Dataset Information

Fuentealb2016 - Genome-scale metabolic reconstruction (iPF215) of Piscirickettsia salmonis LF-89

ABSTRACT: Fuentealb2016 - Genome-scale metabolic reconstruction (iPF215) of Piscirickettsia salmonis LF-89 This model is described in the article: Genome-scale metabolic reconstruction for the insidious bacterium in aquaculture Piscirickettsia salmonis. Fuentealba P, Aros C, Latorre Y, Martínez I, Marshall S, Ferrer P, Albiol J, Altamirano C. Bioresour. Technol. 2017 Jan; 223: 105-114 Abstract: Piscirickettsia salmonis is a fish bacterium that causes the disease piscirickettsiosis in salmonids. This pathology is partially controlled by vaccines. The lack of knowledge has hindered its culture on laboratory and industrial scale. The study describes the metabolic phenotype of P. salmonis in culture. This study presents the first genome-scale model (iPF215) of the LF-89 strain of P. salmonis, describing the central metabolic pathway, biosynthesis and molecule degradation and transport mechanisms. The model was adjusted with experiment data, allowing the identification of the capacities that were not predicted by the automatic annotation of the genome sequences. The iPF215 model is comprised of 417 metabolites, 445 reactions and 215 genes, was used to reproduce the growth of P. salmonis (?max 0.052±0.005h(-1)). The metabolic reconstruction of the P. salmonis LF-89 strain obtained in this research provides a baseline that describes the metabolic capacities of the bacterium and is the basis for developing improvements to its cultivation for vaccine formulation. This model is hosted on BioModels Database and identified by: MODEL1610250000. 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: Pablo Fuentealba

PROVIDER: MODEL1610250000 | BioModels | 2016-12-06

REPOSITORIES: BioModels

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Publications

Genome-scale metabolic reconstruction for the insidious bacterium in aquaculture Piscirickettsia salmonis.

Fuentealba Pablo P Aros Camila C Latorre Yesenia Y Martínez Irene I Marshall Sergio S Ferrer Pau P Albiol Joan J Altamirano Claudia C

Bioresource technology 20161015

Piscirickettsia salmonis is a fish bacterium that causes the disease piscirickettsiosis in salmonids. This pathology is partially controlled by vaccines. The lack of knowledge has hindered its culture on laboratory and industrial scale. The study describes the metabolic phenotype of P. salmonis in culture. This study presents the first genome-scale model (iPF215) of the LF-89 strain of P. salmonis, describing the central metabolic pathway, biosynthesis and molecule degradation and transport mech ...[more]

PMID: 27788423

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Project description:Becker2005 - Genome-scale metabolic network of Staphylococcus aureus (iSB619) This model is described in the article: Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. Becker SA, Palsson BØ. BMC Microbiol. 2005; 5: 8 Abstract: BACKGROUND: Several strains of bacteria have sequenced and annotated genomes, which have been used in conjunction with biochemical and physiological data to reconstruct genome-scale metabolic networks. Such reconstruction amounts to a two-dimensional annotation of the genome. These networks have been analyzed with a constraint-based formalism and a variety of biologically meaningful results have emerged. Staphylococcus aureus is a pathogenic bacterium that has evolved resistance to many antibiotics, representing a significant health care concern. We present the first manually curated elementally and charge balanced genome-scale reconstruction and model of S. aureus' metabolic networks and compute some of its properties. RESULTS: We reconstructed a genome-scale metabolic network of S. aureus strain N315. This reconstruction, termed iSB619, consists of 619 genes that catalyze 640 metabolic reactions. For 91% of the reactions, open reading frames are explicitly linked to proteins and to the reaction. All but three of the metabolic reactions are both charge and elementally balanced. The reaction list is the most complete to date for this pathogen. When the capabilities of the reconstructed network were analyzed in the context of maximal growth, we formed hypotheses regarding growth requirements, the efficiency of growth on different carbon sources, and potential drug targets. These hypotheses can be tested experimentally and the data gathered can be used to improve subsequent versions of the reconstruction. CONCLUSION: iSB619 represents comprehensive biochemically and genetically structured information about the metabolism of S. aureus to date. The reconstructed metabolic network can be used to predict cellular phenotypes and thus advance our understanding of a troublesome pathogen. This model is hosted on BioModels Database and identified by: MODEL1507180070. 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.

Project description:Liao2011 - Genome-scale metabolic reconstruction of Klebsiella pneumoniae (iYL1228) This model is described in the article: An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. Liao YC, Huang TW, Chen FC, Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson BO, Hsiung CA. J. Bacteriol. 2011 Apr; 193(7): 1710-1717 Abstract: Klebsiella pneumoniae is a Gram-negative bacterium of the family Enterobacteriaceae that possesses diverse metabolic capabilities: many strains are leading causes of hospital-acquired infections that are often refractory to multiple antibiotics, yet other strains are metabolically engineered and used for production of commercially valuable chemicals. To study its metabolism, we constructed a genome-scale metabolic model (iYL1228) for strain MGH 78578, experimentally determined its biomass composition, experimentally determined its ability to grow on a broad range of carbon, nitrogen, phosphorus and sulfur sources, and assessed the ability of the model to accurately simulate growth versus no growth on these substrates. The model contains 1,228 genes encoding 1,188 enzymes that catalyze 1,970 reactions and accurately simulates growth on 84% of the substrates tested. Furthermore, quantitative comparison of growth rates between the model and experimental data for nine of the substrates also showed good agreement. The genome-scale metabolic reconstruction for K. pneumoniae presented here thus provides an experimentally validated in silico platform for further studies of this important industrial and biomedical organism. This model is hosted on BioModels Database and identified by: MODEL1507180054. 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.

Dataset Information

Fuentealb2016 - Genome-scale metabolic reconstruction (iPF215) of Piscirickettsia salmonis LF-89

Publications

Genome-scale metabolic reconstruction for the insidious bacterium in aquaculture Piscirickettsia salmonis.

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