Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network
Open accessAbstract
The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments and the environment were included. A total of 708 structural open reading frames (ORFs) were accounted for in the reconstructed network, corresponding to 1035 metabolic reactions. Further, 140 reactions were included on the basis of biochemical evidence resulting in a genome-scale reconstructed metabolic network containing 1175 metabolic reactions and 584 metabolites. The number of gene functions included in the reconstructed network corresponds to ∼16% of all characterized ORFs in S. cerevisiae . Using the reconstructed network, the metabolic capabilities of S. cerevisiae were calculated and compared with Escherichia coli . The reconstructed metabolic network is the first comprehensive network for a eukaryotic organism, and it may be used as the basis for in silico analysis of phenotypic functions. [Supplemental material is available online at www.genome.org . The detailed genome-scale reconstructed model of Saccharomyces cerevisiae can be found at http://www.cpb.dtu.dk/models/yeastmodel.html or http://geneticcircuits.ucsd.edu/organisms/yeast.html .]
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Earlier modeling with flux balance analysis put net cellular ATP production at about 59 mmol per gDW per hour.
“Previously, using genome-scale models and flux balance analysis it had been estimated that the net production of ATP in the cell forms approximately 59 mmol ATP gDW 1 h 1 (Forster et al., 2003).”
From Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast (2017) · cites this paper as Forster et al., 2003
The net ATP production required for growth and non-growth processes under reference conditions was 59 mmol-ATP gDW−1 h−1.
“ATP requirement (growth and non-growth related ATP net production) under the reference environmental conditions was 59 mmol-ATP gDW 1 h 1 (Forster et al., 2003).”
From Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast (2017) · cites this paper as Forster et al., 2003
Integration of bibliographic, metabolomic, and genomic data has been used to reconstruct the dynamic range of metabolome flow of organisms, first in Escherichia coli and extended to yeast, mice, and humans.
“For example, the integration of bibliographic, metabolomic, and genomic data have been used to reconstruct the dynamic range of metabolome flow of organisms, first performed in Escherichia coli [35] and since extended to yeast [36, 37] and to individual tissues in mice [38] and humans [39].”
From Multi-omics approaches to disease (2017) · cites this paper as [36]
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- Authors
- Förster, J., Famili, I., Fu, P., Palsson, B. Ø., & Nielsen, J.
- Affiliations
- University of California San Diego (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-02-01
- Volume
- 13
- Issue
- 2
- Pages
- 244-253
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC420374
- OpenAlex
- W2128572161
- Cited by
- 1,069
- References
- 62
- Citations by year
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- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (9873384, 9814092)
- National Institutes of Health
- National Institute of General Medical Sciences (GM-57089, R01GM057089)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- Saccharomyces cerevisiae, genome-scale metabolic networks, metabolic network reconstruction, metabolic reactions, metabolites, open reading frames, mitochondrial compartmentalization, transport reactions, eukaryotic metabolism, metabolic capacity, Escherichia coli comparison
- MeSH terms
- Amino Acids, Enzyme Precursors, Escherichia coli, Genes, Fungal, Phenotype, Protein Precursors, Saccharomyces cerevisiae, Open Reading Frames, Genome, Fungal, Computational Biology, Saccharomyces cerevisiae Proteins, Databases, Genetic, Databases, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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