Engineering wetware and software for the predictive design of compressed genetic circuits for higher-state decision-making

Synthetic genetic circuits enable the reprogramming of cells, advancing the study and application of biology with greater precision. However, quantitative circuit design is hampered by the limited modularity of biological parts. As circuit complexity increases, this imposes a greater metabolic burden on chassis cells, which limits circuit design capacity. Here, we present a generalizable wetware and complementary software to enable the quantitative design of genetic circuits that utilize fewer parts for higher-state decision-making. We term the process of designing smaller genetic circuits as compression. To accomplish this, we develop scalable wetware that leverages sets of synthetic transcription factors (i.e., network capable repressors and anti-repressors) and synthetic promoters that facilitate the full development of 3-input Boolean logic compression circuits. Complementary software enables the design of higher-state circuits with a minimal genetic footprint and quantitatively precise performance setpoints. On average the resulting multi-state compression circuits are approximately 4-times smaller than canonical inverter-type genetic circuits. Our quantitative predictions have an average error below 1.4-fold for >50 test cases. Additionally, we successfully apply this technology toward the predictive design of a recombinase genetic memory circuit, and flux through a metabolic pathway with precise setpoints. As the complexity of synthetic genetic circuits increases for biocomputing applications, there is a need to reduce the footprint of circuits to reduce burden on cells. Here, the authors develop wetware and software to design 3-input Boolean logic circuits that utilize fewer genetic parts.