Synthetic Biology Memory Circuits in Non-Traditional Hosts

Breakthroughs in molecular biology and genomic sciences have enabled synthetic biologists to construct genetic parts with circuit-like connectivity that have the ability to process logical operations. However, almost all successful cases have been demonstrated within well characterized laboratory organisms such as Escherichia coli. While useful for the development and demonstration of capabilities, these organisms are limited to particular environmental conditions and have sensitivities (e.g., to solvents and other chemistry) that may limit their robustness in some applications. These organisms are also limited in their metabolic activity, including preferred substrates and byproducts. The challenge is to be able to manipulate the best suited organism for the particular environment or purpose. Our goal is to develop new synthetic biology toolboxes in non-model bacterial chassis capable of harvesting energy and nutrients from complex dynamic environments such as contaminated fresh water reservoirs or soil. These relatively novel chassis include the aquatic cyanobacterium Synechocystis sp. PCC 6803 and the chemoautotrophic/photohetertrophic soil bacterium, Rhodobacter capsulatus. Our current focus is on the development of integrase-based gene circuits and digital event recorders. Integrases are phage recombinases that either flip or excise the genetic code between two recognition sites depending on the orientation of the sites. These devices record events in genomic and/or plasmid DNA, which is retained for many generations and are therefore useful for detecting chemical and environmental cues. This has broad environmental applications where detection and targeted disruption of harmful chemical species is possible.