Designing Genetic Circuits for Memory and Communication

The goal of synthetic biology is to allow the rapid design of organisms that can find diverse uses in environmental remediation, chemical production, or human health. Genetic engineering has traditionally been done by trial and error, but synthetic biology seeks to apply engineering principles and build complex circuits by rationally composing genetic parts together. We envision engineering microbes to form spatial communities for applications such as programmable tissues. We present novel circuit designs for memory and communication, which are basic building blocks for programming these behaviors. Our memory device uses molecular sequestration instead of cooperativity that was used in almost all previously built synthetic switches. In addition, our design allows predictable tuning of the switching boundaries and enables the rapid design of custom bistable switches that can function as a set-reset latch. We also present designs for contact-based communication by utilizing the recently discovered contact-dependent inhibition (CDI) system. Such a communication channel could allow programmed spatial features with micron-scale resolution, which can be advantageous compared to existing communication methods that rely on diffusible molecules. We present two strategies for harnessing the CDI system. In the first method, we fuse a small transcriptional activator to the protein that is delivered during CDI. In the second method, we exploit the known biology that the delivered domain can co-localize two other proteins. We use this co-localization effect to trigger an increase in activity from a split enzyme, and design an ultrasensitive response to the small number of molecules delivered during the CDI process. While we were not able to show control of gene expression in touching E. coli cells, we believe that our circuit designs can guide future engineering efforts