Covalent Leader Peptide Probes Reveal Extra-Cluster Enzymes in Ribosomal Peptide Biosynthesis

Genome-based analyses have enabled widespread discovery and biosynthetic annotation of ribosomally synthesized and post-translationally modified peptides (RiPPs) pathways, yet often fail to capture all participating enzymes, particularly those encoded outside canonical biosynthetic gene clusters. In this study, leveraging the central role of leader peptides (LPs) in RiPP enzyme-substrate recognition, we developed a substrate-guided chemical-proteomic strategy using covalent LP probes to directly identify LP-binding enzymes from native proteomes. Using the LctA-LctM and PatE-LynD systems, we demonstrate that LP probes carrying a photo-cross-linker engage enzymes at their authentic LP-recognition sites while preserving full catalytic competence. Application of this strategy to a model strain Streptomyces sparsogenes uncovered lanthipeptide synthetases encoded outside canonical biosynthetic gene clusters and revealed graded cross-cluster activities among multiple RiPP pathways. This work establishes a proof-of-concept model platform for proteome-level discovery of LP-binding RiPP enzymes and highlights cross-cluster enzymatic crosstalk as a latent mechanism for structural diversification.