Elucidation and activation of native xylose and cellobiose metabolism in Yarrowia lipolytica for high-yield production of organic acids

While the model oleaginous yeast Yarrowia lipolytica is well known for decades to grow mainly on C6 sugars, its native metabolic capability to assimilate xylose and cellobiose, dominant sugars derived from lignocellulosic biomass, is poorly understood. In this study, we elucidated and activated native xylose and cellobiose pathways of Y. lipolytica through comprehensive metabolic and transcriptomic analyses. We identified 7 glucose-specific transporters, 16 xylose-specific transporters, and 4 cellobiose-specific transporters that are transcriptionally upregulated for growth on respective single sugars. While Y. lipolytica is capable of using xylose as a carbon source, xylose dehydrogenase is the key bottleneck of xylose assimilation, which found to be transcriptionally repressed by glucose. Y. lipolytica has a set of 5 extracellular and 6 intracellular beta-glucosidases to assimilate cellobiose via both extra- and intra-cellular mechanisms, but the latter being dominant for growth on cellobiose as a sole carbon source. In the mixture of sugars we observed that Y. lipolytica exhibited carbon catabolite repression (CCR) by glucose as well as carbon catabolite activation for xylose utilization by cellobiose or vice versa. By tuning the expression of metabolic enzyme and transporter genes of sugar assimilation pathways in Y. lipolytica, we demonstrated efficient biotransformation of 1) xylose, cellobiose as well as their mixtures with glucose and 2) lignocellulosic biomass in simultaneous saccharification and fermentation in ionic liquid (SSF-IL) for high-yield production of high-value organic acids (e.g., alpha-ketoglutaric acid).