Developmental and Stress-Mediated Transcriptional Shifts in Riboflavin Metabolism Pathway in Arabidopsis

Background: Flavin cofactors, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), are indispensable for plant metabolism, supporting photosynthesis, photorespiration, mitochondrial electron transport, nitrogen assimilation, and cellular redox balance. Both cofactors derive from riboflavin (vitamin B₂), which plants synthesize de novo, unlike animals, which rely on dietary intake. While the riboflavin biosynthesis pathway has been biochemically well-characterized, its transcriptional regulation and cellular organization remain poorly understood. Methods: Here, using large-scale transcriptomic datasets as well as co-expression and cis-element analyses, we systematically investigated the expression dynamics of riboflavin metabolism genes in Arabidopsis thaliana. In addition, HPLC was employed to monitor flavin level fluctuations in plants under abiotic stresses. Results: Most genes displayed strong expression in photosynthetic and reproductive tissues, consistent with elevated metabolic demands for flavins in redox reactions and energy metabolism. Under osmotic stress, RIBA1, RIBA3, PYRD, PYRR, COS1/LS, and RS, genes encoding enzymes involved in the early and intermediate steps of riboflavin biosynthesis were transcriptionally downregulated. In contrast, RIBA2, FHY1/PYRP1 and FMN/FHY were upregulated, whereas FADS1 and NUDX23, genes encoding enzymes responsible for interconversion between FMN and FAD, were suppressed. Gene expression responses are consistent with the maintenance of flavin homeostasis, affecting flavin level changes under abiotic stress. Conclusions: This study establishes a comprehensive framework for the transcriptional regulation of flavin biosynthesis in plants. The findings reveal stress-responsive reprogramming of flavin metabolism and identify promising strategies for engineering crops for biofortification, metabolic efficiency, and stress resilience.