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Letter

Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model

¹ Department of Bioengineering, University of California–San Diego, La Jolla, California 92093-0412, USA ² Bioinformatics Graduate Program, University of California–San Diego, La Jolla, California 92093-0412, USA

A fully compartmentalized genome-scale metabolic model of Saccharomyces cerevisiae that accounts for 750 genes and their associated transcripts, proteins, and reactions has been reconstructed and validated. All of the 1149 reactions included in this in silico model are both elementally and charge balanced and have been assigned to one of eight cellular locations (extracellular space, cytosol, mitochondrion, peroxisome, nucleus, endoplasmic reticulum, Golgi apparatus, or vacuole). When in silico predictions of 4154 growth phenotypes were compared to two published large-scale gene deletion studies, an 83% agreement was found between iND750's predictions and the experimental studies. Analysis of the failure modes showed that false predictions were primarily caused by iND750's limited inclusion of cellular processes outside of metabolism. This study systematically identified inconsistencies in our knowledge of yeast metabolism that require specific further experimental investigation.

³ These authors contributed equally to this work.

⁴ Corresponding author.
E-MAIL palsson{at}ucsd.edu; FAX (858) 822-3120.

Supplemental material is available online at www.genome.org. The reaction and metabolite lists, metabolic network maps, and gene-protein-reaction associations for Saccharomyces cerevisiae iND750 can be found at http://systemsbiology.ucsd.edu.

⁵ If different isozymes are counted as separate reactions, there is a total of 1175 reactions in the Förster-Famili model; the set of reactions discussed here is a count of the unique enzymatic and transport reactions determined from the published reaction list.

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