Synthetic Regulation of Metabolic Pathways at the Single Cell Level

Cell-to-cell metabolic variations among isogenetic cell populations are ubiquitous and can substantially affect the ensemble bioproduction of cell cultures. We showed that engineered cells grown from a single colony could have ten-fold variations between individual cells in their metabolic activities.1 Methods to control non-genetic variation are lacking, such that low-performing variants arise in all cell cultures and their proportions cannot be regulated, resulting in suboptimal ensemble production. We have developed a synthetic regulatory tool, termed in vivo population quality control (PopQC), which employs an intracellular, product-responsive biosensor to regulate the expression of a survival gene – permitting continuous enrichment of high-performing, non-genetic variants under a given selection pressure and leading to enhanced ensemble production. We validated PopQC in two biosynthetic pathways and tested two alternative design principles, yielding enhanced bioproduction of both free fatty acid (FFA) and tyrosine.  We further confirmed that PopQC improves ensemble performance by selecting for non-genetic high-performers, an avenue unexplored by existing methods. Given the ubiquity of non-genetic phenotype variation, PopQC should be applicable to a variety of metabolic pathways, providing a unique approach to realizing efficient bioproduction for metabolic engineering.

1 Xiao Y., Bowen C.H., Liu D., Zhang F., Exploiting non-genetic, cell-to-cell variation for enhanced biosynthesis. Nat Chem Biol Accepted