Characterization of the uup locus and its role in transposon excisions and tandem repeat deletions in Escherichia coli

Journal of Bacteriology

Volumn 182, Issue 7, 2000, Pages 1978-1986

  Reddy, Manjula ^a   Gowrishankar, J ^a  

^a CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIOPHAGE MU; CONTROLLED STUDY; DNA SEQUENCE; ESCHERICHIA COLI; GENE DELETION; GENE INSERTION; GENE LOCUS; GENE MUTATION; GENE OVEREXPRESSION; MOLECULAR CLONING; NONHUMAN; OPERON; PRIORITY JOURNAL; TANDEM REPEAT; TRANSPOSON;

ATP-BINDING CASSETTE TRANSPORTERS; BACTERIAL PROTEINS; DNA TRANSPOSABLE ELEMENTS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE DOSAGE; GENE EXPRESSION; GENE FREQUENCY; GENES, BACTERIAL; GENES, REPORTER; GENETIC COMPLEMENTATION TEST; MUTAGENESIS, INSERTIONAL; OPERON; PHYSICAL CHROMOSOME MAPPING; PROMOTER REGIONS (GENETICS); REC A RECOMBINASES; RECOMBINATION, GENETIC; RNA, BACTERIAL; SEQUENCE DELETION; TANDEM REPEAT SEQUENCES; TRANSCRIPTION FACTORS;

BACTERIA (MICROORGANISMS); ENTEROBACTERIA PHAGE MU; ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0034102178     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.182.7.1978-1986.2000     Document Type: Article

References (53)

1. Albertini, A. M., M. Hofer, M. P. Calos, and J. H. Miller. 1982. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell 29:319-328.
2. Berlyn, M. K. B. 1998. Linkage map of Escherichia coli K-12, edition 10: the traditional map. Microbiol. Mol. Biol. Rev. 62:814-984.
3. Bierne, H., D. Vilette, S. D. Ehrlich, and B. Michel. 1997. Isolation of a dnaE mutation which enhances RecA-independent homologous recombination in the Escherichia coli chromosome. Mol. Microbiol. 24:1225-1234.
4. Blattner, F. R., G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462.
5. Bzymek, M., C. J. Saveson, V. V. Feschenko, and S. T. Lovett. 1999. Slipped misalignment mechanisms of deletion formation: in vivo susceptibility to nucleases. J. Bacteriol. 181:477-482.
6. Canceill, D., and S. D. Ehrlich. 1996. Copy-choice recombination mediated by DNA polymerase III holoenzyme from Escherichia coli. Proc. Natl. Acad. Sci. USA 93:6647-6652.
7. d'Alencon, E., M. Petranovic, B. Michel, P. Noirot, A. Aucouturier, M. Uzest, and S. D. Ehrlich. 1994. Copy-choice illegitimate DNA recombination revisited. EMBO J. 13:2725-2734.
8. DasGupta, U., K. Weston-Hafer, and D. E. Berg. 1987. Local DNA sequence control of deletion formation in Escherichia coli plasmid pBR322. Genetics 115:41-49.
9. DiNardo, S., K. A. Voelkel, R. Sternglanz, A. E. Reynolds, and A. Wright. 1982. Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes. Cell 31:43-51.
10. Egner, C., and D. E. Berg. 1981. Excision of transposon Tn5 is dependent on the inverted repeats but not on the transposase function of Tn5. Proc. Natl. Acad. Sci. USA 78:459-463.
11. Farabaugh, P. J., and J. H. Miller. 1978. Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli. J. Mol. Biol. 126:847-863.
12. 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.
13. Foster, T. J., V. Lundblad, S. Hanley-Way, S. M. Halling, and N. Kleckner. 1981. Three Tn10-associated excision events: relationship to transposition and role of direct and inverted repeats. Cell 23:215-227.
14. Gifford, C. M., and S. S. Wallace. 1999. The genes encoding formamidopyrimidine and MutY DNA glycosylases in Escherichia coli are transcribed as part of complex operons. J. Bacteriol. 181:4223-4236.
15. Gowrishankar, J. 1985. Identification of osmoresponsive genes in Escherichia coli: evidence for participation of potassium and proline transport systems in osmoregulation. J. Bacteriol. 164:434-445.
16. Hopkins, J. D., M. Clements, and M. Syvanen. 1983. New class of mutations in Escherichia coli (uup) that affect precise excision of insertion elements and bacteriophage Mu growth. J. Bacteriol. 153:384-389.
17. Kleckner, N., J. Bender, and S. Gottesman. 1991. Uses of transposons with emphasis on Tn10. Methods Enzymol. 204:139-180.
18. Koh, Y.-S., and J.-H. Roe. 1995. Isolation of a novel paraquat-inducible (pqi) gene regulated by the soxRS locus in Escherichia coli. J. Bacteriol. 177:2673-2678.
19. Koh, Y.-S., and J.-H. Roe. 1996. Dual regulation of the paraquat-inducible gene pqi-5 by SoxS and RpoS in Escherichia coli. Mol. Microbiol. 22:53-61.
20. Kohara, Y., K. Akiyama, and K. Isono. 1987. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50:495-508.
21. Lerner, C. G., and M. Inouye. 1990. Low copy number plasmids for regulated low-level expression of cloned genes in Escherichia coli with blue/white insert screening capability. Nucleic Acids Res. 18:4631.
22. Levy, M. S., E. Balbinder, and R. Nagel. 1993. Effect of mutations in SOS genes on UV-induced precise excision of Tn10 in Escherichia coli. Mutat. Res. 293:241-247.
23. Linton, K. J., and C. F. Higgins. 1998. The Escherichia coli ATP-binding cassette (ABC) proteins. Mol. Microbiol. 28:5-13.
24. Lohmann, T. M., and M. E. Ferrari. 1994. Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu. Rev. Biochem. 63:527-570.
25. Lundblad, V., and N. Kleckner. 1982. Mutants of Escherichia coli K12 which affect excision of transposon Tn10, p. 245-258. In J. F. Lemontt and W. M. Generoso (ed.), Molecular and cellular mechanisms of mutagenesis. Academic Press, New York, N.Y.
26. Lundblad, V., and N. Kleckner. 1985. Mismatch repair mutations of Escherichia coli K12 enhance transposon excision. Genetics 109:3-19.
27. MacPhee, D. G., and L. M. Hafner. 1988. Antimutagenic effects of chemicals on mutagenesis resulting from excision of a transposon in Salmonella typhimurium. Mutat. Res. 207:99-106.
28. McClellan, J. A., P. Boublikova, E. Palecek, and D. M. J. Lilley. 1990. Superhelical torsion in cellular DNA responds directly to environmental and genetic factors. Proc. Natl. Acad. Sci. USA 87:8373-8377.
29. Meyer, R. R., and P. S. Laine. 1990. The single-stranded DNA-binding protein of Escherichia coli. Microbiol. Rev. 54:342-380.
30. Miller, H. I., and D. I. Friedman. 1980. An E. coli gene product required for λ site-specific recombination. Cell 20:711-719.
31. Miller, J. H. 1992. A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
32. Modrich, P. 1991. Mechanisms and biological effects of mismatch repair. Annu. Rev. Genet. 25:229-253.
33. Murphy, K. C. 1998. Use of bacteriophage λ recombination functions to promote gene replacement in Escherichia coli. J. Bacteriol. 180:2063-2071.
34. Nagel, R., A. Chan, and E. Rosen. 1994. Ruv and recG genes and the induced precise excision of Tn10 in Escherichia coli. Mutat. Res. 311:103-109.
35. Pinder, D. J., C. E. Blake, J. C. Lindsey, and D. R. F. Leach. 1998. Replication strand preference for deletions associated with DNA palindromes. Mol. Microbiol. 28:719-727.
36. Pruss, G. J., S. H. Manes, and K. Drlica. 1982. Escherichia coli DNA topoisomerase I mutants: increased supercoiling is corrected by mutations near gyrase genes. Cell 31:35-42.
37. Reddy, M., and J. Gowrishankar. 1997. A genetic strategy to demonstrate the occurrence of spontaneous mutations in nondividing cells within colonies of Escherichia coli. Genetics 147:991-1001.
38. Reddy, M., and J. Gowrishankar. 1997. Identification and characterization of ssb and uup mutants with increased frequency of precise excision of transposon Tn10 derivatives: nucleotide sequence of uup in Escherichia coli. J. Bacteriol. 179:2892-2899.
39. Richardson, S. M. H., C. F. Higgins, and D. M. J. Lilley. 1984. The genetic control of DNA supercoiling in Salmonella typhimurium. EMBO J. 3:1745-1752.
40. Ripley, L. S. 1990. Frameshift mutation: determinants of specificity. Annu. Rev. Genet. 24:189-213.
41. Rudd, K. E. 1998. Linkage map of Escherichia coli K-12, edition 10: the physical map. Microbiol. Mol. Biol. Rev. 62:985-1019.
42. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
43. + assimilation and osmoregulation in GOGAT (glutamate synthase)-deficient mutants of Escherichia coli. J. Bacteriol. 178:4105-4114.
44. Saveson, C. J., and S. T. Lovett. 1997. Enhanced deletion formation by aberrant DNA replication in Escherichia coli. Genetics 146:457-470.
45. Schaaper, R. M., B. N. Danforth, and B. W. Glickman. 1986. Mechanisms of spontaneous mutagenesis: an analysis of the spectrum of spontaneous mutation in the Escherichia coli lacI gene. J. Mol. Biol. 189:273-284.
46. Singer, M., T. A. Baker, G. Schnitzler, S. M. Deischel, M. Goel, W. Dove, K. J. Jaacks, A. D. Grossman, J. W. Erickson, and C. A. Gross. 1989. A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53:1-24.
47. Studier, F. W., and B. A. Moffatt. 1986. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189:113-130.
48. Syvanen, M. 1988. Bacterial insertion sequences, p. 331-356. In R. Kucherlapati and G. R. Smith (ed.), Genetic recombination. American Society for Microbiology, Washington, D.C.
49. Syvanen, M., J. D. Hopkins, T. J. Griffin IV, T.-Y. Liang, K. Ippen-Ihler, and R. Kolodner. 1986. Stimulation of precise excision and recombination by conjugal proficient F′ plasmids. Mol. Gen. Genet. 203:1-7.
50. Trinh, T. Q., and R. R. Sinden. 1993. The influence of primary and secondary DNA structure in deletion and duplication between direct repeats in Escherichia coli. Genetics 134:409-422.
51. Wang, P., J. Yang, and A. J. Pittard. 1997. Promoters and transcripts associated with the aroP gene of Escherichia coli. J. Bacteriol. 179:4206-4212.
52. Washburn, B. K., and S. R. Kushner. 1991. Construction and analysis of deletions in the structural gene (uvrD) for DNA helicase II of Escherichia coli. J. Bacteriol. 178:2569-2575.
53. Weston-Hafer, K., and D. E. Berg. 1989. Palindromy and the location of deletion endpoints in Escherichia coli. Genetics 121:651-658.