BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051.pdfhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051.mhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051.xpphttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051.pnghttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180051?filename=MODEL1507180051.vcmlprimaryOK200Nicolas Le NovèreNon-curatedconstraint-based modelL3V1https://www.ebi.ac.uk/biomodels/MODEL150718005121609491falseBioModelsSBMLModelsFang2011 Genome scale metabolic network of Burkholderia cenocepacia (iKF1028)2011MODEL1507180051Non KineticFang K, Zhao H, Sun C, Lam CM, Chang S, Zhang K, Panda G, Godinho M, Martins dos Santos VA, Wang JFang K21609491,
BACKGROUND: Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets. RESULTS: We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, iKF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model iKF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets. CONCLUSIONS: As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen.. null, 5.
Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China.n.lenovere@gmail.comThe Babraham Institute<h4>Background</h4>Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets.<h4>Results</h4>We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, iKF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model iKF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets.<h4>Conclusions</h4>As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen.Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction.Fang Kechi K, Zhao Hansheng H, Sun Changyue C, Lam Carolyn M C CM, Chang Suhua S, Zhang Kunlin K, Panda Gurudutta G, Godinho Miguel M, Martins dos Santos Vítor A P VA, Wang Jing Jscale (sensu Metazoa), scale tissue, Burkholderia cepacia genomovar III., scales, scale, Genomes, plant peltate hair, peltate hairprojections, Cystic fibrosis NOS, other disease, scale tissue, Virulence, Materials, Immune Systems, infectious disorder, FESTA-L, FESTA-S, lamellae, Biocatalysts, susceptibility to chronic infection by, peltate hair, Meconium obstruction of intestine in mucoviscidosis, Infestations and Infections, secondary metabolites, Gene, Pancreas Fibrocystic Diseases, infectivity, process of organ, dIKK-gamma, protrusion, lamella, Readability, primary metabolites, resilient, diseases, tough, DmIKK-gamma, Pathogenicity Factor, disease or disorder, cystic fibrosis with other manifestations (disorder), AW048865, diseases and disorders, dmIKKgamma, cystic fibrosis lung disease, IKK[[gamma]], modifier of, Meconium ileus in cystic fibrosis (disorder), U19, IKKg, Pulmonary, KEY, Key, infectious, treatment, infection, strong, study, viral infection, BM040, human disease, FOCUS, cystic fibrosis with meconium ileus, Genetic, enzymes, Genomes, Cystic Fibrosis of Pancreas, cystic fibrosis with other manifestations, plant peltate hair, cystic fibrosis with combined manifestations, virus process, ridges, clinical infection, ecotype, cystic fibrosis with gastrointestinal manifestations, non-neoplastic, Fibrocystic disease, Pathogenicity Factors, CF, Infestation and Infection, Cystic Fibrosis, drugs, Enzyme, Immune, IKK, medicine, Clients, papilla, disease management, Therapies, scale (sensu Metazoa), disorder, Homo sapiens disease, Pulmonary Cystic Fibrosis, Infections and Infestations, laminae, Burkholderia cepacia genomovar III, pseudomonas aeruginosa, Therapy, anatomical protrusion, infectious diseases and manifestations, Traits, anatomical process, drug, lamina, disorders, Mucoviscidosis, flanges, Cystic fibrosis NOS (disorder), enzyme activity, Factor, medical condition, function, Cistrons, Client, results, CF - Cystic fibrosis, strain, cystic fibrosis with pulmonary manifestations, IKKgamma, Virulence Factor, DmIKKgamma, disorder due to infection, dIKK, communicable disease, CYSTIC FIBROS W/O ILEUS, Systems, shelf, Kenny, Diseases, Infection, Pathogenicity, Genetic Materials, condition, cultivar, background, Pancreatic, Fibrosis, scales, disease by infectious agent, flange, Genetic Material, organ process, in cystic fibrosis, Cystic fibrosis (disorder), Pancreatic Cystic Fibrosis, Factors, scale, Dmikkgamma, System, shelves, IKK-gamma, Cystic fibrosis without mention of meconium ileus, metabolite, Infection and Infestation, cystic fibrosis, INSDC_feature:gene, Understanding, cystic fibrosis with meconium ileus (disorder), CG16910, projection, TRAITS, ridge, Treatments, introduction, Fibrocystic Disease of Pancreas, Cystic, processes, process, disease, DmelCG16910, Patient, Therapeutic, spine, Material, mucoviscidosis, Festa, metabolites, Pancreas Fibrocystic Disease, Biocatalyst, processus, Cistron, Treatment, medical condition., virulence, infectious disease, cystic fibrosis with pulmonary manifestations (disorder), transmissible diseaseprojections, extent, Cystic fibrosis NOS, scale tissue, DmelCG6944, Virulence, Materials, Public Sectors, Immune Systems, susceptibility to chronic infection by, DmLamin, Meconium obstruction of intestine in mucoviscidosis, 9630008F14, Infestations and Infections, E(csw)3A, E(csw[CS])3A, infectivity, AW046674, LamDm[[0]], Readability, diseases, AW048865, diseases and disorders, Public Enterprise, modifier of, lymphangio-myomatosis, infectious, treatment, strong, viral infection, human disease, lamin Dm0, enzymes, Genomes, plant peltate hair, 74/76, Name of Epi/Pandemic, Public Domains, virus process, nlam, Gab-1, ecotype, cystic fibrosis with gastrointestinal manifestations, DM[[O]], Fibrocystic disease, Pathogenicity Factors, CF, FBgn0002526, Immune, medicine, papilla, disease management, Therapies, D5, 2459, Lamin Dm[[0]], Homo sapiens disease, Pulmonary Cystic Fibrosis, Infections and Infestations, Lam(Dm0), Burkholderia cepacia genomovar III, Therapy, anatomical protrusion, infectious diseases and manifestations, completeness, lamina, Mucoviscidosis, flanges, DmelCG10236, Cystic fibrosis NOS (disorder), 5]], somatic, results, CF - Cystic fibrosis, Epidemic, lamin, Virulence Factor, Epidemic Disease, epidemic, Dm0, Dm2, Dm1, Dm, Public Domain, CYSTIC FIBROS W/O ILEUS, shelf, Diseases, jf27, Pathogenicity, Domains, CG6944, Genetic Materials, cultivar, Pancreatic, Fibrosis, disease by infectious agent, Genetic Material, Domain, Dm[[2]], R29144/1, in cystic fibrosis, Cystic fibrosis (disorder), misg, Pancreatic Cystic Fibrosis, DmO, Factors, LM-A/alpha1, Su(sev)3A, alpha[[3, System, shelves, lamDm[[0]], Infection and Infestation, cystic fibrosis, INSDC_feature:gene, projection, Treatments, ridge, Fibrocystic Disease of Pancreas, disease, Sector, Dmo, Su(sev[S11])3A, Patient, spine, Material, mucoviscidosis, Festa, Pancreas Fibrocystic Disease, Biocatalyst, Cistron, cystic fibrosis with pulmonary manifestations (disorder), B130007O04Rik, Lam[[Dm0]], other disease, Sectors, infectious disorder, 5430428I19, FESTA-L, FESTA-S, lamellae, Biocatalysts, peltate hair, CT28769, number, Gene, Pancreas Fibrocystic Diseases, Copyrights, CG1044, process of organ, presence, protrusion, lamella, Dm(0), DOS, Dos, resilient, tough, Pathogenicity Factor, disease or disorder, cystic fibrosis with other manifestations (disorder), Dm[[0]], TSC4, cystic fibrosis lung disease, Enterprises, Meconium ileus in cystic fibrosis (disorder), U19, Pulmonary, infection, study, alpha3/5, BM040, FOCUS, cystic fibrosis with meconium ileus, Genetic, Name of Epidemic and/or Pandemic, Cystic Fibrosis of Pancreas, cystic fibrosis with other manifestations, hdln, l(2)gdh-7, cystic fibrosis with combined manifestations, ridges, Public Enterprises, clinical infection, non-neoplastic, Infestation and Infection, Cystic Fibrosis, drugs, Enzyme, Abstract, pulmonary lymphangioleiomyomatosis, laminin alpha3/5, Clients, Lam-A, scale (sensu Metazoa), disorder, Lan, Enterprise, Lam, LAM, laminae, Dm[[1]], CG10236, pseudomonas aeruginosa, Traits, anatomical process, drug, Dm[[mit]], disorders, enzyme activity, l(2)25Ec, Factor, medical condition, function, lam, lamA, Cistrons, Client, lymphangioleiomyomatosis, LamDm[[o]], strain, DmelCG1044, cystic fibrosis with pulmonary manifestations, count in organism, TSC, l(2)04643, 141511_at, disorder due to infection, lung lymphangioleiomyomatosis, Public, communicable disease, Systems, Infection, condition, Dm[[o]], background, scales, flange, organ process, Data Base, lymphangiomyomatosis, Lam A, Epidemic Disorder, scale, l(2)jf27, R29144|1, Name of Epidemic or Pandemic, Cystic fibrosis without mention of meconium ileus, PPP1R160, Understanding, cystic fibrosis with meconium ileus (disorder), lamDm0, EPIDEMIC, Lamp, TRAITS, introduction, Cystic, processes, process, l(2)gdh7, D930023J12Rik, Lam Dm[[0]], Therapeutic, LamA, processus, lamin Dm[[0]], Treatment, virulence, Public., infectious disease, quantitative, lanA, transmissible disease, presence or absence in organismscale (sensu Metazoa), scale tissue, scales, peltate hair., scale, Genomes, Burkholderia cepacia genomovar III, plant peltate hairfalseFang2011 - Genome-scale metabolic network of Burkholderia cenocepacia (iKF1028)
Fang2011 - Genome-scale metabolic network of
Burkholderia cenocepacia (iKF1028)
This model is described in the article:
Exploring the metabolic
network of the epidemic pathogen Burkholderia cenocepacia J2315
via genome-scale reconstruction.
Fang K, Zhao H, Sun C, Lam CM, Chang
S, Zhang K, Panda G, Godinho M, Martins dos Santos VA, Wang
J.
BMC Syst Biol 2011; 5: 83
Abstract:
BACKGROUND: Burkholderia cenocepacia is a threatening
nosocomial epidemic pathogen in patients with cystic fibrosis
(CF) or a compromised immune system. Its high level of
antibiotic resistance is an increasing concern in treatments
against its infection. Strain B. cenocepacia J2315 is the most
infectious isolate from CF patients. There is a strong demand
to reconstruct a genome-scale metabolic network of B.
cenocepacia J2315 to systematically analyze its metabolic
capabilities and its virulence traits, and to search for
potential clinical therapy targets. RESULTS: We reconstructed
the genome-scale metabolic network of B. cenocepacia J2315. An
iterative reconstruction process led to the establishment of a
robust model, iKF1028, which accounts for 1,028 genes, 859
internal reactions, and 834 metabolites. The model iKF1028
captures important metabolic capabilities of B. cenocepacia
J2315 with a particular focus on the biosyntheses of key
metabolic virulence factors to assist in understanding the
mechanism of disease infection and identifying potential drug
targets. The model was tested through BIOLOG assays. Based on
the model, the genome annotation of B. cenocepacia J2315 was
refined and 24 genes were properly re-annotated. Gene and
enzyme essentiality were analyzed to provide further insights
into the genome function and architecture. A total of 45
essential enzymes were identified as potential therapeutic
targets. CONCLUSIONS: As the first genome-scale metabolic
network of B. cenocepacia J2315, iKF1028 allows a systematic
study of the metabolic properties of B. cenocepacia and its key
metabolic virulence factors affecting the CF community. The
model can be used as a discovery tool to design novel drugs
against diseases caused by this notorious pathogen.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180051.
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.
2015-07-282015-07-302015-07-18MODEL150718005121609491MODEL1507180051