Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation

The internal ribosome entry site (IRES) element located at the 5’untranslated genomic region of various RNA viruses mediates cap-independent initiation of translation. Picornavirus IRES activity is highly dependent on both its structural organization and its interaction with host factors. Small mole...

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Detalles Bibliográficos
Autores: Lozano, Gloria, Trapote, Alejandro, Ramajo, Jorge, Elduque, Xavier, Grandas, Anna, Robles, Jordi, Pedroso, Enrique, Martínez-Salas, Encarnación
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2015
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/139584
Acceso en línea:http://hdl.handle.net/10261/139584
Access Level:acceso abierto
Palabra clave:antiviral molecules
fluorescence binding assay
IRES elements
picornavirus
RNA ligands
RNA structure
SHAPE probing
translation initiation
2-aminobenzimidazole
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repository_id_str
spelling Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translationLozano, GloriaTrapote, AlejandroRamajo, JorgeElduque, XavierGrandas, AnnaRobles, JordiPedroso, EnriqueMartínez-Salas, Encarnaciónantiviral moleculesfluorescence binding assayIRES elementspicornavirusRNA ligandsRNA structureSHAPE probingtranslation initiation2-aminobenzimidazoleThe internal ribosome entry site (IRES) element located at the 5’untranslated genomic region of various RNA viruses mediates cap-independent initiation of translation. Picornavirus IRES activity is highly dependent on both its structural organization and its interaction with host factors. Small molecules able to interfere with RNA function are valuable candidates for antiviral agents. Here we show that a small molecule based on benzimidazole (IRAB) inhibited foot-andmouth disease virus (FMDV) IRES-dependent protein synthesis in cells transfected with infectious RNA leading to a decrease of the virus titer, which was higher than that induced by a structurally related benzimidazole derivative. Interestingly, IRAB preferentially inhibited IRES-dependent translation in cell free systems in a dose-dependent manner. RNA structural analysis by SHAPE demonstrated an increased local flexibility of the IRES structure upon incubation with IRAB, which affected 3 stem-loops (SL) of domain 3. Fluorescence binding assays conducted with individual aminopurinelabeled oligoribonucleotides indicated that the SL3A binds IRAB (EC 18 μM). Taken together, the results derived from SHAPE reactivity and fluorescence binding assays suggested that the target site of IRAB within the FMDV IRES might be a folded RNA structure that involves the entire apical region of domain 3. Our data suggest that the conformational changes induced by this compound on a specific region of the IRES structure which is essential for its activity is, at least in part, responsible for the reduced IRES efficiency observed in cell free lysates and, particularly, in RNA-transfected cells.Ministerio de Economia y Competitividad (MINECO), and by an Institutional grant from Fundación Ramón ArecesPeer ReviewedLandes BioscienceMinisterio de Economía y Competitividad (España)Fundación Ramón ArecesConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2016201620152016info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/139584reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1395842026-05-22T06:33:51Z
dc.title.none.fl_str_mv Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation
title Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation
spellingShingle Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation
Lozano, Gloria
antiviral molecules
fluorescence binding assay
IRES elements
picornavirus
RNA ligands
RNA structure
SHAPE probing
translation initiation
2-aminobenzimidazole
title_short Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation
title_full Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation
title_fullStr Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation
title_full_unstemmed Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation
title_sort Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation
dc.creator.none.fl_str_mv Lozano, Gloria
Trapote, Alejandro
Ramajo, Jorge
Elduque, Xavier
Grandas, Anna
Robles, Jordi
Pedroso, Enrique
Martínez-Salas, Encarnación
author Lozano, Gloria
author_facet Lozano, Gloria
Trapote, Alejandro
Ramajo, Jorge
Elduque, Xavier
Grandas, Anna
Robles, Jordi
Pedroso, Enrique
Martínez-Salas, Encarnación
author_role author
author2 Trapote, Alejandro
Ramajo, Jorge
Elduque, Xavier
Grandas, Anna
Robles, Jordi
Pedroso, Enrique
Martínez-Salas, Encarnación
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Economía y Competitividad (España)
Fundación Ramón Areces
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv antiviral molecules
fluorescence binding assay
IRES elements
picornavirus
RNA ligands
RNA structure
SHAPE probing
translation initiation
2-aminobenzimidazole
topic antiviral molecules
fluorescence binding assay
IRES elements
picornavirus
RNA ligands
RNA structure
SHAPE probing
translation initiation
2-aminobenzimidazole
description The internal ribosome entry site (IRES) element located at the 5’untranslated genomic region of various RNA viruses mediates cap-independent initiation of translation. Picornavirus IRES activity is highly dependent on both its structural organization and its interaction with host factors. Small molecules able to interfere with RNA function are valuable candidates for antiviral agents. Here we show that a small molecule based on benzimidazole (IRAB) inhibited foot-andmouth disease virus (FMDV) IRES-dependent protein synthesis in cells transfected with infectious RNA leading to a decrease of the virus titer, which was higher than that induced by a structurally related benzimidazole derivative. Interestingly, IRAB preferentially inhibited IRES-dependent translation in cell free systems in a dose-dependent manner. RNA structural analysis by SHAPE demonstrated an increased local flexibility of the IRES structure upon incubation with IRAB, which affected 3 stem-loops (SL) of domain 3. Fluorescence binding assays conducted with individual aminopurinelabeled oligoribonucleotides indicated that the SL3A binds IRAB (EC 18 μM). Taken together, the results derived from SHAPE reactivity and fluorescence binding assays suggested that the target site of IRAB within the FMDV IRES might be a folded RNA structure that involves the entire apical region of domain 3. Our data suggest that the conformational changes induced by this compound on a specific region of the IRES structure which is essential for its activity is, at least in part, responsible for the reduced IRES efficiency observed in cell free lysates and, particularly, in RNA-transfected cells.
publishDate 2015
dc.date.none.fl_str_mv 2015
2016
2016
2016
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/139584
url http://hdl.handle.net/10261/139584
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Landes Bioscience
publisher.none.fl_str_mv Landes Bioscience
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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