Chapter 37 : DNA Repair Systems

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

DNA Repair Systems, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818388/9781555810535_Chap37-1.gif /docserver/preview/fulltext/10.1128/9781555818388/9781555810535_Chap37-2.gif


has served as the principal model for investigations into DNA repair mechanisms. The DNA repair systems identified in this paradigm have also been discovered in most other organisms studied. This chapter attempts to look at these repair systems with respect to differentiation processes and developmental biology as studied in the gram-positive bacterium . Originally, DNA repair systems were considered integral parts of an organism's ability to survive the effects of environmental insults and metabolic processes. However, as the molecular characterization of these repair systems proceeded it became obvious that in addition to determining mutation frequency and cell survival, DNA repair systems also play important roles in viral activation, DNA replication, genetic recombination, metabolism, and cancer. In order to investigate systematically the interrelationship(s) between DNA repair systems and these other phenomena, an appropriate model system must be identified. These systems are generally linked in their expression and activity with one or more of the developmental states that have been identified for the bacterium. It is in the elucidation of this linkage that becomes a critical model for the understanding of how organisms respond at the molecular level to stressful situations. Similar characterizations of these repair systems in other gram-positive bacteria, especially among the extremely resistant bacteria, will determine whether or not represents a paradigm for gram-positive bacteria or for bacteria that have distinct developmental cycles.

Citation: Yasbin R, Cheo D, Bol D. 1993. DNA Repair Systems, p 529-537. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch37

Key Concept Ranking

Transcription Start Site
DNA Synthesis
Genetic Recombination
Nucleotide Excision Repair
Base Excision Repair
DNA Polymerase I
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Alonso, J. E.,, G. Luder,, and R. H. Tailor. 1991. Characterization of Bacillus subtilis recombinational pathways. J. Bacteriol. 173: 3977 3980.
2. Bayles, K. W. 1991. Cloning of the Staphylococcus aureus recA gene and generation and characterization of a recA mutant. Plasmid 25: 154 161.
3.. Bibor, V.,, and W. G. Verly. 1978. Purification and properties of the endonuclease specific for apurinic sites of Bacillus stearothermophilus. J. Biol. Chem. 253: 850 855.
4. Bol, D. K. 1991. Bacillus subtilis responses and mechanisms of resistance to hydrogen peroxide. Ph.D. thesis. University of Maryland Baltimore County, Baltimore. 1992.
5. Bol, D. K.,, and R. E. Yasbin. 1990. Characterization of an inducible oxidative stress system in Bacillus subtilis. J. Bacteriol. 172: 3503 3506.
6. Bol, D. K.,, and R. E. Yasbin. 1991. The isolation and identification of a vegetative catalase gene from Bacillus subtilis. Gene 109: 31 37.
7. Chen, Nt.-Y.,, J.-J. Zhang,, and H. Paulus. 1989. Chromosomal location of the Bacillus subtilis aspartokinase II gene and nucleotide sequence of the adjacent genes homologous to uvrC and trx of Escherichia coli. J. Gen. Microbiol. 135: 2931 2940.
8. Cheo, D. L.,, K. W. Bayles,, and R. E. Yasbin. 1991. Cloning and characterization of DNA damage-inducible promoter regions from Bacillus subtilis. J. Bacteriol. 173: 1696 1703.
9. Cheo, D. L.,, K. W. Bayles,, and R. E. Yasbin. 1992. Molecular characterization of regulatory elements controlling expression of the Bacillus subtilis recA + gene. Biochimie 74: 755 762.
10. Cheo, D. L.,, K. W. Bayles,, and R. E. Yasbin. Elucidation of regulatory elements that control damage induction and competence-induction of the Bacillus subtilis SOS system. Submitted for publication.
11. Christman, M. F.,, R. W. Morgan,, F. S. Jacobson,, and B. N. Ames. 1985. Positive control of a regulon for defense against oxidative stress and some heat shock proteins in Salmonella typhimurium. Cell 41: 753 762.
12. Demple, B.,, J. Halbrook,, and S. Linn. 1983. Escherichia coli xth mutants are hypersensitive to hydrogen peroxide. J. Bacteriol. 153: 1079 1082.
13. Demple, B.,, A. Johnson,, and D. Fung. 1986. Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H 202-damaged E. coli. Proc. Natl. Acad. Sci. USA 83: 7731 7735.
14. Dodson, L. A.,, and C. T. Hadden. 1980. Capacity for postreplication repair correlated with transducibility in Rec" mutants of Bacillus subtilis. J. Bacteriol. 144: 608 615.
15. Donnellan, J. E., Jr.,, and R. B. Setlow. 1965. Thymine photoproducts but not thymine dimers are found in ultraviolet irradiated bacterial spores. Science 149: 308 310.
16. Dowds, B. C. A.,, and J. A. Hoch. 1991. Regulation of the oxidative stress response by the hpr gene in Bacillus subtilis. . J. Gen. Microbiol. 137: 1121 1125.
17. Dowds, B. C. A.,, P. Murphy,, D. J. McConnell,, and K. M. Devine. 1987. Relationship among oxidative stress, growth cycle, and sporulation in Bacillus subtilis. J. Bacteriol. 169: 5771 5775.
18. Dubnau, D. 1991. Genetic competence in Bacillus subtilis. Microbiol. Rev. 55: 395 424.
19. Epstein, H. T.,, and I. Mahler. 1968. Mechanism of enhancement of SP82 transfection. J. Virol. 2: 710 715.
20. Evans, D. M.,, and B. E. B. Moseley. 1983. Roles of uvsC, uvsD, uvsE, and mtcA genes in the two pyrimidine dimer excision repair pathways of Deinococcus radiodurans. J. Bacteriol. 156: 576 583.
21. Fields, P. I.,, and R. E. Yasbin. 1980. Involvement of deoxyribonucleic acid polymerase III in W-reactivation in Bacillus subtilis. J. Bacteriol. 144: 473 475.
22. Fridovich, I. 1978. The biology of oxygen radicals. Science 201: 875 900.
23. Friedberg, E. C., 1981. Base excision repair of DNA, p. 77 83. In E. Seeberg, and K. Kleppi (ed.), Chromosome Damage and Repair. Plenum Press, New York.
24. Friedberg, E. C. 1985. DNA Repair, p. 141 211. W. H. Freeman and Co., New York.
25. Ganesan, A. K. 1974. Persistence of pyrimidine dimers during post-replication repair in ultraviolet light-irradiated Escherichia coli K-12. J. Mol. Biol. 87: 102 119.
26. Germaine, G. R.,, and W. G. Murrel. 1973. Effect of dipicolinic acid on the ultraviolet radiation resistance of Bacillus cereus spores. Photochem. Photobiol. 17: 145 153.
27. Goering, R. V. 1979. Mutants of Staphylococcus aureus deficient in recombinational repair. Improved isolation by selecting for mutants exhibiting concurrent sensitivity to ultraviolet radiation and N-methyl-N'-nitro-N-nitrosoguanidine. Mutat. Res. 60: 279 289.
28. Goering, R. V.,, and P. A. Pattee. 1971. Mutants of Staphylococcus aureus with increased sensitivity to ultraviolet radiation. J. Bacteriol. 106: 157 161.
29. Grossman, L.,, and A. T. Yeung. 1990. The UvrABC endonuclease system of Escherichia coli: a view from Baltimore. Mutat. Res. 236: 213 221.
30. Hadden, C. T. 1979. Gap-filling repair synthesis induced by ultraviolet light in a Bacillus subtilis Uvr -mutant. J. Bacteriol. 139: 239 246.
31. Hadden, C. T. 1979. Pyrimidine dimer excision in a Bacillus subtilis Uvr- mutant. J. Bacteriol. 139: 247 255.
32. Hadden, C. T.,, R. S. Foote,, and S. Mitra. 1983. Adaptive response of Bacillus subtilis to N-methyl-N-nitro-N-nitrosoguanidine. J. Bacteriol. 153: 756 762.
33. Hagensee, M.,, and R. E. Moses. 1989. Multiple pathways for repair of H2O2-induced damage in Escherichia coli. J. Bacteriol. 171: 991 995.
34. Hanawalt, P. C. 1989. Concepts and models for DNA repair: from E. coli to mammalian cells. Environ. Mol. Mutagen. 14: 90 98.
35. Harris, W. J.,, and G. C. Barr. 1971. Mechanism of transformation in Bacillus subtilis. Mol. Gen. Genet. 113: 316 330.
36. Inoue, M.,, H. Oshima,, T. Okubo,, and S. Mitsuhashi. 1972. Isolation of the rec mutants in Staphylococcus aureus. J. Bacteriol. 112: 1169 1176.
37. Inoue, T.,, and T. Kada. 1978. Purification and properties of a Bacillus subtilis endonuclease specific for apurinic sites in DNA. J. Biol. Chem. 253: 8559 8563.
38. Juan, J.-Y.,, S. N. Keeney,, and E. M. Gregory. 1991. Reconstitution of the Deinococcus radiodurans aposuperoxide dismutase. Arch. Biochem. Biophys. 286: 257 263.
39. Kaasen, I.,, P. Falkenberg,, O. B. Styrvold,, and A. R. Strem. 1992. Molecular cloning and physical mapping of the otsBA genes, which encode the osmoregulatory trehalose pathway of Escherichia coli: evidence that transcription is activated by KatF (AppR). J. Bacteriol. 174: 889 898.
40. Kallio, P. T.,, J. E. Fagelson,, J. A. Hoch,, and M. A. Strauch. 1991. The transition state regulator Hpr of Bacillus subtilis is a DNA-binding protein. J. Biol. Chem. 266: 13411 13417.
41. Kelner, A. 1949. Effect of visible light on the recovery of Streptomyces griseus conidia from ultraviolet irradiation injury. Proc. Natl. Acad. Sci. USA 35: 73 79.
42. Kushner, S. R., 1987. DNA repair, p. 1044 1053. In F. C. Neidhardt,, J. L. Ingraham,, K. B. Low,, B. Magasanik,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C..
43. Lindahl, T. 1979. DNA glycosylases, endonucleases, endonucleases for apurinic/apyrimidinic sites, and base excision repair. Prog. Nucleic Acids Res. Mol. Biol. 22: 135 192.
44. Lindahl, T. 1982. DNA repair enzymes. Annu. Rev. Biochem. 51: 61 87.
45. Lindahl, T.,, B. Sedgwick,, M. Sekiguchi,, and Y. Nakabeppu. 1988. Regulation and expression of the adaptive response to alkylating agents. Annu. Rev. Biochem. 57: 133 157.
46. Little, J. W.,, and D. W. Mount. 1982. The SOS regulatory system of Escherichia coli. Cell 29: 11 22.
47. Loewen, P. C.,, J. Switala,, and B. L. Triggs-Rlane. 1985. Catalases HPI and HPII in E. coli are induced independently. Arch. Biochem. Biophys. 243: 144 149.
48. Love, P. E.,, M. J. Lyle,, and R. E. Yasbin. 1985. DNA damage inducible (DIN) loci are transcriptionally activated in competent Bacillus subtilis. Proc. Natl. Acad. Sci. USA 82: 6201 6205.
49. Love, P. E.,, and R. E. Yasbin. 1984. Genetic characterization of the inducible "SOS-like" system of Bacillus subtilis. J. Bacteriol. 160: 910 920.
50. Lovett, C. M., Jr.,, P. E. Love,, and R. E. Yasbin. 1989. Competence-specific induction of the Bacillus subtilis RecA protein analog: evidence for dual regulation of a recombination protein. J Bacteriol. 171: 2318 2322.
51. Lovett, C. M., Jr.,, and J. W. Roberts. 1985. Purification of a RecA protein analogue from Bacillus subtilis. J. Biol. Chem. 260: 3305 3313.
52. Malvy, C.,, J. Pierre,, M. Lefrancois,, and J. Markovits. 1990. Low concentrations of acridine dimers inhibit Micrococcus AP endonuclease through interaction with apurinic sites in DNA. Chem-Biol. Interact. 73: 249 260.
53. Marrero, R.,, and R. E. Yasbin. 1988. Cloning of the Bacillus subtilis recE + gene and functional expression of recE + in B. subtilis. J. Bacteriol. 170: 335 344.
54. Mason, J. M.,, and P. Setlow. 1986. Essential role of small acid-soluble spore proteins in resistance of Bacillus subtilis spores to UV light. J. Bacteriol. 167: 174 178.
55. Masters, C. I.,, B. E. B. Moseley,, and K. W. Minton. 1991. AP endonuclease and uracil DNA glycosylase activities in Deinococcus radiodurans. Mutat. Res. 254: 263 272.
56. McAllister, W. T.,, and D. M. Green. 1972. Bacteriophage SP82G inhibition of intracellular deoxyribonucleic acid inactivation process of Bacillus subtilis. J. Virol. 10: 51 59.
57. McCann, M. P.,, J. P. Kidwell,, and A. Matin. 1991. The putative sigma factor KatF has a central role in development of starvation-mediated general resistance in Escherichia coli. J. Bacteriol. 173: 4188 4194.
58. Mohr, S. C.,, N. V. H. A. Sokolov,, C. He,, and P. Setlow. 1991. Binding of small acid-soluble spore proteins from Bacillus subtilis changes the conformation of DNA from B to A. Proc. Natl. Acad. Sci. USA 88: 77 81.
59. Morohoshi, F.,, K. Hayashi,, and N. Munakata. 1991. Molecular analysis of Bacillus subtilis ada mutants deficient in the adaptive response to simple alkylating agents. J. Bacteriol. 173: 7834 7840.
60. Morohoshi, F.,, and X. Munakata. 1986. Two classes of Bacillus subtilus mutants deficient in the adaptive response to simple alkylating agents. Mol. Gen. Genet. 202: 200 206.
61. Morohoshi, F.,, and N. Munakata. 1987. Multiple species of Bacillus subtilis DNA alkyltransferase involved in the adaptive response to simple alkylating agents. J. Bacteriol. 169: 587 592.
62. Moseley, B. E. B. 1983. Photobiology and radiobiology of Micrococcus (Deinococcus) radiodurans. Photochem. Photobiol. Rev. 7: 223 274.
63. Munakata, N. 1974. Ultraviolet sensitivity of Bacillus subtilis spores upon germination and outgrowth. J. Bacteriol. 120: 59 65.
64. Munakata, N. 1977. Mapping of the genes controlling excision repair of pyrimidine photoproducts in Bacillus subtilis. Mol. Gen. Genet. 156: 49 54.
65. Munakata, N.,, and C. S. Rupert. 1972. Genetically controlled removal of "spore photoproduct" from deoxyribonucleic acid of ultraviolet-irradiated Bacillus subtilis spores. J. Bacteriol. 111: 192 198.
66. Munakata, N.,, and C. S. Rupert. 1974. Dark repair of DNA containing "spore photoproduct" in Bacillus subtilis. Mol. Gen. Genet. 130: 239 250.
67. Munakata, N.,, and C. S. Rupert. 1975. Effects of DNA-polymerase-defective and recombination-deficient mutations on the ultraviolet sensitivity of Bacillus subtilis spores. Mutat. Res. 27: 157 169.
68. Nakayama, H.,, S. Shiota,, and K. Umezu. 1992. UV endonuclease-mediated enhancement of UV survival in Micrococcus luteus: evidence revealed by deficiency in the Uvr homolog. Mutat. Res. 273: 43 48.
69. Nicholson, W. Personal communication.
70. Nicholson, W. L.,, B. Setlow,, and P. Setlow. 1990. Binding of DNA in vitro by a small, acid-soluble spore protein and its effect on DNA topology. J. Bacteriol. 172: 6900 6906.
71. Nicholson, W. L.,, B. Setlow,, and P. Setlow. 1991. Ultraviolet irradiation of DNA complexed with alpha/ beta-type small, acid-soluble proteins from spores of Bacillus or Clostridium species makes spore photoproduct but not thymine dimers. Proc. Natl. Acad. Sci. USA 88: 8288 8292.
72. Pierre, J.,, and J. Laval. 1980. Micrococcus luteus endonucleases for apurinic/apyrimidinic sites in deoxyribonucleic acid. I. Purification and general properties. Biochemistry 19: 5018 5024.
73. Radany, E. H.,, G. Malanoski,, N. Ambulos,, E. C. Friedberg,, and R. E. Yasbin. 1988. Transfection enhancement of bacteriophage DNA may reflect a novel repair pathway for UV-irradiated DNA in Bacillus subtilis. J. Cell. Biochem. ( Suppl.) 12A: 323.
74. Radman, M., 1974. Phenomenology of an inducible mutagenic DNA repair pathway in Escherichia coli: SOS repair hypothesis, p. 128 142. In S. Prakash,, F. Sherman,, M. Miller,, C. Lawrence,, and H. W. Tabor (ed.), Molecular and Environmental Aspects of Mutagenesis. Charles C. Thomas, Publisher, Springfield, Ill..
75. Raymond-Denise, A.,, and N. Guillen. 1991. Identification of dinR, a DNA damage-inducible regulator gene of Bacillus subtilis. J. Bacteriol. 173: 7084 7091.
76. Richter, H. E.,, and P. C. Loewen. 1981. Induction of catalase in E. coli by ascorbic acid involves hydrogen peroxide. Biochem. Biophys. Res. Commun. 100: 1039 1046.
77. Roca, A. I.,, and M. M. Cox. 1990. The RecA protein: structure and function. Crit. Rev. Biochem. 25: 415 456.
78. Rupp, W. D.,, and P. Howard-Flanders. 1968. Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet irradiation. J. Mol. Biol. 31: 291 304.
79. Sancar, A.,, K. A. Franklin,, and G. B. Sancar. 1984. Escherichia coli photolyase stimulates Uvr ABC excision nuclease in vitro. Proc. Natl. Acad. Sci. USA 81: 7397 7401.
80. Sancar, A.,, and W. D. Rupp. 1983. A novel repair enzyme: UVRABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region. Cell 33: 249 260.
81. Schellhorn, H. E.,, and V. L. Stones. 1992. Regulation of katF and katE in Escherichia coli K-12 by weak acids. J. Bacteriol. 174: 4769 4776.
82. Setlow, B.,, and P. Setlow. 1987. Thymine-containing dimers as well as spore photoproducts are found in ultraviolet-irradiated Bacillus subtilis spores that lack small, acid-soluble proteins. Proc. Natl. Acad. Sci. USA 84: 421 423.
83. Setlow, P. 1988. Small acid-soluble, spore proteins of Bacillus species: structure, synthesis, genetics, function and degradation. Annu. Rev. Microbiol. 42: 319 338.
84. Setlow, R. B.,, P. A. Swenson,, and W. L. Carrier. 1963. Thymine dimers and inhibition of DNA synthesis by ultraviolet irradiation of cells. Science 142: 1464 1466.
85. Shevell, D. E.,, B. M. Friedman,, and G. C. Walker. 1990. Resistance to alkylation damage in Escherichia coli: role of the Ada protein in induction of the adaptive response. Mutat. Res. 223: 53 72.
86. Shuster, R. C. 1967. Fate of thymine-containing dimers in the deoxyribonucleic acid of ultraviolet-irradiated Bacillus subtilis. J. Bacteriol. 93: 811 815.
87. Sicard, N.,, and A. M. Estevenon. 1990. Excision-repair capacity in Streptococcus pneumoniae: cloning and expression of a uvr-like gene. Mutat. Res. 235: 195 201.
88. Sicard, N.,, J. Oreglia,, and A.-M. Estevenon. 1992. Structure of the gene complementing uvr-402 in Streptococcus pneumoniae: homology with Escherichia coli uvrB and the homologous gene in Micrococcus luteus. J. Bacteriol. 174: 2412 2415.
89. Smith, M. D.,, C. I. Masters,, and B. E. B. Moseley,. 1992. Molecular biology of radiation-resistant bacteria, p. 258 280. In R. A. Herbert, and R. J. Sharp (ed.). Molecular Biology and Biotechnology of Extremophiles. Blackie & Son Limited, Glasgow.
90. Stafford, R. S.,, and J. E. Donnellan, Jr. 1968. Photochemical evidence for conformation changes in DNA during germination of bacterial spores. Proc. Natl. Acad. Set. USA 59: 822 828.
91. Tartaglia, L. A.,, G. Store,, and B. N. Ames. 1989. Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress. J. Mol. Biol. 209: 709 719.
92. van Houten, B. 1990. Nucleotide excision repair in Escherichia coli. Microbiol. Rev. 54: 18 51.
93. Varghese, A. J. 1970. 5-Thyminyl-5,6-dihydrothymine from DNA irradiated with ultraviolet light. Biochem. Biophys. Res. Commun. 38: 484 490.
94. Visse, R.,, M. de Ruijter,, and J. Brouwer. 1991. Uvr excision repair protein complex of Escherichia coli binds to the convex side of a cisplatin-induced kink in the DNA. J. Biol. Chem. 266: 7609 7617.
95. Walker, G. C. 1984. Mutagenic and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol. Rev. 48: 60 93.
96. Walkup, L. K. B.,, and T. Kogoma. 1989. Escherichia coli proteins inducible by oxidative stress mediated by the superoxide radical. J. Bacteriol. 171: 1476 1484.
97. Wallace, S. S. 1988. AP endonucleases and DNA glycosylases that recognize oxidative DNA damage. Environ. Mol. Mutagen. 12: 431 477.
98. Wang, T.-C. V.,, and C. S. Rupert. 1977. Transitory germinative excision repair in Bacillus subtilis. J. Bacteriol. 129: 1313 1319.
99. Witkin, E. M. 1976. Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli. Bacteriol. Rev. 40: 869 907.
100. Yagi, Y.,, and D. B. Clewell. 1980. Recombination-deficient mutant of Streptococcus faecalis. J. Bacteriol. 143: 966 970.
101. Yasbin, R. E. 1977. DNA repair in Bacillus subtilis. II. Activation of the inducible system in competent bacteria. Mol. Gen. Genet. 153: 219 225.
102. Yasbin, R. E., 1985. DNA repair in Bacillus subtilis, p. 33 52. In D. Dubnau (ed.), Molecular Biology of the Bacilli, vol. II. Academic Press, Inc., New York.
103. Yasbin, R. E.,, D. L. Cheo,, and K. W. Bayies. 1992. Inducible DNA repair and differentiation in Bacillus subtilis: interactions between global regulons. Mol. Microbiol. 6: 1263 1270.
104. Yasbin, R. E.,, P. I. Fields,, and B. J. Andersen. 1980. Properties of Bacillus subtilis 168 derivatives freed of their natural prophages. Gene 12: 155 159.
105. Yasbin, R. E.,, P. Love,, J. Jackson,, and C. M. Lovett, Jr., 1988. Evolutionary divergence of the SOS-like (SOB) system of Bacillus subtilis, p. 485 490. In E. C. Friedberg, and P. Hanawalt (ed.), Mechanisms and Consequences of DNA Damage Processing. Alan R. Liss, Inc., New York.
106. Yasbin, R. E.,, and R. Miehl. 1980. Deoxyribonucleic acid repair in Bacillus subtilis: development of competent cells into a tester for carcinogens. Appl. Environ. Microbiol. 39: 854 858.
107. Yasbin, R. E.,, M. Stranathan,, and K. W. Bayies. 1991. The : recE(A) + : gene of : B. subtilis : and its gene product: further characterization of this universal protein. Biochimie 73: 245 250.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error