Rules of Coexistence: 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 new family of RiPPs, named linear polyphosphorylated peptides (LPPs). Their biosynthetic gene clusters are widespread in the Bacillota genomes and often co-localize with those of lasso peptides, a distinct class of RiPPs. Both LPP and lasso peptide biosyntheses rely on specific interactions between precursor peptides and small adapter protein domains known as RiPP recognition elements (RREs). Since LPP and lasso peptide precursors 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 systems evolved to discriminate between their cognate precursors and leader peptidases, allowing them to coexist within a single host. Thus, our study provides new insights into the evolutionary diversification of RiPP families.