Reference : Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in sili...
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/13039
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.
English
Thiele, Ines mailto []
Vo, Thuy D. [> >]
Price, Nathan D. [> >]
Palsson, Bernhard O. [> >]
2005
Journal of Bacteriology
187
16
5818-30
Yes (verified by ORBilu)
0021-9193
1098-5530
United States
[en] Biotin/biosynthesis ; Energy Metabolism/genetics ; Gene Deletion ; Genes, Lethal ; Genome, Bacterial ; Helicobacter pylori/genetics/growth & development/metabolism ; Models, Genetic ; Mutagenesis ; Phenotype ; Reproducibility of Results
[en] Helicobacter pylori is a human gastric pathogen infecting almost half of the world population. Herein, we present an updated version of the metabolic reconstruction of H. pylori strain 26695 based on the revised genome annotation and new experimental data. This reconstruction, iIT341 GSM/GPR, represents a detailed review of the current literature about H. pylori as it integrates biochemical and genomic data in a comprehensive framework. In total, it accounts for 341 metabolic genes, 476 intracellular reactions, 78 exchange reactions, and 485 metabolites. Novel features of iIT341 GSM/GPR include (i) gene-protein-reaction associations, (ii) elementally and charge-balanced reactions, (iii) more accurate descriptions of isoprenoid and lipopolysaccharide metabolism, and (iv) quantitative assessments of the supporting data for each reaction. This metabolic reconstruction was used to carry out in silico deletion studies to identify essential and conditionally essential genes in H. pylori. A total of 128 essential and 75 conditionally essential metabolic genes were identified. Predicted growth phenotypes of single knockouts were validated using published experimental data. In addition, in silico double-deletion studies identified a total of 47 synthetic lethal mutants involving 67 different metabolic genes in rich medium.
http://hdl.handle.net/10993/13039

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