PMC:3091627 / 10729-16244 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3091627","sourcedb":"PMC","sourceid":"3091627","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091627","text":"Main features of the B38 genome\nThe genome of the B38 strain consists of a circular chromosome containing 1,576,758 base pairs (bp) and an average GC content of 39.2% (Figure 3). It is the smallest H. pylori genome sequenced to date (Table 1). The B38 genome sequence was first automatically and then manually annotated using the MaGe system [28]http://www.genoscope.cns.fr/agc/mage and was then compared with the other sequenced H. pylori genomes. It contains 1,528 CDSs with a coding density (85.0%) similar to that found in the other Helicobacter sequenced strains. Among the 1528 CDSs, 1393 were predicted to be protein-coding genes (complete CDSs) with an average length of 971 bp; 135 correspond to partial CDSs, of which 133 are pseudogenes (i.e. 133 fragments representing 62 genes) and two are remnant genes (corresponding to truncated genes for which we cannot find the missing sections in close proximity) (Table 1).\nTable 1 Summary of comparative features of Helicobacter genomes\naThese genomes have got a 9,369 bp (HPAG1), a 10,031 bp (G27), a 10,225 bp (P12), a 3,661 bp (Sheeba) plasmid and a 10,031 bp (G27) and a 10,225 bp (P12). Plasmids were not counted\nbRevised number with the MaGe system and manual curation\ncPercentage of fragments of genes/total CDSs\ndPercentage of fragmented genes/total CDSs\ne Number of copies\nFigure 3 Genome map of Helicobacter pylori strain B38. From outside to inside: -\tGC skew (window 2500, step 500) in blue. -\tTotal CDSs (green) with pseudogenes/partial genes (purple). -\tCDSs coding for hypothetical restriction/modification systems (purple), phage proteins (orange), or insertion sequences (ISHp609) (green). -\tTotal CDSs according to the matrix defined for gene identification (matrix n°1 in red, matrix N°2 in black, matrix n°3 in green). -\tRNA (rRNA in green, tRNA in purple and misc_RNA in red). -\tRule. -\tGC% (window 5000, step 2000) in yellow. Red arrow indicates the position of the origin of replication. Of the 1,528 annotated CDSs, a function was assigned to 989 CDSs (64.7%). For 784 of them (79.3%), a function was experimentally demonstrated either in the Helicobacter species (188, 12.3%) or in another organism (596, 39%). Two hundred and five CDSs (20.7% of 989) received a function based on the presence of a conserved amino acid motif, a structural feature, or limited homology. A total of 378 CDSs have homologs in previously reported sequences of the genus Helicobacter (43.6% of 378), in the epsilon proteobacteria (35.2% of 378), or in other distant bacteria (21.2% of 378). Protein function classification based on the cluster orthologous genes classification (COG) database allowed us to place 1189 of the 1528 CDSs (77.81%) in at least one of the COG functional groups (Table 2): 454 were assigned to cellular processes and signaling systems, 342 to information storage and processing, while 595 were involved in metabolism. The B38 genome exhibits the highest percentage of CDSs associated with a COG group (77.97% vs 73.38% for 26695, 76.48% for J99, 76.15% for HPAG1 and, 73.49 for Shi470), with the number of CDSs involved in defense mechanisms slightly higher than in the other sequenced Helicobacter strains.\nTable 2 Automatic distribution of protein functions, based on the COG classification, between Helicobacter strains\n*The CDSs were manually curated in the MaGe system for the elimination of artifacts. There are a significant number of restriction/modification systems present in H. pylori; their composition and activity have been shown to be strain-specific [29]. In the B38 strain, 63 CDSs were involved in restriction/modification systems. Among them, 30 elements were fragmented into pseudogenes corresponding to 12 potential genes, and three elements appeared to be partial genes (Additional file 2). Thus, the proportion of potentially active genes (52%) appeared to be higher in B38 than in strains J99 and 26695, in which only 30% of type II R-M systems were reported to be functional [30].\nThe B38 genome harbors five complete copies of the four-gene insertion sequence ISHp609. This insertion sequence was frequently found in H. pylori strains from Europe, Americas, India and Africa, but was almost always absent in strains from East Asia [31]. Three of the four genes (orf1, orf2, ORFA) demonstrated 100% of identity in the five B38 ISHp609 copies, whereas ORFB from one of the five B38 ISHp609 copies (HELPY1334) exhibited a single mutation. Among the sequenced genomes (Table 1), a single and complete copy of this element was found in strain HPAG1, but it differed slightly from that found in B38 (6, 8, and 9 mutations are present in orf1, ORFA, and ORFB of HPAG1, respectively). This consistency in the five copies of ISHp609 in B38 indicated that it has been acquired very recently, and that it is probably an active element that is capable of transposition, a property never experimentally demonstrated for a transposable element in H. pylori.\nAnother property associated with the B38 genome relates to the complete absence of four of the 45 genes encoding outer membrane proteins (OMPs) from the four conserved OMP families (Hop, Hor, Hof et Hom) (Additional file 3). B38 lacks babB, babC, sabB, and homB, four OMPs known to play a major role in adhesion to gastric epithelial cells and possibly in long-term persistence of strains in the human gastric mucosa when associated with peptic ulcer diseases or gastric metaplasia [32]. B38 lacks a high number of adhesin genes among the sequenced genomes.","divisions":[{"label":"title","span":{"begin":0,"end":31}},{"label":"p","span":{"begin":32,"end":927}},{"label":"table caption","span":{"begin":928,"end":1337}},{"label":"p","span":{"begin":937,"end":992}},{"label":"p","span":{"begin":993,"end":1173}},{"label":"p","span":{"begin":1174,"end":1230}},{"label":"p","span":{"begin":1231,"end":1275}},{"label":"p","span":{"begin":1276,"end":1318}},{"label":"p","span":{"begin":1319,"end":1337}},{"label":"figure caption","span":{"begin":1338,"end":1967}},{"label":"p","span":{"begin":1348,"end":1967}},{"label":"p","span":{"begin":1968,"end":3194}},{"label":"table caption","span":{"begin":3195,"end":3395}},{"label":"p","span":{"begin":3204,"end":3310}},{"label":"p","span":{"begin":3311,"end":3395}},{"label":"p","span":{"begin":3396,"end":3993}},{"label":"p","span":{"begin":3994,"end":4957}}],"tracks":[{"project":"2_test","denotations":[{"id":"20537153-16407324-10781736","span":{"begin":343,"end":345},"obj":"16407324"},{"id":"20537153-10944229-10781737","span":{"begin":3555,"end":3557},"obj":"10944229"},{"id":"20537153-11226310-10781738","span":{"begin":3989,"end":3991},"obj":"11226310"},{"id":"20537153-15516563-10781739","span":{"begin":4246,"end":4248},"obj":"15516563"},{"id":"20537153-16790815-10781740","span":{"begin":5441,"end":5443},"obj":"16790815"}],"attributes":[{"subj":"20537153-16407324-10781736","pred":"source","obj":"2_test"},{"subj":"20537153-10944229-10781737","pred":"source","obj":"2_test"},{"subj":"20537153-11226310-10781738","pred":"source","obj":"2_test"},{"subj":"20537153-15516563-10781739","pred":"source","obj":"2_test"},{"subj":"20537153-16790815-10781740","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93a8ec","default":true}]}]}}