Engineered Gene Circuits: From Oscillators to Synchronized Clocks and Biopixels
Synthetic biology can be broadly parsed into the “top-down” synthesis of genomes and the “bottom-up” engineering of relatively small genetic circuits. In the genetic circuits arena, toggle switches and oscillators have progressed into triggers, counters and synchronized clocks. Sensors have arisen as a major focus in the context of biotechnology, while oscillators have provided insights into the basic-science functionality of cyclic regulatory processes. A common theme is the concurrent development of mathematical modeling that can be used for experimental design and characterization, as in physics and the
engineering disciplines. In this talk, I will describe the development of genetic oscillators over increasingly longer length scales. I will first describe an engineered intracellular oscillator that is fast, robust, and persistent, with tunable oscillatory periods as fast as 13 minutes. Experiments show remarkable robustness and persistence of oscillations in the designed circuit; almost every cell exhibits large-amplitude fluorescence oscillations throughout each experiment. Computational modeling reveals that the key design principle for constructing a robust oscillator is a small time delay in the negative feedback loop, which can mechanistically arise from the cascade of cellular processes involved in forming a functional transcription factor. I will then describe an engineered network with intercellular coupling that is capable of generating synchronized oscillations in a growing population of cells. Microfluidic devices tailored for cellular populations at differing length scales are used to demonstrate collective synchronization properties along with spatiotemporal waves occurring on millimeter scales. While quorum sensing proves to be a promising design strategy for reducing variability through coordination across a cellular population, the length scales are limited by the diffusion time of the small molecule governing the intercellular communication. I will conclude with our recent progress in engineering the synchronization of thousands of oscillating colony “biopixels” over centimeter length scales through the use of redox signaling that is mediated by hydrogen peroxide vapor. We have used the redox communication to construct a frequency modulated biosensor by coupling the synchronized oscillators to the output of an arsenic sensitive promoter that modulates the frequency of colony-level oscillations due to quorum sensing.