1887

Chapter 24 : Excision Repair and Bypass

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

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Excision Repair and Bypass, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817640/9781555812324_Chap24-1.gif /docserver/preview/fulltext/10.1128/9781555817640/9781555812324_Chap24-2.gif

Abstract:

In excision repair, damaged DNA is recognized as altered and the damage is cut out. Two types of excision repair, each with important variations, can be distinguished. The first, base excision repair (BER), uses particular enzymes, the DNA N-glycosylases to sense specific damaged bases. The second, nucleotide excision repair is a multiprotein system which recognizes generalized deformation in the DNA. The clear requirement for the RecA protein is explained by the need to support the strand exchanges required for recombination and for the filling of gaps left by the blockage of DNA synthesis along one strand only at the site of pyrimidine dimer or other lesion. The genome codes for at least five different DNA polymerases. The dynamics of the bypass process involving the different DNA polymerases are described in this chapter. The complete replication system is in place and DNA is being replicated, either by progression of the complex along a chromosome, as usually thought, or, as has been suggested for , by the chromosomal DNA moving through a fixed replication site. has a variety of enzymes which cooperate to detect and remove damage from the DNA. Operation of these mechanisms is dependent on the location of the lesions with respect to DNA growing points. Lesions far from such growing points are detected either by small DNA glycosylases that continually test the DNA for aberrant bases or by the UvrAUvrB protein complex, which detects helix distortions and searches the distorted helix for altered bases.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24

Key Concept Ranking

DNA Synthesis
0.5410264
Genetic Recombination
0.53596705
DNA Polymerase III
0.4890545
Chromosomal DNA
0.45604908
0.5410264
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Pyrimidine dimers.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Some bases recognized by DNA glycosylases as abnormal.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Four methods by which organisms deal with damaged DNA.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Model for the nucleotide excision repair of nontranscribed DNA in . Reproduced from reference (copyright 2000) with permission from Elsevier and R. D. Wood.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Pathways for DNA repair of a stalled replication fork. Reproduced from reference (copyright 2001 National Academy of Sciences) with permission.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

The isomerization step in lesion avoidance ( ).

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817640.chap24
1. Aas, P. A.,, M. Otterlei,, P. O. Falnes,, C. B. Vagbo,, F. Skorpen,, M. Akbari,, O. Sundheim,, M. Bjoras,, G. Slupphaug,, E. Seeberg,, and H. E. Krokan. 2003. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 421:859863.
2. Artsimovitch, I.,, and R. Landick. 2000. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl. Acad. Sci. USA 97:70907095.
3. Batty, D. P.,, and R. D. Wood. 2000. Damage recognition in nucleotide excision repair of DNA. Gene 241:193204.
4. Becherel, O.,, and R. P. Fuchs. 2001. Mechanism of DNA polymerase II-mediated frameshift mutagenesis. Proc. Natl. Acad. Sci. USA 98:85668571.
5. Berdal, K. G.,, R. F. Johansen,, and E. Seeberg. 1998. Release of normal bases from intact DNA by a native DNA repair enzyme. EMBO J. 17:363367.
6. Bonner, C. A.,, P. T. Stukenberg,, M. Rajagopalan,, R. Eritja,, M. O´Donnell,, K. McEntee,, H. Echols,, and M. F. Goodman. 1992. Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins. J. Biol. Chem. 267:1143111438.
7. Branum, M. E.,, J. T. Reardon,, and A. Sancar. 2001. DNA repair excision nuclease attacks undamaged DNA. A potential source of spontaneous mutations. J. Biol. Chem. 276: 2542125426.
8. 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 85:18111815.
9. Chabes, A.,, B. Georgieva,, V. Domkin,, X. Zhao,, R. Rothstein,, and L. Thelander. 2003. Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase. Cell 112:391401.
10. Cooper, P. K. 1982. Characterization of long patch excision repair of DNA in ultraviolet-irradiated Escherichia coli: an inducible function under rec-lex control. Mol. Gen. Genet. 185:189197.
11. Courcelle, J.,, D. J. Crowley,, and P. C. Hanawalt. 1999. Recovery of DNA replication in UV-irradiated Escherichia coli requires both excision repair and recF protein function. J. Bacteriol. 181:916922.
12. 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 299:10641067.
13. Courcelle, J.,, A. K. Ganesan,, and P. C. Hanawalt. 2001. Therefore, what are recombination proteins there for? Bioessays 23:463470.
14. Courcelle, J.,, and P. C. Hanawalt. 2001. Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination. Proc. Natl. Acad. Sci. USA 98:81968202.
15. 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 158:4164.
16. Cox, M. M. 2001. Historical overview: searching for replication help in all of the rec places. Proc. Natl. Acad. Sci. USA 98:81738180.
17. 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 404:3741.
18. Cupples, C. G.,, M. Cabrera,, C. Cruz,, and J. H. Miller. 1990. A set of lacZ mutations in Escherichia coli that allow rapid detection of specific frameshift mutations. Genetics 125:275280.
19. Dorrell, N.,, D. J. Davies,, and S. H. Moss. 1995. Evidence of photoenzymatic repair due to the phrA gene in a phrB mutant of Escherichia coli K-12. J. Photochem. Photobiol. B28:8792.
20. Eisen, J. A. 1998. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 26:42914300.
21. Eisen, J. A.,, and P. C. Hanawalt. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat. Res. 435:171213.
22. Falnes, P. O.,, R. F. Johansen,, and E. Seeberg. 2002. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419:178182.
23. Ferentz, A. E.,, G. C. Walker,, and G. Wagner. 2001. Converting a DNA damage checkpoint effector (UmuD(2)C) into a lesion bypass polymerase (UmuD´(2)C). EMBO J. 20:42874298.
24. Fersht, A. R.,, J. W. Knill-Jones,, and W. C. Tsui. 1982. Kinetic basis of spontaneous mutation. Misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli. J. Mol. Biol. 156:3751.
25. Fortini, P.,, E. Parlanti,, O. M. Sidorkina,, J. Laval,, and E. Dogliotti. 1999. The type of DNA glycosylase determines the base excision repair pathway in mammalian cells. J. Biol. Chem. 274:1523015236.
26. Friedberg, E. 1997. Correcting the Blueprint of Life. An Historical Account of the Discovery of DNA Repair Mechanisms. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
27. Gerlach, V. L.,, L. Aravind,, G. Gotway,, R. A. Schultz,, E. V. Koonin,, and E. C. Friedberg. 1999. Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily. Proc. Natl. Acad. Sci. USA 96:1192211927.
28. Goodman, M. F. 2002. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71:1750.
29. Goosen, N.,, and G. Moolenar. 2001. Role of ATP hydrolysis by UvrA and UvrB during nucleotide excision repair. Res. Microbiol. 152:401409.
30. Hang, B.,, and B. Singer. 2003. Protein-protein interactions involving DNA glycosylases. Chem. Res. Toxicol. 16:11811195.
31. Heelis, P. F.,, S. T. Kim,, T. Okamura,, and A. Sancar. 1993. The photo repair of pyrimidine dimers by DNA photolyase and model systems. J. Photochem. Photobiol. B 17:219228.
32. Hess, M. T.,, U. Schwitter,, M. Petretta,, B. Giese,, and H. Naegeli. 1997. Bipartite substrate discrimination by human nucleotide excision repair. Proc. Natl. Acad. Sci. USA 94:66646669.
33. Higashitani, N.,, A. Higashitani,, and K. Horiuchi. 1995. SOS induction in Escherichia coli by single-stranded DNA of mutant filamentous phage: monitoring by cleavage of LexA repressor. J. Bacteriol. 177:36103612.
34. Higgins, N. P.,, K. Kato,, and B. Strauss. 1976. A model for replication repair in mammalian cells. J. Mol. Biol. 101:417425.
35. Hingorani, M. M.,, and M. O´Donnell. 2000. Sliding clamps: a (tail)ored fit. Curr. Biol. 10:R25R29.
36. Holmquist, G. P. 1998. Endogenous lesions, S-phase-independent spontaneous mutations, and evolutionary strategies for base excision repair. Mutat. Res. 400:5968.
37. Howard-Flanders, P.,, and R. P. Boyce. 1966. DNA repair and genetic recombination: studies on mutants of Escherichia coli defective in these processes. Radiat. Res. Suppl. 6:156184.
38. Iyer, V. N.,, and W. D. Rupp. 1971. Usefulness of benzoylated naphthoylated DEAE-cellulose to distinguish and fractionate double-stranded DNA bearing different extents of single-stranded regions. Biochim. Biophys. Acta 228:117126.
39. Johnson, K. A. 1993. Conformational coupling in DNA polymerase fidelity. Annu. Rev. Biochem. 62:685713.
40. Johnson, R. E.,, G. K. Kovvali,, S. N. Guzder,, N. S. Amin,, C. Holm,, Y. Habraken,, P. Sung,, L. Prakash,, and S. Prakash. 1996. Evidence for involvement of yeast proliferating cell nuclear antigen in DNA mismatch repair. J. Biol. Chem. 271:2798727990.
41. Joyce, C. M.,, and N. D. Grindley. 1984. Method for determining whether a gene of Escherichia coli is essential: application to the polA gene. J. Bacteriol. 158:636643.
42. Kadyk, L. C.,, and L. H. Hartwell. 1993. Replication-dependent sister chromatid recombination in rad1 mutants of Saccharomyces cerevisiae. Genetics 133:469487.
43. Kelman, Z.,, and M. O´Donnell. 1995. DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu. Rev. Biochem. 64:171200.
44. Khidhir, M. A.,, S. Casaregola,, and I. B. Holland. 1985. Mechanism of transient inhibition of DNA synthesis in ultraviolet-irradiated E. coli: inhibition is independent of recA whilst recovery requires RecA protein itself and an additional, inducible SOS function. Mol. Gen. Genet. 199:133140.
45. Kim, S.,, K. Matsui,, M. Yamada,, P. Gruz,, and T. Nohmi. 2001. Role of chromosomal and episomal dinB genes encoding DNA pol IV in targeted and untargeted mutagenesis in Escherichia coli. Mol. Genet. Genom. 266:207215.
46. Kowalczykowski, S. C. 2000. Some assembly required. Nat. Struct. Biol. 7:10871089.
47. Krokan, H. E.,, R. Standal,, and G. Slupphaug. 1997. DNA glycosylases in the base excision repair of DNA. Biochem. J.325:116.
48. Kuzminov, A. 2001. DNA replication meets genetic exchange: chromosomal damage and its repair by homologous recombination. Proc. Natl. Acad. Sci. USA 98:84618468.
49. Kuzminov, A. 1999. Recombinational repair of DNA damage in Escherichia coli and bacteriophage l. Microbiol. Mol. Biol. Rev. 63:751813.
50. Lemon, K. P.,, and A. D. Grossman. 2000. Movement of replicating DNA through a stationary replisome. Mol. Cell 6:13211330.
51. Lenne-Samuel, N.,, J. Wagner,, H. Etienne,, and R. P. Fuchs. 2002. The processivity factor beta controls DNA polymerase IV traffic during spontaneous mutagenesis and translesion synthesis in vivo. EMBO Rep. 3:4549.
52. Lin, J. J.,, A. M. Phillips,, J. E. Hearst,, and A. Sancar. 1992. Active site of (A)BC excinuclease. II. Binding, bending, and catalysis mutants of UvrB reveal a direct role in 3´ and an indirect role in 5´ incision. J. Biol. Chem. 267:1769317700.
53. Lin, J. J.,, and A. Sancar. 1992. Active site of (A)BC excinuclease. I. Evidence for 5´ incision by UvrC through a catalytic site involving Asp399, Asp438, Asp466, and His538 residues. J. Biol. Chem. 267:1768817692.
54. Lin, J. J.,, and A. Sancar. 1992. (A)BC excinuclease: the Escherichia coli nucleotide excision repair enzyme. Mol. Microbiol. 6:22192224.
55. Lindahl, T. 1996. The Croonian Lecture, 1996: endogenous damage to DNA. Philos. Trans. R. Soc. Lond. B 351:15291538.
56. Lindahl, T.,, B. Sedgwick,, M. Sekiguchi,, and Y. Nakabeppu. 1988. Regulation and expression of the adaptive response to alkylating agents. Annu. Rev. Biochem. 57:133157.
57. Lindahl, T.,, and R. D. Wood. 1999. Quality control by DNA repair. Science 286:18971905.
58. Lopez De Saro, F. J.,, and M. O´Donnell. 2001. Interaction of the beta sliding clamp with MutS, ligase, and DNA polymerase I. Proc. Natl. Acad. Sci. USA 98:83768380.
59. Marnett, L. J.,, and P. C. Burcham. 1993. Endogenous DNA adducts: potential and paradox. Chem. Res. Toxicol. 6:771785.
60. Mazia, D., 1952. Physiology of the cell nucleus, p. 77122. In E. S. G. Barron (ed.), Modern Trends in Physiology and Biochemistry. Academic Press, Inc., New York, N.Y.
61. McCullough, A. K.,, M. L. Dodson,, and R. S. Lloyd. 1999. Initiation of base excision repair: glycosylase mechanisms and structures. Annu. Rev. Biochem. 68:255285.
62. McGlynn, P.,, R. G. Lloyd,, and K. J. Marians. 2001. Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication forks: RecG stimulates regression even when the DNA is negatively supercoiled. Proc. Natl. Acad. Sci. USA 98:82358240.
63. McKenzie, G. J.,, D. B. Magner,, P. L. Lee,, and S. M. Rosenberg. 2003. The dinB operon and spontaneous mutation in Escherichia coli. J. Bacteriol. 185:39723977.
64. Michel, B.,, M. J. Flores,, E. Viguera,, G. Grompone,, M. Seigneur,, and V. Bidnenko. 2001. Rescue of arrested replication forks by homologous recombination. Proc. Natl. Acad. Sci. USA 98:81818188.
65. Mizrahi, V.,, and S. J. Benkovic. 1988. The dynamics of DNA polymerase-catalyzed reactions. Adv. Enzymol. Relat. Areas Mol. Biol. 61:437457.
66. Moore, P.,, and B. S. Strauss. 1979. Sites of inhibition of in vitro DNA synthesis in carcinogen- and UV-treated phi X174 DNA. Nature 278:664666.
67. 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. 19:62596265.
68. 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 85:18161820.
69. 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 96:92189223.
70. Orren, D. K.,, and A. Sancar. 1989. The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC subunits in the incision complex. Proc. Natl. Acad. Sci. USA 86:52375241.
71. Orren, D. K.,, and A. Sancar. 1990. Formation and enzymatic properties of the UvrB.DNA complex. J. Biol. Chem. 265:1579615803.
72. Park, J. S.,, M. T. Marr,, and J. W. Roberts. 2002. E. coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell 109:757767.
73. Peterson, K. R.,, and D. W. Mount. 1987. Differential repression of SOS genes by unstable LexA41 (tsl-1) protein causes a “split-phenotype” in Escherichia coli K-12. J. Mol. Biol. 193:2740.
74. Pham, P.,, J. G. Bertram,, M. O´Donnell,, R. Woodgate,, and M. F. Goodman. 2001. A model for SOS-lesion-targeted mutations in Escherichia coli. Nature 409:366370.
75. Pham, P.,, S. Rangarajan,, R. Woodgate,, and M. F. Goodman. 2001. Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli. Proc. Natl. Acad. Sci. USA 98:83508354.
76. Pham, P.,, E. M. Seitz,, S. Saveliev,, X. Shen,, R. Woodgate,, M. M. Cox,, and M. F. Goodman. 2002. Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis. Proc. Natl. Acad. Sci. USA 99:1106111066.
77. 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. 272:86118617.
78. Radman, M., 1974. Phenomenology of an inducible mutagenic DNA repair pathway in Escherichia coli: SOS repair hypothesis, p. 128142. In L. Prakash,, F. Sherman,, M. Miller,, C. Lawrence,, and H. W. Tabor (ed.), Molecular and Environmental Aspects of Mutagenesis. Charles C Thomas, Springfield, Ill.
79. 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 96:92249229.
80. 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. 43:617628.
81. Reuven, N. B.,, G. Arad,, A. Maor-Shoshani,, and Z. Livneh. 1999. The mutagenesis protein UmuC is a DNA polymerase activated by UmuD0, RecA, and SSB and is specialized for translesion replication. J. Biol. Chem. 274:3176331766.
82. 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. 31:291304.
83. Rupp, W. D.,, C. E. Wilde III,, D. L. Reno,, and P. Howard-Flanders. 1971. Exchanges between DNA strands in ultraviolet- irradiated Escherichia coli. J. Mol. Biol. 61:2544.
84. Sandigursky, M.,, G. A. Freyer,, and W. A. Franklin. 1998. The post-incision steps of the DNA base excision repair pathway in Escherichia coli: studies with a closed circular DNA substrate containing a single U:G base pair. Nucleic Acids Res. 26:12821287.
85. Sandler, S. J.,, and K. J. Marians. 2000. Role of PriA in replication fork reactivation in Escherichia coli. J. Bacteriol. 182:913.
86. Santos, M. E.,, and J. W. Drake. 1994. Rates of spontaneous mutation in bacteriophage T4 are independent of host fidelity determinants. Genetics 138:553564.
87. Sassanfar, M.,, and J. W. Roberts. 1990. Nature of the SOS-inducing signal in Escherichia coli. The involvement of DNA replication. J. Mol. Biol. 212:7996.
88. Scudiero, D.,, and B. Strauss. 1976. Increased repair in DNA growing point regions after treatment of human lymphoma cells with N-methyl-N´-nitro-N-nitrosoguanidine. Mutat. Res. 35:311324.
89. Selby, C. P.,, and A. Sancar. 1997. Human transcription-repair coupling factor CSB/ERCC6 is a DNA-stimulated ATPase but is not a helicase and does not disrupt the ternary transcription complex of stalled RNA polymerase II. J. Biol. Chem. 272:18851890.
90. Selby, C. P.,, and A. Sancar. 1993. Molecular mechanism of transcription-repair coupling. Science 260:5358.
91. Selby, C. P.,, and A. Sancar. 1995. Structure and function of transcription-repair coupling factor. II. Catalytic properties. J. Biol. Chem. 270:48904895.
92. Sexton, D. J.,, A. J. Berdis,, and S. J. Benkovic. 1997. Assembly and disassembly of DNA polymerase holoenzyme. Curr. Opin. Chem. Biol. 1:316322.
93. Strauss, B. S.,, R. Roberts,, L. Francis,, and P. Pouryazdanparast. 2000. Role of the dinB gene product in spontaneous mutation in Escherichia coli with an impaired replicative polymerase. J. Bacteriol. 182:67426750.
94. Sutton, M. D.,, M. F. Farrow,, B. M. Burton,, and G. C. Walker. 2001. Genetic interactions between the Escherichia coli umuDC gene products and the beta processivity clamp of the replicative DNA polymerase. J. Bacteriol. 183:28972909.
95. 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 404:10141018.
96. Tang, M.,, X. Shen,, E. G. Frank,, M. O´Donnell,, R. Woodgate,, and M. F. Goodman. 1999. UmuD0(2)C is an error-prone DNA polymerase, Escherichia coli pol V. Proc. Natl. Acad. Sci. USA 96:89198924.
97. Todo, T.,, H. Takemori,, H. Ryo,, M. Ihara,, T. Matsunaga,, O. Nikaido,, K. Sato,, and T. Nomura. 1993. A new photo-reactivating enzyme that specifically repairs ultraviolet light-induced (6-4)photoproducts. Nature 361:371374.
98. Tompkins, J. D.,, J. L. Nelson,, J. C. Hazel,, S. L. Leugers,, J. D. Stumpf,, and P. L. Foster. 2003. Error-prone polymerase, DNA polymerase IV, is responsible for transient hypermutation during adaptive mutation in Escherichia coli. J. Bacteriol. 185:34693472.
99. Tornaletti, S.,, and P. C. Hanawalt. 1999. Effect of DNA lesions on transcription elongation. Biochimie 81:139146.
100. Trewick, S. C.,, T. F. Henshaw,, R. P. Hausinger,, T. Lindahl,, and B. Sedgwick. 2002. Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature 419:174178.
101. Umar, A.,, A. B. Buermeyer,, J. A. Simon,, D. C. Thomas,, A. B. Clark,, R. M. Liskay,, and T. A. Kunkel. 1996. Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis. Cell 87:6573.
102. Verhoeven, E. E.,, M. van Kesteren,, G. F. Moolenaar,, R. Visse,, and N. Goosen. 2000. Catalytic sites for 3´ and 5´ incision of Escherichia coli nucleotide excision repair are both located in UvrC. J. Biol. Chem. 275:51205123.
103. Verhoeven, E. E.,, C. Wyman,, G. F. Moolenaar,, J. H. Hoeijmakers,, and N. Goosen. 2001. Architecture of nucleotide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition. EMBO J. 20: 601611.
104. Wagner, J.,, H. Etienne,, R. Janel-Bintz,, and R. P. Fuchs. 2002. Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II, IV and V) deal with lesion/sequence context diversity. DNA Repair 1:159167.
105. Wagner, J.,, S. Fujii,, P. Gruz,, T. Nohmi,, and R. P. Fuchs. 2000. The beta clamp targets DNA polymerase IV to DNA and strongly increases its processivity. EMBO Rep. 1:484488.
106. Wagner, J.,, and T. Nohmi. 2000. Escherichia coli DNA polymerase IV mutator activity: genetic requirements and mutational specificity. J. Bacteriol. 182:45874595.
107. Wang, Y.,, D. Cortez,, P. Yazdi,, N. Neff,, S. J. Elledge,, and J. Qin. 2000. BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. Genes Dev. 14:927939.
108. Witkin, E. M. 1974. Thermal enhancement of ultraviolet mutability in a tif-1 uvrA derivative of Escherichia coli B-r: evidence that ultraviolet mutagenesis depends upon an inducible function. Proc. Natl. Acad. Sci. USA 71:19301934.
109. Woodgate, R.,, and D. G. Ennis. 1991. Levels of chromosomally encoded Umu proteins and requirements for in vivo UmuD cleavage. Mol. Gen. Genet. 229:1016.
110. Wu, Y. H.,, M. A. Franden,, J. R. Hawker, Jr.,, and C. S. McHenry. 1984. Monoclonal antibodies specific for the alpha subunit of the Escherichia coli DNA polymerase III holoenzyme. J. Biol. Chem. 259:1211712122.
111. Zou, Y.,, C. Luo,, and N. E. Geacintov. 2001. Hierarchy of DNA damage recognition in Escherichia coli nucleotide excision repair. Biochemistry 40:29232931.
112. Zou, Y.,, and B. Van Houten. 1999. Strand opening by the UvrA(2)B complex allows dynamic recognition of DNA damage. EMBO J. 18:48894901.

Tables

Generic image for table
Table 1

Dose of radiation at which 37% of bacteria form colonies

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Generic image for table
Table 2

Glycosylases of

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Generic image for table
Table 3

Increased amounts of transcript following UV irradiation

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Generic image for table
Table 4

Proteins that may participate in replication fork reactivation

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24

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