Fig 1.
(A) Comparison of shared reactions among iGC535 and template models (iHN637, iPC815, iML1515). (B) Comparison of shared genes among iGC535 and other Ne models. (C) Reactions distribution through the subsystems in the genome-scale model. (D) Electron transport chain simulated using fructose at high concentrations or HCO3- as the sole carbon source. Abbreviations: NADH16pp, NADH dehydrogenase; AMO, ammonia monooxygenase; HAO, hydroxylamine oxidoreductase; CYTEX, cytochrome exchange; Q8H2ASE, ubiquinol synthase; CYTbc1, CytCbc1 reductase using ubiquinol-8; C552oxi, cytochrome c552 oxidase; ATPS, ATP synthase; QH2, ubiquinol; Q, ubiquinone; HAM, hydroxylamine; C554red, cytochrome c554 reduced; C554ox, cytochrome c554 oxidized; c552mox, membrane cytochrome c552 oxidized; c552mred, membrane cytochrome c552 reduced; C552ox, cytochrome c552 oxidized; C552red, cytochrome c552 reduced; Fru, fructose.
Table 1.
Comparative table of the properties of the genome-scale model of Ne (iGC535) and other models.
Table 2.
Comparative table of simulations performed under different growth conditions of the Ne genome-scale model (iGC535) and other models.
Fig 2.
Map of the metabolic flux distributions predicted under chemolithoorganotrophic and chemolithotrophic conditions.
The map shows the changes in the flux distributions under four different growth conditions. Ammonium is present under all conditions but changing the carbon source (fructose, pyruvate, and HCO3-). (A) Chemolithoorganotrophy metabolism. The fructose uptake rate was constrained to 0.746 mmol/gDW/h, and the ammonium uptake rate was 0.5mmol/gDW/h. (B) Chemolithotrophy metabolism. HCO3- uptake rates were constrained to 4.35 mmol/gDW/h for high and 1.43 mmol/gDW/h for low. Abbreviations: HCO3E, carbonic anhydrase; PYK, pyruvate kinase; PPS, phosphoenolpyruvate synthasePGK, phosphoglycerate kinase; GAPD, glyceraldehyde 3-phosphate dehydrogenase; PFK, phosphofructokinase; PGI, glucose 6-phosphate isomerase; G6PDH2r, glucose 6-phosphate dehydrogenase; PGL, 6-phosphogluconolactonase; GND, phosphogluconate dehydrogenase; RPI, ribose-5-phosphate isomerase; RPE, ribulose 5-phosphate 3-epimerase; TKT, transketolase; TPI, triose-phosphate isomerase; PRUK, phosphoribulokinase; RBPC, ribulose 1,5-bisphosphate carboxylase-oxygenase; PDH, pyruvate dehydrogenase; CS, citrate synthase; MDH, malate dehydrogenase; SUCDi, succinate dehydrogenase; SUCOAS, succinyl-CoA synthetase; AKGDH, 2-oxoglutarate dehydrogenase; ICDHyr, isocitrate dehydrogenase; ORNTAC, ornithine transacetylase; G6P, D-Glucose 6-phosphate; F6P, D-Fructose 6-phosphate; FDP, D-Fructose 1,6-bisphosphate; G3P, Glyceraldehyde 3-phosphate; 13DPG, 3-Phospho-D-glyceroyl phosphate; 3PG, 3-Phospho-D-glycerate; 2PG, D-Glycerate 2-phosphate; PEP, Phosphoenolpyruvate; Pyr, Pyruvate; AcCoA, Acetyl-CoA; Fru, D-Fructose; Cit, citrate; Acon, Aconitate; iCit, Isocitrate; AKG, 2-Oxoglutarate; SucCoA, Succinyl-CoA; Suc, Succinate; Fum, Fumarate; Mal, L-Malate; OAA,Oxaloacetate; ArgSuc, L-Argininosuccinate; L-Citr, L-Citrulline; Orn, Ornithine; AcOrn, Acetylornithine; AcGlu, Acetyl-L-glutamate; AcG5P, Acetyl-L-glutamate 5-phosphate; AcG5SA, Acetyl-L-glutamate 5-semialdehyde; L-Glu, L-Glutamate; RuBP, D-Ribose 1,5-bisphosphate; Ru5P, D-Ribulose 5-phosphate; Xu5P, D-Xylulose 5-phosphate; DHAP, Dihydroxyacetone phosphate; E4P, Erythrose 4-phosphate dehydrogenase; S7P, Sedoheptulose 7-phosphate; S17BP, Sedoheptulose 1,7-bisphosphate; R5P, Ribose 5-phosphate; 6PGC, 6-Phospho-D-gluconate; 6PGL, 6-phospho-D-glucono-1,5-lactone.
Fig 3.
Flux distribution analysis under different growth conditions.
(A) Hierarchical clustering of flux distributions under different carbon sources and growth conditions. The HCO3- uptake rates were established at low and high levels, as we mentioned in Section 3.5.1. The pyruvate uptake flux (0.0773 mmol/gDW/h) used as a constraint in the simulations, resulted from the experimentally observed growth rate of 0.034 1/h [16] when Ne is grown using pyruvate as the organic carbon source. The methane and pollutant uptake rates were constrained to 1 mmol/gDW/h under the low HCO3- level condition. We used standararized Z-scores to normalize predicted fluxes. Z-scores represent negative and positive values in a blue to red color scale. The X-axis shows the metabolic reactions, and the Y-axis shows different growth conditions. * means low uptake rates; ** means high uptake rates. Group 1: 24 reactions; Group 2: 353 reactions; Group 3: 16 reactions; Group 4: 15 reactions. (B) Change in flux predictions of CBB cycle, glycolysis, rPPP reactions when fructose uptake is at low or high concentration. (C) Change in flux predictions of TCA cycle reactions when fructose uptake is at low or high concentration. (D) Change in flux predictions of energy metabolism reactions when fructose uptake is at low or high concentration. Abbreviations: FBA, Fructose-bisphosphate aldolase; PYK, pyruvate kinase; RPE, ribulose 5-phosphate 3-epimerase; RPI, ribose-5-phosphate isomerase; TALA, transaldolase; TKT, transketolase; TPI, triose-phosphate isomerase; PGI, glucose 6-phosphate isomerase; RBPC, ribulose 1,5-bisphosphate carboxylase-oxygenase; PRUK, phosphoribulokinase; PFK, phosphofructokinase; ACONT, aconitate hydratase; CS, citrate synthase; FUM, fumarase; MDH, malate dehydrogenase; AKGDH, 2-oxoglutarate dehydrogenase; ICDHyr, isocitrate dehydrogenase; SUCDi, succinate dehydrogenase; SUCOAS, succinyl-CoA synthetase; THD2pp, NAD(P)+transhydrogenase; AMO, ammonia monooxygenase; HAO, hydroxylamine oxidoreductase; Q8H2ASE, ubiquinol synthase; CYTEX, cytochrome exchange; NADH16pp, NADH dehydrogenase.