Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.

TitleExpanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.
Publication TypeJournal Article
Year of Publication2005
AuthorsThiele I, Vo TD, Price ND, Palsson BØ
JournalJ Bacteriol
Volume187
Issue16
Pagination5818-30
Date Published2005 Aug
ISSN0021-9193
KeywordsBiotin, Energy Metabolism, Gene Deletion, Genes, Lethal, Genome, Bacterial, Helicobacter pylori, Models, Genetic, Mutagenesis, Phenotype, Reproducibility of Results
Abstract

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.

DOI10.1128/JB.187.16.5818-5830.2005
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/16077130?dopt=Abstract
PMCPMC1196094
Alternate JournalJ. Bacteriol.
PubMed ID16077130