Dataset Information

Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics

ABSTRACT: [1] Transcription profiling of one Burkholderia cenocepacia clinical isolate, J2315, versus a soil isolate, HI2424, in conditions mimicking CF sputum [2] Transcription profiling of Burkholderia cenocepacia isolates J2315 and HI2424 in media mimicking CF sputum or the soil environment Overall design: [1] J2315 vs. HI2424 cells in the same condition. [2] Two-condition experiment. Biological replicates: 4 replicates.

INSTRUMENT(S): Agilent Burkholderia cenocepacia 017397 microarray

ORGANISM(S): Burkholderia cenocepacia

SUBMITTER: Deborah R. Yoder-Himes

PROVIDER: GSE15817 | GEO | 2009-12-01

SECONDARY ACCESSION(S): PRJNA116735

REPOSITORIES: GEO

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Project description: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.