Fig. 4
From: Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism
Suboptimal pathway usage limits allocation of carbon to biomass precursors. Toy network schematic of flux distribution in Ref (a) and in uKO (b). A reaction knockout is highlighted in red. The flux distribution in eKO could be categorized as c changed flux distribution (i.e., the pathway usage was changed) or d changed flux capacity (i.e., the same pathways was used but at a higher level, see Methods). Four examples of changed flux distribution and changed flux capacity for f gnd, g sdhCB, h ptsHIcrr, and i pgi lineages. f flux was initially re-routed through the ED pathway after removing the gnd gene The ED pathway has a net yield of one ATP, NADH, and NADPH per molecule of glucose, whereas glycolysis has a net yield of two ATP and NADH40. Instead, the evolved gnd endpoints limited the use of the PPP and increased the flux capacity through the higher energy and redox equivalent producing pathway of glycolysis. g flux was initially re-routed through the TCA cycle in uSdhCB by diverting flux through the anaplerotic reactions phosphoenolpyruvate carboxylase (PPC) and inverting the direction of flux through malate dehydrogenase (MDH). The eSdhCB re-inverted the direction of malate dehydrogenase towards production of nadh or quinone reduction, and downregulated flux through the rest of the TCA cycle. h A significant portion of flux was bifurcated between the methylglyoxal pathway and lower glycolysis in uPtsHIcrr in response to elevated levels of dihydroxyacetone phosphate (DHAP) and depletion of lower glycolytic intermediates that inhibit the activity of methylglyoxal synthase114, 115. The flux through the methylglyoxal pathway was essentially eliminated in endpoints 2 and 4, and significantly decreased in replicates 1 and 3, in order to utilize the less toxic and more energy and redox producing lower glycolytic pathway. i The abnormally high levels of flux directed through the oxidative Pentose Phosphate Pathway (oxPPP) in uPgi was initially re-routed through the ED pathway. Several evolved pgi endpoints retained the flux through the ED pathway to varying degrees, but most re-distributed flux through GND, and all increased the flux capacity through the non-oxidative Pentose Phosphate Pathway (non-oxPPP). Green and orange colored reaction lines in f–i correspond to the grouping of changed flux distribution or changed flux capacity shown in the bar plot in h. Color bars for all flux values are shown next to their corresponding reaction(s)
