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Sabei A, Hognon C, Martin J, Frezza E. Dynamics of Protein-RNA Interfaces Using All-Atom Molecular Dynamics Simulations. J Phys Chem B 2024; 128:4865-4886. [PMID: 38740056 DOI: 10.1021/acs.jpcb.3c07698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Facing the current challenges posed by human health diseases requires the understanding of cell machinery at a molecular level. The interplay between proteins and RNA is key for any physiological phenomenon, as well protein-RNA interactions. To understand these interactions, many experimental techniques have been developed, spanning a very wide range of spatial and temporal resolutions. In particular, the knowledge of tridimensional structures of protein-RNA complexes provides structural, mechanical, and dynamical pieces of information essential to understand their functions. To get insights into the dynamics of protein-RNA complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on nine different protein-RNA complexes with different functions and interface size by taking into account the bound and unbound forms. First, we characterized structural changes upon binding and, for the RNA part, the change in the puckering. Second, we extensively analyzed the interfaces, their dynamics and structural properties, and the structural waters involved in the binding, as well as the contacts mediated by them. Based on our analysis, the interfaces rearranged during the simulation time showing alternative and stable residue-residue contacts with respect to the experimental structure.
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Affiliation(s)
- Afra Sabei
- Université Paris Cité, CiTCoM, CNRS, Paris F-75006, France
| | - Cécilia Hognon
- Université Paris Cité, CiTCoM, CNRS, Paris F-75006, France
| | - Juliette Martin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5086 MMSB, Lyon 69367, France
- Laboratory of Biology and Modeling of the Cell, Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, Lyon 69367, France
| | - Elisa Frezza
- Université Paris Cité, CiTCoM, CNRS, Paris F-75006, France
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2
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Roca-Martínez J, Kang HS, Sattler M, Vranken W. Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: connecting experimental with AlphaFold2 predicted models. NAR Genom Bioinform 2024; 6:lqae002. [PMID: 38288375 PMCID: PMC10823583 DOI: 10.1093/nargab/lqae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/07/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
The RNA recognition motif (RRM) is the most prevalent RNA binding domain in eukaryotes and is involved in most RNA metabolism processes. Single RRM domains have a limited RNA specificity and affinity and tend to be accompanied by other RNA binding domains, frequently additional RRMs that contribute to an avidity effect. Within multi-RRM proteins, the most common arrangement are tandem RRMs, with two domains connected by a variable linker. Despite their prevalence, little is known about the features that lead to specific arrangements, and especially the role of the connecting linker. In this work, we present a novel and robust way to investigate the relative domain orientation in multi-domain proteins using inter-domain vectors referenced to a stable secondary structure element. We apply this method to tandem RRM domains and cluster experimental tandem RRM structures according to their inter-domain and linker-domain contacts, and report how this correlates with their orientation. By extending our analysis to AlphaFold2 predicted structures, with particular attention to the inter-domain predicted aligned error, we identify new orientations not reported experimentally. Our analysis provides novel insights across a range of tandem RRM orientations that may help for the design of proteins with a specific RNA binding mode.
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Affiliation(s)
- Joel Roca-Martínez
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Hyun-Seo Kang
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, 85764 Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, 85747 Garching, Germany
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, 85764 Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, 85747 Garching, Germany
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
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3
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Liu Y, Hu B, Pei X, Li J, Qi D, Xu Y, Ou H, Wu Y, Xue L, Huang JH, Wu E, Hu X. A Non-G-Quadruplex DNA Aptamer Targeting NCL for Diagnosis and Therapy in Bladder Cancer. Adv Healthc Mater 2023; 12:e2300791. [PMID: 37262080 DOI: 10.1002/adhm.202300791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 06/03/2023]
Abstract
Bladder cancer (BC) is a highly aggressive malignant tumor affecting the urinary system, characterized by metastasis and a poor prognosis that often leads to limited therapeutic success. This study aims to develop a novel DNA aptamer for the diagnosis and treatment of BC using a tissue-based systematic evolution of ligands by an exponential enrichment (SELEX) process. By using SELEX, this work successfully generates a new aptamer named TB-5, which demonstrates a remarkable and specific affinity for nucleolin (NCL) in BC tissues and displays marked biocompatibility both in vitro and in vivo. Additionally, this work shows that NCL is a reliable tissue-specific biomarker in BC. Moreover, according to circular dichroism spectroscopy, TB-5 forms a non-G-quadruplex structure, distinguishing it from the current NCL-targeting aptamer AS1411, and exhibits a distinct binding region on NCL compared to AS1411. Notably, this study further reveals that TB-5 activates NCL function by promoting autophagy and suppressing the migration and invasion of BC cells, which occurs by disrupting mRNA transcription processes. These findings highlight the critical role of NCL in the pathological examination of BC and warrant more comprehensive investigations on anti-NCL aptamers in BC imaging and treatment.
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Affiliation(s)
- Yunyi Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Bei Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xiaming Pei
- Department of Urology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine. Changsha, Hunan, 410013, China
| | - Juan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
| | - Yuxi Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Hailong Ou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Yatao Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Lei Xue
- Department of Pathology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine. Changsha, Hunan, 410013, China
| | - Jason H Huang
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
- Department of Medical Education, Texas A&M University School of Medicine, College Station, TX, 77843, USA
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
- Department of Medical Education, Texas A&M University School of Medicine, College Station, TX, 77843, USA
- Department of Pharmaceutical Sciences, Texas A&M University School of Pharmacy, College Station, TX, 77843, USA
- LIVESTRONG Cancer Institutes and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Xiaoxiao Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Research Institute of Hunan University in Chongqing, Chongqing, 401120, China
- Shenzhen Research Institute, Hunan University, Shenzhen, Guangdong, 518000, China
- Hunan Yonghe-sun Biotechnology Co. Ltd., Changsha, Hunan, 410082, China
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4
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Che X, Wu J, Liu H, Su J, Chen X. Cellular liquid-liquid phase separation: Concept, functions, regulations, and detections. J Cell Physiol 2023; 238:847-865. [PMID: 36870067 DOI: 10.1002/jcp.30980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023]
Abstract
Liquid-liquid phase separation is a multicomponent system separated into phases with different compositions and structures. It has been identified and explored in organisms after being introduced from the thermodynamic field. Condensate, the product of phase separation, exists in different scales of cellular structures, such as nucleolus, stress granules, and other organelles in nuclei or cytoplasm. And also play critical roles in different cellular behaviors. Here, we review the concept, thermodynamical and biochemical principles of phase separation. We summarized the main functions including the adjustment of biochemical reaction rates, the regulation of macromolecule folding state, subcellular structural support, the mediation of subcellular location, and intimately linked to different kinds of diseases, such as cancer and neurodegeneration. Advanced detection methods to investigate phase separation are collected and analyzed. We conclude with the discussion of anxiety of phase separation, and thought about how progress can be made to develop precise detection methods and disclose the potential application of condensates.
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Affiliation(s)
- Xuanlin Che
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Jiajun Wu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Hua Liu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
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5
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Bie L, Wang Y, Jiang F, Xiao Z, Zhang L, Wang J. Insights into the binding mode of AS1411 aptamer to nucleolin. Front Mol Biosci 2022; 9:1025313. [PMID: 36262475 PMCID: PMC9574071 DOI: 10.3389/fmolb.2022.1025313] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 11/23/2022] Open
Abstract
AS1411 aptamer can function as a recognition probe to detect the cell surface nucleolin overexpressed in cancer cells, however, little is known about their binding process. This study proposed a feasible binding mode for the first time and provided atomic-level descriptions for the high affinity and specific binding of AS1411. The binding pose predicted by docking was screened using knowledge-based criteria, and a microsecond molecular dynamics (MD) simulation showed the stable existence of the predicted structure in the solution. Structural analysis shows that the unique capping of the 5′ end of AS1411 provides the specific binding with RBD1, and the interactions of hydrogen bond, salt bridge, and water-mediated network between AS1411 and RBD1,2 stabilize the binding. The calculation of per-residue decomposition emphasizes the dominant contribution of van der Waals energy and critical residues are screened. Our study provides the molecular basis of this specific binding and can guide rational AS1411-based aptamers design. Further insights require tight collaborations between the experiments and in silico studies.
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Affiliation(s)
- Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Yue Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Fuze Jiang
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Zhen Xiao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Lianjun Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Jing Wang
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
- *Correspondence: Jing Wang,
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6
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Santos T, Lopes-Nunes J, Alexandre D, Miranda A, Figueiredo J, Silva MS, Mergny JL, Cruz C. Stabilization of a DNA aptamer by ligand binding. Biochimie 2022; 200:8-18. [PMID: 35550917 DOI: 10.1016/j.biochi.2022.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/03/2022] [Accepted: 05/05/2022] [Indexed: 12/17/2022]
Abstract
G-rich aptamers such as AS1411 are small oligonucleotides that present several benefits comparatively to monoclonal antibodies, since they are easier to manufacture and store, have small size and do not stimulate an immune response. We analyzed AT11-B1, a modified sequence of AT11 (itself a modified version of AS1411), in which one thymine was removed from the bulge region. We studied G-quadruplex (G4) formation/stabilization using PhenDC3, PDS, BRACO-19, TMPyP4 and 360A ligands by different biophysical techniques, namely circular dichroism (CD), Förster resonance energy transfer (FRET-melting) and nuclear magnetic resonance (NMR). The CD spectra showed that AT11-B1 adopts a predominant G4 of parallel topology when the buffer contains KCl or when ligands are added. PhenDC3 induced a ΔTm of 30 °C or more of the G4 structure as shown by CD- and FRET-melting experiments. The ligands demonstrate high affinity for AT11-B1 G4 and the NMR studies revealed that the AT11-B1 G4 involves four G-tetrad layers. The in silico studies suggest that all ligands bind AT11-B1 G4, namely, by stacking interactions, except PDS that may bind to the loop/groove interface. In addition, molecular dynamics simulations revealed that nucleolin (NCL) interacts with the AT11-B1 G4 structure through the RNA binding domain (RBD) 2 and the 12-residue linker between RBD1,2. Moreover, AT11-B1 G4 was internalized into a NCL-positive tongue squamous cell carcinoma cell line. In a nutshell, this study may help the identification of the ligands scaffolds to bind and stabilize AT11-B1, improving the targeting towards NCL that is overexpressed in cancer cells.
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Affiliation(s)
- Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Jéssica Lopes-Nunes
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Daniela Alexandre
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Joana Figueiredo
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Micael S Silva
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Jean-Louis Mergny
- Institute of Biophysics of the CAS, v.v.i, Královopolská 135, 612 65, Brno, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal.
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7
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Santos T, Miranda A, Imbert L, Jardim A, Caneira CRF, Chu V, Conde JP, Campello MPC, Paulo A, Salgado G, Cabrita EJ, Cruz C. Pre-miRNA-149 G-quadruplex as a molecular agent to capture nucleolin. Eur J Pharm Sci 2022; 169:106093. [PMID: 34922315 DOI: 10.1016/j.ejps.2021.106093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/14/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023]
Abstract
One of the most significant challenges in capturing and detecting biomarkers is the choice of an appropriate biomolecular receptor. Recently, RNA G-quadruplexes emerged as plausible receptors due to their ability to recognize with high-affinity proteins. Herein, we have unveiled and characterized the capability of the precursor microRNA 149 to form a G-quadruplex structure and determined the role that some ligands may have in its folding and binding capacity to nucleolin. The G-quadruplex formation was induced by K+ ions and stabilized by ligands, as demonstrated by nuclear magnetic resonance and circular dichroism experiments. Surface plasmon resonance measurements showed a binding affinity of precursor microRNA 149 towards ligands in the micromolar range (10-5-10-6 M) and a strong binding affinity to nucleolin RNA-binding domains 1 and 2 (8.38 × 10-10 M). Even in the presence of the ligand PhenDC3, the binding remains almost identical and in the same order of magnitude (4.46 × 10-10 M). The molecular interactions of the RNA G-quadruplex motif found in precursor miRNA 149 (5'-GGGAGGGAGGGACGGG- 3') and nucleolin RNA-binding domains 1 and 2 were explored by means of molecular docking and molecular dynamics studies. The results showed that RNA G-quadruplex binds to a cavity between domains 1 and 2 of the protein. Then, complex formation was also evaluated through polyacrylamide gel electrophoresis. The results suggest that precursor microRNA 149/ligands and precursor microRNA 149/nucleolin RNA-binding domains 1 and 2 form stable molecular complexes. The in vitro co-localization of precursor microRNA 149 and nucleolin in PC3 cells was demonstrated using confocal microscopy. Finally, a rapid and straightforward microfluidic strategy was employed to check the ability of precursor microRNA 149 to capture nucleolin RNA-binding domains 1 and 2. The results revealed that precursor microRNA 149 can capture nucleolin RNA-binding domains 1 and 2 labeled with Fluorescein 5-isothiocyanate in a concentration-dependent manner, but PhenDC3 complexation seems to decrease the ability of precursor microRNA 149 to capture the protein. Overall, our results proved the formation of the G-quadruplex structure in the precursor microRNA 149 and the ability to recognize and detect nucleolin. This proof-of-concept study could open up a new framework for developing new strategies to design improved molecular receptors for capture and detection of nucleolin in complex biological samples.
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Affiliation(s)
- Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Lionel Imbert
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France; Univ. Grenoble Alpes, CNRS, CEA, EMBL Integrated Structural Biology Grenoble (ISBG), Grenoble, France
| | - Andreia Jardim
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Catarina R F Caneira
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Virgínia Chu
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - João P Conde
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Paula Cabral Campello
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 1397), 2695-066 Bobadela LRS, Portugal; DECN -Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - António Paulo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 1397), 2695-066 Bobadela LRS, Portugal; DECN -Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Gilmar Salgado
- Univ. Bordeaux, ARNA Laboratory INSERM, U1212, CNRS UMR 5320, IECB, Pessac, France
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal.
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8
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Soubise B, Jiang Y, Douet-Guilbert N, Troadec MB. RBM22, a Key Player of Pre-mRNA Splicing and Gene Expression Regulation, Is Altered in Cancer. Cancers (Basel) 2022; 14:cancers14030643. [PMID: 35158909 PMCID: PMC8833553 DOI: 10.3390/cancers14030643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 01/05/2023] Open
Abstract
RNA-Binding Proteins (RBP) are very diverse and cover a large number of functions in the cells. This review focuses on RBM22, a gene encoding an RBP and belonging to the RNA-Binding Motif (RBM) family of genes. RBM22 presents a Zinc Finger like and a Zinc Finger domain, an RNA-Recognition Motif (RRM), and a Proline-Rich domain with a general structure suggesting a fusion of two yeast genes during evolution: Cwc2 and Ecm2. RBM22 is mainly involved in pre-mRNA splicing, playing the essential role of maintaining the conformation of the catalytic core of the spliceosome and acting as a bridge between the catalytic core and other essential protein components of the spliceosome. RBM22 is also involved in gene regulation, and is able to bind DNA, acting as a bona fide transcription factor on a large number of target genes. Undoubtedly due to its wide scope in the regulation of gene expression, RBM22 has been associated with several pathologies and, notably, with the aggressiveness of cancer cells and with the phenotype of a myelodysplastic syndrome. Mutations, enforced expression level, and haploinsufficiency of RBM22 gene are observed in those diseases. RBM22 could represent a potential therapeutic target in specific diseases, and, notably, in cancer.
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Affiliation(s)
- Benoît Soubise
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
| | - Yan Jiang
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- Department of Hematology, The First Hospital of Jilin University, Changchun 130021, China
| | - Nathalie Douet-Guilbert
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- CHRU Brest, Service de Génétique, Laboratoire de Génétique Chromosomique, F-29200 Brest, France
| | - Marie-Bérengère Troadec
- Université de Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (B.S.); (Y.J.); (N.D.-G.)
- CHRU Brest, Service de Génétique, Laboratoire de Génétique Chromosomique, F-29200 Brest, France
- Correspondence: ; Tel.: +33-2-98-01-64-55
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9
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Nikulin AD. Characteristic Features of Protein Interaction with Single- and Double-Stranded RNA. BIOCHEMISTRY (MOSCOW) 2021; 86:1025-1040. [PMID: 34488578 DOI: 10.1134/s0006297921080125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses differences between the specific protein interactions with single- and double-stranded RNA molecules using the data on the structure of RNA-protein complexes. Proteins interacting with the single-stranded RNAs form contacts with RNA bases, which ensures recognition of specific nucleotide sequences. Formation of such contacts with the double-stranded RNAs is hindered, so that the proteins recognize unique conformations of the RNA spatial structure and interact mainly with the RNA sugar-phosphate backbone.
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Affiliation(s)
- Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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10
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Santos T, Miranda A, Campello MPC, Paulo A, Salgado G, Cabrita EJ, Cruz C. Recognition of nucleolin through interaction with RNA G-quadruplex. Biochem Pharmacol 2021; 189:114208. [PMID: 32860827 DOI: 10.1016/j.bcp.2020.114208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The development of novel biomarkers for early-stage diagnosis of prostate cancer (PCa) has attracted the attention of researchers in the last decade. Nucleolin (NCL) has emerged as a possible biomarker of PCa due to its high expression levels in the surface of PCa cells and affinity towards parallel G4s since it contains four RNA-binding domains (RBDs). Herein, we developed a novel strategy based on a microfluidic platform for the detection of NCL in biological samples, such as human plasma. The RNA G4 (rG4) sequence found in human precursor microRNA 92b (pre-miR-92b) was used as a molecular recognition probe since it forms a single dominant parallel rG4 conformation in the presence of 0.1 mM K+ as confirmed by NMR spectroscopy. The additional stability of the rG4 structure was provided by the acridine orange derivative ligand C8, which stabilizes the pre-miR-92b rG4 structure, as denoted by an increase in more than 30 °C of its melting temperature. FRET-melting assay revealed a remarkable synergistic effect of NCL RBD1,2 and C8 on the stabilization of the pre-miR-92b rG4. The binding of pre-miR-92b to NCL RBD1,2 was determined by in silico studies, which revealed a binding pocket formed by a 12-residue linker between RBD1 and RBD2. Both, pre-miR-92b rG4 and pre-miR-92b rG4/C8 complex demonstrated high affinity towards NCL RBD1,2, as proved by fluorimetric titrations (KD range between 10-12 and 10-9 M). The stability and nuclease resistance of pre-miR-92b rG4 and pre-miR-92b rG4/C8 complex were evaluated as molecular recognition probes to capture and detect NCL. Finally, the microfluidic platform detects NCL in complex biological samples, such as human plasma. Overall, this work demonstrates the usefulness of the microfluidic platform based on the pre-miR-92b to detect NCL and the possibility to be used as a valuable biomedical tool in PCa diagnosis.
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Affiliation(s)
- Tiago Santos
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Maria P C Campello
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139,7), 2695-066 Bobadela LRS, Portugal
| | - António Paulo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139,7), 2695-066 Bobadela LRS, Portugal
| | - Gilmar Salgado
- Univ. Bordeaux, ARNA Laboratory, INSERM, U1212, CNRS UMR 5320, IECB, F-33600 Pessac, France
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal.
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11
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Saha A, Duchambon P, Masson V, Loew D, Bombard S, Teulade-Fichou MP. Nucleolin Discriminates Drastically between Long-Loop and Short-Loop Quadruplexes. Biochemistry 2020; 59:1261-1272. [PMID: 32191439 DOI: 10.1021/acs.biochem.9b01094] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We investigate herein the interaction between nucleolin (NCL) and a set of G4 sequences derived from the CEB25 human minisatellite that adopt a parallel topology while differing in the length of the central loop (from nine nucleotides to one nucleotide). It is revealed that NCL strongly binds to long-loop (five to nine nucleotides) G4 while interacting weakly with the shorter variants (loop with fewer than three nucleotides). Photo-cross-linking experiments using 5-bromo-2'-deoxyuridine (BrU)-modified sequences further confirmed the loop-length dependency, thereby indicating that the WT-CEB25-L191 (nine-nucleotide loop) is the best G4 substrate. Quantitative proteomic analysis (LC-MS/MS) of the product(s) obtained by photo-cross-linking NCL to this sequence enabled the identification of one contact site corresponding to a 15-amino acid fragment located in helix α2 of RNA binding domain 2 (RBD2), which sheds light on the role of this structural element in G4-loop recognition. Then, the ability of a panel of benchmark G4 ligands to prevent the NCL-G4 interaction was explored. It was found that only the most potent ligand PhenDC3 can inhibit NCL binding, thereby suggesting that the terminal guanine quartet is also a strong determinant of G4 recognition, putatively through interaction with the RGG domain. This study describes the molecular mechanism by which NCL recognizes G4-containing long loops and leads to the proposal of a model implying a concerted action of RBD2 and RGG domains to achieve specific G4 recognition via a dual loop-quartet interaction.
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Affiliation(s)
- Abhijit Saha
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Patricia Duchambon
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Vanessa Masson
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
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12
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Dickerhoff J, Onel B, Chen L, Chen Y, Yang D. Solution Structure of a MYC Promoter G-Quadruplex with 1:6:1 Loop Length. ACS OMEGA 2019; 4:2533-2539. [PMID: 30842981 PMCID: PMC6396123 DOI: 10.1021/acsomega.8b03580] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
The important MYC oncogene is deregulated in many cancer cells and comprises one of the most prominent G-quadruplex (G4) forming sequences in its promoter regions, the NHE III1 motif. Formation of G4s suppresses MYC transcription and can be modulated by drug binding, establishing these DNA structures as promising targets in cancer therapy. The NHE III1 motif can fold into more than one parallel G4s, including 1:2:1 and 1:6:1 loop length conformers, with the 1:2:1 conformer shown as the major species under physiological conditions in solution. However, additional factors such as protein interactions may affect the cellular folding equilibrium. Nucleolin, a protein shown to bind MYC G4 and repress MYC transcription, is reported herein to preferably bind to the 1:6:1 loop length conformer suggesting a physiological significance of this species. The high-resolution NMR solution structure of the 1:6:1 conformer is determined, which reveals a 5'-capping structure distinctive from the 1:2:1 form, with the 6 nt central loop playing an essential role for this specific capping structure. This suggests that each parallel G-quadruplex likely adopts unique capping and loop structures determined by the specific central loop and flanking sequences. The resulting structural information at the molecular level will help to understand protein recognition of different G4s, contribution of G4 polymorphism to gene regulation, and to rationally design small molecules selectively targeting the 1:6:1 MYC G4.
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Affiliation(s)
- Jonathan Dickerhoff
- College
of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 W Stadium Avenue, West
Lafayette, Indiana 47907, United States
| | - Buket Onel
- College
of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 W Stadium Avenue, West
Lafayette, Indiana 47907, United States
| | - Luying Chen
- College
of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 W Stadium Avenue, West
Lafayette, Indiana 47907, United States
| | - Yuwei Chen
- Department
of Chemistry and Biochemistry, College of Science, University of Arizona, 1306 E. University Blvd, Tucson, Arizona 85721, United
States
| | - Danzhou Yang
- College
of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 W Stadium Avenue, West
Lafayette, Indiana 47907, United States
- Center
for Cancer Research, Purdue University, 201 S University Street, West Lafayette, Indiana 47906, United States
- Purdue
Institute for Drug Discovery, 720 Clinic Dr, West Lafayette, Indiana 47907, United
States
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13
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Sofi S, Stehling S, Niewienda A, Janek K, Kuhn H, Ufer C. Functional characterization of isolated RNA-binding domains of the GRSF1 protein. Biochim Biophys Acta Gen Subj 2017; 1862:946-957. [PMID: 29288125 DOI: 10.1016/j.bbagen.2017.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/20/2017] [Accepted: 12/22/2017] [Indexed: 11/26/2022]
Abstract
The Guanine-rich RNA sequence binding factor 1 (GRSF1) is a member of the heterogeneous nuclear ribonucleoprotein F/H family and has been implicated in RNA processing, RNA transport and translational regulation. Amino acid alignments and homology modeling suggested the existence of three distinct RNA-binding domains and two auxiliary domains. Unfortunately, little is known about the molecular details of GRSF1/RNA interactions. To explore the RNA-binding mechanisms we first expressed full-length human GRSF1 and several truncation mutants, which include the three separated qRRM domains in E. coli, purified the recombinant proteins and quantified their RNA-binding affinity by RNA electrophoretic mobility shift assays. The expression levels varied between 1 and 10mg purified protein per L bacterial liquid culture and for full-length human GRSF1 a binding constant (KD-value) of 0.5μM was determined. In addition, our mechanistic experiments with different truncation mutants allowed the following conclusions: i) Deletion of either of the three RNA-binding domains impaired the RNA-binding affinity suggesting that the simultaneous presence of the three domains is essential for high-affinity RNA-binding. ii) Deletion of the Ala-rich auxiliary domain did hardly affect RNA-binding. Thus, this structural subunit may not be involved in RNA interaction. iii) Deletion of the acidic auxiliary domain improved the RNA-binding suggesting a regulatory role for this structural motif. iv) The isolated RNA-binding domains did not exhibit sizeable RNA-binding affinities. Taken together these data suggest that a cooperative interaction of the three qRRMs is required for high affinity RNA-binding.
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Affiliation(s)
- Sajad Sofi
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, CCO-Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Sabine Stehling
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, CCO-Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Agathe Niewienda
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Shared Facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Katharina Janek
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Shared Facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Hartmut Kuhn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, CCO-Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Christoph Ufer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, CCO-Building, Virchowweg 6, D-10117 Berlin, Germany.
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14
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Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition. Methods 2017; 118-119:119-136. [PMID: 28315749 DOI: 10.1016/j.ymeth.2017.03.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/19/2017] [Accepted: 03/13/2017] [Indexed: 12/20/2022] Open
Abstract
Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain arrangements and dynamics. Principles of protein-RNA recognition and current approaches are reviewed and illustrated with recent studies.
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15
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Krepl M, Cléry A, Blatter M, Allain FHT, Sponer J. Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs. Nucleic Acids Res 2016; 44:6452-70. [PMID: 27193998 PMCID: PMC5291263 DOI: 10.1093/nar/gkw438] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/30/2016] [Accepted: 05/05/2016] [Indexed: 01/28/2023] Open
Abstract
RNA recognition motif (RRM) proteins represent an abundant class of proteins playing key roles in RNA biology. We present a joint atomistic molecular dynamics (MD) and experimental study of two RRM-containing proteins bound with their single-stranded target RNAs, namely the Fox-1 and SRSF1 complexes. The simulations are used in conjunction with NMR spectroscopy to interpret and expand the available structural data. We accumulate more than 50 μs of simulations and show that the MD method is robust enough to reliably describe the structural dynamics of the RRM-RNA complexes. The simulations predict unanticipated specific participation of Arg142 at the protein-RNA interface of the SRFS1 complex, which is subsequently confirmed by NMR and ITC measurements. Several segments of the protein-RNA interface may involve competition between dynamical local substates rather than firmly formed interactions, which is indirectly consistent with the primary NMR data. We demonstrate that the simulations can be used to interpret the NMR atomistic models and can provide qualified predictions. Finally, we propose a protocol for 'MD-adapted structure ensemble' as a way to integrate the simulation predictions and expand upon the deposited NMR structures. Unbiased μs-scale atomistic MD could become a technique routinely complementing the NMR measurements of protein-RNA complexes.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Blatter
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel CH-4002, Switzerland
| | - Frederic H T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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16
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Mitrea DM, Kriwacki RW. Phase separation in biology; functional organization of a higher order. Cell Commun Signal 2016; 14:1. [PMID: 26727894 PMCID: PMC4700675 DOI: 10.1186/s12964-015-0125-7] [Citation(s) in RCA: 467] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/29/2015] [Indexed: 12/18/2022] Open
Abstract
Inside eukaryotic cells, macromolecules are partitioned into membrane-bounded compartments and, within these, some are further organized into non-membrane-bounded structures termed membrane-less organelles. The latter structures are comprised of heterogeneous mixtures of proteins and nucleic acids and assemble through a phase separation phenomenon similar to polymer condensation. Membrane-less organelles are dynamic structures maintained through multivalent interactions that mediate diverse biological processes, many involved in RNA metabolism. They rapidly exchange components with the cellular milieu and their properties are readily altered in response to environmental cues, often implicating membrane-less organelles in responses to stress signaling. In this review, we discuss: (1) the functional roles of membrane-less organelles, (2) unifying structural and mechanistic principles that underlie their assembly and disassembly, and (3) established and emerging methods used in structural investigations of membrane-less organelles.
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Affiliation(s)
- Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA.
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17
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Abstract
RRM-containing proteins are involved in most of the RNA metabolism steps. Their functions are closely related to their mode of RNA recognition, which has been studied by structural biologists for more than 20 years. In this chapter, we report on high-resolution structures of single and multi RRM-RNA complexes to explain the numerous strategies used by these domains to interact specifically with a large repertoire of RNA sequences. We show that multiple variations of their canonical fold can be used to adapt to different single-stranded sequences with a large range of affinities. Furthermore, we describe the consequences on RNA binding of the different structural arrangements found in tandem RRMs and higher order RNPs. Importantly, these structures also reveal with very high accuracy the RNA motifs bound specifically by RRM-containing proteins, which correspond very often to consensus sequences identified with genome-wide approaches. Finally, we show how structural and cellular biology can benefit from each other and pave a way for understanding, defining, and predicting a code of RNA recognition by the RRMs.
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18
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Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution. Methods Enzymol 2015; 558:279-331. [DOI: 10.1016/bs.mie.2015.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Davlieva M, Donarski J, Wang J, Shamoo Y, Nikonowicz EP. Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis. Nucleic Acids Res 2014; 42:10795-808. [PMID: 25140011 PMCID: PMC4176348 DOI: 10.1093/nar/gku743] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure.
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Affiliation(s)
- Milya Davlieva
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
| | - James Donarski
- Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Jiachen Wang
- Department of Physics, East China Normal University, 200062 Shanghai, P. R. China
| | - Yousif Shamoo
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
| | - Edward P Nikonowicz
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
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20
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Woo HH, Baker T, Laszlo C, Chambers SK. Nucleolin mediates microRNA-directed CSF-1 mRNA deadenylation but increases translation of CSF-1 mRNA. Mol Cell Proteomics 2013; 12:1661-77. [PMID: 23471483 PMCID: PMC3675821 DOI: 10.1074/mcp.m112.025288] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/03/2013] [Indexed: 11/06/2022] Open
Abstract
CSF-1 mRNA 3'UTR contains multiple unique motifs, including a common microRNA (miRNA) target in close proximity to a noncanonical G-quadruplex and AU-rich elements (AREs). Using a luciferase reporter system fused to CSF-1 mRNA 3'UTR, disruption of the miRNA target region, G-quadruplex, and AREs together dramatically increased reporter RNA levels, suggesting important roles for these cis-acting regulatory elements in the down-regulation of CSF-1 mRNA. We find that nucleolin, which binds both G-quadruplex and AREs, enhances deadenylation of CSF-1 mRNA, promoting CSF-1 mRNA decay, while having the capacity to increase translation of CSF-1 mRNA. Through interaction with the CSF-1 3'UTR miRNA common target, we find that miR-130a and miR-301a inhibit CSF-1 expression by enhancing mRNA decay. Silencing of nucleolin prevents the miRNA-directed mRNA decay, indicating a requirement for nucleolin in miRNA activity on CSF-1 mRNA. Downstream effects followed by miR-130a and miR-301a inhibition of directed cellular motility of ovarian cancer cells were found to be dependent on nucleolin. The paradoxical effects of nucleolin on miRNA-directed CSF-1 mRNA deadenylation and on translational activation were explored further. The nucleolin protein contains four acidic stretches, four RNA recognition motifs (RRMs), and nine RGG repeats. All three domains in nucleolin regulate CSF-1 mRNA and protein levels. RRMs increase CSF-1 mRNA, whereas the acidic and RGG domains decrease CSF-1 protein levels. This suggests that nucleolin has the capacity to differentially regulate both CSF-1 RNA and protein levels. Our finding that nucleolin interacts with Ago2 indirectly via RNA and with poly(A)-binding protein C (PABPC) directly suggests a nucleolin-Ago2-PABPC complex formation on mRNA. This complex is in keeping with our suggestion that nucleolin may work with PABPC as a double-edged sword on both mRNA deadenylation and translational activation. Our findings underscore the complexity of nucleolin's actions on CSF-1 mRNA and describe the dependence of miR-130a- and miR-301a-directed CSF-1 mRNA decay and inhibition of ovarian cancer cell motility on nucleolin.
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Affiliation(s)
- Ho-Hyung Woo
- Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, USA.
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21
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Barraud P, Allain FHT. Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling: how the relative orientation between RRMs influences the nucleic acid binding topology. JOURNAL OF BIOMOLECULAR NMR 2013; 55:119-38. [PMID: 23247503 DOI: 10.1007/s10858-012-9696-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/11/2012] [Indexed: 05/21/2023]
Abstract
Human hnRNP A1 is a multi-functional protein involved in many aspects of nucleic-acid processing such as alternative splicing, micro-RNA biogenesis, nucleo-cytoplasmic mRNA transport and telomere biogenesis and maintenance. The N-terminal region of hnRNP A1, also named unwinding protein 1 (UP1), is composed of two closely related RNA recognition motifs (RRM), and is followed by a C-terminal glycine rich region. Although crystal structures of UP1 revealed inter-domain interactions between RRM1 and RRM2 in both the free and bound form of UP1, these interactions have never been established in solution. Moreover, the relative orientation of hnRNP A1 RRMs is different in the free and bound crystal structures of UP1, raising the question of the biological significance of this domain movement. In the present study, we have used NMR spectroscopy in combination with segmental isotope labeling techniques to carefully analyze the inter-RRM contacts present in solution and subsequently determine the structure of UP1 in solution. Our data unambiguously demonstrate that hnRNP A1 RRMs interact in solution, and surprisingly, the relative orientation of the two RRMs observed in solution is different from the one found in the crystal structure of free UP1 and rather resembles the one observed in the nucleic-acid bound form of the protein. This strongly supports the idea that the two RRMs of hnRNP A1 have a single defined relative orientation which is the conformation previously observed in the bound form and now observed in solution using NMR. It is likely that the conformation in the crystal structure of the free form is a less stable form induced by crystal contacts. Importantly, the relative orientation of the RRMs in proteins containing multiple-RRMs strongly influences the RNA binding topologies that are practically accessible to these proteins. Indeed, RRM domains are asymmetric binding platforms contacting single-stranded nucleic acids in a single defined orientation. Therefore, the path of the nucleic acid molecule on the multiple RRM domains is strongly dependent on whether the RRMs are interacting with each other. The different nucleic acid recognition modes by multiple-RRM domains are briefly reviewed and analyzed on the basis of the current structural information.
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Affiliation(s)
- Pierre Barraud
- Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, 8093 Zurich, Switzerland
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Abdelmohsen K, Tominaga K, Lee EK, Srikantan S, Kang MJ, Kim MM, Selimyan R, Martindale JL, Yang X, Carrier F, Zhan M, Becker KG, Gorospe M. Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs. Nucleic Acids Res 2011; 39:8513-30. [PMID: 21737422 PMCID: PMC3201861 DOI: 10.1093/nar/gkr488] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 05/25/2011] [Accepted: 05/27/2011] [Indexed: 01/26/2023] Open
Abstract
RNA-binding proteins (RBPs) regulate gene expression at many post-transcriptional levels, including mRNA stability and translation. The RBP nucleolin, with four RNA-recognition motifs, has been implicated in cell proliferation, carcinogenesis and viral infection. However, the subset of nucleolin target mRNAs and the influence of nucleolin on their expression had not been studied at a transcriptome-wide level. Here, we globally identified nucleolin target transcripts, many of which encoded cell growth- and cancer-related proteins, and used them to find a signature motif on nucleolin target mRNAs. Surprisingly, this motif was very rich in G residues and was not only found in the 3'-untranslated region (UTR), but also in the coding region (CR) and 5'-UTR. Nucleolin enhanced the translation of mRNAs bearing the G-rich motif, since silencing nucleolin did not change target mRNA stability, but decreased the size of polysomes forming on target transcripts and lowered the abundance of the encoded proteins. In summary, nucleolin binds G-rich sequences in the CR and UTRs of target mRNAs, many of which encode cancer proteins, and enhances their translation.
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Affiliation(s)
- Kotb Abdelmohsen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging - Intramural Research Program, NIH, Baltimore, MD 21224, USA.
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23
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Tominaga K, Srikantan S, Lee EK, Subaran SS, Martindale JL, Abdelmohsen K, Gorospe M. Competitive regulation of nucleolin expression by HuR and miR-494. Mol Cell Biol 2011; 31:4219-31. [PMID: 21859890 PMCID: PMC3187287 DOI: 10.1128/mcb.05955-11] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 08/10/2011] [Accepted: 08/12/2011] [Indexed: 11/20/2022] Open
Abstract
The RNA-binding protein (RBP) nucleolin promotes the expression of several proliferative proteins. Nucleolin levels are high in cancer cells, but the mechanisms that control nucleolin expression are unknown. Here, we show that nucleolin abundance is controlled posttranscriptionally via factors that associate with its 3' untranslated region (3'UTR). The RBP HuR was found to interact with the nucleolin (NCL) 3'UTR and specifically promoted nucleolin translation without affecting nucleolin mRNA levels. In human cervical carcinoma HeLa cells, analysis of a traceable NCL 3'UTR bearing MS2 RNA hairpins revealed that NCL RNA was mobilized to processing bodies (PBs) after silencing HuR, suggesting that the repression of nucleolin translation may occur in PBs. Immunoprecipitation of MS2-tagged NCL 3'UTR was used to screen for endogenous repressors of nucleolin synthesis. This search identified miR-494 as a microRNA that potently inhibited nucleolin expression, enhanced NCL mRNA association with argonaute-containing complexes, and induced NCL RNA transport to PBs. Importantly, miR-494 and HuR functionally competed for modulation of nucleolin expression. Moreover, the promotion of cell growth previously attributed to HuR was due in part to the HuR-elicited increase in nucleolin expression. Our collective findings indicate that nucleolin expression is positively regulated by HuR and negatively regulated via competition with miR-494.
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Affiliation(s)
- Kumiko Tominaga
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224
| | - Subramanya Srikantan
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224
| | - Eun Kyung Lee
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224
| | - Sarah S. Subaran
- Laboratory of Cardiovascular Science, NIA-IRP, NIH, Baltimore, Maryland 21224
| | | | - Kotb Abdelmohsen
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224
| | - Myriam Gorospe
- Laboratory of Molecular Biology and Immunology, NIA-IRP, NIH, Baltimore, Maryland 21224
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24
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Ruwe H, Kupsch C, Teubner M, Schmitz-Linneweber C. The RNA-recognition motif in chloroplasts. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1361-71. [PMID: 21330002 DOI: 10.1016/j.jplph.2011.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 01/25/2011] [Accepted: 01/26/2011] [Indexed: 05/10/2023]
Abstract
Chloroplast RNA metabolism is characterized by multiple RNA processing steps that require hundreds of RNA binding proteins. A growing number of RNA binding proteins have been shown to mediate specific RNA processing steps in the chloroplast, but little do we know about their regulatory importance or mode of molecular action. This review summarizes knowledge on chloroplast proteins that contain an RNA recognition motif, a classical RNA binding domain widespread in pro- and eukaryotes. Several members of this family respond to external and internal stimuli by changes in their expression levels and protein modification state. They therefore appear as ideal candidates for regulating chloroplast RNA processing under shifting environmental conditions.
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Affiliation(s)
- Hannes Ruwe
- Institute of Biology, Humboldt University of Berlin, Chausseestrasse 117, Berlin, Germany
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25
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Cancio-Lonches C, Yocupicio-Monroy M, Sandoval-Jaime C, Galvan-Mendoza I, Ureña L, Vashist S, Goodfellow I, Salas-Benito J, Gutiérrez-Escolano AL. Nucleolin interacts with the feline calicivirus 3' untranslated region and the protease-polymerase NS6 and NS7 proteins, playing a role in virus replication. J Virol 2011; 85:8056-68. [PMID: 21680514 PMCID: PMC3147956 DOI: 10.1128/jvi.01878-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 05/29/2011] [Indexed: 12/19/2022] Open
Abstract
Cellular proteins play many important roles during the life cycle of all viruses. Specifically, host cell nucleic acid-binding proteins interact with viral components of positive-stranded RNA viruses and regulate viral translation, as well as RNA replication. Here, we report that nucleolin, a ubiquitous multifunctional nucleolar shuttling phosphoprotein, interacts with the Norwalk virus and feline calicivirus (FCV) genomic 3' untranslated regions (UTRs). Nucleolin can also form a complex in vitro with recombinant Norwalk virus NS6 and -7 (NS6/7) and can be copurified with the analogous protein from feline calicivirus (p76 or NS6/7) from infected feline kidney cells. Nucleolin RNA levels or protein were not modified during FCV infection; however, as a consequence of the infection, nucleolin was seen to relocalize from the nucleoli to the nucleoplasm, as well as to the perinuclear area where it colocalizes with the feline calicivirus NS6/7 protein. In addition, antibodies to nucleolin were able to precipitate viral RNA from feline calicivirus-infected cells, indicating a direct or indirect association of nucleolin with the viral RNA during virus replication. Small interfering RNA (siRNA)-mediated knockdown of nucleolin resulted in a reduction of the cytopathic effect and virus yield in CrFK cells. Taken together, these results demonstrate that nucleolin is a nucleolar component that interacts with viral RNA and NS6/7 and is required for feline calicivirus replication.
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Affiliation(s)
- Clotilde Cancio-Lonches
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
- Departamento de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, IPN, Distrito Federal, México
| | - Martha Yocupicio-Monroy
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Distrito Federal, México
| | - Carlos Sandoval-Jaime
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
| | - Iván Galvan-Mendoza
- Laboratorios Centrales, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
| | - Luis Ureña
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Surender Vashist
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Ian Goodfellow
- Section of Virology, Faculty of Medicine, Imperial College of London, St. Mary's Campus, Norkfolk Place, London W2 1PG, United Kingdom
| | - Juan Salas-Benito
- Departamento de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, IPN, Distrito Federal, México
| | - Ana Lorena Gutiérrez-Escolano
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Distrito Federal, México
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26
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Multistep kinetics of the U1A-SL2 RNA complex dissociation. J Mol Biol 2011; 408:896-908. [PMID: 21419778 DOI: 10.1016/j.jmb.2011.02.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 02/20/2011] [Accepted: 02/22/2011] [Indexed: 11/23/2022]
Abstract
The U1A-SL2 RNA complex is a model system for studying interactions between RNA and the RNA recognition motif (RRM), which is one of the most common RNA binding domains. We report here kinetic studies of dissociation of the U1A-SL2 RNA complex, using laser temperature jump and stopped-flow fluorescence methods with U1A proteins labeled with the intrinsic chromophore tryptophan. An analysis of the kinetic data suggests three phases of dissociation with time scales of ∼100 μs, ∼50 ms, and ∼2 s. We propose that the first step of dissociation is a fast rearrangement of the complex to form a loosely bound complex. The intermediate step is assigned to be the dissociation of the U1A-SL2 RNA complex, and the final step is assigned to a reorganization of the U1A protein structure into the conformation of the free protein. These assignments are consistent with previous proposals based on thermodynamic, NMR, and surface plasmon resonance experiments and molecular dynamics simulations. Together, these results begin to build a comprehensive model of the complex dynamic processes involved in the formation and dissociation of an RRM-RNA complex.
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27
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Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA. J Mol Biol 2011; 408:99-117. [PMID: 21333656 DOI: 10.1016/j.jmb.2011.02.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 02/03/2011] [Accepted: 02/04/2011] [Indexed: 01/28/2023]
Abstract
In Gram-positive bacteria, the RNA transcripts of many amino acid biosynthetic and aminoacyl tRNA synthetase genes contain 5' untranslated regions, or leader RNAs, that function as riboswitches. These T-box riboswitches bind cognate tRNA molecules and regulate gene expression by a transcription attenuation mechanism. The Specifier Loop domain of the leader RNA contains nucleotides that pair with nucleotides in the tRNA anticodon loop and is flanked on one side by a kink-turn (K-turn), or GA, sequence motif. We have determined the solution NMR structure of the K-turn sequence element within the context of the Specifier Loop domain. The K-turn sequence motif has several noncanonical base pairs typical of K-turn structures but adopts an extended conformation. The Specifier Loop domain contains a loop E structural motif, and the single-strand Specifier nucleotides stack with their Watson-Crick edges displaced toward the minor groove. Mg(2+) leads to a significant bending of the helix axis at the base of the Specifier Loop domain, but does not alter the K-turn. Isothermal titration calorimetry indicates that the K-turn sequence causes a small enhancement of the interaction between the tRNA anticodon arm and the Specifier Loop domain. One possibility is that the K-turn structure is formed and stabilized when tRNA binds the T-box riboswitch and interacts with Stem I and the antiterminator helix. This motif in turn anchors the orientation of Stem I relative to the 3' half of the leader RNA, further stabilizing the tRNA-T box complex.
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28
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Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Cyril Dominguez
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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29
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Galloway CA, Kumar A, Krucinska J, Smith HC. APOBEC-1 complementation factor (ACF) forms RNA-dependent multimers. Biochem Biophys Res Commun 2010; 398:38-43. [PMID: 20541536 DOI: 10.1016/j.bbrc.2010.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 06/06/2010] [Indexed: 10/19/2022]
Abstract
Limited proteolysis of APOBEC-1 complementation factor (ACF) and computational secondary structure modeling were used to guide the construction of a well-folded, truncation protein spanning residues 1-320 and containing three RNA recognition motifs (RRMs). ACF320 bound preferentially to apoB mRNA and supported APOBEC-1 dependent editing at 40% of the activity of full length ACF. Live cell FRET and immunoprecipitation assays revealed that ACF320 formed homomultimers in situ that were bridged by RNA. Our study predicted that the C to U editosome may be assembled on the mooring sequence of apoB mRNA as a dimer of ACF bound to a dimer of APOBEC-1.
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Affiliation(s)
- C A Galloway
- University of Rochester, School of Medicine and Dentistry, Department of Biochemistry and Biophysics, 601 Elmwood Ave., Rochester, NY 14642, USA
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30
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Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing. Proc Natl Acad Sci U S A 2010; 107:10062-7. [PMID: 20479262 DOI: 10.1073/pnas.1000848107] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human Cleavage Factor Im (CFI(m)) is an essential component of the pre-mRNA 3' processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI(m)25) of the CFI(m) complex possesses a characteristic alpha/beta/alpha Nudix fold, CFI(m)25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI(m)25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI(m)25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap(4)A (diadenosine tetraphosphate) by CFI(m)25 suggests a potential role for small molecules in the regulation of mRNA 3' processing.
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31
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Arumugam S, Miller MC, Maliekal J, Bates PJ, Trent JO, Lane AN. Solution structure of the RBD1,2 domains from human nucleolin. JOURNAL OF BIOMOLECULAR NMR 2010; 47:79-83. [PMID: 20376532 DOI: 10.1007/s10858-010-9412-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Accepted: 03/22/2010] [Indexed: 05/29/2023]
Affiliation(s)
- Sengodagounder Arumugam
- JG Brown Cancer Center, University of Louisville, 505 South Hancock St., Louisville, KY 40202, USA
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32
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Wang J, Henkin TM, Nikonowicz EP. NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA. Nucleic Acids Res 2010; 38:3388-98. [PMID: 20110252 PMCID: PMC2879506 DOI: 10.1093/nar/gkq020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Gram-positive bacteria utilize a tRNA-responsive transcription antitermination mechanism, designated the T box system, to regulate expression of many amino acid biosynthetic and aminoacyl-tRNA synthetase genes. The RNA transcripts of genes controlled by this mechanism contain 5′ untranslated regions, or leader RNAs, that specifically bind cognate tRNA molecules through pairing of nucleotides in the tRNA anticodon loop with nucleotides in the Specifier Loop domain of the leader RNA. We have determined the solution structure of the Specifier Loop domain of the tyrS leader RNA from Bacillus subtilis. Fifty percent of the nucleotides in the Specifier Loop domain adopt a loop E motif. The Specifier Sequence nucleotides, which pair with the tRNA anticodon, stack with their Watson–Crick edges rotated toward the minor groove and exhibit only modest flexibility. We also show that a Specifier Loop domain mutation that impairs the function of the B. subtilis glyQS T box RNA disrupts the tyrS loop E motif. Our results suggest a mechanism for tRNA–Specifier Loop binding in which the phosphate backbone kink created by the loop E motif causes the Specifier Sequence bases to rotate toward the minor groove, which increases accessibility for pairing with bases in the anticodon loop of tRNA.
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Affiliation(s)
- Jiachen Wang
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
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33
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Kainov DE, Selth LA, Svejstrup JQ, Egly JM, Poterzsman A. Interacting partners of the Tfb2 subunit from yeast TFIIH. DNA Repair (Amst) 2010; 9:33-9. [PMID: 19897425 DOI: 10.1016/j.dnarep.2009.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 10/03/2009] [Accepted: 10/06/2009] [Indexed: 11/29/2022]
Abstract
TFIIH is an evolutionary conserved eukaryotic multi-protein complex composed of ten subunits. It is involved in transcription, cell cycle regulation, RNA splicing and the nucleotide excision DNA repair pathway (NER). Depending on the process in which it is functioning, the composition of TFIIH varies and activities of its subunits are differentially regulated. Here we focused on interplay between the Ssl2, Tfb2 and Tfb5 subunits of TFIIH from Saccharomyces cerevisiae. We found that Tfb2 bridges the Ssl2 helicase and the NER-specific Tfb5 subunit. Moreover, the Tfb5-interacting domain of Tfb2 also binds nucleic acids (NA), although the addition of Tfb5 triggers dissociation of NA from Tfb2. In yeast cells, deletion of TFB5 is more detrimental to NER than loss of the Tfb5/NA-interacting domain of Tfb2, while combining these mutations resulted in suppression of the UV sensitivity of tfb5Delta. The implications of our findings in regards to TFIIH function and group A trichothiodystrophy, an inherited disease associated with mutations in the human TFB5 gene, are discussed.
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Affiliation(s)
- Denis E Kainov
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
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34
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Routsias JG, Kyriakidis N, Latreille M, Tzioufas AG. RNA recognition motif (RRM) of La/SSB: the bridge for interparticle spreading of autoimmune response to U1-RNP. Mol Med 2010; 16:19-26. [PMID: 19838329 PMCID: PMC2762815 DOI: 10.2119/molmed.2009.00106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 10/12/2009] [Indexed: 11/06/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is characterized by the production of grouped sets of autoantibodies targeting mainly the U1 ribonucleoprotein (RNP) and/or Ro/La RNP particles. Intraparticle diversification of the autoimmune response is believed to occur via epitope spreading. So far, it is not known how the autoimmune response "jumps" from one particle to another. To the extent that the majority of nuclear autoantigens in SLE are RNA binding proteins and major epitopes were previously mapped within their RRM (RNA recognition motifs), conserved sequences within RRM could be involved in the intermolecular and inter-particle diversification process of the autoimmune response. We investigated the potential of RRM of the La/SSB autoantigen to induce antibodies that cross-recognize components of the U1-RNP particle and therefore its capacity to produce interparticle epitope spreading. We immunized New Zealand white rabbits with a peptide corresponding to the epitope 145-164 of La/SSB (belonging to the RRM of La/SSB), attached in four copies on a scaffold carrier. Sera were drawn from 20 sera of patients with SLE and anti-U1-RNP antibodies and 26 sera of primary Sjögren syndrome patients with anti-La/SSB antibodies. All sera were evaluated for reactivity against the major epitope of La/SSB (pep349-364), the RNP antigen and the RRM-related epitope of La/SSB (pep145-164). Specific antibodies against pep145-164 were purified with immunoaffinity columns from selected sera. After the immunization of the animals with pep145-164, a specific IgG antibody response was detected, directed against the La/SSB autoantigen (wks 3-7), the immunizing peptide (wks 3-27), and the RNP autoantigen (wks 7-20). This response gradually decreased to low levels between postimmunization wks 27-42. Purified antibodies against pep145-164 recognized La/SSB and a 70-kD autoantigen in Western blot and exhibited significant reactivity in anti-U1-RNP ELISA. Depletion of anti-pep145-164 antibodies eliminated anti-U1-RNP reactivity from immunized rabbit sera but not from human sera. In addition, pep145-164 was recognized to a greater extent by autoimmune sera with anti-RNP reactivity compared with anti-La/SSB-positive sera, in contrast to pep349-364 of La/SSB, which was recognized almost exclusively by sera with anti-La/SSB reactivity. These data suggest that the RRM region of La/SSB can trigger interparticle B-cell diversification to U1-RNP-70 autoantigen via molecular mimicry. Identification of key sequences that trigger and perpetuate the autoimmune process is particularly important for understanding pathogenetic mechanisms in autoimmunity.
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Affiliation(s)
- John G Routsias
- Department of Pathophysiology, School of Medicine, National University of Athens, 115 27 Athens, Greece.
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35
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Cléry A, Blatter M, Allain FHT. RNA recognition motifs: boring? Not quite. Curr Opin Struct Biol 2008; 18:290-8. [PMID: 18515081 DOI: 10.1016/j.sbi.2008.04.002] [Citation(s) in RCA: 460] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 04/09/2008] [Indexed: 01/10/2023]
Abstract
The RNA recognition motif (RRM) is one of the most abundant protein domains in eukaryotes. While the structure of this domain is well characterized by the packing of two alpha-helices on a four-stranded beta-sheet, the mode of protein and RNA recognition by RRMs is not clear owing to the high variability of these interactions. Here we report recent structural data on RRM-RNA and RRM-protein interactions showing the ability of this domain to modulate its binding affinity and specificity using each of its constitutive elements (beta-strands, loops, alpha-helices). The extreme structural versatility of the RRM interactions explains why RRM-containing proteins have so diverse biological functions.
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Affiliation(s)
- Antoine Cléry
- Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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36
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Nucleolin – Characteristics of Protein and its Role in Biology of Cancers and Viral Infections. ACTA ACUST UNITED AC 2008. [DOI: 10.2478/v10052-008-0003-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Homann M. Editing Reactions from the Perspective of RNA Structure. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2008. [DOI: 10.1007/978-3-540-73787-2_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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38
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Schmid N, Zagrovic B, van Gunsteren WF. Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA. Biochemistry 2007; 46:6500-12. [PMID: 17497933 DOI: 10.1021/bi6026133] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polypyrimidine tract binding protein (PTB) is involved in many physiological processes, including alternative splicing, internal ribosomal entry side (IRES)-mediated initiation of translation, and polyadenylation, as well as in ensuring mRNA stability. However, the role of PTB in these processes is not fully understood, and this has motivated us to undertake a computational study of the protein. PTB RNA binding domains (RBDs) 3 and 4 and their complexes with oligopyrimidine RNAs were simulated using the GROMOS simulation software using the GROMOS 45A4 force field. First, the stability and fluctuations of the tertiary fold and of the secondary structural elements in individual domains, the combined RBD34 domain, and their complexes with RNA were studied. Second, the simulation results were validated against the experimental NMR NOE data. The analysis of hydrogen bonding patterns, salt bridge networks, and stacking interactions of the RNA to the binding pockets of the protein domains showed that binding is not sequence-specific and that many RNA fragments can bind to them successfully. Further calculations of the relative free energy of binding for different polypyrimidine sequences were carried out using the thermodynamic integration (TI) and single-step perturbation (SSP) methods. It is was not possible to calculate the relative free energies with high accuracy, but the obtained results do give qualitative insights into PTB's affinity for different RNA sequences. Furthermore, the low-energy conformations of the complexes that were found provided additional information about the mechanism of binding.
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Affiliation(s)
- Nathan Schmid
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH-8093 Zürich, Switzerland
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39
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Soler N, Fourmy D, Yoshizawa S. Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB. J Mol Biol 2007; 370:728-41. [PMID: 17537456 DOI: 10.1016/j.jmb.2007.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 04/20/2007] [Accepted: 05/01/2007] [Indexed: 11/16/2022]
Abstract
Elongation factor SelB is responsible for co-translational incorporation of selenocysteine (Sec) into proteins. The UGA stop codon is recoded as a Sec codon in the presence of a downstream mRNA hairpin. In prokaryotes, in addition to the EF-Tu-like N-terminal domains, a C-terminal extension containing four tandem winged-helix motifs (WH1-4) recognizes the mRNA hairpin. The 2.3-A resolution crystal structure of the Escherichia coli WH3/4 domains bound to mRNA with mutagenesis data reveal that the two WH motifs use the same structural elements to bind RNA. The structure together with the 2.6-A resolution structure of the WH1-4 domains from Moorella thermoacetica bound to RNA revealed that a salt bridge connecting WH2 to WH3 modules is disrupted upon mRNA binding. The results provide a structural basis for the molecular switch that may allow communication between tRNA and mRNA binding sites and illustrate how RNA acts as an activator of the switch. The structures show that tandem WH motifs not only provide an excellent scaffold for RNA binding but can also have an active role in the function of protein-RNA complexes.
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Affiliation(s)
- Nicolas Soler
- Laboratoire de Chimie et Biologie Structurales, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France
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40
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Petricka JJ, Nelson TM. Arabidopsis nucleolin affects plant development and patterning. PLANT PHYSIOLOGY 2007; 144:173-86. [PMID: 17369435 PMCID: PMC1913809 DOI: 10.1104/pp.106.093575] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 03/13/2007] [Indexed: 05/14/2023]
Abstract
Nucleolin is a major nucleolar protein implicated in many aspects of ribosomal biogenesis, including early events such as processing of the large 35S preribosomal RNA. We found that the Arabidopsis (Arabidopsis thaliana) parallel1 (parl1) mutant, originally identified by its aberrant leaf venation, corresponds to the Arabidopsis nucleolin gene. parl1 mutants display parallel leaf venation, aberrant localization of the provascular marker Athb8:beta-glucuronidase, the auxin-sensitive reporter DR5:beta-glucuronidase, and auxin-dependent growth defects. PARL1 is highly similar to the yeast (Saccharomyces cerevisiae) nucleolin NUCLEAR SIGNAL RECOGNITION 1 (NSR1) multifunctional protein; the Arabidopsis PARL1 gene can rescue growth defects of yeast nsr1 null mutants. This suggests that PARL1 protein may have roles similar to those of the yeast nucleolin in nuclear signal recognition, ribosomal processing, and ribosomal subunit accumulation. Based on the range of auxin-related defects in parl1 mutants, we propose that auxin-dependent organ growth and patterning is highly sensitive to the efficiency of nucleolin-dependent ribosomal processing.
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Affiliation(s)
- Jalean Joyanne Petricka
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104, USA
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41
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Auweter SD, Oberstrass FC, Allain FHT. Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res 2006; 34:4943-59. [PMID: 16982642 PMCID: PMC1635273 DOI: 10.1093/nar/gkl620] [Citation(s) in RCA: 227] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A code predicting the RNA sequence that will be bound by a certain protein based on its amino acid sequence or its structure would provide a useful tool for the design of RNA binders with desired sequence-specificity. Such de novo designed RNA binders could be of extraordinary use in both medical and basic research applications. Furthermore, a code could help to predict the cellular functions of RNA-binding proteins that have not yet been extensively studied. A comparative analysis of Pumilio homology domains, zinc-containing RNA binders, hnRNP K homology domains and RNA recognition motifs is performed in this review. Based on this, a set of binding rules is proposed that hints towards a code for RNA recognition by these domains. Furthermore, we discuss the intermolecular interactions that are important for RNA binding and summarize their importance in providing affinity and specificity.
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Affiliation(s)
- Sigrid D. Auweter
- Department of Biology, Institute for Molecular Biology and BiophysicsETH Zürich, CH-8093 Zürich, Switzerland
- Molecular Life Science PhD ProgramZürich, Switzerland
| | - Florian C. Oberstrass
- Department of Biology, Institute for Molecular Biology and BiophysicsETH Zürich, CH-8093 Zürich, Switzerland
- Molecular Life Science PhD ProgramZürich, Switzerland
| | - Frédéric H.-T. Allain
- Department of Biology, Institute for Molecular Biology and BiophysicsETH Zürich, CH-8093 Zürich, Switzerland
- To whom correspondence should be addressed. Tel: +41 44 633 3940; Fax: +41 44 63 31294;
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42
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Zhao Y, Kormos BL, Beveridge DL, Baranger AM. Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface. Biopolymers 2006; 81:256-69. [PMID: 16278830 DOI: 10.1002/bip.20408] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The RNA recognition motif (RRM) is one of the most common RNA binding domains. We have investigated the contribution of three highly conserved aromatic amino acids to RNA binding by the N-terminal RRM of the U1A protein. Recently, we synthesized a modified base (A-4CPh) in which a phenyl group is tethered to adenine using a linker of 4 methylene groups. The substitution of this base for adenine in the target RNA selectively stabilizes the complex formed with a U1A protein in which one of the conserved aromatic amino acids is replaced with Ala (Phe56Ala). In this article, we report molecular dynamics (MD) simulations that probe the structural consequences of the substitution of A-4CPh for adenine in the wild type and Phe56Ala U1A-RNA complexes and in the free RNA. The simulations suggest that A-4CPh stabilizes the complex formed with Phe56Ala by adopting a folded conformation in which the tethered phenyl group fills the site occupied by the phenyl group of Phe56 in the wild-type complex. In contrast, an extended conformation of A-4CPh is predicted to be most stable in the complex formed with the wild-type protein. The calculations indicate A-4CPh is in an extended conformation in the free RNA. Therefore, preorganizing the structure of the phenyl-tethered base for binding may improve both the affinity and specificity of the RNA containing A-4CPh for the Phe56Ala U1A protein. Taken together, the previous experimental work and the calculations reported here suggest a general design strategy for altering RRM-RNA complex stability.
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Affiliation(s)
- Ying Zhao
- Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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43
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Wang S, Hu Y, Overgaard MT, Karginov FV, Uhlenbeck OC, McKay DB. The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold. RNA (NEW YORK, N.Y.) 2006; 12:959-67. [PMID: 16611943 PMCID: PMC1464845 DOI: 10.1261/rna.5906] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The YxiN protein of Bacillus subtilis is a member of the DbpA subfamily of prokaryotic DEAD-box RNA helicases. Like DbpA, it binds with high affinity and specificity to segments of 23S ribosomal RNA as short as 32 nucleotides (nt) that include hairpin 92. Several experiments have shown that the 76-residue carboxy-terminal domain of YxiN is responsible for the high-affinity RNA binding. The domain has been crystallized and its structure has been solved to 1.7 Angstroms resolution. The structure reveals an RNA recognition motif (RRM) fold that is found in many eukaryotic RNA binding proteins; the RRM fold was not apparent from the amino acid sequence. The domain has two solvent exposed aromatic residues at sites that correspond to the aromatic residues of the ribonucleoprotein (RNP) motifs RNP1 and RNP2 that are essential for RNA binding in many RRMs. However, mutagenesis of these residues (Tyr404 and Tyr447) to alanine has little effect on RNA affinity, suggesting that the YxiN domain binds target RNAs in a manner that differs from the binding mode commonly found in many eukaryotic RRMs.
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MESH Headings
- Amino Acid Motifs
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Crystallization
- Crystallography, X-Ray
- DEAD-box RNA Helicases
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- Protein Folding
- Protein Structure, Tertiary
- RNA/chemistry
- RNA/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Spliceosomes/metabolism
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Affiliation(s)
- Shuying Wang
- Department of Structural Biology, Stanford University School of Medicine, California 94305, USA
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44
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Curry S, Conte MR. A terminal affair: 3'-end recognition by the human La protein. Trends Biochem Sci 2006; 31:303-5. [PMID: 16679019 DOI: 10.1016/j.tibs.2006.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 03/15/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
Abstract
The La protein, an autoantigen in rheumatic disease, orchestrates several aspects of the metabolism of noncoding RNA molecules. More than 20 years ago it was shown that La primarily binds the 3' UUU-OH tails of nascent transcripts of RNA polymerase III. A recent study now reveals how the structure of the amino-terminal domain of the human La protein achieves specific 3'-end recognition.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Blackett Laboratory, Faculty of Natural Sciences, Imperial College, Exhibition Road, London SW7 2AZ, UK
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45
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Sjöberg MK, Shestakova E, Mansuroglu Z, Maccioni RB, Bonnefoy E. Tau protein binds to pericentromeric DNA: a putative role for nuclear tau in nucleolar organization. J Cell Sci 2006; 119:2025-34. [PMID: 16638814 DOI: 10.1242/jcs.02907] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The microtubule-associated tau protein participates in the organization and integrity of the neuronal cytoskeleton. A nuclear form of tau has been described in neuronal and non-neuronal cells, which displays a nucleolar localization during interphase but is associated with nucleolar-organizing regions in mitotic cells. In the present study, based on immunofluorescence, immuno-FISH and confocal microscopy, we show that nuclear tau is mainly present at the internal periphery of nucleoli, partially colocalizing with the nucleolar protein nucleolin and human AT-rich alpha-satellite DNA sequences organized as constitutive heterochromatin. By using gel retardation, we demonstrate that tau not only colocalizes with, but also specifically binds to, AT-rich satellite DNA sequences apparently through the recognition of AT-rich DNA stretches. Here we propose a functional role for nuclear tau in relation to the nucleolar organization and/or heterochromatinization of a portion of RNA genes. Since nuclear tau has also been found in neurons from patients with Alzheimer's disease (AD), aberrant nuclear tau could affect the nucleolar organization during the course of AD. We discuss nucleolar tau associated with AT-rich alpha-satellite DNA sequences as a potential molecular link between trisomy 21 and AD.
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Affiliation(s)
- Marcela K Sjöberg
- Laboratory of Cellular, Molecular Biology and Neurosciences, Millennium Institute for Advanced Studies in Cell Biology and Biotechnology (CBB), Faculty of Sciences, University of Chile, Las Encinas 3370, Nuñoa, Santiago, Chile.
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46
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Bonvin AMJJ, Boelens R, Kaptein R. NMR analysis of protein interactions. Curr Opin Chem Biol 2006; 9:501-8. [PMID: 16122968 DOI: 10.1016/j.cbpa.2005.08.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Accepted: 08/09/2005] [Indexed: 11/28/2022]
Abstract
Recent technological advances in NMR spectroscopy have alleviated the size limitations for the determination of biomolecular structures in solution. At the same time, novel NMR parameters such as residual dipolar couplings are providing greater accuracy. As this review shows, the structures of protein-protein and protein-nucleic acid complexes up to 50 kDa can now be accurately determined. Although de novo structure determination still requires considerable effort, information on interaction surfaces from chemical shift perturbations is much easier to obtain. Advances in modelling and data-driven docking procedures allow this information to be used for determining approximate structures of biomolecular complexes. As a result, a wealth of information has become available on the way in which proteins interact with other biomolecules. Of particular interest is the fact that these NMR-based methods can be applied to weak and transient protein-protein complexes that are difficult to study by other structural methods.
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Affiliation(s)
- Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Utrecht University, NL-3584 CH Utrecht, The Netherlands
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47
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Navratilova I, Myszka DG. Investigating Biomolecular Interactions and Binding Properties Using SPR Biosensors. SPRINGER SERIES ON CHEMICAL SENSORS AND BIOSENSORS 2006. [DOI: 10.1007/5346_018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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48
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Stefl R, Skrisovska L, Allain FHT. RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle. EMBO Rep 2005; 6:33-8. [PMID: 15643449 PMCID: PMC1299235 DOI: 10.1038/sj.embor.7400325] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 11/26/2004] [Indexed: 11/09/2022] Open
Abstract
At all stages of its life (from transcription to translation), an RNA transcript interacts with many different RNA-binding proteins. The composition of this supramolecular assembly, known as a ribonucleoprotein particle, is diverse and highly dynamic. RNA-binding proteins control the generation, maturation and lifespan of the RNA transcript and thus regulate and influence the cellular function of the encoded gene. Here, we review our current understanding of protein-RNA recognition mediated by the two most abundant RNA-binding domains (the RNA-recognition motif and the double-stranded RNA-binding motif) plus the zinc-finger motif, the most abundant nucleic-acid-binding domain. In addition, we discuss how not only the sequence but also the shape of the RNA are recognized by these three classes of RNA-binding protein.
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Affiliation(s)
- Richard Stefl
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Lenka Skrisovska
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Frédéric H.-T. Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
- Tel: +41 (0)1 63 33940; Fax: +41 (0)1 63 31294;
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49
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Maris C, Dominguez C, Allain FHT. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J 2005; 272:2118-31. [PMID: 15853797 DOI: 10.1111/j.1742-4658.2005.04653.x] [Citation(s) in RCA: 790] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The RNA recognition motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is one of the most abundant protein domains in eukaryotes. Based on the comparison of more than 40 structures including 15 complexes (RRM-RNA or RRM-protein), we reviewed the structure-function relationships of this domain. We identified and classified the different structural elements of the RRM that are important for binding a multitude of RNA sequences and proteins. Common structural aspects were extracted that allowed us to define a structural leitmotif of the RRM-nucleic acid interface with its variations. Outside of the two conserved RNP motifs that lie in the center of the RRM beta-sheet, the two external beta-strands, the loops, the C- and N-termini, or even a second RRM domain allow high RNA-binding affinity and specific recognition. Protein-RRM interactions that have been found in several structures reinforce the notion of an extreme structural versatility of this domain supporting the numerous biological functions of the RRM-containing proteins.
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Affiliation(s)
- Christophe Maris
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zurich, ETH-Hönggerberg, Zürich, Switzerland
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50
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Law MJ, Chambers EJ, Katsamba PS, Haworth IS, Laird-Offringa IA. Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction. Nucleic Acids Res 2005; 33:2917-28. [PMID: 15914668 PMCID: PMC1140079 DOI: 10.1093/nar/gki602] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The A protein of the U1 small nuclear ribonucleoprotein particle, interacting with its stem-loop RNA target (U1hpII), is frequently used as a paradigm for RNA binding by recognition motif domains (RRMs). U1A/U1hpII complex formation has been proposed to consist of at least two steps: electrostatically mediated alignment of both molecules followed by locking into place, based on the establishment of close-range interactions. The sequence of events between alignment and locking remains obscure. Here we examine the roles of three critical residues, Tyr13, Phe56 and Gln54, in complex formation and stability using Biacore. Our mutational and kinetic data suggest that Tyr13 plays a more important role than Phe56 in complex formation. Mutational analysis of Gln54, combined with molecular dynamics studies, points to Arg52 as another key residue in association. Based on our data and previous structural and modeling studies, we propose that electrostatic alignment of the molecules is followed by hydrogen bond formation between the RNA and Arg52, and the sequential establishment of interactions with loop bases (including Tyr13). A quadruple stack, sandwiching two bases between Phe56 and Asp92, would occur last and coincide with the rearrangement of a C-terminal helix that partially occludes the RRM surface in the free protein.
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Affiliation(s)
| | - Eric J. Chambers
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | | | - Ian S. Haworth
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Ite A. Laird-Offringa
- To whom correspondence should be addressed. Tel: +1 323 865 0655; Fax: +1 323 865 0158;
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