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Canela-Pérez I, Azuara-Liceaga E, Cuéllar P, Saucedo-Cárdenas O, Valdés J. Multiple types of nuclear localization signals in Entamoeba histolytica. Biochem Biophys Rep 2024; 39:101770. [PMID: 39055170 PMCID: PMC11269297 DOI: 10.1016/j.bbrep.2024.101770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Entamoeba histolytica is a protozoan parasite that belongs to the Amoebozoa supergroup whose study related to the nucleocytoplasmic transport of proteins through the nucleus is poorly studied. In this work, we have performed in silico predictions of the potential nuclear localization signals (NLS) corresponding to the proteome of 8201 proteins from Entamoeba histolytica annotated in the AmoebaDB database. We have found the presence of monopartite nuclear localization signals (MNLSs), bipartite nuclear localization signals (BNLSs), and non-canonical monopartite NLSs with lengths exceeding 20 amino acid residues. Additionally, we detected a new type of NLS consisting of multiple juxtaposed bipartite NLSs (JNLSs) that have not been described in any eukaryotic organism. Also, we have generated consensus sequences for the nuclear import of proteins with the NLSs obtained. Docking experiments between EhImportin α and an MNLS, BNLS, and JNLS outlined the interacting residues between the Importin and cargo proteins, emphasizing their putative roles in nuclear import. By transfecting HA-tagged protein constructs, we assessed the nuclear localization of MNLS (U1A and U2AF1), JMNLS (U2AF2), and non-canonical NLS (N-terminus of Pol ll) in vivo. Our data provide the basis for understanding the nuclear transport process in E. histolytica.
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Affiliation(s)
- Israel Canela-Pérez
- Departamento de Bioquímica, CINVESTAV-México, Av. IPN 2508 colonia San Pedro Zacatenco, GAM, CDMX, 07360, Mexico
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, 03100, Mexico
| | - Patricia Cuéllar
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, 03100, Mexico
| | - Odila Saucedo-Cárdenas
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, 67700, Mexico
| | - Jesús Valdés
- Departamento de Bioquímica, CINVESTAV-México, Av. IPN 2508 colonia San Pedro Zacatenco, GAM, CDMX, 07360, Mexico
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2
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Surynt P, Wojtczak BA, Chrominski M, Panecka-Hofman J, Kwapiszewska K, Kalwarczyk T, Kubacka D, Spiewla T, Kasprzyk R, Holyst R, Kowalska J, Jemielity J. Trimethylguanosine cap-fluorescent molecular rotor (TMG-FMR) conjugates are potent, specific snurportin1 ligands enabling visualization in living cells. Org Biomol Chem 2024. [PMID: 39105613 DOI: 10.1039/d4ob01019a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
The trimethylguanosine (TMG) cap is a motif present inter alia at the 5' end of small nuclear RNAs, which are involved in RNA splicing. The TMG cap plays a crucial role in RNA processing and stability as it protects the RNA molecule from degradation by exonucleases and facilitates its export from the nucleus. Additionally, the TMG cap plays a role in the recognition of snRNA by snurportin, a protein that facilitates nuclear import. TMG cap analogs are used in biochemical experiments as molecular tools to substitute the natural TMG cap. To expand the range of available TMG-based tools, here we conjugated the TMG cap to Fluorescent Molecular Rotors (FMRs) to open the possibility of detecting protein-ligand interactions in vitro and, potentially, in vivo, particularly visualizing interactions with snurportin. Consequently, we report the synthesis of 34 differently modified TMG cap-FMR conjugates and their evaluation as molecular probes for snurportin. As FMRs we selected three GFP-like chromophores (derived from green fluorescent protein) and one julolidine derivative. The evaluation of binding affinities for snurportin showed unexpectedly a strong stabilizing effect for TMGpppG-derived dinucleotides containing the FMR at the 2'-O-position of guanosine. These newly discovered compounds are potent snurportin ligands with nanomolar KD (dissociation constant) values, which are two orders of magnitude lower than that of natural TMGpppG. The effect is diminished by ∼50-fold for the corresponding 3'-regioisomers. To deepen the understanding of the structure-activity relationship, we synthesized and tested FMR conjugates lacking the TMG cap moiety. These studies, supported by molecular docking, suggested that the enhanced affinity arises from additional hydrophobic contacts provided by the FMR moiety. The strongest snurportin ligand, which also gave the greatest fluorescence enhancement (Fm/F0) when saturated with the protein, were tested in living cells to detect interactions and visualize complexes by fluorescence lifetime monitoring. This approach has potential applications in the study of RNA processing and RNA-protein interactions.
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Affiliation(s)
- Piotr Surynt
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| | - Blazej A Wojtczak
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| | - Mikolaj Chrominski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| | - Joanna Panecka-Hofman
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Dorota Kubacka
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Tomasz Spiewla
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
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Iruzubieta P, Damborenea A, Ioghen M, Bajew S, Fernandez-Torrón R, Töpf A, Herrero-Reiriz Á, Epure D, Vill K, Hernández-Laín A, Manterola M, Azkargorta M, Pikatza-Menoio O, Pérez-Fernandez L, García-Puga M, Gaina G, Bastian A, Streata I, Walter MC, Müller-Felber W, Thiele S, Moragón S, Bastida-Lertxundi N, López-Cortajarena A, Elortza F, Gereñu G, Alonso-Martin S, Straub V, de Sancho D, Teleanu R, López de Munain A, Blázquez L. Biallelic variants in SNUPN cause a limb girdle muscular dystrophy with myofibrillar-like features. Brain 2024; 147:2867-2883. [PMID: 38366623 PMCID: PMC11292911 DOI: 10.1093/brain/awae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024] Open
Abstract
Alterations in RNA-splicing are a molecular hallmark of several neurological diseases, including muscular dystrophies, where mutations in genes involved in RNA metabolism or characterized by alterations in RNA splicing have been described. Here, we present five patients from two unrelated families with a limb-girdle muscular dystrophy (LGMD) phenotype carrying a biallelic variant in SNUPN gene. Snurportin-1, the protein encoded by SNUPN, plays an important role in the nuclear transport of small nuclear ribonucleoproteins (snRNPs), essential components of the spliceosome. We combine deep phenotyping, including clinical features, histopathology and muscle MRI, with functional studies in patient-derived cells and muscle biopsies to demonstrate that variants in SNUPN are the cause of a new type of LGMD according to current definition. Moreover, an in vivo model in Drosophila melanogaster further supports the relevance of Snurportin-1 in muscle. SNUPN patients show a similar phenotype characterized by proximal weakness starting in childhood, restrictive respiratory dysfunction and prominent contractures, although inter-individual variability in terms of severity even in individuals from the same family was found. Muscle biopsy showed myofibrillar-like features consisting of myotilin deposits and Z-disc disorganization. MRI showed predominant impairment of paravertebral, vasti, sartorius, gracilis, peroneal and medial gastrocnemius muscles. Conservation and structural analyses of Snurportin-1 p.Ile309Ser variant suggest an effect in nuclear-cytosol snRNP trafficking. In patient-derived fibroblasts and muscle, cytoplasmic accumulation of snRNP components is observed, while total expression of Snurportin-1 and snRNPs remains unchanged, which demonstrates a functional impact of SNUPN variant in snRNP metabolism. Furthermore, RNA-splicing analysis in patients' muscle showed widespread splicing deregulation, in particular in genes relevant for muscle development and splicing factors that participate in the early steps of spliceosome assembly. In conclusion, we report that SNUPN variants are a new cause of limb girdle muscular dystrophy with specific clinical, histopathological and imaging features, supporting SNUPN as a new gene to be included in genetic testing of myopathies. These results further support the relevance of splicing-related proteins in muscle disorders.
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Affiliation(s)
- Pablo Iruzubieta
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Alberto Damborenea
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Mihaela Ioghen
- Clinical Neurosciences Department, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Paediatric Neurology, 020021 Bucharest, Romania
| | - Simon Bajew
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Roberto Fernandez-Torrón
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, NE4 5NR Newcastle Upon Tyne, UK
| | - Álvaro Herrero-Reiriz
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Diana Epure
- Department of Paediatric Neurology, Doctor Victor Gomoiu Children’s Hospital, 022102 Bucharest, Romania
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children’s Hospital, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Aurelio Hernández-Laín
- Neuropathology Unit, Department of Pathology, 12 de Octubre University Hospital, 28041 Madrid, Spain
- Department of Neuro-oncology, Instituto de Investigación Sanitaria imas12, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Universidad Complutense de Madrid, Facultad de Medicina, 28040 Madrid, Spain
| | - María Manterola
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
- Centre for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Oihane Pikatza-Menoio
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Laura Pérez-Fernandez
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014 San Sebastián, Spain
| | - Mikel García-Puga
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Gisela Gaina
- Department of Cell Biology, Neurosciences and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
| | - Alexandra Bastian
- Department of Pathology, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Ioana Streata
- Human Genomics Laboratory, Regional Centre of Medical Genetics, Craiova University of Medicine and Pharmacy, 200349 Dolj, Romania
| | - Maggie C Walter
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Wolfgang Müller-Felber
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Simone Thiele
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Saioa Moragón
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
| | - Nerea Bastida-Lertxundi
- Department of Clinical Genetics, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
| | - Aitziber López-Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014 San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
- Centre for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Gorka Gereñu
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Sonia Alonso-Martin
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, NE4 5NR Newcastle Upon Tyne, UK
| | - David de Sancho
- Donostia International Physics Center, 20018 San Sebastián, Spain
- Faculty of Chemistry, University of the Basque Country, 20018 San Sebastián, Spain
| | - Raluca Teleanu
- Clinical Neurosciences Department, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Paediatric Neurology, 020021 Bucharest, Romania
| | - Adolfo López de Munain
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Faculty of Medicine, University of the Basque Country, 20014 San Sebastián, Spain
- Faculty of Medicine, University of Deusto, 48007 Bilbao, Spain
| | - Lorea Blázquez
- Department of Neurosciences, Biogipuzkoa Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
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4
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Nashabat M, Nabavizadeh N, Saraçoğlu HP, Sarıbaş B, Avcı Ş, Börklü E, Beillard E, Yılmaz E, Uygur SE, Kayhan CK, Bosco L, Eren ZB, Steindl K, Richter MF, Bademci G, Rauch A, Fattahi Z, Valentino ML, Connolly AM, Bahr A, Viola L, Bergmann AK, Rocha ME, Peart L, Castro-Rojas DL, Bültmann E, Khan S, Giarrana ML, Teleanu RI, Gonzalez JM, Pini A, Schädlich IS, Vill K, Brugger M, Zuchner S, Pinto A, Donkervoort S, Bivona SA, Riza A, Streata I, Gläser D, Baquero-Montoya C, Garcia-Restrepo N, Kotzaeridou U, Brunet T, Epure DA, Bertoli-Avella A, Kariminejad A, Tekin M, von Hardenberg S, Bönnemann CG, Stettner GM, Zanni G, Kayserili H, Oflazer ZP, Escande-Beillard N. SNUPN deficiency causes a recessive muscular dystrophy due to RNA mis-splicing and ECM dysregulation. Nat Commun 2024; 15:1758. [PMID: 38413582 PMCID: PMC10899626 DOI: 10.1038/s41467-024-45933-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
SNURPORTIN-1, encoded by SNUPN, plays a central role in the nuclear import of spliceosomal small nuclear ribonucleoproteins. However, its physiological function remains unexplored. In this study, we investigate 18 children from 15 unrelated families who present with atypical muscular dystrophy and neurological defects. Nine hypomorphic SNUPN biallelic variants, predominantly clustered in the last coding exon, are ascertained to segregate with the disease. We demonstrate that mutant SPN1 failed to oligomerize leading to cytoplasmic aggregation in patients' primary fibroblasts and CRISPR/Cas9-mediated mutant cell lines. Additionally, mutant nuclei exhibit defective spliceosomal maturation and breakdown of Cajal bodies. Transcriptome analyses reveal splicing and mRNA expression dysregulation, particularly in sarcolemmal components, causing disruption of cytoskeletal organization in mutant cells and patient muscle tissues. Our findings establish SNUPN deficiency as the genetic etiology of a previously unrecognized subtype of muscular dystrophy and provide robust evidence of the role of SPN1 for muscle homeostasis.
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Affiliation(s)
- Marwan Nashabat
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Nasrinsadat Nabavizadeh
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Hilal Pırıl Saraçoğlu
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Burak Sarıbaş
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Şahin Avcı
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
| | - Esra Börklü
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
| | | | - Elanur Yılmaz
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Seyide Ecesu Uygur
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Cavit Kerem Kayhan
- Pathology Laboratory, Acıbadem Maslak Hospital, Istanbul, Turkey
- Department of Biotechnology, Nişantaşı University, Istanbul, Turkey
| | - Luca Bosco
- Unit of Muscular and Neurodegenerative Disorders and Developmental Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Science, University "Roma Tre", Rome, Italy
| | - Zeynep Bengi Eren
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | | | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
- Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Centre, Tehran, Iran
| | - Maria Lucia Valentino
- IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Anne M Connolly
- Division of Neurology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Laura Viola
- Unit of Clinical Pediatrics, State Hospital, San Marino Republic, Italy
| | | | | | - LeShon Peart
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derly Liseth Castro-Rojas
- Genomics Laboratory, Center of Immunology and Genetics (CIGE), SURA Ayudas Diagnosticas, Medellín, Colombia
| | - Eva Bültmann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | | | | | - Raluca Ioana Teleanu
- Dr Victor Gomoiu Children's Hospital, Bucharest, Romania
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Joanna Michelle Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Antonella Pini
- Neuromuscular Pediatric Unit, IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy
| | - Ines Sophie Schädlich
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-University, Munich, Germany
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | - Melanie Brugger
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Ann Bivona
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anca Riza
- Human Genomics Laboratory, University of Medicine and Pharmacy, Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital, Craiova, Romania
| | - Ioana Streata
- Human Genomics Laboratory, University of Medicine and Pharmacy, Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital, Craiova, Romania
| | | | | | | | - Urania Kotzaeridou
- Division of Child Neurology and Inherited Metabolic Diseases, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Theresa Brunet
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-University, Munich, Germany
- Department of Human Genetics, Technical University of Munich, School of Medicine, Munich, Germany
| | | | | | | | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- John P. Hussmann Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Georg M Stettner
- Neuromuscular Center Zurich and Department of Pediatric Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Developmental Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Hülya Kayserili
- Diagnostic Center for Genetic Diseases, Department of Medical Genetics, Koç University Hospital, Istanbul, Turkey
- Department of Medical Genetics, Koç University School of Medicine (KUSoM), Istanbul, Turkey
| | - Zehra Piraye Oflazer
- Department of Neurology, Koç University Hospital Muscle Center, Istanbul, Turkey
| | - Nathalie Escande-Beillard
- Laboratory of Functional Genomics, Department of Medical Genetics, Koç University, School of Medicine (KUSoM), Istanbul, Turkey.
- Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine (KUSoM), Istanbul, Turkey.
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5
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Zucko D, Boris-Lawrie K. Blocking tri-methylguanosine synthase 1 (TGS1) stops anchorage-independent growth of canine sarcomas. Cancer Gene Ther 2023; 30:1274-1284. [PMID: 37386121 PMCID: PMC10501901 DOI: 10.1038/s41417-023-00636-9] [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: 11/17/2022] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 07/01/2023]
Abstract
Tri methylguanosine synthase 1 (TGS1) is the enzyme that hyper methylates the hallmark 7-methyl-guanosine cap (m7G-cap) appended to the transcription start site of RNAs. The m7G-cap and the eIF4E-cap binding protein guide canonical cap-dependent translation of mRNAs, whereas hyper methylated cap, m2,2,7G-cap (TMG) lacks adequate eIF4E affinity and licenses entry into a different translation initiation pathway. The potential role for TGS1 and TMG-capped mRNA in neoplastic growth is unknown. Canine sarcoma has high translational value to the human disease. Cumulative downregulation of protein synthesis in osteosarcoma OSCA-40 was achieved cooperatively by siTGS1 and Torin-1. Torin-1 inhibited the proliferation of three canine sarcoma explants in a reversible manner that was eliminated by siRNA-downregulation of TGS1. TGS1 failure prevented the anchorage-independent growth of osteo- and hemangio-sarcomas and curtailed sarcoma recovery from mTOR inhibition. RNA immunoprecipitation studies identified TMG-capped mRNAs encoding TGS1, DHX9 and JUND. TMG-tgs1 transcripts were downregulated by leptomycin B and TGS1 failure was compensated by eIF4E mRNP-dependent tgs1 mRNA translation affected by mTOR. The evidence documents TMG-capped mRNAs are hallmarks of the investigated neoplasms and synergy between TGS1 specialized translation and canonical translation is involved in sarcoma recovery from mTOR inhibition. Therapeutic targeting of TGS1 activity in cancer is ripe for future exploration.
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Affiliation(s)
- Dora Zucko
- University of Minnesota - Twin Cities, Department of Veterinary and Biomedical Sciences, Saint Paul, MN, 55108, USA
| | - Kathleen Boris-Lawrie
- University of Minnesota - Twin Cities, Department of Veterinary and Biomedical Sciences, Saint Paul, MN, 55108, USA.
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6
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Wojtczak BA, Bednarczyk M, Sikorski PJ, Wojtczak A, Surynt P, Kowalska J, Jemielity J. Synthesis and Evaluation of Diguanosine Cap Analogs Modified at the C8-Position by Suzuki-Miyaura Cross-Coupling: Discovery of 7-Methylguanosine-Based Molecular Rotors. J Org Chem 2023. [PMID: 37209102 DOI: 10.1021/acs.joc.3c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Chemical modifications of the mRNA cap structure can enhance the stability, translational properties, and half-life of mRNAs, thereby altering the therapeutic properties of synthetic mRNA. However, cap structure modification is challenging because of the instability of the 5'-5'-triphosphate bridge and N7-methylguanosine. The Suzuki-Miyaura cross-coupling reaction between boronic acid and halogen compound is a mild, convenient, and potentially applicable approach for modifying biomolecules. Herein, we describe two methods to synthesize C8-modified cap structures using the Suzuki-Miyaura cross-coupling reaction. Both methods employed phosphorimidazolide chemistry to form the 5',5'-triphosphate bridge. However, in the first method, the introduction of the modification via the Suzuki-Miyaura cross-coupling reaction at the C8 position occurs postsynthetically, at the dinucleotide level, whereas in the second method, the modification was introduced at the level of the nucleoside 5'-monophosphate, and later, the triphosphate bridge was formed. Both methods were successfully applied to incorporate six different groups (methyl, cyclopropyl, phenyl, 4-dimethylaminophenyl, 4-cyanophenyl, and 1-pyrene) into either the m7G or G moieties of the cap structure. Aromatic substituents at the C8-position of guanosine form a push-pull system that exhibits environment-sensitive fluorescence. We demonstrated that this phenomenon can be harnessed to study the interaction with cap-binding proteins, e.g., eIF4E, DcpS, Nudt16, and snurportin.
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Affiliation(s)
- Blazej A Wojtczak
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| | - Marcelina Bednarczyk
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| | - Anna Wojtczak
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Piotr Surynt
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Joanna Kowalska
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
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7
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4-Methylumbelliferone Targets Revealed by Public Data Analysis and Liver Transcriptome Sequencing. Int J Mol Sci 2023; 24:ijms24032129. [PMID: 36768453 PMCID: PMC9917189 DOI: 10.3390/ijms24032129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
4-methylumbelliferone (4MU) is a well-known hyaluronic acid synthesis inhibitor and an approved drug for the treatment of cholestasis. In animal models, 4MU decreases inflammation, reduces fibrosis, and lowers body weight, serum cholesterol, and insulin resistance. It also inhibits tumor progression and metastasis. The broad spectrum of effects suggests multiple and yet unknown targets of 4MU. Aiming at 4MU target deconvolution, we have analyzed publicly available data bases, including: 1. Small molecule library Bio Assay screening (PubChemBioAssay); 2. GO pathway databases screening; 3. Protein Atlas Database. We also performed comparative liver transcriptome analysis of mice on normal diet and mice fed with 4MU for two weeks. Potential targets of 4MU public data base analysis fall into two big groups, enzymes and transcription factors (TFs), including 13 members of the nuclear receptor superfamily regulating lipid and carbohydrate metabolism. Transcriptome analysis revealed changes in the expression of genes involved in bile acid metabolism, gluconeogenesis, and immune response. It was found that 4MU feeding decreased the accumulation of the glycogen granules in the liver. Thus, 4MU has multiple targets and can regulate cell metabolism by modulating signaling via nuclear receptors.
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8
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Chen L, Roake CM, Maccallini P, Bavasso F, Dehghannasiri R, Santonicola P, Mendoza-Ferreira N, Scatolini L, Rizzuti L, Esposito A, Gallotta I, Francia S, Cacchione S, Galati A, Palumbo V, Kobin MA, Tartaglia G, Colantoni A, Proietti G, Wu Y, Hammerschmidt M, De Pittà C, Sales G, Salzman J, Pellizzoni L, Wirth B, Di Schiavi E, Gatti M, Artandi S, Raffa GD. TGS1 impacts snRNA 3'-end processing, ameliorates survival motor neuron-dependent neurological phenotypes in vivo and prevents neurodegeneration. Nucleic Acids Res 2022; 50:12400-12424. [PMID: 35947650 PMCID: PMC9757054 DOI: 10.1093/nar/gkac659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
Trimethylguanosine synthase 1 (TGS1) is a highly conserved enzyme that converts the 5'-monomethylguanosine cap of small nuclear RNAs (snRNAs) to a trimethylguanosine cap. Here, we show that loss of TGS1 in Caenorhabditis elegans, Drosophila melanogaster and Danio rerio results in neurological phenotypes similar to those caused by survival motor neuron (SMN) deficiency. Importantly, expression of human TGS1 ameliorates the SMN-dependent neurological phenotypes in both flies and worms, revealing that TGS1 can partly counteract the effects of SMN deficiency. TGS1 loss in HeLa cells leads to the accumulation of immature U2 and U4atac snRNAs with long 3' tails that are often uridylated. snRNAs with defective 3' terminations also accumulate in Drosophila Tgs1 mutants. Consistent with defective snRNA maturation, TGS1 and SMN mutant cells also exhibit partially overlapping transcriptome alterations that include aberrantly spliced and readthrough transcripts. Together, these results identify a neuroprotective function for TGS1 and reinforce the view that defective snRNA maturation affects neuronal viability and function.
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Affiliation(s)
- Lu Chen
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cancer Signaling and Epigenetics Program and Cancer Epigenetics Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Caitlin M Roake
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paolo Maccallini
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Francesca Bavasso
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Natalia Mendoza-Ferreira
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute for Genetics, University of Cologne, 50931 Cologne, Germany
| | - Livia Scatolini
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Ludovico Rizzuti
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | | | - Ivan Gallotta
- Institute of Genetics and Biophysics, IGB-ABT, CNR, Naples, Italy
| | - Sofia Francia
- IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy
- Istituto di Genetica Molecolare, CNR-Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Stefano Cacchione
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Alessandra Galati
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Valeria Palumbo
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Marie A Kobin
- Cancer Signaling and Epigenetics Program and Cancer Epigenetics Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Gian Gaetano Tartaglia
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy
- Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Alessio Colantoni
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy
- Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Gabriele Proietti
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy
- Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Yunming Wu
- Cancer Signaling and Epigenetics Program and Cancer Epigenetics Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Matthias Hammerschmidt
- Institute for Zoology, Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | | | - Gabriele Sales
- Department of Biology, University of Padova, Padua, Italy
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Columbia University, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University, NY 10032, USA
- Department of Neurology, Columbia University, NY 10032, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute for Genetics, University of Cologne, 50931 Cologne, Germany
- Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Elia Di Schiavi
- Institute of Biosciences and BioResources, IBBR, CNR, Naples, Italy
- Institute of Genetics and Biophysics, IGB-ABT, CNR, Naples, Italy
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
- Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Rome, Italy
| | - Steven E Artandi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Grazia D Raffa
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
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9
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Cheng L, Zhang Y, Zhang Y, Chen T, Xu YZ, Rong YS. Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development. PLoS Genet 2020; 16:e1009098. [PMID: 33085660 PMCID: PMC7605716 DOI: 10.1371/journal.pgen.1009098] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 11/02/2020] [Accepted: 09/07/2020] [Indexed: 12/31/2022] Open
Abstract
The 2,2,7-trimethylguanosine (TMG) cap is one of the first identified modifications on eukaryotic RNAs. TMG, synthesized by the conserved Tgs1 enzyme, is abundantly present on snRNAs essential for pre-mRNA splicing. Results from ex vivo experiments in vertebrate cells suggested that TMG ensures nuclear localization of snRNAs. Functional studies of TMG using tgs1 mutations in unicellular organisms yield results inconsistent with TMG being indispensable for either nuclear import or splicing. Utilizing a hypomorphic tgs1 mutation in Drosophila, we show that TMG reduction impairs germline development by disrupting the processing, particularly of introns with smaller sizes and weaker splice sites. Unexpectedly, loss of TMG does not disrupt snRNAs localization to the nucleus, disputing an essential role of TMG in snRNA transport. Tgs1 loss also leads to defective 3' processing of snRNAs. Remarkably, stronger tgs1 mutations cause lethality without severely disrupting splicing, likely due to the preponderance of TMG-capped snRNPs. Tgs1, a predominantly nucleolar protein in Drosophila, likely carries out splicing-independent functions indispensable for animal development. Taken together, our results suggest that nuclear import is not a conserved function of TMG. As a distinctive structure on RNA, particularly non-coding RNA, we suggest that TMG prevents spurious interactions detrimental to the function of RNAs that it modifies.
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Affiliation(s)
- Lin Cheng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Hengyang College of Medicine, University of South China, Hengyang, China
| | - Yu Zhang
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Zhang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States of America
| | - Tao Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Hengyang College of Medicine, University of South China, Hengyang, China
| | - Yong-Zhen Xu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yikang S. Rong
- Hengyang College of Medicine, University of South China, Hengyang, China
- * E-mail:
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10
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Warminski M, Sikorski PJ, Kowalska J, Jemielity J. Applications of Phosphate Modification and Labeling to Study (m)RNA Caps. Top Curr Chem (Cham) 2017; 375:16. [PMID: 28116583 PMCID: PMC5396385 DOI: 10.1007/s41061-017-0106-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023]
Abstract
The cap is a natural modification present at the 5' ends of eukaryotic messenger RNA (mRNA), which because of its unique structural features, mediates essential biological functions during the process of gene expression. The core structural feature of the mRNA cap is an N7-methylguanosine moiety linked by a 5'-5' triphosphate chain to the first transcribed nucleotide. Interestingly, other RNA 5' end modifications structurally and functionally resembling the m7G cap have been discovered in different RNA types and in different organisms. All these structures contain the 'inverted' 5'-5' oligophosphate bridge, which is necessary for interaction with specific proteins and also serves as a cleavage site for phosphohydrolases regulating RNA turnover. Therefore, cap analogs containing oligophosphate chain modifications or carrying spectroscopic labels attached to phosphate moieties serve as attractive molecular tools for studies on RNA metabolism and modification of natural RNA properties. Here, we review chemical, enzymatic, and chemoenzymatic approaches that enable preparation of modified cap structures and RNAs carrying such structures, with emphasis on phosphate-modified mRNA cap analogs and their potential applications.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
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11
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Xu C, Ishikawa H, Izumikawa K, Li L, He H, Nobe Y, Yamauchi Y, Shahjee HM, Wu XH, Yu YT, Isobe T, Takahashi N, Min J. Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. Genes Dev 2016; 30:2376-2390. [PMID: 27881600 PMCID: PMC5131778 DOI: 10.1101/gad.288340.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/26/2016] [Indexed: 12/26/2022]
Abstract
Xu et al. show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs. They also determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA. In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)4–6G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m7G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays. We further determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m7G cap of pre-snRNAs via two distinct binding sites by respective base-specific interactions. In addition, we also uncovered a novel role of Gemin5 in escorting the truncated forms of U1 pre-snRNAs for proper disposal. Overall, the elucidated Gemin5 structures will contribute to a better understanding of Gemin5 in small nuclear ribonucleic protein (snRNP) biogenesis as well as, potentially, other cellular activities.
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Affiliation(s)
- Chao Xu
- Hefei National Laboratory for Physical Sciences at Microscale, Hefei Science Center of CAS, Chinese Academy of Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hideaki Ishikawa
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Keiichi Izumikawa
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Li Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hao He
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yuko Nobe
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Hanief M Shahjee
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Xian-Hui Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Toshiaki Isobe
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Nobuhiro Takahashi
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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12
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Molecular recognition of mRNA 5' cap by 3' poly(A)-specific ribonuclease (PARN) differs from interactions known for other cap-binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:331-45. [PMID: 26772900 DOI: 10.1016/j.bbapap.2016.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/23/2015] [Accepted: 01/05/2016] [Indexed: 12/30/2022]
Abstract
The mRNA 5' cap structure plays a pivotal role in coordination of eukaryotic translation and mRNA degradation. Poly(A)-specific ribonuclease (PARN) is a dimeric exoribonuclease that efficiently degrades mRNA 3' poly(A) tails while also simultaneously interacting with the mRNA 5' cap. The cap binding amplifies the processivity of PARN action. We used surface plasmon resonance kinetic analysis, quantitative equilibrium fluorescence titrations and circular dichroism to study the cap binding properties of PARN. The molecular mechanism of 5' cap recognition by PARN has been demonstrated to differ from interactions seen for other known cap-binding proteins in that: i) the auxiliary biological function of 5' cap binding by the 3' degrading enzyme is accomplished by negative cooperativity of PARN dimer subunits; ii) non-coulombic interactions are major factors in the complex formation; and iii) PARN has versatile activity toward alternative forms of the cap. These characteristics contribute to stabilization of the PARN-cap complex needed for the deadenylation processivity. Our studies provide a consistent biophysical basis for elucidation of the processive mechanism of PARN-mediated 3' mRNA deadenylation and provide a new framework to interpret the role of the 5' cap in mRNA degradation.
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13
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Honcharenko M, Bestas B, Jezowska M, Wojtczak BA, Moreno PMD, Romanowska J, Bächle SM, Darzynkiewicz E, Jemielity J, Smith CIE, Strömberg R. Synthetic m3G-CAP attachment necessitates a minimum trinucleotide constituent to be recognised as a nuclear import signal. RSC Adv 2016. [DOI: 10.1039/c6ra09568b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Minimal requirement for Snurportin based nuclear uptake is the inclusion of a trinucleotide sequence between the m3G-CAP and the artificial linker.
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14
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Christie M, Chang CW, Róna G, Smith KM, Stewart AG, Takeda AAS, Fontes MRM, Stewart M, Vértessy BG, Forwood JK, Kobe B. Structural Biology and Regulation of Protein Import into the Nucleus. J Mol Biol 2015; 428:2060-90. [PMID: 26523678 DOI: 10.1016/j.jmb.2015.10.023] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/16/2015] [Accepted: 10/24/2015] [Indexed: 11/28/2022]
Abstract
Proteins are translated in the cytoplasm, but many need to access the nucleus to perform their functions. Understanding how these nuclear proteins are transported through the nuclear envelope and how the import processes are regulated is therefore an important aspect of understanding cell function. Structural biology has played a key role in understanding the molecular events during the transport processes and their regulation, including the recognition of nuclear targeting signals by the corresponding receptors. Here, we review the structural basis of the principal nuclear import pathways and the molecular basis of their regulation. The pathways involve transport factors that are members of the β-karyopherin family, which can bind cargo directly (e.g., importin-β, transportin-1, transportin-3, importin-13) or through adaptor proteins (e.g., importin-α, snurportin-1, symportin-1), as well as unrelated transport factors such as Hikeshi, involved in the transport of heat-shock proteins, and NTF2, involved in the transport of RanGDP. Solenoid proteins feature prominently in these pathways. Nuclear transport factors recognize nuclear targeting signals on the cargo proteins, including the classical nuclear localization signals, recognized by the adaptor importin-α, and the PY nuclear localization signals, recognized by transportin-1. Post-translational modifications, particularly phosphorylation, constitute key regulatory mechanisms operating in these pathways.
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Affiliation(s)
- Mary Christie
- The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales Faculty of Medicine, Darlinghurst, NSW 2010, Australia
| | - Chiung-Wen Chang
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gergely Róna
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Kate M Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Alastair G Stewart
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Agnes A S Takeda
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Marcos R M Fontes
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Murray Stewart
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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15
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Dickmanns A, Monecke T, Ficner R. Structural Basis of Targeting the Exportin CRM1 in Cancer. Cells 2015; 4:538-68. [PMID: 26402707 PMCID: PMC4588050 DOI: 10.3390/cells4030538] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/07/2015] [Accepted: 09/11/2015] [Indexed: 12/19/2022] Open
Abstract
Recent studies have demonstrated the interference of nucleocytoplasmic trafficking with the establishment and maintenance of various cancers. Nucleocytoplasmic transport is highly regulated and coordinated, involving different nuclear transport factors or receptors, importins and exportins, that mediate cargo transport from the cytoplasm into the nucleus or the other way round, respectively. The exportin CRM1 (Chromosome region maintenance 1) exports a plethora of different protein cargoes and ribonucleoprotein complexes. Structural and biochemical analyses have enabled the deduction of individual steps of the CRM1 transport cycle. In addition, CRM1 turned out to be a valid target for anticancer drugs as it exports numerous proto-oncoproteins and tumor suppressors. Clearly, detailed understanding of the flexibility, regulatory features and cooperative binding properties of CRM1 for Ran and cargo is a prerequisite for the design of highly effective drugs. The first compound found to inhibit CRM1-dependent nuclear export was the natural drug Leptomycin B (LMB), which blocks export by competitively interacting with a highly conserved cleft on CRM1 required for nuclear export signal recognition. Clinical studies revealed serious side effects of LMB, leading to a search for alternative natural and synthetic drugs and hence a multitude of novel therapeutics. The present review examines recent progress in understanding the binding mode of natural and synthetic compounds and their inhibitory effects.
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Affiliation(s)
- Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany.
| | - Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany.
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany.
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16
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Piecyk K, Niedzwiecka A, Ferenc-Mrozek A, Lukaszewicz M, Darzynkiewicz E, Jankowska-Anyszka M. How to find the optimal partner--studies of snurportin 1 interactions with U snRNA 5' TMG-cap analogues containing modified 2-amino group of 7-methylguanosine. Bioorg Med Chem 2015; 23:4660-4668. [PMID: 26118337 DOI: 10.1016/j.bmc.2015.05.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/26/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
Abstract
Snurportin 1 is an adaptor protein that mediates the active nuclear import of uridine-rich small nuclear RNAs (U snRNA) by the importin-β receptor pathway. Its cellular activity influences the overall transport yield of small ribonucleoprotein complexes containing N(2),N(2),7-trimethylguanosine (TMG) capped U snRNA. So far little is still known about structural requirements related to molecular recognition of the trimethylguanosine moiety by snurportin in solution. Since these interactions are of a great biomedical importance, we synthesized a series of new 7-methylguanosine cap analogues with extended substituents at the exocyclic 2-amino group to gain a deeper insight into how the TMG-cap is adapted into the snurportin cap-binding pocket. Prepared chemical tools were applied in binding assays using emission spectroscopy. Surprisingly, our results revealed strict selectivity of snurportin towards the TMG-cap structure that relied mainly on its structural stiffness and compactness.
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Affiliation(s)
- Karolina Piecyk
- Faculty of Chemistry, University of Warsaw, 1 Pasteura St., 02-093 Warsaw, Poland
| | - Anna Niedzwiecka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, 32/46 Lotników Ave., 02-668 Warsaw, Poland; Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 93 Żwirki I Wigury St., 02-089 Warsaw, Poland
| | | | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 93 Żwirki I Wigury St., 02-089 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 93 Żwirki I Wigury St., 02-089 Warsaw, Poland; Centre of New Technologies, University of Warsaw, 2C Banacha St., 02-097 Warsaw, Poland
| | - Marzena Jankowska-Anyszka
- Faculty of Chemistry, University of Warsaw, 1 Pasteura St., 02-093 Warsaw, Poland; Department of Biochemistry, Second Faculty of Medicine, Medical University of Warsaw, 101 Zwirki & Wigury Str., 02-089 Warsaw, Poland.
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17
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Zytek M, Kowalska J, Lukaszewicz M, Wojtczak BA, Zuberek J, Ferenc-Mrozek A, Darzynkiewicz E, Niedzwiecka A, Jemielity J. Towards novel efficient and stable nuclear import signals: synthesis and properties of trimethylguanosine cap analogs modified within the 5',5'-triphosphate bridge. Org Biomol Chem 2015; 12:9184-99. [PMID: 25296894 DOI: 10.1039/c4ob01579g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A trimethylguanosine (TMG) cap is present at the 5' end of several small nuclear and nucleolar RNAs. Recently, it has been reported that the TMG cap is a potential nuclear import signal for nucleus-targeting therapeutic nucleic acids and proteins. The import is mediated by recognition of the TMG cap by the snRNA transporting protein, snurportin1. This work describes the synthesis and properties of a series of dinucleotide TMG cap (m3(2,2,7)GpppG) analogs modified in the 5',5'-triphosphate bridge as tools to study TMG cap-dependent biological processes. The bridge was altered at different positions by introducing either bridging (imidodiphosphate, O to NH and methylenebisphosphonate, O to CH2) or non-bridging (phosphorothioate, O to S and boranophosphate, O to BH3) modifications, or by elongation to tetraphosphate. The stability of novel analogs in blood serum was studied to reveal that the α,β-bridging O to NH substitution (m3(2,2,7)GppNHpG) confers the highest resistance. Short RNAs capped with analogs containing α,β-bridging (m3(2,2,7)GppNHpG) or β-non-bridging (m3(2,2,7)GppSpG D2) modifications were resistant to decapping pyrophosphatase, hNudt16. Preliminary studies on binding by human snurportin1 revealed that both O to NH and O to S substitutions support this binding. Due to favorable properties in all three assays, m3(2,2,7)GppNHpG was selected as a promising candidate for further studies on the efficiency of the TMG cap as a nuclear import signal.
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Affiliation(s)
- Malgorzata Zytek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
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18
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Fung HYJ, Chook YM. Atomic basis of CRM1-cargo recognition, release and inhibition. Semin Cancer Biol 2014; 27:52-61. [PMID: 24631835 PMCID: PMC4108548 DOI: 10.1016/j.semcancer.2014.03.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/01/2014] [Indexed: 11/19/2022]
Abstract
CRM1 or XPO1 is the major nuclear export receptor in the cell, which controls the nuclear-cytoplasmic localization of many proteins and RNAs. CRM1 is also a promising cancer drug target as the transport receptor is overexpressed in many cancers where some of its cargos are misregulated and mislocalized to the cytoplasm. Atomic level understanding of CRM1 function has greatly facilitated recent drug discovery and development of CRM1 inhibitors to target a variety of malignancies. Numerous atomic resolution CRM1 structures are now available, explaining how the exporter recognizes nuclear export signals in its cargos, how RanGTP and cargo bind with positive cooperativity, how RanBP1 causes release of export cargos in the cytoplasm and how diverse inhibitors such as Leptomycin B and the new KPT-SINE compounds block nuclear export. This review summarizes structure-function studies that explain CRM1-cargo recognition, release and inhibition.
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Affiliation(s)
- Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, TX 75390-9041, USA.
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, TX 75390-9041, USA.
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19
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Hales CM, Dammer EB, Diner I, Yi H, Seyfried NT, Gearing M, Glass JD, Montine TJ, Levey AI, Lah JJ. Aggregates of small nuclear ribonucleic acids (snRNAs) in Alzheimer's disease. Brain Pathol 2014; 24:344-51. [PMID: 24571648 DOI: 10.1111/bpa.12133] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 02/13/2014] [Indexed: 01/04/2023] Open
Abstract
We recently discovered that protein components of the ribonucleic acid (RNA) spliceosome form cytoplasmic aggregates in Alzheimer's disease (AD) brain, resulting in widespread changes in RNA splicing. However, the involvement of small nuclear RNAs (snRNAs), also key components of the spliceosome complex, in the pathology of AD remains unknown. Using immunohistochemical staining of post-mortem human brain and spinal cord, we identified cytoplasmic tangle-shaped aggregates of snRNA in both sporadic and familial AD cases but not in aged controls or other neurodegenerative disorders. Immunofluorescence using antibodies reactive with the 2,2,7-trimethylguanosine cap of snRNAs and transmission electron microscopy demonstrated snRNA localization with tau and paired helical filaments, the main component of neurofibrillary tangles. Quantitative real-time polymerase chain reaction (PCR) showed U1 snRNA accumulation in the insoluble fraction of AD brains whereas other U snRNAs were not enriched. In combination with our previous results, these findings demonstrate that aggregates of U1 snRNA and U1 small nuclear ribonucleoproteins represent a new pathological hallmark of AD.
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Affiliation(s)
- Chadwick M Hales
- Center for Neurodegenerative Disease, Emory University, Atlanta, GA; Department of Neurology, Emory University School of Medicine, Atlanta, GA
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20
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Monecke T, Buschmann J, Neumann P, Wahle E, Ficner R. Crystal structures of the novel cytosolic 5'-nucleotidase IIIB explain its preference for m7GMP. PLoS One 2014; 9:e90915. [PMID: 24603684 PMCID: PMC3946280 DOI: 10.1371/journal.pone.0090915] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/04/2014] [Indexed: 12/13/2022] Open
Abstract
5′-nucleotidases catalyze the hydrolytic dephosphorylation of nucleoside monophosphates. As catabolic enzymes they contribute significantly to the regulation of cellular nucleotide levels; misregulation of nucleotide metabolism and nucleotidase deficiencies are associated with a number of diseases. The seven human 5′-nucleotidases differ with respect to substrate specificity and cellular localization. Recently, the novel cytosolic 5′-nucleotidase III-like protein, or cN-IIIB, has been characterized in human and Drosophila. cN-IIIB exhibits a strong substrate preference for the modified nucleotide 7-methylguanosine monophosphate but the structural reason for this preference was unknown. Here, we present crystal structures of cN-IIIB from Drosophila melanogaster bound to the reaction products 7-methylguanosine or cytidine. The structural data reveal that the cytosine- and 7-methylguanine moieties of the products are stacked between two aromatic residues in a coplanar but off-centered position. 7-methylguanosine is specifically bound through π-π interactions and distinguished from unmodified guanosine by additional cation-π coulomb interactions between the aromatic side chains and the positively charged 7-methylguanine. Notably, the base is further stabilized by T-shaped edge-to-face stacking of an additional tryptophan packing perpendicularly against the purine ring and forming, together with the other aromates, an aromatic slot. The structural data in combination with site-directed mutagenesis experiments reveal the molecular basis for the broad substrate specificity of cN-IIIB but also explain the substrate preference for 7-methylguanosine monophosphate. Analyzing the substrate specificities of cN-IIIB and the main pyrimidine 5′-nucleotidase cN-IIIA by mutagenesis studies, we show that cN-IIIA dephosphorylates the purine m7GMP as well, hence redefining its substrate spectrum. Docking calculations with cN-IIIA and m7GMP as well as biochemical data reveal that Asn69 does not generally exclude the turnover of purine substrates thus correcting previous suggestions.
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Affiliation(s)
- Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail:
| | - Juliane Buschmann
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Piotr Neumann
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Elmar Wahle
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
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21
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Abstract
Cap analogs are chemically modified derivatives of the unique cap structure present at the 5´ end of all eukaryotic mRNAs and several non-coding RNAs. Until recently, cap analogs have served primarily as tools in the study of RNA metabolism. Continuing advances in our understanding of cap biological functions (including RNA stabilization, pre-mRNA splicing, initiation of mRNA translation, as well as cellular transport of mRNAs and snRNAs) and the consequences of the disruption of these processes - resulting in serious medical disorders - have opened new possibilities for pharmaceutical applications of these compounds. In this review, the medicinal potential of cap analogs in areas, such as cancer treatment (including eIF4E targeting and mRNA-based immunotherapy), spinal muscular atrophy treatment, antiviral therapy and the improvement of the localization of nucleus-targeting drugs, are highlighted. Advances achieved to date, challenges, plausible solutions and prospects for the future development of cap analog-based drug design are described.
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22
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Honcharenko M, Zytek M, Bestas B, Moreno P, Jemielity J, Darzynkiewicz E, Smith CIE, Strömberg R. Synthesis and evaluation of stability of m3G-CAP analogues in serum-supplemented medium and cytosolic extract. Bioorg Med Chem 2013; 21:7921-8. [PMID: 24184216 DOI: 10.1016/j.bmc.2013.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 02/02/2023]
Abstract
Increased efficiency in splice-correction (splice-switching) has been shown by use of a synthetic RNA 5'-end nuclear localization signal composed of an m3G-CAP. Use of the m3G-CAP as an NLS signal for therapeutic compounds in vivo is likely to require additional stability towards enzymatic degradation. For this reason introduction of stabilizing modifications into the triphosphate bridge may be beneficial. Here we report on synthesis of three m3G-CAP derivatives with a 'native' (m3GpppAOMe) as well as with a methylenephosphonate stabilized triphosphate bridge (m3GpCH2ppAOMe, m3GppCH2pAOMe) and the investigation of the enzymatic stability of these compounds in 10% (v/v) fetal bovine serum (FBS) and cytosolic extract from HeLa cells, thus mimicking in vivo conditions. Our results indicate that introduction of methylene group between the β and γ phosphates in m3GpCH2ppAOMe improves to some extent stability of this analogue in 10% serum but does not prolong life of this compound in the cytosolic extract. In contrast the stabilization introduced between α and β phosphates in m3GppCH2pAOMe offers threefold longer life in 10% serum and almost complete protection in cytosolic extract.
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Affiliation(s)
- Malgorzata Honcharenko
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, SE-14183 Huddinge, Sweden.
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23
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Ohkubo A, Kondo Y, Suzuki M, Kobayashi H, Kanamori T, Masaki Y, Seio K, Nagai K, Sekine M. Chemical synthesis of U1 snRNA derivatives. Org Lett 2013; 15:4386-9. [PMID: 23952175 PMCID: PMC3901379 DOI: 10.1021/ol401917r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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U1 snRNA is an interesting biological tool for splicing correction and regulation of gene expression. However, U1 snRNA has never been chemically synthesized. In this study, the first chemical synthesis of U1snRNA and its analogues was carried out. Moreover, it was found that the binding affinity of the modified U1 snRNA with an ethylene glycol linkage to snurportin 1 (nuclear import adaptor) was as high as that of the unmodified RNA.
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Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
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24
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Natalizio AH, Matera AG. Identification and characterization of Drosophila Snurportin reveals a role for the import receptor Moleskin/importin-7 in snRNP biogenesis. Mol Biol Cell 2013; 24:2932-42. [PMID: 23885126 PMCID: PMC3771954 DOI: 10.1091/mbc.e13-03-0118] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Previous work established Importin-β and Snurportin1 as the vertebrate snRNP import receptor and adaptor proteins, respectively. This study identifies Drosophila Snurportin and shows that it uses an alternative import receptor, Importin7/Moleskin. Moleskin is required for the stability of other snRNP biogenesis factors. Nuclear import is an essential step in small nuclear ribonucleoprotein (snRNP) biogenesis. Snurportin1 (SPN1), the import adaptor, binds to trimethylguanosine (TMG) caps on spliceosomal small nuclear RNAs. Previous studies indicated that vertebrate snRNP import requires importin-β, the transport receptor that binds directly to SPN1. We identify CG42303/snup as the Drosophila orthologue of human snurportin1 (SNUPN). Of interest, the importin-β binding (IBB) domain of SPN1, which is essential for TMG cap–mediated snRNP import in humans, is not well conserved in flies. Consistent with its lack of an IBB domain, we find that Drosophila SNUP (dSNUP) does not interact with Ketel/importin-β. Fruit fly snRNPs also fail to bind Ketel; however, the importin-7 orthologue Moleskin (Msk) physically associates with both dSNUP and spliceosomal snRNPs and localizes to nuclear Cajal bodies. Strikingly, we find that msk-null mutants are depleted of the snRNP assembly factor, survival motor neuron, and the Cajal body marker, coilin. Consistent with a loss of snRNP import function, long-lived msk larvae show an accumulation of TMG cap signal in the cytoplasm. These data indicate that Ketel/importin-β does not play a significant role in Drosophila snRNP import and demonstrate a crucial function for Msk in snRNP biogenesis.
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Affiliation(s)
- Amanda Hicks Natalizio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Departments of Biology, University of North Carolina, Chapel Hill, NC 27599 Departments of Genetics, University of North Carolina, Chapel Hill, NC 27599 Program in Molecular Biology and Biotechnology, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
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25
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Piecyk K, Davis RE, Jankowska-Anyszka M. Synthesis of N²-modified 7-methylguanosine 5'-monophosphates as nematode translation inhibitors. Bioorg Med Chem 2012; 20:4781-9. [PMID: 22748379 PMCID: PMC3636719 DOI: 10.1016/j.bmc.2012.05.078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/25/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
Abstract
Preparative scale synthesis of 14 new N(2)-modified mononucleotide 5' mRNA cap analogues was achieved. The key step involved use of an S(N)Ar reaction with protected 2-fluoro inosine and various primary and secondary amines. The derivatives were tested in a parasitic nematode, Ascaris suum, cell-free system as translation inhibitors. The most effective compound with IC(50) ∼0.9μM was a N(2)-p-metoxybenzyl-7-methylguanosine-5'-monophosphate 35.
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Affiliation(s)
- Karolina Piecyk
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
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26
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Chemical approaches for structure and function of RNA in postgenomic era. J Nucleic Acids 2012; 2012:369058. [PMID: 22347623 PMCID: PMC3278928 DOI: 10.1155/2012/369058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 06/21/2011] [Accepted: 07/05/2011] [Indexed: 01/11/2023] Open
Abstract
In the study of cellular RNA chemistry, a major thrust of research focused upon sequence determinations for decades. Structures of snRNAs (4.5S RNA I (Alu), U1, U2, U3, U4, U5, and U6) were determined at Baylor College of Medicine, Houston, Tex, in an earlier time of pregenomic era. They show novel modifications including base methylation, sugar methylation, 5′-cap structures (types 0–III) and sequence heterogeneity. This work offered an exciting problem of posttranscriptional modification and underwent numerous significant advances through technological revolutions during pregenomic, genomic, and postgenomic eras. Presently, snRNA research is making progresses involved in enzymology of snRNA modifications, molecular evolution, mechanism of spliceosome assembly, chemical mechanism of intron removal, high-order structure of snRNA in spliceosome, and pathology of splicing. These works are destined to reach final pathway of work “Function and Structure of Spliceosome” in addition to exciting new exploitation of other noncoding RNAs in all aspects of regulatory functions.
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27
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Honcharenko M, Romanowska J, Alvira M, Jezowska M, Kjellgren M, Edvard Smith CI, Strömberg R. Capping of oligonucleotides with “clickable” m3G-CAPs. RSC Adv 2012. [DOI: 10.1039/c2ra22345g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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28
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Liu W, Jankowska-Anyszka M, Piecyk K, Dickson L, Wallace A, Niedzwiecka A, Stepinski J, Stolarski R, Darzynkiewicz E, Kieft J, Zhao R, Jones DNM, Davis RE. Structural basis for nematode eIF4E binding an m(2,2,7)G-Cap and its implications for translation initiation. Nucleic Acids Res 2011; 39:8820-32. [PMID: 21965542 PMCID: PMC3203607 DOI: 10.1093/nar/gkr650] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Metazoan spliced leader (SL) trans-splicing generates mRNAs with an m2,2,7G-cap and a common downstream SL RNA sequence. The mechanism for eIF4E binding an m2,2,7G-cap is unknown. Here, we describe the first structure of an eIF4E with an m2,2,7G-cap and compare it to the cognate m7G-eIF4E complex. These structures and Nuclear Magnetic Resonance (NMR) data indicate that the nematode Ascaris suum eIF4E binds the two different caps in a similar manner except for the loss of a single hydrogen bond on binding the m2,2,7G-cap. Nematode and mammalian eIF4E both have a low affinity for m2,2,7G-cap compared with the m7G-cap. Nematode eIF4E binding to the m7G-cap, m2,2,7G-cap and the m2,2,7G-SL 22-nt RNA leads to distinct eIF4E conformational changes. Additional interactions occur between Ascaris eIF4E and the SL on binding the m2,2,7G-SL. We propose interactions between Ascaris eIF4E and the SL impact eIF4G and contribute to translation initiation, whereas these interactions do not occur when only the m2,2,7G-cap is present. These data have implications for the contribution of 5′-UTRs in mRNA translation and the function of different eIF4E isoforms.
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Affiliation(s)
- Weizhi Liu
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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29
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Dinucleotide cap analogue affinity resins for purification of proteins that specifically recognize the 5' end of mRNA. Bioorg Med Chem Lett 2011; 21:6131-4. [PMID: 21889340 DOI: 10.1016/j.bmcl.2011.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/02/2011] [Accepted: 08/04/2011] [Indexed: 11/22/2022]
Abstract
Here we present first dinucleotide affinity resins for purification of proteins that specifically recognize the 5' end of mRNA. Constructed resins possess either a naturally occurring mono- or trimethylated cap or their analogues resistant towards enzymatic degradation, bearing a CH(2) bridge between β and γ position of the 5',5'-triphosphate chain. All cap analogues were attached to a polymer support (EAH-Sepharose) through the carboxylic group that had been generated by derivatization of the 2',3'-cis diol of the second nucleotide in the cap structure with levulinic acid.
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30
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Fischer U, Englbrecht C, Chari A. Biogenesis of spliceosomal small nuclear ribonucleoproteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:718-31. [PMID: 21823231 DOI: 10.1002/wrna.87] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Virtually, all eukaryotic mRNAs are synthesized as precursor molecules that need to be extensively processed in order to serve as a blueprint for proteins. The three most prevalent processing steps are the capping reaction at the 5'-end, the removal of intervening sequences by splicing, and the formation of poly (A)-tails at the 3'-end of the message by polyadenylation. A large number of proteins and small nuclear ribonucleoprotein complexes (snRNPs) interact with the mRNA and enable the different maturation steps. This chapter focuses on the biogenesis of snRNPs, the major components of the pre-mRNA splicing machinery (spliceosome). A large body of evidence has revealed an intricate and segmented pathway for the formation of snRNPs that involves nucleo-cytoplasmic transport events and elaborates assembly strategies. We summarize the knowledge about the different steps with an emphasis on trans-acting factors of snRNP maturation of higher eukaryotes. WIREs RNA 2011 2 718-731 DOI: 10.1002/wrna.87 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Utz Fischer
- Department of Biochemistry, University of Wuerzburg, Germany.
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31
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Lott K, Cingolani G. The importin β binding domain as a master regulator of nucleocytoplasmic transport. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:1578-92. [PMID: 21029753 DOI: 10.1016/j.bbamcr.2010.10.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 10/11/2010] [Accepted: 10/19/2010] [Indexed: 12/16/2022]
Abstract
Specific and efficient recognition of import cargoes is essential to ensure nucleocytoplasmic transport. To this end, the prototypical karyopherin importin β associates with import cargoes directly or, more commonly, through import adaptors, such as importin α and snurportin. Adaptor proteins bind the nuclear localization sequence (NLS) of import cargoes while recruiting importin β via an N-terminal importin β binding (IBB) domain. The use of adaptors greatly expands and amplifies the repertoire of cellular cargoes that importin β can efficiently import into the cell nucleus and allows for fine regulation of nuclear import. Accordingly, the IBB domain is a dedicated NLS, unique to adaptor proteins that functions as a molecular liaison between importin β and import cargoes. This review provides an overview of the molecular role played by the IBB domain in orchestrating nucleocytoplasmic transport. Recent work has determined that the IBB domain has specialized functions at every step of the import and export pathway. Unexpectedly, this stretch of ~40 amino acids plays an essential role in regulating processes such as formation of the import complex, docking and translocation through the nuclear pore complex (NPC), release of import cargoes into the cell nucleus and finally recycling of import adaptors and importin β into the cytoplasm. Thus, the IBB domain is a master regulator of nucleocytoplasmic transport, whose complex molecular function is only recently beginning to emerge. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.
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Affiliation(s)
- Kaylen Lott
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
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Marfori M, Mynott A, Ellis JJ, Mehdi AM, Saunders NFW, Curmi PM, Forwood JK, Bodén M, Kobe B. Molecular basis for specificity of nuclear import and prediction of nuclear localization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:1562-77. [PMID: 20977914 DOI: 10.1016/j.bbamcr.2010.10.013] [Citation(s) in RCA: 307] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 10/15/2010] [Accepted: 10/19/2010] [Indexed: 01/03/2023]
Abstract
Although proteins are translated on cytoplasmic ribosomes, many of these proteins play essential roles in the nucleus, mediating key cellular processes including but not limited to DNA replication and repair as well as transcription and RNA processing. Thus, understanding how these critical nuclear proteins are accurately targeted to the nucleus is of paramount importance in biology. Interaction and structural studies in the recent years have jointly revealed some general rules on the specificity determinants of the recognition of nuclear targeting signals by their specific receptors, at least for two nuclear import pathways: (i) the classical pathway, which involves the classical nuclear localization sequences (cNLSs) and the receptors importin-α/karyopherin-α and importin-β/karyopherin-β1; and (ii) the karyopherin-β2 pathway, which employs the proline-tyrosine (PY)-NLSs and the receptor transportin-1/karyopherin-β2. The understanding of specificity rules allows the prediction of protein nuclear localization. We review the current understanding of the molecular determinants of the specificity of nuclear import, focusing on the importin-α•cargo recognition, as well as the currently available databases and predictive tools relevant to nuclear localization. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.
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Affiliation(s)
- Mary Marfori
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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Ruszczyńska-Bartnik K, Maciejczyk M, Stolarski R. Dynamical insight into Caenorhabditis elegans eIF4E recognition specificity for mono-and trimethylated structures of mRNA 5' cap. J Mol Model 2010; 17:727-37. [PMID: 20535623 PMCID: PMC3076583 DOI: 10.1007/s00894-010-0773-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 05/06/2010] [Indexed: 12/01/2022]
Abstract
Specific recognition and binding of the ribonucleic acid 5′ termini (mRNA 5′ cap) by the eukaryotic translation initiation factor 4E (eIF4E) is a key, rate limiting step in translation initiation. Contrary to mammalian and yeast eIF4Es that discriminate in favor of 7-methylguanosine cap, three out of five eIF4E isoforms from the nematode Caenorhabditis elegans as well as eIF4Es from the parasites Schistosome mansoni and Ascaris suum, exhibit dual binding specificity for both 7-methylguanosine-and N2,N2,7-trimethylguanosine cap. To address the problem of the differences in the mechanism of the cap recognition by those highly homologic proteins, we carried out molecular dynamics simulations in water of three factors, IFE-3 and IFE-5 isoforms from C. elegans and murine eIF4E, in the apo form as well as in the complexes with 7-methyl-GDP and N2,N2,7-trimethyl-GDP. The results clearly pointed to a dynamical mechanism of discrimination between each type of the cap, viz. differences in mobility of the loops located at the entrance into the protein binding pockets during the cap association and dissociation. Additionally, our data showed that the hydrogen bond involving the N2-amino group of 7-methylguanosine and the carboxylate of glutamic acid was not stable. The dynamic mechanism proposed here differs from a typical, static one in that the differences in the protein-ligand binding specificity cannot be ascribed to formation and/or disruption of well defined stabilizing contacts.
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Affiliation(s)
- Katarzyna Ruszczyńska-Bartnik
- Nuclear Magnetic Resonance Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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Kühn-Hölsken E, Lenz C, Dickmanns A, Hsiao HH, Richter FM, Kastner B, Ficner R, Urlaub H. Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry. Nucleic Acids Res 2010; 38:5581-93. [PMID: 20421206 PMCID: PMC2938196 DOI: 10.1093/nar/gkq272] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mass spectrometry allows the elucidation of molecular details of the interaction domains of the individual components in macromolecular complexes subsequent to cross-linking of the individual components. Here, we applied chemical and UV cross-linking combined with tandem mass-spectrometric analysis to identify contact sites of the nuclear import adaptor snurportin 1 to the small ribonucleoprotein particle U1 snRNP in addition to the known interaction of m3G cap and snurportin 1. We were able to define previously unknown sites of protein–protein and protein–RNA interactions on the molecular level within U1 snRNP. We show that snurportin 1 interacts with its central m3G-cap-binding domain with Sm proteins and with its extreme C-terminus with stem-loop III of U1 snRNA. The crosslinking data support the idea of a larger interaction area between snurportin 1 and U snRNPs and the contact sites identified prove useful for modeling the spatial arrangement of snurportin 1 domains when bound to U1 snRNP. Moreover, this suggests a functional nuclear import complex that assembles around the m3G cap and the Sm proteins only when the Sm proteins are bound and arranged in the proper orientation to the cognate Sm site in U snRNA.
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Affiliation(s)
- Eva Kühn-Hölsken
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Lott K, Bhardwaj A, Mitrousis G, Pante N, Cingolani G. The importin beta binding domain modulates the avidity of importin beta for the nuclear pore complex. J Biol Chem 2010; 285:13769-80. [PMID: 20197273 DOI: 10.1074/jbc.m109.095760] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Importin beta mediates active passage of cellular substrates through the nuclear pore complex (NPC). Adaptors such as importin alpha and snurportin associate with importin beta via an importin beta binding (IBB) domain. The intrinsic structural flexibility of importin beta allows its concerted interactions with IBB domains, phenylalanine-glycine nucleoporins, and the GTPase Ran during transport. In this paper, we provide evidence that the nature of the IBB domain modulates the affinity of the import complex for the NPC. In permeabilized cells, importin beta imports a cargo fused to the snurportin IBB (sIBB) with approximately 70% reduced energy requirement as compared with the classical importin alpha IBB. At the molecular level, this is explained by approximately 200-fold reduced affinity of importin beta for Nup62, when bound to the sIBB. Consistently, in vivo, the importin beta.sIBB complex has greatly reduced persistence inside the central channel of the NPC. We propose that by controlling the degree of strain in the tertiary structure of importin beta, the IBB domain modulates the affinity of the import complex for nucleoporins, thus dictating its persistence inside the NPC.
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Affiliation(s)
- Kaylen Lott
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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Curry S, Kotik-Kogan O, Conte MR, Brick P. Getting to the end of RNA: structural analysis of protein recognition of 5' and 3' termini. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:653-66. [PMID: 19619683 DOI: 10.1016/j.bbagrm.2009.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022]
Abstract
The specific recognition by proteins of the 5' and 3' ends of RNA molecules is an important facet of many cellular processes, including RNA maturation, regulation of translation initiation and control of gene expression by degradation and RNA interference. The aim of this review is to survey recent structural analyses of protein binding domains that specifically bind to the extreme 5' or 3' termini of RNA. For reasons of space and because their interactions are also governed by catalytic considerations, we have excluded enzymes that modify the 5' and 3' extremities of RNA. It is clear that there is enormous structural diversity among the proteins that have evolved to bind to the ends of RNA molecules. Moreover, they commonly exhibit conformational flexibility that appears to be important for binding and regulation of the interaction. This flexibility has sometimes complicated the interpretation of structural results and presents significant challenges for future investigations.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London, SW7 2AZ, UK.
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Goette M, Stumpe MC, Ficner R, Grubmüller H. Molecular determinants of snurportin 1 ligand affinity and structural response upon binding. Biophys J 2009; 97:581-9. [PMID: 19619473 PMCID: PMC2711343 DOI: 10.1016/j.bpj.2009.04.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 04/24/2009] [Accepted: 04/27/2009] [Indexed: 10/20/2022] Open
Abstract
The transport of large biomolecules such as proteins and RNA across nuclear pore complexes is a field of strong interest and research. Although the basic mechanisms are fairly well understood, the details of the underlying intermolecular interaction within these transport complexes are still unclear. The recognition dynamics and energetics of cargo binding to the transport receptor are not yet resolved. Here, the binding of dimethylated RNA-caps to snurportin 1 is studied by molecular-dynamics simulations. The simulations reveal a strong structural response of the protein upon RNA-cap release. In particular, major rearrangements occur in regions already intrinsically flexible in the holo structure. Additionally, the difference in free energy of binding to snurportin 1 between the two methylation states of the RNA-cap, responsible for the directionality of the transport is quantified. In particular, desolvation of the ligand is revealed as the key-step in binding to snurportin 1. These findings suggest that the binding of m(3)G-capped RNA is mainly driven by the enhanced water entropy gain of the solvation shell.
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Affiliation(s)
- Maik Goette
- Theoretical and Computational Biophysics Department, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Martin C. Stumpe
- Theoretical and Computational Biophysics Department, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik and GZMB, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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38
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Evidence that the AAA+ proteins TIP48 and TIP49 bridge interactions between 15.5K and the related NOP56 and NOP58 proteins during box C/D snoRNP biogenesis. Mol Cell Biol 2009; 29:4971-81. [PMID: 19620283 DOI: 10.1128/mcb.00752-09] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The box C/D small nucleolar RNPs (snoRNPs) are essential for the processing and modification of rRNA. TIP48 and TIP49 are two related AAA(+) proteins that are essential for the formation of box C/D snoRNPs. These proteins are key components of the pre-snoRNP complexes, but their exact role in box C/D snoRNP biogenesis is largely uncharacterized. Here we report that TIP48 and TIP49 interact with one another in vitro, and only the TIP48/TIP49 complex, but not the individual proteins, possesses significant ATPase activity. Loss of TIP48 and TIP49 results in a change in pre-snoRNA levels and a loss of U3 snoRNA signal in the Cajal body. We show that TIP48 and TIP49 make multiple interactions with core snoRNP proteins and biogenesis factors and that these interactions are often regulated by the presence of ATP. Furthermore, we demonstrate that TIP48 and TIP49 efficiently bridge interactions between the core box C/D proteins NOP56 or NOP58 and 15.5K. Our data imply that the snoRNP assembly factor NUFIP can regulate the interactions between TIP48 and TIP49 and the core box C/D proteins. We suggest that snoRNP assembly involves an intricate series of interactions that are mediated/regulated by bridging factors and chaperones.
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Monecke T, Güttler T, Neumann P, Dickmanns A, Görlich D, Ficner R. Crystal structure of the nuclear export receptor CRM1 in complex with Snurportin1 and RanGTP. Science 2009; 324:1087-91. [PMID: 19389996 DOI: 10.1126/science.1173388] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CRM1 mediates nuclear export of numerous unrelated cargoes, which may carry a short leucine-rich nuclear export signal or export signatures that include folded domains. How CRM1 recognizes such a variety of cargoes has been unknown up to this point. Here we present the crystal structure of the SPN1.CRM1.RanGTP export complex at 2.5 angstrom resolution (where SPN1 is snurportin1 and RanGTP is guanosine 5' triphosphate-bound Ran). SPN1 is a nuclear import adapter for cytoplasmically assembled, m(3)G-capped spliceosomal U snRNPs (small nuclear ribonucleoproteins). The structure shows how CRM1 can specifically return the cargo-free form of SPN1 to the cytoplasm. The extensive contact area includes five hydrophobic residues at the SPN1 amino terminus that dock into a hydrophobic cleft of CRM1, as well as numerous hydrophilic contacts of CRM1 to m(3)G cap-binding domain and carboxyl-terminal residues of SPN1. The structure suggests that RanGTP promotes cargo-binding to CRM1 solely through long-range conformational changes in the exportin.
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Affiliation(s)
- Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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40
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Dong X, Biswas A, Chook YM. Structural basis for assembly and disassembly of the CRM1 nuclear export complex. Nat Struct Mol Biol 2009; 16:558-60. [PMID: 19339972 PMCID: PMC3437629 DOI: 10.1038/nsmb.1586] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 03/05/2009] [Indexed: 11/08/2022]
Abstract
CRM1 (or exportin 1, Xpo1) transports proteins out of the cell nucleus through the nuclear pore complex. In the cytoplasm, GTP hydrolysis and consequent dissociation of Ran from CRM1 releases low-affinity substrates, while additional factors facilitate release of high-affinity substrates. Here we provide a model for human CRM1 export complex assembly and disassembly through structural and biochemical analyses of CRM1 bound to the substrate snurportin 1 (SNUPN, also called snuportin 1).
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Affiliation(s)
- Xiuhua Dong
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, USA
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42
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Dong X, Biswas A, Süel KE, Jackson LK, Martinez R, Gu H, Chook YM. Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature 2009; 458:1136-41. [PMID: 19339969 PMCID: PMC3437623 DOI: 10.1038/nature07975] [Citation(s) in RCA: 254] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 03/06/2009] [Indexed: 01/17/2023]
Abstract
CRM1 (also known as XPO1 and exportin 1) mediates nuclear export of hundreds of proteins through the recognition of the leucine-rich nuclear export signal (LR-NES). Here we present the 2.9 A structure of CRM1 bound to snurportin 1 (SNUPN). Snurportin 1 binds CRM1 in a bipartite manner by means of an amino-terminal LR-NES and its nucleotide-binding domain. The LR-NES is a combined alpha-helical-extended structure that occupies a hydrophobic groove between two CRM1 outer helices. The LR-NES interface explains the consensus hydrophobic pattern, preference for intervening electronegative residues and inhibition by leptomycin B. The second nuclear export signal epitope is a basic surface on the snurportin 1 nucleotide-binding domain, which binds an acidic patch on CRM1 adjacent to the LR-NES site. Multipartite recognition of individually weak nuclear export signal epitopes may be common to CRM1 substrates, enhancing CRM1 binding beyond the generally low affinity LR-NES. Similar energetic construction is also used in multipartite nuclear localization signals to provide broad substrate specificity and rapid evolution in nuclear transport.
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Affiliation(s)
- Xiuhua Dong
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, Texas 75390-9041, USA
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Wu M, Nilsson P, Henriksson N, Niedzwiecka A, Lim MK, Cheng Z, Kokkoris K, Virtanen A, Song H. Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease. Structure 2009; 17:276-86. [PMID: 19217398 DOI: 10.1016/j.str.2008.11.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 11/04/2008] [Accepted: 11/18/2008] [Indexed: 10/21/2022]
Abstract
Poly(A)-specific ribonuclease (PARN) is a homodimeric, processive, and cap-interacting 3' exoribonuclease that efficiently degrades eukaryotic mRNA poly(A) tails. The crystal structure of a C-terminally truncated PARN in complex with m(7)GpppG reveals that, in one subunit, m(7)GpppG binds to a cavity formed by the RRM domain and the nuclease domain, whereas in the other subunit, it binds almost exclusively to the RRM domain. Importantly, our structural and competition data show that the cap-binding site overlaps with the active site in the nuclease domain. Mutational analysis demonstrates that residues involved in m(7)G recognition are crucial for cap-stimulated deadenylation activity, and those involved in both cap and poly(A) binding are important for catalysis. A modeled PARN, which shows that the RRM domain from one subunit and the R3H domain from the other subunit enclose the active site, provides a structural foundation for further studies to elucidate the mechanism of PARN-mediated deadenylation.
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Affiliation(s)
- Mousheng Wu
- Institute of Molecular and Cell Biology, Proteos, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
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44
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Monecke T, Dickmanns A, Ficner R. Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1. Nucleic Acids Res 2009; 37:3865-77. [PMID: 19386620 PMCID: PMC2709555 DOI: 10.1093/nar/gkp249] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The 5′-cap of spliceosomal small nuclear RNAs, some small nucleolar RNAs and of telomerase RNA was found to be hypermethylated in vivo. The Trimethylguanosine Synthase 1 (TGS1) mediates this conversion of the 7-methylguanosine-cap to the 2,2,7-trimethylguanosine (m3G)-cap during maturation of the RNPs. For mammalian UsnRNAs the generated m2,2,7G-cap is one part of a bipartite import signal mediating the transport of the UsnRNP-core complex into the nucleus. In order to understand the structural organization of human TGS1 as well as substrate binding and recognition we solved the crystal structure of the active TGS1 methyltransferase domain containing both, the minimal substrate m7GTP and the reaction product S-adenosyl-l-homocysteine (AdoHcy). The methyltransferase of human TGS1 harbors the canonical class 1 methyltransferase fold as well as an unique N-terminal, α-helical domain of 40 amino acids, which is essential for m7G-cap binding and catalysis. The crystal structure of the substrate bound methyltransferase domain as well as mutagenesis studies provide insight into the catalytic mechanism of TGS1.
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Affiliation(s)
- Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
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45
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Moreno PMD, Wenska M, Lundin KE, Wrange O, Strömberg R, Smith CIE. A synthetic snRNA m3G-CAP enhances nuclear delivery of exogenous proteins and nucleic acids. Nucleic Acids Res 2009; 37:1925-35. [PMID: 19208638 PMCID: PMC2665231 DOI: 10.1093/nar/gkp048] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Accessing the nucleus through the surrounding membrane poses one of the major obstacles for therapeutic molecules large enough to be excluded due to nuclear pore size limits. In some therapeutic applications the large size of some nucleic acids, like plasmid DNA, hampers their access to the nuclear compartment. However, also for small oligonucleotides, achieving higher nuclear concentrations could be of great benefit. We report on the synthesis and possible applications of a natural RNA 5′-end nuclear localization signal composed of a 2,2,7-trimethylguanosine cap (m3G-CAP). The cap is found in the small nuclear RNAs that are constitutive part of the small nuclear ribonucleoprotein complexes involved in nuclear splicing. We demonstrate the use of the m3G signal as an adaptor that can be attached to different oligonucleotides, thereby conferring nuclear targeting capabilities with capacity to transport large-size cargo molecules. The synthetic capping of oligos interfering with splicing may have immediate clinical applications.
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Affiliation(s)
- Pedro M D Moreno
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, SE-141 86 Huddinge, Sweden.
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46
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Goette M, Grubmüller H. Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. J Comput Chem 2009; 30:447-56. [DOI: 10.1002/jcc.21073] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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47
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Worch R, Stolarski R. Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins. Proteins 2008; 71:2026-37. [PMID: 18186485 DOI: 10.1002/prot.21882] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recognition of the ribonucleic acid 5' termini (RNA 5' cap) by a wide class of cap-binding proteins is largely accomplished by cation-pi stacking that involves the positively charged 7-methylguanine ring and aromatic amino acid side chains. Quantum calculations of the stacking energy were performed by means of MP2 perturbation method for binary and ternary associates composed of the 7-methylguanine moiety and tryptophan, tyrosine, or phenylalanine, in their spatial orientations known from the crystalline cap-protein complexes. The results clearly pointed to an enhancement of the stacking energy due to a net positive charge in the cap guanine moiety and allowed analysis of a role of various amino acids in stabilization of the complexes. Conformational flexibility of the aromatic amino acids taking part in binding ligands to a wide class of RNA-recognizing proteins, including the cap-binding proteins, was determined by regional order neural network (RONN) algorithm that provides results close to those of the crystallographic B-factors analysis. Interestingly, some of the tyrosines that are classified in general as "rigid" showed high flexibility when engaged in binding the cap to nuclear cap-binding protein complex CBC and to viral methyltransferase VP39. Parallel analyses of the binding energy and flexibility of the protein fragments engaged in the binding leads to understanding differences in molecular mechanisms of the cap recognition by various proteins, CBC compared with the eukaryotic initiation factor eIF4E, and enzymes vs. other protein factors.
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Affiliation(s)
- Remigiusz Worch
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, Warsaw University, 02-089 Warszawa, Poland
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48
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Mitrousis G, Olia AS, Walker-Kopp N, Cingolani G. Molecular basis for the recognition of snurportin 1 by importin beta. J Biol Chem 2008; 283:7877-84. [PMID: 18187419 DOI: 10.1074/jbc.m709093200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The nuclear import of uridine-rich ribonucleoproteins is mediated by the transport adaptor snurportin 1 (SNP1). Similar to importin alpha, SNP1 uses an N-terminal importin beta binding (sIBB) domain to recruit the receptor importin beta and gain access to the nucleus. In this study, we demonstrate that the sIBB domain has a bipartite nature, which contains two distinct binding determinants for importin beta. The first determinant spans residues 25-65 and includes the previously identified importin alpha IBB (alphaIBB) region of homology. The second binding determinant encompasses residues 1-24 and resembles region 1011-1035 of the nucleoporin 153 (Nup153). The two binding determinants synergize within the sIBB domain to confer a low nanomolar binding affinity for importin beta (K(d) approximately 2 nm) in an interaction that, in vitro, is displaced by RanGTP. We propose that in vivo the synergy of Nup153 and nuclear RanGTP promotes translocation of uridine-rich ribonucleoproteins into the nucleus.
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Affiliation(s)
- Gregory Mitrousis
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210, USA
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Kubota T, Maezawa S, Koiwai K, Hayano T, Koiwai O. Identification of functional domains in TdIF1 and its inhibitory mechanism for TdT activity. Genes Cells 2007; 12:941-59. [PMID: 17663723 DOI: 10.1111/j.1365-2443.2007.01105.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
TdT interacting factor 1 (TdIF1) was identified as a protein that binds to terminal deoxynucleotidyltransferase (TdT) to negatively regulate TdT activity. TdT is a template-independent DNA polymerase that catalyzes the incorporation of deoxynucleotides to the 3'-hydroxyl end of DNA templates to increase the junctional diversity of immunoglobulin or T-cell receptor (TcR) genes. Here, using bioinformatics analysis, we identified the TdT binding, DNA binding and dimerization regions, and nuclear localization signal (NLS) in TdIF1. TdIF1 bound to double-stranded DNA (dsDNA) through three DNA binding regions: residues 1-75, the AT-hook-like motif (ALM) and the predicted helix-turn-helix (HTH) motif. ALM in TdIF1 preferentially bound to AT-rich DNA regions. NLS was of the bipartite type and overlapped ALM. TdIF1 bound to the Pol beta-like region in TdT and blocked TdT access to DNA ends. In the presence of dsDNA, however, TdIF1 bound to dsDNA to release TdT from the TdIF1/TdT complex and to exhibit TdT activity, implying that active TdT released microenvironmentally concentrates around AT-rich DNA to synthesize DNA.
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Affiliation(s)
- Takashi Kubota
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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Structural basis for RanGTP independent entry of spliceosomal U snRNPs into the nucleus. J Mol Biol 2007; 374:1129-38. [PMID: 18028944 DOI: 10.1016/j.jmb.2007.09.065] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/14/2007] [Accepted: 09/18/2007] [Indexed: 12/22/2022]
Abstract
The nuclear import of assembled spliceosomal subunits, the uridine-rich small nuclear ribonucleoprotein particles (U snRNPs), is mediated by a nuclear import receptor adaptor couple of importin beta (Imp beta) and snurportin1 (SPN1). In contrast to any other characterized active nuclear import, the Imp beta/SPN1/U snRNP complex does not require RanGTP for the terminal release from the nuclear basket of the nuclear pore complex (NPC). The crystal structure of Imp beta (127-876) in complex with the Imp beta-binding (IBB) domain of SPN1 (1-65) at 2.8-A resolution reveals that Imp beta adopts an open conformation, which is unique for a functional Imp beta/cargo complex, and rather surprisingly, it resembles the conformation of the Imp beta/RanGTP complex. As binding of RanGTP to Imp beta usually triggers the release of import complexes from the NPC, we propose that by already mimicking a conformation similar to Imp beta/RanGTP the independent dissociation of Imp beta/SPN1 from the nuclear basket is energetically aided.
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