System-level metabolic and enzyme engineering enables high-titer gastrodin biosynthesis in yeast.

Gastrodin is a clinically used neuroprotective phenolic glycoside for the treatment of migraine and other neurovascular disorders, yet its sustainable and scalable production remains challenging. Microbial biosynthesis of gastrodin is intrinsically limited by restricted carbon flux into the shikimate pathway, strong metabolic competition at the chorismate node, and the low catalytic efficiency of plant-derived UDP-glycosyltransferases toward 4-hydroxybenzyl alcohol. In this work, a mechanism-guided metabolic and enzyme reprogramming strategy was established to overcomes these bottlenecks and enables industrial-level production of gastrodin in Saccharomyces cerevisiae. Carbon entry into the shikimate pathway was strengthened by engineering a strongly feedback-insensitive Aro3 variant, together with structure-guided attenuation of Aro7 that reduced l-phenylalanine and l-tyrosine formation while preserving essential physiological function. To sustain high-flux precursor generation, central carbon metabolism was systematically reconfigured by enhancing pentose phosphate pathway activity and tuning phosphoenolpyruvate-pyruvate partitioning, thereby elevating erythrose-4-phosphate, phosphoenolpyruvate, and NADPH availability. To resolve the terminal bottleneck, structure-guided evolution of AtUGT72B1 yielded a glycosyltransferase variant with a 26.6-fold increase in catalytic efficiency relative to the wild-type enzyme, while reinforcement of UDP-glucose biosynthesis further supported efficient glycosylation under elevated pathway flux. Integration of these multi-layered engineering strategies enabled production of 19.01 mM (5.44 g/L) gastrodin in shake flasks and 90.34 g/L in fed-batch fermentation, representing the highest microbial titer reported to date. Overall, this work demonstrates that synchronizing central metabolic architecture with tailored enzyme performance provides a generalizable framework for unlocking industrial-scale microbial biosynthesis of complex plant natural products.