Abstract Background Apilactobacillus kunkeei is a fructophilic lactic acid bacterium adapted to honeybees, their food sources and products. These bacteria synthesize exopolysaccharides thought to promote host colonization and protection against toxic compounds and stressful conditions. Homopolysaccharides consisting of glucose residues are synthesized by enzymes in the glycoside hydrolase family 70 (GH70), whereas polysaccharides that contain fructose are synthesized by family 32 (GH32) enzymes. However, the mechanisms whereby these enzymes diversify are not well understood. Here, we used a comparative genomics approach to investigate the evolution of GH70 and GH32 enzymes in the A. kunkeei population. Results Based on phylogenetic inferences, the GH70 proteins in 38 reference A. kunkeei strains were sorted into glucan-binding enzymes, which were predicted to have glucansucrase and branching sucrase activities, and non-glucan binding enzymes of unknown enzymatic functions. Genes for the glucan sucrases and the branching sucrases are clustered in a chromosomal segment that also contains genes for GH32 enzymes. The number and combination of genes for the glucan-binding GH70 enzymes were mostly strain-specific, indicative of high rates of gene turnover. Neighboring genes often displayed a dramatic variability in synonymous and nonsynonymous substitution frequencies and have only rarely co-diverged. We identified short recombination tracts and a few long tracts that spanned across the cluster of genes for GH70 and GH32 enzymes. Genes encoding GH70 and GH32 enzymes evolve faster than genes encoding core proteins. The ratios of the relative effect of recombination to mutation for the core genome were estimated to 1.6 to 5.2 for A. kunkeei strains assigned to phylogroups A and B-C, respectively. Conclusions Our results suggest genes for GH32 and GH70 proteins have a unique evolutionary history in each A. kunkeei strain and have diverged by duplications, deletions, fusions, recombination events and nucleotide substitutions. We suggest that genes for GH70 enzymes have escaped the homogenizing effects of homologous recombination to a greater extent than the core genes due to rampant gene gain and loss. The results imply that the clustering of the A. kunkeei- related strains into phylogroups mostly reflects the impact of homologous recombination on the core genome.
Mota-Merlo et al. (Mon,) studied this question.