Dynamics of bacterial insertion sequences: can transposition bursts help the elements persist?

Abstract

BackgroundCurrently there is no satisfactory explanation for why bacterial insertion sequences (ISs) widely occur across prokaryotes despite being mostly harmful to their host genomes. Rates of horizontal gene transfer are likely to be too low to maintain ISs within a population. IS-induced beneficial mutations may be important for both prevalence of ISs and microbial adaptation to changing environments but may be too rare to sustain IS elements in the long run. Environmental stress can induce elevated rates of IS transposition activities; such episodes are known as ‘transposition bursts’. By examining how selective forces and transposition events interact to influence IS dynamics, this study asks whether transposition bursts can lead to IS persistence.ResultsWe show through a simulation model that ISs are gradually eliminated from a population even if IS transpositions occasionally cause advantageous mutations. With beneficial mutations, transposition bursts create variation in IS copy numbers and improve cell fitness on average. However, these benefits are not usually sufficient to overcome the negative selection against the elements, and transposition bursts amplify the mean fitness effect which, if negative, simply accelerates the extinction of ISs. If down regulation of transposition occurs, IS extinctions are reduced while ISs still generate variation amongst bacterial genomes.ConclusionsTransposition bursts do not help ISs persist in a bacterial population in the long run because most burst-induced mutations are deleterious and therefore not favoured by natural selection. However, bursts do create more genetic variation through which occasional advantageous mutations can help organisms adapt. Regulation of IS transposition bursts and stronger positive selection of the elements interact to slow down the burst-induced extinction of ISs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0560-5) contains supplementary material, which is available to authorized users.

Functional and Comparative Genomics of Niche-Specific Adapted ActinomycetesKocuria rhizophilaStrain D2 Isolated from Healthy Human Gut

“…Insertion sequences (ISs) and bacteriophages contribute actively to bacterial evolution by integrating and exciting from the genome. In certain conditions, they provide new genetic properties such as virulence factors and antibiotic resistance (41–45). In K. rhizophila no such observations for IS elements with respect to virulence and antibiotic determinates could be done, also the bacteriophage did not harbour important genes related to the bacterial cellular functions.…”

The Divided Bacterial Genome: Structure, Function, and Evolution

“…5); i.e., putative chromids appeared most like chromosomes, followed by megaplasmids, with plasmids being very different from the others. Given that the gain of insertion elements is generally deleterious (138)(139)(140), perhaps the biases in transposase prevalence reflect differences in the expendabilities of genes on each type of replicon and differences in purifying selection (98).…”

How genetic parasites persist despite the purge of natural selection

“…2). Even in the case of transposons, a small amount of HGT is required to compensate for the overall fitness cost of these genetic elements, which explains why transposition bursts in the absence of HGT do not facilitate transposon persistence in microbial populations [53].…”