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Open Access Highly Accessed Research article

Genomic comparisons among Escherichia coli strains B, K-12, and O157:H7 using IS elements as molecular markers

Dominique Schneider1*, Esther Duperchy2, Joëlle Depeyrot1, Evelyne Coursange3, Richard E Lenski4 and Michel Blot3

Author Affiliations

1 Laboratoire Plasticité et Expression des Génomes Microbiens, Team "Contrôle de l'Expression des Gènes", CNRS FRE2383, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France

2 Zentrum für Molekulare Biologie der Universität Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany

3 Laboratoire Plasticité et Expression des Génomes Microbiens, CNRS FRE2383, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France

4 Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA

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BMC Microbiology 2002, 2:18  doi:10.1186/1471-2180-2-18

Published: 9 July 2002

Abstract

Background

Insertion Sequence (IS) elements are mobile genetic elements widely distributed among bacteria. Their activities cause mutations, promoting genetic diversity and sometimes adaptation. Previous studies have examined their copy number and distribution in Escherichia coli K-12 and natural isolates. Here, we map most of the IS elements in E. coli B and compare their locations with the published genomes of K-12 and O157:H7.

Results

The genomic locations of IS elements reveal numerous differences between B, K-12, and O157:H7. IS elements occur in hok-sok loci (homologous to plasmid stabilization systems) in both B and K-12, whereas these same loci lack IS elements in O157:H7. IS elements in B and K-12 are often found in locations corresponding to O157:H7-specific sequences, which suggests IS involvement in chromosomal rearrangements including the incorporation of foreign DNA. Some sequences specific to B are identified, as reported previously for O157:H7. The extent of nucleotide sequence divergence between B and K-12 is <2% for most sequences adjacent to IS elements. By contrast, B and K-12 share only a few IS locations besides those in hok-sok loci. Several phenotypic features of B are explained by IS elements, including differential porin expression from K-12.

Conclusions

These data reveal a high level of IS activity since E. coli B, K-12, and O157:H7 diverged from a common ancestor, including IS association with deletions and incorporation of horizontally acquired genes as well as transpositions. These findings indicate the important role of IS elements in genome plasticity and divergence.