Homologous recombination between tandem paralogues drives evolution of a subset of type VII secretion system immunity genes in firmicute bacteria.

The type VII secretion system (T7SS) is found in many Gram-positive firmicutes and secretes protein toxins that mediate bacterial antagonism. Two T7SS toxins have been identified in , EsaD a nuclease toxin that is counteracted by the EsaG immunity protein, and TspA, which has membrane depolarising activity and is neutralised by TsaI. Both toxins are polymorphic, and strings of non-identical and immunity genes are encoded in all strains. To investigate the evolution of repertoires, we analysed the sequences of the tandem genes and their encoded proteins. We identified three blocks of high sequence similarity shared by all genes and identified evidence of extensive recombination events between paralogues facilitated through these conserved sequence blocks. Recombination between these blocks accounts for loss and expansion of genes in genomes and we identified evidence of such events during evolution of strains in clonal complex 8. TipC, an immunity protein for the TelC lipid II phosphatase toxin secreted by the streptococcal T7SS, is also encoded by multiple gene paralogues. Two blocks of high sequence similarity locate to the 5' and 3' end of genes, and we found strong evidence for recombination between paralogues encoded by BCC08. By contrast, we found only a single homology block across genes, and little evidence for intergenic recombination within this gene family. We conclude that homologous recombination is one of the drivers for the evolution of T7SS immunity gene clusters.