Computational analyses, molecular genetics and biochemical approaches performed in collaboration between D. Mazel and Mobi’VIR teams reveal that integron cassettes integrate into bacterial genomes at widespread non-classical attG sites. This process enables the acquisition of genetic material and disruption of existing genes with potential consequences for bacterial evolution. Loot et al., Nature Microbiology 2024

Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites. Once integrated, these cassettes can be expressed if located near bacterial promoters and can be excised at the integration point or outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 10⁵ independent integration events revealed a very large genomic integration landscape. We identified consensus recombination sequences, named attG sites, which differ greatly in sequence and structure from classical att sites. These results unveil an alternative route for dissemination of adaptive functions in bacteria and expand the role of integrons in bacterial evolution.