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Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins
Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311958/ https://www.ncbi.nlm.nih.gov/pubmed/28205536 http://dx.doi.org/10.1038/srep42471 |
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author | Vale, Filipa F. Nunes, Alexandra Oleastro, Mónica Gomes, João P. Sampaio, Daniel A. Rocha, Raquel Vítor, Jorge M. B. Engstrand, Lars Pascoe, Ben Berthenet, Elvire Sheppard, Samuel K. Hitchings, Matthew D. Mégraud, Francis Vadivelu, Jamuna Lehours, Philippe |
author_facet | Vale, Filipa F. Nunes, Alexandra Oleastro, Mónica Gomes, João P. Sampaio, Daniel A. Rocha, Raquel Vítor, Jorge M. B. Engstrand, Lars Pascoe, Ben Berthenet, Elvire Sheppard, Samuel K. Hitchings, Matthew D. Mégraud, Francis Vadivelu, Jamuna Lehours, Philippe |
author_sort | Vale, Filipa F. |
collection | PubMed |
description | Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6–33.0 Kbp, consisting of 27–39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3′ end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes. |
format | Online Article Text |
id | pubmed-5311958 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-53119582017-02-23 Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins Vale, Filipa F. Nunes, Alexandra Oleastro, Mónica Gomes, João P. Sampaio, Daniel A. Rocha, Raquel Vítor, Jorge M. B. Engstrand, Lars Pascoe, Ben Berthenet, Elvire Sheppard, Samuel K. Hitchings, Matthew D. Mégraud, Francis Vadivelu, Jamuna Lehours, Philippe Sci Rep Article Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6–33.0 Kbp, consisting of 27–39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3′ end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes. Nature Publishing Group 2017-02-16 /pmc/articles/PMC5311958/ /pubmed/28205536 http://dx.doi.org/10.1038/srep42471 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Vale, Filipa F. Nunes, Alexandra Oleastro, Mónica Gomes, João P. Sampaio, Daniel A. Rocha, Raquel Vítor, Jorge M. B. Engstrand, Lars Pascoe, Ben Berthenet, Elvire Sheppard, Samuel K. Hitchings, Matthew D. Mégraud, Francis Vadivelu, Jamuna Lehours, Philippe Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins |
title | Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins |
title_full | Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins |
title_fullStr | Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins |
title_full_unstemmed | Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins |
title_short | Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins |
title_sort | genomic structure and insertion sites of helicobacter pylori prophages from various geographical origins |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311958/ https://www.ncbi.nlm.nih.gov/pubmed/28205536 http://dx.doi.org/10.1038/srep42471 |
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