Corrigendum to “In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways”

Comparison of carbon fixation pathways using methanol as a substrate for the production of pyruvate with the Enzyme Cost Minimization algorithm. “(w/o SHMT)” indicates that the costs of the serine hydroxymethyltransferase are not included in the respective pathway’s activity. The concentration of CO₂ was assumed to be 1 mM and the concentration of HCO₃^- to be 10 mM. (a) Pathway-specific activities with standard deviations and the full name of the main pathways and the connecting modules to transform their primary product to pyruvate. Pathway abbreviations: CBB(PTS): phosphatase-free CBB cycle; HP-bicycle(glyox): glyoxylate producing subcycle of the 3-HP bicycle; GAPtoPyr: glycolysis; FCL: formaldehyde:NADP+ oxidoreductase (formyl-CoA-forming); GlyoxToPyr: GCL/GDH route; b-OH-AspCycle: β-hydroxyaspartate cycle; AcCoAtoOAA(HP): acetyl-CoA to oxaloacetate-converting module derived from the 3-HP/4-HB cycle using either ADP- or AMP-producing CoA-ester synthases; rCC-AcCoAtoPyr: acetyl-CoA to pyruvate-converting module derived from the rCCC; GlyoxToOAA: glyoxylate- to oxaloacetate-converting module based on the serine cycle. (b) Pathway-specific activities compared to product-substrate yield. The overall stoichiometries of all pathways and modules are listed in Table 1 and supplementary Tables S4 and S5. The small letters label each pathway and correspond to the labels and the respective pathway combinations in (a).

Comparison carbon fixation pathways using formate as a substrate for the production of pyruvate with the Enzyme Cost Minimization algorithm. “(w/o SHMT)” indicates that the cost of the serine hydroxymethyltransferase is not included in the respective pathway’s activity. The concentration of CO₂ was assumed to be 1 mM and the concentration of HCO₃^- to be 10 mM. (a) Pathway-specific activities with standard deviations and the full name of the main pathways and the connecting modules to transform their primary product to pyruvate. Pathway abbreviations: CBB(PTS): phosphatase-free CBB cycle; HP-bicycle(glyox): glyoxylate producing subcycle of the 3-HP bicycle; GAPtoPyr: glycolysis; FCL: formaldehyde:NADP+ oxidoreductase (formyl-CoA-forming); GlyoxToPyr: GCL/GDH route; b-OH-AspCycle: β-hydroxyaspartate cycle; AcCoAtoOAA(HP): acetyl-CoA- to oxaloacetate-converting module derived from the 3-HP/4-HB cycle using either ADP- or AMP-producing CoA-ester synthases; rCC-AcCoAtoPyr: acetyl-CoA- to pyruvate-converting module derived from the rCCC; GlyoxToOAA: glyoxylate to oxaloacetate converting module based on the serine cycle. (b) Pathway-specific activities compared to product-substrate yield. The overall stoichiometries of all pathways and modules are listed in Table 1 and supplementary Tables S4 and S5. The small letters label each pathway and correspond to the labels and the respective pathway combinations in (a).

Enzyme demands to sustain a total pathway activity of 1 mmol product per second. Contribution of the capacity, the reversibility, and the saturation with substrates or products of each reaction to the demand of enzymes for the CBB cycle, the rCCC, and the 2-HG-rTCA cycle. The figure follows the wording of Noor et al. [29]. “Capacity”: demand of enzyme caused by a limitation by the catalytic rate constant; “Reversibility”: extra amount of enzyme needed because of a backward flux; “Saturation”: additional enzyme necessary because of undersaturation with a substrate or oversaturation with a product. The values present the optimized state as predicted by the ECM algorithm assuming a CO₂ concentration of 10 μM and HCO₃^- concentration of 100 μM. Pyruvate was chosen as a product and formate as a substrate for the pathways. Reaction names correspond to their identifiers in the SBtab model file (Supplementary file Reactions_Composite22_model.tsv (available here)).

Comparison carbon fixation pathways using H₂/CO₂ as a substrate for the production of pyruvate with the Enzyme Cost Minimization algorithm. “(w/o SHMT)” indicates that the cost of the serine hydroxymethyltransferase is not included in the respective pathway’s activity. The concentration of CO₂ was assumed to be 1 mM and the concentration of HCO₃^- to be 10 mM. (a) Pathway-specific activities with standard deviations and the full name of the main pathways and the connecting modules to transform their primary product to pyruvate. Pathway abbreviations: CBB(PTS): phosphatase-free CBB cycle; HP-bicycle(glyox): glyoxylate-producing subcycle of the 3-HP bicycle; GAPtoPyr: glycolysis; FCL: formaldehyde:NADP+ oxidoreductase (formyl-CoA-forming); GlyoxToPyr: GCL/GDH route; b-OH-AspCycle: β-hydroxyaspartate cycle; AcCoAtoOAA(HP): acetyl-CoA- to oxaloacetate-converting module derived from the 3-HP/4-HB cycle using either ADP- or AMP-producing CoA-ester synthases; rCC-AcCoAtoPyr: acetyl-CoA- to pyruvate-converting module derived from the rCCC; GlyoxToOAA: glyoxylate- to oxaloacetate-converting module based on the serine cycle. (b) Pathway-specific activities compared to product-substrate yield. The overall stoichiometries of all pathways and modules are listed in Table 1 and supplementary Tables S4 and S5. The small letters label each pathway and correspond to the labels and the respective pathway combinations in (a).