RiPP recognition elements evolved to prevent pathway interference through leader peptide discrimination

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are natural products with diverse structures and functions. Here, we report the discovery of a family of RiPPs whose biosynthetic gene clusters are widespread in the Bacillota genomes and often co-localize with those of lasso peptides, another distinct family of RiPPs. The synthesis of both kinds of RiPPs relies on specific interactions between small adapter protein domains known as RiPP recognition elements (RREs) with their precursor peptides. As these latter share a conserved RRE-binding motif, conflicts between the two biosynthetic pathways may emerge. Through biochemical and structural studies, we reveal how the two RiPP biosynthetic systems evolved to discriminate between their cognate precursors and leader peptidases, allowing them to coexist within a single host. Thus, our study provides insights into the evolutionary diversification of RiPP families.