Deletions at stalled replication forks occur by two different pathways

EMBO Journal

Volumn 16, Issue 11, 1997, Pages 3332-3340

  Bierne, Hélène ^a,b   Ehrlich, S Dusko ^a   Michel, Bénédicte ^a  

^a CEMAGREF   (France)

^b INSTITUT PASTEUR   (France)

Author keywords

Double strand break; Illegitimate recombination; RecBCD; Replication terminators; Topoisomerase I

Indexed keywords

DNA; DNA TOPOISOMERASE; EXONUCLEASE;

ARTICLE; BACTERIUM MUTANT; CONTROLLED STUDY; DNA REPLICATION; DNA STRAND BREAKAGE; ESCHERICHIA COLI; GENE DELETION; GENE FUSION; NONHUMAN; PLASMID; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

BASE SEQUENCE; DNA REPLICATION; DNA TOPOISOMERASES, TYPE I; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EXODEOXYRIBONUCLEASE V; EXODEOXYRIBONUCLEASES; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PLASMIDS; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

EID: 0030946855     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.11.3332     Document Type: Article

References (52)

1. Albertini, A.M., Hofer, M., Calos, M.P. and Miller, J. (1982) On the formation of spontaneous deletions: the importance of short sequences of homologies in the generation of large deletions. Cell, 29, 319-328.
2. Bierne, H. and Michel, B. (1994) When replication forks stop. Mol. Microbiol., 13, 17-23.
3. Bierne, H., Ehrlich, S.D. and Michel, B. (1991) The replication termination signal TerB of the Escherichia coli chromosome is a deletion hotspot. EMBO J., 10, 2699-2705.
4. Canceill, D. and Ehrlich, S.D. (1996) Copy-choice recombination mediated by DNA polymerase III holoenzyme from Escherichia coli. Proc. Natl Acad. Sci. USA, 93, 6647-6652.
5. Champoux, J.J. and Bullock, P.A. (1988) Possible role for the eucaryotic type I topoisomerase in illegitimate recombination. In Kucherlapati, R. and Smith, R. (eds), Genetic Recombination. American Society for Microbiology, Washington, DC, pp. 655-666.
6. Chedin, R, Dervyn, E., Dervyn, R., Ehrlich, S.D. and Noirot, P. (1994) Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol. Microbiol., 12, 561-569.
7. Christiansen, K., Svejstrup, A.B.D., Andersen, A.H. and Westergaard, O. (1993) Eukaryotic topoisomerase I-mediated cleavage requires bipartite DNA interaction. J. Biol. Chem., 268, 9690-9701.
8. Conley, E.C., Saunders, V.A., Jackson, V. and Saunders, J.R. (1986) Mechanism of intramolecular recyclization and deletion formation following transformation of Escherichia coli with linearized plasmid DNA. Nucleic Acids Res., 14, 8919-8932.
9. Dabert, P., Ehrlich, S.D. and Gruss, S. (1992) χ sequence protects against RecBCD degradation of DNA in vivo. Proc. Natl Acad. Sci. USA, 89, 12073-12077.
10. D'Alençon, E., Petranovic, M., Michel, B., Noirot, P, Aucouturier, A., Uzest, M. and Ehrlich, S.D. (1994) Copy-choice illegitimate recombination revisited. EMBO J., 13, 2725-2734.
11. Deshpande, A.M. and Newlon, C.S. (1996) DNA replication fork pause sites dependent on transcription. Science, 272, 1030-1033.
12. Ehrlich, S.D. (1989) Illegitimate recombination in bacteria. In Berg, D.E. and Howe, M.M. (eds), Mobile DNA. American Society for Microbiology, Washington, DC, pp. 799-832.
13. Gordenin, D.A., Malkova, A.L., Peterzen, A., Kulikov, V.N., Pavlov, Y.I., Perkins, E. and Resnick, M.A. (1992) Transposon Tn5 excision in yeast: influence of DNA polymerase α, δ, and ε and repair genes. Proc. Natl Acad. Sci. USA, 89, 3785-3789.
14. Henningfel, K.A. and Hecht, S.M. (1995) A model for topoisomerase I-mediated insertions and deletions with duplex DNA substrates containing branches, nicks and gaps. Biochemistry, 34, 6120-6129.
15. Hiasa, H., Digates, R.J. and Marians, K.J. (1994) Decatening activity of Escherichia coli DNA gyrase and topoisomerases I and III during oriC and pBR322 DNA replication in vitro. J. Biol. Chem., 269, 2093-2099.
16. Hill, T.M. (1992) Arrest of bacterial DNA replication. Annu. Rev. Microbiol., 46, 603-633.
17. Hill, T.M., Pelletier, A.J., Tecklenburg, M.L. and Kuempel, P.L. (1988) Identification of the DNA sequence from the E. coli terminus region that halts replication forks. Cell, 55, 459-466.
18. Horinouchi, S. and Weisblum, B. (1982) Nucleotide sequence and functional analysis of pE194. J. Bacteriol, 150, 804-814.
19. Horiuchi, T. and Fujimura, Y. (1995) Recombinational rescue of the stalled DNA replication fork: a model based on analysis of an Escherichia coli strain with a chromosome region difficult to replicate. J. Bacteriol., 177, 783-791.
20. Horiuchi, T., Fujimara, Y., Nishitani, H., Kobayashi, T. and Hidaka, M. (1994) The DNA replication fork blocked at the Ter site may be an entrance for the RecBCD enzyme into duplex DNA. J. Bacteriol., 176, 4656-4663.
21. Hutchinson, F. (1993) Induction of large DNA deletion by persistent nicks: a new hypothesis. Mutat. Res., 299, 211-218.
22. Ikeda, H. (1990) In Cozarelli, N.R. and Wang, J.C. (eds). DNA Topology and its Biological Effects. Cold Spring Harbor Laboratory Press, Cold Spring Harbor. NY, pp. 341-359.
23. King, J.S., Fairley, C.F. and Morgan, W.F. (1994) Bridging the gap. J. Biol. Chem., 269, 13061-13064.
24. Kirkegaard, K. and Wang, J.C. (1985) Bacterial DNA topoisomerases I can relax positively supercoiled DNA containing a single-stranded loop. J. Mol. Biol., 185, 625-637.
25. Kong, D. and Masker, W. (1994) Deletion between direct repeats in T7 DNA stimulated by double-strand breaks. J. Bacteriol., 176, 5904-5911.
26. Krawczack, M. and Cooper, D.N. (1991) Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment. Hum. Genet., 86, 425-441.
27. Kuzminov, A. (1995) Collapse and repair of replication forks in Escherichia coli. Mol Microbiol., 16, 373-384.
28. Lin, F.L., Sperle, K. and Sternberg, N. (1984) Model for homologous recombination during transfer of DNA into mouse L cells: role for DNA ends in the recombination process. Mol. Cell. Biol., 4, 1020-1034.
29. Liu, B. and Alberts, B.M. (1995) Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science, 267, 1131-1137.
30. Messer, W., Bellekes, U. and Lother, H. (1985) Effect of dam methylation on the activity of the E.coli replication origin, oriC. EMBO J., 4, 1327-1332.
31. Meuth, M. (1989) Illegitimate recombination in mammalian cells. In Berg, D.E. and Howe, M.M. (eds), Mobile DNA. American Society for Microbiology, Washington, DC, pp. 833-860.
32. Michel, B., Ehrlich, S.D. and Uzest, M. (1997) DNA double-strand breaks caused by replication arrests. EMBO J., 16, 430-438.
33. Moore, J.K. and Haber, J.E. (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol. Cell. Biol., 16, 2164-2173.
34. Painter, R.B. and Kapp, L.N. (1991) Replication intermediates as substrates for DNA rearrangements. Mutat. Res., 262, 21-23.
35. Prentki, P. and Krisch, H.M. (1984) In vitro insertional mutagenesis with a selectable DNA fragment. Gene, 29, 303-313.
36. Roth, D. and Wilson, J. (1988) Illegitimate recombination in mammalian cells. In Kucherlapati, R. and Smith, G.R. (eds), Genetic Recombination. American Society for Microbiology, Washington, DC, pp. 621-653.
37. Schielst, R.H. and Petes, T.D. (1991) Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA. 88, 7585-7589.
38. Sharma, B. and Hill, T.M. (1995) Insertion of inverted Ter sites into the terminus region of the Escherichia coli chromosome delays completion of DNA replication and disrupts the cell cycle. Mol. Microbiol., 18, 45-61.
39. Shuman, S. (1992) Two classes of DNA end-joining reactions catalyzed by vaccinia topoisomerase I. J. Biol. Chem., 267, 16755-16758.
40. Singer, B.S. and Westlye, J. (1988) Deletion formation in bacteriophage T4. J. Mol. Biol., 202, 233-243.
41. Sorokin, A., Serror, P., Pujic, P., Azevedo, V. and Ehrlich, S.D. (1995) The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mssA and rpsA gene products. Microbiology, 141, 311-319.
42. Stary, A. and Sarasin, A. (1992) Molecular analysis of DNA junctions produced by illegitimate recombination in human cells. Nucleic Acids Res., 20, 4269-4274.
43. Steck, T.R., Franco, R.J., Wang, J.-Y. and Drlica, K. (1993) Topoisomerase mutations affect the relative abundance of many Escherichia coli proteins. Mol. Microbiol., 10, 473-481.
44. Sternglanz, R., Dinardo, S., Voekel, K.A., Nishimura, Y., Hirota, Y., Becherer, K., Zumstein, L. and Wang, J.C. (1981) Mutations in the gene coding for Escherichia coli DNA topoisomerase I affect transcription and transposition. Proc. Natl Acad. Sci. USA, 78, 2747-2751.
45. Te Riele, H., Michel, B. and Ehrlich, S.D. (1986) Are single-stranded circles intermediates in plasmid DNA replication? EMBO J., 5, 631-637.
46. Thode, S., Schäfer, A., Pfeiffer, P. and Vielmetter, W. (1990) A novel pathway of end-to-end joining. Cell, 60, 921-928.
47. Tse-Dinh, Y.C., McCarron, B.G., Arentzen, R. and Chowdhry, V. (1983) Mechanistic study of E. coli DNA topoisomerase I: cleavage of oligonucleotides. Nucleic Acids Res., 11, 8691-8701.
48. Uzest, M., Ehrlich, S.D. and Michel, B. (1995) Lethality of rep recB and rep recC double mutants of Escherichia coli. Mol. Microbiol., 17, 1177-1188.
49. Vilette, D., Uzest, M., Ehrlich, S.D. and Michel, B. (1992) DNA transcription and repressor binding affect deletion formation in Escherichia coli plasmids. EMBO J., 11, 3629-3634.
50. Vilette, D., Ehrlich, S.D. and Michel, B. (1995) Transcription-induced deletions in Escherichia coli plasmids. Mol. Microbiol., 17, 493-504.
51. Zhu, J. and Schiestl, R.H. (1996) Topoisomerase I involvement in illegitimate recombination in Saccharomyces cerevisiae. Mol. Cell. Biol., 16, 1805-1812.
52. Zipursky, S.L. and Marians, K.J. (1980). Identification of two Escherichia coli factor Y effector sites near the origins of replication of plasmids ColE1 and pBR322. Proc. Natl Acad. Sci USA, 77, 6521-6525.