| The goal of this thesis is to uncover operating principles in Escherichia coli metabolism and regulation. Due to the highly complex nature of biological systems, fundamental principles are often masked by secondary effects. To uncover various design principles, different research approaches were taken; systems and synthetic.;Using the systems approach, we uncovered a relationship where the growth rate is less than or equals to the square-root of the product among the biomass yield, the protein synthesis rate of the carbon source transporter and its turnover number. Through theoretical analysis, this relationship appears to be evolutionary optimal. We further demonstrated that adaptively evolved strain, knockout mutants, and ethanol challenged strains also follow the square-root relationship. Moreover this relationship provides an explanation to why the maximal growth rate does not occur at the maximal yield, and a design principle for engineering product formation strains.;Through the synthetic approach, a gene-metabolic oscillator, termed metabolator, was designed and constructed. Autonomous oscillations found in neuronal, cardiac, metabolic and gene expression systems have attracted significant attention because of their biological significance and their intriguing dynamics. We constructed a synthetic gene-metabolic oscillator in Escherichia coli K12 using the glycolytic flux to drive transcriptional and metabolic oscillation through a signaling metabolite, acetyl phosphate. We showed that metabolic oscillation can be generated from metabolic flux imbalance.;Furthermore, single-cell characterization of the proteolysis system used in the metabolator showed zeroth-order kinetics. In addition, we showed that zeroth-order degradation kinetics, coupled with long-tailed initial protein distribution, will generate first-order population degradation kinetics. Through simulation, we demonstrated that zeroth-order kinetics can significantly enhance the robustness of the metabolator. This result highlights the importance of single-cell measurements in determining the dynamics of a process. |
