Chemoinformatic exploration of RiPP biosynthetic gene clusters in Lecanoromycetes

Background Ribosomally synthesized and posttranslationally modified peptides (RiPPs) constitute a relatively newly discovered biosynthetic gene cluster (BGC) class involved in defense-related functions in fungi, with significant therapeutic potential. While only a few fungal RiPPs have been characterized, and primarily from a few model fungi, genome mining approaches have revealed that RiPPs are nearly ubiquitous across fungi, spanning fungal classes from Saccharomycetes to Eurotiomycetes. However, the RiPP biosynthetic landscape of fungi, such as lichen-forming fungi (LFFs), involved in intricate symbiotic relationships remains largely unexplored. Results This study presents the first comprehensive analysis of RiPP BGCs across 111 LFF genomes via an integrative approach combining whole-genome mining, phylogenetic inference, and sequence similarity network analysis. We identified 987 RiPP BGCs, constituting approximately 17% of the total biosynthetic diversity in LFF, a proportion significantly higher than previously estimated. We found most RiPP BGCs to be unique, as they do not cluster with any known RiPP gene clusters. Two conserved RiPP clans were identified in the family Parmeliaceae (Lecanoromycetes), with the core gene putatively homologous to ustY, indicating a relationship with fungal mycotoxins. While Clan R1 BGCs contain the accessory genes for dikaritin synthesis (tyrosinase and methyltransferase), the accessory genes of Clan R2 have not yet been reported from any characterized fungal RiPP BGC but only from bacteria. Additionally, we report the widespread distribution of dikaritin homologs across Lecanoromycetes, expanding the known range of these biosynthetic pathways beyond model Ascomycetes. Conclusions This study highlights the chemical diversity of RiPPs in Lecanoromycetes and identifies two conserved RiPP BGC clans within the Parmeliaceae family which are linked to dikaritins, mostly mycotoxins. This study highlights lichenized fungi such as Lecanoromycetes as promising sources of novel RiPPs.