Connecting extracellular metabolomic measurements to intracellular flux states in yeast

We used an updated genome-scale metabolic network model of Saccharomyces cerevisiae, iMM904, to investigate how changes in the extracellular metabolome can be used to study systemic changes in intracellular metabolic states. The iMM904 metabolic network was reconstructed based on an existing genome-scale network, iND750, and includes 904 genes and 1,412 reactions. The network model was first validated by comparing 2,888 in silico single-gene deletion strain growth phenotype predictions to published experimental data. Extracellular metabolome data measured in response to environmental and genetic perturbations of ammonium assimilation pathways was then integrated with the iMM904 network in the form of relative overflow secretion constraints and a flux sampling approach was used to characterize candidate flux distributions allowed by these constraints. Predicted intracellular flux changes were consistent with published measurements on intracellular metabolite levels and fluxes. Patterns of predicted intracellular flux changes could also be used to correctly identify the regions of the metabolic network that were perturbed.Our results indicate that integrating quantitative extracellular metabolomic profiles in a constraint-based framework enables inferring changes in intracellular metabolic flux states. Similar methods could potentially be applied towards analyzing biofluid metabolome variations related to human physiological and disease states."Omics" technologies are rapidly generating high amounts of data at varying levels of biological detail. In addition, there is a rapidly growing literature and accompanying databases that compile this information. This has provided the basis for the assembly of genome-scale metabolic networks for various microbial and eukaryotic organisms [1-11]. These network reconstructions serve as manually curated knowledge bases of biological information as well as mathematical representations of biochemical components and interactions spec