Development of a Synthetic 3‑Dehydroshikimate Biosensor in Escherichia coli for Metabolite Monitoring and Genetic Screening

Biosensors for target metabolites provide powerful high-throughput screening tools to obtain high-performing strains. However, well-characterized metabolite-sensing modules are often unavailable and limit rapid access to the robust biosensors with successful applications. In this study, we developed a strategy of transcriptome-assisted metabolite-sensing (TAMES) to identify the target metabolite-sensing module based on selectively comparative transcriptome analysis between the target metabolite producing and nonproducing strains and a subsequent quantative reverse transcription (RT-qPCR) evaluation. The strategy was applied to identify the sensing module cusR that responds positively to the metabolite 3-dehydroshikimate (DHS) and proved it was effective to narrow down the candidates. We further constructed the cusR-based synthetic biosensor and established the DHS biosensor-based high-throughput screening (HTS) platform to screen higher DHS-producing strains and successfully increased DHS production by more than 90%. This study demonstrated that the TAMES strategy was effective at exploiting the metabolite-sensing transcriptional regulator, and this could likely be extended to develop the biosensor-based HTS platforms for other molecules.