The distribution of insertion sequences in the genome ofShigella flexneristrain 2457T

Abstract

Shigella flexneri, which causes shigellosis in humans, evolved from Escherichia coli. The sequencing of Shigella genomes has revealed that a large number of insertion sequence (IS) elements (over 200 elements) reside in the genome. Although the presence of these elements has been noted previously and summarized, more detailed analyses are required to understand their evolutionary significance. Here, the genome of S. flexneri strain 2457T is used to investigate the spatial distribution of IS copies around the chromosome and the location of elements with respect to genes. It is found that most IS isoforms occur essentially randomly around the genome. Two exceptions are IS91 and IS911, which appear to cluster due to local hopping. The location of IS elements with respect to genes is biased, however, revealing the action of natural selection. The non-coding regions of the genome (no more than 21%) carry disproportionally more IS elements (at least 28%) than the coding regions, implying that selection acts against insertion into genes. Of the genes disrupted by ISs, those involved in signal transduction, intracellular trafficking, and cell motility are most commonly targeted, suggesting selection against genes in these categories.

Structural Characterization of IS CR8 , IS CR22 , and IS CR23 , Subgroups of IS 91 -Like Insertion Elements

“…In this aspect the elements studied here seem to resemble IS91 in Shigella flexneri 2457T. In a genome-wide survey investigating the spatial distribution of over 200 insertion sequences in this strain, only IS91 and IS911 appeared to be nonrandomly distributed (24). This was explained with local hopping, i.e., the transposition mechanism is biased toward placing new copies near the parent copy, rather than natural selection favoring insertion into particular regions of the genome.…”

“…Transposition of canonical IS91 elements is site specific and takes place at the 5Ј end of this tetranucleotide (13). The lack of the tetranucleotide at ISCR insertion sites has led to speculation about differences in the transposition mechanism of these elements (24). However, these hypotheses await experimental confirmation.…”

Antibiotics Shaping Bacterial Genome: Deletion of an IS91 Flanked Virulence Determinant upon Exposure to Subinhibitory Antibiotic Concentrations

“…Interestingly, the six IS 91 copies present in the chromosome of the S. flexneri strain 2457T cluster together and flank several virulence determinants [43]. Local hopping was proposed to explain the clustering pattern of these determinants.…”

Intergenic Transposable Elements Are Not Randomly Distributed in Bacteria

“…Therefore, an IS that causes a deleterious mutation by disrupting an essential gene will probably be quickly eliminated from most natural populations, whereas an IS that inserts into a selectively neutral location will have a much greater chance of long-term survival (Lynch 2006). As a general rule, intergenic IS elements probably enjoy higher survival than those that integrate within genes, simply because they have a lower likelihood of disrupting native genes (Campbell 2002; Zaghloul et al 2007). However, the question then arises: are all intergenic regions selectively equivalent for IS occupancy?…”