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. 1994 Nov 8;91(23):11276–11280. doi: 10.1073/pnas.91.23.11276

Nucleotide polymorphism in colicin E1 and Ia plasmids from natural isolates of Escherichia coli.

M A Riley 1, Y Tan 1, J Wang 1
PMCID: PMC45210  PMID: 7972047

Abstract

We examined DNA sequence polymorphism for the colicin gene clusters of seven ColE1 and six ColIa plasmids obtained from natural isolates of Escherichia coli. These gene clusters harbor levels of nucleotide diversity ranging from 0.006 (ColIa) to 0.054 (ColE1). This level of diversity is similar to that observed for chromosomally encoded E. coli genes. However, the variance associated with these estimates is severalfold higher for the plasmid-encoded genes. This increased variance may be due to the differing plasmid population sizes. The pattern of colicin gene cluster polymorphism suggests that the two colicins are evolving in different fashions. ColE1 accumulates polymorphism at an elevated rate in the central domain of the colicin protein, while ColIa polymorphism is distributed evenly along the gene cluster. Comparison of the patterns of divergence between colicin and related proteins of ColIa and Ib and patterns of polymorphism within ColIa suggest that this gene cluster is not evolving in a neutral fashion. These data lend support to the hypothesis that colicin gene clusters may evolve under the influence of diversifying selection.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Achtman M., Mercer A., Kusecek B., Pohl A., Heuzenroeder M., Aaronson W., Sutton A., Silver R. P. Six widespread bacterial clones among Escherichia coli K1 isolates. Infect Immun. 1983 Jan;39(1):315–335. doi: 10.1128/iai.39.1.315-335.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bisercić M., Feutrier J. Y., Reeves P. R. Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus. J Bacteriol. 1991 Jun;173(12):3894–3900. doi: 10.1128/jb.173.12.3894-3900.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chak K. F., James R. Localization and characterization of a gene on the ColE3-CA38 plasmid that confers immunity to colicin E8. J Gen Microbiol. 1984 Mar;130(3):701–710. doi: 10.1099/00221287-130-3-701. [DOI] [PubMed] [Google Scholar]
  4. Chan P. T., Ohmori H., Tomizawa J., Lebowitz J. Nucleotide sequence and gene organization of ColE1 DNA. J Biol Chem. 1985 Jul 25;260(15):8925–8935. [PubMed] [Google Scholar]
  5. DuBose R. F., Dykhuizen D. E., Hartl D. L. Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1988 Sep;85(18):7036–7040. doi: 10.1073/pnas.85.18.7036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dykhuizen D. E., Green L. Recombination in Escherichia coli and the definition of biological species. J Bacteriol. 1991 Nov;173(22):7257–7268. doi: 10.1128/jb.173.22.7257-7268.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hall B. G., Sharp P. M. Molecular population genetics of Escherichia coli: DNA sequence diversity at the celC, crr, and gutB loci of natural isolates. Mol Biol Evol. 1992 Jul;9(4):654–665. doi: 10.1093/oxfordjournals.molbev.a040751. [DOI] [PubMed] [Google Scholar]
  8. Hartl D. L., Medhora M., Green L., Dykhuizen D. E. The evolution of DNA sequences in Escherichia coli. Philos Trans R Soc Lond B Biol Sci. 1986 Jan 29;312(1154):191–204. doi: 10.1098/rstb.1986.0001. [DOI] [PubMed] [Google Scholar]
  9. Konisky J. Colicins and other bacteriocins with established modes of action. Annu Rev Microbiol. 1982;36:125–144. doi: 10.1146/annurev.mi.36.100182.001013. [DOI] [PubMed] [Google Scholar]
  10. Lawrence J. G., Ochman H., Hartl D. L. The evolution of insertion sequences within enteric bacteria. Genetics. 1992 May;131(1):9–20. doi: 10.1093/genetics/131.1.9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Mankovich J. A., Hsu C. H., Konisky J. DNA and amino acid sequence analysis of structural and immunity genes of colicins Ia and Ib. J Bacteriol. 1986 Oct;168(1):228–236. doi: 10.1128/jb.168.1.228-236.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Masaki H., Akutsu A., Uozumi T., Ohta T. Identification of a unique specificity determinant of the colicin E3 immunity protein. Gene. 1991 Oct 30;107(1):133–138. doi: 10.1016/0378-1119(91)90306-v. [DOI] [PubMed] [Google Scholar]
  13. McDonald J. H., Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 1991 Jun 20;351(6328):652–654. doi: 10.1038/351652a0. [DOI] [PubMed] [Google Scholar]
  14. Milkman R., Bridges M. M. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics. 1990 Nov;126(3):505–517. doi: 10.1093/genetics/126.3.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Milkman R., Crawford I. P. Clustered third-base substitutions among wild strains of Escherichia coli. Science. 1983 Jul 22;221(4608):378–380. doi: 10.1126/science.6346486. [DOI] [PubMed] [Google Scholar]
  16. Milkman R., Stoltzfus A. Molecular evolution of the Escherichia coli chromosome. II. Clonal segments. Genetics. 1988 Oct;120(2):359–366. doi: 10.1093/genetics/120.2.359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Nelson K., Selander R. K. Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli. J Bacteriol. 1992 Nov;174(21):6886–6895. doi: 10.1128/jb.174.21.6886-6895.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Nelson K., Whittam T. S., Selander R. K. Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6667–6671. doi: 10.1073/pnas.88.15.6667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Pugsley A. P. Escherichia coli K12 strains for use in the identification and characterization of colicins. J Gen Microbiol. 1985 Feb;131(2):369–376. doi: 10.1099/00221287-131-2-369. [DOI] [PubMed] [Google Scholar]
  21. Pugsley A. P. The ins and outs of colicins. Part I: Production, and translocation across membranes. Microbiol Sci. 1984 Oct;1(7):168–175. [PubMed] [Google Scholar]
  22. Reanney D. Extrachromosomal elements as possible agents of adaptation and development. Bacteriol Rev. 1976 Sep;40(3):552–590. doi: 10.1128/br.40.3.552-590.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Riley M. A., Gordon D. M. A survey of Col plasmids in natural isolates of Escherichia coli and an investigation into the stability of Col-plasmid lineages. J Gen Microbiol. 1992 Jul;138(7):1345–1352. doi: 10.1099/00221287-138-7-1345. [DOI] [PubMed] [Google Scholar]
  24. Riley M. A. Molecular mechanisms of colicin evolution. Mol Biol Evol. 1993 Nov;10(6):1380–1395. doi: 10.1093/oxfordjournals.molbev.a040081. [DOI] [PubMed] [Google Scholar]
  25. Riley M. A. Positive selection for colicin diversity in bacteria. Mol Biol Evol. 1993 Sep;10(5):1048–1059. doi: 10.1093/oxfordjournals.molbev.a040054. [DOI] [PubMed] [Google Scholar]
  26. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  27. Stoltzfus A., Leslie J. F., Milkman R. Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB. Genetics. 1988 Oct;120(2):345–358. doi: 10.1093/genetics/120.2.345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Tajima F. The effect of change in population size on DNA polymorphism. Genetics. 1989 Nov;123(3):597–601. doi: 10.1093/genetics/123.3.597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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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