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      1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

      research-article
      Author(s): 1 , 2 , 1 , 2 , 1 , 2 , 3 , 1 , 2 , 1 , 2 , 1 , 2 , 4 , 1 , 2 , 2 , 5 , 1 , 2 , 1 , 2 , 1 , 2 , 6 , 1 , 2 , 1 , 2 , 1 , 2 , 1 , 2 , 2 , 5 , 1 , 2 , 2 , 7 , 8 , 1 , 2 , 1 , 2 , 9 , 2 , 5 , 1 , 2 , 10 , 1 , 2 , 1 , 2 , 2 , 5 , 8 , 1 , 2 , 1 , 2 , 2 , 5 , 1 , 2 , , 1 , 2 ,
      Publication date (Electronic):
      Journal: Biomolecular Nmr Assignments
      Publisher: Springer Netherlands
      Keywords: SARS-CoV-2, 5'-UTR, SL1, Solution NMR spectroscopy, COVID19-NMR

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          Abstract

          The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7–33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.

          Supplementary Information

          The online version contains supplementary material available at 10.1007/s12104-021-10047-2.

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          Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy

          Geoffrey Bodenhausen, David Ruben (1980)
          Article 0 comments Cited 206 times – based on 0 reviews     Review now
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            The SARS-CoV-2 RNA–protein interactome in infected human cells

            Nora Schmidt, Caleb Lareau, Hasmik Keshishian … (2020)
            Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.
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              Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid

              Christiane Iserman, Christine A. Roden, Mark A Boerneke … (2020)
              We report that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with viral RNA. N-protein condenses with specific RNA genomic elements under physiological buffer conditions and condensation is enhanced at human body temperatures (33°C and 37°C) and reduced at room temperature (22°C). RNA sequence and structure in specific genomic regions regulate N-protein condensation while other genomic regions promote condensate dissolution, potentially preventing aggregation of the large genome. At low concentrations, N-protein preferentially crosslinks to specific regions with single-stranded RNA flanked by structure and these features specify the location, number, and strength of N-protein binding sites (valency). Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is RNA sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules, and presents a screenable process for identifying antiviral compounds effective against SARS-CoV-2.
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                Author and article information

                Contributors
                Harald Schwalbe:
                ORCID: http://orcid.org/0000-0001-5693-7909
                schwalbe@nmr.uni-frankfurt.de
                Anna Wacker: wacker@nmr.uni-frankfurt.de
                Journal
                Journal ID (nlm-ta): Biomol NMR Assign
                Journal ID (iso-abbrev): Biomol NMR Assign
                Title: Biomolecular Nmr Assignments
                Publisher: Springer Netherlands (Dordrecht )
                ISSN (Print): 1874-2718
                ISSN (Electronic): 1874-270X
                Publication date (Electronic): 28 August 2021
                Publication date PMC-release: 28 August 2021
                Pages: 1-8
                Affiliations
                [1 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Institute for Organic Chemistry and Chemical Biology, , Goethe-University Frankfurt, ; Max-von-Laue- Straße 7, 60438 Frankfurt, Germany
                [2 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Center for Biomolecular Magnetic Resonance (BMRZ), , Goethe-University Frankfurt, ; Max-von-Laue- Straße 7, 60438 Frankfurt, Germany
                [3 ]GRID grid.423218.e, Bruker BioSpin, ; Silberstreifen 4, 76287 Rheinstetten, Germany
                [4 ]GRID grid.434484.b, ISNI 0000 0004 4692 2203, Present Address: BioNTech SE, ; An der Goldgrube 12, 55131 Mainz, Germany
                [5 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Institute for Molecular Biosciences, , Goethe-University Frankfurt, ; Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
                [6 ]GRID grid.13992.30, ISNI 0000 0004 0604 7563, Present Address: Faculty of Chemistry, , Weizmann Institute of Science, ; 7610001 Rehovot, Israel
                [7 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Institute for Biophysical Chemistry, , Goethe-University Frankfurt, ; Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
                [8 ]GRID grid.6546.1, ISNI 0000 0001 0940 1669, Department of Biology, , Technical University of Darmstadt, ; Schnittspahnstraße 10, 64287 Darmstadt, Germany
                [9 ]GRID grid.4709.a, ISNI 0000 0004 0495 846X, Present Address: EMBL Heidelberg, ; Meyerhofstraße 1, 69117 Heidelberg, Germany
                [10 ]Present Address: Deutero GmbH, Am Ring 29, 56288 Kastellaun, Germany
                Author information
                http://orcid.org/0000-0001-5693-7909
                Article
                Publisher ID: 10047
                DOI: 10.1007/s12104-021-10047-2
                PMC ID: 8401371
                PubMed ID: 34453696
                SO-VID: 93afcd43-89be-4f8d-90b3-797895aabece
                Copyright © © The Author(s) 2021
                License:

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 29 June 2021
                Date accepted : 19 August 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100003495, hessisches ministerium für wissenschaft und kunst;
                Award ID: BMRZ
                Award ID: IWB-EFRE-programme 20007375
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001659, deutsche forschungsgemeinschaft;
                Award ID: CRC 902
                Award ID: CLIC
                Award ID: SPP2002
                Award ID: SPP1879
                Award ID: TRR 267
                Award ID: FOR2509
                Award ID: 277478796
                Award ID: 277479031
                Award ID: 392682309
                Award ID: 452632086
                Award ID: 70653611
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100005687, goethe-universität frankfurt am main;
                Award ID: Goethe Corona Fonds
                Funded by: Johann Wolfgang Goethe-Universität, Frankfurt am Main (1022)
                Open Access :

                Open Access funding enabled and organized by Projekt DEAL.

                Categories
                Subject: Article

                ScienceOpen disciplines: Biophysics
                Keywords: sars-cov-2,5'-utr,sl1,solution nmr spectroscopy,covid19-nmr
                Data availability:
                ScienceOpen disciplines: Biophysics
                Keywords: sars-cov-2, 5'-utr, sl1, solution nmr spectroscopy, covid19-nmr

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