Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems

CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has b...

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Autores: Rubio Valle, Alejandro, Sprang, Maximilian, Garzón, Andrés, Moreno Rodriguez, Antonio, Pachón Ibáñez, Maria Eugenia, Pachón, Jerónimo, Andrade Navarro, Miguel A., Pérez-Pulido, Antonio J.
Tipo de recurso: artículo
Fecha de publicación:2023
País:España
Institución:Universidad Pablo de Olavide (UPO)
Repositorio:RIO. Repositorio Institucional Olavide
Idioma:inglés
OAI Identifier:oai:rio.upo.es:10433/25477
Acceso en línea:https://hdl.handle.net/10433/25477
Access Level:acceso abierto
Palabra clave:CRISPR-Cas
Membrane
Phage
Pangenome
ESKAPE
Machine learning
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spelling Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systemsRubio Valle, AlejandroSprang, MaximilianGarzón, AndrésMoreno Rodriguez, AntonioPachón Ibáñez, Maria EugeniaPachón, JerónimoAndrade Navarro, Miguel A.Pérez-Pulido, Antonio J.CRISPR-CasMembranePhagePangenomeESKAPEMachine learningCRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter. By analyzing the spacers of tens of thousands of genomes from six bacterial species, we have been able to reduce the CRISPR dark matter from 80% to as low as 15% in some of the species. In addition, we have observed that, when a genome presents CRISPR-Cas systems, this is accompanied by particular sets of membrane proteins. Our results suggest that when bacteria present membrane proteins that make it compete better in its environment and these proteins are, in turn, receptors for specific phages, they would be forced to acquire CRISPR-Cas.American Association for the Advancement of Science20262026-01-1220232023-01-0120232023-01-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10433/25477reponame:RIO. Repositorio Institucional Olavideinstname:Universidad Pablo de Olavide (UPO)InglésengAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2020-114861GB-I00 ESTUDIO DEL CRISPROMA DEL GRUPO ESKAPE DE BACTERIAS DE INTERES CLINICO Y SU RELACION CON GENES DE LA PROPIA BACTERIAopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial 4.0 Internationalhttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:rio.upo.es:10433/254772026-06-13T12:46:27Z
dc.title.none.fl_str_mv Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
title Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
spellingShingle Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
Rubio Valle, Alejandro
CRISPR-Cas
Membrane
Phage
Pangenome
ESKAPE
Machine learning
title_short Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
title_full Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
title_fullStr Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
title_full_unstemmed Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
title_sort Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
dc.creator.none.fl_str_mv Rubio Valle, Alejandro
Sprang, Maximilian
Garzón, Andrés
Moreno Rodriguez, Antonio
Pachón Ibáñez, Maria Eugenia
Pachón, Jerónimo
Andrade Navarro, Miguel A.
Pérez-Pulido, Antonio J.
author Rubio Valle, Alejandro
author_facet Rubio Valle, Alejandro
Sprang, Maximilian
Garzón, Andrés
Moreno Rodriguez, Antonio
Pachón Ibáñez, Maria Eugenia
Pachón, Jerónimo
Andrade Navarro, Miguel A.
Pérez-Pulido, Antonio J.
author_role author
author2 Sprang, Maximilian
Garzón, Andrés
Moreno Rodriguez, Antonio
Pachón Ibáñez, Maria Eugenia
Pachón, Jerónimo
Andrade Navarro, Miguel A.
Pérez-Pulido, Antonio J.
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv
dc.subject.none.fl_str_mv CRISPR-Cas
Membrane
Phage
Pangenome
ESKAPE
Machine learning
topic CRISPR-Cas
Membrane
Phage
Pangenome
ESKAPE
Machine learning
description CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter. By analyzing the spacers of tens of thousands of genomes from six bacterial species, we have been able to reduce the CRISPR dark matter from 80% to as low as 15% in some of the species. In addition, we have observed that, when a genome presents CRISPR-Cas systems, this is accompanied by particular sets of membrane proteins. Our results suggest that when bacteria present membrane proteins that make it compete better in its environment and these proteins are, in turn, receptors for specific phages, they would be forced to acquire CRISPR-Cas.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-01-01
2023
2023-01-01
2026
2026-01-12
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/10433/25477
url https://hdl.handle.net/10433/25477
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2020-114861GB-I00 ESTUDIO DEL CRISPROMA DEL GRUPO ESKAPE DE BACTERIAS DE INTERES CLINICO Y SU RELACION CON GENES DE LA PROPIA BACTERIA
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial 4.0 International
http://creativecommons.org/licenses/by-nc/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial 4.0 International
http://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv American Association for the Advancement of Science
publisher.none.fl_str_mv American Association for the Advancement of Science
dc.source.none.fl_str_mv reponame:RIO. Repositorio Institucional Olavide
instname:Universidad Pablo de Olavide (UPO)
instname_str Universidad Pablo de Olavide (UPO)
reponame_str RIO. Repositorio Institucional Olavide
collection RIO. Repositorio Institucional Olavide
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.81155

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