Rapid and tunable post-translational coupling of genetic circuits

One promise of synthetic biology is the creation of genetic circuitry that enables the execution of logical programming in living cells. Such “wet programming” is positioned to transform a wide and diverse swath of biotechnology ranging from therapeutics and diagnostics to water treatment strategies. While progress in the development of a library of genetic modules continues apace(1–4), a major challenge for their integration into larger circuits is the generation of sufficiently fast and precise communication between modules(5,6). An attractive approach is to integrate engineered circuits with host processes that facilitate robust cellular signaling(7). In this context, recent studies have demonstrated that bacterial protein degradation can trigger a precise response to stress by overloading a limited supply of intracellular proteases(8–10). Here, we use protease competition to engineer rapid and tunable coupling of genetic circuits across multiple spatial and temporal scales. We characterize coupling delay times that are more than an order of magnitude faster than standard transcription-factor based coupling methods (less than one minute compared with ~20–40 minutes) and demonstrate tunability through manipulation of the linker between the protein and its degradation tag. We use this mechanism as a platform to couple genetic clocks at the intracellular and colony level, then synchronize the multi-colony dynamics to reduce variability in both clocks. We show how the coupled clock network can be used to encode independent environmental inputs into a single time series output, thus enabling the possibility of frequency multiplexing in a genetic circuit context. Our results establish a general framework for the rapid and tunable coupling of genetic circuits through the use of native queueing processes such as protein degradation.