Dataset Information


Oh2007 - Genome-scale metabolic network of Bacillus subtilis (iYO844)

ABSTRACT: Oh2007 - Genome-scale metabolic network of Bacillus subtilis (iYO844) This model is described in the article: Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. J. Biol. Chem. 2007 Sep; 282(39): 28791-28799 Abstract: In this report, a genome-scale reconstruction of Bacillus subtilis metabolism and its iterative development based on the combination of genomic, biochemical, and physiological information and high-throughput phenotyping experiments is presented. The initial reconstruction was converted into an in silico model and expanded in a four-step iterative fashion. First, network gap analysis was used to identify 48 missing reactions that are needed for growth but were not found in the genome annotation. Second, the computed growth rates under aerobic conditions were compared with high-throughput phenotypic screen data, and the initial in silico model could predict the outcomes qualitatively in 140 of 271 cases considered. Detailed analysis of the incorrect predictions resulted in the addition of 75 reactions to the initial reconstruction, and 200 of 271 cases were correctly computed. Third, in silico computations of the growth phenotypes of knock-out strains were found to be consistent with experimental observations in 720 of 766 cases evaluated. Fourth, the integrated analysis of the large-scale substrate utilization and gene essentiality data with the genome-scale metabolic model revealed the requirement of 80 specific enzymes (transport, 53; intracellular reactions, 27) that were not in the genome annotation. Subsequent sequence analysis resulted in the identification of genes that could be putatively assigned to 13 intracellular enzymes. The final reconstruction accounted for 844 open reading frames and consisted of 1020 metabolic reactions and 988 metabolites. Hence, the in silico model can be used to obtain experimentally verifiable hypothesis on the metabolic functions of various genes. This model is hosted on BioModels Database and identified by: MODEL1507180013. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

SUBMITTER: Nicolas Le Novère  

PROVIDER: MODEL1507180013 | BioModels | 2015-07-30


Similar Datasets

2015-07-30 | MODEL1507180015 | BioModels
2016-03-09 | E-GEOD-74926 | ArrayExpress
2015-07-30 | MODEL1507180023 | BioModels
2013-06-06 | BIOMD0000000461 | BioModels
2013-06-06 | BIOMD0000000460 | BioModels
2013-06-06 | BIOMD0000000459 | BioModels
2009-09-20 | GSE12873 | GEO
2015-07-30 | MODEL1507180068 | BioModels
2013-08-06 | E-GEOD-47184 | ArrayExpress
2013-08-06 | E-GEOD-47183 | ArrayExpress