Abstract

Synthetic biology, which combines tools from engineering, molecular biology and computation, aims to
explore the biological systems available in nature and engineer new ones that can better serve our needs.
Yet, there are many challenges in designing and in building a biological system that will perform the desired
functions. Optimization of these newly engineered systems requires careful control over the levels and
timing of gene expression. Optogenetic tools are ideal to dynamically control gene expression since only
light is required to enable precise control and it provides a convenient interface between digital control
software and microbial culture. In this thesis, I present a fully automated closed-loop system which controls
gene expression and growth rates in Escherichia coli by using the engineered CcaR-CcaS two component
system that is activated or repressed by illumination of green or red light respectively. Using an in-house
designed computer-controlled light system, we periodically record culture density and fluorescence
measurements related to open- and closed-loop control of green fluorescent protein expression. We also
verify our experimental results with simulation models - with and without feedback. These results presented
here highlight the efficacy of our system, illustrating how it will potentially be used for other applications
that require gene expression control such as metabolic pathway engineering and designing biofuelproducing microbes.