Table 3

Comparison of tricarboxylic acid and glyoxylate cycle reactions in Arabidopsis reconstructions.

Reaction

Radrich

Poolman

AraGEM


Succinate + Ubiquinone ↔ Fumarate + Ubiquinol

OK

OK

With FAD/FADH2

Fumarate + H2O ↔ Malate

OK

OK

OK

Malate + NAD ↔ Oxaloacetate + NADH + H

Malate + NADP ↔ Oxaloacetate + NADPH + H

No H

Only with NAD/NADH

OK

Oxaloacetate + ADP + Orthophosphate + Acetyl-CoA ↔ Citrate + ATP + CoA

OK

OK

OK

Citrate ↔ cis-Aconitate + H2O

OK

No H2O

OK

cis-Aconitate + H2O ↔ Isocitrate

OK

No H2O

OK

Isocitrate ↔ Succinate + Glyoxylate

OK

OK

OK

Glyoxylate + H2O +Acetyl-CoA ↔ Malate + CoA

OK

No H2O

OK

Isocitrate + NAD ↔ 2-oxoglutarate + CO2 + NADH + H

Isocitrate + NADP ↔ 2-oxoglutarate + CO2 + NADPH + H

No H

Only with NAD/NADH;

2 H

OK

Isocitrate + NADP ↔ Oxalosuccinate + NADPH + H

No H

NA

NA

Oxalosuccinate + NADP ↔ 2-oxoglutarate + CO2 + NADPH + H

No H

NA

NA

2-oxoglutarate + CoA + NAD ↔ Succinyl-CoA + CO2 + NADH

OK

OK

With ferredoxin

2-oxoglutarate + Thiamine-pyrophosphate ↔ 3-carboxy-1-hydroxypropyl-ThPP + Co2

OK

NA

OK

3-carboxy-1-hydroxypropyl-ThPP + Lipoamide-E ↔ Succinyldihydrolipoamide-E + Thiamine-pyrophosphate

OK

NA

OK

Succinyldihydrolipoamide-E + CoA ↔ Succinyl-CoA + Dihydropiloamide-E

OK

NA

OK

Succinyl-CoA + ADP + Orthophosphate ↔ Succinate + ATP + CoA

Succinyl-CoA + GDP + Orthophosphate ↔ Succinate + GTP + CoA

OK

OK

Only with ADP/ATP


"Radrich" refers to this work, "Poolman" to the model by Poolman et al. [16] and "AraGEM" to the model by de Oliveira Dal'Molin et al. [17]. OK indicates that the reaction in the model is identical to the first column, NA that it is not included in the model; other differences are explicitly described.

Radrich et al. BMC Systems Biology 2010 4:114   doi:10.1186/1752-0509-4-114

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