cox, and, R. B. Inman. 1997. Recombinational DNA repair: the RecF and RecR proteins limit the extension of RecA filaments beyond single-strand DNA gaps. Cell 91: 347– 356.
277. West, S. C. 1997. Processing of recombination intermediates by the RuvABC proteins. Annu. Rev. Genet. 31: 213– 244.
278. Whitby, M. C., and, R. G. Lloyd. 1995. Altered SOS induction associated with mutations in recF, recO and recR. Mol. Gen. Genet. 246: 174– 179.
279. White, M. F. 2009. Structure, function and evolution of the XPD family of iron-sulfur-containing 5′—.3′ DNA helicases. Biochem. Soc. Trans. 37: 547– 551.
280. Winterling,, K. W.,, A. S. Levine,, R. E. Yasbin, and, R. Woodgate. 1997. Characterization of DinR, the Bacillus subtilis SOS repressor. J. Bacteriol. 179: 1698– 1703.
281. Winterling,, K. W.,, D. Chafin,, J. J. Hayes,, J. Sun,, A. S. Levine,, R. E. Yasbin, and, R. Woodgate. 1998. The Bacillus subtilis DinR binding site: redefinition of the consensus sequence. J. Bacteriol. 180: 2201– 2211.
282. Witkin, E. M. 1967. The radiation sensitivity of Escherichia coli B: a hypothesis relating filament formation and prophage induction. Proc. Natl. Acad. Sci. USA 57: 1275– 1279.
283. Witkin, E. M. 1976. Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli. Bacteriol. Rev. 40: 869– 907.
284. Woodgate, R., and, D. G. Ennis. 1991. Levels of chromosomally encoded Umu proteins and requirements for in vivo UmuD cleavage. Mol. Gen. Genet. 229: 10– 16.
285. Yang,, C. Y.,, K. H. Chin,, M. T. Yang,, A. H. Wang, and, S. H. Chou. 2009. Crystal structure of RecX: a potent regulatory protein of RecA from Xanthomonas campestris. Proteins 74: 530– 537.
286. Yang,, H., E. Wolff,, M. Kim,, A. Diep, and, J. H. Miller. 2004. Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach. Mol. Microbiol. 53: 283– 295.
287. Yang, W., and, R. Woodgate. 2007. What a difference a decade makes: insights into translesion DNA synthesis. Proc. Natl. Acad. Sci. USA 104: 15591– 15598.
288. Yasuda, T.,, K. Morimatsu,, T. Horii,, T. Nagata, and, H. Ohmori. 1998. Inhibition of Escherichia coli RecA coprotease activities by DinI. EMBO J. 17: 3207– 3216.
289. Yasuda,, T., K. Morimatsu,, R. Kato,, J. Usukura,, M.