Two D-loop resolution systems enable natural genetic transformation in bacteria

Natural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds from the capture of extracellular DNA released by other cells. Internalized in linear single strands, this exogenous DNA is ultimately integrated into the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has coevolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. The wide distribution of this dual system indicates that recombination of exogenous DNA by natural transformation is an ancestral and pervasive feature of bacteria.