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

Anna Delgado-Tejedor, Rebeca Medina, Oguzhan Begik, Luca Cozzuto, Judith López, Sandra Blanco, Julia Ponomarenko and Eva Maria Novoa ()
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Anna Delgado-Tejedor: The Barcelona Institute of Science and Technology
Rebeca Medina: The Barcelona Institute of Science and Technology
Oguzhan Begik: The Barcelona Institute of Science and Technology
Luca Cozzuto: The Barcelona Institute of Science and Technology
Judith López: Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca
Sandra Blanco: Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca
Julia Ponomarenko: The Barcelona Institute of Science and Technology
Eva Maria Novoa: The Barcelona Institute of Science and Technology

Nature Communications, 2024, vol. 15, issue 1, 1-19

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-54368-x

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