Reducing Recon 2 for steady-state flux analysis of HEK cell culture

• Reduced Recon 2 into a concise metabolic model for flux analysis in four overall steps.
• Original model has 7440 reactions; reduced model has 357 reactions.
• Curated Recon 2's metabolites and reactions for inconsistencies and duplication.
• Glutaminolysis rate increased when l-alanyl-l-glutamine dipeptide was depleted.

A representative stoichiometric model is essential to perform metabolic flux analysis (MFA) using experimentally measured consumption (or production) rates as constraints. For Human Embryonic Kidney (HEK) cell culture, there is the opportunity to use an extremely well-curated and annotated human genome-scale model Recon 2 for MFA. Performing MFA using Recon 2 without any modification would have implied that cells have access to all functionality encoded by the genome, which is not realistic. The majority of intracellular fluxes are poorly determined as only extracellular exchange rates are measured. This is compounded by the fact that there is no suitable metabolic objective function to suppress non-specific fluxes. We devised a heuristic to systematically reduce Recon 2 to emphasize flux through core metabolic reactions. This implies that cells would engage these dominant metabolic pathways to grow, and any significant changes in gross metabolic phenotypes would have invoked changes in these pathways. The reduced metabolic model becomes a functionalized version of Recon 2 used for identifying significant metabolic changes in cells by flux analysis.