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...
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doaj-145d541650a948c4b6eb1c2eba10cf642020-11-25T03:57:09ZengMDPI AGViruses1999-49152020-10-01121232123210.3390/v12111232New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus GenomeMariola Dutkiewicz0Jakub Kuczynski1Michal Jarzab2Aleksandra Stachowiak3Agata Swiatkowska4Institute of Bioorganic Chemistry Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, PolandInstitute of Bioorganic Chemistry Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, PolandInstitute of Bioorganic Chemistry Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, PolandInstitute of Bioorganic Chemistry Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, PolandInstitute of Bioorganic Chemistry Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, PolandHere 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 <i>cis</i>-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<sup>2+</sup>, 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.https://www.mdpi.com/1999-4915/12/11/1232enterovirusCoxsackie B3 viruscoxsackievirus B3CVB3RNA secondary structureRNA motif |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Mariola Dutkiewicz Jakub Kuczynski Michal Jarzab Aleksandra Stachowiak Agata Swiatkowska |
spellingShingle |
Mariola Dutkiewicz Jakub Kuczynski Michal Jarzab Aleksandra Stachowiak Agata Swiatkowska New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome Viruses enterovirus Coxsackie B3 virus coxsackievirus B3 CVB3 RNA secondary structure RNA motif |
author_facet |
Mariola Dutkiewicz Jakub Kuczynski Michal Jarzab Aleksandra Stachowiak Agata Swiatkowska |
author_sort |
Mariola Dutkiewicz |
title |
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_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_sort |
new rna structural elements identified in the coding region of the coxsackie b3 virus genome |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2020-10-01 |
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 <i>cis</i>-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<sup>2+</sup>, 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. |
topic |
enterovirus Coxsackie B3 virus coxsackievirus B3 CVB3 RNA secondary structure RNA motif |
url |
https://www.mdpi.com/1999-4915/12/11/1232 |
work_keys_str_mv |
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