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Chapter 8 : Illegitimate Recombination in Bacteria

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Abstract:

Illegitimate recombination is a ubiquitous phenomenon and includes three types of events. In the first class, rearrangements occur by recombination between short homologous sequences. A second class is associated with site-specific elements. A last class groups all rearrangements in which the newly linked sequences share less than 3 bp of homology and have no homology with known specific sites. Oxidative lesions are known to induce rearrangements. Deletions by illegitimate recombination between short homologous sequences were reported in mutants, in which a defect in iron metabolism regulation results in increased oxidative damage. In bacteria, transcription inhibits deletion between tandemly repeated sequences 10-fold. In contrast, transcription was shown to increase recombination between nonhomologous sequence. The stimulation of transposon excision by rolling-circle replication adds to the long list of indirect evidence that supports the occurrence of the replication slippage events in vivo. Most of the genetic studies of illegitimate recombination were performed in , either on the chromosome or with bacteriophages. Most of the recombination events between short homologous sequences occur independently from the action of RecA, since the length considered is far below the minimum efficient processing segment (MEPS). Topoisomerases are enzymes that modify the supercoiling of molecules through transient breakage and ligation of DNA strands. The first evidence that topoisomerases may promote rearrangements in bacteria came from the work of Ikeda and collaborators. Illegitimate recombination is a major issue in eukaryotes, because it is at the origin of numerous pathological disorders.

Citation: Michel B. 1999. Illegitimate Recombination in Bacteria, p 129-150. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch8

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DNA Synthesis
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Type II Topoisomerase
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Replication Fork
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Type I Topoisomerase
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Figures

Image of FIGURE 1
FIGURE 1

Model of deletion by replication slippage between two short homologous sequences. The directly repeated (DR) sequences are indicated by shaded boxes and the arrows above the boxes. The hatched lines represent newly synthesized DNA strands, and a, b, and с are the DNA regions flanking (a and c) and between (b) the repeated sequences. A pause of the DNA polymerase during the synthesis of the first DR encountered allows the opening of the DNA. Erroneous pairing with the other DR leads to the loss of the b region and of one of the repeated sequences. The deletion is stabilized by replication continuation. Duplication of the b sequence and of one of the DR occurs when DNA synthesis pauses at the second DR encountered and the newly synthesized DNA folds back, allowing erroneous pairing with the first DR and a second replication of the b region (not shown).

Citation: Michel B. 1999. Illegitimate Recombination in Bacteria, p 129-150. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch8
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Image of FIGURE 2
FIGURE 2

Model of deletion between two short homologous sequences by SSA. The directly repeated (DR) sequences are indicated by grey boxes and the arrows above the boxes. The initiating event is a DNA DSB occurring between the repeated sequences. Exonucleolytic degradation of one of the strands renders short homologous sequences single stranded, which allows them to pair. Degradation by exonucleases of the single-stranded tails, gap filling by a polymerase, and ligation lead to the deletion of the b region (defined in the legend to Fig. 1 ) and of one DR.

Citation: Michel B. 1999. Illegitimate Recombination in Bacteria, p 129-150. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch8
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Image of FIGURE 3
FIGURE 3

Repair of a broken replication fork by SSA (reproduced from reference ). A replication fork arrested at a (T) site is represented. Short repeated sequences (1 and 2) are shown as bold lines. (a) Breakage of the lagging-strand template in the vicinity of , generating a DSB. (b) Nucleolytic degradation of the exposed 5′ ends, generating a 3′-tailed single-stranded region, (c) Annealing of complementary sequences 1 and 2. (d) The intermediate is repaired by removal of the 3′ tail, gap filling, and ligation. A round of replication produces the deletant plasmid molecule. Arrows indicate the 3′ ends of leading and lagging strands.

Citation: Michel B. 1999. Illegitimate Recombination in Bacteria, p 129-150. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch8
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Image of FIGURE 4
FIGURE 4

Model of SbcCD action (reproduced, with permission, from reference ). During the replication of a palindromic sequence, intrastrand base pairing can cause pausing of DNA replication and is a potential precursor for deletion. To reinitiate replication, the SbcCD protein removes the secondary structure and generates a DSB. This DSB is repaired by homologous recombination with the sister chromosome to allow the reconstitution of a replication fork. This model specifically predicts that the intact copy of the palindromic sequence is replicated again after reconstitution of the replication fork.

Citation: Michel B. 1999. Illegitimate Recombination in Bacteria, p 129-150. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch8
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Image of FIGURE 5
FIGURE 5

Schematic model of deletion formation by one-ended transposition. The transposon is shown as a shaded box; the bound transposase is shown as an oval. One end of the transposon and the target (T) are acted upon by the transposase. The region (b) between the transposon end and the target is excised by the transposase and deleted. Regions a and с are the regions flanking the deleted sequences.

Citation: Michel B. 1999. Illegitimate Recombination in Bacteria, p 129-150. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch8
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Image of FIGURE 6
FIGURE 6

Model for deletion formation by erroneous action of gyrase. Gyrase is shown as two rectangles, corresponding to the two subunits of the enzyme. Gyrase binds to double-stranded DNA and introduces a double-strand cut. Exchange of subunits between two gyrase molecules, acting at different places on a DNA molecule or on two different DNA molecules, and resealing by gyrase lead to rearrangement. Bold and thin lines are two different DNA molecules. White and gray rectangles are two different gyrase molecules.

Citation: Michel B. 1999. Illegitimate Recombination in Bacteria, p 129-150. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch8
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Image of FIGURE 7
FIGURE 7

Models for TopA-mediated deletion formation between divergent replication forks blocked at sites (reproduced from reference ). The 1- 2 replication intermediate is partially represented; template strands are shown as thin lines, and newly synthesized leading and lagging strands are shown as continuous and interrupted thick arrows, respectively. О and T represent and replication terminators, respectively. The 5′ and 3′ ends generated by topoisomerase cleavage are represented by a point and a thin arrow, respectively. Deletion can result either from the junction of the template strands (model A) or from the junction of the newly synthesized strands (model B). In model A, topoisomerase-mediated cleavage occurs at each of the two replication forks, in the vicinity of sites (A1); a topoisomerase molecule (a) covalently linked to the 5′ end generated on the leading-strand template catalyzes by error ligation with the 3′ end created by another topoisomerase molecule (b) at the other replication fork (A2); this leads to the excision of a gap-containing molecule, which is converted into a circular double-stranded plasmid by continuation of leading-strand synthesis (A3). In model B, a topoisomerase molecule cleaves the lagging strand in the vicinity of a site (B1); this molecule, bound to the 5′ end, catalyzes the joining to the 3′ end of the leading strand at the other blocked replication fork (B2); a circular double-stranded deletant plasmid is generated by another round of replication (B3).

Citation: Michel B. 1999. Illegitimate Recombination in Bacteria, p 129-150. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch8
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References

/content/book/10.1128/9781555818180.chap8
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. Allgood, N. D.,, and T. J. Silhavy. 1991. Escherichia coli xonA (sbcB) mutants enhance illegitimate recombination. Genetics 127: 671 680.
3. Anagnostopoulos, C., 1990. Genetic rearrangements in Bacillus subtilis , p. 361 371. In K. Drlika, and M. Riley (ed.), The Bacterial Chromosome. American Society for Microbiology, Washington, D.C..
4. Ashley, C. T., Jr.,, and S. T. Warren. 1995. Trinucleotide repeat expansion and human disease. Annu. Rev. Genet. 29: 703 728.
5. Bachellier, S.,, E. Gilson,, M. Hofîhung,, and C. W. Hill,. 1996. Repeated sequences, p. 2012 2040. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. American Society for Microbiology, Washington, D.C..
6. Bachellier, S.,, J. M. Clement,, M. Hofhung,, and E. Gilson. 1997. Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence. Genetics 145: 551 562.
7. Balbinder, E.,, B. Coll,, J. Hutchinson,, A. S. Bianchi,, T. Groman,, K. A. Wheeler,, and M. Meyer. 1993. Participation of the SOS system in producing deletions in E. coli plasmids. Mutat. Res. 286: 253 265.
8. Bashkirov, V. I.,, F. K. Khasanov,, and A. A. Prozorov. 1987. Illegitimate recombination in Bacillus subtilis: nucleotide sequences at recombinant DNA junctions. Mol. Gen. Genet. 210: 578 580.
9. Bedinger, P.,, M. Munn,, and B. M. Alberts. 1989. Sequence-specific pausing during in vitro DNA replication on double-stranded DNA templates. J. Biol. Chem. 264: 16880 16886.
10. Berg, D. E.,, C. Egner,, and J. B. Lowe. 1983. Mechanism of F factor-enhanced excision of transposon Tn 5 . Gene 22: 1 7.
11. 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.
12. Bichara, M.,, S. Schumacher,, and R. P. P. Fuchs. 1995. Genetic instability within monotonous runs of CpG sequences in Escherichia coli . Genetics 140: 897 907.
13. Bierne, H.,, S. D. Ehrlich,, and B. Michel. 1995. Competition between parental and recombinant plasmids affects the measure of recombination frequencies. Plasmid 33: 101 112.
14. Bierne, H.,, S. D. Ehrlich,, and B. Michel. 1997. Deletions at stalled replication forks occur by two different pathways. EMBO J. 16: 3332 3340.
15. Bierne, H.,, S. D. Ehrlich,, and B. Michel. 1991. The replication termination signal TerB of the Escherichia coli chromosome is a deletion hot spot. EMBO J. 10: 2699 2705.
16. Bierne, H.,, and B. Michel. 1994. When replication forks stop. Mol. Microbiol. 13: 17 23.
17. 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 1474.
18. Bowater, R. P.,, W. A. Rosche,, A. Jaworski,, R. R. Sinden,, and R. D. Wells. 1996. Relationship between Escherichia coli growth and deletions of CTG • CAG triplet repeats in plasmids. J. Mol. Biol. 264: 82 96.
19. Canceill, D.,, E. Viguera,, and S. D. Ehrlich. Replication slippage of different DNA polymerases is inversely related to their strand displacement efficiency. Submitted for publication.
20. 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.
21. Cao, Y.,, and T. Kogoma. 1995. The mechanism of recA polA lethality: suppression by RecA-independent recombination repair activated by the lexA (Def) mutation in Escherichia coli . Genetics 139: 1483 1494.
22. Chalker, A. F.,, E. A. Okely,, A. Davison,, and D. R. F. Leach. 1993. The effects of central asymmetry on the propagation of palindromic DNA in bacteriophage lambda are consistent with cruciform extrusion in vivo . Genetics 133: 143 148.
23. Chalmers, R. ML, and N. Kleckner. 1996. IS 10/Tn 10 transposition efficiently accommodates diverse transposon end configurations. EMBO J. 15: 5112 5122.
24. Chan, A.,, M. S. Levy,, and R. Nagel. 1994. RecN SOS gene and induced precise excision of Tn 10 in Escherichia coli . Mutat. Res. Lett. 325: 75 79.
25. Chedin, F.,, E. Dervyn,, R. Dervyn,, S. D. Ehrlich,, and P. Noirot. 1994. Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol. Microbiol. 12: 561 569.
26. Chedin, F.,, R. Dervyn,, S. D. Ehrlich,, and P. Noirot. 1997. Apparent and real recombination frequencies in multicopy plasmids: the need for a novel approach in frequency determination. J. Bacteriol. 179: 754 761.
27. Conley, E. C.,, and J. R. Saunders. 1984. Recombination-dependent recircularization of linearized pBR322 plasmid DNA following transformation of Escherichia coli . Mol. Gen. Genet. 194: 211 218.
28. Conley, E. C.,, V. A. Saunders,, V. Jackson,, and J. R. Saunders. 1986. Mechanism of intramolecular recyclization and deletion formation following transformation of Escherichia coli with linearized plasmid DNA. Nucleic Acids Res. 14: 8919 8932.
29. Conley, E. C.,, V. A. Saunders,, and J. R. Saunders. 1986. Deletion and rearrangement of plasmid DNA during transformation of Escherichia coli with linear plasmid molecules. Nucleic Acids Res. 14: 8905 8917.
30. Connelly, J. C.,, E. S. de Leau,, E. A. Okely,, and D. R. Leach. 1997. Overexpression, purification and characterisation of the SbcCD protein from Escherichia coli . J. Biol. Chem. 272: 19819 19826.
31. 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.
32. Darlow, J. M.,, and D. R. F. Leach. 1995. The effects of trinucleotide repeats found in human inherited disorders on palindrome inviability in Escherichia coli suggest hairpin folding preferences in vivo . Genetics 141: 825 832.
33. Davison, A.,, and D. R. Leach. 1994. The effects of nucleotide sequence changes on DNA secondary structure formation in Escherichia coli are consistent with cruciform extrusion in vivo . Genetics 137: 361 368.
34. Dempsey, L. A.,, and D. A. Dubnau. 1989. Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration. J. Bacteriol. 171: 2856 2865.
35. Desomer, J.,, M. Crespi,, and M. Van Montagu. 1991. Illegitimate integration of non-replicative vectors in the genome of Rhodococcus fascians upon electrotransformation as an insertional mutagenesis system. Mol. Microbiol. 5: 2115 2124.
36. DiGate, R. J.,, and K. J. Marians. 1988. Identification of a potent decatenating enzyme from Escherichia coli . J. Biol. Chem. 263: 13366 13373.
37. DiGate, R. J.,, and K. J. Marians. 1989. Molecular cloning and DNA sequence analysis of Escherichia coli topB, the gene encoding topoisomerase III. J. Biol. Chem. 264: 17924 17930.
38. Ehrlich, S. D., 1989. Illegitimate recombination in bacteria, p. 799 832. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C..
39. Ehrlich, S. D.,, H. Bierne,, E. d'Alencon,, D. Vilette,, M. Petranovic,, P. Noirot,, and B. Michel. 1993. Mechanisms of illegitimate recombination. Gene 135: 161 166.
40. 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 lad gene of Escherichia coli . J. Mol. Biol. 126: 847 857.
41. Foster, P. L.,, and J. Cairns. 1994. The occurrence of heritable Mu excisions in starving cells of Escherichia coli . EMBO J. 13: 5240 5244.
42. Foster, T. J.,, V. Lundblad,, S. Hanley-Way,, S. M. Hailing,, and N. Kleckner. 1981. Three Tn 10 -associated excision events: relationship to transposition and role of direct and inverted repeats. Cell 23: 215 227.
43. Gibson, F. P.,, D. R. F. Leach,, and R. G. Lloyd. 1992. Identification of sbcD mutations as cosuppressors of recBC that allow propagation of DNA palindromes in Escherichia coli K-12. J. Bacteriol. 174: 1222 1228.
44. Gilson, E.,, W. Saurin,, D. Perrin,, S. Bachellier,, and M. Hofhung. 1991. Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res. 19: 1375 1383.
45. Glickman, B. W.,, and L. S. Ripley. 1984. Structural intermediates of deletion mutagenesis: a role for palindromic DNA. Proc. Natl. Acad. Sci. USA 81: 512 516.
46. Haber, J. E. 1995. In vivo biochemistry: physical monitoring of recombination induced by site-specific endonucleases. Bioessays 17: 609 620.
47. Hanada, K.,, T. Ukita,, Y. Kohno,, K. Saito,, J. Kato,, and H. Ikeda. 1997. RecQ DNA helicase is a suppressor of illegitimate recombination in Escherichia coli . Proc. Natl. Acad. Sci. USA 94: 3860 3865.
48. Herrmann, R.,, K. Neugebauer,, H. Zentgraf,, and H. Schaller. 1978. Transposition of a DNA sequence determining kanamycin resistance into the single-stranded genome of bacteriophage fd. Mol. Gen. Genet. 159: 171 178.
49. Higgins, C. F.,, C. J. Dorman,, D. A. Stirling,, L. Waddell,, I. R. Booth,, G. May,, and E. Bremer. 1988. A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli . Cell 52: 569 584.
50. Hill, T. M., 1996. Features of the chromosomal terminus region, p. 1602 1614. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (éd.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. American Society for Microbiology, Washington, D.C..
51. Hulton, C. S.,, C. F. Higgins,, and P. M. Sharp. 1991. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5: 825 834.
52. Hutchinson, F. 1993. Induction of large DNA deletions by persistent nicks—a new hypothesis. Mutat. Res. 299: 211 218.
53. Ikeda, H., 1990. DNA topoisomerase-mediated illegitimate recombination, p. 341 356. In N. R. Cozarelli, and J. C. Wang (ed.) DNA Topology and Its Biological Effects . Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
54. Ikeda, H.,, K. Moriya,, and T. Matsumoto. 1981. In vitro study of illegitimate recombination: involvement of DNA gyrase. Cold Spring Harbor Symp. Quant. Biol. 45: 399 408.
55. Ishiura, M.,, N. Hazumi,, H. Shinagawa,, A. Nakata,, T. Uchida,, and Y. Okada. 1990. RecA-independent high-frequency deletion of recombinant cosmid DNA in Escherichia coli . J. Gen. Microbiol. 136: 69 79.
55a.. Jackson, A.,, R. Chen,, and L. A. Loeb. 1998. Induction of microsatellite instability by oxidative DNA damage. Proc. Natl. Acad. Sci. USA 95: 12468 12473.
56. Janniere, L.,, C. Bruand,, and S. D. Ehrlich. 1990. Structurally stable Bacillus subtilis cloning vectors. Gene 87: 53 61.
57. Jarvis, E. D.,, S. Cheng,, and R. Rudner. 1990. Genetic structure and DNA sequences at junctions involved in the rearrangements of Bacillus subtilis strains carrying the Trp26 mutation. Genetics 126: 785 797.
58. Jilk, R. A.,, J. C. Makris,, L. Borchardt,, and W. S. Reznikoff. 1993. Implications of Tn5-associated adjacent deletions. J. Bacteriol. 175: 1264 1271.
59. Kalpana, G. V.,, B. R. Bloom,, and W. R. Jacobs. 1991. Insertional mutagenesis and illegitimate recombination in mycobacteria. Proc. Natl. Acad. Sci. USA 88: 5433 5437.
60. Kang, S. M.,, K. Ohshima,, M. Shimizu,, S. Amirhaeri,, and R. D. Wells. 1995. Pausing of DNA synthesis in vitro at specific loci in CTG and CGG triplet repeats from human hereditary disease genes. J. Biol. Chem. 270: 27014 27021.
61. Khasanov, F. K.,, D. J. Zvingila,, A. A. Zainullin,, A. A. Prozorov,, and V. I. Bashkirov. 1992. Homologous recombination between plas-mid and chromosomal DNA in Bacillus subtilis requires approximately 70 bp of homology. Mol. Gen. Genet. 234: 494 497.
62. King, S. R.,, and J. P. Richardson. 1986. Role of homology and pathway specificity for recombination between plasmids and bacteriophage lambda. Mol. Gen. Genet. 204: 141 147.
63. Kleckner, N.,, R. M., Chalmers,, D. Kwon,, J. Sakai,, and S. Bolland,. 1996. Tn10 and IS1O transposition and chromosome rearrangements: mechanisms and regulation in vivo and in vitro, p. 49 84. In H. Saedler, and A. Gierl(ed.), Transposable Elements, vol. 204. Springer, Berlin, Germany.
64. Kolodner, R. 1996. Biochemistry and genetics of eukaryotic mismatch repair. Genes Dev. 10: 1433 1442.
65. Kong, D. C, and W. Masker. 1994. Deletion between direct repeats in T7 DNA stimulated by double-strand breaks. J. Bacteriol. 176: 5904 5911.
66. Kunst, F.,, N. Ogasawara,, I. Moszer,, A. M. Albertini,, G. Alloni,, V. Azevedo,, M. G. Bertero,, P. Bessières,, A. Bolotin,, S. Borchert,, R. Borriss,, L. Boursier,, A. Brans,, M. Braun,, S. C. Brignell,, S. Bron,, S. Brouillet,, C. V. Bruschi,, B. Caldwell,, V. Capuano,, N. M. Carter,, S.-K. Choi,, J.-J. Codani,, I. F. Connerton,, N. J. Cummings,, R. A. Daniel,, F. Denizot,, K. M. Devine,, A. Düsterhöft,, S. D. Ehrlich,, P. T. Emmerson,, K. D. Entian,, J. Errington,, C. Fabret,, E. Ferrari,, D. Foulger,, C. Fritz,, M. Fujita,, Y. Fujita,, S. Fuma,, A. Galizzi,, N. Galleron,, S.-Y. Ghim,, P. Glaser,, A. Goffeau,, E. J. Golightly,, G. Grandi,, G. Giuseppi,, B. J. Guy,, K. Haga,, J. Haiech,, C. R. Harwood,, A. Hénaut,, H. Hubert,, S. Holsappel,, S. Hosono,, M.-F. Hullo,, M. Itaya,, L. Jones,, B. Joris,, D. Karamata,, Y. Kasahara,, M. Klaerr-Blanchard,, C. Klein,, Y. Kobayashi,, P. Koetter,, G. Koningstein,, S. Krogh,, M. Kumano,, K. Kurita,, A. Lapidus,, S. Lardinois,, J. Lauber,, V. Lazarevic,, S.-M. Lee,, A. Levine,, H. Liu,, S. Masuda,, C. Mauël,, C. Médigue,, N. Medina,, R. P. Mellado,, M. Mizuno,, D. Moestl,, S. Nakai,, M. Noback,, D. Noone,, M. O'Reilly,, K. Ogawa,, A. Ogiwara,, B. Oudega,, S.-H. Park,, V. Parro,, T. M. Pohl,, D. Portetelle,, S. Porwollik,, A. M. Prescott,, E. Presecan,, P. Pujic,, B. Purnelle,, G. Rapoport,, M. Rey,, S. Reynolds,, M. Rieger,, C. Rivolta,, E. Rocha,, B. Roche,, M. Rose,, Y. Sadaie,, T. Sato,, E. Scanlan,, S. Schleich,, R. Schroeter,, F. Scoffone,, J. Sekiguchi,, A. Sekowska,, S. J. Seror,, P. Serror,, B.-S. Shin,, B. Soldo,, A. Sorokin,, E. Tacconi,, T. Takagi,, H. Takahashi,, K. Takemaru,, M. Takeuchi,, A. Tamakoshi,, T. Tanaka,, P. Terpstra,, A. Tognoni,, V. Tosato,, S. Uchiyama,, M. Vandenbol,, F. Vannier,, A. Vassarotti,, A. Viari,, R. Wambutt,, E. Wedler,, H. Wedler,, T. Weitzenegger,, P. Winters,, A. Wipat,, H. Yamamoto,, K. Yamane,, K. Yasumoto,, K. Yata,, K. Yoshida,, H.-F. Yoshikawa,, E. Zumstein,, H. Yoshikawa,, and A. Danchin. 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis . Nature 390: 249 256.
67. LaDuca, R. J.,, P. J. Fay,, C. Chuang,, C. S. McHenry,, and R. A. Bambara. 1983. Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III. Biochemistry 22: 5177 5188.
68. Leach, D. R.,, and F. W. Stahl. 1983. Viability of lambda phages carrying a perfect palindrome in the absence of recombination nucleases. Nature (London) 305: 448 451.
69. Leach, D. R. F., 1996. Cloning and characterisation of DNAs with palindromic sequences, p. 1 11. In J. K. Sedow (ed.), Genetic Engineering, vol. 18. Plenum Press, New York, N.Y..
70. Leach, D.R.F. 1996. Genetic Recombination . Blackwell Science, Oxford, England.
71. Leach, D. R. F. 1994. Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. Bioessays 16: 893 900.
72. Leach, D. R. L.,, E. A. Okely,, and D. J. Pinder. 1997. Repair by recombination of DNA containing a palindromic sequence. Mol Microbiol. 26: 597 606.
73. Lejeune, P.,, and A. Danchin. 1990. Mutations in the bglY gene increase the frequency of spontaneous deletions in Escherichia coli K-12. Proc. Natl Acad. Sci. USA 87: 360 363.
74. Levinson, G.,, and G. A. Gutman. 1987. High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12. Nucleic Acids Res. 15: 5323 5338.
75. Lin, F. L.,, K. Sperle,, and N. Sternberg. 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.
76. Liu, L. F.,, and J. C. Wang. 1987. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84: 7024 7027.
77. Louarn, J.,, F. Cornet,, V. Francois,, J. Patte,, and J. M. Louarn. 1994. Hyperrecombination in the terminus region of the Escherichia coli chromosome: possible relation to nucleoid organization. J. Bacteriol. 176: 7524 7531.
78. Lovett, S. T.,, T. J. Gluckman,, P. J. Simon,, V. A. Sutera,, and P. T. Drapkin. 1994. Recombination between repeats in Escherichia coli by a recA -independent, proximity-sensitive mechanism. Mol. Gen. Genet. 245: 294 300.
79. Lundblad, V.,, and N. Kleckner. 1984. Mismatch repair mutations of Escherichia coli K12 enhance transposon excision. Genetics 109: 3 19.
80. Maenhaut-Michel, G.,, C. E. Blake,, D. R. F. Leach,, and J. A. Shapiro. 1997. Different structures of selected and unselected araB-lacZ fusions. Mol. Microbiol. 23: 1133 1145.
81. Maenhaut-Michel, G.,, and J. A. Shapiro. 1994. The roles of starvation and selective substrates in the emergence of araB-lacZ fusion clones. EMBO J. 13: 5229 5239.
82. 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.
83. McFadden, J. 1996. Recombination in mycobacteria. Mol. Miaobiol. 21: 205 211.
84. Mcmurray, C. T. 1995. Mechanisms of DNA expansion. Chromosoma 104: 2 13.
85. Meima, R.,, B. J. Haijema,, H. Dijkstra,, G. J. Haan,, G. Venema,, and S. Bron. 1997. Role of enzymes of homologous recombination in illegitimate plasmid recombination in Bacillus subtilis . J. Bacteriol. 179: 1219 1229.
86. Michel, B.,, E. D'Alencon,, and S. D. Ehrlich. 1989. Deletion hot spots in chimeric Escherichia coli plasmids. J. Bacteriol. 171: 1846 1853.
87. Michel, B.,, and S. D. Ehrlich. 1986. Illegitimate recombination at the replication origin of bacteriophage M13. Proc. Natl. Acad. Sci. USA 83: 386 390.
88. Michel, B.,, S. D. Ehrlich,, and M. Uzest. 1997. DNA double-strand breaks caused by replication arrest. EMBO J. 16: 430 438.
89. Mizuuchi, K. 1992. Transpositional recombination—mechanistic insights from studies of Mu and other elements. Annu. Rev. Biochem. 61: 1011 1051.
90. Mollet, B.,, and M. Delley. 1991. A beta-galactosidase deletion mutant of Lactobacillus bulgaricus reverts to generate an active enzyme by internal DNA sequence duplication. Mol. Gen. Genet. 227: 17 21.
91. Morel P.,, C. Reverdy,, B. Michel,, S. D. Ehrlich,, and E. Cassuto. The role of SOS and flap processing in microsatellite instability in E. coli . Proc. Natl. Acad. Sci. USA 95: 10003 10008.
92. Mukaihara, T.,, and M. Enomoto. 1997. Deletion formation between the two Salmonella typhimurium flagellin genes encoded on the mini F plasmid: Escherichia coli ssb alleles enhance deletion rates and change hot-spot preference for deletion endpoints. Genetics 145: 563 572.
93. Naas, T.,, M. Blot,, W. M. Fitch,, and W. Arber. 1995. Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol. Biol. Evol. 12: 198 207.
94. Naas, T.,, M. Blot,, W. M. Fitch,, and W. Arber. 1994. Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics 136: 721 730.
95. Nagel, R.,, A. Chan,, and E. Rosen. 1994. ruv and recG genes and the induced precise excision of Tn 10 in Escherichia coli . Mutat. Res. 311: 103 109.
96. Ohshima, K.,, and R. D. Wells. 1997. Hairpin formation during DNA synthesis primer realignment in vitro in triplet repeat sequences from human hereditary disease genes. J. Biol. Chem. 272: 16798 16806.
97. Ouchane, S.,, M. Picaud,, C. Vernotte,, and C. Astier. 1997. Photooxidative stress stimulates illegitimate recombination and mutability in carotenoid-less mutants of Rubrivivax gelatinosus . EMBO J. 16: 4777 4787.
98. Papanicolaou, C.,, and L. S. Ripley. 1989. Polymerase-specific differences in the DNA intermediates of frameshift mutagenesis. In vitro synthesis errors of Escherichia coli DNA polymerase I and its large fragment derivative. J. Mol. Biol. 207: 335 353.
99. Peeters, B. P.,, J. H. de Boer,, S. Bron,, and G. Venema. 1988. Structural plasmid instability in Bacillus subtilis: effect of direct and inverted repeats. Mol. Gen. Genet. 212: 450 458.
100. Pierce, J. C.,, D. C. Kong,, and W. Masker. 1991. The effect of the length of direct repeats and the presence of palindromes on deletion between direcdy repeated DNA sequences in bacteriophage T7. Nucleic Acids Res. 19: 3901 3905.
101. Pinder, D. J.,, C. E. Blake,, and D. R. F. Leach. 1997. DIR: a novel DNA rearrangement associated with inverted repeats. Nucleic Acids Res. 25: 523 529.
10la.. Pinder, D. J.,, C. E. Blake,, J. C. Lindsey,, and D. R. F. Leach. 1998. Replication strand preference for deletions associated with palindromes. Mol. Microbiol. 28: 719 727.
102. Polard, P.,, L. Seroude,, O. Fayet,, M. F. Prere,, and M. Chandler. 1994. One-ended insertion of IS 911 . J. Bacteriol. 176: 1192 1196.
103. Reddy, M.,, and J. Gowrishankar. 1997. Identification and characterization of ssb and uup mutants with increased frequency of precise excision of transposon Tn 10 derivatives: nucleotide sequence of uup in Escherichia coli . J. Bacteriol. 179: 2892 2899.
104. Richardson, P. T.,, and S. F. Park. 1997. Integration of heterologous plasmid DNA into multiple sites on the genome of Campylobacter coli following natural transformation. J. Bacteriol. 179: 1809 1812.
105. Rosche, W. A.,, T. Q. Trinh,, and R. R. S inden. 1997. Leading strand specific spontaneous mutation corrects a quasipalindrome by an intermolecular strand switch mechanism. J. Mol. Biol. 269: 176 187.
106. Roth, J. R.,, N. Benson,, T. Galinski,, K. Haack,, J. G. Lawrence,, and L. Miesel,. 1996. Rearrangements of the bacterial chromosome: formation and applications, p. 2256 2276. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. American Society for Microbiology, Washington, D.C..
107. Rozsa, F. W.,, P. Viollier,, M. Fussenegger,, R. Hiestand-Nauer,, and W. Arber. 1995. Gin-mediated recombination at secondary crossover sites on the Escherichia coli chromosome. J. Bacteriol. 177: 1159 1168.
108. Rupp, W. D., 1996. DNA repair mechanisms, p. 2277 2294. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. American Society for Microbiology, Washington, D.C..
109. 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: 291 304.
109a.. Sarkar, P. S.,, H. C. Chang,, F. B. Boudi,, and S. Reddy. 1998. CTG repeats show bimodal amplification in E. coli . Cell 95: 531 540.
110. Scearce, L. M.,, J. C. Pierce,, B. Mcinroy,, and W. Masker. 1991. Deletion mutagenesis independent of recombination in bacteriophage T7. J. Bacteriol. 173: 869 878.
111. Schaaper, R. M.,, and R. L. Dunn. 1991. Spontaneous mutation in the Escherichia coli lacI gene. Genetics 129: 317 326.
112. Schofield, M. A.,, R. Agbunag,, M. L. Michaels,, and J. H. Miller. 1992. Cloning and sequencing of Escherichia coli mutR shows its identity to topB, encoding topoisomerase III. J. Bacteriol. 174: 5168 5170.
113. Schofield, M. A.,, R. Agbunag,, and J. H. Miller. 1992. DNA inversions between short inverted repeats in Escherichia coli . Genetics 132: 295 302.
114. Schumacher, S.,, R. P. P. Fuchs,, and M. Bichara. 1997. Two distinct models account for short and long deletions within sequence repeats in Escherichia coli . J. Bacteriol. 179: 6512 6517.
115. Seigneur, M.,, S. D. Ehrlich,, and B. Michel. 1997. Blocking rolling circle replication with a UV lesion creates a deletion hotspot. Mol. Microbiol. 26: 569 580.
116. Shanado, Y.,, J. Kato,, and H. Ikeda. 1997. Fis is required for illegitimate recombination during formation of lambda bio transducing phage. J. Bacteriol. 179: 4239 4245.
117. Shapiro, J. A. 1997. Genome organization, natural genetic engineering and adaptive mutation. Trends Genet. 13: 98 104.
118. Sharp, P. M.,, and D. R. F. Leach. 1996. Palindrome-induced deletion in enterobacterial repetitive sequences. Mol. Microbiol. 22: 1055 1056.
119. Sharpies, G. J.,, and R. G. Lloyd. 1990. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 18: 6503 6508.
120. Shen, P.,, and H. V. Huang. 1986. Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics 112: 441 457.
121. Shimizu, H.,, H. Yamaguchi,, Y. Ashizawa,, Y. Kohno,, M. Asami,, J. Kato,, and H. Ikeda. 1997. Short-homology-independent illegitimate recombination in Escherichia coli: distinct mechanism from short-homology-dependent illegitimate recombination. J. Mol. Biol. 266: 297 305.
122. Shurvinton, C. E.,, M. M. Stahl,, and F. W. Stahl. 1987. Large palindromes in the lambda phage genome are preserved in a rec+ host by inhibiting lambda DNA replication. Proc. Natl. Acad. Sci. USA 84: 1624 1628.
123. Sinden, R. R.,, G. X. Zheng,, R. G. Brankamp,, and K. N. Allen. 1991. On the deletion of inverted repeated DNA in Escherichia coli: effects of length, thermal stability, and cruciform formation in vivo. Genetics 129: 991 1005.
124. Singer, B. S.,, and J. Wesdye. 1988. Deletion formation in bacteriophage T4. J. Mol. Biol. 202: 233 243.
125. 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.
126. Touati, D. Personal communication.
127. Touati, D.,, M. Jacques,, B. Tardat,, L. Bouchard,, and S. Despied. 1995. Lethal oxidative damage and mutagenesis are generated by iron in delta fur mutants of Escherichia coli: protective role of superoxide dismutase. J. Bacteriol. 177: 2305 2314.
128. Tse-Dinh, Y. C.,, B. G. McCarron,, R. Arentzen,, and V. Chowdhry. 1983. Mechanistic study of E. coli DNA topoisomerase I: cleavage of oligonucleotides. Nucleic Acids Res. 11: 8691 8701.
129. Turlan, C.,, and M. Chandler. 1995. IS1-mediated intramolecular rearrangements: formation of excised transposon circles and replicative deletions. EMBO J. 14: 5410 5421.
130. Uematsu, N.,, S. Eda,, and K. Yamamoto. 1997. An Escherichia coli topB mutant increases deletion and frameshift mutations in the supF target gene. Mutat. Res. 383: 223 230.
131. Ukita, T.,, and H. Ikeda. 1996. Role of the recJ gene product in UV-induced illegitimate recombination at the hotspot. J. Bacteriol. 178: 2362 2367.
132. Usdin, K.,, and K. J. Woodford. 1995. CGG repeats associated with DNA instability and chromosome fragility form structures that block DNA synthesis in vitro . Nucleic Acids Res. 23: 4202 4209.
133. Vilette, D.,, S. D. Ehrlich,, and B. Michel. 1995. Transcription-induced deletions in Escherichia coli plasmids. Mol. Microbiol. 17: 493 504.
134. Vilette, D.,, S. D. Ehrlich,, and B. Michel. 1996. Transcription-induced deletions in plasmid vectors: M13 DNA replication as a source of instability. Mol. Gen. Genet. 252: 398 403.
135. Vilette, D.,, M. Uzest,, S. D. Ehrlich,, and B. Michel. 1992. DNA transcription and repressor binding affect deletion formation in Escherichia coli plasmids. EMBO J. 11: 3629 3634.
136. Wang, J. C. 1996. DNA topoisomerases. Annu. Rev. Biochem. 65: 635 692.
137. Wang, T. C.,, and K. C. Smith. 1986. Inviability of dam recA and dam recB cells of Escherichia coli is correlated with their inability to repair DNA double-strand breaks produced by mismatch repair. J. Bacteriol. 165: 1023 1025.
138. Wang, T. C.,, and K. C. Smith. 1983. Mechanisms for recF -dependent and recB -dependent pathways of postreplication repair in UV-irradiated Escherichia coli uvrB . J. Bacteriol. 156: 1093 1098.
139. Watt, V., M. C. J. Ingles,, M. S. Urdea,, and W. J. Rutter. 1985. Homology requirements for recombination in Escherichia coli . Proc. Natl. Acad. Sci. USA 82: 4768 4772.
140. Weinert, T. A.,, N. A. Schaus,, and N. D. Grindley. 1983. Insertion sequence duplication in transpositional recombination. Science 222: 755 765.
141. Weston-Hafer, K.,, and D. E. Berg. 1991. Deletions in plasmid pBR322: replication slippage involving leading and lagging strands. Genetics 127: 649 655.
142. Weston-Hafer, K.,, and D. E. Berg. 1991. Limits to the role of palindromy in deletion formation. J. Bacteriol. 173: 315 318.
143. Weston-Hafer, K.,, and D. E. Berg. 1989. Palindromy and the location of deletion end-points in Escherichia coli . Genetics 121: 651 658.
144. 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.
145. Whoriskey, S. K.,, M. A. Schofield,, and J. H. Miller. 1991. Isolation and characterization of Escherichia coli mutants with altered rates of deletion formation. Genetics 127: 21 30.
146. Wilson, T. E.,, U. Grawunder,, and M. R. Lieber. 1997. Yeast DNA ligase IV mediates non-homologous DNA end joining. Nature (London) 388: 495 498.
147. Yamaguchi, H.,, T. Yamashita,, H. Shimizu,, and H. Ikeda. 1995. A hotspot of spontaneous and UV-induced illegitimate recombination during formation of lambda bio transducing phage. Mol. Gen. Genet. 248: 637 643.
148. Yang, Y.,, and W. Masker. 1997. Double-strand breaks increase the incidence of genetic deletion associated with intermolecular recombination in bacteriophage T7. Mol. Gen. Genet. 255: 277 284.
149. Yang, Y.,, and W. Masker. 1996. Instability of repeated dinucleotides in bacteriophage T7 genomes. Mutat. Res. 354: 113 122.

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