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New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome
Here we present a set of new structural elements formed within the open reading frame of the virus, which are highly probable, evolutionarily conserved and may interact with host proteins. This work focused on the coding regions of the CVB3 genome (particularly the V4-, V1-, 2C-, and 3D-coding regio...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7692623/ https://www.ncbi.nlm.nih.gov/pubmed/33143071 http://dx.doi.org/10.3390/v12111232 |
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author | Dutkiewicz, Mariola Kuczynski, Jakub Jarzab, Michal Stachowiak, Aleksandra Swiatkowska, Agata |
author_facet | Dutkiewicz, Mariola Kuczynski, Jakub Jarzab, Michal Stachowiak, Aleksandra Swiatkowska, Agata |
author_sort | Dutkiewicz, Mariola |
collection | PubMed |
description | Here we present a set of new structural elements formed within the open reading frame of the virus, which are highly probable, evolutionarily conserved and may interact with host proteins. This work focused on the coding regions of the CVB3 genome (particularly the V4-, V1-, 2C-, and 3D-coding regions), which, with the exception of the cis-acting replication element (CRE), have not yet been subjected to experimental analysis of their structures. The SHAPE technique, chemical modification with DMS and RNA cleavage with Pb(2+), were performed in order to characterize the RNA structure. The experimental results were used to improve the computer prediction of the structural models, whereas a phylogenetic analysis was performed to check universality of the newly identified structural elements for twenty CVB3 genomes and 11 other enteroviruses. Some of the RNA motifs turned out to be conserved among different enteroviruses. We also observed that the 3′-terminal region of the genome tends to dimerize in a magnesium concentration-dependent manner. RNA affinity chromatography was used to confirm RNA–protein interactions hypothesized by database searches, leading to the discovery of several interactions, which may be important for virus propagation. |
format | Online Article Text |
id | pubmed-7692623 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-76926232020-11-28 New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome Dutkiewicz, Mariola Kuczynski, Jakub Jarzab, Michal Stachowiak, Aleksandra Swiatkowska, Agata Viruses Article Here we present a set of new structural elements formed within the open reading frame of the virus, which are highly probable, evolutionarily conserved and may interact with host proteins. This work focused on the coding regions of the CVB3 genome (particularly the V4-, V1-, 2C-, and 3D-coding regions), which, with the exception of the cis-acting replication element (CRE), have not yet been subjected to experimental analysis of their structures. The SHAPE technique, chemical modification with DMS and RNA cleavage with Pb(2+), were performed in order to characterize the RNA structure. The experimental results were used to improve the computer prediction of the structural models, whereas a phylogenetic analysis was performed to check universality of the newly identified structural elements for twenty CVB3 genomes and 11 other enteroviruses. Some of the RNA motifs turned out to be conserved among different enteroviruses. We also observed that the 3′-terminal region of the genome tends to dimerize in a magnesium concentration-dependent manner. RNA affinity chromatography was used to confirm RNA–protein interactions hypothesized by database searches, leading to the discovery of several interactions, which may be important for virus propagation. MDPI 2020-10-30 /pmc/articles/PMC7692623/ /pubmed/33143071 http://dx.doi.org/10.3390/v12111232 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Dutkiewicz, Mariola Kuczynski, Jakub Jarzab, Michal Stachowiak, Aleksandra Swiatkowska, Agata New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome |
title | New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome |
title_full | New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome |
title_fullStr | New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome |
title_full_unstemmed | New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome |
title_short | New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome |
title_sort | new rna structural elements identified in the coding region of the coxsackie b3 virus genome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7692623/ https://www.ncbi.nlm.nih.gov/pubmed/33143071 http://dx.doi.org/10.3390/v12111232 |
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