Fig 1.
Representation of the ME-model.
The E-matrix reconstruction accounted for transcription, translation, and translocation as well as associated reactions to produce functional enzymes. Integration of the E-matrix (colored arrows) with the M-model (grey arrows) resulted in the ME-model.
Fig 2.
Predicted growth rate and yield.
Maximum growth rate (solid line), acetate secretion rate (dashed line), and ethanol secretion rate (dotted line) changed as functions of (A) CO, (B) CO2, and (C) fructose uptake rate.
Fig 3.
Predictions of growth rate and product production.
(A) Two sets of predicted growth rates, from iJL680 and iJL965-ME, were plotted against in vivo measured growth rates for arginine, xylose, pyruvate, glucose, CO, and fructose growth conditions (±std, n = 3). Linear regressions and 95% confidence intervals were represented by dashed lines and shaded areas, respectively. In iJL680, carbon atom uptake was constrained to 30 mmol*gDW-1*h-1, while in iJL965-ME, the optimal carbon uptake was constrained by inherent proteome limitations. r and p represent Pearson's correlation and p-value. (B) Predicted maximum acetate secretion rate (Ac; mmol*gDW-1*h-1) to substrate uptake rate (SUR; mmol*gDW-1*h-1) was plotted against measured averaged values. (C) Predicted pathway mechanism for observed glycerol production in spent media. Glycerol was a byproduct of cell membrane formation during cardiolipin production. While the cell was carbon-limited, glycerol was recycled into biomass using the pathway highlighted in green. When cells were proteome-limited, C. ljungdahlii secreted glycerol (purple arrow). Abbreviations: 1 = phosphatidylglycerol (n-C14:0), 2 = cardiolipin (n-C14:0), 3 = glycerol, 4 = dihydroxyacetone, 5 = dihydroxyacetone phosphate, CLPNS140 = cardiolipin synthase (n-C14:0), GLYCt = glycerol transport, GLYCDx = glycerol dehydrogenase, DHAK = dihydroxyacetone kinase.
Fig 4.
Predicted and experimental gene expression.
Categorized by RAST subsystem and summed, predicted gene expression (transcription flux reactions * gDW of RNA molecule; mmol* h-1) was compared to RNA-seq data for C. ljungdahlii grown on (A) CO, (B) CO2+H2, and (C) fructose. Linear regressions, 95% confidence intervals of the regression, and 95% prediction intervals are represented by lines, dark shaded areas, and light shaded areas respectively. Scatter plots shown are for the highest Pearson r between predicted and experimental data. Normalized total transcription flux (mmol*gDW-1*h-1) of the Wood-Ljungdahl pathway was plotted against carbon substrate uptake rate for (D) CO, (E) CO2+H2, and (F) fructose. Pearson r reflects correlation with growth rate.
Fig 5.
Effects of nickel availability on C. ljungdahlii grown on CO.
(A) Maximum predicted growth rate was plotted against relative nickel uptake (line), and in vivo maximum growth rate verses the concentration of added nickel was plotted on the opposite axes (dot, ±std, n = 3). (B) Predicted protein activity of the nickel-containing enzymes, carbon monoxide dehydrogenase (CODH4) and carbon monoxide dehydrogenase:acetyl-CoA synthase (CODH_ACS), was plotted against relative nickel uptake.
Fig 6.
Effects of nickel availability on C. ljungdahlii grown on fructose.
(A) Predicted growth rate and protein activity of carbon monoxide dehydrogenase:acetyl-CoA synthase (CODH_ACS) were plotted against relative nickel uptake (mmol*gDW-1*h-1). (B) Predicted ethanol (EtOH) secretion at optimal nickel uptake (WT) and no available nickel (-Ni2+) were plotted against relative fructose uptake (mmol*gDW-1*h-1). (C) Predicted acetate (Ac) secretion at optimal nickel uptake and no available nickel were plotted against relative fructose uptake (mmol*gDW-1*h-1). Measured (D) growth rate, (E) fructose consumption, (F) final ethanol concentration, and (G) final acetate concentration of fructose-grown C. ljungdahlii without added nickel and with ten times the concentration of nickel were plotted (±std, n = 3). Gray asterisk indicates difference significance is p = 0.06, and three black asterisk indicates significance of p<0.001.