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Figure 6 | EURASIP Journal on Bioinformatics and Systems Biology

Figure 6

From: Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

Figure 6

Yields for alternative pyruvate formation. Possible reactions to produce pyruvate (sorted by model predicted biomass yield on glycerol) computed by the proposed algorithm. The black bars show the predicted biomass yields on glycerol without regulation, gray bars with the regulatory network iMC1010v2. The bars for wild type and F41malE::pyc use combinations of reactions to pyruvate. Other bars are tagged by their final reaction to pyruvate: DHAPT - Dihydroxyacetone phosphotransferase (DhaK, DhaL, DhaM), SERD-L - L-Serine deaminase (TdcG, SdaA, SdaB, TnaA), SERD-D - D-Serine deaminase (DsdA), TRPAS2 - Tryptophanase-L-tryptophan (TnaA), EDA - 2-Dehydro-3-deoxyphosphogluconate aldolase (Eda), CYSDS - Cysteine desulfhydrase (TnaA, MetC), LDH-D - D-lactate dehydrogenase (Ldh), LACD2 - L-lactate dehydrogenase using ubiquinone (LldD), LACD3 - L-lactate dehydrogenase using menaquinone (LldD), LDH-D2 - D-lactate dehydrogenase (Dld), OAADC - Oxaloacetate decarboxylase (Eda), ME2 - Malic enzyme NADP (MaeB), ME1 - Malic enzyme NAD (MaeA), MCITL2 - Methylisocitrate lyase (PrpB), ICHORT - Isochorismatase (EntB), CHRPL - Chorismate pyruvate-lyase (UbiC), ADCL - 4-aminobenzoate synthase (PabC), ANS - Anthranilate synthase (TrpD, TrpE), CYSTL - Cystathionine-b-lyase (MalY, MetC), SHCHCS2 - 2-Succinyl-6-hydroxy-2-4-cyclohexadiene-1-carboxylate synthase (MenD). In all cases either ALATA-L - Alanine transaminase (AlaABC) (shown yields) or DXPS - Deoxy-D-xylulose-5-phosphate synthase (Dxs) contributed to pyruvate production similar to J3 and J4 in Figure5. Other essential reactions similar to J8 in Figure5 were: ACLS - Acetolactate synthase (IlvH or IlvB), ACHBS - 2-Aceto-2-hydroxybutanoate synthase (IlvH or IlvB) and DHDPS - Dihydrodipicolinate synthase (DapA).

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