Processing two environmental chemical signals with a synthetic genetic IMPLY gate, a 2‐input‐2‐output integrated logic circuit, and a process pipeline to optimize its systems chemistry in Escherichia coli

Abstract

Synthetic genetic devices can perform molecular computation in living bacteria, which may sense more than one environmental chemical signal, perform complex signal processing in a human‐designed way, and respond in a logical manner. IMPLY is one of the four fundamental logic functions and unlike others, it is an “IF‐THEN” constraint‐based logic. By adopting physical hierarchy of electronics in the realm of in‐cell systems chemistry, a full‐spectrum transcriptional cascaded synthetic genetic IMPLY gate, which senses and integrates two environmental chemical signals, is designed, fabricated, and optimized in a single Escherichia coli cell. This IMPLY gate is successfully integrated into a 2‐input‐2‐output integrated logic circuit and showed higher signal‐decoding efficiency. Further, we showed simple application of those devices by integrating them with an inherent cellular process, where we controlled the cell morphology and color in a logical manner. To fabricate and optimize the genetic devices, a new process pipeline named NETWORK Brick is developed. This pipeline allows fast parallel kinetic optimization and reduction in the unwanted kinetic influence of one DNA module over another. A mathematical model is developed and it shows that response of the genetic devices are digital‐like and are mathematically predictable. This single‐cell IMPLY gate provides the fundamental constraint‐based logic and completes the in‐cell molecular logic processing toolbox. The work has significance in the smart biosensor, artificial in‐cell molecular computation, synthetic biology, and microbiorobotics.

Synthetic Genetic Reversible Feynman Gate in a Single E. coli Cell and Its Application in Bacterial to Mammalian Cell Information Transfer

“…Thus, by tuning the extracellular aTc and IPTG, the expression of EGFP and E2Crimson can be logically controlled. The bioparts were assembled using the Network Brick approach, 26 and the whole circuit was engineered in two plasmids and inserted into E. coli DH5αZ1 cells (Figure 1B). A detailed description of the plasmids can be found in Table S2.…”

Multilayer Genetic Circuits for Dynamic Regulation of Metabolic Pathways

“…Refined regulation of metabolic pathways often requires the cooperation of multiple signals to synthesize the target product efficiently, and therefore logic gates have a high potential in metabolic control. − However, it is impractical to use small molecules as inducers on a large scale. Moser et al showed that the same set of sensors could be integrated by different combinational logic circuits, which changes when genes are turned on and off during growth .…”

A Synthetic Genetic Reversible Feynman Gate in a Single E.coli Cell and its Application in Bacterial to Mammalian Cell Information Transfer

“…Thus by tuning the extracellular aTc and IPTG, the expression of EGFP and E2-crimson can be logically controlled. The bioparts were assembled using Network Brick approach 21 and the whole circuit was engineered in two plasmids and inserted into E.coli DH5αZ1 cells (Fig. 1B).…”

“…The individual expression cassettes were then assembled using network brick assembly process. A detailed process pipeline can be found elsewhere 21 . PCR amplifications were performed using KOD Hot Start DNA polymerase (Merck Millipore).…”