Table 1.
Network property comparisons between iCN1361 and RehMBEL1391.
Fig 1.
Experimental validation of central carbon metabolic fluxes for the iCN1361 GSM for growth on fructose.
a) GSM prediction of substrate uptake rates and growth rate using iCN1361 for growth data provided in [9]. Units for the substrates are in mmol/gDCW/h, whereas the growth rate is h-1. Note that the uptake rate of fructose was constrained in the model using the experimentally determined value. b) Comparison of the fluxes predicted by iCN1361 (blue bars) and 13C metabolic flux analysis (red bars) for growth on fructose mineral media. The flux in the GSM have been normalised to correspond to a fructose uptake of 1 mmol/gDCW/h to allow comparison with the 13C-MFA data. c) Minimum and maximum flux values for each reaction, calculated using flux variability analysis. Blue data points correspond to the pFBA flux prediction, whereas red dots correspond to the 13C-MFA flux prediction. d) Two feasible routes through the electron transport chain of C. necator H16 predicted using iCN1361 growing at the maximum growth rate. The flux units are all in mmol/gDCW/h. See the abbreviations section for the metabolite and reaction names.
Table 2.
Comparison of transposon mutant library sizes and average insertion frequencies between TraDIS and the Tn-Seq analysis from [24].
Table 3.
Confusion matrix showing the number of true positives (TP), true negatives (TN), false positives (FP) and false negatives (FN), obtained by comparing TraDIS results with GSM predictions.
Fig 2.
Growth of C. necator H16 wild type (H16 wt) and its isogenic mutants ΔA0792, ΔA3038, ΔA3084, ΔA3165, ΔA3408 and ΔA3434 on a) SOB (top panel) and FMM (bottom panel) plates, and liquid SOB (b) and FMM (c). Details about cultures set up are reported in the Methods section.
Fig 3.
The predicted range of fluxes for by-products in iCN1361 using flux variability analysis, whilst simulating nitrogen-limited conditions.
Fig 4.
The number of reactions predicted to be up-regulated (orange) or down-regulated (green) in the nitrogen-limited conditions using the genome-scale metabolic model analysis.
Fig 5.
Flux diagram of the central carbon metabolism, electron transport chain and the PHB cycle comparing the predicted flux in the growth and nitrogen-limited phase.
The bar charts show the mean flux value from the flux sampling simulated on iCN1361-f16 (red) and iCN1361-f26 (blue). Reactions that were predicted to have significantly up-regulated or down-regulated flux in iCN1361-f26 are highlighted with an asterisk. See the abbreviations section for the metabolite and reaction names.