Clade-wide fungal proteome analysis reveals structure–function conservation in divergent Dicer proteins

Dicers (Dcrs) are central proteins involved in the biogenesis of small RNAs (sRNAs) in eukaryotes. Most of the knowledge on Dcr structure, function and evolution comes from studies conducted in animal and plant species. Comparatively, much less is known in fungi, which are a genetically and ecologically diverse group with important roles in ecosystems, agriculture, medicine, and biotechnology. While canonical Dcrs in plants and animals contain a well-defined domain architecture, most fungal Dcrs with experimentally validated functions lack one or more identifiable canonical domains, raising questions about how RNA-binding and precise sRNA processing is retained. Here, we conducted the most extensive survey of fungal Dcr proteins, analyzing 1,593 proteomes across eight phyla. We found a diversity of Dcr domain architectures, with some of them lacking an identifiable PAZ, Helicase, and/or double-stranded RNA binding domains. Phylogenetic analyses showed that different Dcr classes are distributed across distinct clades that often align with fungal taxonomic groups. Despite the lack of canonical domain architectures, we found that fungal Dcrs fold into a characteristic L-shaped structure and show PAZ-like folds, even in proteins without detectable PAZ sequences. Molecular docking and electrostatic analyses further indicate that these divergent Dcrs maintain key RNA-binding surfaces for proper sRNA processing. Our results indicate a remarkable evolutionary plasticity of Dcr in fungi, showing that essential sRNA processing functions can be retained through structural conservation, and highlighting fungi as models to study the modular evolution of the RNAi machinery in eukaryotes.