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Table 1 Physiological constraints used in constraints-based flux analysis for simulating metabolism of wild-type and lpdA knockout mutant of E. coli

From: Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network

Enzyme Metabolism Condition v13Cor vfmt (mmol/g dry cell weight/h) σ
Phosphotransferase system for D-glucose transport Transport Wild-type -3.04 0.01824
   ΔlpdA mutant -2.48 0.1488
Cell growth rate - Wild-type 0.20 0.0100
   ΔlpdA mutant 0.22 0.0110
Glucose-6-phosphate isomerase Glycolysis/Gluconeogenesis Wild-type 2.39 0.3107
   ΔlpdA mutant 1.79 0.2327
Pyruvate kinase Glycolysis/Gluconeogenesis Wild-type 1.09 0.0109
   ΔlpdA mutant 0.26 0.0026
Glucose 6-phosphate dehydrogenase Pentose phosphate pathway Wild-type 0.61 0.0732
   ΔlpdA mutant 0.64 0.0768
Phosphogluconate dehydrogenase Pentose phosphate pathway Wild-type 0.61 0.0732
   ΔlpdA mutant 0.32 0.0384
Phosphoenolpyruvate carboxylase Anaplerotic reactions Wild-type 0.67 0.0469
   ΔlpdA mutant 1.61 0.1127
Phosphoenolpyruvate carboxykinase Anaplerotic reactions Wild-type 0.07 0.0070
   ΔlpdA mutant 0.93 0.0930
Pyruvate dehydrogenase Glycolysis/Gluconeogenesis Wild-type 3.56 0.2136
   ΔlpdA mutant 0.00 0.0000
α-ketoglutarate dehydrogenase Citrate Cycle (TCA) Wild-type Not constrained Not constrained
   ΔlpdA mutant 0.00 0.0000
glycine cleavage system Folate Metabolism Wild-type Not constrained Not constrained
   ΔlpdA mutant 0.00 0.0000
  1. Mean values (v13C or vfmt) of physiological constraints are based on 13C-based metabolic flux and cell culture data for the wild-type and lpdA knockout mutant of E. coli, both grown in continuous culture at dilution rate 0.2 h-1[33]. Standard deviations (σ) were calculated by multiplying these mean values with average error percentage associated with each reaction, taken from [43]. In addition to these, flux values of α-ketoglutarate dehydrogenase and glycine cleavage system were additionally constrained to zero due to the knockout of lpdA gene.