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Article

New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome

Institute of Bioorganic Chemistry Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland
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Viruses 2020, 12(11), 1232; https://doi.org/10.3390/v12111232
Received: 6 October 2020 / Revised: 27 October 2020 / Accepted: 28 October 2020 / Published: 30 October 2020
(This article belongs to the Special Issue Enteroviruses 2021)
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 Pb2+, 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. View Full-Text
Keywords: enterovirus; Coxsackie B3 virus; coxsackievirus B3; CVB3; RNA secondary structure; RNA motif; RNA structural element; RNA structure of coding region; RNA virus; RNA–protein interaction enterovirus; Coxsackie B3 virus; coxsackievirus B3; CVB3; RNA secondary structure; RNA motif; RNA structural element; RNA structure of coding region; RNA virus; RNA–protein interaction
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MDPI and ACS Style

Dutkiewicz, M.; Kuczynski, J.; Jarzab, M.; Stachowiak, A.; Swiatkowska, A. New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome. Viruses 2020, 12, 1232. https://doi.org/10.3390/v12111232

AMA Style

Dutkiewicz M, Kuczynski J, Jarzab M, Stachowiak A, Swiatkowska A. New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome. Viruses. 2020; 12(11):1232. https://doi.org/10.3390/v12111232

Chicago/Turabian Style

Dutkiewicz, Mariola, Jakub Kuczynski, Michal Jarzab, Aleksandra Stachowiak, and Agata Swiatkowska. 2020. "New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome" Viruses 12, no. 11: 1232. https://doi.org/10.3390/v12111232

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