Date of Award

Summer 8-15-2022

Author's School

McKelvey School of Engineering

Author's Department

Energy, Environmental & Chemical Engineering

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Microbes live in complex and continually changing environments. Rapid shifts in nutrient availability are a common challenge for microbes, and cause changes in intracellular metabolite levels. Microbial response to dynamic environments requires coordination of multiple levels of cellular machinery including gene expression and metabolite concentrations. This coordination is achieved through metabolic control systems, which sense metabolite concentrations and direct cellular activity in response. Several reoccurring control architectures are found throughout diverse metabolic systems, which suggests underlying evolutionary advantages for using these control systems to coordinate metabolism. One common, yet understudied, control architecture is the positive feedback metabolite uptake loop, which features a metabolite responsive-transcription factor (MRTF) that activates genes necessary to uptake its cognate metabolite. Understanding the design principles behind these complex metabolic control systems is a fundamental issue across many biological sub-disciplines since metabolism is a central feature of cellular behavior.The goal of this dissertation is to elucidate how the architecture and parameters of a MRTF-based control system shape metabolite dynamics and heterogenous metabolic response to changing nutrient environments. This dissertation focuses on the Escherichia coli fatty acid degradation system, which employs the positive feedback uptake loop architecture. The function and performance of these control systems to three common metabolic tasks was evaluated. First, after a nutrient depletion, microbes must rapidly turn off metabolic pathways to conserve resources. Second, microbes must maintain sensing ability in the face of metabolic conditions which impact cellular growth rate. Finally, upon abrupt shifts between nutrients, microbes must shift metabolic resources to uptake the new nutrient or otherwise cease growth. This shifting process can be heterogenous, with a sub-population which maintains a non-growing state that confers tolerance to antimicrobial compounds. Taken together, this work provides deeper understanding of the design principles for the control of metabolite dynamics and heterogeneity for applications in metabolic engineering and synthetic biology.


English (en)


Fuzhong Zhang

Committee Members

Petra Levin, Diego Oyarzún, Yinjie Tang, Joshua Yuan,