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

Schneider D, Duperchy E, Depeyrot J, Coursange E, Lenski R, Blot M - BMC Microbiol. (2002)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire Plasticité et Expression des Génomes Microbiens, CNRS FRE2383, Université Joseph Fourier, Grenoble, Fance. dominique.schneider@ujf-grenoble.fr

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.

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Location of IS elements on the E. coli B chromosome. IS elements are represented by black dots. The position of the different IS elements is given in minutes. For clarity, in the two regions (between 8 and 15 min, and near 98 min) where several IS elements are closely located, their number is also given. The precise data are given in Table 1 (see Additional file: Table 1).
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Figure 1: Location of IS elements on the E. coli B chromosome. IS elements are represented by black dots. The position of the different IS elements is given in minutes. For clarity, in the two regions (between 8 and 15 min, and near 98 min) where several IS elements are closely located, their number is also given. The precise data are given in Table 1 (see Additional file: Table 1).

Mentions: In B, there are apparent clusters of IS elements in the chromosomal regions between 12 and 15 min, 58 and 65 min, and 97 and 0.5 min (Figure 1). The 12–15 min region corresponds to a region of high IS density in K-12 [13]. On the other hand, no IS elements were found in B between 65 and 75 min, nor between 85 and 97 min. Chromosomal regions devoid of IS elements were reported in K-12 between 53 and 67 min, and between 83 and 92 min [12-14,28]; the 83–92 min region corresponds to a low IS-density region in B, but IS elements are not underrepresented in the 53–67 min region of B.


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

Schneider D, Duperchy E, Depeyrot J, Coursange E, Lenski R, Blot M - BMC Microbiol. (2002)

Location of IS elements on the E. coli B chromosome. IS elements are represented by black dots. The position of the different IS elements is given in minutes. For clarity, in the two regions (between 8 and 15 min, and near 98 min) where several IS elements are closely located, their number is also given. The precise data are given in Table 1 (see Additional file: Table 1).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC117601&req=5

Figure 1: Location of IS elements on the E. coli B chromosome. IS elements are represented by black dots. The position of the different IS elements is given in minutes. For clarity, in the two regions (between 8 and 15 min, and near 98 min) where several IS elements are closely located, their number is also given. The precise data are given in Table 1 (see Additional file: Table 1).
Mentions: In B, there are apparent clusters of IS elements in the chromosomal regions between 12 and 15 min, 58 and 65 min, and 97 and 0.5 min (Figure 1). The 12–15 min region corresponds to a region of high IS density in K-12 [13]. On the other hand, no IS elements were found in B between 65 and 75 min, nor between 85 and 97 min. Chromosomal regions devoid of IS elements were reported in K-12 between 53 and 67 min, and between 83 and 92 min [12-14,28]; the 83–92 min region corresponds to a low IS-density region in B, but IS elements are not underrepresented in the 53–67 min region of B.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire Plasticité et Expression des Génomes Microbiens, CNRS FRE2383, Université Joseph Fourier, Grenoble, Fance. dominique.schneider@ujf-grenoble.fr

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.

Show MeSH
Related in: MedlinePlus