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Soni K, Jagtap PKA, Martínez-Lumbreras S, Bonnal S, Geerlof A, Stehle R, Simon B, Valcárcel J, Sattler M. Structural basis for specific RNA recognition by the alternative splicing factor RBM5. Nat Commun 2023; 14:4233. [PMID: 37454201 PMCID: PMC10349855 DOI: 10.1038/s41467-023-39961-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The RNA-binding motif protein RBM5 belongs to a family of multi-domain RNA binding proteins that regulate alternative splicing of genes important for apoptosis and cell proliferation and have been implicated in cancer. RBM5 harbors structural modules for RNA recognition, such as RRM domains and a Zn finger, and protein-protein interactions such as an OCRE domain. Here, we characterize binding of the RBM5 RRM1-ZnF1-RRM2 domains to cis-regulatory RNA elements. A structure of the RRM1-ZnF1 region in complex with RNA shows how the tandem domains cooperate to sandwich target RNA and specifically recognize a GG dinucleotide in a non-canonical fashion. While the RRM1-ZnF1 domains act as a single structural module, RRM2 is connected by a flexible linker and tumbles independently. However, all three domains participate in RNA binding and adopt a closed architecture upon RNA binding. Our data highlight how cooperativity and conformational modularity of multiple RNA binding domains enable the recognition of distinct RNA motifs, thereby contributing to the regulation of alternative splicing. Remarkably, we observe surprising differences in coupling of the RNA binding domains between the closely related homologs RBM5 and RBM10.
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Affiliation(s)
- Komal Soni
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Pravin Kumar Ankush Jagtap
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Santiago Martínez-Lumbreras
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sophie Bonnal
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
| | - Arie Geerlof
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Ralf Stehle
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85748, Garching, Germany.
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Neuhaus D. Zinc finger structure determination by NMR: Why zinc fingers can be a handful. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:62-105. [PMID: 36113918 PMCID: PMC7614390 DOI: 10.1016/j.pnmrs.2022.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 06/07/2023]
Abstract
Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.
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Affiliation(s)
- David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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Lugo-Reyes SO, Pastor N, González-Serrano E, Yamazaki-Nakashimada MA, Scheffler-Mendoza S, Berron-Ruiz L, Wakida G, Nuñez-Nuñez ME, Macias-Robles AP, Staines-Boone AT, Venegas-Montoya E, Alaez-Verson C, Molina-Garay C, Flores-Lagunes LL, Carrillo-Sanchez K, Niemela J, Rosenzweig SD, Gaytan P, Yañez JA, Martinez-Duncker I, Notarangelo LD, Espinosa-Padilla S, Cruz-Munoz ME. Clinical Manifestations, Mutational Analysis, and Immunological Phenotype in Patients with RAG1/2 Mutations: First Cases Series from Mexico and Description of Two Novel Mutations. J Clin Immunol 2021; 41:1291-1302. [PMID: 33954879 DOI: 10.1007/s10875-021-01052-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/20/2021] [Indexed: 11/25/2022]
Abstract
Mutations in recombinase activating genes 1 and 2 (RAG1/2) result in human severe combined immunodeficiency (SCID). The products of these genes are essential for V(D)J rearrangement of the antigen receptors during lymphocyte development. Mutations resulting in null-recombination activity in RAG1 or RAG2 are associated with the most severe clinical and immunological phenotypes, whereas patients with hypomorphic mutations may develop leaky SCID, including Omenn syndrome (OS). A group of previously unrecognized clinical phenotypes associated with granulomata and/or autoimmunity have been described as a consequence of hypomorphic mutations. Here, we present six patients from unrelated families with missense variants in RAG1 or RAG2. Phenotypes observed in these patients ranged from OS to severe mycobacterial infections and granulomatous disease. Moreover, we report the first evidence of two variants that had not been associated with immunodeficiency. This study represents the first case series of RAG1- or RAG2-deficient patients from Mexico and Latin America.
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Affiliation(s)
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | | | | | | | - Laura Berron-Ruiz
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Guillermo Wakida
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | | | | | - Edna Venegas-Montoya
- Unidad Médica de Alta Especialidad 25, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | | | | | - Julie Niemela
- Laboratory of Clinical Immunology and Microbiology, National Institute of Health, Mexico City, Mexico
| | - Sergio D Rosenzweig
- Laboratory of Clinical Immunology and Microbiology, National Institute of Health, Mexico City, Mexico
| | - Paul Gaytan
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge A Yañez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ivan Martinez-Duncker
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Health, Mexico City, Mexico
| | - Sara Espinosa-Padilla
- Laboratorio de Inmunodeficiencias, Instituto Nacional de Pediatría, Mexico City, Mexico.
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