Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation
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].