Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.

TitleReconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.
Publication TypeJournal Article
Year of Publication2004
AuthorsDuarte NC, Herrgard MJ, Palsson BØ
JournalGenome research
Volume14
Issue7
Pagination1298-309
PubMed Date2004 Jul
ISSN1088-9051
KeywordsCell Compartmentation, Computational Biology, Cytoplasm, Endoplasmic Reticulum, Extracellular Space, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Fungal, Genes, Fungal, Genome, Fungal, Golgi Apparatus, Mitochondria, Models, Genetic, Peroxisomes, Saccharomyces cerevisiae, Vacuoles
Abstract

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.

Alternate JournalGenome Res.
PubMed ID15197165

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