De novo biosynthesis of eriocitrin in Saccharomyces cerevisiae through deep learning-guided enzyme screening and systematic metabolic engineering

Eriocitrin, a flavanone-7- O -disaccharide known for its antioxidant and anti-inflammatory properties, holds considerable promise for use in functional foods and pharmaceuticals. However, its large-scale production is constrained by the limitations of conventional plant extraction, including low abundance of active compounds and seasonal variability. Here, we established a de novo biosynthetic pathway for eriocitrin from glucose in engineered Saccharomyces cerevisiae through combinatorial metabolic engineering. First, to verify the feasibility of glycosylation in the eriocitrin synthesis process, two highly efficient flavonoid-7- O -glucosyltransferases were identified using an integrated bioinformatics and deep learning approach. Subsequently, through the reconstruction of the UDP-rhamnose synthesis pathway and enhancement of the key glycosylation precursor UDP-glucose supply, an eriocitrin titer of 147.9 mg/L was achieved following supplementation with 300 mg/L eriodictyol. To further achieve the de novo synthesis of eriocitrin, an eriodictyol-producing strain was developed by screening the optimal F3′H/CPR pair, engineering promoters, and pathway integration, achieving an eriodictyol titer of 237.8 mg/L. Finally, combining the eriodictyol-producing chassis strain with the previously optimized glycosylation module enabled the de novo production of eriocitrin, reaching a titer of 30.5 mg/L. This work demonstrates a proof-of-concept for microbial production of flavonoid disaccharides, providing a foundation for a sustainable and scalable supply of eriocitrin.