Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites

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  • dc.contributor.author Delgado-Tejedor, Anna
  • dc.contributor.author Medina, Rebeca
  • dc.contributor.author Begik, Oguzhan
  • dc.contributor.author Cozzuto, Luca
  • dc.contributor.author López, Judith
  • dc.contributor.author Blanco, Sandra
  • dc.contributor.author Ponomarenko, Julia
  • dc.contributor.author Novoa, Eva Maria
  • dc.date.accessioned 2025-02-06T08:00:40Z
  • dc.date.available 2025-02-06T08:00:40Z
  • dc.date.issued 2024
  • dc.description.abstract The biological relevance and dynamics of mRNA modifications have been extensively studied; however, whether rRNA modifications are dynamically regulated, and under which conditions, remains unclear. Here, we systematically characterize bacterial rRNA modifications upon exposure to diverse antibiotics using native RNA nanopore sequencing. To identify significant rRNA modification changes, we develop NanoConsensus, a novel pipeline that is robust across RNA modification types, stoichiometries and coverage, with very low false positive rates, outperforming all individual algorithms tested. We then apply NanoConsensus to characterize the rRNA modification landscape upon antibiotic exposure, finding that rRNA modification profiles are altered in the vicinity of A and P-sites of the ribosome, in an antibiotic-specific manner, possibly contributing to antibiotic resistance. Our work demonstrates that rRNA modification profiles can be rapidly altered in response to environmental exposures, and provides a robust workflow to study rRNA modification dynamics in any species, in a scalable and reproducible manner.
  • dc.description.sponsorship The work of S.B. work was supported by the Spanish Ministry of Science and Innovation MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe” (PID2019-111692RB-I00 and PID2022-139598OB-I00), and The Scientific Foundation AECC AECC (LABAE19040BLAN). J.L-L. was supported by the AECC (PRDSA19002LÓPE) and MIU (FPU19/01190). This work was supported by funds from the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) (PID2021-128193NB-100 to EMN) and the European Research Council (ERC-StG-2021 No 101042103 to EMN). We acknowledge the support of the MEIC to the EMBL partnership, Centro de Excelencia Severo Ochoa and CERCA Program / Generalitat de Catalunya.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Delgado-Tejedor A, Medina R, Begik O, Cozzuto L, López J, Blanco S, et al. Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites. Nat Commun. 2024 Nov 29;15(1):10054. DOI: 10.1038/s41467-024-54368-x
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-024-54368-x
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/69510
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Commun. 2024 Nov 29;15(1):10054
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101042103
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2019-111692RB-I00
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2022-139598OB-I00
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2021-128193NB-100
  • dc.rights © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
  • dc.subject.keyword Antibiotics
  • dc.subject.keyword Computational biology and bioinformatics
  • dc.subject.keyword Microbiology
  • dc.title Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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