Genome-Wide Exploration\nof Thiamin Pyrophosphate Riboswitches\nin Medically Relevant Fungi Reveals Diverse Distribution and Implications\nfor Antimicrobial Drug Targeting

The rising incidence of fungal infections coupled with\nlimited\ntreatment options underscores the urgent need for novel antifungal\ntherapies. Riboswitches, particularly thiamin pyrophosphate (TPP)\nclass, have emerged as promising antimicrobial targets. This study\npresents a comprehensive genome-wide analysis of TPP riboswitches\nin 156 medically relevant fungi utilizing advanced covariance models\n(CMs) tailored for fungal sequences. Our investigation identified\n378 conserved TPP riboswitch sequences distributed across 140 distinct\nspecies, revealing a broader prevalence than that previously recognized.\nNotably, we provide evidence for a novel putative group of TPP riboswitches,\ndesignated TPPsw<sup>SUGAR</sup>, associated with sugar transporters\nin Mucoromycota and Basidiomycota. This group exhibits distinctive\nstructural features while maintaining key TPP-binding motifs, potentially\nexpanding our understanding of the riboswitch diversity in fungi.\nOur analysis highlights the impact of P3 stem variability on riboswitch\ndetection and characterization, demonstrating the superiority of fungal-specific\nCMs over generic models. We observed multiple TPP riboswitches in\nover 50% of the examined species, including clinically significant\npathogens involved in aspergillosis and mucormycosis. Remarkably, Aspergillus latus, a species associated with COVID-19\ncoinfections, harbors six distinct TPP riboswitch sequences, whereas\nthe extremophilic black fungus Hortaea werneckii possesses nine. These findings not only elucidate the diverse distribution\nof TPP riboswitches in pathogenic fungi but also emphasize their potential\nas multifaceted targets for antifungal drug development. By addressing\nkey limitations of previous detection methods and providing insights\ninto riboswitch structural diversity, this study lays a foundation\nfor future investigations into riboswitch-mediated regulation in fungi\nand the development of novel antifungal strategies.