Transhydrogenase Promotes the Robustness and Evolvability of E. coli Deficient in NADPH Production

Abstract

Metabolic networks revolve around few metabolites recognized by diverse enzymes and involved in myriad reactions. Though hub metabolites are considered as stepping stones to facilitate the evolutionary expansion of biochemical pathways, changes in their production or consumption often impair cellular physiology through their system-wide connections. How does metabolism endure perturbations brought immediately by pathway modification and restore hub homeostasis in the long run? To address this question we studied laboratory evolution of pathway-engineered Escherichia coli that underproduces the redox cofactor NADPH on glucose. Literature suggests multiple possibilities to restore NADPH homeostasis. Surprisingly, genetic dissection of isolates from our twelve evolved populations revealed merely two solutions: (1) modulating the expression of membrane-bound transhydrogenase (mTH) in every population; (2) simultaneously consuming glucose with acetate, an unfavored byproduct normally excreted during glucose catabolism, in two subpopulations. Notably, mTH displays broad phylogenetic distribution and has also played a predominant role in laboratory evolution of Methylobacterium extorquens deficient in NADPH production. Convergent evolution of two phylogenetically and metabolically distinct species suggests mTH as a conserved buffering mechanism that promotes the robustness and evolvability of metabolism. Moreover, adaptive diversification via evolving dual substrate consumption highlights the flexibility of physiological systems to exploit ecological opportunities.

Author Summary

The structure of biological networks, like traffic systems or the Internet, features few hubs connected by numerous components. Though the conservation and high connectivity of hubs serve as key junctions to promote network expansion, addition or removal of connections surrounding hubs may disturb the whole system through their global linkage. How do biological networks mitigate hub perturbations during evolution? Using metabolism as an example, we studied the physiological and evolutionary consequences of genetically perturbed production of a hub metabolite NADPH in E. coli. We found that the expression of mTH, a phylogenetically conserved enzyme, was immediately upregulated and essential to counteract the hub perturbation. Moreover, long-term evolution of this pathway-modified E. coli in glucose growth media recurrently selected for mTH-upregulating mutations to restore the NADPH balance in all twelve replicate populations, regardless of several alternative solutions suggested in the literature. Corroborated by similar findings from laboratory evolution of a highly diverged species M. extorquens, our study suggests that mechanisms dedicated to mitigating hub perturbations promote both the robustness and evolvability of biological networks.