A riboswitch separated from its ribosome-binding site still regulates translation
Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crys...
Published in: | Nucleic Acids Research |
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Oxford University Press (OUP)
2023
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Online Access: | http://dx.doi.org/10.1093/nar/gkad056 https://academic.oup.com/nar/article-pdf/51/5/2464/49538015/gkad056.pdf |
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croxfordunivpr:10.1093/nar/gkad056 2024-06-23T07:47:54+00:00 A riboswitch separated from its ribosome-binding site still regulates translation Schroeder, Griffin M Akinyemi, Olayinka Malik, Jeffrey Focht, Caroline M Pritchett, Elizabeth M Baker, Cameron D McSally, James P Jenkins, Jermaine L Mathews, David H Wedekind, Joseph E National Institutes of Health Elon Huntington Hooker Fellowship U.S. Department of Energy Basic Energy Sciences DOE Office of Biological and Environmental Research National Institute of General Medical Sciences University of Rochester Center for Integrated Research Computing 2023 http://dx.doi.org/10.1093/nar/gkad056 https://academic.oup.com/nar/article-pdf/51/5/2464/49538015/gkad056.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by-nc/4.0/ Nucleic Acids Research volume 51, issue 5, page 2464-2484 ISSN 0305-1048 1362-4962 journal-article 2023 croxfordunivpr https://doi.org/10.1093/nar/gkad056 2024-06-04T06:13:49Z Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10–G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch—akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold. Article in Journal/Newspaper Antarc* Oxford University Press Nucleic Acids Research |
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Oxford University Press |
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English |
description |
Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10–G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch—akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold. |
author2 |
National Institutes of Health Elon Huntington Hooker Fellowship U.S. Department of Energy Basic Energy Sciences DOE Office of Biological and Environmental Research National Institute of General Medical Sciences University of Rochester Center for Integrated Research Computing |
format |
Article in Journal/Newspaper |
author |
Schroeder, Griffin M Akinyemi, Olayinka Malik, Jeffrey Focht, Caroline M Pritchett, Elizabeth M Baker, Cameron D McSally, James P Jenkins, Jermaine L Mathews, David H Wedekind, Joseph E |
spellingShingle |
Schroeder, Griffin M Akinyemi, Olayinka Malik, Jeffrey Focht, Caroline M Pritchett, Elizabeth M Baker, Cameron D McSally, James P Jenkins, Jermaine L Mathews, David H Wedekind, Joseph E A riboswitch separated from its ribosome-binding site still regulates translation |
author_facet |
Schroeder, Griffin M Akinyemi, Olayinka Malik, Jeffrey Focht, Caroline M Pritchett, Elizabeth M Baker, Cameron D McSally, James P Jenkins, Jermaine L Mathews, David H Wedekind, Joseph E |
author_sort |
Schroeder, Griffin M |
title |
A riboswitch separated from its ribosome-binding site still regulates translation |
title_short |
A riboswitch separated from its ribosome-binding site still regulates translation |
title_full |
A riboswitch separated from its ribosome-binding site still regulates translation |
title_fullStr |
A riboswitch separated from its ribosome-binding site still regulates translation |
title_full_unstemmed |
A riboswitch separated from its ribosome-binding site still regulates translation |
title_sort |
riboswitch separated from its ribosome-binding site still regulates translation |
publisher |
Oxford University Press (OUP) |
publishDate |
2023 |
url |
http://dx.doi.org/10.1093/nar/gkad056 https://academic.oup.com/nar/article-pdf/51/5/2464/49538015/gkad056.pdf |
genre |
Antarc* |
genre_facet |
Antarc* |
op_source |
Nucleic Acids Research volume 51, issue 5, page 2464-2484 ISSN 0305-1048 1362-4962 |
op_rights |
https://creativecommons.org/licenses/by-nc/4.0/ |
op_doi |
https://doi.org/10.1093/nar/gkad056 |
container_title |
Nucleic Acids Research |
_version_ |
1802638149481922560 |