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Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain

The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading f...

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Autores principales: Koch, Miriam, Willi, Jessica, Pradère, Ugo, Hall, Jonathan, Polacek, Norbert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499644/
https://www.ncbi.nlm.nih.gov/pubmed/28369621
http://dx.doi.org/10.1093/nar/gkx195
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author Koch, Miriam
Willi, Jessica
Pradère, Ugo
Hall, Jonathan
Polacek, Norbert
author_facet Koch, Miriam
Willi, Jessica
Pradère, Ugo
Hall, Jonathan
Polacek, Norbert
author_sort Koch, Miriam
collection PubMed
description The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson–Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation.
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spelling pubmed-54996442017-07-10 Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain Koch, Miriam Willi, Jessica Pradère, Ugo Hall, Jonathan Polacek, Norbert Nucleic Acids Res RNA The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson–Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation. Oxford University Press 2017-06-20 2017-03-21 /pmc/articles/PMC5499644/ /pubmed/28369621 http://dx.doi.org/10.1093/nar/gkx195 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle RNA
Koch, Miriam
Willi, Jessica
Pradère, Ugo
Hall, Jonathan
Polacek, Norbert
Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain
title Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain
title_full Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain
title_fullStr Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain
title_full_unstemmed Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain
title_short Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain
title_sort critical 23s rrna interactions for macrolide-dependent ribosome stalling on the ermcl nascent peptide chain
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499644/
https://www.ncbi.nlm.nih.gov/pubmed/28369621
http://dx.doi.org/10.1093/nar/gkx195
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