Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications

Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field. •Highlights the bottleneck of Design-Build-Test (DBT) cycle in synthetic biology and metabolic engineering•Summarizes the current status of high throughput screening technologies for metabolite detection•Methods to transduce chemical concentrations to absorbance or fluorescence for high throughput screening•Includes metabolic engineering applications that benefit from the developed tools•Provides tables that include metabolites and their corresponding sensing tools for high throughput screening