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The asymmetry and cooperativity of tandem glycine riboswitch aptamers
Glycine riboswitches utilize both single- and tandem-aptamer architectures. In the tandem system, the relative contribution of each aptamer toward gene regulation is not well understood. To dissect these contributions, the effects of 684 single mutants of a tandem ON switch from Bacillus subtilis we...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161355/ https://www.ncbi.nlm.nih.gov/pubmed/31992591 http://dx.doi.org/10.1261/rna.073577.119 |
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author | Torgerson, Chad D. Hiller, David A. Strobel, Scott A. |
author_facet | Torgerson, Chad D. Hiller, David A. Strobel, Scott A. |
author_sort | Torgerson, Chad D. |
collection | PubMed |
description | Glycine riboswitches utilize both single- and tandem-aptamer architectures. In the tandem system, the relative contribution of each aptamer toward gene regulation is not well understood. To dissect these contributions, the effects of 684 single mutants of a tandem ON switch from Bacillus subtilis were characterized for the wild-type construct and binding site mutations that selectively restrict ligand binding to either the first or second aptamer. Despite the structural symmetry of tandem aptamers, the response to these mutations was frequently asymmetrical. Mutations in the first aptamer often significantly weakened the K(1/2), while several mutations in the second aptamer improved the amplitude. These results demonstrate that this ON switch favors ligand binding to the first aptamer. This is in contrast to the tandem OFF switch variant from Vibrio cholerae, which was previously shown to have preferential binding to its second aptamer. A bioinformatic analysis of tandem glycine riboswitches revealed that the two binding pockets are differentially conserved between ON and OFF switches. Altogether, this indicates that tandem ON switch variants preferentially utilize binding to the first aptamer to promote helical switching, while OFF switch variants favor binding to the second aptamer. The data set also revealed a cooperative glycine response when both binding pockets were maximally stabilized with three GC base pairs. This indicates a cooperative response may sometimes be obfuscated by a difference in the affinities of the two aptamers. This conditional cooperativity provides an additional layer of tunability to tandem glycine riboswitches that adds to their versatility as genetic switches. |
format | Online Article Text |
id | pubmed-7161355 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-71613552021-05-01 The asymmetry and cooperativity of tandem glycine riboswitch aptamers Torgerson, Chad D. Hiller, David A. Strobel, Scott A. RNA Article Glycine riboswitches utilize both single- and tandem-aptamer architectures. In the tandem system, the relative contribution of each aptamer toward gene regulation is not well understood. To dissect these contributions, the effects of 684 single mutants of a tandem ON switch from Bacillus subtilis were characterized for the wild-type construct and binding site mutations that selectively restrict ligand binding to either the first or second aptamer. Despite the structural symmetry of tandem aptamers, the response to these mutations was frequently asymmetrical. Mutations in the first aptamer often significantly weakened the K(1/2), while several mutations in the second aptamer improved the amplitude. These results demonstrate that this ON switch favors ligand binding to the first aptamer. This is in contrast to the tandem OFF switch variant from Vibrio cholerae, which was previously shown to have preferential binding to its second aptamer. A bioinformatic analysis of tandem glycine riboswitches revealed that the two binding pockets are differentially conserved between ON and OFF switches. Altogether, this indicates that tandem ON switch variants preferentially utilize binding to the first aptamer to promote helical switching, while OFF switch variants favor binding to the second aptamer. The data set also revealed a cooperative glycine response when both binding pockets were maximally stabilized with three GC base pairs. This indicates a cooperative response may sometimes be obfuscated by a difference in the affinities of the two aptamers. This conditional cooperativity provides an additional layer of tunability to tandem glycine riboswitches that adds to their versatility as genetic switches. Cold Spring Harbor Laboratory Press 2020-05 /pmc/articles/PMC7161355/ /pubmed/31992591 http://dx.doi.org/10.1261/rna.073577.119 Text en © 2020 Torgerson et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Article Torgerson, Chad D. Hiller, David A. Strobel, Scott A. The asymmetry and cooperativity of tandem glycine riboswitch aptamers |
title | The asymmetry and cooperativity of tandem glycine riboswitch aptamers |
title_full | The asymmetry and cooperativity of tandem glycine riboswitch aptamers |
title_fullStr | The asymmetry and cooperativity of tandem glycine riboswitch aptamers |
title_full_unstemmed | The asymmetry and cooperativity of tandem glycine riboswitch aptamers |
title_short | The asymmetry and cooperativity of tandem glycine riboswitch aptamers |
title_sort | asymmetry and cooperativity of tandem glycine riboswitch aptamers |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161355/ https://www.ncbi.nlm.nih.gov/pubmed/31992591 http://dx.doi.org/10.1261/rna.073577.119 |
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