Mammalian Metabolism Reaction Network Model

The reaction network model of mammalian metabolism by Henry et al. [31 (link)] consists of central carbon metabolic pathways, including glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, anaplerotic and cataplerotic reactions, as well as metabolism of amino acids. Reversible reactions and intracellular compartmentation were not taken into account in this model; however, scrambling of ¹³C-labeling due to rotational symmetry of fumarate and succinate was considered. In total, the model contains 29 reactions and 29 metabolites, with 15 balanced intracellular metabolites and 13 measured extracellular metabolites (see Additional file 1). The thirteen fluxes fixed by the external measurements are shown with dashed arrows in Figure 1. The model has two degrees of freedom, the oxidative pentose phosphate flux (oxPPP, G6P → R5P + CO₂) and pyruvate carboxylase flux (PC, Pyr + CO₂ → OAC). Lactate mass isotopomers provide the additional constraints needed to determine the two free fluxes in the model. The Henry network model contains several substrates, including glucose and various amino acids. In this work, glucose and glutamine were considered the main carbon sources that could be ¹³C-labeled, while the remaining amino acids were treated as unlabeled. The identities of unlabeled amino acid substrates were collectively referred to as “non-tracer” substrates in the EMU decomposition. The two flux maps estimated by Henry et al. for HEK-293 cells (WT) and PC-expressing HEK-293 cells (PYC) were used as reference in this study. The PYC flux map was used for simulations and for optimal tracer experiment design.