Answering the call: Coping with DNA damage at the most inopportune time

Journal of Biomedicine and Biotechnology

Volumn 2002, Issue 2, 2002, Pages 66-74

  Crowley, David J ^a   Courcelle, Justin ^b  

^a MERCER UNIVERSITY   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT;

BIOCHEMISTRY; CELL DEATH; CHROMOSOME REPLICATION; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; ESCHERICHIA COLI; GENOMICS; LETHALITY; MUTAGENESIS; NONHUMAN; REVIEW; UPREGULATION;

ESCHERICHIA COLI;

EID: 0346191761     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/S1110724302202016     Document Type: Review

References (84)

1. Radman M. Phenomenology of an inducible mutagenic DNA repair pathway in Escherichia coli: SOS repair hypothesis. In: Prakash L, Sherman F, Miller M, Lawrence C, Tabor, HW, eds. Molecular and Environmental Aspects of Mutagenesis. Springfield, Ill: Charles C Thomas; 1999:128-142.
2. Friedberg EC, Walker GC, Siede W. DNA Repair and Mutagenesis. Washington, D.C.: ASM Press; 1995.
3. Koch WH, Woodgate R. The SOS response. In: Nickoloff JA, Hoekstra MF, eds. DNA Damage and Repair: DNA Repair in Prokaryotes and Lower Eukaryotes. Totowa, NJ: Humana Press; 1998:107-134.
4. Sassanfar M, Roberts JW. Nature of the SOS-inducing signal in Escherichia coli. The involvement of DNA replication. J Mol Biol. 1990;212(1):79-96.
5. Brent R, Ptashne M. Mechanism of action of the lexA gene product. Proc Natl Acad Sci USA. 1981; 78(7):4204-4208.
6. Little JW, Mount DW, Yanisch-Perron CR. Purified lexA protein is a repressor of the recA and lexA genes. Proc Natl Acad Sci USA. 1981;78(7):4199-4203.
7. Kenyon CJ, Walker GC. DNA-damaging agents stimulate gene expression at specific loci in Escherichia colt. Proc Natl Acad Sci USA. 1980;77(5):2819-2823.
8. Walker GC. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol Rev. 1984;48(1):60-93.
9. Bagg A, Kenyon CJ, Walker GC. Inducibility of a gene product required for UV and chemical mutagenesis in Escherichia coli. Proc Natl Acad Sci USA. 1981;78(9):5749-5753.
10. Bonner CA, Hays S, McEntee K, Goodman MF. DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli. Proc Natl Acad Sci USA. 1990;87(19):7663-7667.
11. Fogliano M, Schendel PF. Evidence for the inducibility of the uvrB operon. Nature. 1981;289(5794):196-198.
12. Huisman O, D'Ari R. An inducible DNA replication-cell division coupling mechanism in E. coli. Nature. 1981;290(5809):797-799.
13. Iwasaki H, Nakata A, Walker GC, Shinagawa H. The Escherichia coli polB gene, which encodes DNA polymerase II, is regulated by the SOS system. J Bacteriol 1990;172(11):6268-6273.
14. Kenyon CJ, Walker GC. Expression of the E. coli uvrA gene is inducible. Nature. 1981;289(5800):808-810.
15. Lloyd RG, Picksley SM, Prescott C. Inducible expression of a gene specific to the RecF pathway for recombination in Escherichia coli K12. Mol Gen Genet. 1983;190(1):162-167.
16. Ohmori H, Hatada E, Qiao Y, Tsuji M, Fukuda R. dinP, a new gene in Escherichia coli, whose product shows similarities to UmuC and its homologues. Mutat Res. 1995;347(1):1-7.
17. Shurvinton CE, Lloyd RG. Damage to DNA induces expression of the ruv gene of Escherichia coli. Mol Gen Genet. 1982;185(2):352-355.
18. Siegel EC. The Escherichia coli uvrD gene is inducible by DNA damage. Mol Gen Genet. 1983;191(3):397-400.
19. Ohmori H, Saito M, Yasuda T, et al. The pcsA gene is identical to dinD in Escherichia coli. J Bacteriol. 1995;177(1):156-165.
20. Lewis LK, Harlow GR, Gregg-Jolly LA, Mount DW. Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli. J Mol Biol 1994;241(4):507-523.
21. Courcelle J, Khodursky A, Peter B1 Brown PO, Hanawalt PC. Comparative gene expression profiles following UV exposure in wild type and SOS deficient. Escherichia coli Genetics. 2001;158(1):41-64.
22. Satta G, Gudas LJ, Pardee AB. Degradation of Escherichia coli DNA: evidence for limitation in vivo by protein X, the recA gene product. Mol Gen Genet. 1979;168(1):69-80.
23. Horii Z, Suzuki K. Degradation of the DNA of Escherichia coli K12 rec- (JC1569b) after irradiation with ultraviolet light. Photochem photobiol. 1968;8(2):93-105.
24. Clark AJ, Margulies AD. Isolation and characterization of recombination-deficient mutants of Escherichia coli K12. Proc Natl Acad Sci USA. 1965;53(2):451-459.
25. Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev. 1994;58(3):401-i65.
26. Roca AI, Cox MM. RecA protein: structure, function, and role in recombinationa repair. Prog Nucleic Acid Res Mol Biol. 1997;56:129-223.
27. Smith GR. Homologous recombination in procaryotes. Microbiol Rev. 1988;52(1):1-28.
28. Courcelle J, Ganesan AK, Hanawalt PC. Therefore, what are recombination proteins there for?. Bioessays. 2001;23(5):463-470.
29. Courcelle J, Carswell-Crumpton C, Hanawalt PC. recF and recR are required for the resumption of replication at DNA replication forks in Escherichia coli. Proc Natl Acad Sci USA. 1997;94(8):3714-3719.
30. Courcelle J, Crowley DJ, Hanawalt PC. Recovery of DNA replication in UV-irradiated Escherichia coli requires both excision repair and recF protein function. J Bacteriol. 1999;181(3):916-922.
31. Courcelle J, Hanawalt PC. Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination. Proc Natl Acad Sci USA. 2001;98(15):8196-8202.
32. McGlynn P, Mahdi AA, Lloyd RG. Characterisation of the catalytically active form of RecG helicase. Nucleic Acids Res. 2000;28(12):2324-2332.
33. Eggleston AK, West SC. Cleavage of Holliday junctions by the E. coli RuvABC complex. J Biol Chem. 2000;275(34):26467-26476.
34. McGlynn P, Lloyd RG. RecG helicase activity at three- and four-strand DNA structures. Nucleic Acids Res. 1999;27(15):3049-3056.
35. McGlynn P, Lloyd RG. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell. 2000;101(1):35-45.
36. Crowley DJ, Hanawalt PC. Induction of the SOS response increases the efficiency of global-nucleotide excision repair of cyclobutane pyrimidine dimers, but not 6-4 photoproducts, in UV-irradiated Escherichia coli. J Bacteriol. 1998;180(13):3345-3352.
37. Crowley DJ, Hanawalt PC. The SOS-dependent up-regulation of uvrD is not required for efficient nucleotide excision repair of ultraviolet light induced DNA photoproducts in Escherichia coli. Mutat Res. 2001;485(4):319-329.
38. Siegel EC. Ultraviolet-sensitive mutator mutU4 of Escherichia coli inviable with polA. J Bacteriol. 1973;113(1):161-166.
39. Washburn BK, Kushner SR. Construction and analysis of deletions in the structural gene (uvrD) for DNA helicase II of Escherichia coli. J Bacteriol. 1991;173(8):2569-2575.
40. Bruand C, Ehrlich SD. UvrD-dependent replication of rolling-circle plasmids in Escherichia coli. Mol Microbiol. 2000;35(1):204-210.
41. George JW, Brosh RM Jr, Matson SW. A dominant negative allele of the Escherichia coli uvrD gene encoding DNA helicase II. A biochemical and genetic characterization. J Mol Biol. 1994;235(2):424-435.
42. Moolenaar GF, Moorman C, Goosen N. Role of the Escherichia coli nucleotide excision repair proteins in DNA replication. J Bacteriol. 2000;182(20):5706-5714.
43. SaiSree L, Reddy M, Gowrishankar J. Ion incompatibility associated with mutations causing SOS induction: null uvrD alleles induce an SOS response in Escherichia coli. J Bacteriol. 2000;182(11):3151-3157.
44. Tang M, Pham P, Shen X, et al. Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature. 2000;404(6781):1014- 1018.
45. Livneh Z. Replication of UV-irradiated single-stranded DNA by DNA polymerase III holoenzyme of Escherichia coli: evidence for bypass of pyrimidine photodimers. Proc Natl Acad Sci USA. 1986;83(13):4599-4603.
46. Wagner J, Nohmi T. Escherichia coli DNA polymerase IV mutator activity: genetic requirements and mutational specificity. J Bacteriol. 2000;182(16):4587-4595.
47. Wagner J, Gruz P, Kim SR, et al. The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis. Mol Cell. 1999;4(2):281-286.
48. Tang M, Shen X, Frank EG, O'Donnell M, Woodgate R, Goodman MF. UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V. Proc Natl Acad Sci USA. 1999;96(16):8919-8924.
49. Reuven NB, Arad G, Maor-Shoshani A, Livneh Z. The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication. J Biol Chem. 1999;274(45):1763-31766.
50. Perry KL, Elledge SJ, Mitchell BB, Marsh L, Walker GC. umuDC and mucAB operons whose products are required for UV light- and chemical-induced mutagenesis: UmuD, MucA, and LexA proteins share homology. Proc Natl Acad Sci USA. 1985;82(13):4331-4335.
51. Nelson JR, Lawrence CW, Hinkle DC. Deoxycytidyl transferase activity of yeast REV1 protein. Nature. 1996;382(6593):729-731.
52. Chen H, Bryan SK, Moses RE. Cloning the polB gene of Escherichia coli and identification of its product. J Biol Chem. 1989;264(34):20591-20595.
53. Kornberg T, Gefter ML. DNA synthesis in cell-free extracts of a DNA polymerase-defective mutant. Biochem BiophysRes Commun. 1970;40(6):1348-1355.
54. Kornberg T, Gefter ML. Purification and DNA synthesis in cell-free extracts: properties of DNA polymerase II. Proc Natl Acad Sci USA. 1971;68(4):761-764.
55. Qiu Z, Goodman MF. 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. 1997;272(13):8611-8617.
56. Rangarajan S, Woodgate R, Goodman MF. A phenotype for enigmatic DNA polymerase II: a pivotal role for pol II in replication restart in UV-irradiated Escherichia colt. Proc Natl Acad Sci USA. 1999;96(16):9224-9229.
57. Napolitano R, Janel-Bintz R, Wagner J, Fuchs RR All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. EMBO J. 2000;19(22):6259-6265.
58. Marsh L, Walker GC. New phenotypes associated with mucAB: alteration of a MucA sequence homologous to the LexA cleavage site. J Bacteriol. 1987;169(5):1818-1823.
59. Shinagawa H, Iwasaki H, Kato T, Nakata A. RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis. Proc Natl Acad Sci USA. 1988;85(6):1806-1810.
60. Burckhardt SE, Woodgate R, Scheuermann RH, Echols H. UmuD mutagenesis protein of Escherichia coli: over-production, purification, and cleavage by RecA. Proc Natl Acad Sci USA. 1988;85(6):1811-1815.
61. Nohmi T, Battista JR, Dodson LA, Walker GC. RecA-mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. Proc Natl Acad Sci USA. 1988;85(6):1816-1820.
62. Ferentz AE, Walker GC, Wagner G. Converting a DNA damage, checkpoint effector (UmuD2C) into a lesion bypass polymerase (UmuD'2C). EMBO J. 2001;20(15):4287-4298.
63. Opperman T, Murli S, Smith BT, Walker GC. A model for a umuDC-dependent prokaryotic DNA damage checkpoint. Proc Natl Acad Sci USA. 1999;96(16):9218- 9223.
64. Marsh L, Walker GC. Cold sensitivity induced by over-production of UmuDC in Escherichia coli. J Bacteriol. 1985;162(1):155-161.
65. Opperman T, Murli S, Walker GC. The genetic requirements for UmuDC-mediated cold sensitivity are distinct from those for SOS mutagenesis. J Bacteriol. 1996;178(15):4400-4411.
66. Sutton MD, Walker GC. umuDC-mediated cold sensitivity is a manifestation of functions of the UmuD(2)C complex involved in a DNA damage checkpoint control. J Bacteriol. 2001;183(4):1215-1224.
67. Sutton MD, Opperman T, Walker GC. The Escherichia coli SOS mutagenesis proteins UmuD and UmuD' interact physically with the replicative DNA polymerase. Proc Natl Acad Sci USA. 1999;96(22):12373-12378.
68. Sutton MD, Murli S, Opperman T, Klein C, Walker GC. umuDC-dnaQ Interaction and its implications for cell cycle regulation and SOS mutagenesis in Escherichia coli. J Bacteriol. 2001;183(3):1085-1089.
69. Li R, Waga S, Hannon GJ, Beach D, Stillman B. Differential effects by the p21 CDK inhibitor on PCNA-dependent DNA replication and repair. Nature. 1994;371(6497):534-537.
70. George J, Castellazzi M, Buttin G. Prophage induction and cell division in E. coli. III. Mutations sfiA and sfiB restore division in tif and Ion strains and permit the expression of mutator properties of tif. Mol Gen Genet. 1975;140(4):309-332.
71. Bi EF, Lutkenhaus J. FtsZ ring structure associated with division in Escherichia coli. Nature. 1991;354(6349):161-164.
72. Lutkenhaus JF. Coupling of DNA replication and cell division: sulB is an allele of ftsZ. J Bacteriol. 1983;154(3):1339-1346.
73. Schoemaker JM, Gayda RC, Markovitz A. Regulation of cell division in Escherichia coli: SOS induction and cellular location of the sulA protein, a key to Ion-associated filamentation and death. J Bacteriol. 1984;158(2):551-561.
74. Jones C, Holland IB. Role of the SuIB (FtsZ) protein in division inhibition during the SOS response in Escherichia coli: FtsZ stabilizes the inhibitor SulA in maxi-cells. Proc Natl Acad Sci USA. 1985;82(18):6045-6049.
75. Hill TM, Sharma B, Valjavec-Gratian M, Smith J. sfi-independent filamentation in Escherichia coli is lexA dependent and requires DNA damage for induction. J Bacteriol. 1997;179(6):1931-1939.
76. Dorazi R, Dewar SJ. The SOS promoter dinH is essential for ftsK transcription during cell division. Microbiology. 2000;146(11):2891-2899.
77. Wang L, Lutkenhaus J. FtsK is an essential cell division protein that is localized to the septum and induced as part of the SOS response. Mol Microbiol. 1998;29(3):731-740.
78. Chen JC, Beckwith J. FtsQ, FtsL and FtsI require FtsK, but not FtsN, for co-localization with FtsZ during Escherichia coli cell division. Mol Microbiol. 2001;42(2):395-413.
79. Brent R, Ptashne M. The lexA gene product represses its own promoter. Proc Natl Acad Sci USA. 1980;77(4):1932-1936.
80. Yasuda T, Nagata T, Ohmori H. Multicopy suppressors of the cold-sensitive phenotype of the pcsA68 (dinD68) mutation in Escherichia coli. J Bacteriol. 1996;178(13):3854-3859.
81. Yasuda T, Morimatsu K, Kato R, Usukura J, Takahashi M, Ohmori H. Physical interactions between DinI and RecA nucleoprotein filament for the regulation of SOS mutagenesis. EMBO J. 2001;20(5):1192-11202.
82. Yasuda T, Morimatsu K, Horii T, Nagata T, Ohmori H. Inhibition of Escherichia coli RecA coprotease activities by DinI. EMBO J. 1998;17(11):3207-3216.
83. Ramirez BE, Voloshin ON, Camerini-Otero RD, Bax A. Solution structure of DinI provides insight into its mode of RecA inactivation. Protein Sci. 2000;9(11):2161-2169.
84. Voloshin ON, Ramirez BE, Bax A, Camerini-Otero RD. 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. 2001;15(4):415-427.