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

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Issue Date
2020-12-21Author
Zhao, Junxing
Qiu, Jianming
Aryal, Sadikshya
Hackett, Jennifer L.
Wang, Jingxin
Publisher
MDPI
Type
Article
Article Version
Scholarly/refereed, publisher version
Rights
© 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.
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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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Citation
Zhao, J.; Qiu, J.; Aryal, S.; Hackett, J.L.; Wang, J. The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region. Viruses 2020, 12, 1473. https://doi.org/10.3390/v12121473
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