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Blechar J, de Jesus V, Fürtig B, Hengesbach M, Schwalbe H. Shine-Dalgarno Accessibility Governs Ribosome Binding to the Adenine Riboswitch. ACS Chem Biol 2024; 19:607-618. [PMID: 38412235 DOI: 10.1021/acschembio.3c00435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Translational riboswitches located in the 5' UTR of the messenger RNA (mRNA) regulate translation through variation of the accessibility of the ribosome binding site (RBS). These are the result of conformational changes in the riboswitch RNA governed by ligand binding. Here, we use a combination of single-molecule colocalization techniques (Single-Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) and Single-Molecule Kinetic Analysis of Ribosome Binding (SiM-KARB)) and microscale thermophoresis (MST) to investigate the adenine-sensing riboswitch in Vibrio vulnificus, focusing on the changes of accessibility between the ligand-free and ligand-bound states. We show that both methods faithfully report on the accessibility of the RBS within the riboswitch and that both methods identify an increase in accessibility upon adenine binding. Expanding on the regulatory context, we show the impact of the ribosomal protein S1 on the unwinding of the RNA secondary structure, thereby favoring ribosome binding even for the apo state. The determined rate constants suggest that binding of the ribosome is faster than the time required to change from the ON state to the OFF state, a prerequisite for efficient regulation decision.
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Affiliation(s)
- Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
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2
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Duchardt-Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Schwalbe H. The COVID19-NMR Consortium: A Public Report on the Impact of this New Global Collaboration. Angew Chem Int Ed Engl 2023; 62:e202217171. [PMID: 36748955 DOI: 10.1002/anie.202217171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 02/08/2023]
Abstract
The outbreak of COVID-19 in December 2019 required the formation of international consortia for a coordinated scientific effort to understand and combat the virus. In this Viewpoint Article, we discuss how the NMR community has gathered to investigate the genome and proteome of SARS-CoV-2 and tested them for binding to low-molecular-weight binders. External factors including extended lockdowns due to the global pandemic character of the viral infection triggered the transition from locally focused collaborative research conducted within individual research groups to digital exchange formats for immediate discussion of unpublished results and data analysis, sample sharing, and coordinated research between more than 50 groups from 18 countries simultaneously. We discuss key lessons that might pertain after the end of the pandemic and challenges that we need to address.
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Affiliation(s)
- Elke Duchardt-Ferner
- Institute for Biomolecular Sciences, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Andreas Schlundt
- Institute for Biomolecular Sciences, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Julia E Weigand
- Philipps-University Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037, Marburg, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, UK
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3
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Duchardt‐Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Schwalbe H. Das COVID19‐NMR‐Konsortium: Ein öffentlicher Bericht über den Einfluss dieser neuen globalen Kollaboration. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202217171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- Elke Duchardt‐Ferner
- Institute for Biomolecular Sciences Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt/M. Deutschland
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Andreas Schlundt
- Institute for Biomolecular Sciences Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt/M. Deutschland
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Julia E. Weigand
- Philipps-University Marburg Department of Pharmacy Institute of Pharmaceutical Chemistry Marbacher Weg 6 35037 Marburg Deutschland
| | - Julia Wirmer‐Bartoschek
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
- Instruct-ERIC Oxford House, Parkway Court John Smith Drive Oxford OX4 2JY Großbritannien
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4
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Sudakov A, Knezic B, Hengesbach M, Fürtig B, Stirnal E, Schwalbe H. Site-Specific Labeling of RNAs with Modified and 19 F-Labeled Nucleotides by Chemo-Enzymatic Synthesis. Chemistry 2023; 29:e202203368. [PMID: 36594705 DOI: 10.1002/chem.202203368] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/04/2023]
Abstract
More than 170 post-transcriptional modifications of RNAs have currently been identified. Detailed biophysical investigations of these modifications have been limited since large RNAs containing these post-transcriptional modifications are difficult to produce. Further, adequate readout of spectroscopic fingerprints are important, necessitating additional labeling procedures beyond the naturally occurring RNA modifications. Here, we report the chemo-enzymatic synthesis of RNA modifications and several structurally similar fluorine-modified analogs further optimizing a recently developed methodology.[1] This chemo-enzymatic method allows synthesis of also large RNAs. We were able to incorporate 16 modified nucleotides and 6 19 F-labeled nucleotides. To showcase the applicability of such modified large RNAs, we incorporated a 19 F-labeled cytidine into the aptamer domain of the 2'dG sensing riboswitch (2'dG-sw) from Mesoplasma florum, enabling characterizing RNA fold, ligand binding and kinetics. Thanks to the large chemical shift dispersion of 19 F, we can detect conformational heterogeneity in the apo state of the riboswitch.
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Affiliation(s)
- Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
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5
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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6
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022; 61:e202205858. [PMID: 36115062 PMCID: PMC9539013 DOI: 10.1002/anie.202205858] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 11/17/2022]
Abstract
SARS‐CoV‐2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti‐virals. Within the international Covid19‐NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80% of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR‐detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure‐based drug design against the SCoV2 proteome.
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Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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7
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Fuks C, Falkner S, Schwierz N, Hengesbach M. Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch. Front Mol Biosci 2022; 9:826505. [PMID: 35573739 PMCID: PMC9094411 DOI: 10.3389/fmolb.2022.826505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Riboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction between the P1 and P2 hairpins. While an interaction was shown for isolated hairpins in crystallization and electron paramagnetic resonance experiments, an intrastrand kissing loop formation has not been demonstrated. Here, we report the first evidence of this interaction in cis in a ligand and Mg2+ dependent manner. Using single-molecule FRET spectroscopy and detailed structural information from coarse-grained simulations, we observe and characterize three interconvertible states representing an open and kissing loop conformation as well as a novel Mg2+ dependent state for the guanidine-II riboswitch from E. coli. The results further substantiate the proposed switching mechanism and provide detailed insight into the regulation mechanism for the guanidine-II riboswitch class. Combining single molecule experiments and coarse-grained simulations therefore provides a promising perspective in resolving the conformational changes induced by environmental conditions and to yield molecular insights into RNA regulation.
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Affiliation(s)
- Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Sebastian Falkner
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Computational and Soft Matter Physics, University of Vienna, Vienna, VIA, Austria
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main, Germany
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8
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Mertinkus KR, Grün JT, Altincekic N, Bains JK, Ceylan B, Ferner JP, Frydman L, Fürtig B, Hengesbach M, Hohmann KF, Hymon D, Kim J, Knezic B, Novakovic M, Oxenfarth A, Peter SA, Qureshi NS, Richter C, Scherf T, Schlundt A, Schnieders R, Schwalbe H, Stirnal E, Sudakov A, Vögele J, Wacker A, Weigand JE, Wirmer-Bartoschek J, Martin MAW, Wöhnert J. 1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2022; 16:17-25. [PMID: 35178672 PMCID: PMC8853908 DOI: 10.1007/s12104-021-10053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/16/2021] [Indexed: 06/14/2023]
Abstract
The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5'- and 3'-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5'-untranslated region (5'-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5'-UUUCGU-3' hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1H, 13C and 15N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy.
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Affiliation(s)
- Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jan-Peter Ferner
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Božana Knezic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
- Institute for Biochemistry, ETH Zürich, Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | | | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Tali Scherf
- Department of Chemical Research Support, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Deutero GmbH, Am Ring 29, 56288, Kastellaun, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| | - Elke Stirnal
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jennifer Vögele
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
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9
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Broft P, Rosenkranz R, Schleiff E, Hengesbach M, Schwalbe H. Structural analysis of temperature-dependent alternative splicing of HsfA2 pre-mRNA from tomato plants. RNA Biol 2022; 19:266-278. [PMID: 35130120 PMCID: PMC8824230 DOI: 10.1080/15476286.2021.2024034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Temperature-dependent alternative splicing was recently demonstrated for intron 2 of the gene coding for heat shock factor HsfA2 of the tomato plant Solanum lycopersicum, but the molecular mechanism regulating the abundance of such temperature-dependent splice variants is still unknown. We report here on regulatory pre-mRNA structures that could function as regulators by controlling the use of splice sites in a temperature-dependent manner. We investigate pre-mRNA structures at the splice sites of intron 2 of the gene coding for HsfA2 from S. lycopersicum using NMR- and CD-spectroscopy as well as in-line probing. The pre-mRNA undergoes conformational changes between two different secondary structures at the 3ʹ splice site of the intron in a temperature-dependent manner. Previously, it was shown that three single nucleotide polymorphisms (SNPs) in intron 2 of the HsfA2 pre-mRNA affect the splicing efficiency of its pre-mRNA and are linked to the thermotolerance in different tomato species. By comparing pre-mRNA fragments of the tomato species S. lycopersicum and S. peruvianum, we show that these SNPs result in substantial structural differences between the pre-mRNAs of the two species.
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Affiliation(s)
- Patrizia Broft
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main, Germany
| | - Remus Rosenkranz
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main, Germany
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10
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Richter C, Hohmann KF, Toews S, Mathieu D, Altincekic N, Bains JK, Binas O, Ceylan B, Duchardt-Ferner E, Ferner J, Fürtig B, Grün JT, Hengesbach M, Hymon D, Jonker HRA, Knezic B, Korn SM, Landgraf T, Löhr F, Peter SA, Pyper DJ, Qureshi NS, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Vögele J, Weigand JE, Wirmer-Bartoschek J, Witt K, Wöhnert J, Schwalbe H, Wacker A. 1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2021; 15:467-474. [PMID: 34453696 PMCID: PMC8401371 DOI: 10.1007/s12104-021-10047-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/19/2021] [Indexed: 05/27/2023]
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.
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Affiliation(s)
- Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Sabrina Toews
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Daniel Mathieu
- Bruker BioSpin, Silberstreifen 4, 76287, Rheinstetten, Germany
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- BioNTech SE, An der Goldgrube 12, 55131, Mainz, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Faculty of Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Hendrik R A Jonker
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Sophie M Korn
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Frank Löhr
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Biophysical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Dennis J Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Andreas Schlundt
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Deutero GmbH, Am Ring 29, 56288, Kastellaun, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Jennifer Vögele
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Kerstin Witt
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
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11
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Vögele J, Ferner JP, Altincekic N, Bains JK, Ceylan B, Fürtig B, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Löhr F, Peter SA, Pyper D, Qureshi NS, Richter C, Schlundt A, Schwalbe H, Stirnal E, Sudakov A, Wacker A, Weigand JE, Wirmer-Bartoschek J, Wöhnert J, Duchardt-Ferner E. 1H, 13C, 15N and 31P chemical shift assignment for stem-loop 4 from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2021; 15:335-340. [PMID: 33928512 PMCID: PMC8083917 DOI: 10.1007/s12104-021-10026-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/16/2021] [Indexed: 06/01/2023]
Abstract
The SARS-CoV-2 virus is the cause of the respiratory disease COVID-19. As of today, therapeutic interventions in severe COVID-19 cases are still not available as no effective therapeutics have been developed so far. Despite the ongoing development of a number of effective vaccines, therapeutics to fight the disease once it has been contracted will still be required. Promising targets for the development of antiviral agents against SARS-CoV-2 can be found in the viral RNA genome. The 5'- and 3'-genomic ends of the 30 kb SCoV-2 genome are highly conserved among Betacoronaviruses and contain structured RNA elements involved in the translation and replication of the viral genome. The 40 nucleotides (nt) long highly conserved stem-loop 4 (5_SL4) is located within the 5'-untranslated region (5'-UTR) important for viral replication. 5_SL4 features an extended stem structure disrupted by several pyrimidine mismatches and is capped by a pentaloop. Here, we report extensive 1H, 13C, 15N and 31P resonance assignments of 5_SL4 as the basis for in-depth structural and ligand screening studies by solution NMR spectroscopy.
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Affiliation(s)
- Jennifer Vögele
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Jan-Peter Ferner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Nadide Altincekic
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Betül Ceylan
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Boris Fürtig
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - J Tassilo Grün
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Martin Hengesbach
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Katharina F Hohmann
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Daniel Hymon
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Bozana Knezic
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Frank Löhr
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Biophysical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Dennis Pyper
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | | | - Christian Richter
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Elke Stirnal
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Alexey Sudakov
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Anna Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany.
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12
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Schmidt A, Hanspach G, Hengesbach M. Structural dynamics govern substrate recruitment and catalytic turnover in H/ACA RNP pseudouridylation. RNA Biol 2021; 18:1300-1309. [PMID: 33111609 PMCID: PMC8354600 DOI: 10.1080/15476286.2020.1842984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/01/2020] [Accepted: 10/22/2020] [Indexed: 01/17/2023] Open
Abstract
H/ACA ribonucleoproteins catalyse the sequence-dependent pseudouridylation of ribosomal and spliceosomal RNAs. Here, we reconstitute site-specifically fluorophore labelled H/ACA complexes and analyse their structural dynamics using single-molecule FRET spectroscopy. Our results show that the guide RNA is distorted into a substrate-binding competent conformation by specific protein interactions. Analysis of the reaction pathway using atomic mutagenesis establishes a new model how individual protein domains contribute to catalysis. Taken together, these results identify and characterize individual roles for all accessory proteins on the assembly and function of H/ACA RNPs.
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Affiliation(s)
- Andreas Schmidt
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt, Germany
| | - Gerd Hanspach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt, Germany
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13
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Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome. Angew Chem Int Ed Engl 2021; 60:19191-19200. [PMID: 34161644 PMCID: PMC8426693 DOI: 10.1002/anie.202103693] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 contains a positive single-stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS-CoV and SARS-CoV-2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex-vivo structural probing experiments. These elements contain non-base-paired regions that potentially harbor ligand-binding pockets. Here, we performed an NMR-based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1 H-based 1D NMR binding assays. The screening identified common as well as RNA-element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS-CoV-2.
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15
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Wacker A, Weigand JE, Akabayov SR, Altincekic N, Bains JK, Banijamali E, Binas O, Castillo-Martinez J, Cetiner E, Ceylan B, Chiu LY, Davila-Calderon J, Dhamotharan K, Duchardt-Ferner E, Ferner J, Frydman L, Fürtig B, Gallego J, Grün JT, Hacker C, Haddad C, Hähnke M, Hengesbach M, Hiller F, Hohmann KF, Hymon D, de Jesus V, Jonker H, Keller H, Knezic B, Landgraf T, Löhr F, Luo L, Mertinkus KR, Muhs C, Novakovic M, Oxenfarth A, Palomino-Schätzlein M, Petzold K, Peter SA, Pyper DJ, Qureshi NS, Riad M, Richter C, Saxena K, Schamber T, Scherf T, Schlagnitweit J, Schlundt A, Schnieders R, Schwalbe H, Simba-Lahuasi A, Sreeramulu S, Stirnal E, Sudakov A, Tants JN, Tolbert BS, Vögele J, Weiß L, Wirmer-Bartoschek J, Wirtz Martin MA, Wöhnert J, Zetzsche H. Correction to 'Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy'. Nucleic Acids Res 2021; 49:7204-7205. [PMID: 34161581 PMCID: PMC8266613 DOI: 10.1093/nar/gkab568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sabine R Akabayov
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Erhan Cetiner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | | | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Lucio Frydman
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - José Gallego
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Carolin Hacker
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Martin Hähnke
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Fabian Hiller
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Henry Jonker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Le Luo
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Christina Muhs
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Mihajlo Novakovic
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Dennis J Pyper
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Magdalena Riad
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tali Scherf
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | | | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alvaro Simba-Lahuasi
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Heidi Zetzsche
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
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16
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Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci 2021; 8:653148. [PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sophie Marianne Korn
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Martí Ninot-Pedrosa
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Jose Abi Saad
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Fabio C. L. Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisele Cardoso de Amorim
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil
| | - Thomas K. Anderson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cristiane D. Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chelsea Anorma
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Bax
- LCP, NIDDK, NIH, Bethesda, MD, United States
| | | | - Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Louis Brigandat
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Anna Bula
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Matthias Bütikofer
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Teresa Carlomagno
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Icaro Putinhon Caruso
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Marquise G. Crosby
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karthikeyan Dhamotharan
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Isabella C. Felli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yanick Fleischmann
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dhiman Ghosh
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | | | - Sabine Häfner
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Bruno Hargittay
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - K. Henzler-Wildman
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie T. Hutchison
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Katarina Jović
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Kaņepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert N. Kirchdoerfer
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - John Kirkpatrick
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Robin Krishnathas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Felicitas Kutz
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andras Lang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Douglas Laurents
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Nathane Cunha Mebus-Antunes
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beat H. Meier
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Mompeán
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Celine Moser
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Thais Cristtina Neves-Martins
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xiamonin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Roberta Pierattelli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Riek
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Chad M. Rienstra
- Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anderson S. Pinheiro
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Linda Schulte
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Schiavina
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mara Silber
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcius da Silva Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | | | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Niklas Tants
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabrina Töws
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Á. Treviño
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Ying Wang
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Marco E. Weber
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Julia E. Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Zehnder
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Schlundt
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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Trucks S, Hanspach G, Hengesbach M. Eukaryote specific RNA and protein features facilitate assembly and catalysis of H/ACA snoRNPs. Nucleic Acids Res 2021; 49:4629-4642. [PMID: 33823543 PMCID: PMC8096250 DOI: 10.1093/nar/gkab177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/16/2021] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
H/ACA Box ribonucleoprotein complexes (RNPs) play a major role in modification of rRNA and snRNA, catalyzing the sequence specific pseudouridylation in eukaryotes and archaea. This enzymatic reaction takes place on a substrate RNA recruited via base pairing to an internal loop of the snoRNA. Eukaryotic snoRNPs contain the four proteins Nop10, Cbf5, Gar1 and Nhp2, with Cbf5 as the catalytic subunit. In contrast to archaeal H/ACA RNPs, eukaryotic snoRNPs contain several conserved features in both the snoRNA as well as the protein components. Here, we reconstituted the eukaryotic H/ACA RNP containing snR81 as a guide RNA in vitro and report on the effects of these eukaryote specific features on complex assembly and enzymatic activity. We compare their contribution to pseudouridylation activity for stand-alone hairpins versus the bipartite RNP. Using single molecule FRET spectroscopy, we investigated the role of the different eukaryote-specific proteins and domains on RNA folding and complex assembly, and assessed binding of substrate RNA to the RNP. Interestingly, we found diverging effects for the two hairpins of snR81, suggesting hairpin-specific requirements for folding and RNP formation. Our results for the first time allow assessing interactions between the individual hairpin RNPs in the context of the full, bipartite snoRNP.
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Affiliation(s)
- Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Gerd Hanspach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
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18
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Salvi N, Bessa LM, Guseva S, Camacho-Zarco A, Maurin D, Perez LM, Malki A, Hengesbach M, Korn SM, Schlundt A, Schwalbe H, Blackledge M. 1H, 13C and 15N backbone chemical shift assignments of SARS-CoV-2 nsp3a. Biomol NMR Assign 2021; 15:173-176. [PMID: 33475934 PMCID: PMC7819138 DOI: 10.1007/s12104-020-10001-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/24/2020] [Indexed: 05/25/2023]
Abstract
The non-structural protein nsp3 from SARS-CoV-2 plays an essential role in the viral replication transcription complex. Nsp3a constitutes the N-terminal domain of nsp3, comprising a ubiquitin-like folded domain and a disordered acidic chain. This region of nsp3a has been linked to interactions with the viral nucleoprotein and the structure of double membrane vesicles. Here, we report the backbone resonance assignment of both domains of nsp3a. The study is carried out in the context of the international covid19-nmr consortium, which aims to characterize SARS-CoV-2 proteins and RNAs, providing for example NMR chemical shift assignments of the different viral components. Our assignment will provide the basis for the identification of inhibitors and further functional and interaction studies of this essential protein.
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Affiliation(s)
- Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | | | - Serafima Guseva
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | | | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | | | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Sophie Marianne Korn
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
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19
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Schnieders R, Peter SA, Banijamali E, Riad M, Altincekic N, Bains JK, Ceylan B, Fürtig B, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Oxenfarth A, Petzold K, Qureshi NS, Richter C, Schlagnitweit J, Schlundt A, Schwalbe H, Stirnal E, Sudakov A, Vögele J, Wacker A, Weigand JE, Wirmer-Bartoschek J, Wöhnert J. 1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2021; 15:203-211. [PMID: 33484403 PMCID: PMC7822759 DOI: 10.1007/s12104-021-10007-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/08/2021] [Indexed: 05/27/2023]
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.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum, Solnavägen 9, 17177, Stockholm, Sweden
| | - Magdalena Riad
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum, Solnavägen 9, 17177, Stockholm, Sweden
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum, Solnavägen 9, 17177, Stockholm, Sweden
| | | | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum, Solnavägen 9, 17177, Stockholm, Sweden
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany.
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jennifer Vögele
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
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20
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Kubatova N, Qureshi NS, Altincekic N, Abele R, Bains JK, Ceylan B, Ferner J, Fuks C, Hargittay B, Hutchison MT, de Jesus V, Kutz F, Wirtz Martin MA, Meiser N, Linhard V, Pyper DJ, Trucks S, Fürtig B, Hengesbach M, Löhr F, Richter C, Saxena K, Schlundt A, Schwalbe H, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Wöhnert J. 1H, 13C, and 15N backbone chemical shift assignments of coronavirus-2 non-structural protein Nsp10. Biomol NMR Assign 2021; 15:65-71. [PMID: 33159807 PMCID: PMC7648550 DOI: 10.1007/s12104-020-09984-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
The international Covid19-NMR consortium aims at the comprehensive spectroscopic characterization of SARS-CoV-2 RNA elements and proteins and will provide NMR chemical shift assignments of the molecular components of this virus. The SARS-CoV-2 genome encodes approximately 30 different proteins. Four of these proteins are involved in forming the viral envelope or in the packaging of the RNA genome and are therefore called structural proteins. The other proteins fulfill a variety of functions during the viral life cycle and comprise the so-called non-structural proteins (nsps). Here, we report the near-complete NMR resonance assignment for the backbone chemical shifts of the non-structural protein 10 (nsp10). Nsp10 is part of the viral replication-transcription complex (RTC). It aids in synthesizing and modifying the genomic and subgenomic RNAs. Via its interaction with nsp14, it ensures transcriptional fidelity of the RNA-dependent RNA polymerase, and through its stimulation of the methyltransferase activity of nsp16, it aids in synthesizing the RNA cap structures which protect the viral RNAs from being recognized by the innate immune system. Both of these functions can be potentially targeted by drugs. Our data will aid in performing additional NMR-based characterizations, and provide a basis for the identification of possible small molecule ligands interfering with nsp10 exerting its essential role in viral replication.
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Affiliation(s)
- N Kubatova
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - R Abele
- Institute for Biochemistry, Biocentre, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J K Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J Ferner
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - C Fuks
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Hargittay
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M T Hutchison
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - V de Jesus
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - F Kutz
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N Meiser
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - V Linhard
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - D J Pyper
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - S Trucks
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany.
| | - F Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - C Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - K Saxena
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - A Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - H Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany.
| | - S Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - A Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr 10, 64287, Darmstadt, Germany
| | - J Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
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21
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Korn SM, Lambertz R, Fürtig B, Hengesbach M, Löhr F, Richter C, Schwalbe H, Weigand JE, Wöhnert J, Schlundt A. 1H, 13C, and 15N backbone chemical shift assignments of the C-terminal dimerization domain of SARS-CoV-2 nucleocapsid protein. Biomol NMR Assign 2021; 15:129-135. [PMID: 33270159 PMCID: PMC7711055 DOI: 10.1007/s12104-020-09995-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 11/25/2020] [Indexed: 05/25/2023]
Abstract
The current outbreak of the highly infectious COVID-19 respiratory disease is caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). To fight the pandemic, the search for promising viral drug targets has become a cross-border common goal of the international biomedical research community. Within the international Covid19-NMR consortium, scientists support drug development against SARS-CoV-2 by providing publicly available NMR data on viral proteins and RNAs. The coronavirus nucleocapsid protein (N protein) is an RNA-binding protein involved in viral transcription and replication. Its primary function is the packaging of the viral RNA genome. The highly conserved architecture of the coronavirus N protein consists of an N-terminal RNA-binding domain (NTD), followed by an intrinsically disordered Serine/Arginine (SR)-rich linker and a C-terminal dimerization domain (CTD). Besides its involvement in oligomerization, the CTD of the N protein (N-CTD) is also able to bind to nucleic acids by itself, independent of the NTD. Here, we report the near-complete NMR backbone chemical shift assignments of the SARS-CoV-2 N-CTD to provide the basis for downstream applications, in particular site-resolved drug binding studies.
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Affiliation(s)
- Sophie M Korn
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt/M, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt/M, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt/M, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt/M, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt/M, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt/M, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt/M, Germany.
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22
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Alriquet M, Calloni G, Martínez-Limón A, Delli Ponti R, Hanspach G, Hengesbach M, Tartaglia GG, Vabulas RM. The protective role of m1A during stress-induced granulation. J Mol Cell Biol 2021; 12:870-880. [PMID: 32462207 PMCID: PMC7883823 DOI: 10.1093/jmcb/mjaa023] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional methylation of N6-adenine and N1-adenine can affect transcriptome turnover and translation. Furthermore, the regulatory function of N6-methyladenine (m6A) during heat shock has been uncovered, including the enhancement of the phase separation potential of RNAs. In response to acute stress, e.g. heat shock, the orderly sequestration of mRNAs in stress granules (SGs) is considered important to protect transcripts from the irreversible aggregation. Until recently, the role of N1-methyladenine (m1A) on mRNAs during acute stress response remains largely unknown. Here we show that the methyltransferase complex TRMT6/61A, which generates the m1A tag, is involved in transcriptome protection during heat shock. Our bioinformatics analysis indicates that occurrence of the m1A motif is increased in mRNAs known to be enriched in SGs. Accordingly, the m1A-generating methyltransferase TRMT6/61A accumulated in SGs and mass spectrometry confirmed enrichment of m1A in the SG RNAs. The insertion of a single methylation motif in the untranslated region of a reporter RNA leads to more efficient recovery of protein synthesis from that transcript after the return to normal temperature. Our results demonstrate far-reaching functional consequences of a minimal RNA modification on N1-adenine during acute proteostasis stress.
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Affiliation(s)
- Marion Alriquet
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Adrían Martínez-Limón
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Riccardo Delli Ponti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Gerd Hanspach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Gian G. Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Department of Biology ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - R. Martin Vabulas
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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23
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Wacker A, Weigand JE, Akabayov SR, Altincekic N, Bains JK, Banijamali E, Binas O, Castillo-Martinez J, Cetiner E, Ceylan B, Chiu LY, Davila-Calderon J, Dhamotharan K, Duchardt-Ferner E, Ferner J, Frydman L, Fürtig B, Gallego J, Grün JT, Hacker C, Haddad C, Hähnke M, Hengesbach M, Hiller F, Hohmann KF, Hymon D, de Jesus V, Jonker H, Keller H, Knezic B, Landgraf T, Löhr F, Luo L, Mertinkus KR, Muhs C, Novakovic M, Oxenfarth A, Palomino-Schätzlein M, Petzold K, Peter SA, Pyper DJ, Qureshi NS, Riad M, Richter C, Saxena K, Schamber T, Scherf T, Schlagnitweit J, Schlundt A, Schnieders R, Schwalbe H, Simba-Lahuasi A, Sreeramulu S, Stirnal E, Sudakov A, Tants JN, Tolbert BS, Vögele J, Weiß L, Wirmer-Bartoschek J, Wirtz Martin MA, Wöhnert J, Zetzsche H. Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy. Nucleic Acids Res 2020; 48:12415-12435. [PMID: 33167030 PMCID: PMC7736788 DOI: 10.1093/nar/gkaa1013] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/08/2020] [Accepted: 10/14/2020] [Indexed: 12/24/2022] Open
Abstract
The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
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Affiliation(s)
- Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sabine R Akabayov
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Erhan Cetiner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | | | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Lucio Frydman
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - José Gallego
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Carolin Hacker
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Martin Hähnke
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Fabian Hiller
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Henry Jonker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Le Luo
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Christina Muhs
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Mihajlo Novakovic
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Dennis J Pyper
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Magdalena Riad
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tali Scherf
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | | | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alvaro Simba-Lahuasi
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Heidi Zetzsche
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
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24
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Meiser N, Mench N, Hengesbach M. RNA secondary structure dependence in METTL3-METTL14 mRNA methylation is modulated by the N-terminal domain of METTL3. Biol Chem 2020; 402:89-98. [PMID: 33544495 DOI: 10.1515/hsz-2020-0265] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022]
Abstract
N 6-methyladenosine (m6A) is the most abundant modification in mRNA. The core of the human N 6-methyltransferase complex (MTC) is formed by a heterodimer consisting of METTL3 and METTL14, which specifically catalyzes m6A formation within an RRACH sequence context. Using recombinant proteins in a site-specific methylation assay that allows determination of quantitative methylation yields, our results show that this complex methylates its target RNAs not only sequence but also secondary structure dependent. Furthermore, we demonstrate the role of specific protein domains on both RNA binding and substrate turnover, focusing on postulated RNA binding elements. Our results show that one zinc finger motif within the complex is sufficient to bind RNA, however, both zinc fingers are required for methylation activity. We show that the N-terminal domain of METTL3 alters the secondary structure dependence of methylation yields. Our results demonstrate that a cooperative effect of all RNA-binding elements in the METTL3-METTL14 complex is required for efficient catalysis, and that binding of further proteins affecting the NTD of METTL3 may regulate substrate specificity.
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Affiliation(s)
- Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438Frankfurt, Germany
| | - Nicole Mench
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438Frankfurt, Germany
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25
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Cantini F, Banci L, Altincekic N, Bains JK, Dhamotharan K, Fuks C, Fürtig B, Gande SL, Hargittay B, Hengesbach M, Hutchison MT, Korn SM, Kubatova N, Kutz F, Linhard V, Löhr F, Meiser N, Pyper DJ, Qureshi NS, Richter C, Saxena K, Schlundt A, Schwalbe H, Sreeramulu S, Tants JN, Wacker A, Weigand JE, Wöhnert J, Tsika AC, Fourkiotis NK, Spyroulias GA. 1H, 13C, and 15N backbone chemical shift assignments of the apo and the ADP-ribose bound forms of the macrodomain of SARS-CoV-2 non-structural protein 3b. Biomol NMR Assign 2020; 14:339-346. [PMID: 32803496 PMCID: PMC7428200 DOI: 10.1007/s12104-020-09973-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/31/2020] [Indexed: 06/02/2023]
Abstract
The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project COVID19-NMR, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein Nsp3b, a domain of Nsp3. The 217-kDa large Nsp3 protein contains multiple structurally independent, yet functionally related domains including the viral papain-like protease and Nsp3b, a macrodomain (MD). In general, the MDs of SARS-CoV and MERS-CoV were suggested to play a key role in viral replication by modulating the immune response of the host. The MDs are structurally conserved. They most likely remove ADP-ribose, a common posttranslational modification, from protein side chains. This de-ADP ribosylating function has potentially evolved to protect the virus from the anti-viral ADP-ribosylation catalyzed by poly-ADP-ribose polymerases (PARPs), which in turn are triggered by pathogen-associated sensing of the host immune system. This renders the SARS-CoV-2 Nsp3b a highly relevant drug target in the viral replication process. We here report the near-complete NMR backbone resonance assignment (1H, 13C, 15N) of the putative Nsp3b MD in its apo form and in complex with ADP-ribose. Furthermore, we derive the secondary structure of Nsp3b in solution. In addition, 15N-relaxation data suggest an ordered, rigid core of the MD structure. These data will provide a basis for NMR investigations targeted at obtaining small-molecule inhibitors interfering with the catalytic activity of Nsp3b.
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Affiliation(s)
- F Cantini
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy
| | - L Banci
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy.
| | - N Altincekic
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - J K Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - K Dhamotharan
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - C Fuks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - B Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | | | - B Hargittay
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - M Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - M T Hutchison
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - S M Korn
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - N Kubatova
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - F Kutz
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - V Linhard
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - F Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - N Meiser
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - D J Pyper
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - N S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - C Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - K Saxena
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - A Schlundt
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - H Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| | - S Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - J-N Tants
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - A Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - J E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - J Wöhnert
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - A C Tsika
- Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - N K Fourkiotis
- Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - G A Spyroulias
- Department of Pharmacy, University of Patras, 26504, Patras, Greece.
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26
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Korn SM, Dhamotharan K, Fürtig B, Hengesbach M, Löhr F, Qureshi NS, Richter C, Saxena K, Schwalbe H, Tants JN, Weigand JE, Wöhnert J, Schlundt A. 1H, 13C, and 15N backbone chemical shift assignments of the nucleic acid-binding domain of SARS-CoV-2 non-structural protein 3e. Biomol NMR Assign 2020; 14:329-333. [PMID: 32770392 PMCID: PMC7414254 DOI: 10.1007/s12104-020-09971-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
The ongoing pandemic caused by the Betacoronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) demonstrates the urgent need of coordinated and rapid research towards inhibitors of the COVID-19 lung disease. The covid19-nmr consortium seeks to support drug development by providing publicly accessible NMR data on the viral RNA elements and proteins. The SARS-CoV-2 genome encodes for approximately 30 proteins, among them are the 16 so-called non-structural proteins (Nsps) of the replication/transcription complex. The 217-kDa large Nsp3 spans one polypeptide chain, but comprises multiple independent, yet functionally related domains including the viral papain-like protease. The Nsp3e sub-moiety contains a putative nucleic acid-binding domain (NAB) with so far unknown function and consensus target sequences, which are conceived to be both viral and host RNAs and DNAs, as well as protein-protein interactions. Its NMR-suitable size renders it an attractive object to study, both for understanding the SARS-CoV-2 architecture and drugability besides the classical virus' proteases. We here report the near-complete NMR backbone chemical shifts of the putative Nsp3e NAB that reveal the secondary structure and compactness of the domain, and provide a basis for NMR-based investigations towards understanding and interfering with RNA- and small-molecule-binding by Nsp3e.
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Affiliation(s)
- Sophie M Korn
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Karthikeyan Dhamotharan
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Jan-Niklas Tants
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, 60438, Frankfurt, Germany.
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27
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Schnieders R, Knezic B, Zetzsche H, Sudakov A, Matzel T, Richter C, Hengesbach M, Schwalbe H, Fürtig B. NMR Spectroscopy of Large Functional RNAs: From Sample Preparation to Low-Gamma Detection. ACTA ACUST UNITED AC 2020; 82:e116. [PMID: 32960489 DOI: 10.1002/cpnc.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
NMR spectroscopy is a potent method for the structural and biophysical characterization of RNAs. The application of NMR spectroscopy is restricted in RNA size and most often requires isotope-labeled or even selectively labeled RNAs. Additionally, new NMR pulse sequences, such as the heteronuclear-detected NMR experiments, are introduced. We herein provide detailed protocols for the preparation of isotope-labeled RNA for NMR spectroscopy via in vitro transcription. This protocol covers all steps, from the preparation of DNA template to the transcription of milligram RNA quantities. Moreover, we present a protocol for a chemo-enzymatic approach to introduce a single modified nucleotide at any position of any RNA. Regarding NMR methodology, we share protocols for the implementation of a suite of heteronuclear-detected NMR experiments including 13 C-detected experiments for ribose assignment and amino groups, the CN-spin filter heteronuclear single quantum coherence (HSQC) for imino groups and the 15 N-detected band-selective excitation short transient transverse-relaxation-optimized spectroscopy (BEST-TROSY) experiment. © 2020 The Authors. Basic Protocol 1: Preparation of isotope-labeled RNA samples with in vitro transcription using T7 RNAP, DEAE chromatography, and RP-HPLC purification Alternate Protocol 1: Purification of isotope-labeled RNA from in vitro transcription with preparative PAGE Alternate Protocol 2: Purification of isotope-labeled RNA samples from in vitro transcription via centrifugal concentration Support Protocol 1: Preparation of DNA template from plasmid Support Protocol 2: Preparation of PCR DNA as template Support Protocol 3: Preparation of T7 RNA Polymerase (T7 RNAP) Support Protocol 4: Preparation of yeast inorganic pyrophosphatase (YIPP) Basic Protocol 2: Preparation of site-specific labeled RNAs using a chemo-enzymatic synthesis Support Protocol 5: Synthesis of modified nucleoside 3',5'-bisphosphates Support Protocol 6: Preparation of T4 RNA Ligase 2 Support Protocol 7: Setup of NMR spectrometer for heteronuclear-detected NMR experiments Support Protocol 8: IPAP and DIPAP for homonuclear decoupling Basic Protocol 3: 13 C-detected 3D (H)CC-TOCSY, (H)CPC, and (H)CPC-CCH-TOCSY experiments for ribose assignment Basic Protocol 4: 13 C-detected 2D CN-spin filter HSQC experiment Basic Protocol 5: 13 C-detected C(N)H-HDQC experiment for the detection of amino groups Support Protocol 9: 13 C-detected CN-HSQC experiment for amino groups Basic Protocol 6: 13 C-detected "amino"-NOESY experiment Basic Protocol 7: 15 N-detected BEST-TROSY experiment.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Heidi Zetzsche
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Germany
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28
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Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
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Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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29
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Schlundt A, Wirtz MA, Knezic B, Hengesbach M, Fürtig B, Weigand JE, Wöhnert J, Ferner J, Saxena K, Wacker A, Richter C, Sreeramulu S, Wirmer-Bartoschek J, Schwalbe H. Gemeinschaftlich in Krisenzeiten: NMR-Strukturbiologie gegen COVID-19. Biospektrum 2020; 26:440-441. [PMID: 32834541 PMCID: PMC7318729 DOI: 10.1007/s12268-020-1396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Universität Frankfurt a. M., Max-von-Laue-Straße 7, D-60438 Frankfurt a. M., Deutschland
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30
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Altincekic N, Löhr F, Meier-Credo J, Langer JD, Hengesbach M, Richter C, Schwalbe H. Site-Specific Detection of Arginine Methylation in Highly Repetitive Protein Motifs of Low Sequence Complexity by NMR. J Am Chem Soc 2020; 142:7647-7654. [PMID: 32233470 DOI: 10.1021/jacs.0c02308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational modifications of proteins are widespread in eukaryotes. To elucidate the functional role of these modifications, detection methods need to be developed that provide information at atomic resolution. Here, we report on the development of a novel Arg-specific NMR experiment that detects the methylation status and symmetry of each arginine side chain even in highly repetitive RGG amino acid sequence motifs found in numerous proteins within intrinsically disordered regions. The experiment relies on the excellent resolution of the backbone H,N correlation spectra even in these low complexity sequences. It requires 13C, 15N labeled samples.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Jakob Meier-Credo
- Max Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Julian D Langer
- Max Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
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31
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Hegelein A, Müller D, Größl S, Göbel M, Hengesbach M, Schwalbe H. Cover Feature: Genetic Code Expansion Facilitates Position‐Selective Labeling of RNA for Biophysical Studies (Chem. Eur. J. 8/2020). Chemistry 2020. [DOI: 10.1002/chem.201905368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andreas Hegelein
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Sylvester Größl
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Michael Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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32
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Hegelein A, Müller D, Größl S, Göbel M, Hengesbach M, Schwalbe H. Genetic Code Expansion Facilitates Position-Selective Labeling of RNA for Biophysical Studies. Chemistry 2020; 26:1800-1810. [PMID: 31692134 PMCID: PMC7027469 DOI: 10.1002/chem.201904623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Indexed: 12/13/2022]
Abstract
Nature relies on reading and synthesizing the genetic code with high fidelity. Nucleic acid building blocks that are orthogonal to the canonical A-T and G-C base-pairs are therefore uniquely suitable to facilitate position-specific labeling of nucleic acids. Here, we employ the orthogonal kappa-xanthosine-base-pair for in vitro transcription of labeled RNA. We devised an improved synthetic route to obtain the phosphoramidite of the deoxy-version of the kappa nucleoside in solid phase synthesis. From this DNA template, we demonstrate the reliable incorporation of xanthosine during in vitro transcription. Using NMR spectroscopy, we show that xanthosine introduces only minor structural changes in an RNA helix. We furthermore synthesized a clickable 7-deaza-xanthosine, which allows to site-specifically modify transcribed RNA molecules with fluorophores or other labels.
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Affiliation(s)
- Andreas Hegelein
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Sylvester Größl
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Michael Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
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33
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Hengesbach M. The how & why of looking at individual RNAs. RNA Biol 2019; 16:1075-1076. [DOI: 10.1080/15476286.2019.1637607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt, Germany
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34
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Alriquet M, Martínez-Limón A, Hanspach G, Hengesbach M, Tartaglia GG, Calloni G, Vabulas RM. Assembly of Proteins by Free RNA during the Early Phase of Proteostasis Stress. J Proteome Res 2019; 18:2835-2847. [PMID: 31244213 DOI: 10.1021/acs.jproteome.9b00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
At any stage of their lifecycle, mRNAs are coated by specialized proteins. One of few circumstances when free mRNA appears in the cytosol is the disassembly of polysomes during the stress-induced shutdown of protein synthesis. Using quantitative mass spectrometry, we sought to identify the free RNA-interacting cellular machinery in heat-shocked mammalian cells. Free RNA-associated proteins displayed higher disorder and larger size, which supports the role of multivalent interactions during the initial phase of the association with RNAs during stress. Structural features of the free RNA interactors defined them as a subset of RNA-binding proteins. The interaction between these assembled proteins in vivo required RNA. Reconstitution of the association process in vitro indicated a multimolecular basis for increased binding to RNA upon heat shock in the cytosol. Our study represents a step toward understanding how free RNA is processed in the cytosol during proteostasis stress.
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Affiliation(s)
- Marion Alriquet
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Adrían Martínez-Limón
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Gerd Hanspach
- Institute for Organic Chemistry and Chemical Biology , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Universitat Pompeu Fabra (UPF), Institucio Catalana de Recerca i Estudis Avançats (ICREA) , 08002 Barcelona , Spain
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - R Martin Vabulas
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
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35
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Abstract
Most single-molecule techniques observing RNA in vitro or in vivo require fluorescent labels that have to be connected to the RNA of interest. In recent years, a plethora of methods has been developed to achieve site-specific labelling, in many cases under near-native conditions. Here, we review chemical as well as enzymatic labelling methods that are compatible with single-molecule fluorescence spectroscopy or microscopy and show how these can be combined to offer a large variety of options to site-specifically place one or more labels in an RNA of interest. By either chemically forming a covalent bond or non-covalent hybridization, these techniques are prerequisites to perform state-of-the-art single-molecule experiments.
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Affiliation(s)
- Gerd Hanspach
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
| | - Sven Trucks
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
| | - Martin Hengesbach
- a Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology , Frankfurt , Germany
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36
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Schmidt A, Altincekic N, Gustmann H, Wachtveitl J, Hengesbach M. The Protein Microenvironment Governs the Suitability of Labeling Sites for Single-Molecule Spectroscopy of RNP Complexes. ACS Chem Biol 2018; 13:2472-2483. [PMID: 30060648 DOI: 10.1021/acschembio.8b00348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-molecule techniques allow unique insights into biological systems as they provide unrivaled access to structural dynamics and conformational heterogeneity. One major bottleneck for reliable single-molecule Förster resonance energy transfer (smFRET) analysis is the identification of suitable fluorophore labeling sites that neither impair the function of the biological system nor cause photophysical artifacts of the fluorophore. To address this issue, we identified the contribution of virtually all individual parameters that affect Förster resonance energy transfer between two fluorophores attached to a ribonucleoprotein complex consisting of the RNA-binding protein L7Ae and a cognate kink turn containing RNA. A non-natural amino acid was incorporated at various positions of the protein using an amber suppression system (pEVOL) to label the protein via copper(I)-catalyzed alkyne-azide cycloaddition. On the basis of simulations followed by functional, structural, and multiparameter fluorescence analysis of five different smFRET RNPs, new insights into the design of smFRET RNPs were obtained. From this, a correlation between the photophysical properties of fluorophores attached to the protein and the predictability of the corresponding smFRET construct was established. Additionally, we identify a straightforward experimental method for characterizing selected labeling sites. Overall, this protocol allows fast generation and assessment of functional RNPs for accurate single-molecule experiments.
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Affiliation(s)
- Andreas Schmidt
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Henrik Gustmann
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
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37
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Warhaut S, Mertinkus KR, Höllthaler P, Fürtig B, Heilemann M, Hengesbach M, Schwalbe H. Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy. Nucleic Acids Res 2017; 45:5512-5522. [PMID: 28204648 PMCID: PMC5605240 DOI: 10.1093/nar/gkx110] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/06/2017] [Indexed: 01/20/2023] Open
Abstract
The full-length translation-regulating add adenine riboswitch (Asw) from Vibrio vulnificus has a more complex conformational space than its isolated aptamer domain. In addition to the predicted apo (apoA) and holo conformation that feature the conserved three-way junctional purine riboswitch aptamer, it adopts a second apo (apoB) conformation with a fundamentally different secondary structure. Here, we characterized the ligand-dependent conformational dynamics of the full-length add Asw by NMR and by single-molecule FRET (smFRET) spectroscopy. Both methods revealed an adenine-induced secondary structure switch from the apoB-form to the apoA-form that involves no tertiary structural interactions between aptamer and expression platform. This strongly suggests that the add Asw triggers translation by capturing the apoA-form secondary structure in the holo state. Intriguingly, NMR indicated a homogenous, docked aptamer kissing loop fold for apoA and holo, while smFRET showed persistent aptamer kissing loop docking dynamics between comparably stable, undocked and docked substates of the apoA and the holo conformation. Unraveling the folding of large junctional riboswitches thus requires the integration of complementary solution structural techniques such as NMR and smFRET.
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Affiliation(s)
- Sven Warhaut
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Klara Rebecca Mertinkus
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Philipp Höllthaler
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Martin Hengesbach
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
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38
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Helmling C, Wacker A, Wolfinger MT, Hofacker IL, Hengesbach M, Fürtig B, Schwalbe H. NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations. J Am Chem Soc 2017; 139:2647-2656. [PMID: 28134517 DOI: 10.1021/jacs.6b10429] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene repression induced by the formation of transcriptional terminators represents a prime example for the coupling of RNA synthesis, folding, and regulation. In this context, mapping the changes in available conformational space of transcription intermediates during RNA synthesis is important to understand riboswitch function. A majority of riboswitches, an important class of small metabolite-sensing regulatory RNAs, act as transcriptional regulators, but the dependence of ligand binding and the subsequent allosteric conformational switch on mRNA transcript length has not yet been investigated. We show a strict fine-tuning of binding and sequence-dependent alterations of conformational space by structural analysis of all relevant transcription intermediates at single-nucleotide resolution for the I-A type 2'dG-sensing riboswitch from Mesoplasma florum by NMR spectroscopy. Our results provide a general framework to dissect the coupling of synthesis and folding essential for riboswitch function, revealing the importance of metastable states for RNA-based gene regulation.
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Affiliation(s)
- Christina Helmling
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
| | - Anna Wacker
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
| | - Michael T Wolfinger
- Medical University of Vienna , Center for Anatomy and Cell Biology, Währingerstraße 13, 1090 Vienna, Austria
| | | | - Martin Hengesbach
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
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39
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Helmling C, Keyhani S, Sochor F, Fürtig B, Hengesbach M, Schwalbe H. Rapid NMR screening of RNA secondary structure and binding. J Biomol NMR 2015; 63:67-76. [PMID: 26188386 DOI: 10.1007/s10858-015-9967-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/13/2015] [Indexed: 05/10/2023]
Abstract
Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3' end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA.
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Affiliation(s)
- Christina Helmling
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Sara Keyhani
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Florian Sochor
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany.
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40
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Silvers R, Keller H, Schwalbe H, Hengesbach M. Inside Cover: Differential Scanning Fluorimetry for Monitoring RNA Stability (ChemBioChem 7/2015). Chembiochem 2015. [DOI: 10.1002/cbic.201590016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Silvers R, Keller H, Schwalbe H, Hengesbach M. Differential Scanning Fluorimetry for Monitoring RNA Stability. Chembiochem 2015; 16:1109-14. [DOI: 10.1002/cbic.201500046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/05/2022]
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Hengesbach M, Schwalbe H. Strukturelle Grundlage der Regulation der 2′-O-Methylierung ribosomaler RNA. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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43
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Abstract
Methods that interrogate different, yet overlapping structural-size ranges were integrated to gain high-resolution information on the Pyrococcus furiosus box C/D ribonucleoprotein complex. The new structure shows how 2'-O-methylation of RNA substrates through four active methyltransferases occurs in a strictly sequential manner.
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Affiliation(s)
- Martin Hengesbach
- Institut für Organische Chemie und Chemische Biologie, Biomolekulares Magnetresonanz-Zentrum (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
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Hengesbach M, Kim NK, Feigon J, Stone MD. Single-molecule FRET reveals the folding dynamics of the human telomerase RNA pseudoknot domain. Angew Chem Int Ed Engl 2012; 51:5876-9. [PMID: 22544760 DOI: 10.1002/anie.201200526] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/10/2012] [Indexed: 12/30/2022]
Affiliation(s)
- Martin Hengesbach
- Department of Chemistry and Biochemistry, Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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45
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Hengesbach M, Kim NK, Feigon J, Stone MD. Single-Molecule FRET Reveals the Folding Dynamics of the Human Telomerase RNA Pseudoknot Domain. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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46
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Hengesbach M, Stone MD. Single Molecule Analysis of Human Telomerase RNA Pseudoknot Folding and Dynamics. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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47
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Hengesbach M, Akiyama BM, Stone MD. Single-molecule analysis of telomerase structure and function. Curr Opin Chem Biol 2011; 15:845-52. [PMID: 22057212 DOI: 10.1016/j.cbpa.2011.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 10/05/2011] [Accepted: 10/17/2011] [Indexed: 02/06/2023]
Abstract
The telomerase ribonucleoprotein is a specialized reverse transcriptase required to maintain protective chromosome end-capping structures called telomeres. In most cells, telomerase is not active and the natural shortening of telomeres with each round of DNA replication ultimately triggers cell growth arrest. In contrast, the presence of telomerase confers a high level of renewal capacity upon rapidly dividing cells. Telomerase is aberrantly activated in 90% of human cancers and thus represents an important target for anticancer therapeutics. However, the naturally low abundance of telomerase has hampered efforts to obtain high-resolution models for telomerase structure and function. To circumvent these challenges, single-molecule techniques have recently been employed to investigate telomerase assembly, structure, and catalysis.
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Affiliation(s)
- Martin Hengesbach
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
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48
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Kobitski A, Hengesbach M, Seidu-Larry S, Dammertz K, Chow C, van Aerschot A, Nienhaus GU, Helm M. Single-Molecule FRET Reveals a Cooperative Effect of Two Methyl Group Modifications in the Folding of Human Mitochondrial tRNALys. ACTA ACUST UNITED AC 2011; 18:928-36. [DOI: 10.1016/j.chembiol.2011.03.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 03/14/2011] [Accepted: 03/29/2011] [Indexed: 10/17/2022]
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49
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Dammertz K, Hengesbach M, Helm M, Nienhaus GU, Kobitski AY. Single-Molecule FRET Studies of Counterion Effects on the Free Energy Landscape of Human Mitochondrial Lysine tRNA. Biochemistry 2011; 50:3107-15. [DOI: 10.1021/bi101804t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Martin Hengesbach
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
- Institute of Pharmacy and Biochemistry, University of Mainz, 55128 Mainz, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrei Yu. Kobitski
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany
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Hengesbach M, Voigts-Hoffmann F, Hofmann B, Helm M. Formation of a stalled early intermediate of pseudouridine synthesis monitored by real-time FRET. RNA 2010; 16:610-620. [PMID: 20106954 PMCID: PMC2822925 DOI: 10.1261/rna.1832510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 12/03/2009] [Indexed: 05/28/2023]
Abstract
Pseudouridine is the most abundant of more than 100 chemically distinct natural ribonucleotide modifications. Its synthesis consists of an isomerization reaction of a uridine residue in the RNA chain and is catalyzed by pseudouridine synthases. The unusual reaction mechanism has become the object of renewed research effort, frequently involving replacement of the substrate uridines with 5-fluorouracil (f(5)U). f(5)U is known to be a potent inhibitor of pseudouridine synthase activity, but the effect varies among the target pseudouridine synthases. Derivatives of f(5)U have previously been detected, which are thought to be either hydrolysis products of covalent enzyme-RNA adducts, or isomerization intermediates. Here we describe the interaction of pseudouridine synthase 1 (Pus1p) with f(5)U-containing tRNA. The interaction described is specific to Pus1p and position 27 in the tRNA anticodon stem, but the enzyme neither forms a covalent adduct nor stalls at a previously identified reaction intermediate of f(5)U. The f(5)U27 residue, as analyzed by a DNAzyme-based assay using TLC and mass spectrometry, displayed physicochemical properties unaltered by the reversible interaction with Pus1p. Thus, Pus1p binds an f(5)U-containing substrate, but, in contrast to other pseudouridine synthases, leaves the chemical structure of f(5)U unchanged. The specific, but nonproductive, interaction demonstrated here thus constitutes an intermediate of Pus turnover, stalled by the presence of f(5)U in an early state of catalysis. Observation of the interaction of Pus1p with fluorescence-labeled tRNA by a real-time readout of fluorescence anisotropy and FRET revealed significant structural distortion of f(5)U-tRNA structure in the stalled intermediate state of pseudouridine catalysis.
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Affiliation(s)
- Martin Hengesbach
- Institute of Pharmacy and Molecular Biotechnology, Department of Chemistry, Heidelberg University, 69120 Heidelberg, Germany
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