Quantitative Studies of Bacterial Growth Physiology

University Of California, San Diego, La Jolla CA

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Abstract

? 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.