In silico characterization of unique fungal modular rhodopsin expands the horizon of novel optobiological and biomedical applications
Microbial modular rhodopsins, in which light-sensing rhodopsin domains are fused with effector modules, have emerged as promising tools for optogenetic regulation in algae and other systems. However, the diversity and potential regulatory roles of fungal modular rhodopsins remain largely unexplored. Here, we performed a comprehensive in-silico analysis to identify previously uncharacterized fungal modular-rhodopsins that pair a conserved light-sensing core with diverse effector domains, including RPEL-motif, NADP-binding Rossmann fold domain, MCM (Mini-Chromosome Maintenance) domain, and GC-cAT (Carnitine O-Acetyltransferase) modules. In Aureobasidium pullulans, the representative modular rhodopsin (ApRh-RPEL) contains RPEL-motif associated with actin-related and transcriptional regulatory processes, suggesting light-driven fungal signaling pathway involved in transcriptional and cellular regulation, respectively. Rhodopsins fused with NADP-binding Rossmann fold and MCM domains further indicate possible applications in light-programmable metabolic and cell-cycle signaling. Genome mining additionally revealed that A. pullulans harbours a diverse but underexplored array of biosynthetic gene clusters (BGCs), raising the intriguing possibility that light perception may regulate secondary metabolite pathways. Supporting this, multisource protein-protein interaction network analysis links ApRh-RPEL to enzymes involved in terpenoid and sphingolipid biosynthesis, indicating potential cross-talk between light-sensing module and metabolic regulation. These findings outline a computationally derived model in which fungal modular rhodopsins (ApRh-RPEL) function as opto-synthetic regulators of biosynthetic processes. Structural predictions confirmed conserved Schiff-base lysine and retinal-binding pocket, highlighting functional diversity across fungal rhodopsins. Together, these findings expand the optogenetic toolkit and provide a framework for engineering light-driven signaling in fungi, with applications in optobiological and biomedical applications.