Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden

To build therapeutic strains, Escherichia coli Nissle (EcN) have been engineered to express antibiotics, toxin-degrading enzymes, immunoregulators, and anti-cancer chemotherapies. For efficacy, the recombinant genes need to be highly expressed, but this imposes a burden on the cell, and plasmids are difficult to maintain in the body. To address these problems, we have developed landing pads in the EcN genome and genetic circuits to control therapeutic gene expression. These tools were applied to EcN SYNB1618, undergoing clinical trials as a phenylketonuria treatment. The pathway for converting phenylalanine to trans-cinnamic acid was moved to a landing pad under the control of a circuit that keeps the pathway off during storage. The resulting strain (EcN SYN8784) achieved higher activity than EcN SYNB1618, reaching levels near when the pathway is carried on a plasmid. This work demonstrates a simple system for engineering EcN that aids quantitative strain design for therapeutics. •Improvement of a bacterium for PKU therapy•Genetic circuit design automation for human probiotic E. coli Nissle•Library of NOT gates based on orthogonal protein repressors•Genomic circuits and landing pads for improved activity and stability The probiotic Escherichia coli Nissle has been engineered as a living treatment for human diseases, from metabolic disorders to cancer. Here, we develop genome-encoded genetic circuits that control when therapeutic genes are expressed. This advance was applied to a treatment for phenylketonuria (PKU) that showed improved activity and simplified manufacturing.