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Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene

Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluo...

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Autores principales: Lee, Juhyun, Sung, Si-Eun, Lee, Janghyun, Kang, Jin Young, Lee, Joon-Hwa, Choi, Byong-Seok
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8004769/
https://www.ncbi.nlm.nih.gov/pubmed/33810132
http://dx.doi.org/10.3390/ijms22063234
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author Lee, Juhyun
Sung, Si-Eun
Lee, Janghyun
Kang, Jin Young
Lee, Joon-Hwa
Choi, Byong-Seok
author_facet Lee, Juhyun
Sung, Si-Eun
Lee, Janghyun
Kang, Jin Young
Lee, Joon-Hwa
Choi, Byong-Seok
author_sort Lee, Juhyun
collection PubMed
description Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.
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spelling pubmed-80047692021-03-29 Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene Lee, Juhyun Sung, Si-Eun Lee, Janghyun Kang, Jin Young Lee, Joon-Hwa Choi, Byong-Seok Int J Mol Sci Article Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism. MDPI 2021-03-22 /pmc/articles/PMC8004769/ /pubmed/33810132 http://dx.doi.org/10.3390/ijms22063234 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lee, Juhyun
Sung, Si-Eun
Lee, Janghyun
Kang, Jin Young
Lee, Joon-Hwa
Choi, Byong-Seok
Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene
title Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene
title_full Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene
title_fullStr Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene
title_full_unstemmed Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene
title_short Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene
title_sort base-pair opening dynamics study of fluoride riboswitch in the bacillus cereus crcb gene
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8004769/
https://www.ncbi.nlm.nih.gov/pubmed/33810132
http://dx.doi.org/10.3390/ijms22063234
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