Quantitative Studies of Bacterial Growth Physiology

 描述（由申请人提供）：了解细胞应激反应是系统生物学的重大挑战之一。以前的细菌应激反应研究主要集中在特定的途径或遗传反应的全系统调查。在这个建议中，我们描述了一个定量的生理研究E。大肠杆菌的渗透压反应，解决渗透压如何影响细菌的生长，细菌的反应如何破坏施加的压力，以及压力反应对生长造成的问题。结果将被用来构建一个成本效益分析的渗透反应，在一个定量的，预测的理论，准确地描述了细胞资源的协调对对抗渗透胁迫和维持生物量增长的冲突的需求的背景下。本研究的实验部分将涉及现代组学方法和经典生物化学分析的结合。蛋白质组学和核糖测序方法将用于获得细胞蛋白质组资源分配的定量、蛋白质组范围的图片，代谢组学方法将用于表征营养素的使用，朝向渗透反应与生物量生长。传统的生物化学方法将用于监测细胞质和细胞膜的拥挤，并检测维持在非常高的内部浓度的渗透剂的可能泄漏。这些研究将在各种营养物质和介质渗透压下进行，并针对不同的遗传背景进行设计，以探索渗透反应的各个方面。生成的数据将使用Hwa实验室开创的粗粒化方法进行分析，以获得蛋白质组和代谢资源分配的定量模型，在理论和实验之间进行迭代对话。

 DESCRIPTION (provided by applicant): Understanding cellular stress response is one of the grand challenges of systems biology. Previous studies of bacterial stress response have focused mostly on either specific pathways or system-wide survey of genetic responses. In this proposal, we describe a quantitative physiological study of E. coli's osmotic response, addressing how osmotic stress affects bacterial growth, how bacterial response alleviates the imposed stress, and what problems the stress response imposes on growth. The results will be used to construct a cost-benefit analysis of the osmotic response, in the context of a quantitative, predictive theory that accurately describes the coordination of cellular resources towards the conflicting demands of combating osmotic stress and maintaining biomass growth. The experimental component of this research will involve a combination of modern 'omic methodologies and classical biochemical analysis. Proteomics and ribo-seq methods will be used to obtain quantitative, proteome-wide picture of the cell's allocation of proteomic resources, and metabolomics methods will be used to characterize the use of nutrients, towards osmotic response vs biomass growth. Traditional biochemical methods will be used to monitor the crowding of the cytoplasm and the membrane, and detect possible leakage of osmolytes maintained at very high internal concentrations. These studies will be done at a variety of nutrient and medium osmolarities, and for different genetic backgrounds designed to probe various aspects of the osmotic response. The data generated will be analyzed using a coarse-graining approach pioneered by the Hwa lab to derive a quantitative model of proteomic and metabolic resource allocation, in an iterative dialogue between theory and experiment.