Quantitative studies of metabolic switches in enteric bacteria

肠道细菌代谢开关的定量研究

• 批准号: 8997108
• 负责人: TERENCE HWA
• 金额: $ 35.79万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-02-17 至 2018-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8997108
• 关键词: Address; Adopted; Affect; Age; Animal Model; Antibiotics; Bacteria; Behavior; Binding; Biochemical; Biology; Carbon; Cells; Cereals; Complement; Consumption; Data; Development; Enterobacteriaceae; Environment; Enzymes; Equilibrium; Escherichia coli; Excision; Exhibits; Experimental Designs; Experimental Models; Feedback; Formulation; Gene Expression; Gene Expression Regulation; Genetic; Glucose; Glycerol; Goals; Growth; Health; Human; Kinetics; Knowledge; Lead; Learning; Length; Link; Metabolic; Metabolism; Microbe; Microfluidics; Modeling; Molecular; Molecular Biology; Monitor; Nitrogen; Nutrient; Output; Phase; Physiological; Physiology; Process; Protein Biosynthesis; Proteins; Proteome; Proteomics; Qualifying; Recovery; Repression; Research; Role; Running; Scheme; Signal Transduction; Signaling Molecule; Solid; Source; Speed; Stress; System; Systems Biology; Testing; Variant; Work; antimicrobial; base; cell growth; cell type; decision-making capacity; exhaust; fitness; mathematical model; metabolic abnormality assessment; metabolic engineering; model development; mutant; novel; novel strategies; predictive modeling; preference; protein degradation; protein expression; prototype; research study; response; theories

DESCRIPTION (provided by applicant): This research addresses the hierarchical usage of carbon sources by enteric bacteria, and the kinetic of growth transition that occurs when bacteria switch from one to another carbon source. This phenomenon, known as diauxic growth, was discovered by Jacques Monod 65 years ago. It was commonly thought to result from "catabolite repression", a regulatory response well characterized molecularly in E. coli and wide spread among microbes. However, recent studies establish that catabolite repression is about coordinating carbon metabolism with other sectors of metabolism and cell growth, and not about prioritizing the use of carbons. This research aims to elucidate the regulatory strategies enteric bacteria employ to choose among an infinite combination of carbon sources in the environment (often taking the fast-metabolizing carbons first), and the kinetic mechanism that enable them to switch carbon source rapidly when the preferred one runs out. The research will be carried out using a combination of approaches: traditional biochemical and molecular biology approaches to quantify the pools of key signaling molecules; quantitative proteomics to characterize protein synthesis and turnover that result in proteome-wide remodeling during growth transitions; synthetic genetic constructs that allow one to quantitatively probe the effect of changing metabolic fluxes and protein loads on growth transitions; microfluidic-based approaches to characterize cell growth, gene expression, and signaling molecules at a cell-by-cell level; and quantitative phenomenological approaches to develop coarse- grained kinetic models that capture the physiological responses and relate them to the underlying regulatory mechanisms. The proposed work is in essence a major extension of the highly successful approach our lab has developed in recent years to relate gene expression to growth physiology, but from the steady state to the kinetic domains. The output of this research, a quantitative predictive model of diauxic growth relating key molecular interactions to physiological behaviors, will provide a prototype for modeling the kinetics of growth transitions relevant to a wide variety of other problems ranging from the response of bacteria to antibiotic, to the kinetics of differentiation an development after entering the stationary phase. The specific knowledge on how enteric bacteria select their carbon preferences may be exploited in metabolic engineering applications to remove or alter the order of carbon consumption, while knowledge on the regulatory strategies of growth transitions may lead to new classes of antimicrobial strategies aimed at slowing down growth recovery.

描述（由申请人提供）：本研究介绍了肠细菌对碳源的层次使用，以及当细菌从一种切换到另一个碳源时发生的生长转变的动力学。这种现象被称为Diauxic Growth，由65年前的Jacques Monod发现。人们通常认为这是由“分解代谢物抑制”引起的，这种调节反应很好地表征了大肠杆菌的分子和微生物之间的广泛蔓延。然而，最近的研究表明，分解代谢物的抑制是关于将碳代谢与其他代谢和细胞生长领域进行协调，而不是优先考虑使用碳。这项研究旨在阐明肠道细菌采用的调节策略在环境中无限组合（通常首先采用快速代谢的碳）和动力学机制，从而使它们能够在偏爱时迅速切换碳源。该研究将使用多种方法进行：传统的生化和分子生物学方法来量化关键信号分子的池；定量蛋白质组学表征蛋白质合成和周转，从而导致生长过渡过程中蛋白质组的重塑；合成的遗传构建体可以定量探测改变代谢通量和蛋白质负荷对生长转变的影响；基于微流体的方法来表征细胞生长，基因表达和信号分子在细胞水平上；以及开发粗颗粒动力学模型的定量现象学方法，以捕获生理反应并将其与潜在的调节机制联系起来。拟议的工作本质上是我们实验室近年来开发的非常成功的方法的主要扩展，该方法将基因表达与生长生理学联系起来，但从稳态到动力学领域。这项研究的输出是将关键分子相互作用与生理行为相关的数字生长的定量预测模型，将提供一个原型，用于建模与从细菌对抗生素的反应到抗生素的反应，再到分化的发展阶段的生长转变动力学的动力学。有关肠细菌如何选择其碳偏好的特定知识可能会在代谢工程应用中被利用，以消除或改变碳消耗的顺序，而对生长过渡的调节策略的知识可能会导致旨在减缓生长恢复的新类别的抗菌策略。