Engineering Schizochytrium for tailored omega-3 production: Mechanistic insights into dehydratase domains and integrated metabolic optimization

Abstract

Schizochytrium is a premier industrial platform for polyunsaturated fatty acid (PUFA) production; however, simultaneously achieving high total content and an optimized ω-3/ω-6 quality ratio remains a significant metabolic engineering challenge. In this study, we elucidate the critical role of the dehydratase (DH) domain in PUFA biosynthesis through systematic domain-swapping between Schizochytrium and Shewanella. We first demonstrated that while the native SsDH_FabA domain contributes to both docosahexaenoic acid (DHA) and docosapentaenoic acid (DPA) formation, the bacterial SoDH_FabA specifically catalyzes DHA synthesis, thereby acting as a determinant for the ω-3/ω-6 ratio. Secondly, we expressed heterologously the SoDH_FabA in Schizochytrium to selectively improve PUFA composition. To further maximize productivity, we implemented an integrated “Push–Pull–Environmental Adaptation” strategy, which combined precursor supply enhancement, pathway flux redistribution, and intracellular physiological optimization. Finally, the engineered strain achieved a 42.26% increase in total fatty acids and a 54.54% increase in total PUFA, reaching concentrations of 0.44 g/g and 0.29 g/g dry cell weight, respectively. Notably, the ω-3/ω-6 ratio was significantly improved from 2.05 to 2.68–2.80. These results provide a novel engineering paradigm for the sustainable production of high-quality, tailored microbial oils for the industrial applications.