Modular control of multiple pathways using engineered orthogonal T7 polymerases

TLDR

Synthetic genetic sensors and circuits provide programmable control of gene expression and are increasingly used to regulate complex multigene pathways and cellular functions. The authors propose a design strategy that genetically separates sensing/circuitry functions from the pathway to be controlled. They achieve this separation by having circuit outputs drive expression of engineered orthogonal T7 RNA polymerases that activate pathway genes from polymerase‑specific promoters, with all components encoded on a controller plasmid and using toxicity‑reduced T7 variants to create four orthogonal polymerases. The resulting orthogonal polymerases exhibit 8‑ to 75‑fold higher activation of cognate promoters than off‑target promoters, enabling four independent channels that link circuit outputs to distinct cellular functions, as demonstrated by a controller plasmid that implements AND logic to toggle between metabolic pathways that change E.

Abstract

Synthetic genetic sensors and circuits enable programmable control over the timing and conditions of gene expression. They are being increasingly incorporated into the control of complex, multigene pathways and cellular functions. Here, we propose a design strategy to genetically separate the sensing/circuitry functions from the pathway to be controlled. This separation is achieved by having the output of the circuit drive the expression of a polymerase, which then activates the pathway from polymerase-specific promoters. The sensors, circuits and polymerase are encoded together on a 'controller' plasmid. Variants of T7 RNA polymerase that reduce toxicity were constructed and used as scaffolds for the construction of four orthogonal polymerases identified via part mining that bind to unique promoter sequences. This set is highly orthogonal and induces cognate promoters by 8- to 75-fold more than off-target promoters. These orthogonal polymerases enable four independent channels linking the outputs of circuits to the control of different cellular functions. As a demonstration, we constructed a controller plasmid that integrates two inducible systems, implements an AND logic operation and toggles between metabolic pathways that change Escherichia coli green (deoxychromoviridans) and red (lycopene). The advantages of this organization are that (i) the regulation of the pathway can be changed simply by introducing a different controller plasmid, (ii) transcription is orthogonal to host machinery and (iii) the pathway genes are not transcribed in the absence of a controller and are thus more easily carried without invoking evolutionary pressure.