Metabolic Repair through Emergence of New Pathways in Escherichia coli

E.coli can derive all essential metabolites and cofactors through a highly evolved metabolic system. Damage of pathways may significantly affect cell growth and physiology, but the strategies by which damaged metabolic pathways can be circumvented remain intriguing. Here, we use a ΔpanD (encoding for aspartate 1-decarboxylase) strain of E. coli, unable to produce the β-alanine required for CoA biosynthesis, to demonstrate that metabolic systems can overcome pathway damage by extensively rerouting metabolic pathways and modifying existing enzymes for unnatural functions. Using directed cell evolution, significant rewiring and repurposing of uracil metabolism allowed formation of an alternative β-alanine biosynthetic pathway. After this pathway was deleted, a second was evolved that utilized a gain of function mutation on ornithine decarboxylase (SpeC) to alter reaction and substrate specificity towards an oxidative decarboxylation-deamination reaction. After deletion of both pathways, yet another independent pathway emerged using polyamine biosynthesis, demonstrating the vast capacity of metabolic repair.