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. Overall design: Comparative gene expression profiling analysis of RNA-seq data for WT E. coli Nissle 1917 cells and engineered derivatives (EcN_SensorArrayOnly EcN_NOTgate_PsrA, EcN_NOTgate_HlyIIR, EcN_NOTgate_BM3R1, EcN_NOTgate_AmtR, EcN_NOTgate_QacR, EcN_NOTgate_LitR, EcN_NOTgate_AmeR, EcN_NOTgate_IcaR, EcN_NOTgate_BetI, EcN_NOTgate_PhlF)