Table 3 Natural and synthetic biological carbon fixation cycles and pathways. References [145,146,147,148,149,150,151,152,153,154,155,156,157,158,159] were used to compile this table
From: Electrical energy storage with engineered biological systems
Cycle or Pathway | Substrate(s) | Product | ATP requirements | NAD(P)H | Number of substrate molecules | Number of each product | ATPs per substrate molecules | Key enzyme(s) | Specific activity of key enzyme(s) (μmol/min/mg protein) | Note | Reference |
|---|---|---|---|---|---|---|---|---|---|---|---|
Naturally Evolved, Operates Under Aerobic Conditions | |||||||||||
 Calvin cycle (CBB) or Reductive pentose phosphate pathway | CO2 | Glyceraldehyde-3-phosphate (C3H7O6P) | 9 | 6 | 3 | 1 | 3 | A. RuBisCO (EC 4.1.1.39) (e.g. Gossypium hirsutum) | A. 0.01 | The dominant autotrophic pathway, which loss of fixed carbon and thus photosynthetic energy by photorespiration. | Bar-even et al. [145], Dietz et al. [146], Claassens et al. [149] |
Pyruvate (C3H3O3-) | 7 | 5 | 2.3 | ||||||||
 3-hydroxypropionate bicycle (3HP) | Bicarbonate (HCO3-) | Pyruvate (C3H3O3-) | 5 | 6 | 3 | 1 | 1.6 | A. Malonyl-CoA reductase (EC 1.2.1.75) (e.g. Chloroflexus aurantiacus, 55°C, pH 7.8) | A. 10 | This pathway occurs only in photosynthetic organisms in non-sulfur bacteria of the Chloroflexaceae family. | Herter et al. [147], Zarzycki et al. [148], Claassens et al. [149] |
B. Propionyl-CoA synthase (EC 6.2.1.17) (e.g. Chloroflexus aurantiacus, 55°C, pH 7.8) | B. 2.5 | ||||||||||
C. Acetyl-CoA carboxylase (EC 6.4.1.2) (e.g. Chloroflexus aurantiacus, 55°C, pH 7.8) | C. 0.015 | ||||||||||
 3-hydroxypropionate-4-hydroxybutyrate cycle (3HP-4HB) | Bicarbonate (HCO3-) | Acetyl-CoA (C2H3O-CoA) | 4 | 6 | 2 | 1 | 2 | A. Acetyl-CoA carboxylase (EC 6.4.1.2) (e.g. Chloroflexus aurantiacus, 55°C, pH 7.8) | A. 0.015 | This pathway has been found in hyperthermophilic microorganisms. | |
Pyruvate (C3H3O3-) | 5 | 5 | 2.5 | ||||||||
B. Propionyl-CoA carboxylase (EC 6.4.1.3) (e.g. Metallosphaera sedula, 65°C, pH 7.5) | B. 3.3 | ||||||||||
Naturally Evolved, Operates Under Anaerobic Conditions | |||||||||||
 Reductive Tricarboxylic Acid cycle (rTCA) or Arnon–Buchanan cycle | CO2 | Acetyl-CoA (C2H3O-CoA) | 2 | 4 | 2 | 1 | 1 | A. Isocitrate dehydrogenase (ICDH) (EC 1.1.1.41) (e.g. Ostreococcus ‘lucimarinus’, 25°C, pH 7.5) | A. 3.8 | This pathway is reversible and limited to microorganisms that are difficult to manipulate and engineer. | |
Pyruvate (C3H3O3-) | 2 | 3 | 1 | ||||||||
B. 2-oxoglutarate synthase (EC 1.2.7.3) (r.g. Thauera aromatica, 30°C, pH 7.8) | B. 4.8 | ||||||||||
 Reductive acetyl-coenzyme A (acetyl-CoA) or Wood-Ljungdahl pathway (WL) | CO2 | Acetyl-CoA (C2H3O-CoA) | 1 | 4 | 2 | 1 | 0.5 | A. CO dehydrogenase/acetyl-CoA synthase (EC 1.2.7.4) (e.g. Archaeoglobus fulgidus, 65°C, pH 7.5 ) | A. 5.2 | This reversible pathway is the most energetically favorable autotrophic carbon fixation pathway, but deactivates under ambient CO2 concentration. | Bar-even et al. [145], Claassens et al. [149], Liao et al. [152], Berg et al. [153], Fast et al. [154] |
Pyruvate (C3H3O3-) | 1 | 2 | 0.5 | ||||||||
 dicarboxylate/4-hydroxybutyrate cycle (Di-4HB) | Bicarbonate (HCO3-) + CO2 | Acetyl-CoA (C2H3O-CoA) | 3 | 1 | 1 + 1 | 1 | 1.5 | A. Pyruvate synthase (EC 1.2.7.1) (e.g. Archaeoglobus fulgidus, 65°C, pH 7.5 ) | A. 0.7 | The microorganisms with this pathway may require an electron acceptor such as elemental sulfur for anaerobic respiration. | Huber et al. [155] |
Pyruvate (C3H3O3-) | 5 | 3 | 2.5 | ||||||||
B. 4-hydroxybutanoyl-CoA dehydratase (EC 4.2.1.120) (Clostridium aminobutyricum, 25°C, pH 9) | B. 12.5 | ||||||||||
 Reversed oxidative Tricarboxylic Acid cycle (roTCA) | CO2 | Acetyl-CoA (C2H3O-CoA) | 1 | N.D | 2 | 1 | 0.5 | A. Reverse oxidative malate dehydrogenase (roMDH) (EC 1.1.1.37) (e.g. Thermoplasma acidophilum) | A. 180 | This pathway has been found in two thermophilic bacteria, Desulfurella acetivorans and Thermosulfidibacter. | |
B. Reverse oxidative citrate synthase (roCS) (EC 2.3.3.16) (e.g. Thermoplasma acidophilum) | B. 0.172 | ||||||||||
 Reductive hexulosephosphate (RHP) pathway | CO2 | Glyceraldehyde-3-phosphate (C3H7O6P) | 3 | 2 | 1 | 1 | 3 | A. RuBisCO (EC 4.1.1.39) (e.g. Cupriavidus necator) | A. 1.56 | The RHP pathway and the Calvin–Benson cycle only differ in a few steps, namely from F6P to Ru5P, without the release of carbon, but whether the RHP pathway allows for autotrophy remains unknown. | Kono et al. [158] |
B. Phosphoribulokinase (PRK) (EC 2.7.1.19) (e.g. Cupriavidus necator) | B. 7.59 | ||||||||||
Synthetic, Operates Under Aerobic Conditions | |||||||||||
 Malonyl-CoA oxaloacetate glyoxylate (MOG) | Bicarbonate (HCO3-) | Glyceraldehyde-3-phosphate (C3H7O6P) | 8 | 6 | 1 | 1 | 8 | A. PEP carboxylase (EC 4.1.1.31) (e.g. Escherichia coli) | A. 30 | MOG pathway has not been established as functional CO2 fixation pathway yet. | Bar-even et al. [145] |
Pyruvate (C3H3O3-) | 6 | 5 | 6 | ||||||||
 Crotonyl–coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH 5.4) | CO2 | Glyoxylate (C2HO3-) | 1 | 4 | 2 | 1 | 0.5 | A. Engineered enzymes: succinyl-CoA reductase, methylmalonyl-CoA mutase, ethylmalonyl-CoA mutase, 4-hydroxybutyryl-CoA synthetase | A. 0.05 (total cycle activity) | The 13 core reactions catalyzed by 17 enzymes for the continuous fixation of CO2 in vitro. | Schwander et al. [159] |
 HydrOxyPropionyl-CoA/ ACrylyl-CoA (HOPAC) | CO2 | Glyoxylate (C2HO3-) | 2 | 3 | 2 | 1 | 1 | A. Theoretical network for 12 reactions have been defined, but specific enzyme for each reaction has not been defined. | A. Not measured. | Network reaction for CO2 fixation which has not been synthesized yet. | Schwander et al. [159] |
 Crotonyl-CoA/ HYdroxyethylmalonyl-CoA/ MEthylmalonyl-CoA (CHYME) | CO2 | Acetaldehyde (C2H4O) | 3 | 6 | 2 | 1 | 1.5 | A. Theoretical network for 15 reactions have been defined, but specific enzyme for each reaction has not been defined. | A. Not measured. | Network reaction for CO2 fixation which has not been synthesized yet. | Schwander et al. [159] |