Trait tacking for predictive evolution of metabolic phenotypes

Adaptive laboratory evolution has been successfully used to obtain cells with improved properties through natural selection. While being conceptually and operationally simple, it can provide access to complex traits without any knowledge of the involved genetic and regulatory elements. Yet , the method is inherently limited to growth-associated traits like utilization of difficult-to-assimilate nutrients. This precludes a large range of phenotypes of interest, e.g. metabolite secretion, that incur a fitness cost. Here, we introduce the concept of tacking trait, which enables model-guided design of evolution conditions – evolution niche – for enhancing a costly metabolic trait through natural selection. The concept is inspired from the tacking maneuver in sailing allowing traversing upwind, a situation analogous to selecting for a fitness-costly trait. In the present formulation, we define tacking trait as a set of metabolic fluxes that are coupled to the desired trait (e.g. production of a metabolite of interest) in the target niche (i.e. the environment in which the cells are desired to manifest the trait of interest). The evolution experiment is, however, carried out in the model-designed evolution niche wherein the tacking trait, but not necessarily the desired trait, is coupled to the cell growth. Adaptive evolution in the evolution niche then drives the enhancement in the tacking trait; thanks to the thermodynamic coupling between the tacking and the desired traits, the evolved cells are primed to exhibit improved desired trait when grown in the target niche. We demonstrate the validity of this strategy – the EvolveX algorithm – by evolving a wine yeast strain for selective increase in the aroma compounds originating from either branched-chain or aromatic amino acid pathway. Our results show how fitness-costly traits can be selected for by using first-principle models and pave the way for precision laboratory evolution for biotechnological and ecological applications.