Understanding Functional Roles of Native Pentose-Specific Transporters for Activating Dormant Pentose Metabolism in Yarrowia lipolytica (2017)

Pentoses, including xylose and arabinose, are the second most prevalent sugars in lignocellulosic biomass that can be harnessed for biological conversion. Although <i>Yarrowia lipolytica</i> has emerged as a promising industrial microorganism for production of high-value chemicals and biofuels, its native pentose metabolism is poorly understood. Our previous study demonstrated that <i>Y. lipolytica</i> (ATCC MYA-2613) has endogenous enzymes for d-xylose assimilation, but inefficient xylitol dehydrogenase causes <i>Y. lipolytica</i> to assimilate xylose poorly. In this study, we investigated the functional roles of native sugar-specific transporters for activating the dormant pentose metabolism in <i>Y. lipolytica</i> By screening a comprehensive set of 16 putative pentose-specific transporters, we identified two candidates, YALI0C04730p and YALI0B00396p, that enhanced xylose assimilation. The engineered mutants YlSR207 and YlSR223, overexpressing YALI0C04730p and YALI0B00396p, respectively, improved xylose assimilation approximately 23% and 50% in comparison to YlSR102, a parental engineered strain overexpressing solely the native xylitol dehydrogenase gene. Further, we activated and elucidated a widely unknown native l-arabinose assimilation pathway in <i>Y. lipolytica</i> through transcriptomic and metabolic analyses. We discovered that <i>Y. lipolytica</i> can coconsume xylose and arabinose, where arabinose utilization shares transporters and metabolic enzymes of some intermediate steps of the xylose assimilation pathway. Arabinose assimilation is synergistically enhanced in the presence of xylose, while xylose assimilation is competitively inhibited by arabinose. l-Arabitol dehydrogenase is the rate-limiting step responsible for poor arabinose utilization in <i>Y. lipolytica</i> Overall, this study sheds light on the cryptic pentose metabolism of <i>Y. lipolytica</i> and, further, helps guide strain engineering of <i>Y. lipolytica</i> for enhanced assimilation of pentose sugars.<b>IMPORTANCE</b> The oleaginous yeast <i>Yarrowia lipolytica</i> is a promising industrial-platform microorganism for production of high-value chemicals and fuels. For decades since its isolation, <i>Y. lipolytica</i> has been known to be incapable of assimilating pentose sugars, xylose and arabinose, that are dominantly present in lignocellulosic biomass. Through bioinformatic, transcriptomic, and enzymatic studies, we have uncovered the dormant pentose metabolism of <i>Y. lipolytica</i> Remarkably, unlike most yeast strains, which share the same transporters for importing hexose and pentose sugars, we discovered that <i>Y. lipolytica</i> possesses the native pentose-specific transporters. By overexpressing these transporters together with the rate-limiting d-xylitol and l-arabitol dehydrogenases, we activated the dormant pentose metabolism of <i>Y. lipolytica</i> Overall, this study provides a fundamental understanding of the dormant pentose metabolism of <i>Y. lipolytica</i> and guides future metabolic engineering of <i>Y. lipolytica</i> for enhanced conversion of pentose sugars to high-value chemicals and fuels.