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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...

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Autores principales: García-Sacristán, Ana, Moreno, Miguel, Ariza-Mateos, Ascensión, López-Camacho, Elena, Jáudenes, Rosa M., Vázquez, Luis, Gómez, Jordi, Martín-Gago, José Ángel, Briones, Carlos
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
RNA
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.
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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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