Impact of xylose feeding on transcriptome profiles of anaerobically fed-batch xylodextrins consumption in Saccharomyces cerevisiae

Saccharomyces cerevisiae cannot metabolize xylodextrins in nature. One engineered S. cerevisiae strain, which expresses XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, and cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa, can utilize xylodextrins in aerobic condtions but not anaerobic conditions. We sequenced mRNA from anaerobically fed-batch cultures of the engineered S. cerevisiae grown on xylodextrins with or without the continuous feeding of xylose in biological duplicate. Dynamic changes of gene expression during xylose feeding experiment revealed by RNA deep sequencing indicated that xylose helps anaerobically xylodextrin-grown cells to recover mithondrial function thereby resuming xylodextrin consumption. Furthermore, different portions of genes involved in ribosome biogenesis showed either decreased or increased transcriptions. The underlying mechanism remains to be elucidated.野生型酿酒酵母（Saccharomyces cerevisiae）在自然环境中无法代谢木糖糊精。本研究构建的一株工程化酿酒酵母菌株，可表达来自斯氏假丝酵母（Scheffersomyces stipitis）的木糖还原酶基因（xylose reductase gene, XYL1）、木糖醇脱氢酶基因（xylitol dehydrogenase gene, XYL2）与木酮糖激酶基因（xylulose kinase gene, XKS1），以及来自粗糙脉孢霉（Neurospora crassa, N. crassa）的纤维糊精转运蛋白2编码基因（cellodextrin transporter 2, cdt-2）、β-木糖苷酶编码基因（β-xylosidase, gh43-2）与木糖基-木糖醇特异性β-木糖苷酶编码基因（xylosyl-xylitol-specific β-xylosidase, gh43-7）；该工程菌株可在有氧条件下利用木糖糊精，但无法在厌氧条件下完成该代谢过程。我们对以木糖糊精为碳源、添加或不添加持续补加木糖的厌氧补料分批培养体系中的工程酿酒酵母的mRNA进行了测序，实验设置生物学重复。通过RNA深度测序（RNA deep sequencing）分析木糖补加实验过程中的基因表达动态变化，结果显示：木糖可帮助厌氧环境中以木糖糊精为碳源生长的细胞恢复线粒体功能，进而恢复木糖糊精的消耗。此外，参与核糖体生物发生（ribosome biogenesis）的不同基因子集的转录水平呈现上调或下调趋势，其背后的潜在分子机制仍有待进一步阐明。