Reconstruction of genome-scale metabolic model for Helicobacter pylori

Helicobacter pylori is a gram-negative bacteria that specifically colonizes gastric epithelium of more than half ofthe world population. The presents of H. pylori evokes various diseases including peptic ulcers, gastric ulcers, ade nocarcinoma, MALT lymphoma, and gastric cancer . Based on the H. pylori’s species and host characteristics,the type of disease and intensity may be highly variable . The genome sequence of H. pylori is well character ized as NCBI reports more than ۵۰۰ di↵erent strains around the world. Despite that, these genome analysesmerely supply information about the overall metabolism of helicobacter pylori. On the other hand, the survivalof H. pylori in human host could reflect its unique capability of physiological response which displays the needof crucial research in this field. Genome-scale metabolic model is an approach which extensively used for analy sis of metabolic pathways of di↵erent organisms. It defines gene-protein-reaction associations for metabolic genesby contextualizing di↵erent types of Big Data (e.g., genomics, metabolomics, and transcriptomics) . Therefore, inthis study various omics data of helicobacter pylori ۲۶۶۹۵ were utilized to construct and contextualize metabolicmodel of H. pylori. In this way, the existed genome scale metabolic model of helicobacter pylori ۲۶۶۹۵, Ilt۳۴۱ ,was used as template model in RAVEN Toolbox, which combined draft GEM from KEGG and MetaCyc path way databases. Based on comparison between the combined draft model and Ilt۳۴۱model, the reactions that wereabsent in Ilt۳۴۱, were incorporated in to the model. Subsequently, transport DB, UniProt and other available exper imental data were utilized for improving and validating of model. According to amino acid auxotrophy, Biologphenotype microarray and gene essentiality simulation, the model shows approximately ۸۵%, ۸۰% and ۷۹% accuracyrespectively. This model can be used for deeply understanding mechanistic underlying H. pylori’s metabolic pathway

کلیدواژه ها:

Helicobacter pylori ، Genome scale metabolic model