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Tants JN, Schlundt A. Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA. Chembiochem 2023; 24:e202300110. [PMID: 37466350 DOI: 10.1002/cbic.202300110] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/22/2023] [Indexed: 07/20/2023]
Abstract
RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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2
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Korn SM, Von Ehr J, Dhamotharan K, Tants JN, Abele R, Schlundt A. Insight into the Structural Basis for Dual Nucleic Acid-Recognition by the Scaffold Attachment Factor B2 Protein. Int J Mol Sci 2023; 24:ijms24043286. [PMID: 36834708 PMCID: PMC9958909 DOI: 10.3390/ijms24043286] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
The family of scaffold attachment factor B (SAFB) proteins comprises three members and was first identified as binders of the nuclear matrix/scaffold. Over the past two decades, SAFBs were shown to act in DNA repair, mRNA/(l)ncRNA processing and as part of protein complexes with chromatin-modifying enzymes. SAFB proteins are approximately 100 kDa-sized dual nucleic acid-binding proteins with dedicated domains in an otherwise largely unstructured context, but whether and how they discriminate DNA and RNA binding has remained enigmatic. We here provide the SAFB2 DNA- and RNA-binding SAP and RRM domains in their functional boundaries and use solution NMR spectroscopy to ascribe DNA- and RNA-binding functions. We give insight into their target nucleic acid preferences and map the interfaces with respective nucleic acids on sparse data-derived SAP and RRM domain structures. Further, we provide evidence that the SAP domain exhibits intra-domain dynamics and a potential tendency to dimerize, which may expand its specifically targeted DNA sequence range. Our data provide a first molecular basis of and a starting point towards deciphering DNA- and RNA-binding functions of SAFB2 on the molecular level and serve a basis for understanding its localization to specific regions of chromatin and its involvement in the processing of specific RNA species.
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Affiliation(s)
- Sophie M. Korn
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Julian Von Ehr
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Karthikeyan Dhamotharan
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Jan-Niklas Tants
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
- Correspondence:
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3
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Tants JN, Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A. NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res 2022; 50:4083-4099. [PMID: 35357505 PMCID: PMC9023295 DOI: 10.1093/nar/gkac212] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 12/31/2022] Open
Abstract
Control of posttranscriptional mRNA decay is a crucial determinant of cell homeostasis and differentiation. mRNA lifetime is governed by cis-regulatory elements in their 3′ untranslated regions (UTR). Despite ongoing progress in the identification of cis elements we have little knowledge about the functional and structural integration of multiple elements in 3′UTR regulatory hubs and their recognition by mRNA-binding proteins (RBPs). Structural analyses are complicated by inconsistent mapping and prediction of RNA fold, by dynamics, and size. We here, for the first time, provide the secondary structure of a complete mRNA 3′UTR. We use NMR spectroscopy in a divide-and-conquer strategy complemented with SAXS, In-line probing and SHAPE-seq applied to the 3′UTR of Ox40 mRNA, which encodes a T-cell co-receptor repressed by the protein Roquin. We provide contributions of RNA elements to Roquin-binding. The protein uses its extended bi-modal ROQ domain to sequentially engage in a 2:1 stoichiometry with a 3′UTR core motif. We observe differential binding of Roquin to decay elements depending on their structural embedment. Our data underpins the importance of studying RNA regulation in a full sequence and structural context. This study serves as a paradigm for an approach in analysing structured RNA-regulatory hubs and their binding by RBPs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Lea Marie Becker
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - François McNicoll
- Goethe University Frankfurt, Institute for Molecular Biosciences, Max-von-Laue-Str. 13, 60438 Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Goethe University Frankfurt, Institute for Molecular Biosciences, Max-von-Laue-Str. 13, 60438 Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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4
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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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5
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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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6
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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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7
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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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8
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Binas O, Tants JN, Peter SA, Janowski R, Davydova E, Braun J, Niessing D, Schwalbe H, Weigand JE, Schlundt A. Structural basis for the recognition of transiently structured AU-rich elements by Roquin. Nucleic Acids Res 2020; 48:7385-7403. [PMID: 32491174 PMCID: PMC7367199 DOI: 10.1093/nar/gkaa465] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/16/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Adenylate/uridylate-rich elements (AREs) are the most common cis-regulatory elements in the 3′-untranslated region (UTR) of mRNAs, where they fine-tune turnover by mediating mRNA decay. They increase plasticity and efficacy of mRNA regulation and are recognized by several ARE-specific RNA-binding proteins (RBPs). Typically, AREs are short linear motifs with a high content of complementary A and U nucleotides and often occur in multiple copies. Although thermodynamically rather unstable, the high AU-content might enable transient secondary structure formation and modify mRNA regulation by RBPs. We have recently suggested that the immunoregulatory RBP Roquin recognizes folded AREs as constitutive decay elements (CDEs), resulting in shape-specific ARE-mediated mRNA degradation. However, the structural evidence for a CDE-like recognition of AREs by Roquin is still lacking. We here present structures of CDE-like folded AREs, both in their free and protein-bound form. Moreover, the AREs in the UCP3 3′-UTR are additionally bound by the canonical ARE-binding protein AUF1 in their linear form, adopting an alternative binding-interface compared to the recognition of their CDE structure by Roquin. Strikingly, our findings thus suggest that AREs can be recognized in multiple ways, allowing control over mRNA regulation by adapting distinct conformational states, thus providing differential accessibility to regulatory RBPs.
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Affiliation(s)
- Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany
| | - Jan-Niklas Tants
- Institute for Molecular Biosciences, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Elena Davydova
- Institute of Structural Biology, Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Braun
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz-Zentrum München, 85764 Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany
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Heber S, Gáspár I, Tants JN, Günther J, Moya SMF, Janowski R, Ephrussi A, Sattler M, Niessing D. Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains. Nat Commun 2019; 10:1659. [PMID: 30971701 PMCID: PMC6477676 DOI: 10.1038/s41467-019-09655-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/20/2019] [Indexed: 11/08/2022] Open
Abstract
Throughout metazoans, Staufen (Stau) proteins are core factors of mRNA localization particles. They consist of three to four double-stranded RNA binding domains (dsRBDs) and a C-terminal dsRBD-like domain. Mouse Staufen2 (mStau2)-like Drosophila Stau (dmStau) contains four dsRBDs. Existing data suggest that only dsRBDs 3-4 are necessary and sufficient for mRNA binding. Here, we show that dsRBDs 1 and 2 of mStau2 bind RNA with similar affinities and kinetics as dsRBDs 3 and 4. While RNA binding by these tandem domains is transient, all four dsRBDs recognize their target RNAs with high stability. Rescue experiments in Drosophila oocytes demonstrate that mStau2 partially rescues dmStau-dependent mRNA localization. In contrast, a rescue with mStau2 bearing RNA-binding mutations in dsRBD1-2 fails, confirming the physiological relevance of our findings. In summary, our data show that the dsRBDs 1-2 play essential roles in the mRNA recognition and function of Stau-family proteins of different species.
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Affiliation(s)
- Simone Heber
- Institute of Pharmaceutical Biotechnology, 89081 Ulm University, Ulm, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Imre Gáspár
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
- Institute of Molecular Biotechnology, 1030, Vienna, Austria
| | - Jan-Niklas Tants
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemistry, Technische Universität München, 85747, Garching, Germany
| | - Johannes Günther
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemistry, Technische Universität München, 85747, Garching, Germany
| | - Sandra M Fernandez Moya
- Biomedical Center Munich, Department of Cell Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemistry, Technische Universität München, 85747, Garching, Germany
| | - Dierk Niessing
- Institute of Pharmaceutical Biotechnology, 89081 Ulm University, Ulm, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.
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Falk S, Tants JN, Basquin J, Thoms M, Hurt E, Sattler M, Conti E. Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53. RNA 2017; 23:1780-1787. [PMID: 28883156 PMCID: PMC5688999 DOI: 10.1261/rna.062901.117] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 09/05/2017] [Indexed: 05/24/2023]
Abstract
The nuclear exosome and the associated RNA helicase Mtr4 participate in the processing of several ribonucleoprotein particles (RNP), including the maturation of the large ribosomal subunit (60S). S. cerevisiae Mtr4 interacts directly with Nop53, a ribosomal biogenesis factor present in late pre-60S particles containing precursors of the 5.8S rRNA. The Mtr4-Nop53 interaction plays a pivotal role in the maturation of the 5.8S rRNA, providing a physical link between the nuclear exosome and the pre-60S RNP. An analogous interaction between Mtr4 and another ribosome biogenesis factor, Utp18, directs the exosome to an earlier preribosomal particle. Nop53 and Utp18 contain a similar Mtr4-binding motif known as the arch-interacting motif (AIM). Here, we report the 3.2 Å resolution crystal structure of S. cerevisiae Mtr4 bound to the interacting region of Nop53, revealing how the KOW domain of the helicase recognizes the AIM sequence of Nop53 with a network of hydrophobic and electrostatic interactions. The AIM-interacting residues are conserved in Mtr4 and are not present in the related cytoplasmic helicase Ski2, rationalizing the specificity and versatility of Mtr4 in the recognition of different AIM-containing proteins. Using nuclear magnetic resonance (NMR), we show that the KOW domain of Mtr4 can simultaneously bind an AIM-containing protein and a structured RNA at adjacent surfaces, suggesting how it can dock onto RNPs. The KOW domains of exosome-associated helicases thus appear to have evolved from the KOW domains of ribosomal proteins and to function as RNP-binding modules in the context of the nuclear exosome.
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Affiliation(s)
- Sebastian Falk
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
| | - Jan-Niklas Tants
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jerôme Basquin
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
| | - Matthias Thoms
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Michael Sattler
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Elena Conti
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, D-82152 Martinsried, Germany
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Tants JN, Fesser S, Kern T, Stehle R, Geerlof A, Wunderlich C, Juen M, Hartlmüller C, Böttcher R, Kunzelmann S, Lange O, Kreutz C, Förstemann K, Sattler M. Molecular basis for asymmetry sensing of siRNAs by the Drosophila Loqs-PD/Dcr-2 complex in RNA interference. Nucleic Acids Res 2017; 45:12536-12550. [PMID: 29040648 PMCID: PMC5716069 DOI: 10.1093/nar/gkx886] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/22/2017] [Accepted: 09/22/2017] [Indexed: 12/26/2022] Open
Abstract
RNA interference defends against RNA viruses and retro-elements within an organism's genome. It is triggered by duplex siRNAs, of which one strand is selected to confer sequence-specificity to the RNA induced silencing complex (RISC). In Drosophila, Dicer-2 (Dcr-2) and the double-stranded RNA binding domain (dsRBD) protein R2D2 form the RISC loading complex (RLC) and select one strand of exogenous siRNAs according to the relative thermodynamic stability of base-pairing at either end. Through genome editing we demonstrate that Loqs-PD, the Drosophila homolog of human TAR RNA binding protein (TRBP) and a paralog of R2D2, forms an alternative RLC with Dcr-2 that is required for strand choice of endogenous siRNAs in S2 cells. Two canonical dsRBDs in Loqs-PD bind to siRNAs with enhanced affinity compared to miRNA/miRNA* duplexes. Structural analysis, NMR and biophysical experiments indicate that the Loqs-PD dsRBDs can slide along the RNA duplex to the ends of the siRNA. A moderate but notable binding preference for the thermodynamically more stable siRNA end by Loqs-PD alone is greatly amplified in complex with Dcr-2 to initiate strand discrimination by asymmetry sensing in the RLC.
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Affiliation(s)
- Jan-Niklas Tants
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Stephanie Fesser
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Thomas Kern
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Christoph Wunderlich
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Michael Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Hartlmüller
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Romy Böttcher
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Stefan Kunzelmann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Oliver Lange
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Klaus Förstemann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
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