The recombination efficiency of the bacterial integron depends on the mechanical stability of the synaptic complex

Abstract

The predominant tool for adaptation in Gram-negative bacteria is a genetic system called integron. Under conditions of stress, it rearranges gene cassettes, ensuring their sampling through expression, to offer a solution for overcoming the initial stress. Integrons are a major actor of multiple antibiotic resistances, a recognized major global health threat. Cassettes are recombined by a unique recombination process involving a tyrosine recombinase - the IntI integrase - and folded single-stranded DNA hairpins - the attC sites which terminate each cassette. Four recombinases and two attC sites form a macromolecular synaptic complex, which is key to the recombination process and the focus of our study. The bottom strand of all attC sites shows highest recombination efficiency in vivo than the top one, however, the efficiency still varies several orders of magnitude and the underlying reason remains unclear. Here, we established an optical tweezers force-spectroscopy assay that allows us to probe the synaptic complex stability. We found for seven combinations of attC sites great variability in the mechanical stability. Two protein variants also showed a strong influence on the mechanical stability. We then determined the in vivo recombination efficiencies of the different attC site combinations and protein variants and discovered a strong correlation between recombination efficiency and mechanical stability of the synaptic complex, indicating a regulatory mechanism from the DNA sequence to the macromolecular complex stability. Taking into account known forces during DNA metabolism, we suggest that the variation of the in vivo recombination efficiency is mediated strongly by the synaptic complex stability.