New Aspects of Lanthipeptide Evolution Revealed by Phylogeny-guided Genome Mining of Roseocin Family Lantibiotics
Lantibiotics are a rapidly expanding class of RiPPs, which have proved their antimicrobial potential against the drug-resistant Gram-positive strains. The hallmark of lantibiotics is the ring structures installed by lanthipeptide synthetases, which have evolved in a phylum-dependent manner in bacteria. These enzymes are specific for a particular type of lanthipeptides as they recognize the leader region of precursor peptides for their core decoration by installing thioether rings. Lanthipeptide precursors possess a natural diversity in their core region with a conserved target binding motif and the signature of leader region for recognition by the synthetase. While assessing the diversity of roseocin homologs among the phylum actinobacteria, we carried out the phylogenetic analysis using lanthipeptide synthetase RosM, which led to the identification of twelve other members of the roseocin family, which diverged into three different types of biosynthetic gene clusters. We hypothesized that such naturally diverse congeners should be screened to reach a conclusive hit with the best antimicrobial potential. The identified roseocin peptide homologs were carefully aligned to identify the conserved sites in their core and the substitutions allowed by nature. Using the heterologous expression system of roseocin established earlier, its alpha peptide was bioengineered to have the permitted substitutions only, which were all found to be bioactive, in synergism with Rosβ peptide. The lanthipeptides from four other phyla were also analysed to reveal many undermined aspects of lanthipeptide evolution and a phylum-dependent coevolutionary relation between lanthipeptide leader and their synthetases.