Biosensor-guided indexing of genome evolution for boosting microbial chemical synthesis

Microbial synthesis of chemicals still faces low production due to the complicated metabolic networks, which generally cannot be tackled by rational engineering strategies. In this study, we report on a workflow, biosensor-guided indexing of genome evolution (BRIDGE), to obtain marker-free engineered strains with improved chemical production. We adopt the BRIDGE system to achieve high-level protocatechuic acid (PCA) production in Pseudomonas putida, reaching 4.67 g l^-1 in shake flasks. Transcriptomics analysis reveals a synergy between metabolic pathway activation and the secretion system, allowing PCA overproduction. Furthermore, we demonstrate that the engineered P. putida can serve as a platform for de novo synthesis of other chemicals with high titers, achieving 2.97 g l^-1cis,cis-muconate in shake flasks. Since the BRIDGE system gives marker-free engineered strains, it would greatly favor downstream industrial applications. Considering the great variety of available biosensors, we envision that our BRIDGE approach will accelerate other microbial synthesis processes with enhanced productivity.