Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites
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 a...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54368-x |
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| author | Anna Delgado-Tejedor Rebeca Medina Oguzhan Begik Luca Cozzuto Judith López Sandra Blanco Julia Ponomarenko Eva Maria Novoa |
| author_facet | Anna Delgado-Tejedor Rebeca Medina Oguzhan Begik Luca Cozzuto Judith López Sandra Blanco Julia Ponomarenko Eva Maria Novoa |
| author_sort | Anna Delgado-Tejedor |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-df6cb01d20354a90b7f1c25f8b404d7d |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-df6cb01d20354a90b7f1c25f8b404d7d2025-01-12T12:29:32ZengNature PortfolioNature Communications2041-17232024-11-0115111910.1038/s41467-024-54368-xNative RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sitesAnna Delgado-Tejedor0Rebeca Medina1Oguzhan Begik2Luca Cozzuto3Judith López4Sandra Blanco5Julia Ponomarenko6Eva Maria Novoa7Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyMolecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of SalamancaMolecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of SalamancaCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyAbstract 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.https://doi.org/10.1038/s41467-024-54368-x |
| spellingShingle | Anna Delgado-Tejedor Rebeca Medina Oguzhan Begik Luca Cozzuto Judith López Sandra Blanco Julia Ponomarenko Eva Maria Novoa Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites Nature Communications |
| title | Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites |
| title_full | Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites |
| title_fullStr | Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites |
| title_full_unstemmed | Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites |
| title_short | Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites |
| title_sort | native rna nanopore sequencing reveals antibiotic induced loss of rrna modifications in the a and p sites |
| url | https://doi.org/10.1038/s41467-024-54368-x |
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