Thesis Defense: Reed McCardell

Genetic circuits for the control of multi-strain bacterial populations

Microbes together in their communities are incredibly powerful actors wherever they are found; they perform small miracles---the conversion of milk into yogurt---and large ones---production of most of the planet's oxygen and organic carbon. This thesis presents a body of work which explores the manipulation of microbial communities using the intersectional bio-engineering approach of synthetic biology. We demonstrate how molecular tools evolved by bacteria can be repurposed to create rationally designed systems for controlling features of bacterial populations.

We begin by examining a genetic circuit that controls the size of a bacterial population by coordinating the deaths of population members in response to a density signal---the "pop cap" circuit. To improve the circuit's performance and reduce the influence of the environment on the circuit, we add machinery for the active degradation of the density signal. Additionally, we explore mechanisms to sequester the death-causing toxin---inactivating it---allowing us to release a population cap---creating the "cap and release" circuit. Using the scalable "cap and release motif", we design a genetic circuit to regulate a multi-strain community---the "A=B" circuit. Our implementation of "A=B" can successfully regulate the composition of a community, with interesting additional effects on total population density.

We conclude with a discussion of the bacteriocin exotoxins. Increasingly popular in engineering microbial community control, bacteriocins are powerful tools for regulating groups of microbes and present an exceedingly versatile chassis for protein design innovation.