Fig. 3: Systems-level examination of ETS variants.

a Aero-type classification of the ETS variants. Broken lines on the aero-type plot show growth rate isoclines. b ME-model-based examination of the ATP production (left y-axis) and proteome allocation (right y-axis) in the ETS variants. The ATP produced per ATS proteome is approximately the same. c Contributions of different ATP-producing reactions towards total ATP production. ATP production by (i) ATP synthase (ATPS) in oxidative phosphorylation, (ii) acetate kinase (ACKr) in mixed acid fermentation, (iii) succinyl-CoA synthetase (SUCOAS) in the TCA cycle, and (iv) phosphoglycerate kinase (PGK) in the glycolysis pathway is shown in the histogram. The mean and standard deviation values are calculated using four independently evolved replicates of each strain. d Tradeoffs in the expression levels of genes of iModulons associated with anoxic (y-axis) and oxic (x-axis) energetics underlie the rewiring of the ATS to allow all variants to achieve approximately the same growth rate. The lowest aerotype (ETS-1H) has high anoxic/low oxic gene expression while the highest aerotype (ETS-4) exhibits the opposite. The gene composition of the iModulons is shown in Supplementary Table 4. The outliers of the replicates for an ETS variant are reflections of the differences in their genotypes (Supplementary Fig. 2, Supplementary Data 1). e Estimation of the number of protons required for the phosphorylation of ADP by ATP synthase (proton-to-ATP ratio) using the ME-model and the experimental data. Individual values of four independently evolved replicates of each ETS variant have been shown on the plot and corresponding median and range of values have been presented. Source Data available in Supplementary Table 3 and provided RNA-seq data.