Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

Significance Understanding how microbes adapt to changing conditions is fundamental to biological science and engineering. For example, adaptation is a key driver of antimicrobial resistance, and adaptive laboratory evolution has become a key tool in biotechnology. Here, we present a comprehensive genetic and fluxomic analysis of 10 adaptively evolved Escherichia coli phosphoglucose isomerase ( pgi ) knockout strains. The loss of PGI, a key enzyme in glycolysis, results in massive redirection of carbon catabolic flux and reduction in growth rate. Adaptive evolution results in a 3.6-fold increase in growth rate, enabled by key mutations and metabolic flux rewiring. These include global transcriptional regulators, cofactor transhydrogenases, and the phosphotransferase system component crr . Overcoming key bottlenecks, rather than a broad metabolic response, is the dominant mechanism of adaptation.