Fig 1.
Outline of central aerobic metabolism.
Reaction nomenclature according to iJO1366 [14]. Pyr, pyruvate; ICit, Isocitric acid; α-KG, α-ketoglutaric acid; Suc-CoA, succinyl-coenzyme A; Succ, succinic acid; Mal, malic acid; OxAc, oxaloacetic acid; UQ, ubiquinone; UQH2, ubiquinol; only redox cofactors are considered.
Fig 2.
Correlation of transcriptional fold changes with FBA flux rate differences.
The difference between the sums of absolute FBA fluxes with identical enzyme composition between anaerobic and aerobic conditions is plotted against the logFC of the associated transcripts. Spearman rank coefficient and P-values are indicated. Linear regression is shown as black line with 95% confidence bands in red.
Table 1.
Parameters for dddFBA modeling.
Fig 3.
Fluxes of balanced genes in dddFBA.
Fluxes are depicted as green lines, upper flux bounds as dashed light green lines, flux variability as shadowed areas and correspond to the left axis; measured mRNA expression as blue dots with standard deviations, and simulated mRNA expression in light blue correspond to the right axis. 0 min denote the onset of aeration.
Table 2.
Alternative pathways for reoxidation of NADH.
Fig 4.
Fluxes of unbalanced reactions in dddFBA.
The pFBA solution with minimized squared fluxes is given in black. The shadowed area indicates flux variability.
Fig 5.
Expression of unbalanced genes.
RPKM values of the indicated genes are given with standard deviation. ∞ denotes the aerobic steady-state expression level.