Genomic and phenotypic characterization of a refactored xylose utilizing Saccharomyces cerevisiae for lignocellulosic biofuels/biochemicals production

To understand the mechanisms of enhanced xylose metabolism of XUSE, we reported transcriptome analysis of XUS (rationally engineered strain) and XUSE (evolved XUS strain) grown on xylose by performing RNA-sequencing. Compared with XUS, XUSE showed significantly different gene expression landscape with 463 up-regulated and 675 down-regulated genes (>2-fold, p-value<0.05). While the genes involved in non-oxidative pentose phosphate pathway, such as TKL1, TKL2 and TAL1, were down-regulated in XUSE, it shows the decreased transcriptional patterns of a number of genes encoding TCA cycle and respiratory enzymes. Also, the genes involved in the cellular metal ion regulation and sugar transporters showed significantly changed expression levels in XUSE. This study shows the gene expression landscape of XUSE revealing engineering strategies for the enhanced xylose metabolism in S. cerevisiae.为解析XUSE木糖代谢增强的分子机制，本研究对以木糖为碳源培养的XUS（理性工程菌株）与XUSE（经进化得到的XUS菌株）开展RNA测序（RNA-sequencing），并进行转录组分析。与XUS相比，XUSE的基因表达谱存在显著差异，共鉴定出463个上调表达基因与675个下调表达基因（差异倍数>2倍，p值<0.05）。尽管XUSE中参与非氧化戊糖磷酸途径（non-oxidative pentose phosphate pathway）的TKL1、TKL2及TAL1等基因呈下调表达，但该菌株中编码三羧酸循环（TCA cycle）与呼吸酶的多数基因的转录水平同样出现下调。此外，XUSE中参与细胞金属离子调控及糖转运蛋白（sugar transporters）的相关基因，其表达水平也发生了显著改变。本研究明确了XUSE的基因表达谱特征，为酿酒酵母（S. cerevisiae）木糖代谢增强的工程改造策略提供了理论依据。