1
|
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.
Collapse
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
| |
Collapse
|
2
|
Comparative Proteomic Analysis of Drug Trichosanthin Addition to BeWo Cell Line. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051603. [PMID: 35268705 PMCID: PMC8911981 DOI: 10.3390/molecules27051603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/17/2022]
Abstract
Trichosanthin (TCS) is a traditional Chinese herbal medicine used to treat some gynecological diseases. Its effective component has diverse biological functions, including antineoplastic activity. The human trophoblast cell line BeWo was chosen as an experimental model for in vitro testing of a drug screen for anticancer properties of TCS. The MTT method was used in this study to get a primary screen result. The result showed that 100 mM had the best IC50 value. Proteomics analysis was then performed for further investigation of the drug effect of TCS on the BeWo cell line. In this differential proteomic expression analysis, the total proteins extracted from the BeWo cell line and their protein expression level after the drug treatment were compared by 2DE. Then, 24 unique three-fold differentially expressed proteins (DEPs) were successfully identified by MALDI-TOF/TOF MS. Label-free proteomics was run as a complemental method for the same experimental procedure. There are two proteins that were identified in both the 2DE and label-free methods. Among those identified proteins, bioinformatics analysis showed the importance of pathway and signal transduction and gives us the potential possibility for the disease treatment hypothesis.
Collapse
|
3
|
Campagne S, de Vries T, Malard F, Afanasyev P, Dorn G, Dedic E, Kohlbrecher J, Boehringer D, Cléry A, Allain FHT. An in vitro reconstituted U1 snRNP allows the study of the disordered regions of the particle and the interactions with proteins and ligands. Nucleic Acids Res 2021; 49:e63. [PMID: 33677607 PMCID: PMC8216277 DOI: 10.1093/nar/gkab135] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022] Open
Abstract
U1 small nuclear ribonucleoparticle (U1 snRNP) plays a central role during RNA processing. Previous structures of U1 snRNP revealed how the ribonucleoparticle is organized and recognizes the pre-mRNA substrate at the exon–intron junction. As with many other ribonucleoparticles involved in RNA metabolism, U1 snRNP contains extensions made of low complexity sequences. Here, we developed a protocol to reconstitute U1 snRNP in vitro using mostly full-length components in order to perform liquid-state NMR spectroscopy. The accuracy of the reconstitution was validated by probing the shape and structure of the particle by SANS and cryo-EM. Using an NMR spectroscopy-based approach, we probed, for the first time, the U1 snRNP tails at atomic detail and our results confirm their high degree of flexibility. We also monitored the labile interaction between the splicing factor PTBP1 and U1 snRNP and validated the U1 snRNA stem loop 4 as a binding site for the splicing regulator on the ribonucleoparticle. Altogether, we developed a method to probe the intrinsically disordered regions of U1 snRNP and map the interactions controlling splicing regulation. This approach could be used to get insights into the molecular mechanisms of alternative splicing and screen for potential RNA therapeutics.
Collapse
Affiliation(s)
- Sébastien Campagne
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Florian Malard
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | | | - Daniel Boehringer
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Antoine Cléry
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| |
Collapse
|
4
|
Domain Requirements and Genetic Interactions of the Mud1 Subunit of the Saccharomyces cerevisiae U1 snRNP. G3-GENES GENOMES GENETICS 2019; 9:145-151. [PMID: 30413416 PMCID: PMC6325900 DOI: 10.1534/g3.118.200781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mud1 is an inessential 298-amino acid protein subunit of the Saccharomyces cerevisiae U1 snRNP. Mud1 consists of N-terminal and C-terminal RRM domains (RRM1 and RRM2) separated by a linker domain. Synthetic lethal interactions of mud1∆ with deletions of inessential spliceosome components Nam8, Mud2, and Msl1, or missense mutations in the branchpoint-binding protein Msl5 enabled us to dissect genetically the domain requirements for Mud1 function. We find that the biological activities of Mud1 can be complemented by co-expressing separately the RRM1 (aa 1-127) and linker-RRM2 (aa 128-298) modules. Whereas RRM1 and RRM2 (aa 197-298) per se are inactive in all tests of functional complementation, the linker-RRM2 by itself partially complements a subset of synthetic lethal mud1∆ interactions. Linker segment aa 155 to 196 contains a nuclear localization signal rich in basic amino acids that is necessary for RRM2 activity in mud1∆ complementation. Alanine scanning mutagenesis indicates that none of the individual RRM1 amino acid contacts to U1 snRNA in the cryo-EM model of the yeast U1 snRNP is necessary for mud1∆ complementation activity.
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- Utz Fischer
- Department of Biochemistry, University of Wuerzburg, Germany.
| | | | | |
Collapse
|
6
|
Vázquez-Iglesias L, Lostalé-Seijo I, Martínez-Costas J, Benavente J. Avian reovirus sigmaA localizes to the nucleolus and enters the nucleus by a nonclassical energy- and carrier-independent pathway. J Virol 2009; 83:10163-75. [PMID: 19640987 PMCID: PMC2747991 DOI: 10.1128/jvi.01080-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 07/16/2009] [Indexed: 12/24/2022] Open
Abstract
Avian reovirus sigmaA is a double-stranded RNA (dsRNA)-binding protein that has been shown to stabilize viral core particles and to protect the virus against the antiviral action of interferon. To continue with the characterization of this viral protein, we have investigated its intracellular distribution in avian cells. Most sigmaA accumulates into cytoplasmic viral factories of infected cells, and yet a significant fraction was detected in the nucleolus. The protein also localizes in the nucleolus of transfected cells, suggesting that nucleolar targeting is not facilitated by the viral infection or by viral factors. Assays performed in both intact cells and digitonin-permeabilized cells demonstrate that sigmaA is able to enter the nucleus via a nucleoporin-dependent nondiffusional mechanism that does not require added cytosolic factors or energy input. These results indicate that sigmaA by itself is able to penetrate into the nucleus using a process that is mechanistically different from the classical nuclear localization signal/importin pathway. On the other hand, two sigmaA arginines that are necessary for dsRNA binding are also required for nucleolar localization, suggesting that dsRNA-binding and nucleolar targeting are intimately linked properties of the viral protein.
Collapse
Affiliation(s)
- Lorena Vázquez-Iglesias
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | | | | | | |
Collapse
|
7
|
|
8
|
Lorković ZJ, Barta A. Role of Cajal bodies and nucleolus in the maturation of the U1 snRNP in Arabidopsis. PLoS One 2008; 3:e3989. [PMID: 19098980 PMCID: PMC2600615 DOI: 10.1371/journal.pone.0003989] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 11/21/2008] [Indexed: 01/31/2023] Open
Abstract
Background The biogenesis of spliceosomal snRNPs takes place in both the cytoplasm where Sm core proteins are added and snRNAs are modified at the 5′ and 3′ termini and in the nucleus where snRNP-specific proteins associate. U1 snRNP consists of U1 snRNA, seven Sm proteins and three snRNP-specific proteins, U1-70K, U1A, and U1C. It has been shown previously that after import to the nucleus U2 and U4/U6 snRNP-specific proteins first appear in Cajal bodies (CB) and then in splicing speckles. In addition, in cells grown under normal conditions U2, U4, U5, and U6 snRNAs/snRNPs are abundant in CBs. Therefore, it has been proposed that the final assembly of these spliceosomal snRNPs takes place in this nuclear compartment. In contrast, U1 snRNA in both animal and plant cells has rarely been found in this nuclear compartment. Methodology/Principal Findings Here, we analysed the subnuclear distribution of Arabidopsis U1 snRNP-specific proteins fused to GFP or mRFP in transiently transformed Arabidopsis protoplasts. Irrespective of the tag used, U1-70K was exclusively found in the nucleus, whereas U1A and U1C were equally distributed between the nucleus and the cytoplasm. In the nucleus all three proteins localised to CBs and nucleoli although to different extent. Interestingly, we also found that the appearance of the three proteins in nuclear speckles differ significantly. U1-70K was mostly found in speckles whereas U1A and U1C in ∼90% of cells showed diffuse nucleoplasmic in combination with CBs and nucleolar localisation. Conclusions/Significance Our data indicate that CBs and nucleolus are involved in the maturation of U1 snRNP. Differences in nuclear accumulation and distribution between U1-70K and U1A and U1C proteins may indicate that either U1-70K or U1A and U1C associate with, or is/are involved, in other nuclear processes apart from pre-mRNA splicing.
Collapse
Affiliation(s)
- Zdravko J Lorković
- Department of Medical Biochemistry, Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria.
| | | |
Collapse
|
9
|
Andrake MD, Sauter MM, Boland K, Goldstein AD, Hussein M, Skalka AM. Nuclear import of Avian Sarcoma Virus integrase is facilitated by host cell factors. Retrovirology 2008; 5:73. [PMID: 18687138 PMCID: PMC2527327 DOI: 10.1186/1742-4690-5-73] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 08/07/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Integration of retroviral DNA into the host cell genome is an obligatory step in the virus life cycle. In previous reports we identified a sequence (amino acids 201-236) in the linker region between the catalytic core and C-terminal domains of the avian sarcoma virus (ASV) integrase protein that functions as a transferable nuclear localization signal (NLS) in mammalian cells. The sequence is distinct from all known NLSs but, like many, contains basic residues that are essential for activity. RESULTS Our present studies with digitonin-permeabilized HeLa cells show that nuclear import mediated by the NLS of ASV integrase is an active, saturable, and ATP-dependent process. As expected for transport through nuclear pore complexes, import is blocked by treatment of cells with wheat germ agglutinin. We also show that import of ASV integrase requires soluble cellular factors but does not depend on binding the classical adapter Importin-alpha. Results from competition studies indicate that ASV integrase relies on one or more of the soluble components that mediate transport of the linker histone H1. CONCLUSION These results are consistent with a role for ASV integrase and cytoplasmic cellular factors in the nuclear import of its viral DNA substrate, and lay the foundation for identification of host cell components that mediate this reaction.
Collapse
Affiliation(s)
- Mark D Andrake
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
| | | | | | | | | | | |
Collapse
|
10
|
Lobo GP, Waite KA, Planchon SM, Romigh T, Houghton JA, Eng C. ATP modulates PTEN subcellular localization in multiple cancer cell lines. Hum Mol Genet 2008; 17:2877-85. [PMID: 18579579 PMCID: PMC2525500 DOI: 10.1093/hmg/ddn185] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The tumour suppressor gene PTEN plays an important somatic role in both hereditary and sporadic breast carcinogenesis. While the role of PTEN's lipid phosphatase activity, as a negative regulator of the cytoplasmic phosphatidylinositol-3-kinase/Akt pathway is well known, it is now well established that PTEN exists and functions in the nucleus. Multiple mechanisms of regulating PTEN's subcellular localization have been reported. However none are ubiquitous across multiple cancer cell lines and tissue types. We show here that adenosine triphosphate (ATP) regulates PTEN subcellular localization in a variety of different cancer cell lines, including those derived from breast, colon and thyroid carcinomas. Cells deficient in ATP show an increased level of nuclear PTEN protein. This increase in PTEN is reversed when cells are supplemented with ATP, ADP or AMP. In contrast, the addition of the non-hydrolyzable analogue ATPgammaS, did not reverse nuclear PTEN protein levels in all the cell types tested. To our knowledge, this is the first report that describes a regulation of PTEN subcellular localization that is not specific to one cell line or tissue type, but appears to be common across a variety of cell lineages.
Collapse
Affiliation(s)
- Glenn P Lobo
- Genomic Medicine Institute, Cleveland Clinic Foundation, 9500 Euclid Ave, NE-50, Cleveland, OH 44195, USA
| | | | | | | | | | | |
Collapse
|
11
|
Matsuoka T, Sato M, Tokoro M, Shin SW, Uenoyama A, Ito K, Hitomi S, Amano T, Anzai M, Kato H, Mitani T, Saeki K, Hosoi Y, Iritani A, Matsumoto K. Identification of ZAG1, a novel protein expressed in mouse preimplantation, and its putative roles in zygotic genome activation. J Reprod Dev 2008; 54:192-7. [PMID: 18360097 DOI: 10.1262/jrd.20008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated a mouse cDNA, zag1 (zygotic gene activation-associated gene 1), that has an open reading frame of 1,728-bp encoding a protein of 66.2 kDa including both a bipartite nuclear targeting sequence and a P-loop motif containing nucleoside triphosphate hydrolase motifs. Northern blot analysis of mouse tissues showed that zag1 was widely expressed but was especially prominent in the ovary and testis. RT-PCR analysis of in vitro fertilized embryos showed that the abundance of zag1 transcripts in oocytes decreased after fertilization, and zag1 mRNA was detected at 15 h post insemination (hpi) in fertilized embryos indicating that the gene was expressed at the start of zygotic gene activation at the mouse 1-cell stage. The nuclear-localization of ZAG1 protein in mouse preimplantation embryos at 15 hpi was confirmed by both subcellular analysis of enhanced green fluorescent protein (EGFP)-tagged ZAG1 and immunocytochemical analysis with anti-ZAG1 antibody. Subsequently, using yeast two-hybrid screening, we identified U2 small nuclear ribonucleoprotein B (U2B"), which is associated with pre-mRNA splicing, as a putative interacting partner of ZAG1 protein. Furthermore, knockdown of zag1 expression by an antisense DNA plasmid induced arrest and/or delay of embryonic development in injected 1-cell embryos. These results suggest that ZAG1 may be closely associated with zygotic gene expression in mouse preimplantation embryos.
Collapse
Affiliation(s)
- Toshiki Matsuoka
- Division of Biological Science, Graduate School of Biology-Oriented Science and Technology, Kinki University, Wakayama, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
prp8 mutations that cause human retinitis pigmentosa lead to a U5 snRNP maturation defect in yeast. Nat Struct Mol Biol 2007; 14:1077-83. [PMID: 17934474 DOI: 10.1038/nsmb1303] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 08/28/2007] [Indexed: 12/12/2022]
Abstract
Prp8 protein (Prp8p) is a highly conserved pre-mRNA splicing factor and a component of spliceosomal U5 small nuclear ribonucleoproteins (snRNPs). Although it is ubiquitously expressed, mutations in the C terminus of human Prp8p cause the retina-specific disease retinitis pigmentosa (RP). The biogenesis of U5 snRNPs is poorly characterized. We present evidence for a cytoplasmic precursor U5 snRNP in yeast that lacks the mature U5 snRNP component Brr2p and depends on a nuclear localization signal in Prp8p for its efficient nuclear import. The association of Brr2p with the U5 snRNP occurs within the nucleus. RP mutations in Prp8p in yeast result in nuclear accumulation of the precursor U5 snRNP, apparently as a consequence of disrupting the interaction of Prp8p with Brr2p. We therefore propose a novel assembly pathway for U5 snRNP complexes that is disrupted by mutations that cause human RP.
Collapse
|
13
|
Abstract
RNA-binding proteins play crucial roles in many biological processes, such as transcription, pre-mRNA splicing, nuclear-cytoplasmic transport of RNA, and translation of mRNA. Specific RNA-protein interactions are key to the correct assembly of ribonucleoprotein complexes and their biological functions. To date, more than 100 unique RNA-protein crystals have been prepared and there are more than 300 entries of RNA-protein complex structures in the Protein Data Bank. This chapter focuses on methods of RNA-protein complex crystallization discussed in six sections: determination of protein-binding sites in RNA, preparation of RNA, preparation of protein, annealing of RNA, reconstitution of RNA-protein complex, and searching crystallization conditions.
Collapse
Affiliation(s)
- Eiji Obayashi
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | | | | |
Collapse
|
14
|
Bahia D, Aviñó A, Darzynkiewicz E, Eritja R, Bach-Elias M. Trimethylguanosine nucleoside inhibits cross-linking between Snurportin 1 and m3G-CAPPED U1 snRNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:909-23. [PMID: 16901822 DOI: 10.1080/15257770600793901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Macromolecular nuclear import is an energy-and signal-dependent process. The best characterized type of nuclear import consists of proteins carrying the classical NLS that is mediated by the heterodimeric receptor importin alpha/beta. Spliceosomal snRNPs U1, U2, U4, and U5 nuclear import depend both on the 5' terminal m3G (trimethylguanosine) cap structure of the U snRNA and the Sm core domain. Snurportin 1 recognizes the m3G-cap structure of m3G-capped U snRNPs. In this report, we show how a synthesized trimethylguanosine nucleoside affects the binding of Snurportin 1 to m3G-capped U1 snRNA in a UV-cross-linking assay. The data indicated that TMG nucleoside is an essential component required in the recognition by Snurportin 1, thus suggesting that interaction of Snurportin 1 with U1 snRNA is not strictly dependent on the presence of the whole cap structure, but rather on the presence of the TMG nucleoside structure. These results indicate that the free nucleoside TMG could be a candidate to be an inhibitor of the interaction between Snurportin 1 and U snRNAs. We also show the behavior of free TMG nucleoside in in vitro U snRNPs nuclear import.
Collapse
Affiliation(s)
- Diana Bahia
- Institut de Biología Molecular de Barcelona, CSIC (IBMB-CSIC), Barcelona.
| | | | | | | | | |
Collapse
|
15
|
Lemm I, Girard C, Kuhn AN, Watkins NJ, Schneider M, Bordonné R, Lührmann R. Ongoing U snRNP biogenesis is required for the integrity of Cajal bodies. Mol Biol Cell 2006; 17:3221-31. [PMID: 16687569 PMCID: PMC1483051 DOI: 10.1091/mbc.e06-03-0247] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cajal bodies (CBs) have been implicated in the nuclear phase of the biogenesis of spliceosomal U small nuclear ribonucleoproteins (U snRNPs). Here, we have investigated the distribution of the CB marker protein coilin, U snRNPs, and proteins present in C/D box small nucleolar (sno)RNPs in cells depleted of hTGS1, SMN, or PHAX. Knockdown of any of these three proteins by RNAi interferes with U snRNP maturation before the reentry of U snRNA Sm cores into the nucleus. Strikingly, CBs are lost in the absence of hTGS1, SMN, or PHAX and coilin is dispersed in the nucleoplasm into numerous small foci. This indicates that the integrity of canonical CBs is dependent on ongoing U snRNP biogenesis. Spliceosomal U snRNPs show no detectable concentration in nuclear foci and do not colocalize with coilin in cells lacking hTGS1, SMN, or PHAX. In contrast, C/D box snoRNP components concentrate into nuclear foci that partially colocalize with coilin after inhibition of U snRNP maturation. We demonstrate by siRNA-mediated depletion that coilin is required for the condensation of U snRNPs, but not C/D box snoRNP components, into nucleoplasmic foci, and also for merging these factors into canonical CBs. Altogether, our data suggest that CBs have a modular structure with distinct domains for spliceosomal U snRNPs and snoRNPs.
Collapse
Affiliation(s)
- Ira Lemm
- *Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Cyrille Girard
- Institut de Génétique Moléculaire, UMR5535 CNRS, Montpellier, France; and
| | - Andreas N. Kuhn
- *Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Nicholas J. Watkins
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Marc Schneider
- *Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Rémy Bordonné
- Institut de Génétique Moléculaire, UMR5535 CNRS, Montpellier, France; and
| | - Reinhard Lührmann
- *Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| |
Collapse
|
16
|
Hirano M, Furiya Y, Asai H, Yasui A, Ueno S. ALADINI482S causes selective failure of nuclear protein import and hypersensitivity to oxidative stress in triple A syndrome. Proc Natl Acad Sci U S A 2006; 103:2298-303. [PMID: 16467144 PMCID: PMC1413683 DOI: 10.1073/pnas.0505598103] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Triple A syndrome is an autosomal recessive neuroendocrinological disease caused by mutations in a gene that encodes 546 amino acid residues. The encoded protein is the nucleoporin ALADIN, a component of nuclear pore complex (NPC). We identified a mutant ALADIN(I482S) that fails to target NPC and investigated the consequences of mistargeting using cultured fibroblasts (I482Sf) from a patient with triple A syndrome. ALADIN(I482S) affected a karyopherin-alpha/beta-mediated import pathway and decreased nuclear accumulations of aprataxin (APTX), a repair protein for DNA single-strand breaks (SSBs), and of DNA ligase I in I482Sf. This decrease was restored by wild-type ALADIN. ALADIN(I482S) had no effect on imports of M9/kap-beta2, BIB/kap-beta3, histone H1/importin 7, the ubiquitin conjugating enzyme UbcM2/importin 11, or the spliceosome protein U1A, indicating that ALADIN(I482S) selectively impaired transport of discrete import complexes through NPC. Cell survival assay showed hypersensitivity of I482Sf to l-buthionine-(S,R)-sulfoximine (BSO), a glutathione-depleting agent. BSO decreased nuclear APTX and ligase I levels in I482Sf and normal control fibroblasts, but increased SSBs only in I482Sf. These observations implied that I482Sf are hypersensitive to BSO and no longer sufficiently repair SSBs. Consistent with this notion, I482Sf transfected with both APTX and ligase I had increased resistance to BSO, whereas I482Sf transfected with LacZ vector remained hypersensitive to BSO. We propose that oxidative stress aggravates nuclear import failure, which is already compromised in patient cells. Consequent DNA damage, beyond the limited capacity of DNA repair proteins, i.e., APTX and ligase I, may participate in triggering cell death.
Collapse
Affiliation(s)
- Makito Hirano
- *Department of Neurology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8522, Japan; and
| | - Yoshiko Furiya
- *Department of Neurology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8522, Japan; and
| | - Hirohide Asai
- *Department of Neurology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8522, Japan; and
| | - Akira Yasui
- Department of Molecular Genetics, Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Satoshi Ueno
- *Department of Neurology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8522, Japan; and
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
17
|
Aratani S, Oishi T, Fujita H, Nakazawa M, Fujii R, Imamoto N, Yoneda Y, Fukamizu A, Nakajima T. The nuclear import of RNA helicase A is mediated by importin-α3. Biochem Biophys Res Commun 2006; 340:125-33. [PMID: 16375861 DOI: 10.1016/j.bbrc.2005.11.161] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 11/29/2005] [Indexed: 10/25/2022]
Abstract
RNA helicase A (RHA), an ATPase/helicase, regulates the gene expression at various steps including transcriptional activation and RNA processing. RHA is known to shuttle between the nucleus and cytoplasm. We identified the nuclear localization signal (NLS) of RHA and analyzed the nuclear import mechanisms. The NLS of RHA (RHA-NLS) consisting of 19 amino acid residues is highly conserved through species and does not have the consensus classical NLS. In vitro nuclear import assays revealed that the nuclear import of RHA was Ran-dependent and mediated with the classical importin-alpha/beta-dependent pathway. The binding assay indicated that the basic residues in RHA-NLS were used for interaction with importin-alpha. Furthermore, the nuclear import of RHA-NLS was supported by importin-alpha1 and preferentially importin-alpha3. Our results indicate that the nuclear import of RHA is mediated by the importin-alpha3/importin-beta-dependent pathway and suggest that the specificity for importin may regulate the functions of cargo proteins.
Collapse
Affiliation(s)
- Satoko Aratani
- Department of Genome Science, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Krämer A, Ferfoglia F, Huang CJ, Mulhaupt F, Nesic D, Tanackovic G. Structure-function analysis of the U2 snRNP-associated splicing factor SF3a. Biochem Soc Trans 2005; 33:439-42. [PMID: 15916536 DOI: 10.1042/bst0330439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Human splicing factor SF3a is a part of the 17 S U2 snRNP (small nuclear ribonucleoprotein), which interacts with the pre-mRNA branch site early during spliceosome formation. The SF3a subunits of 60, 66 and 120 kDa are all required for SF3a function in vitro. Depletion of individual subunits from HeLa cells by RNA interference results in a global inhibition of splicing, indicating that SF3a is a constitutive splicing factor. Structure-function analyses have defined domains necessary for interactions within the SF3a heterotrimer, association with the U2 snRNP and spliceosome assembly. Studies aimed at the identification of regions in SF3a60 and SF3a66, required for proper intracellular localization, have led to a model for the final steps in U2 snRNP biogenesis and the proposal that SF3a is incorporated into the U2 snRNP in Cajal bodies.
Collapse
Affiliation(s)
- A Krämer
- Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
| | | | | | | | | | | |
Collapse
|
19
|
Dickmanns A, Ficner R. Role of the 5’-cap in the biogenesis of spliceosomal snRNPs. FINE-TUNING OF RNA FUNCTIONS BY MODIFICATION AND EDITING 2005. [DOI: 10.1007/b106799] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
20
|
Narayanan U, Achsel T, Lührmann R, Matera AG. Coupled in vitro import of U snRNPs and SMN, the spinal muscular atrophy protein. Mol Cell 2004; 16:223-34. [PMID: 15494309 DOI: 10.1016/j.molcel.2004.09.024] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Revised: 07/08/2004] [Accepted: 08/18/2004] [Indexed: 10/26/2022]
Abstract
Cytoplasmic assembly of Sm-class small nuclear ribonucleoproteins (snRNPs) is a central process in eukaryotic gene expression. A large macromolecular complex containing the survival of motor neurons (SMN) protein is required for proper snRNP assembly in vivo. Defects in SMN function lead to a human neuromuscular disorder, spinal muscular atrophy (SMA). SMN protein localizes to both nuclear and cytoplasmic compartments, and a reduction in nuclear levels of SMN is correlated with the disease. The mechanism of SMN nuclear import, however, is unknown. Using digitonin-permeabilized cells, we show that SMN import depends on the presence of Sm snRNPs. Conversely, import of labeled U1 snRNPs was SMN complex dependent. Thus, import of SMN and U snRNPs are coupled in vitro. Furthermore, we identify nuclear import defects in SMA patient-derived SMN mutants, uncovering a potential mechanism for SMN dysfunction.
Collapse
Affiliation(s)
- Usha Narayanan
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | | | | | | |
Collapse
|
21
|
Nesic D, Tanackovic G, Krämer A. A role for Cajal bodies in the final steps of U2 snRNP biogenesis. J Cell Sci 2004; 117:4423-33. [PMID: 15316075 DOI: 10.1242/jcs.01308] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The biogenesis of Sm-type small nuclear ribonucleoproteins (snRNPs) involves the export of newly transcribed small nuclear RNAs (snRNAs) to the cytoplasm, assembly with seven common proteins and modification at the 5' and 3' termini. Binding of snRNP-specific proteins and snRNA modification complete the maturation process. This is thought to occur after reimport of the core snRNPs into the nucleus. The heterotrimeric splicing factor SF3a converts a pre-mature 15S U2 snRNP into the functional 17S particle. To analyze cellular aspects of this process, we studied domains in SF3a60 and SF3a66 that are required for their localization to nuclear speckles. Regions in SF3a60 and SF3a66 that mediate the binding to SF3a120 are necessary for nuclear import of the proteins, suggesting that the SF3a heterotrimer forms in the cytoplasm. SF3a60 and SF3a66 deleted for zinc finger domains required for the incorporation of SF3a into the U2 snRNP are nuclear, indicating that the 17S U2 snRNP is assembled in the nucleus. However, these proteins show an aberrant nuclear distribution. Endogenous SF3a subunits colocalize with U2 snRNP in nuclear speckles, but cannot be detected in Cajal bodies, unlike core U2 snRNP components. By contrast, SF3a60 and SF3a66 lacking the zinc finger domains accumulate in Cajal bodies and are diffusely distributed in the cytoplasm, suggesting a function for Cajal bodies in the final maturation of the U2 snRNP.
Collapse
Affiliation(s)
- Dobrila Nesic
- Department of Cell Biology, Faculty of Sciences, University of Geneva, 30, quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | | | | |
Collapse
|
22
|
Miyamoto Y, Hieda M, Harreman MT, Fukumoto M, Saiwaki T, Hodel AE, Corbett AH, Yoneda Y. Importin alpha can migrate into the nucleus in an importin beta- and Ran-independent manner. EMBO J 2002; 21:5833-42. [PMID: 12411501 PMCID: PMC131066 DOI: 10.1093/emboj/cdf569] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A classical nuclear localization signal (NLS)-containing protein is transported into the nucleus via the formation of a NLS-substrate/importin alpha/beta complex. In this study, we found that importin alpha migrated into the nucleus without the addition of importin beta, Ran or any other soluble factors in an in vitro transport assay. A mutant importin alpha lacking the importin beta-binding domain efficiently entered the nucleus. Competition experiments showed that this import pathway for importin alpha is distinct from that of importin beta. These results indicate that importin alpha alone can enter the nucleus via a novel pathway in an importin beta- and Ran-independent manner. Furthermore, this process is evolutionarily conserved as similar results were obtained in Saccharomyces cerevisiae. Moreover, the import rate of importin alpha differed among individual nuclei of permeabilized cells, as demonstrated by time-lapse experiments. This heterogeneous nuclear accumulation of importin alpha was affected by the addition of ATP, but not ATPgammaS. These results suggest that the nuclear import machinery for importin alpha at individual nuclear pore complexes may be regulated by reaction(s) that require ATP hydrolysis.
Collapse
Affiliation(s)
| | | | - Michelle T. Harreman
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, 2-2 Yamada-oka, Suita,Osaka 565-0871, Japan and
Department of Biochemistry,Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA 30322, USA Corresponding author e-mail: Y.Miyamoto and M.Hieda contributed equally to this work
| | | | | | - Alec E. Hodel
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, 2-2 Yamada-oka, Suita,Osaka 565-0871, Japan and
Department of Biochemistry,Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA 30322, USA Corresponding author e-mail: Y.Miyamoto and M.Hieda contributed equally to this work
| | - Anita H. Corbett
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, 2-2 Yamada-oka, Suita,Osaka 565-0871, Japan and
Department of Biochemistry,Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA 30322, USA Corresponding author e-mail: Y.Miyamoto and M.Hieda contributed equally to this work
| | - Yoshihiro Yoneda
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, 2-2 Yamada-oka, Suita,Osaka 565-0871, Japan and
Department of Biochemistry,Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, GA 30322, USA Corresponding author e-mail: Y.Miyamoto and M.Hieda contributed equally to this work
| |
Collapse
|
23
|
Affiliation(s)
- George Simos
- Biochemie-Zentrum Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | | | | |
Collapse
|
24
|
Dzeja PP, Bortolon R, Perez-Terzic C, Holmuhamedov EL, Terzic A. Energetic communication between mitochondria and nucleus directed by catalyzed phosphotransfer. Proc Natl Acad Sci U S A 2002; 99:10156-61. [PMID: 12119406 PMCID: PMC126640 DOI: 10.1073/pnas.152259999] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Exchange of information between the nucleus and cytosol depends on the metabolic state of the cell, yet the energy-supply pathways to the nuclear compartment are unknown. Here, the energetics of nucleocytoplasmic communication was determined by imaging import of a constitutive nuclear protein histone H1. Translocation of H1 through nuclear pores in cardiac cells relied on ATP supplied by mitochondrial oxidative phosphorylation, but not by glycolysis. Although mitochondria clustered around the nucleus, reducing the distance for energy transfer, simple nucleotide diffusion was insufficient to meet the energetic demands of nuclear transport. Rather, the integrated phosphotransfer network was required for delivery of high-energy phosphoryls from mitochondria to the nucleus. In neonatal cardiomyocytes with low creatine kinase activity, inhibition of adenylate kinase-catalyzed phosphotransfer abolished nuclear import. With deficient adenylate kinase, nucleoside diphosphate kinase, which secures phosphoryl exchange between ATP and GTP, was unable to sustain nuclear import. Up-regulation of creatine kinase phosphotransfer, to mimic metabolic conditions of adult cardiac cells, rescued H1 import, suggesting a developmental plasticity of the cellular energetic system. Thus, mitochondrial oxidative phosphorylation coupled with phosphotransfer relays provides an efficient energetic unit in support of nuclear transport.
Collapse
Affiliation(s)
- Petras P Dzeja
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | | |
Collapse
|
25
|
Abstract
A central aspect of cellular function is the proper regulation of nucleocytoplasmic transport. In recent years, significant progress has been made in identifying and characterizing the essential components of the transport machinery. Despite these advances, some facets of this process are still unclear. Furthermore, recent work has uncovered novel molecules and mechanisms of nuclear transport. This review focuses on the unresolved and novel aspects of nuclear transport and explores issues in tRNA, snRNA, and mRNA export that highlight the diversity of nuclear transport mechanisms.
Collapse
Affiliation(s)
- A Komeili
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA.
| | | |
Collapse
|
26
|
Rudt F, Pieler T. Cytosolic import factor- and Ran-independent nuclear transport of ribosomal protein L5. Eur J Cell Biol 2001; 80:661-8. [PMID: 11824785 DOI: 10.1078/0171-9335-00212] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomal protein L5 is a shuttling protein that, in Xenopus oocytes, is involved in the nucleocytoplasmic transport of 5S rRNA. As demonstrated earlier, L5 contains three independent nuclear import signals (NLSs), which function in oocytes as well as in somatic cells. Upon physical separation, these NLSs differ in respect to their capacity to bind to nuclear import factors in vitro and to mediate the nuclear import of a heterologous RNP in vivo. As reported in this communication, analysis of the in vitro nuclear import activity of these three NLSs reveals that they also differ in respect to their requirements for cytosolic import factors and Ran. Nuclear import mediated by the N-terminal and the central NLS depends on cytosolic import factor(s) and Ran, whereas import via the C-terminal NLS occurs independently from these factors. Thus, the presence of multiple NLSs in ribosomal protein L5 appears to allow for efficient nuclear transport via utilisation of multiple, mechanistically different import pathways.
Collapse
Affiliation(s)
- F Rudt
- Institut für Biochemie und Molekulare Zellbiologie, Georg-August-Universität, Göttingen/Germany
| | | |
Collapse
|
27
|
Miller ME, Cross FR. Mechanisms controlling subcellular localization of the G(1) cyclins Cln2p and Cln3p in budding yeast. Mol Cell Biol 2001; 21:6292-311. [PMID: 11509671 PMCID: PMC87357 DOI: 10.1128/mcb.21.18.6292-6311.2001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Different G(1) cyclins confer functional specificity to the cyclin-dependent kinase (Cdk) Cdc28p in budding yeast. The Cln3p G(1) cyclin is localized primarily to the nucleus, while Cln2p is localized primarily to the cytoplasm. Both binding to Cdc28p and Cdc28p-dependent phosphorylation in the C-terminal region of Cln2p are independently required for efficient nuclear depletion of Cln2p, suggesting that this process may be physiologically regulated. The accumulation of hypophosphorylated Cln2 in the nucleus is an energy-dependent process, but may not involve the RAN GTPase. Phosphorylation of Cln2p is inefficient in small newborn cells obtained by elutriation, and this lowered phosphorylation correlates with reduced Cln2p nuclear depletion in newborn cells. Thus, Cln2p may have a brief period of nuclear residence early in the cell cycle. In contrast, the nuclear localization pattern of Cln3p is not influenced by Cdk activity. Cln3p localization requires a bipartite nuclear localization signal (NLS) located at the C terminus of the protein. This sequence is required for nuclear localization of Cln3p and is sufficient to confer nuclear localization to green fluorescent protein in a RAN-dependent manner. Mislocalized Cln3p, lacking the NLS, is much less active in genetic assays specific for Cln3p, but more active in assays normally specific for Cln2p, consistent with the idea that Cln3p localization explains a significant part of Clnp functional specificity.
Collapse
Affiliation(s)
- M E Miller
- The Rockefeller University, New York, New York 10021, USA
| | | |
Collapse
|
28
|
|
29
|
Abstract
Significant advances have been made in elucidating the biogenesis pathway and three-dimensional structure of the UsnRNPs, the building blocks of the spliceosome. U2 and U4/U6*U5 tri-snRNPs functionally associate with the pre-mRNA at an earlier stage of spliceosome assembly than previously thought, and additional evidence supporting UsnRNA-mediated catalysis of pre-mRNA splicing has been presented.
Collapse
MESH Headings
- Animals
- Crystallography
- Humans
- Macromolecular Substances
- Protein Structure, Tertiary/physiology
- Protein Transport/physiology
- RNA Splicing/genetics
- RNA Splicing/physiology
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U1 Small Nuclear/biosynthesis
- Ribonucleoprotein, U1 Small Nuclear/chemistry
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/biosynthesis
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Spliceosomes/chemistry
- Spliceosomes/genetics
- Spliceosomes/metabolism
Collapse
Affiliation(s)
- C L Will
- Max Planck Institute of Biophysical Chemistry, Department of Cellular Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | | |
Collapse
|
30
|
Depienne C, Mousnier A, Leh H, Le Rouzic E, Dormont D, Benichou S, Dargemont C. Characterization of the nuclear import pathway for HIV-1 integrase. J Biol Chem 2001; 276:18102-7. [PMID: 11278458 DOI: 10.1074/jbc.m009029200] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The karyophilic properties of the human immunodeficiency virus, type I (HIV-1) pre-integration complex (PIC) allow the virus to infect non-dividing cells. To better understand the mechanisms responsible for nuclear translocation of the PIC, we investigated nuclear import of HIV-1 integrase (IN), a PIC-associated viral enzyme involved in the integration of the viral genome in the host cell DNA. Accumulation of HIV-1 IN into nuclei of digitonin-permeabilized cells does not result from passive diffusion but rather from an active transport that occurs through the nuclear pore complexes. HIV-1 IN is imported by a saturable mechanism, implying that a limiting cellular factor is responsible for this process. Although IN has been previously proposed to contain classical basic nuclear localization signals, we found that nuclear accumulation of IN does not involve karyopherins alpha, beta1, and beta2-mediated pathways. Neither the non-hydrolyzable GTP analog, guanosine 5'-O-(thiotriphosphate), nor the GTP hydrolysis-deficient Ran mutant, RanQ69L, significantly affects nuclear import of IN, which depends instead on ATP hydrolysis. Therefore these results support the idea that IN import is not mediated by members of the karyopherin beta family. More generally, in vitro nuclear import of IN does not require addition of cytosolic factors, suggesting that cellular factor(s) involved in this active but atypical pathway process probably remain associated with the nuclear compartment or the nuclear pore complexes from permeabilized cells.
Collapse
Affiliation(s)
- C Depienne
- Institut Jacques Monod, Unité Mixte de Recherche 7592, CNRS, Université Paris VI, Université Paris VII, Paris 75251, France
| | | | | | | | | | | | | |
Collapse
|
31
|
Hieda M, Tachibana T, Fukumoto M, Yoneda Y. Nuclear import of the U1A splicesome protein is mediated by importin alpha /beta and Ran in living mammalian cells. J Biol Chem 2001; 276:16824-32. [PMID: 11278401 DOI: 10.1074/jbc.m008299200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
U1A is a component of the uracil-rich small nuclear ribonucleoprotein. The molecular mechanism of nuclear import of U1A was investigated in vivo and in vitro. When recombinant deletion mutants of U1A are injected into the BHK21 cell cytoplasm, the nuclear localization signal (NLS) of U1A is found in the N-terminal half of the central domain (residues 100-144 in mouse U1A). In an in vitro assay, it was found that the U1A-NLS accumulated in only a portion of the nuclei in the absence of cytosolic extract. In contrast, the addition of importin alpha/beta and Ran induced the uniform nuclear accumulation of U1A-NLS in all cells. Furthermore, U1A was found to bind the C-terminal portion of importin alpha. In addition, the in vitro nuclear migration of full-length U1A was found to be exclusively dependent on importin alpha/beta and Ran. Moreover, in living cells, the full-length U1A accumulated in the nucleus in a Ran-dependent manner, and nuclear accumulation was inhibited by the importin beta binding domain of importin alpha. These results suggest that the nuclear import of U1A is mediated by at least two distinct pathways, an importin alpha/beta and Ran-dependent and an -independent pathway in permeabilized cells, and that the latter pathway may be suppressed in intact cells.
Collapse
Affiliation(s)
- M Hieda
- Department of Cell Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka and Institute for Molecular and Cellular Biology, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan
| | | | | | | |
Collapse
|
32
|
Bunn CF, Neidig JA, Freidinger KE, Stankiewicz TA, Weaver BS, McGrew J, Allison LA. Nucleocytoplasmic shuttling of the thyroid hormone receptor alpha. Mol Endocrinol 2001; 15:512-33. [PMID: 11266504 DOI: 10.1210/mend.15.4.0619] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The thyroid hormone receptor alpha (TR alpha) exhibits a dual role as an activator or repressor of gene transcription in response to thyroid hormone (T(3)). Our studies show that TR alpha, formerly thought to reside solely in the nucleus tightly bound to DNA, actually shuttles rapidly between the nucleus and cytoplasm. The finding that TR alpha shuttles reveals an additional checkpoint in receptor control of gene expression. Using Xenopus oocyte microinjection assays, we show that there are two coexisting mechanisms for nuclear entry of TR alpha. First, nuclear import of TR alpha (molecular mass 46 kDa) was not sensitive to general inhibitors of signal-mediated transport, indicating that TR alpha can enter the oocyte nucleus by passive diffusion. Second, when TR alpha was tagged with glutathione-S:-transferase, import of the fusion protein (molecular mass 73 kDa) was completely blocked by these inhibitors, demonstrating that an alternative, signal-mediated import pathway exists for TR alpha. Nuclear retention of TR alpha in oocytes is enhanced in the presence of T(3), suggesting that more intranuclear binding sites are available for the ligand-bound receptor. Using mammalian cells, we show that shuttling of green fluorescent protein (GFP)-tagged and untagged TR alpha is inhibited in both chilled and energy-depleted cells, suggesting that there is an energy-requiring step in the nuclear retention/export process. Nuclear export of TR alpha is not blocked by leptomycin B, a specific inhibitor of the export receptor CRM1, indicating that TR alpha does not require the CRM1 pathway to exit the nucleus. Dominant negative mutants of TR with defects in DNA binding and transactivation accumulate in the cytoplasm at steady state, illustrating that even single amino acid changes in functional domains may alter the subcellular distribution of TR. In contrast to TR alpha, nuclear export of its oncogenic homolog v-ErbA is sensitive to leptomycin B, suggesting that the oncoprotein follows a CRM1-mediated export pathway. Acquisition of altered nuclear export capabilities may contribute to the oncogenic properties of v-ErbA.
Collapse
Affiliation(s)
- C F Bunn
- Department of Zoology, University of Canterbury, Christchurch, New Zealand 8001
| | | | | | | | | | | | | |
Collapse
|
33
|
Wu X, Kasper LH, Mantcheva RT, Mantchev GT, Springett MJ, van Deursen JM. Disruption of the FG nucleoporin NUP98 causes selective changes in nuclear pore complex stoichiometry and function. Proc Natl Acad Sci U S A 2001; 98:3191-6. [PMID: 11248054 PMCID: PMC30629 DOI: 10.1073/pnas.051631598] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2000] [Accepted: 12/29/2000] [Indexed: 11/18/2022] Open
Abstract
The NUP98 gene encodes precursor proteins that generate two nucleoplasmically oriented nucleoporins, NUP98 and NUP96. By using gene targeting, we have selectively disrupted the murine NUP98 protein, leaving intact the expression and localization of NUP96. We show that NUP98 is essential for mouse gastrulation, a developmental stage that is associated with rapid cell proliferation, but dispensable for basal cell growth. NUP98-/- cells had an intact nuclear envelope with a normal number of embedded nuclear pore complexes. Typically, NUP98-deficient cells contained on average approximately 5-fold more cytoplasmic annulate lamellae than control cells. We found that a set of cytoplasmically oriented nucleoporins, including NUP358, NUP214, NUP88, and p62, assembled inefficiently into nuclear pores of NUP98-/- cells. Instead, these nucleoporins were prominently associated with the annulate lamellae. By contrast, a group of nucleoplasmically oriented nucleoporins, including NUP153, NUP50, NUP96, and NUP93, had no affinity for annulate lamellae and assembled normally into nuclear pores. Mutant pores were significantly impaired in transport receptor-mediated docking of proteins with a nuclear localization signal or M9 import signal and showed weak nuclear import of such substrates. In contrast, the ability of mutant pores to import ribosomal protein L23a and spliceosome protein U1A appeared intact. These observations show that NUP98 disruption selectively impairs discrete protein import pathways and support the idea that transport of distinct import complexes through the nuclear pore complex is mediated by specific subsets of nucleoporins.
Collapse
Affiliation(s)
- X Wu
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | | | | |
Collapse
|
34
|
Abstract
In eukaryotic cells, cell functions are maintained in an orderly manner through the continuous traffic of various proteins between the cell nucleus and the cytoplasm. The nuclear import and export of proteins occurs through nuclear pore complexes and typically requires specific signals: the nuclear localization signal and nuclear export signal, respectively. The transport pathways have been found to be highly divergent, but are known to be largely mediated by importin beta-like transport receptor family molecules. These receptor molecules bind to and carry their cargoes directly or via adapter molecules. A small GTPase Ran ensures the directionality of nuclear transport by regulating the interaction between the receptors and their cargoes through its GTP/GDP cycle. Moreover, it has been recently elucidated how the transport system is involved in various functions of cell physiology, such as cell cycle control.
Collapse
Affiliation(s)
- Y Yoneda
- Department of Cell Biology and Neuroscience, Graduate School of Medicine, Osaka University, Japan.
| |
Collapse
|
35
|
Hood JK, Silver PA. Diverse nuclear transport pathways regulate cell proliferation and oncogenesis. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1471:M31-41. [PMID: 10967423 DOI: 10.1016/s0304-419x(00)00018-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- J K Hood
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and the Dana-Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA
| | | |
Collapse
|
36
|
Abstract
Nuclear pore complexes (NPCs) form the site for entry and exit from the nucleus. A convergence of studies have defined the physical framework for the nuclear transport mechanism. This includes definition of the soluble transport machinery required for protein and RNA movement, x-ray structure analysis of transport factors, definitive compositional analysis of yeast NPCs, and documentation of the relative steady state arrangement of NPC components within the portal. With this information, researchers are now in the exciting position to examine the dynamic interplay between shuttling transport factors and the static pore complex.
Collapse
Affiliation(s)
- S R Wente
- Department of Cell Biology and Physiology, Box 8228, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
| |
Collapse
|
37
|
|