Helicobacter pylori의 minimal genome 분석
Analysis of helicobacter pylori minimal genome
HELICOBACTER PYLORI GENOME 위염 위암 위점막 신경생물학;
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Helicobacter pylori is an etiological agent of various stomach disorders, including type B chronic gastritis, peptic ulcers, and gastric cancers. H. pylori colonizes near the surface of gastric epithelial tissues which are enclosed with gastric mucus layer. H. pylori can pass through and move in gastric mucus layer which is the barrier capable of protecting gastric epithelial tissues from the corrosive gastric juice of the stomach lumen. And host defense mechanisms cannot reach intra-mucus layer. Therefore, H. pylori in the gastric mucous layer might be protected from both antibiotic treatments and host defense mechanisms. This means that control of H. pylori in gastric mucosa might be difficult by using conventional bacteriological concepts and techniques. Genome project presents us the entire sequence informations of bacterial DNA. The genomic sequences of 3 H. pylori strains have been determined up to date. The entire sequence information is supposed to be critical to understand the pathophysiology of H. pylori infections. H. pylori infects and colonizes human gastric mucus layer in which H. pylori's physiological properties are not shown in other pathogenic bacteria, demonstrating that a lot of pathophysiological properties of H. pylori remain unclear. Therefore, availability of complete genomic sequence is limited to elucidate the physiological and pathological roles of H. pylroi in the gastroduodenal disorders. A minimal genome is generally defined as the smallest set of genes that allow for replication of the organism in a particular environment. H. pylori minimal genome will throw light on availability of complete genome sequence. This study aims to analyse H. pylori minimal genomes for physiological life using H. pylori strain 26695. The analysis of minimal genome for physiological life of H. pylori can define and classify biological roles of all genetic elements harbored in the genome. The integration vector pBK, consists of aph3'-Ⅲ and ColEI sequence for inducing global mutagenesis of H. pylori in which allelic exchange mutagenesis via homologous recombination is involved. pBK library of H. pylori strain 26695 genome was prepared to transform H. pylori strain 219 of which transformation yield is high. The mutants were grown and their genomic DNA were isolated, treated with HindIII, self-ligated, and transformed to Eschechia coli DB10B for rescuing the pBK DNAs that were inserted into the mutants genome. The nucleotide sequences of pBK inserts were determined and analyzed what target genes were disrupted using NCBI Conserved Domain Search and TIGRFAM and PFAM Hit comparison. As a result, the nucleotide sequences of the 1,536 rescued plasmids were determined, which represented 293 genes. Two hundreds and fifty seven out of 293 genes were classified in COGs (clusters of orthologous groups). But 36 genes still were not categorized in any COGs. Two hundreds and ninetieth-three genes covered 18.4% of H. pylori 26695 total ORFs. Two hundreds and eight genes covered 13.1% of H. pylori 26695 total ORFs were knockout. Fourteen point two percent of 237 genes included an information storage and processing, 18.8% of 285 genes included an cellular processes, 20.5% of an metabolism and 5.5% of an poorly characterized proteins were knocked out. And 3.1% of 32 genes, involved in a defence mechanism and 10% of 40 genes related to a intracellular trafficking and secretion were knockout. Conclusively, 208 genes (13.1%) among 1,591 ORF of H. pylori strain 26695 were known to be dispensible for a physiological life of H. pylori. These results will give us an insight for functional annotation of complete genome sequence, which leads to understand pathophysilogical behavior of H. pylori.