UC San Diego

Survival through periods of starvation is crucial for bacterial fitness. The role of gene expression in sustaining the viability of starving bacteria has been extensively studied, including the identification and investigation of 'stress response' proteins regulated by the general stress sigma factor RpoS in E. coli. However, less is known about the costs and benefits of metabolic processes sustaining gene expression during starvation. This thesis work describes a comprehensive physiological study of E. coli cells under glucose starvation, quantifying the temporal dynamics of resource generation and utilization, and connecting them to cell viability. We focus on a preparatory period, the stationary phase, where the proteome is remodeled after entering starvation, before the onset of significant population death. We find two proteins are degraded for every protein synthesized, and five-six proteins degraded for every protein accumulated, resulting in the turnover of over half of the proteome for a moderate gain in stress proteins. Such extensive global proteolysis is enabled by a little-known member of the RpoS regulon, YeaG, which works in concert with well-known members of the proteolytic machineries. The total amount of protein synthesis is dictated by the amount of protein degradation, reflecting a dominant, supply-driven strategy of resource allocation for starving cells. YeaG-mediated proteome remodeling accounts for a major share of the viability boost provided by RpoS. In a mutant where energy can be supplemented without cell growth, YeaG activity is largely unnecessary, suggesting that a major physiological function of proteome remodeling is to increase the energy efficiency of starving cells for survival. Such knowledge of the physiology and molecular biology of starving bacteria offers new insights on bacterial vulnerabilities and inspires new strategies for engineering efficient bacterial bio-factories.