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Toews S, Wacker A, Faison EM, Duchardt-Ferner E, Richter C, Mathieu D, Bottaro S, Zhang Q, Schwalbe H. The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH. Nucleic Acids Res 2024; 52:7971-7986. [PMID: 38842942 PMCID: PMC11260494 DOI: 10.1093/nar/gkae477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 07/23/2024] Open
Abstract
We present the nuclear magnetic resonance spectroscopy (NMR) solution structure of the 5'-terminal stem loop 5_SL1 (SL1) of the SARS-CoV-2 genome. SL1 contains two A-form helical elements and two regions with non-canonical structure, namely an apical pyrimidine-rich loop and an asymmetric internal loop with one and two nucleotides at the 5'- and 3'-terminal part of the sequence, respectively. The conformational ensemble representing the averaged solution structure of SL1 was validated using NMR residual dipolar coupling (RDC) and small-angle X-ray scattering (SAXS) data. We show that the internal loop is the major binding site for fragments of low molecular weight. This internal loop of SL1 can be stabilized by an A12-C28 interaction that promotes the transient formation of an A+•C base pair. As a consequence, the pKa of the internal loop adenosine A12 is shifted to 5.8, compared to a pKa of 3.63 of free adenosine. Furthermore, applying a recently developed pH-differential mutational profiling (PD-MaP) approach, we not only recapitulated our NMR findings of SL1 but also unveiled multiple sites potentially sensitive to pH across the 5'-UTR of SARS-CoV-2.
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Affiliation(s)
- Sabrina Toews
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
| | - Anna Wacker
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
| | - Edgar M Faison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599, USA
| | - Elke Duchardt-Ferner
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Institute of Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
| | - Christian Richter
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
| | - Daniel Mathieu
- Bruker BioSpin GmbH, Ettlingen, Baden-Württemberg 76275, Germany
| | - Sandro Bottaro
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599, USA
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
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5
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He S, Huang R, Townley J, Kretsch RC, Karagianes TG, Cox DBT, Blair H, Penzar D, Vyaltsev V, Aristova E, Zinkevich A, Bakulin A, Sohn H, Krstevski D, Fukui T, Tatematsu F, Uchida Y, Jang D, Lee JS, Shieh R, Ma T, Martynov E, Shugaev MV, Bukhari HST, Fujikawa K, Onodera K, Henkel C, Ron S, Romano J, Nicol JJ, Nye GP, Wu Y, Choe C, Reade W, Das R. Ribonanza: deep learning of RNA structure through dual crowdsourcing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581671. [PMID: 38464325 PMCID: PMC10925082 DOI: 10.1101/2024.02.24.581671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity of experimental data. Here, we present Ribonanza, a dataset of chemical mapping measurements on two million diverse RNA sequences collected through Eterna and other crowdsourced initiatives. Ribonanza measurements enabled solicitation, training, and prospective evaluation of diverse deep neural networks through a Kaggle challenge, followed by distillation into a single, self-contained model called RibonanzaNet. When fine tuned on auxiliary datasets, RibonanzaNet achieves state-of-the-art performance in modeling experimental sequence dropout, RNA hydrolytic degradation, and RNA secondary structure, with implications for modeling RNA tertiary structure.
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Affiliation(s)
- Shujun He
- Department of Chemical Engineering, Texas A&M University, TX, USA
| | - Rui Huang
- Department of Biochemistry, Stanford CA, USA
| | | | | | | | - David B T Cox
- Department of Biochemistry, Stanford CA, USA
- Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA
| | | | - Dmitry Penzar
- AIRI, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow 119991, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Valeriy Vyaltsev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
| | - Elizaveta Aristova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
| | - Arsenii Zinkevich
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
| | - Artemy Bakulin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
| | - Hoyeol Sohn
- Department of Chemical Engineering, Texas A&M University, TX, USA
- Department of Biochemistry, Stanford CA, USA
- Eterna Massive Open Laboratory
- Biophysics Program, Stanford CA, USA
- Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA
- Department of Mathematics, Stanford CA, USA
- AIRI, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow 119991, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
- GO Inc., Tokyo, Japan
- Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea
- DeltaX, Seoul, Republic of Korea
- Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA
- Vergesense, CA
- DeNA, Tokyo, Japan
- NVIDIA, Tokyo, Japan
- NVIDIA, Munich
- Howard Hughes Medical Institute
- Department of Bioengineering, Stanford CA, USA
- Kaggle, San Francisco CA, USA
| | - Daniel Krstevski
- Department of Chemical Engineering, Texas A&M University, TX, USA
- Department of Biochemistry, Stanford CA, USA
- Eterna Massive Open Laboratory
- Biophysics Program, Stanford CA, USA
- Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA
- Department of Mathematics, Stanford CA, USA
- AIRI, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow 119991, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
- GO Inc., Tokyo, Japan
- Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea
- DeltaX, Seoul, Republic of Korea
- Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA
- Vergesense, CA
- DeNA, Tokyo, Japan
- NVIDIA, Tokyo, Japan
- NVIDIA, Munich
- Howard Hughes Medical Institute
- Department of Bioengineering, Stanford CA, USA
- Kaggle, San Francisco CA, USA
| | | | | | | | - Donghoon Jang
- Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea
| | | | - Roger Shieh
- Department of Chemical Engineering, Texas A&M University, TX, USA
- Department of Biochemistry, Stanford CA, USA
- Eterna Massive Open Laboratory
- Biophysics Program, Stanford CA, USA
- Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA
- Department of Mathematics, Stanford CA, USA
- AIRI, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow 119991, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
- GO Inc., Tokyo, Japan
- Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea
- DeltaX, Seoul, Republic of Korea
- Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA
- Vergesense, CA
- DeNA, Tokyo, Japan
- NVIDIA, Tokyo, Japan
- NVIDIA, Munich
- Howard Hughes Medical Institute
- Department of Bioengineering, Stanford CA, USA
- Kaggle, San Francisco CA, USA
| | - Tom Ma
- Department of Chemical Engineering, Texas A&M University, TX, USA
- Department of Biochemistry, Stanford CA, USA
- Eterna Massive Open Laboratory
- Biophysics Program, Stanford CA, USA
- Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA
- Department of Mathematics, Stanford CA, USA
- AIRI, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow 119991, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
- GO Inc., Tokyo, Japan
- Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea
- DeltaX, Seoul, Republic of Korea
- Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA
- Vergesense, CA
- DeNA, Tokyo, Japan
- NVIDIA, Tokyo, Japan
- NVIDIA, Munich
- Howard Hughes Medical Institute
- Department of Bioengineering, Stanford CA, USA
- Kaggle, San Francisco CA, USA
| | - Eduard Martynov
- Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation
| | - Maxim V Shugaev
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA
| | | | | | | | | | - Shlomo Ron
- Department of Chemical Engineering, Texas A&M University, TX, USA
- Department of Biochemistry, Stanford CA, USA
- Eterna Massive Open Laboratory
- Biophysics Program, Stanford CA, USA
- Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA
- Department of Mathematics, Stanford CA, USA
- AIRI, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow 119991, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
- GO Inc., Tokyo, Japan
- Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea
- DeltaX, Seoul, Republic of Korea
- Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA
- Vergesense, CA
- DeNA, Tokyo, Japan
- NVIDIA, Tokyo, Japan
- NVIDIA, Munich
- Howard Hughes Medical Institute
- Department of Bioengineering, Stanford CA, USA
- Kaggle, San Francisco CA, USA
| | - Jonathan Romano
- Eterna Massive Open Laboratory
- Howard Hughes Medical Institute
| | | | - Grace P Nye
- Department of Biochemistry, Stanford CA, USA
| | - Yuan Wu
- Department of Biochemistry, Stanford CA, USA
- Howard Hughes Medical Institute
| | | | | | - Rhiju Das
- Department of Biochemistry, Stanford CA, USA
- Biophysics Program, Stanford CA, USA
- Howard Hughes Medical Institute
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