Tags

Type your tag names separated by a space and hit enter

The RNA Architecture of the SARS-CoV-2 3'-Untranslated Region.
Viruses. 2020 12 21; 12(12)V

Abstract

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.

Authors+Show Affiliations

Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA.Department of Microbiology, Molecular Genetics & Immunology, University of Kansas Medical Center, Kansas, KS 66160, USA.Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA.Genome Sequencing Core, University of Kansas, Lawrence, KS 66045, USA.Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA.

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

33371200

Citation

Zhao, Junxing, et al. "The RNA Architecture of the SARS-CoV-2 3'-Untranslated Region." Viruses, vol. 12, no. 12, 2020.
Zhao J, Qiu J, Aryal S, et al. The RNA Architecture of the SARS-CoV-2 3'-Untranslated Region. Viruses. 2020;12(12).
Zhao, J., Qiu, J., Aryal, S., Hackett, J. L., & Wang, J. (2020). The RNA Architecture of the SARS-CoV-2 3'-Untranslated Region. Viruses, 12(12). https://doi.org/10.3390/v12121473
Zhao J, et al. The RNA Architecture of the SARS-CoV-2 3'-Untranslated Region. Viruses. 2020 12 21;12(12) PubMed PMID: 33371200.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The RNA Architecture of the SARS-CoV-2 3'-Untranslated Region. AU - Zhao,Junxing, AU - Qiu,Jianming, AU - Aryal,Sadikshya, AU - Hackett,Jennifer L, AU - Wang,Jingxin, Y1 - 2020/12/21/ PY - 2020/10/23/received PY - 2020/12/11/revised PY - 2020/12/15/accepted PY - 2020/12/29/entrez PY - 2020/12/30/pubmed PY - 2021/1/12/medline KW - 3′ UTR KW - COVID-19 KW - DMS KW - DMS-MaPseq KW - DREEM KW - SARS-CoV-2 KW - ShapeKnots KW - minigene KW - pseudoknot KW - three-helix junction JF - Viruses JO - Viruses VL - 12 IS - 12 N2 - 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. SN - 1999-4915 UR - https://www.unboundmedicine.com/medline/citation/33371200/The_RNA_Architecture_of_the_SARS_CoV_2_3'_Untranslated_Region_ L2 - https://www.mdpi.com/resolver?pii=v12121473 DB - PRIME DP - Unbound Medicine ER -