Enhanced deletion formation by aberrant DNA replication in Escherichia coli

Genetics

Volumn 146, Issue 2, 1997, Pages 457-470

  Saveson, Catherine J ^a   Lovett, Susan T ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE;

ARTICLE; BASE MISPAIRING; DNA REPLICATION; ESCHERICHIA COLI; GENE DELETION; GENE REARRANGEMENT; GENE SEQUENCE; GENOTYPE; PRIORITY JOURNAL; REPLICON; STRAIN DIFFERENCE;

BACTERIOCIN PLASMIDS; CHROMOSOMES, BACTERIAL; DNA POLYMERASE III; DNA REPLICATION; DNA, SINGLE-STRANDED; ESCHERICHIA COLI; GENES, BACTERIAL; GENOTYPE; MODELS, GENETIC; MUTATION; REC A RECOMBINASES; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE DELETION; SOS RESPONSE (GENETICS);

ESCHERICHIA COLI;

EID: 0030902447     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (60)

1. ALBERTINI, A. M., M. HOFER, M. P. CALOS and J. H. MILLER, 1982 On the formation of spontaneous deletion: the importance of short sequence homologies in the generation of large deletions. Cell 29: 319-328.
2. ARAI, K., and A. KORNBERG, 1981 Unique primed start of phage ΦX174 DNA replication and mobility of the primosome in a direction opposite chain synthesis. Proc. Natl. Acad. Sci. USA 78: 69-73.
3. ASAI, T., D. BATES and T. KOGOMA, 1994 DNA replication triggered by double-strand breaks in E. coli: dependence on homologous recombination functions. Cell 78: 1051-1061.
4. BACHMANN, B. J., 1996 Derivations and genotypes of some mutant derivatives of Escherichia coli K-12, pp. 2460-2488 in Escherichia coli and Salmonella: Cellular and Molecular Biology, edited by F. C. NEIDHARDT. ASM Press, Washington, DC.
5. BAKER, T. A., and S. H. WICKNKR, 1992 Genetics and enzymology of DNA replication in Escherichia coli. Annu. Rev. Genet. 26: 447-477.
6. BI, X., and L. F. LIU, 1994 recA-independent and recA-dependent intramolecular plasmid recombination. Differential homology requirement and distance effect. J. Mol. Biol. 235: 414-423.
7. BI, X., and L. F. LIU, 1996 A replicational model for DNA recombination between direct repeats. J. Mol. Biol. 256: 849-858.
8. CARL, P. L., 1970 Escherichia coli mutants with temperature-sensitive synthesis of DNA. Mol. Gen. Genet. 109: 107-122.
9. CHASE, J., J. L'ITALIEN, J. MURPHY, E. SPICER and K. WILLIAMS, 1984 Characterization of the Escherichia coli SSB-113 mutant single-stranded DNA binding protein. Cloning of the gene, DNA and protein sequence analysis, high pressure liquid chromatography peptide mapping and DNA binding studies. J. Biol. Chem. 259: 805-814.
10. CLARK, A. J., and S. J. SANDLER, 1994 Homologous genetic recombination: the pieces begin to fall into place. Crit. Rev. Microbiol. 20: 125-142.
11. CSONKA, L., and A. J. CLARK, 1979 Deletions generated by the transposon Tn 10 in the srl recA region of the Escherichia coli K-12 chromosome. Genetics 93: 321-343.
12. DIANOV, G. L., A. V. KUZMINOV, A. V. MAZIN and R. I. SALGANIK, 1991 Molecular mechanisms of deletion formation in Escherichia coli plasmids. I. Deletion formation mediated by long direct repeats. Mol. Gen. Genet. 228: 153-159.
13. DIXON, W. J., and F. J. MASSEY, 1969 Introduction to Statistical Analysis. McGraw-Hill, New York.
14. DOWER, W. J., J. F. MILLER and C. W. RAGSDALE, 1988 High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 16: 6127-6145.
15. ESCARCELLER, M., J. HICKS, G. GUDMUNDSSON, G. TRUMP, D. TOUATI et al., 1994 Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation. J. Bacteriol. 176: 6221-6228.
16. FIJALKOWSKA, I. J., and R. M. SCHAAPER, 1995 Effects of Escherichia coli dnaE antimutator alleles in a proofreading-deficient mutD5 strain. J. Bacteriol. 177: 5979-5986.
17. FILIP, C., J. ALLEN, R. GUSTAFSON, R. ALLEN and J. WALKER, 1974 Bacterial cell division regulation: characterization of the dnaH locus of Escherichia coli. J. Bacteriol. 119: 443-449.
18. FUNNELL, B. E., T. A. BAKER and A. KORNBERG, 1987 In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome. J. Biol. Chem. 262: 10327-10334.
19. HORIUCHI, T., H. MAKI and M. SEKIGUCHI, 1981 Conditional lethality of Escherichia coli strains carrying dnaE and dnaQ mutations. Mol. Gen. Genet. 181: 24-28.
20. Hu, X., and R. G. WORTON, 1992 Partial gene duplication as a cause of human disease. Hum. Mutat. 1: 3-12.
21. JOHANSON, K., and C. MCHENRY, 1984 Adenosine 5′-O-(3-thiotriphosphate) can support the formation of an initiation complex between the DNA polymerase III holoenzyme and primed DNA. J. Biol. Chem. 259: 4589-4595.
22. 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: 636-643.
23. KELMAN, Z., and M. O'DOXNELL, 1995 DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu. Rev. Biochem. 64: 171-200.
24. KORNBERG, A., and T. A. BAKER, 1992 DNA Replication. W. H. Freeman and Company, New York.
25. KRAWCZAK, M., and D. N. COOPER, 1991 Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environments. Hum. Genet. 86: 425-441.
26. KUZMINOV, A., 1995a Collapse and repair of replication forks in Escherichia coli. Mol. Microbiol. 16: 373-384.
27. KUZMINOV, A., 1995b Instability of inhibited replication forks in E. coli. BioEssays 17: 733-741.
28. LEA, D. E., and C. A. COULSON, 1949 The distribution of the numbers of mutants in bacterial populations. J. Genet. 49: 264-285.
29. LOVETT, S. T., and V. V. FESCHENKO, 1996 Stabilization of diverged tandem repeats by mismatch repair: evidence for deletion formation via a misaligned replication intermediate. Proc. Natl. Acad. Sci. USA 93: 7120-7124.
30. LOVETT, S. T., P. T. DRAPKIN, V. A. J. SUTERA and T. J. GLUCKMAN-PESKIND, 1993 A sister-strand exchange mechanism for recA-independent deletion of repeated DNA sequences in Escherichia coli. Genetics 135: 631-642.
31. MARIANS, K., 1992 Prokaryotic DNA replication. Annu. Rev. Biochem. 61: 673-719.
32. MARIANS, K. J., 1996 Replication fork propagation, pp. 749-763 in Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology, edited by F. C. NEIDHARDT, R. I. CURTISS, J. L. INGRAHAM, E. C. C. LIN, K. B. Low et al. ASM Press, Washington, DC.
33. MASAI, H., N. NOMURA and K. ARAI, 1990 The ABC-primosome: a novel priming system employing dnaA, dnaB, dnaC, and primase on a hairpin containing a dnaA box sequence. J. Biol. Chem. 265: 15134-15144.
34. MASAI, H., T. ASAI, Y. KUBOTA, K. ARAI and T. KOGOMA, 1994 Escherichia coli PriA protein is essential for inducible and constitutive stable DNA replication. EMBO J. 13: 5338-5345.
35. MAZIN, A. V., A. V. KUZMINOV, G. L. DIANOV and R. I. SALGANIK, 1991 Mechanisms of deletion formation in Escherichia coli plasmids. II. Deletions mediated by short direct repeats. Mol. Gen. Genet. 228: 209-214.
36. MCHENRY, C. S., 1982 Purification and characterization of DNA polymerase III′. Identification of τ as a subunit of the DNA Polymerase III holoenzyme. J. Biol. Chem. 257: 2657-2663.
37. MEUTH, M., 1989 Illegitimate recombination in mammalian cells, pp. 833-860, in Mobile DNA, edited by D. E. BERG, and M. M. HOWE. American Society for Microbiology, Washington, DC.
38. MILLER, J. H., 1992 A Short Course in Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
39. MOUNT, D. W., K. B. Low and S. J. EDMISTON, 1972 Dominant mutations (lex) in Escherichia coli K-12 which affect radiation sensitivity and frequency of ultraviolet light-induced mutations. J. Bacteriol. 112: 886-893.
40. NELSON, D. L., 1993 Six human genetic disorders involving mutant trinucleotide repeats, pp. 1-24 in Genome Rearrangement and Stability, edited by K. E. DAVIES and S. T. WARREN. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
41. NURSE, P., K. H. ZAVITZ and K. J. MARIANS, 1991 Inactivation of the Escherichia coli PriA DNA replication protein induces the SOS response. J. Bacteriol. 173: 6686-6693.
42. O'DONNELL, M., 1987 Accessory proteins bind a primed template and mediate rapid cycling of DNA polymerase II holoenzyme from Escherichia coli. J. Biol. Chem. 262: 16558-16565.
43. PIERCE, J. C., D. KONG and W. MASKER, 1991 The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7. Nucleic Acids Res. 19: 3901-3905.
44. RUPP, W. D., C. E. WILDE, D. L. RENO and P. HOWARD-FLANDERS, 1971 Exchanges between DNA strands in ultraviolet-irradiated Escherichia coli. J. Mol. Biol. 61: 24-44.
45. SAKAKIBARA, Y., and T. MIZUKAMI, 1980 A temperature-sensitive Escherichia coli mutant defective in DNA replication: dnaN, a new gene adjacent to the dnaA gene. Mol. Gen. Genet. 178: 541-553.
46. SAMBROOK, J., E. F. FRITSCH and T. MANIATIS, 1989 Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
47. SINGER, M., T. A. BAKER, G. SCHNITZLER, S. M. DEISCHEL, M. GOEL et al., 1989 A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53: 1-24.
48. SLATER, S. C., M. R. LIFSICS, M. O'DONNELL and R. MAURER, 1994 holE, the gene coding for the theta subunit of DNA Polymerase III of Escherichia coli: characterization of a holE mutant and comparison with a dnaQ (∈ subunit) mutant. J. Bacteriol. 176: 815-821.
49. SMITH, G., 1989 Homologous recombination in E. coli: multiple pathways for multiple reasons. Cell 58: 807-809.
50. STREISINGER, G., Y. OKADA, J. EMRICH, J. NEWTON, A. TSUGITA et al., 1967 Frameshift mtations and the genetic code. Cold Spring Harbor Symp. Quant. Biol. 31: 77-84.
51. STUDWELL, P., and M. O'DONNELL, 1990 Processive replication is contingent on the exonuclease subunit of DNA polymerase III holoenzyme. J. Biol. Chem. 265: 71-78.
52. STUDWELL-VAUGHAN, P. S., and M. O'DONNELL, 1991 Constitution of the twin polymerase of DNA polymerase III holoenzyme. J. Biol. Chem. 266: 19833-19841.
53. STUDWELL-VAUGHAN, P. S., and M. O'DONNELL, 1993 DNA polymerase III accessory proteins V. Theta encoded by kolE. J. Biol. Chem. 268: 11785-11791.
54. STUKENBERG, P. T., P. S. STUDWELL-VAUGHAN and M. O'DONNELL, 1991 Mechanism of the sliding β-clamp of DNA polymerase III holoenzyme. J. Biol. Chem. 266: 11328-11334.
55. TOUGU, K., H. PENG and K. MARIANS, 1994 Identification of a domain of Escherichia coli primase required for functional interaction with the DnaB helicase at the replication fork. J. Biol. Chem. 269: 4677-4682.
56. TRINH, T. Q., and R. R. SINDEN, 1991 Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature 352: 544-547.
57. TSENG, Y.-C., J.-L. HUNG and T.-C. V. WANG, 1994 Involvement of RecF pathway recombination genes in postreplication repair in UV-irradiated Escherichia coli cells. Mutat. Res. 315: 1-9.
58. WECHSLER, J. A., and J. D. GROSS, 1971 Escherichia coli mutants temperature-sensitive for DNA synthesis. Mol. Gen. Genet. 113: 273-284.
59. WIERDL, M., C. N. GREENE, A. DATTA, S. JINKS-ROBERTSON and T. D. PETES, 1996 Destabilization of simple repetitive DNA sequences by transcription in yeast. Genetics 143: 713-721.
60. WILLETTS, N. S., A. J. CLARK and B. Low, 1969 Genetic location of certain mutations conferring recombination deficiency in Escherichia coli. J. Bacteriol. 97: 244-249.