Synthetic Gene Circuits in Intestinal Bacteria: Biosensors and Pulse Counters

Abstract

The human microbiome comprises a complex community of microorganisms, residing primarily in the intestine. Variations in the composition of the microbiome have been linked to an increasingly wide array of diseases, leading to a growing interest in the development of microbiome-based clinical interventions. One promising opportunity is the engineering of commensal bacteria to create new strains that can sense disease in the gut and produce therapeutic compounds in response. This dissertation discusses motivations for the construction of synthetic biological circuits in intestinal bacteria and presents developments in two key areas. Because the design of disease-responsive circuits is limited by a relatively small pool of known biosensors, there is a need for expanding the capacity of engineered bacteria to sense and respond to the host environment. Chapter 2 describes the application of a robust genetic memory circuit to identify new bacterial biosensors responding in the healthy and diseased mammalian gut, which may be used to construct diagnostic or therapeutic circuits. Chapter 3 presents novel synthetic circuits that can record multiple pulses of a specific signal, a fundamental capability with many potential applications in biosensing, which has not been reliably demonstrated in synthetic biology thus far. While the clinical application of engineered bacterial strains is still an emerging concept, the advances described herein expand the capabilities of synthetic biology for the creation of increasingly complex, environmentally-responsive systems, representing a practical step toward the construction of clinically useful synthetic tools.