%0 Journal Article
%T Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth
%A Seung Sohn
%A Tae Kim
%A Jay H Lee
%A Sang Lee
%J BMC Systems Biology
%D 2012
%I BioMed Central
%R 10.1186/1752-0509-6-49
%X Here we employed a systematic and iterative process, designated as Reconciling In silico/in vivo mutaNt Growth (RING), to settle discrepancies between in silico prediction and in vivo observations to a newly reconstructed genome-scale metabolic model of the fission yeast, Schizosaccharomyces pombe, SpoMBEL1693. The predictive capabilities of the genome-scale metabolic model in predicting single-gene mutant growth phenotypes were measured against the single-gene mutant library of S. pombe. The use of RING resulted in improving the overall predictive capability of SpoMBEL1693 by 21.5%, from 61.2% to 82.7% (92.5% of the negative predictions matched the observed growth phenotype and 79.7% the positive predictions matched the observed growth phenotype).This study presents validation and refinement of a newly reconstructed metabolic model of the yeast S. pombe, through improving the metabolic model¡¯s predictive capabilities by reconciling the in silico predicted growth phenotypes of single-gene knockout mutants, with experimental in vivo growth data.Genome-scale metabolic models have proven themselves in a wide range of applications in the field of biotechnology, such as system-wide drug targeting, metabolic engineering of microbial systems for production of various chemicals and materials, and system-wide understanding of cellular metabolism [1-5]. Although a large majority of these genome-scale metabolic models are of prokaryotic organisms, genome-scale metabolic models of eukaryotic organisms exist and have contributed in the study of eukaryotic metabolism [2,6]. For instance, the human genome-scale metabolic model has been employed in the study of Alzheimer¡¯s disease, giving insight into the disease and suggesting potential treatments [7]. Other eukaryotic genome-scale metabolic models, in addition to Homo sapiens[8,9], include Mus musculus[10], Leishmania major[11], Aspergillus nidulans[12], Aspergillus niger[13], Saccharomyces cerevisiae[6,14], and Pichia pastoris[1
%K Schizosaccharomyces pombe
%K Genome-scale metabolic model
%K Single-gene mutant growth
%K Essentiality
%U http://www.biomedcentral.com/1752-0509/6/49