Expression data from Saccharomyces cerevisiae

In response to carbon source switching from glucose to non-glucose, such as ethanol and galactose, yeast cells can directionally preprogram cellular metabolism to efficiently utilize the nutrients. However, the understanding of cellular responsive network to utilize a non-natural carbon source, such as xylose, is limited due to the incomplete knowledge on the xylose response mechanisms. Here, through optimization of the xylose assimilation pathway together with combinational evaluation of reported targets, we generated a series of mutants with varied growth ability. However, understanding how cells respond to xylose and remodel cellular metabolic network is far insufficient based on current information. Therefore, genome-scale transcriptional analysis was performed to unravel the cellular reprograming mechanisms underlying the improved growth phenotype. To gain sufficient xylose-metabolism-related information, we designed a sample pool and divided it into three groups: (1) four constructed strains X029, X058, X109 and X158, with gradually improved cellular growth capacity on xylose; (2) X058 with three different preculture mode, on glucose, ethanol, and xylose, respectively; (3) strains X058 and X158 at different OD600 values, in order to track the cellular metabolism rearrangement on time-course当碳源从葡萄糖切换至乙醇、半乳糖等非葡萄糖类物质时，酵母细胞可定向预编程细胞代谢程序，以高效利用此类营养物质。然而，由于对木糖（xylose）响应机制的认知尚不完整，目前学界对细胞利用木糖这类非天然碳源的响应调控网络的理解仍较为有限。本研究通过优化木糖同化途径，并结合已报道靶点的组合筛选，获得了一系列生长能力存在差异的酵母突变株。然而，基于现有研究数据，我们对细胞如何响应木糖并重塑细胞代谢网络的认知仍存在显著不足。因此，本研究通过全基因组转录组分析，解析了提升生长表型背后的细胞重编程机制。为获取足够的木糖代谢相关研究信息，我们设计了样本池并将其划分为三组：(1) 四株工程菌株X029、X058、X109及X158，其在木糖培养基上的细胞生长能力呈逐步提升趋势；(2) 菌株X058分别以葡萄糖、乙醇及木糖为预培养碳源，共三种预培养模式；(3) 菌株X058与X158在不同OD600值下的样本，用于追踪细胞代谢重排的时间动态变化。