A plant-centric investigation of Class B Flavin-dependent Monooxygenase evolution and structural diversity

Class B Flavin-dependent monooxygenases (FMOs) are ancient and ubiquitous enzymes, present throughout diverse kingdoms of life. These enzymes utilize flavin-based coenzymes to incorporate an oxygen atom into their substrate, thereby altering its chemical properties. In plants, FMOs perform crucial catalytic functions essential for plant health, particularly within hormone biosynthesis, defense compound production, and immunogenic responses. Despite the evolutionary significance of class B FMOs across life, their evolution within the plant lineage remains underexplored and underrepresented. Here we present a comprehensive, plant-centric phylogenetic investigation of class B FMOs to uncover lineage-specific evolutionary patterns and structural diversification. Using known Class B FMOs as baits, a large selection of flavin-related proteins was assembled from species representing key lineages across Viridiplantae. Structural domain architecture and motif analysis was used to accurately define different Class B FMOs, resulting in eight distinct class B FMO families. Three families include the canonical YUCCA, N-OX and S-OX FMOs, which remain the most abundant and prevalent across the plant kingdom. Three families are novel, encompassing a small selection of bryophyte FMOs. The analysis also expanded the BVMO family to include monilophyte and angiosperm members, and a potential YUCCA-related family is reclassified as the evolutionary distinct “Seedless FMO” family. Considerable structural diversification within the NADPH-binding domain is observed across the eight families, and by assessing structurally conserved folds rather than amino acid sequence, a refined set of conserved FMO-specific motifs is defined. Overall, this phylogenetic and structural analysis provides new insights into FMO evolution and provides an important foundational framework to aid functional characterization of class B FMOs in plants.