Fig 1.
The workflow of the pathway-consensus metabolic network reconstruction of Pseudomonas putida KT2440.
Table 1.
The optimal growth rates and ATP production rates calculated for the four published models of P. putida KT2440.
Fig 2.
Incorrect reaction loops for unlimited NAD(P)H generation in PpuMBEL1071.
(A) Incorrect reaction R0500 led to a loop to produce NADH without consuming any substrates. (B) Incorrect reaction R0132 led to a loop to produce NADPH and O2. P3H5C, L-1-Pyrroline-3-hydroxy-5-carboxylate; E4HGLU, L-erythro-4-Hydroxyglutamate; HGLUSA, L-4-Hydroxyglutamate semialdehyde; MALCOA, Malonyl-CoA; OPCOA, 3-Oxopropionyl-CoA; HPCOA, 3-Hydroxypropionyl-CoA; PPCOA, Propanoyl-CoA; MCIT, 2-Methylcitrate; MICIT, cis-2-Methylaconitate; PYR, Pyruvate; AcCOA, Acetyl-CoA; SUCC, Succinate; FUM, Fumarate; MAL, (S)-Malate; OA, Oxaloacetate.
Fig 3.
An unconserved reaction sets leading to a net consumption of CoA (defined as an unconserved metabolite) in PpuMBEL1071.
Fig 4.
The respiratory chain reactions in the four models.
‘+’ shows that the complex exists in the model. The numbers of protons pumped from each complex (the value of X and Y) were summarized in Table 2.
Table 2.
The respiratory chain reactions in the four models.
Table 3.
The overall respiratory chain reactions of the four models.
Table 4.
The calculated optimal rates of 20 amino acids from the models.
Fig 5.
Cysteine synthesis pathway in the four models.
Only the pathway in PpuMBEL1071 was right. Green, blue and purple arrows depict reactions in iJN746, iJP815 (iJP962) and PpuMBEL1071 respectively. Wrong directions of R_SER_AL and R_ACSr (in iJN746), IR04850 (in iJP815 and iJP962) led to wrong cysteine synthesis pathways. KDPG: 2-Dehydro-3-deoxy-6-phospho-D-gluconate.
Table 5.
Summary of the number of errors corrected for the pathway-consensus processa.
Fig 6.
Utilization of 48 substrates in the four models for P. putida KT2440.
36 substrates could be utilized in the four original models. Phenylacetate, toluene, gallate and choline could only be utilized in iJN746. Putrescine could be utilized in iJP815 and iJP962. 2dhglcn: 2-Dehydro-D-gluconate, 4abut: 4-Aminobutanoate, Confrl:Conifery-alcohol.
Table 6.
Summary statistics of the updated pathway-consensus models and the original models (in parentheses).
Table 7.
Summary of PpuQY1140 model.
Fig 7.
Experimentally measured and in silico predicted growth rates of P. putida KT2440 and the mutant strains.
(A) Growth rates on glucose M9 medium. (B) Growth rates on toluene M9 medium.