1 H,  13 C and  15 N chemical shift assignment of the stem-loop 5a from the 5′-UTR of SARS-CoV-2

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Abstract

The SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5′- and 3′-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect RNA translation and replication. The 31 nucleotide (nt) long highly conserved stem-loop 5a (SL5a) is located within the 5′-untranslated region (5′-UTR) important for viral replication. SL5a features a U-rich asymmetric bulge and is capped with a 5′-UUUCGU-3′ hexaloop, which is also found in stem-loop 5b (SL5b). We herein report the extensive ¹H, ¹³C and ¹⁵N resonance assignment of SL5a as basis for in-depth structural studies by solution NMR spectroscopy.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12104-021-10007-w.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and pathogenic coronavirus that emerged in late 2019 and has caused a pandemic of acute respiratory disease, named ‘coronavirus disease 2019’ (COVID-19), which threatens human health and public safety. In this Review, we describe the basic virology of SARS-CoV-2, including genomic characteristics and receptor use, highlighting its key difference from previously known coronaviruses. We summarize current knowledge of clinical, epidemiological and pathological features of COVID-19, as well as recent progress in animal models and antiviral treatment approaches for SARS-CoV-2 infection. We also discuss the potential wildlife hosts and zoonotic origin of this emerging virus in detail.

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Coronavirus biology and replication: implications for SARS-CoV-2

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The SARS-CoV-2 pandemic and its unprecedented global societal and economic disruptive impact has marked the third zoonotic introduction of a highly pathogenic coronavirus into the human population. Although the previous coronavirus SARS-CoV and MERS-CoV epidemics raised awareness of the need for clinically available therapeutic or preventive interventions, to date, no treatments with proven efficacy are available. The development of effective intervention strategies relies on the knowledge of molecular and cellular mechanisms of coronavirus infections, which highlights the significance of studying virus–host interactions at the molecular level to identify targets for antiviral intervention and to elucidate critical viral and host determinants that are decisive for the development of severe disease. In this Review, we summarize the first discoveries that shape our current understanding of SARS-CoV-2 infection throughout the intracellular viral life cycle and relate that to our knowledge of coronavirus biology. The elucidation of similarities and differences between SARS-CoV-2 and other coronaviruses will support future preparedness and strategies to combat coronavirus infections.

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NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

Woonghee Lee, Marco Tonelli, John Markley (2014)

Summary: SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for NMR data analysis, despite the fact that development of the package by its originators ceased in 2001. We have taken over the development of this package and describe NMRFAM-SPARKY, which implements new functions reflecting advances in the biomolecular NMR field. NMRFAM-SPARKY has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak simulation and graphical assignment determination. These tools, along with chemical shift predictions from the PACSY database, greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web servers including, PECAN , PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S. Availability and implementation: The software package, along with binary and source codes, if desired, can be downloaded freely from http://pine.nmrfam.wisc.edu/download_packages.html. Instruction manuals and video tutorials can be found at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm. Contact: whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Harald Schwalbe:

ORCID: http://orcid.org/0000-0001-5693-7909

Schwalbe@nmr.uni-frankfurt.de , covid19-nmr@dlist.server.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): 23 January 2021

Publication date PMC-release: 23 January 2021

Pages: 1-9

Affiliations

[1 ]GRID grid.6546.1, ISNI 0000 0001 0940 1669, Department of Biology, , Technical University of Darmstadt, ; Schnittspahnstr. 10, 64287 Darmstadt, Germany

[2 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Institute for Organic Chemistry and Chemical Biology, , Johann Wolfgang Goethe-University Frankfurt, ; Max-von-Laue-Str. 7, 60438 Frankfurt/M., Germany

[3 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Institute for Molecular Biosciences, , Johann Wolfgang Goethe-University Frankfurt, ; Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany

[4 ]GRID grid.7839.5, ISNI 0000 0004 1936 9721, Center for Biomolecular Magnetic Resonance (BMRZ), , Johann Wolfgang Goethe-University Frankfurt, ; Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany

[5 ]GRID grid.4709.a, ISNI 0000 0004 0495 846X, Present Address: EMBL Heidelberg, ; Meyerhofstraße 1, 69117 Heidelberg, Germany

[6 ]GRID grid.4714.6, ISNI 0000 0004 1937 0626, Department of Medical Biochemistry and Biophysics, , Karolinska Institute, ; Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden

Author information

Harald Schwalbe http://orcid.org/0000-0001-5693-7909

Article

Publisher ID: 10007

DOI: 10.1007/s12104-021-10007-w

PMC ID: 7822759

PubMed ID: 33484403

SO-VID: 8323f881-b54c-4fa1-bab6-fe2173efa27e

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 : 9 December 2020

Date accepted : 8 January 2021

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;

Award ID: CRC902

Award ID: GRK 1986

Award ID: Infrastructure program: 277478796, 277479031, 392682309, 452632086, 70653611

Award Recipient : Boris Fürtig Martin Hengesbach Andreas Schlundt Harald Schwalbe Julia E. Weigand Jens Wöhnert

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 : Harald Schwalbe

Funded by: FundRef http://dx.doi.org/10.13039/501100005687, Goethe-Universität Frankfurt am Main;

Funded by: FundRef http://dx.doi.org/10.13039/501100004047, Karolinska Institutet;

Award ID: Start-Up funds

Award Recipient : Katja Petzold

Funded by: Projekt DEAL

Open Access :

Open Access funding enabled and organized by Projekt DEAL.

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