Formation of an F′ plasmid by recombination between imperfectly repeated chromosomal Rep sequences: A closer look at an old friend (F′128 pro lac)

Journal of Bacteriology

Volumn 185, Issue 2, 2003, Pages 660-663

  Kofoid, Eric ^a   Bergthorsson, Ulfar ^a   Slechta, E Susan ^a   Roth, John R ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC RECOMBINATION; LACTOSE OPERON; MUTAGENESIS; NONHUMAN; PLASMID; PRIORITY JOURNAL; BACTERIAL CHROMOSOME; GENETICS; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE;

ESCHERICHIA COLI; NEGIBACTERIA;

ADENOSINE TRIPHOSPHATASE; ESCHERICHIA COLI PROTEIN; F FACTOR; HELICASE; REP PROTEIN, E COLI;

ADENOSINE TRIPHOSPHATASES; BASE SEQUENCE; CHROMOSOMES, BACTERIAL; DNA HELICASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; F FACTOR; LAC OPERON; MOLECULAR SEQUENCE DATA; MUTATION; RECOMBINATION, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 0037207876     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.2.660-663.2003     Document Type: Article

References (50)

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. Anderson, R. P., and J. R. Roth. 1977. Tandem genetic duplications in phage and bacteria. Annu. Rev. Microbiol. 31:473-505.
3. Andersson, D. I., E. S. Slechta, and J. R. Roth. 1998. Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon. Science 282:1133-1135.
4. Bachellier, S., W. Saurin, D. Perrin, M. Hofnung, and E. Gilson. 1994. Structural and functional diversity among bacterial interspersed mosaic elements (BIMEs). Mol. Microbiol. 12:61-70.
5. Bull, H., M.-J. Lombardo, and S. Rosenberg. 2001. Stationary-phase mutation in the bacterial chromosome: recombination protein and DNA polymerase IV dependence. Proc. Natl. Acad. Sci. USA 98:8334-8341.
6. Cairns, J., and P. L. Foster. 1991. Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics 128:695-701.
7. Cairns, J., J. Overbaugh, and S. Miller. 1988. The origin of mutants. Nature 335:142-145.
8. Calos, M. P. 1978. DNA sequence for a low-level promoter of the lac repressor gene and an 'up' promoter mutation. Nature 274:762-765.
9. Coulondre, C., J. H. Miller, P. J. Farabaugh, and W. Gilbert. 1978. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775-780.
10. Deonier, R. C., and N. Davidson. 1976. The sequence organization of the integrated F plasmid in two Hfr strains of Escherichia coli. J. Mol. Biol. 107:207-222.
11. Farabaugh, P. J., U. Schmeissner, M. Hofer, 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. 126:847-857.
12. Foster, P. L. 1999. Mechanisms of stationary phase mutation: a decade of adaptive mutation. Annu. Rev. Genet. 33:57-88.
13. Foster, P. L. 1997. Nonadaptive mutations occur on the F′ episome during adaptive mutation conditions in Escherichia coli. J. Bacteriol. 179:1550-1554.
14. Foster, P. L., and J. M. Trimarchi. 1995. Adaptive reversion of an episomal frameshift mutation in Escherichia coli requires conjugal functions but not actual conjugation. Proc. Natl. Acad. Sci. USA 92:5487-5490.
15. Galitski, T., and J. R. Roth. 1995. Evidence that F plasmid transfer replication underlies apparent adaptive mutation. Science 268:421-423.
16. Gilson, E., W. Saurin, D. Perrin, S. Bachellier, and M. Hofnung. 1991. The BIME family of bacterial highly repetitive sequences. Res. Microbiol. 142: 217-222.
17. Gilson, E., W. Saurin, D. Perrin, S. Bachellier, and M. Hofnung. 1991. Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res. 19:1375-1383.
18. Godoy, V. G., and M. S. Fox. 2000. Transposon stability and a role for conjugational transfer in adaptive mutability. Proc. Natl. Acad. Sci. USA 97:7393-7398.
19. Guyer, M. S., R. R. Reed, J. A. Steitz, and K. B. Low. 1981. Identification of a sex-factor-affinity site in E. coli as gamma delta. Cold Spring Harbor Symp. Quant. Biol. 45:135-140.
20. Hadley, R. G., and R. C. Deonier. 1979. Specificity in formation of type II F′ plasmids. J. Bacteriol. 139:961-976.
21. Hastings, P. J., H. J. Bull, J. R. Klump, and S. M. Rosenberg. 2000. Adaptive amplification. An inducible chromosomal instability mechanism. Cell 103: 723-731.
22. Hendrickson, H., E. S. Slechta, U. Bergthorsson, D. I. Andersson, and J. R. Roth. 2002. Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proc. Natl. Acad. Sci. USA 99:2164-2169.
23. Higgins, C. F., G. F. Ames, W. M. Barnes, J. M. Clement, and M. Hofnung. 1982. A novel intercistronic regulatory element of prokaryotic operons. Nature 298:760-762.
24. Jacob, F., A. Ullmann, and J. Monod. 1965. Délétions fusionnant l'opéron lactose et un opéron purine chez Escherichia coli. J. Mol. Biol. 31:704-719.
25. Kim, S. R., G. Maenhaut-Michel, M. Yamada, Y. Yamamoto, K. Matsui, T. Sofuni, T. Nohmi, and H. Ohmori. 1997. Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA. Proc. Natl. Acad. Sci. USA 94:13792-13797.
26. Kim, S. R., K. Matsui, M. Yamada, P. Gruz, and T. Nohmi. 2001. Roles of chromosomal and episomal dinB genes encoding DNA pol IV in targeted and untargeted mutagenesis in Escherichia coli. Mol. Genet. Genomics 266: 207-215.
27. Koch, W. H., T. A. Cebula, P. L. Foster, and E. Eisenstadt. 1992. UV mutagenesis in Salmonella typhimurium is umuDC dependent despite the presence of samAB. J. Bacteriol. 174:2809-2815.
28. McKenzie, G., P. Lee, M.-J. Lombardo, P. Hastings, and S. Rosenberg. 2001. SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol. Cell 7:571-579.
29. Miller, J. H., and K. B. Low. 1984. Specificity of mutagenesis resulting from the induction of the SOS system in the absence of mutagenic treatment. Cell 37:675-682.
30. Mitchell, D. H., W. S. Reznikoff, and J. R. Beckwith. 1975. Genetic fusions defining trp and lac operon regulatory elements. J. Mol. Biol. 93:331-350.
31. Nohmi, T., M. Yamada, M. Watanabe, S. Y. Murayama, and T. Sofuni. 1992. Roles of Salmonella typhimurium umuDC and samAB in UV mutagenesis and UV sensitivity. J. Bacteriol. 174:6948-6955.
32. Pearson, W. R., and D. J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85:2444-2448.
33. Peters, J. E., I. M. Bartoszyk, S. Dheer, and S. A. Benson. 1996. Redundant homosexual F transfer facilitates selection-induced reversion of plasmid mutations. J. Bacteriol. 178:3037-3043.
34. Radicella, J., P. Park, and M. Fox. 1995. Adaptive mutation in Escherichia coli: a role for conjugation. Science 268:418-420.
35. Rosche, W. A., and P. L. Foster. 1999. The role of transient hypermutators in adaptive mutation in Escherichia coli. Proc. Natl. Acad. Sci. USA 96:6862-6867.
36. Rosenberg, S. 2001. Evolving responsively: adaptive mutation. Nat. Rev. Genet. 2:504-514.
37. Rudd, K. E. 1998. Linkage map of Escherichia coli K-12, edition 10: the physical map. Microbiol. Mol. Biol. Rev. 62:985-1019.
38. Scaife, J. 1967. Episomes. Annu. Rev. Microbiol. 21:601-638.
39. Schofield, M. A., R. Agbunag, and J. H. Miller. 1992. DNA inversions between short inverted repeats in Escherichia coli. Genetics 132:295-302.
40. Shyamala, V., E. Schneider, and G. F. Ames. 1990. Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point. EMBO J. 9:939-946.
41. Slechta, E. S., J. Harold, D. I. Andersson, and J. R. Roth. 2002. Effect of genome position on reversion during growth under selection. Mol. Microbiol. 44:1017-1032.
42. + reversion (adaptive mutation) with or without general hyper-mutability. Genetics 161:945-956.
43. Slupska, M. M., J. H. Chiang, W. M. Luther, J. L. Stewart, L. Amii, A. Conrad, and J. H. Miller. 2000. Genes involved in the determination of the rate of inversions at short inverted repeats. Genes Cells 5:425-437.
44. Tlsty, T. D., A. M. Albertini, and J. H. Miller. 1984. Gene amplification in the lac region of E. coli. Cell 37:217-224.
45. Torkelson, J., R. S. Harris, M.-J. Lombardo, J. Nagendran, C. Thulin, and S. M. Rosenberg. 1997. Genome-wide hypermutation in a subpopulation of stationary phase cells underlies recombination-dependent adaptive mutation. EMBO J. 16:3303-3311.
46. Ullmann, A., D. Perrin, F. Jacob, and J. Monod. 1965. Identification par complémentation in vitro et purification d'un segment peptide de la β-galactosidase d'Escherichia coli. J. Mol. Biol. 12:918-923.
47. van der Ende, A., C. T. Hopman, and J. Dankert. 1999. Deletion of porA by recombination between clusters of repetitive extragenic palindromic sequences in Neisseria meningitidis. Infect. Immun 67:2928-2934.
48. Welply, J. K., A. V. Fowler, J. R. Beckwith, and I. Zabin. 1980. Positions of early nonsense and deletion mutations in lacZ. J. Bacteriol. 142:732-734.
49. Whoriskey, S. K., V. H. Nghiem, P. M. Leong, J. M. Masson, and J. H. Miller. 1987. Genetic rearrangements and gene amplification in Escherichia coli: DNA sequences at the junctures of amplified gene fusions. Genes Dev. 1:227-237.
50. Wu, P. C., P. F. Johnson, and A. Newton. 1970. Operon coordination in different bacterial hosts. J. Bacteriol. 103:318-322.