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A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy
The 5′ untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II–IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still availab...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288189/ https://www.ncbi.nlm.nih.gov/pubmed/25510496 http://dx.doi.org/10.1093/nar/gku1299 |
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author | García-Sacristán, Ana Moreno, Miguel Ariza-Mateos, Ascensión López-Camacho, Elena Jáudenes, Rosa M. Vázquez, Luis Gómez, Jordi Martín-Gago, José Ángel Briones, Carlos |
author_facet | García-Sacristán, Ana Moreno, Miguel Ariza-Mateos, Ascensión López-Camacho, Elena Jáudenes, Rosa M. Vázquez, Luis Gómez, Jordi Martín-Gago, José Ángel Briones, Carlos |
author_sort | García-Sacristán, Ana |
collection | PubMed |
description | The 5′ untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II–IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI. The 574 nt-long molecule analyzed underwent an unexpected, Mg(2+)-induced switch between two alternative conformations: from ‘open’, elongated morphologies at 0–2 mM Mg(2+) concentration to a ‘closed’, comma-shaped conformation at 4–6 mM Mg(2+). This sharp transition, confirmed by gel-shift analysis and partial RNase T1 cleavage, was hindered by the microRNA miR-122. The comma-shaped IRES-574 molecules visualized at 4–6 mM Mg(2+) in the absence of miR-122 showed two arms. Our data support that the first arm would contain domain III, while the second one would be composed of domains (I–II)+(V–VI) thanks to a long-range RNA interaction between the I-II spacer and the basal region of domain VI. This reinforces the previously described structural continuity between the HCV IRES and its flanking domains I, V and VI. |
format | Online Article Text |
id | pubmed-4288189 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-42881892015-02-19 A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy García-Sacristán, Ana Moreno, Miguel Ariza-Mateos, Ascensión López-Camacho, Elena Jáudenes, Rosa M. Vázquez, Luis Gómez, Jordi Martín-Gago, José Ángel Briones, Carlos Nucleic Acids Res RNA The 5′ untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II–IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI. The 574 nt-long molecule analyzed underwent an unexpected, Mg(2+)-induced switch between two alternative conformations: from ‘open’, elongated morphologies at 0–2 mM Mg(2+) concentration to a ‘closed’, comma-shaped conformation at 4–6 mM Mg(2+). This sharp transition, confirmed by gel-shift analysis and partial RNase T1 cleavage, was hindered by the microRNA miR-122. The comma-shaped IRES-574 molecules visualized at 4–6 mM Mg(2+) in the absence of miR-122 showed two arms. Our data support that the first arm would contain domain III, while the second one would be composed of domains (I–II)+(V–VI) thanks to a long-range RNA interaction between the I-II spacer and the basal region of domain VI. This reinforces the previously described structural continuity between the HCV IRES and its flanking domains I, V and VI. Oxford University Press 2015-01-09 2014-12-15 /pmc/articles/PMC4288189/ /pubmed/25510496 http://dx.doi.org/10.1093/nar/gku1299 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | RNA García-Sacristán, Ana Moreno, Miguel Ariza-Mateos, Ascensión López-Camacho, Elena Jáudenes, Rosa M. Vázquez, Luis Gómez, Jordi Martín-Gago, José Ángel Briones, Carlos A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy |
title | A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy |
title_full | A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy |
title_fullStr | A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy |
title_full_unstemmed | A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy |
title_short | A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy |
title_sort | magnesium-induced rna conformational switch at the internal ribosome entry site of hepatitis c virus genome visualized by atomic force microscopy |
topic | RNA |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288189/ https://www.ncbi.nlm.nih.gov/pubmed/25510496 http://dx.doi.org/10.1093/nar/gku1299 |
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