Elucidating and Rewiring Regulation of Terpenoid Biosynthesis in Yarrowia lipolytica Utilizing Renewable Lipid Feedstocks

Abstract

Terpenoids are a group of compounds with many important applications and oleaginous yeast Yarrowia lipolytica is a promising host for terpenoid production because of its highly active mevalonate pathway and high acetyl-CoA fluxes in lipid substrate. Moreover, it is generally recognized as safe (GRAS), and can metabolize renewable lipid feedstocks, in addition to common sugar feedstocks. Lipid is an important substrate as it is underutilized or used to produce low-value products. Our research aims to metabolically engineer Y. lipolytica to convert waste lipid feedstock into terpenes, specifically targeting β-carotene production. Two key aspects of metabolic engineering are emphasized: (1) Optimization of the auxin-inducible degron (AID) system for temporal regulation of protein in lipid substrates, and (2) Investigation into the NADPH supply in Y. lipolytica utilizing lipid substrates, especially its impact on β-carotene production. A unique AID conditional protein degradation system was developed, incorporating a CGD degron tag derived from mini-IAA7 inserted in the open loops of GFP, along with the F74A variant of Oryza sativa TIR1 F-box protein (OsTIR1(F74A)), and 5-Adamantyl-IAA as the inducer. Optimization strategies were employed to minimize leaky degradation by fine-tuning the expression level of the OsTIR1(F74A) F-box protein using the POLE1 medium-strength promoter, effectively improving degradation efficiency during the early culture phase. Metabolomic flux analysis and RNA sequencing suggest the significance of the pentosephosphate pathway and mannitol cycle as the main sources of cellular NADPH, an essential cofactor for β-carotene production. While the pentose-phosphate pathway remains important for NADPH and β-carotene production in lipid substrates, the importance of the mannitol cycle becomes prominent when the pentose-phosphate pathway is knocked out or when mannitol is supplemented to the lipid substrate. However, the correlation between NADPH levels and βcarotene production remains unclear, suggesting that other factors besides NADPH alone may influence β-carotene production.