Figure 1.
Schematic diagram of the metabolic reconstruction and analysis processes.
Solid lines indicate consecutive steps of the reconstruction. Dashed lines represent information transfer. Dotted lines specify planned tasks.
Figure 2.
Schematic representation of various reaction classes and their interdependency.
The areas of the squares correspond to the sizes of the subsets.
Figure 3.
Assignment of the reactions to the particular pathways.
Table 1.
Summary of the main characteristics of the iJP815 metabolic model.
Table 2.
Summary of the comparison with the BIOLOG substrate utilization assay.
Table 3.
List of genes reannotated during the reconstruction process.
Table 4.
Comparison of the in silico predicted growth yields (in gDW⋅gElement−1) with experimental continuous culture data.
Figure 4.
Comparison of FVA calculations with 13C experimental flux data.
The explanation of color codes is given in the figure. “0*” means that the reaction is not included in the particular metabolic network; double-headed arrows depict reversible reactions, the bigger head shows direction of the positive flux.
Figure 5.
Interdependency between the metabolic network, the minimal set and the set of essential reactions.
The set sizes are given for glucose growth conditions.
Figure 6.
Mutational strategies for increased PHA production.
This figure highlights 6 strategies suggested by the modified optknock approach for increased production of AcCoA, a precursor for polyhydroxyalkanoates. (A) AcCoA production ranges vs. growth yield of in silico strains developed using the ‘AcCoA production’ strategy. (B) AcCoA pooling versus growth yield of in silico strains developed using the ‘AcCoA pooling’ strategy.
Table 5.
Summary of the characteristics of the in silico strains generated in the procedure of optimization of the PHA production.