FAMeDB: A Curated Database for the Analysis of Fungal Aromatic Compound Metabolism

Aromatic compounds represent the second most abundant class of organic molecules after carbohydrates, and their microbial metabolism is of broad relevance across multiple research disciplines. Metabolic pathways involving aromatic compounds span from highly conserved anabolic routes to more variable catabolic processes. Numerous peripheral catabolic pathways converge on a small number of central intermediates that undergo aromatic ring opening in the central pathways. Over the past decades, alongside numerous peripheral pathway genes, most of the catabolic genes constituting the central metabolic pathways have finally been characterized in fungi. Here, we present FAMeDB, a manually curated database of proteins involved in fungal aromatic compound metabolism, together with an R-based bioinformatic workflow for orthology data processing. The database currently includes 408 proteins, primarily enzymes, but also includes transcription factors and transporters. Entries span 82 species and 56 genera of fungi. Most entries are from Ascomycota (80%), with a substantial number from Aspergilli (44%). FAMeDB tested and validated the hypothesis that a cross-lineage fungal database can yield meaningful insights into aromatic compound catabolism. Application of FAMeDB and its tools enables the quick and accurate representation of aromatic metabolism across different fungal proteomes. This resource is designed to provide a useful and accessible platform for researchers worldwide, even those without specialized expertise in fungal aromatic catabolism, facilitating omics analysis and genomic comparisons.