Fig. 1
From: Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism
Evolution of knockout (KO) strains from a pre-evolved (i.e., optimized) wild-type strain. a Experimental design using adaptive laboratory evolution (ALE) and enzyme knockouts to investigate system re-optimization following major metabolic perturbations. b An isolated wild-type (wt) E. coli (MG1655 K-12) previously evolved on glucose minimal media at 37 °C31 was used as the starting strain for knockouts of key metabolic genes and subsequent re-evolution, or systems re-optimization. c Reactions disabled by the enzyme knockouts included the phosphotransferase sugar import system (ptsHIcrr), phosphoglucose isomerase (pgi), 6-phosphogluconate dehydrogenase (gnd), triophosphate isomerase (tpi), and succinate dehydrogenase complex (sdhCB). d Adaptive laboratory evolution trajectories of the initial reference knockout and evolved knockout lineages. e Counts of significantly different system components found for each evolved knockout relative to the unevolved knockout. Counts of metabolomic, transcriptomic, and fluxomic data are given as the average and standard deviation of the percent of significant features compared to all features measured for the lineage; counts for mutations are given as the average and standard deviation of the number of significant features (see Methods for criteria for significance)
