Abstract
Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements. Ectopic recombination may also take place between homologous sequences located within transposable element sequences. DNA transposons are typically bounded by terminal inverted repeats (TIRs). Ectopic recombination between TIRs is expected to result in DNA transposon inversions. However, such inversions have barely been documented. In this study, we report natural inversions of the most common prokaryotic DNA transposons: insertion sequences (IS). We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria. We suggest that inversions may impede IS survival and proliferation in the host genome by altering transpositional activity. They may also alter genomic instability by modulating the outcome of ectopic recombination events between IS copies in various orientations. This study represents the first report of TIR-TIR recombination within bacterial IS elements and it thereby uncovers a novel mechanism of structural variation for this class of prokaryotic transposable elements.
Highlights
Transposable elements are discrete pieces of DNA that can move from site to site within genomes
To clarify the evolutionary history of the inversion pattern found in the two Wolbachia strains at the wMel#2 locus, we mapped the distribution of ISWpi1 insertion and inversion patterns onto a phylogeny of Wolbachia strains (Fig. 2)
ISWpi1 inversion events were isolated from natural Wolbachia bacterial strains [20]
Summary
Transposable elements are discrete pieces of DNA that can move from site to site within (and sometimes, between) genomes. They are widely distributed in both eukaryotes and prokaryotes. Recombination often occurs between non-allelic homologous transposable element sequences ( known as ectopic recombination), leading to genomic rearrangements such as deletions, duplications and inversions. This process, which has been widely documented in both eukaryotes and prokaryotes, illustrates the deep impact transposable elements may have on genomic structural variation and instability [1,2,3]
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