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

• Published in: Viruses Vol. 12; no. 12; p. 1473
• Main Authors: Zhao, Junxing, Qiu, Jianming, Aryal, Sadikshya, Hackett, Jennifer, Wang, Jingxin
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 21.12.2020; MDPI
• Subjects: 3' Untranslated regions; 3' Untranslated Regions - genetics; Animals; Base Sequence; Binding sites; Cell Line; Conformation; Conserved Sequence; Coronaviruses; COVID-19; COVID-19 - virology; COVID-19 infection; Cricetinae; Deoxyribonucleic acid; Dimethyl sulfate; DMS; DMS-MaPseq; DNA; DNA methylation; DNA-directed RNA polymerase; DREEM; Genetic analysis; Genomes; High-Throughput Nucleotide Sequencing; Humans; Mesocricetus; Models, Molecular; Nonstructural proteins; Nucleic Acid Conformation; Pandemics; Phylogeny; Plasmids; Point Mutation; Proteins; regulatory sequences; reverse genetics; Reverse Genetics - methods; RNA; RNA polymerase; RNA, Viral - genetics; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - physiology; Sequence Alignment; Sequence Homology, Nucleic Acid; Severe acute respiratory syndrome coronavirus 2; ShapeKnots; Sulfuric Acid Esters; Transcription; Transcription, Genetic; viral genome; Virion - genetics; Virion - physiology; Virions; Viruses; United States > US; COVID-19; SARS-CoV-2; pseudoknot; 3′ UTR; DMS-MaPseq; minigene; three-helix junction; DMS; DREEM; ShapeKnots
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v12121473

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.