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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Authors: Rubio, Alejandro, Sprang, Maximilian, Garzón, Andrés, Moreno-Rodríguez, Antonio, Pachón-Ibáñez, M. E., Pachón, Jerónimo, Andrade-Navarro, Miguel A., Pérez-Pulido, Antonio J.
Format: article
Status:Published version
Publication Date:2023
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/336777
Online Access:http://hdl.handle.net/10261/336777
Access Level:Open access
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network_acronym_str ES
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spelling Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systemsRubio, AlejandroSprang, MaximilianGarzón, AndrésMoreno-Rodríguez, AntonioPachón-Ibáñez, M. E.Pachón, JerónimoAndrade-Navarro, Miguel A.Pérez-Pulido, Antonio J.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.This work was supported by MCIN/AEI/ PID2020-114861GB-I00 (Agencia Estatal de Investigación/Ministry of Science and Innovation of the Spanish Government) and by the European Regional Development Fund and the Consejeria de Transformación Económica, Industria, Conocimiento y Universidades de la Junta de Andalucia (PY20_00871).American Association for the Advancement of ScienceMinisterio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)Junta de AndalucíaConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2023202320232023info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/336777reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114861GB-I00The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI http://dx.doi.org/10.1126/sciadv.add8911http://dx.doi.org/10.1126/sciadv.add8911Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3367772026-05-22T06:33:51Z
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, Alejandro
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, Alejandro
Sprang, Maximilian
Garzón, Andrés
Moreno-Rodríguez, Antonio
Pachón-Ibáñez, M. E.
Pachón, Jerónimo
Andrade-Navarro, Miguel A.
Pérez-Pulido, Antonio J.
author Rubio, Alejandro
author_facet Rubio, Alejandro
Sprang, Maximilian
Garzón, Andrés
Moreno-Rodríguez, Antonio
Pachón-Ibáñez, M. E.
Pachón, Jerónimo
Andrade-Navarro, Miguel A.
Pérez-Pulido, Antonio J.
author_role author
author2 Sprang, Maximilian
Garzón, Andrés
Moreno-Rodríguez, Antonio
Pachón-Ibáñez, M. E.
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 Ministerio de Ciencia, Innovación y Universidades (España)
Agencia Estatal de Investigación (España)
Junta de Andalucía
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
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
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/336777
url http://hdl.handle.net/10261/336777
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114861GB-I00
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI http://dx.doi.org/10.1126/sciadv.add8911
http://dx.doi.org/10.1126/sciadv.add8911
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869419310741454848
score 15,812429

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