Inversion/dimerization of plasmids mediated by inverted repeats

J Mol Biol. 1999 Jan 29;285(4):1485-501. doi: 10.1006/jmbi.1998.2419.


In contrast with earlier studies on the lambda and Escherichia coli genomes, recombination between inverted repeats on plasmids is highly efficient and shown to be recA-independent. In addition, the recombination product is exclusively a head-to-head inverted dimer. Here, we show that this recombination/rearrangement event can occur on different plasmid replicons and is not specific to the particular sequence within the inverted repeats. Transcription readthrough into the inverted repeats has little effect on this event. Genetic analysis has also indicated that most known recombination enzymes are not involved in this process. Specifically, single or double mutants defective in Holliday junction resolution systems (RuvABC and/or RecG/RusA) do not abolish this recombination/rearrangement event. This result does not support the previous models (i.e. the reciprocal-strand-switching and the cruciform-dumbbell models) in which intermediates containing Holliday junctions are proposed. Further analysis has demonstrated that the recombination/rearrangement frequency is dramatically (over 1000-fold) reduced if mismatches (2.8 %) are present within the inverted repeats. Mutations in dam, mutH and mutL genes partially or completely restored the recombination/rearrangement frequency to the level exhibited by the perfect inverted repeats, suggesting the formation of heteroduplexes during recombination/rearrangement. Sequencing analysis of the recombination/rearrangement products have indicated that the majority of the products do not involve crossing-over. We discuss a possible mechanism in which blockage of the lagging strand polymerase by a hairpin triggers recombination/rearrangement mediated by inverted repeats.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • DNA Primers / genetics
  • Dimerization
  • Escherichia coli / genetics
  • Gene Rearrangement
  • Genes, Bacterial
  • Models, Genetic
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation
  • Nucleic Acid Heteroduplexes / chemistry
  • Nucleic Acid Heteroduplexes / genetics
  • Plasmids / chemistry*
  • Plasmids / genetics*
  • Recombination, Genetic*
  • Repetitive Sequences, Nucleic Acid*
  • Replicon
  • Transcription, Genetic


  • DNA Primers
  • Nucleic Acid Heteroduplexes