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. 1987 Jan;115(1):51–63. doi: 10.1093/genetics/115.1.51

Distribution and Abundance of Insertion Sequences among Natural Isolates of Escherichia coli

Stanley A Sawyer 1,2,3,4, Daniel E Dykhuizen 1,2,3,4, Robert F DuBose 1,2,3,4, Louis Green 1,2,3,4, T Mutangadura-Mhlanga 1,2,3,4, David F Wolczyk 1,2,3,4, Daniel L Hartl 1,2,3,4
PMCID: PMC1203063  PMID: 3030884

Abstract

A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been studied with respect to the distribution and abundance of transposable insertion sequences using DNA hybridization. The data include 1173 occurrences of six unrelated insertion sequences (IS 1, IS2, IS3, IS4, IS5 and IS 30). The number of insertion elements per strain, and the sizes of DNA restriction fragments containing them, is highly variable and can be used to discriminate even among closely related strains. The occurrence and abundance of pairs of unrelated insertion sequences are apparently statistically independent, but significant correlations result from stratifications in the reference collection. However, there is a highly significant positive association among the insertion sequences considered in the aggregate. Nine branching process models, which differ in assumptions regarding the regulation of transposition and the effect of copy number on fitness, have been evaluated with regard to their fit of the observed distributions. No single model fits all copy number distributions. The best models incorporate no regulation of transposition and a moderate to strong decrease in fitness with increasing copy number for IS1 and IS5, strong regulation of transposition and a negligible to weak decrease in fitness with increasing copy number for IS3, and less than strong regulation of transposition for IS2, IS 4 and IS30.

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Selected References

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  1. Achtman M., Skurray R. A., Thompson R., Helmuth R., Hall S., Beutin L., Clark A. J. Assignment of tra cistrons to EcoRI fragments of F sex factor DNA. J Bacteriol. 1978 Mar;133(3):1383–1392. doi: 10.1128/jb.133.3.1383-1392.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Foster T. J., Lundblad V., Hanley-Way S., Halling S. M., Kleckner N. Three Tn10-associated excision events: relationship to transposition and role of direct and inverted repeats. Cell. 1981 Jan;23(1):215–227. doi: 10.1016/0092-8674(81)90286-5. [DOI] [PubMed] [Google Scholar]
  3. Green L., Miller R. D., Dykhuizen D. E., Hartl D. L. Distribution of DNA insertion element IS5 in natural isolates of Escherichia coli. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4500–4504. doi: 10.1073/pnas.81.14.4500. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Hartl D. L., Dykhuizen D. E., Miller R. D., Green L., de Framond J. Transposable element IS50 improves growth rate of E. coli cells without transposition. Cell. 1983 Dec;35(2 Pt 1):503–510. doi: 10.1016/0092-8674(83)90184-8. [DOI] [PubMed] [Google Scholar]
  5. Klaer R., Kühn S., Tillmann E., Fritz H. J., Starlinger P. The sequence of IS4. Mol Gen Genet. 1981;181(2):169–175. doi: 10.1007/BF00268423. [DOI] [PubMed] [Google Scholar]
  6. Ochman H., Selander R. K. Standard reference strains of Escherichia coli from natural populations. J Bacteriol. 1984 Feb;157(2):690–693. doi: 10.1128/jb.157.2.690-693.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Ohtsubo H., Nyman K., Doroszkiewicz W., Ohtsubo E. Multiple copies of iso-insertion sequences of IS1 in Shigella dysenteriae chromosome. Nature. 1981 Aug 13;292(5824):640–643. doi: 10.1038/292640a0. [DOI] [PubMed] [Google Scholar]
  8. Orgel L. E., Crick F. H. Selfish DNA: the ultimate parasite. Nature. 1980 Apr 17;284(5757):604–607. doi: 10.1038/284604a0. [DOI] [PubMed] [Google Scholar]
  9. Reed R. R. Resolution of cointegrates between transposons gamma delta and Tn3 defines the recombination site. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3428–3432. doi: 10.1073/pnas.78.6.3428. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Reynolds A. E., Felton J., Wright A. Insertion of DNA activates the cryptic bgl operon in E. coli K12. Nature. 1981 Oct 22;293(5834):625–629. doi: 10.1038/293625a0. [DOI] [PubMed] [Google Scholar]
  11. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  12. Saedler H., Cornelis G., Cullum J., Schumacher B., Sommer H. IS1-mediated DNA rearrangements. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 1):93–98. doi: 10.1101/sqb.1981.045.01.017. [DOI] [PubMed] [Google Scholar]
  13. Whittam T. S., Ochman H., Selander R. K. Multilocus genetic structure in natural populations of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1751–1755. doi: 10.1073/pnas.80.6.1751. [DOI] [PMC free article] [PubMed] [Google Scholar]

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