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Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput...

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Autores principales: Gosavi, Devadatta, Wower, Iwona, Beckmann, Irene K., Hofacker, Ivo L., Wower, Jacek, Wolfinger, Michael T., Sztuba-Solinska, Joanna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8986297/
https://www.ncbi.nlm.nih.gov/pubmed/35380920
http://dx.doi.org/10.1080/15476286.2022.2058818
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author Gosavi, Devadatta
Wower, Iwona
Beckmann, Irene K.
Hofacker, Ivo L.
Wower, Jacek
Wolfinger, Michael T.
Sztuba-Solinska, Joanna
author_facet Gosavi, Devadatta
Wower, Iwona
Beckmann, Irene K.
Hofacker, Ivo L.
Wower, Jacek
Wolfinger, Michael T.
Sztuba-Solinska, Joanna
author_sort Gosavi, Devadatta
collection PubMed
description The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and in silico modelling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA in solution forms a modular architecture composed of three distinct structural domains (I–III). Two regions within domain III are represented in tertiary interactions to form an H-type pseudoknot. Computational modelling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many Pestivirus species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.
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spelling pubmed-89862972022-04-07 Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site Gosavi, Devadatta Wower, Iwona Beckmann, Irene K. Hofacker, Ivo L. Wower, Jacek Wolfinger, Michael T. Sztuba-Solinska, Joanna RNA Biol Research Paper The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and in silico modelling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA in solution forms a modular architecture composed of three distinct structural domains (I–III). Two regions within domain III are represented in tertiary interactions to form an H-type pseudoknot. Computational modelling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many Pestivirus species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element. Taylor & Francis 2022-04-05 /pmc/articles/PMC8986297/ /pubmed/35380920 http://dx.doi.org/10.1080/15476286.2022.2058818 Text en © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://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/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Paper
Gosavi, Devadatta
Wower, Iwona
Beckmann, Irene K.
Hofacker, Ivo L.
Wower, Jacek
Wolfinger, Michael T.
Sztuba-Solinska, Joanna
Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
title Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
title_full Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
title_fullStr Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
title_full_unstemmed Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
title_short Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
title_sort insights into the secondary and tertiary structure of the bovine viral diarrhea virus internal ribosome entry site
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8986297/
https://www.ncbi.nlm.nih.gov/pubmed/35380920
http://dx.doi.org/10.1080/15476286.2022.2058818
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