Marina Mota-Merlo: Evolution of extracellular proteins in a symbiont of honeybees

Abstract

Apilactobacillus kunkeei is a Lactic Acid Bacterium found in the gut and food products of honeybees. A. kunkeei is considered a defensive symbiont because it is believed to protect the honeybees and their larvae from diseases that often have devastating consequences for beekeeping. The protective effect of A. kunkeei is likely caused by the secretion of a bacteriocin called kunkecin. This thesis focuses on extracellular proteins, which are required not only for kunkecin biosynthesis, but also for the interactions between A. kunkeei and the host honeybee.

The evolution of extracellular proteins was studied through multi-omics methods, including genomics, transcriptomics, proteomics and metagenomics, focusing on two groups of proteins, glycosyl hydrolases involved in the synthesis of polysaccharides and “Giant” proteins, likely adhesins, encoded by genes which cover ~6% of the A. kunkeei genome.

While core genes are nearly identical in sequence across strains, genes for extracellular proteins are highly dissimilar and evolve by diversifying selection. Mechanistically, this is best explained by homologous recombination on core genes, whereas gene clusters for glycosyl hydrolases undergo constant gene content turnover that may limit the rate of recombination. Homolog searches showed that Giants1-3 could be involved in the fructophilic lifestyle of A. kunkeei, whereas Giants4-5 lacked homologs from other genera, and therefore evolved more recently. The relative abundance of different variants of the genes for extracellular proteins was similar between A. kunkeei populations from geographically distant sites (Sweden and Malaysia) and honeybee species (Apis mellifera and Apis dorsata, respectively). In addition, a chromosomally-encoded two-component signal transduction system could regulate the synthesis of adhesins and of the plasmid-encoded genes for kunkecin synthesis, which suggests that environmental cues are needed to activate the expression of the defence systems.

Together, these studies provide insights into the evolution and expression of adhesins, bacteriocins and glycosyl hydrolases, all of which are important for the future use of A. kunkeei to promote honeybee health or for industrial applications. More broadly, the results characterize some of the evolutionary processes through which bacteria adapt to new environments.