| Summary: | <p>Abstract</p> <p>Background</p> <p>As one of the best xylose utilization microorganisms, <it>Scheffersomyces stipitis</it> exhibits great potential for the efficient lignocellulosic biomass fermentation. Therefore, a comprehensive understanding of its unique physiological and metabolic characteristics is required to further improve its performance on cellulosic ethanol production.</p> <p>Results</p> <p>A constraint-based genome-scale metabolic model for <it>S. stipitis</it> CBS 6054 was developed on the basis of its genomic, transcriptomic and literature information. The model <it>i</it>TL885 consists of 885 genes, 870 metabolites, and 1240 reactions. During the reconstruction process, 36 putative sugar transporters were reannotated and the metabolisms of 7 sugars were illuminated. Essentiality study was conducted to predict essential genes on different growth media. Key factors affecting cell growth and ethanol formation were investigated by the use of constraint-based analysis. Furthermore, the uptake systems and metabolic routes of xylose were elucidated, and the optimization strategies for the overproduction of ethanol were proposed from both genetic and environmental perspectives.</p> <p>Conclusions</p> <p>Systems biology modelling has proven to be a powerful tool for targeting metabolic changes. Thus, this systematic investigation of the metabolism of <it>S. stipitis</it> could be used as a starting point for future experiment designs aimed at identifying the metabolic bottlenecks of this important yeast.</p>
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