Comparative genomics of van-genes in glycopeptide producing Actinobacteria and beyond

Glycopeptide antibiotics (GPAs) are last resort drugs produced by filamentous actinobacteria mainly from genera Amycolatopsis, Actinoplanes, Nonomuraea and Streptomyces. GPAs are divided into five types, and among them types I-IV are clinically relevant. They are active against Gram-positive bacteria, binding the d-Ala-d-Ala termini of lipid II pentapeptide side chains. This interferes with extracellular stage of peptidoglycan biosynthesis leading to the cell death. GPA-resistant pathogens and GPA producers alike, utilize so-called van-genes for cellwall remodeling to achieve GPA resistance. It was long noticed that GPA biosynthetic gene cluster (BGCs) carry van-genes within. The biological ratio behind seems obvious: GPA producers are avoiding suicide in this way. However, some GPA non-producers (like Streptomyces coelicolor) are also known to carry vangenes, as well as non-harmful soil-inhabitant low G-C Gram-positives do. Consequently, GPAproducers were considered a probable primary source of van-genes for either GPA-nonproducers, low G-C Gram-positives or pathogens. Alternative hypothesis assumed that vangenes evolved independently in soil-dwelling low G-C Gram-positives and then spread to pathogens. In current work we have decided to test these hypotheses. We screened 7108 genome assemblies of the phylum Actinobacteria, either complete or drafts, searching in parallel for van-genes and GPA BGCs. We have discovered van-genes in at least 900 assemblies, coming from 22 orders of Actinobacteria. Only 39 assemblies contained type I-IV GPA BGCs. Peculiarly, genomes with GPA BGCs still tended to have multiple additional van-genes beyond the borders of BGCs. Then we have analyzed 2379 full genomes of the order Bacillales (phylum Firmicutes) and found van-genes only in six species. Finally, we have performed a set of phylogenetic reconstructions to gain insights into the evolution of vangenes from Actinobacteria. Our results suggest that Actinobacteria represent the main source of van-genes. Importantly, van-genes are not a unique feature of GPA producers, being widely distributed in different actinobacteria orders.