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Structure and ion-dependent folding of k-junctions
k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of Arabidopsis and Escherichia coli thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Cold Spring Harbor Laboratory Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10573300/ https://www.ncbi.nlm.nih.gov/pubmed/37311599 http://dx.doi.org/10.1261/rna.079678.123 |
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author | Li, Mengxiao Deng, Jie Peng, Xuemei Wang, Jia Wilson, Timothy J. Huang, Lin Lilley, David M.J. |
author_facet | Li, Mengxiao Deng, Jie Peng, Xuemei Wang, Jia Wilson, Timothy J. Huang, Lin Lilley, David M.J. |
author_sort | Li, Mengxiao |
collection | PubMed |
description | k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of Arabidopsis and Escherichia coli thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the Arabidopsis and E. coli riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding. Using X-ray crystallography, we have determined the structure of the DUF-3268 RNA and thus confirmed that it is a k-junction. It also folds upon the addition of metal ions, though requiring a 40-fold lower concentration of either divalent or monovalent ions. The key difference between the DUF-3268 and riboswitch k-junctions is the lack of nucleotides inserted between G1b and A2b in the former. We show that this insertion is primarily responsible for the difference in folding properties. Finally, we show that the DUF-3268 can functionally substitute for the k-junction in the E. coli TPP riboswitch such that the chimera can bind the TPP ligand, although less avidly. |
format | Online Article Text |
id | pubmed-10573300 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-105733002023-10-14 Structure and ion-dependent folding of k-junctions Li, Mengxiao Deng, Jie Peng, Xuemei Wang, Jia Wilson, Timothy J. Huang, Lin Lilley, David M.J. RNA Articles k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of Arabidopsis and Escherichia coli thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the Arabidopsis and E. coli riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding. Using X-ray crystallography, we have determined the structure of the DUF-3268 RNA and thus confirmed that it is a k-junction. It also folds upon the addition of metal ions, though requiring a 40-fold lower concentration of either divalent or monovalent ions. The key difference between the DUF-3268 and riboswitch k-junctions is the lack of nucleotides inserted between G1b and A2b in the former. We show that this insertion is primarily responsible for the difference in folding properties. Finally, we show that the DUF-3268 can functionally substitute for the k-junction in the E. coli TPP riboswitch such that the chimera can bind the TPP ligand, although less avidly. Cold Spring Harbor Laboratory Press 2023-09 /pmc/articles/PMC10573300/ /pubmed/37311599 http://dx.doi.org/10.1261/rna.079678.123 Text en © 2023 Li et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society https://creativecommons.org/licenses/by/4.0/This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Articles Li, Mengxiao Deng, Jie Peng, Xuemei Wang, Jia Wilson, Timothy J. Huang, Lin Lilley, David M.J. Structure and ion-dependent folding of k-junctions |
title | Structure and ion-dependent folding of k-junctions |
title_full | Structure and ion-dependent folding of k-junctions |
title_fullStr | Structure and ion-dependent folding of k-junctions |
title_full_unstemmed | Structure and ion-dependent folding of k-junctions |
title_short | Structure and ion-dependent folding of k-junctions |
title_sort | structure and ion-dependent folding of k-junctions |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10573300/ https://www.ncbi.nlm.nih.gov/pubmed/37311599 http://dx.doi.org/10.1261/rna.079678.123 |
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