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Genetics. Nov 1993; 135(3): 631–642.
PMCID: PMC1205708

A Sister-Strand Exchange Mechanism for Reca-Independent Deletion of Repeated DNA Sequences in Escherichia Coli


In the genomes of many organisms, deletions arise between tandemly repeated DNA sequences of lengths ranging from several kilobases to only a few nucleotides. Using a plasmid-based assay for deletion of a 787-bp tandem repeat, we have found that a recA-independent mechanism contributes substantially to the deletion process of even this large region of homology. No Escherichia coli recombination gene tested, including recA, had greater than a fivefold effect on deletion rates. The recA-independence of deletion formation is also observed with constructions present on the chromosome. RecA promotes synapsis and transfer of homologous DNA strands in vitro and is indispensable for intermolecular recombination events in vivo measured after conjugation. Because deletion formation in E. coli shows little or no dependence on recA, it has been assumed that homologous recombination contributes little to the deletion process. However, we have found recA-independent deletion products suggestive of reciprocal crossovers when branch migration in the cell is inhibited by a ruvA mutation. We propose a model for recA-independent crossovers between replicating sister strands, which can also explain deletion or amplification of repeated sequences. We suggest that this process may be initiated as post-replicational DNA repair; subsequent strand misalignment at repeated sequences leads to genetic rearrangements.

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Selected References

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  • Albertini AM, Hofer M, Calos MP, Miller JH. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell. 1982 Jun;29(2):319–328. [PubMed]
  • Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. [PMC free article] [PubMed]
  • Cohen A, Laban A. Plasmidic recombination in Escherichia coli K-12: the role of recF gene function. Mol Gen Genet. 1983;189(3):471–474. [PubMed]
  • Csonka LN, Clark AJ. Deletions generated by the transposon Tn10 in the srl recA region of the Escherichia coli K-12 chromosome. Genetics. 1979 Oct;93(2):321–343. [PMC free article] [PubMed]
  • Dianov GL, Kuzminov AV, Mazin AV, Salganik RI. Molecular mechanisms of deletion formation in Escherichia coli plasmids. I. Deletion formation mediated by long direct repeats. Mol Gen Genet. 1991 Aug;228(1-2):153–159. [PubMed]
  • Doherty MJ, Morrison PT, Kolodner R. Genetic recombination of bacterial plasmid DNA. Physical and genetic analysis of the products of plasmid recombination in Escherichia coli. J Mol Biol. 1983 Jul 5;167(3):539–560. [PubMed]
  • Dower WJ, Miller JF, Ragsdale CW. High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 1988 Jul 11;16(13):6127–6145. [PMC free article] [PubMed]
  • Gillen JR, Willis DK, Clark AJ. Genetic analysis of the RecE pathway of genetic recombination in Escherichia coli K-12. J Bacteriol. 1981 Jan;145(1):521–532. [PMC free article] [PubMed]
  • Horii Z, Clark AJ. Genetic analysis of the recF pathway to genetic recombination in Escherichia coli K12: isolation and characterization of mutants. J Mol Biol. 1973 Oct 25;80(2):327–344. [PubMed]
  • Iwasaki H, Takahagi M, Nakata A, Shinagawa H. Escherichia coli RuvA and RuvB proteins specifically interact with Holliday junctions and promote branch migration. Genes Dev. 1992 Nov;6(11):2214–2220. [PubMed]
  • Jones IM, Primrose SB, Ehrlich SD. Recombination between short direct repeats in a recA host. Mol Gen Genet. 1982;188(3):486–489. [PubMed]
  • Kazic T, Berg DE. Context effects in the formation of deletions in Escherichia coli. Genetics. 1990 Sep;126(1):17–24. [PMC free article] [PubMed]
  • Kendal WS, Frost P. Pitfalls and practice of Luria-Delbrück fluctuation analysis: a review. Cancer Res. 1988 Mar 1;48(5):1060–1065. [PubMed]
  • Lloyd RG. Conjugational recombination in resolvase-deficient ruvC mutants of Escherichia coli K-12 depends on recG. J Bacteriol. 1991 Sep;173(17):5414–5418. [PMC free article] [PubMed]
  • Lloyd RG, Benson FE, Shurvinton CE. Effect of ruv mutations on recombination and DNA repair in Escherichia coli K12. Mol Gen Genet. 1984;194(1-2):303–309. [PubMed]
  • Lovett ST, Clark AJ. Cloning of the Escherichia coli recJ chromosomal region and identification of its encoded proteins. J Bacteriol. 1985 Apr;162(1):280–285. [PMC free article] [PubMed]
  • Lovett ST, Luisi-DeLuca C, Kolodner RD. The genetic dependence of recombination in recD mutants of Escherichia coli. Genetics. 1988 Sep;120(1):37–45. [PMC free article] [PubMed]
  • Low B. Formation of merodiploids in matings with a class of Rec- recipient strains of Escherichia coli K12. Proc Natl Acad Sci U S A. 1968 May;60(1):160–167. [PMC free article] [PubMed]
  • Luisi-DeLuca C, Lovett ST, Kolodner RD. Genetic and physical analysis of plasmid recombination in recB recC sbcB and recB recC sbcA Escherichia coli K-12 mutants. Genetics. 1989 Jun;122(2):269–278. [PMC free article] [PubMed]
  • Luria SE, Delbrück M. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics. 1943 Nov;28(6):491–511. [PMC free article] [PubMed]
  • Mahdi AA, Lloyd RG. Identification of the recR locus of Escherichia coli K-12 and analysis of its role in recombination and DNA repair. Mol Gen Genet. 1989 Apr;216(2-3):503–510. [PubMed]
  • Marians KJ. Prokaryotic DNA replication. Annu Rev Biochem. 1992;61:673–719. [PubMed]
  • Mazin AV, Kuzminov AV, Dianov GL, Salganik RI. Mechanisms of deletion formation in Escherichia coli plasmids. II. Deletions mediated by short direct repeats. Mol Gen Genet. 1991 Aug;228(1-2):209–214. [PubMed]
  • Mount DW, Low KB, Edmiston SJ. Dominant mutations (lex) in Escherichia coli K-12 which affect radiation sensitivity and frequency of ultraviolet lght-induced mutations. J Bacteriol. 1972 Nov;112(2):886–893. [PMC free article] [PubMed]
  • Otsuji N, Iyehara H, Hideshima Y. Isolation and characterization of an Escherichia coli ruv mutant which forms nonseptate filaments after low doses of ultraviolet light irradiation. J Bacteriol. 1974 Feb;117(2):337–344. [PMC free article] [PubMed]
  • Picksley SM, Attfield PV, Lloyd RG. Repair of DNA double-strand breaks in Escherichia coli K12 requires a functional recN product. Mol Gen Genet. 1984;195(1-2):267–274. [PubMed]
  • Singer M, Baker TA, Schnitzler G, Deischel SM, Goel M, Dove W, Jaacks KJ, Grossman AD, Erickson JW, Gross CA. A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol Rev. 1989 Mar;53(1):1–24. [PMC free article] [PubMed]
  • Tsaneva IR, Müller B, West SC. ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli. Cell. 1992 Jun 26;69(7):1171–1180. [PubMed]
  • Tsaneva IR, Müller B, West SC. RuvA and RuvB proteins of Escherichia coli exhibit DNA helicase activity in vitro. Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1315–1319. [PMC free article] [PubMed]
  • Way JC, Davis MA, Morisato D, Roberts DE, Kleckner N. New Tn10 derivatives for transposon mutagenesis and for construction of lacZ operon fusions by transposition. Gene. 1984 Dec;32(3):369–379. [PubMed]
  • West SC. Enzymes and molecular mechanisms of genetic recombination. Annu Rev Biochem. 1992;61:603–640. [PubMed]
  • Willetts NS, Clark AJ, Low B. Genetic location of certain mutations conferring recombination deficiency in Escherichia coli. J Bacteriol. 1969 Jan;97(1):244–249. [PMC free article] [PubMed]
  • Yi TM, Stearns D, Demple B. Illegitimate recombination in an Escherichia coli plasmid: modulation by DNA damage and a new bacterial gene. J Bacteriol. 1988 Jul;170(7):2898–2903. [PMC free article] [PubMed]

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