Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering

IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Jongoh Shin , Daniel C. Zielinski , Bernhard O. Palsson
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引用次数: 0

Abstract

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 Vibrio natriegens 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.

Abstract Image

通过知识丰富的转录组学解密营养压力反应,促进微生物工程。
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。在本研究中,我们采用了知识丰富的转录组分析方法来解读纳氏弧菌对所提供营养物质的复杂应激反应,旨在加强微生物工程学的研究。我们计算了 64 个独立调节的基因集,这些基因集构成了转录组动态的定量基础,该转录组数据集包含一系列广泛的营养条件。通过这种方法,我们 i) 发现了用于不同底物的新型转运系统;ii) 详细了解了微量元素如何影响新陈代谢和生长;iii) 广泛鉴定了营养物质诱导的应激反应,包括渗透应激、低糖酵解通量、蛋白稳态和蛋白质表达改变。通过阐明醋酸相关调控子与各种营养物质的糖酵解通量状态之间的关系,我们展示了它在指导最佳碳源选择方面的重要作用。我们的发现深入揭示了细菌营养的转录景观,并强调了其在定制菌株工程策略方面的重要意义,从而促进了生物技术应用领域更高效、更强大的微生物系统的开发。
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来源期刊
Metabolic engineering
Metabolic engineering 工程技术-生物工程与应用微生物
CiteScore
15.60
自引率
6.00%
发文量
140
审稿时长
44 days
期刊介绍: Metabolic Engineering (MBE) is a journal that focuses on publishing original research papers on the directed modulation of metabolic pathways for metabolite overproduction or the enhancement of cellular properties. It welcomes papers that describe the engineering of native pathways and the synthesis of heterologous pathways to convert microorganisms into microbial cell factories. The journal covers experimental, computational, and modeling approaches for understanding metabolic pathways and manipulating them through genetic, media, or environmental means. Effective exploration of metabolic pathways necessitates the use of molecular biology and biochemistry methods, as well as engineering techniques for modeling and data analysis. MBE serves as a platform for interdisciplinary research in fields such as biochemistry, molecular biology, applied microbiology, cellular physiology, cellular nutrition in health and disease, and biochemical engineering. The journal publishes various types of papers, including original research papers and review papers. It is indexed and abstracted in databases such as Scopus, Embase, EMBiology, Current Contents - Life Sciences and Clinical Medicine, Science Citation Index, PubMed/Medline, CAS and Biotechnology Citation Index.
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