Genomics-driven discovery of a family of RiPPs that protect Actinobacteria from phage infection

Bacteria produce a diverse array of natural products, to adapt to changing environments and stress. However, our understanding of the biological functions and ecological roles of the vast majority of these compounds remains limited. Genomic studies have unveiled the untapped metabolic potential of bacteria, with only 3% of natural products being characterized, and millions of molecules yet to be discovered. Recently, it emerged that a few known natural products allow bacteria to resist phage infection, but the prevalence of this defense strategy, called chemical defense, remains unclear. Here we use genomics and synthetic biology to uncover biosynthetic gene clusters that produce unknown natural products involved in anti-phage defense. We found that biosynthetic gene clusters that encode the production of a family of uncharacterized Ribosomally synthesized and post-translationally modified peptides (RiPPs) are often encoded near known anti-phage defense systems. Through heterologous expression in Streptomyces albus, we demonstrate experimentally the anti-phage activity of three representatives of this family of defensive RiPPs, present in hundreds of genomes of Actinobacteria. We further demonstrate the role of these defensive RiPPs in a native strain, allowing us to understand the regulation of their production. Finally, we delve into the anti-phage mechanism of action of these compounds. The discovery of defensive RiPPs paves the way for mining bacterial genomes for compounds involved in anti-phage defense, thus opening avenues for the development of new antiviral drugs derived from natural products.