Understanding diverse bacterial nutritional requirements and responses is foundational in microbial research and biotechnology. In this study, we employed knowledge-enriched transcriptomic analytics to decipher complex stress responses of to supplied nutrients, aiming to enhance microbial engineering efforts. We computed 64 independently modulated gene sets that comprise a quantitative basis for transcriptome dynamics across a comprehensive transcriptomics dataset containing a broad array of nutrient conditions. Our approach led to the i) identification of novel transporter systems for diverse substrates, ii) a detailed understanding of how trace elements affect metabolism and growth, and iii) extensive characterization of nutrient-induced stress responses, including osmotic stress, low glycolytic flux, proteostasis, and altered protein expression. By clarifying the relationship between the acetate-associated regulon and glycolytic flux status of various nutrients, we have showcased its vital role in directing optimal carbon source selection. Our findings offer deep insights into the transcriptional landscape of bacterial nutrition and underscore its significance in tailoring strain engineering strategies, thereby facilitating the development of more efficient and robust microbial systems for biotechnological applications.

中文翻译：

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通过微生物工程知识丰富的转录组学解读营养应激反应


了解不同细菌的营养需求和反应是微生物研究和生物技术的基础。在这项研究中，我们采用知识丰富的转录组分析来破译对所提供营养物质的复杂应激反应，旨在加强微生物工程工作。我们计算了 64 个独立调节的基因集，这些基因集构成了包含广泛营养条件的综合转录组数据集的转录组动态的定量基础。我们的方法导致了i）针对不同底物的新型转运系统的鉴定，ii）对微量元素如何影响代谢和生长的详细了解，以及iii）营养诱导的应激反应的广泛表征，包括渗透应激、低糖酵解通量、蛋白质稳态和蛋白质表达改变。通过阐明乙酸盐相关调节子与各种营养素的糖酵解通量状态之间的关系，我们展示了其在指导最佳碳源选择中的重要作用。我们的研究结果提供了对细菌营养转录景观的深入见解，并强调了其在定制菌株工程策略方面的重要性，从而促进了为生物技术应用开发更高效、更强大的微生物系统。