Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae

• The flux distributions of the genome-scale models of Saccharomyces cerevisiae were evaluated
• Most of the tested models showed fluxes inconsistent with experimental data
• A manual curation process was performed on all reactions including NADH or NADPH
• The curated models showed flux distributions more consistent with experimental data
• Phenotype simulations improved when the curated flux distributions were used

Genome-scale metabolic models (GEMs) can be used to evaluate genotype-phenotype relationships and their application to microbial strain engineering is increasing in popularity. Some of the algorithms used to simulate the phenotypes of mutant strains require the determination of a wild-type flux distribution. However, the accuracy of this reference, when calculated with flux balance analysis, has not been studied in detail before.Here, the wild-type simulations of selected GEMs for Saccharomyces cerevisiae have been analysed and most of the models tested predicted erroneous fluxes in central pathways, especially in the pentose phosphate pathway. Since the problematic fluxes were mostly related to areas of the metabolism consuming or producing NADPH/NADH, we have manually curated all reactions including these cofactors by forcing the use of NADPH/NADP+ in anabolic reactions and NADH/NAD+ for catabolic reactions. The curated models predicted more accurate flux distributions and performed better in the simulation of mutant phenotypes.