Figure 1.
ATP requirements for maintenance and growth.
Panel A shows the model estimated maximum ATP hydrolysis rates needed to match experimentally measured lactate consumption rates and cellular growth rates at four different dilution rates (D = 0.025. 0.04, 0.055, 0.085 h−1). The slope and intercept represent the growth- and non-growth rate dependent ATP requirements, GAR and NGAR, respectively. Panel B shows ATP requirements for various microbes that have been reported in the literature [26]–[32]. The reported GAR values for other microbes were adjusted to remove ATP used for protein polymerization (4 ATP/peptide bond) since ATP used for protein synthesis is accounted for separately in the S. oneidensis MR-1 model and is not part of the MR-1 GAR value. Panel C compares model estimates of maximum growth rates (solid line) at different lactate consumption rates (using ATP requirements as reported in panel A) with experimental data. Additional data points were included that were not used in the estimation of the ATP requirements.
Figure 2.
Classification of reactions and genes for lactate-limited aerobic growth.
Panel A illustrates the classification of reactions based on how fluxes through the reactions affect biomass production. Optimal reactions are ones that can be used to achieve maximal growth rates, these are the most efficient pathways. Suboptimal reactions are ones where non-zero fluxes force a reduction in maximal growth rate. These reactions can be further classified as futile (meaning they participate in futile cycles) or non-futile (they do not participate in futile cycles; these are often less energetically efficient pathways). Blocked reactions are ones that can not carry any flux due to the imposed constraints, so all solutions, optimal and suboptimal, will have zero flux through the reactions. The classification of the reactions is highly dependent on the growth condition. Panel B shows the distribution of reactions in iSO783 for lactate-limited aerobic growth. Panel C shows the distribution of genes in the model based on their association to the classified reactions. For example, if a gene is only associated with optimal reactions then it is classified as optimal, but if it is associated with an optimal reaction and a futile cycle reaction then it is classified as associated with multiple reactions. Panel D shows the expression (reported as RMA, Robust Multichip Average) in lactate limited aerobic conditions versus the change in expression from aerobic conditions to oxygen-limited for genes associated with optimal reactions (black, 387 genes) and with suboptimal reactions (red, 181 genes). The black horizontal and vertical lines show the mean expression and mean expression changes for the optimal set of genes. Only 39 genes associated with suboptimal reactions fall in the upper right quadrant. Gene expression data was obtained from the M3D database [35].
Figure 3.
Oxygen requirements for maximal biomass production.
Panel A shows the maximal biomass yield and oxygen requirements needed to achieve the maximum biomass yields for 30 of the 33 model predicted carbon sources (not shown are fatty acids which lie outside of the region shown, see Table S5 for complete list of values). Blue points correspond to carbon sources that were evaluated experimentally. Panel B shows how the maximum biomass yield is affected as the O2 consumption rate is increased and decreased from its optimal value. All three carbon sources have the same number of carbon atoms, but pyruvate requires the least amount of oxygen and under oxygen limitations will have higher biomass yields than the other two carbon sources. All simulations were done assuming a carbon source consumption rate of 10 mmol ATP/(g AFDW•h). Panel C compares calculated biomass yields with experimental biomass yields as estimated from batch growth in a microplate reader. The model predictions were made assuming a carbon source consumption rate of 10 mmol ATP/(g AFDW•h) with either an unconstrained OUR or a maximum OUR of 20 mmol ATP/(g AFDW•h), based on maximal estimates for E. coli [47].
Figure 4.
Model predicted flux values in central and C1 metabolism.
The figure shows the range of flux values calculated using FVA that correspond to maximal biomass yields in lactate-limited aerobic growth when malate synthase, pyruvate formate lyase, NAD+ dependent isocitrate dehydrogenase, and fumarate reductase are constrained to be zero (see text for details). Flux values are reported as the percentage of the lactate consumption rate, 4.11 mmol/(g AFDW•h). Cellular growth rate was constrained to 0.085 h−1. Metabolite abbreviations are described in text and/or can be found in Table S3.
Table 1.
Enzyme activity for cells grown in lactate-limited aerobic chemostat.