Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance.

Céline Loot,Eduardo P C Rocha,Aleksandra Nivina,David Bikard,José Antonio Escudero,Didier Mazel,Jean Cury,Magaly Ducos-Galand

doi:10.1128/mbio.02296-16

Abstract

ABSTRACTIntegrons ensure a rapid and “on demand” response to environmental stresses driving bacterial adaptation. They are able to capture, store, and reorder functional gene cassettes due to site-specific recombination catalyzed by their integrase. Integrons can be either sedentary and chromosomally located or mobile when they are associated with transposons and plasmids. They are respectively called sedentary chromosomal integrons (SCIs) and mobile integrons (MIs). MIs are key players in the dissemination of antibiotic resistance genes. Here, we used in silico and in vivo approaches to study cassette excision dynamics in MIs and SCIs. We show that the orientation of cassette arrays relative to replication influences attC site folding and cassette excision by placing the recombinogenic strands of attC sites on either the leading or lagging strand template. We also demonstrate that stability of attC sites and their propensity to form recombinogenic structures also regulate cassette excision. We observe that cassette excision dynamics driven by these factors differ between MIs and SCIs. Cassettes with high excision rates are more commonly found on MIs, which favors their dissemination relative to SCIs. This is especially true for SCIs carried in the Vibrio genus, where maintenance of large cassette arrays and vertical transmission are crucial to serve as a reservoir of adaptive functions. These results expand the repertoire of known processes regulating integron recombination that were previously established and demonstrate that, in terms of cassette dynamics, a subtle trade-off between evolvability and genetic capacitance has been established in bacteria.

Highlights

Integrons ensure a rapid and “on demand” response to environmental stresses driving bacterial adaptation
We have previously demonstrated that there is a subtle equilibrium between opposite processes: on one hand, a cassette recombination site (attC) site integrity ensured by the single-stranded DNA binding (SSB) protein which hampers folding of attC sites in the absence of the integrase [30]; on the other hand, attC site folding and recombination favored by the availability of ssDNA and by the propensity to form cruciform structures due to supercoiling [31]
We previously observed that in all 10 analyzed sedentary chromosomally located integrons (SCIs), attC sites were oriented so that their bottom strands were located on the leading strand template, potentially limiting cassette rearrangements [31]

Summary

Introduction

Integrons ensure a rapid and “on demand” response to environmental stresses driving bacterial adaptation They are able to capture, store, and reorder functional gene cassettes due to site-specific recombination catalyzed by their integrase. This is especially true for SCIs carried in the Vibrio genus, where maintenance of large cassette arrays and vertical transmission are crucial to serve as a reservoir of adaptive functions These results expand the repertoire of known processes regulating integron recombination that were previously established and demonstrate that, in terms of cassette dynamics, a subtle trade-off between evolvability and genetic capacitance has been established in bacteria. The aforementioned systems were later named mobile integrons (MIs) as opposed to sedentary chromosomally located integrons (SCIs), which are found in Gram-negative bacteria from various environments and play a general role in bacterial evolution [3]. AttC sites of MI cassette arrays differ in length and sequence [11]

Methods

Results

Conclusion