Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project
Vale, Filipa F. (Universidade de Lisboa)
Roberts, Richard J. (New England Biolabs (Ipswich, Estats Units d'Amèrica))
Kobayashi, Ichizo (University of Tokyo)
Camargo, M. Constanza (National Cancer Institute (Rockville, Estats Units d'Amèrica))
Rabkin, Charles S. (National Cancer Institute (Rockville, Estats Units d'Amèrica))
Brunet, Eduard (Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT))

Fecha:	2024
Resumen:	Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (Hp GP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the Hp GP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29. 5% (298) of the Hp GP genomes contain prophages, of which only 32. 2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.
Ayudas:	European Commission 825832
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Hp GP ; H. pylori ; Prophage ; Mobile elements ; Genome rearrangement ; Phage cycle
Publicado en:	Gut Microbes, Vol. 16 (august 2024) , ISSN 1949-0984

DOI: 10.1080/19490976.2024.2379440
PMID: 39132840

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