Quantitative studies of metabolic switches in enteric bacteria

项目摘要 这项研究解决了肠道细菌对碳源的分级利用，以及生长动力学。 当细菌从一种碳源转换到另一种碳源时发生的过渡。这种现象被称为 双氧体生长，是65年前由雅克·莫诺发现的。人们普遍认为这是由于 “分解代谢抑制”，这是一种在大肠杆菌中很好地描述了分子特征的调节反应，在 微生物。然而，最近的研究证实，分解代谢抑制与协调碳有关。 与新陈代谢的其他部分和细胞生长有关，而不是优先使用碳水化合物。 这项研究旨在阐明肠道细菌在无限的选择中所采用的调控策略。 环境中碳源的组合(通常首先采用快速新陈代谢的碳)，以及 使它们能够在首选碳源耗尽时快速切换碳源的动力学机制。 这项研究将结合使用多种方法：传统的生化方法和分子方法。 量化关键信号分子池的生物学方法；表征的定量蛋白质组学 蛋白质合成和周转，导致生长转变过程中蛋白质组的重塑；合成的 基因结构，使人们能够定量地探索代谢流和蛋白质变化的影响 生长转变的负载；基于微流体的方法来表征细胞生长、基因表达和 在逐个细胞水平上的信号分子；以及发展粗略... 粒化动力学模型，捕捉生理反应，并将它们与潜在的调控联系起来 机械装置。拟议的工作实质上是对我们实验室非常成功的方法的重大扩展 近年来发展起来将基因表达与生长生理联系起来，但从稳定状态到 动态域。本研究的成果，建立了营养生长相关关键字的定量预测模型 分子与生理行为的相互作用，将为建立生长动力学模型提供一个原型 与各种其他问题相关的过渡，从细菌的反应到抗生素，再到 进入稳定期后的分化发育动力学。关于以下方面的具体知识 肠道细菌如何选择它们的碳偏好可以在代谢工程应用中加以利用 消除或改变碳消费的顺序，同时了解增长的监管战略 转型可能会导致旨在减缓增长复苏的新类别的抗菌战略。

Project Summary 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 and 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.