Structural analysis of expressed metabolic subnetworks

Expression of metabolic enzymes increases the metabolic capabilities of the cell, but it also consumes resources, and the gene regulatory systems of cells have to handle this tradeoff. To study whether gene expression patterns reflect the varying metabolic needs of the cell, we translated gene expression profiles into sets of active biochemical reactions, which constitute the expressed metabolic subnetworks. The metabolic capacity of a carbon source denotes the number of metabolites that can be produced from this carbon source and some inorganic nutrients. We studied the metabolic subnetworks that are expressed during diauxic shift in yeast and found that the capacities of different carbon sources tend to decrease during the diauxic shift. The subnetwork expressed in the initial glucose environment shows a high capacity of glucose, much higher than networks of the same size arising in later stages of the diauxic shift or from a random selection of reactions. The same holds for the essential capacity, the number of important, constitutive compounds that can be produced from glucose. These findings indicate that gene regulation increases the range of essential compounds that can be obtained from the available nutrients, while minimising the number of expressed enzymes and therefore the burden of protein synthesis.