BioDesign Research / 2021 / Article / Tab 1

Research Article

In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways

Table 1

Modules connecting pathways that were implemented in the SBtab model file.

Originating pathway eStoichiometry (main substrates underlined, main products bold) (kJ/mol)

Glyoxylate-converting modules
β-Hydroxyaspartate cycle2 glyoxylate+NADH⟶oxaloacetate+NAD+
3-HP-bicycle (modified)glyoxylate+3NADPH+2HCO3-+ATP⟶
oxaloacetate+3NADP++ADP+Pi
Reverse glyoxylate shuntGlyoxylate+ATP+MQH2+NADH+CoA+2H+in
acetyl-CoA+ADP+Pi+MQ+NAD++2H+out
a
Serine cycleGlyoxylate+formate+NADH+NADPH+HCO3-+2ATP⟶
oxaloacetate+NAD++NADP++2ADP+2Pi
Glyoxylate carboligase/glycerate dehydrogenase2 glyoxylate+NADHglycerate+NAD++CO2
Acetyl-CoA-converting modules
Ethylmalonyl-CoA pathway (modified)2 acetyl-CoA+2NADPH+0.5NAD++UQ+MQ+HCO3-+CO2+2H+out
⟶1.5 oxaloacetate+2NADP++0.5NADH+UQH2+MQH2+2CoA+2H+in
a
3-HP/4-HB cycle (modified) bAcetyl-CoA+3ATP+3NADPH+NAD++MQ+2HCO3-+2H+out
oxaloacetate+3ADP+3Pi+3NADP++NADH+MQH2+CoA+2H+in
a
Reductive citramalyl/ethylmalonyl-CoA pathwayAcetyl-CoA+HCO3-+2NADPH+UQ⟶
pyruvate+2NADP++UQH2+CoA
Pyruvate-converting modulesc
4-HB pathwayb (+pyruvate carboxylase)Pyruvate+2CoA+3ATP+HCO3-+MQH2+2NADPH+2H+in
⟶2 acetyl-CoA+3ADP+3Pi+MQ+2NADP++2H+out
a
MCG-like cycled (+pyruvate carboxylase)Pyruvate+3ATP+HCO3-+2CoA+3NADH⟶
⟶2 acetyl-CoA+3ADP+3Pi+3NAD+
General modules
Glycolysis (starting from GAP)Glyceraldehyde-3-phosphate+ADP+NAD(P)++HCO3-
oxaloacetate+NAD(P)H+ATP
Gluconeogenesis (starting from oxaloacetate)Oxaloacetate+2ATP+NADH⟶
glyceraldehyde-3-phosphate+2ADP+Pi+NAD++CO2

aThe free energy was calculated assuming a transmembrane potential of -150 mV. bThis module exists in two variants (like the pathway it is derived from), depending on whether an AMP- or ADP-producing 3-hydroxypropyl-CoA/4-hydroxybutyryl-CoA synthase is used or not. In the here presented form, it corresponds to the crenarchaeal form. Both variants were considered, however, for the following analyses. cIn addition to the modules listed here, single reactions such as the pyruvate dehydrogenase complex or the pyruvate carboxylase were also used to connect metabolites. dThis cycle has the same working principle as the malyl-CoA-glycerate cycle (MCG cycle) presented in Yu et al. [66]. Instead of turning 2 glyoxylate into glycerate which is then converted to oxaloacetate, this cycle directly uses the β-hydroxyaspartate cycle to turn 2 glyoxylate into oxaloacetate. A detailed pathway map can be found in Supplementary Figure S8B. eOriginal pathway in this context relates to the pathway in which the respective enzymes are usually found. Many of the connecting modules are subnetworks of the full, original pathways.