Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.

By Jochen Förster, Iman Famili, P. Fu, Bernhard O. Palsson, Jens Nielsen. Genome Research, 2003

1,116 citations recorded by the source corpus.

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 approximately 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7f677b1d36fc91c37fc68bcc200cf24e481abb73

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Citations in the corpus

Applications of genome-scale metabolic reconstructions (2009, result): “Comparative network-level analysis is not completely new, as some of the first metabolic reconstructions generated were compared with discern phenotypic differences between species (Schilling et al, 2002; Forster et al, 2003).”
Neutralism and selectionism: a network-based reconciliation (2008, background): “Here, many individual mutations that eliminate enzyme-coding genes have very little effect on cell growt”
Single-Cell Metabolomics: Analytical and Biological Perspectives (2013, background): “Even for model organisms such as yeast [the size of the yeastmetabolome is 1168 compounds (90, 91); in the yeast metabolome database, www.”
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Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…be kept in mind that metabolic network data are often still incomplete, and often reflect optimal growth conditions (Edwards & Palsson, 2000a; Forster et al., 2003; Duarte et al., 2007; Ma et al., 2007; Shlomi et al., 2008, 2009; Folger et al., 2011; Holme, 2011; Chavali et al., 2012;…”
Inference of complex biological networks: distinguishability issues and optimization-based solutions (2011, background): “gene expression [5-13], signal transduction [14-17] and metabolic networks [18-25].”
Genome-scale models of microbial cells: evaluating the consequences of constraints (2004, methodology): “The enumeration of optimal biochemical-reaction network states has been used to study several organisms including: Saccharolytic clostridium 39 , E. coli 40–42 , H.pylori 43 , Haemophilus influenzae 44,45 and Saccharomyces cerevisiae 46–48 .”
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. (2004, background): “The first genome-scale metabolic reconstruction of a eukaryotic organism, Saccharomyces cerevisiae iFF708, was recently completed by Förster and Famili [1].”