Cheating the cheater: Suppressing false positive enrichment during biosensor-guided biocatalyst engineering

Abstract

Transcription factor (TF)-based biosensors are very desirable reagents for high-throughput enzyme and strain engineering campaigns. Despite their potential, they are often difficult to deploy effectively as the small molecules being detected can leak out of high-producer cells, into low-producer cells, and activate the biosensor therein. This crosstalk leads to the overrepresentation of false positive/cheater cells in the enriched population. While the host cell can be engineered to minimize crosstalk (e.g., by deleting responsible transporters), this is not easily applicable to all molecules of interest, particularly those that can diffuse passively. One such biosensor recently reported for trans-cinnamic acid (tCA) suffers from crosstalk when used for phenylalanine ammonia-lyase (PAL) enzyme engineering by directed evolution. We report that desensitizing the biosensor (i.e., increasing the limit of detection, LOD) suppresses cheater population enrichment. Further we show that, if we couple the biosensor-based screen with an orthogonal pre-screen that eliminates a large fraction of true negatives, we can successfully reduce the cheater population during the fluorescence-activated cell sorting (FACS). Using the approach developed here, we were successfully able to isolate PAL variants with ~70% high kcat after a single sort. These mutants have tremendous potential in Phenylketonuria (PKU) treatment and flavonoid production.