Compartment-specific metabolome labeling enables the identification of subcellular fluxes that may serve as promising metabolic engineering targets in CHO cells

(13)C labeling data are used to calculate quantitative intracellular flux patterns reflecting in vivo conditions. Given that approaches for compartment-specific metabolomics exist, the benefits they offer compared to conventional non-compartmented (13)C flux studies remain to be determined. Using compartment-specific labeling information of IgG1-producing Chinese hamster ovary cells, this study investigated differences of flux patterns exploiting and ignoring metabolic labeling data of cytosol and mitochondria. Although cellular analysis provided good estimates for the majority of intracellular fluxes, half of the mitochondrial transporters, and NADH and ATP balances, severe differences were found for some reactions. Accurate flux estimations of almost all iso-enzymes heavily depended on the sub-cellular labeling information. Furthermore, key discrepancies were found for the mitochondrial carriers v(AGC1) (Aspartate/Glutamate antiporter), v(DIC) (Malate/H(+) symporter), and v(OGC) (α-ketoglutarate/malate antiporter). Special emphasis is given to the flux of cytosolic malic enzyme (v(ME)): it could not be estimated without the compartment-specific malate labeling information. Interesting enough, cytosolic malic enzyme is an important metabolic engineering target for improving cell-specific IgG1 productivity. Hence, compartment-specific (13)C labeling analysis serves as prerequisite for related metabolic engineering studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00449-021-02628-1.