Diversity of fungal sugar transporters (STs) revealed through integrative omics approaches

The conversion of plant biomass into biofuels, biochemicals, and other bioproducts holds great potential, with fungi being highly effective in breaking down complex carbohydrates into soluble sugars. In fungal plant biomass conversion (FPBC), sugar transporters (STs) are essential for absorbing sugars from enzymatic breakdown of polysaccharide for fungal growth. This thesis integrates bioinformatics methods and omics data to analyze the gene content and diversity of STs across fungal species, providing insights to optimize biomass conversion processes. The first chapter introduces the study, outlining the structure, mechanism, and distribution of STs in fungi, then summarizing the biochemical traits and functions of various STs. It highlights the diversity in ST function, affinity, and specificity. Chapter 2 presents a comparative analysis of genome diversity and transcriptome dynamics among four filamentous fungi: Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens and Trichoderma reesei. Using a domain search with PFAM PF00083, 90, 83, 117, and 52 STs were predicted in each species, respectively, for a total of 342 STs classified into ten clades. The predicted ST specificity was inferred from the known STs in the same phylogenetic clades. Comparative transcriptomics on different sugars revealed complex expression patterns. Moreover, STs often co-expressed with carbohydrate-active enzymes (CAZymes), sugar catabolic enzymes (SCEs), and some transcription factors (TFs). Co-expression analysis confirmed known functions of D-galacturonic acid and D-xylose STs and suggested roles for newly predicted L-rhamnose STs. Chapter 3 investigates the evolutionary genomic origin of fungal STs by phylogenetically analyzing STs across species in Ascomycota, Basidiomycota, Mucoromycota, and Zoopagomycota. Our results showed the total number of STs differed significantly among the studied fungi. Each ST clade had its own unique evolutionary pattern, with expansion of ma