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The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. The 3′ untranslated region (UTR) of this β-CoV contains essential cis-acting RNA elements for the viral genome transcription and replication. These elements include an equilibrium between a...

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Autores principales: Zhao, Junxing, Qiu, Jianming, Aryal, Sadikshya, Hackett, Jennifer L., Wang, Jingxin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766253/
https://www.ncbi.nlm.nih.gov/pubmed/33371200
http://dx.doi.org/10.3390/v12121473
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author Zhao, Junxing
Qiu, Jianming
Aryal, Sadikshya
Hackett, Jennifer L.
Wang, Jingxin
author_facet Zhao, Junxing
Qiu, Jianming
Aryal, Sadikshya
Hackett, Jennifer L.
Wang, Jingxin
author_sort Zhao, Junxing
collection PubMed
description Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. The 3′ untranslated region (UTR) of this β-CoV contains essential cis-acting RNA elements for the viral genome transcription and replication. These elements include an equilibrium between an extended bulged stem-loop (BSL) and a pseudoknot. The existence of such an equilibrium is supported by reverse genetic studies and phylogenetic covariation analysis and is further proposed as a molecular switch essential for the control of the viral RNA polymerase binding. Here, we report the SARS-CoV-2 3′ UTR structures in cells that transcribe the viral UTRs harbored in a minigene plasmid and isolated infectious virions using a chemical probing technique, namely dimethyl sulfate (DMS)-mutational profiling with sequencing (MaPseq). Interestingly, the putative pseudoknotted conformation was not observed, indicating that its abundance in our systems is low in the absence of the viral nonstructural proteins (nsps). Similarly, our results also suggest that another functional cis-acting element, the three-helix junction, cannot stably form. The overall architectures of the viral 3′ UTRs in the infectious virions and the minigene-transfected cells are almost identical.
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spelling pubmed-77662532020-12-28 The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region Zhao, Junxing Qiu, Jianming Aryal, Sadikshya Hackett, Jennifer L. Wang, Jingxin Viruses Article Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. The 3′ untranslated region (UTR) of this β-CoV contains essential cis-acting RNA elements for the viral genome transcription and replication. These elements include an equilibrium between an extended bulged stem-loop (BSL) and a pseudoknot. The existence of such an equilibrium is supported by reverse genetic studies and phylogenetic covariation analysis and is further proposed as a molecular switch essential for the control of the viral RNA polymerase binding. Here, we report the SARS-CoV-2 3′ UTR structures in cells that transcribe the viral UTRs harbored in a minigene plasmid and isolated infectious virions using a chemical probing technique, namely dimethyl sulfate (DMS)-mutational profiling with sequencing (MaPseq). Interestingly, the putative pseudoknotted conformation was not observed, indicating that its abundance in our systems is low in the absence of the viral nonstructural proteins (nsps). Similarly, our results also suggest that another functional cis-acting element, the three-helix junction, cannot stably form. The overall architectures of the viral 3′ UTRs in the infectious virions and the minigene-transfected cells are almost identical. MDPI 2020-12-21 /pmc/articles/PMC7766253/ /pubmed/33371200 http://dx.doi.org/10.3390/v12121473 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
Zhao, Junxing
Qiu, Jianming
Aryal, Sadikshya
Hackett, Jennifer L.
Wang, Jingxin
The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region
title The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region
title_full The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region
title_fullStr The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region
title_full_unstemmed The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region
title_short The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region
title_sort rna architecture of the sars-cov-2 3′-untranslated region
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766253/
https://www.ncbi.nlm.nih.gov/pubmed/33371200
http://dx.doi.org/10.3390/v12121473
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