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Giudice J, Jiang H. Splicing regulation through biomolecular condensates and membraneless organelles. Nat Rev Mol Cell Biol 2024; 25:683-700. [PMID: 38773325 DOI: 10.1038/s41580-024-00739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Biomolecular condensates, sometimes also known as membraneless organelles (MLOs), can form through weak multivalent intermolecular interactions of proteins and nucleic acids, a process often associated with liquid-liquid phase separation. Biomolecular condensates are emerging as sites and regulatory platforms of vital cellular functions, including transcription and RNA processing. In the first part of this Review, we comprehensively discuss how alternative splicing regulates the formation and properties of condensates, and conversely the roles of biomolecular condensates in splicing regulation. In the second part, we focus on the spatial connection between splicing regulation and nuclear MLOs such as transcriptional condensates, splicing condensates and nuclear speckles. We then discuss key studies showing how splicing regulation through biomolecular condensates is implicated in human pathologies such as neurodegenerative diseases, different types of cancer, developmental disorders and cardiomyopathies, and conclude with a discussion of outstanding questions pertaining to the roles of condensates and MLOs in splicing regulation and how to experimentally study them.
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Affiliation(s)
- Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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2
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Garcia-Pardo J, Ventura S. Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies. Trends Biochem Sci 2024; 49:119-133. [PMID: 37926650 DOI: 10.1016/j.tibs.2023.10.005] [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: 07/26/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Amyloids are implicated in neurodegenerative and systemic diseases, yet they serve important functional roles in numerous organisms. Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that control central events of RNA biogenesis in normal and diseased cellular conditions. Many of these proteins contain prion-like sequences of low complexity, which not only assemble into functional fibrils in response to cellular cues but can also lead to disease when missense mutations arise in their sequences. Recent advances in cryo-electron microscopy (cryo-EM) have provided unprecedented high-resolution structural insights into diverse amyloid assemblies formed by hnRNPs and structurally related RBPs, including TAR DNA-binding protein 43 (TDP-43), Fused in Sarcoma (FUS), Orb2, hnRNPA1, hnRNPA2, and hnRNPDL-2. This review provides a comprehensive overview of these structures and explores their functional and pathological implications.
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Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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3
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Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3. Nat Commun 2023; 14:239. [PMID: 36646699 PMCID: PMC9842712 DOI: 10.1038/s41467-023-35854-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
hnRNPDL is a ribonucleoprotein (RNP) involved in transcription and RNA-processing that hosts missense mutations causing limb-girdle muscular dystrophy D3 (LGMD D3). Mammalian-specific alternative splicing (AS) renders three natural isoforms, hnRNPDL-2 being predominant in humans. We present the cryo-electron microscopy structure of full-length hnRNPDL-2 amyloid fibrils, which are stable, non-toxic, and bind nucleic acids. The high-resolution amyloid core consists of a single Gly/Tyr-rich and highly hydrophilic filament containing internal water channels. The RNA binding domains are located as a solenoidal coat around the core. The architecture and activity of hnRNPDL-2 fibrils are reminiscent of functional amyloids, our results suggesting that LGMD D3 might be a loss-of-function disease associated with impaired fibrillation. Strikingly, the fibril core matches exon 6, absent in the soluble hnRNPDL-3 isoform. This provides structural evidence for AS controlling hnRNPDL assembly by precisely including/skipping an amyloid exon, a mechanism that holds the potential to generate functional diversity in RNPs.
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Amodeo ME, Mitchell SPC, Pavan V, Kuehner JN. RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif. G3 (BETHESDA, MD.) 2022; 13:6782960. [PMID: 36315099 PMCID: PMC9836349 DOI: 10.1093/g3journal/jkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Premature transcription termination (i.e. attenuation) is a potent gene regulatory mechanism that represses mRNA synthesis. Attenuation of RNA polymerase II is more prevalent than once appreciated, targeting 10-15% of mRNA genes in yeast through higher eukaryotes, but its significance and mechanism remain obscure. In the yeast Saccharomyces cerevisiae, polymerase II attenuation was initially shown to rely on Nrd1-Nab3-Sen1 termination, but more recently our laboratory characterized a hybrid termination pathway involving Hrp1, an RNA-binding protein in the 3'-end cleavage factor. One of the hybrid attenuation gene targets is DEF1, which encodes a repair protein that promotes degradation of polymerase II stalled at DNA lesions. In this study, we characterized the chromosomal DEF1 attenuator and the functional role of Hrp1. DEF1 attenuator mutants overexpressed Def1 mRNA and protein, exacerbated polymerase II degradation, and hindered cell growth, supporting a biologically significant DEF1 attenuator function. Using an auxin-induced Hrp1 depletion system, we identified new Hrp1-dependent attenuators in MNR2, SNG1, and RAD3 genes. An hrp1-5 mutant (L205S) known to impair binding to cleavage factor protein Rna14 also disrupted attenuation, but surprisingly no widespread defect was observed for an hrp1-1 mutant (K160E) located in the RNA-recognition motif. We designed a new RNA recognition motif mutant (hrp1-F162W) that altered a highly conserved residue and was lethal in single copy. In a heterozygous strain, hrp1-F162W exhibited dominant-negative readthrough defects at several gene attenuators. Overall, our results expand the hybrid RNA polymerase II termination pathway, confirming that Hrp1-dependent attenuation controls multiple yeast genes and may function through binding cleavage factor proteins and/or RNA.
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Affiliation(s)
- Maria E Amodeo
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Shane P C Mitchell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Vincent Pavan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Jason N Kuehner
- Corresponding author: Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA.
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Zhang Q, Zhang J, Ye J, Li X, Liu H, Ma X, Wang C, He K, Zhang W, Yuan J, Zhao Y, Xu H, Liu Q. Nuclear speckle specific hnRNP D-like prevents age- and AD-related cognitive decline by modulating RNA splicing. Mol Neurodegener 2021; 16:66. [PMID: 34551807 PMCID: PMC8456587 DOI: 10.1186/s13024-021-00485-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/12/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Aberrant alternative splicing plays critical role in aging and age-related diseases. Heterogeneous nuclear ribonucleoproteins (hnRNPs) reportedly regulate RNA splicing process. Whether and how hnRNPs contribute to age-related neurodegenerative diseases, especially Alzheimer's disease (AD), remain elusive. METHODS Immunoblotting and immunostaining were performed to determine expression patterns and cellular/subcellular localization of the long isoform of hnRNP D-like (L-DL), which is a hnRNP family member, in mouse hippocampus. Downregulation of L-DL in WT mice was achieved by AAV-mediated shRNA delivery, followed by memory-related behavioural tests. L-DL interactome was analysed by affinity-precipitation and mass spectrometry. Alternative RNA splicing was measured by RNA-seq and analyzed by bioinformatics-based approaches. Downregulation and upregulation of L-DL in APP/PS1 mice were performed using AAV-mediated transduction. RESULTS We show that L-DL is specifically localized to nuclear speckles. L-DL levels are decreased in the hippocampus of aged mouse brains and downregulation of L-DL impairs cognition in mice. L-DL serves as a structural component to recruit other speckle proteins, and regulates cytoskeleton- and synapse-related gene expression by altering RNA splicing. Mechanistically, these splicing changes are modulated via L-DL-mediated interaction of SF3B3, a core component of U2 snRNP, and U2AF65, a U2 spliceosome protein that guides U2 snRNP's binding to RNA. In addition, L-DL levels are decreased in APP/PS1 mouse brains. While downregulation of L-DL deteriorates memory deficits and overexpression of L-DL improves cognitive function in AD mice, by regulating the alternative splicing and expression of synaptic gene CAMKV. CONCLUSIONS Our findings define a molecular mechanism by which hnRNP L-DL regulates alternative RNA splicing, and establish a direct role for L-DL in AD-related synaptic dysfunction and memory decline.
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Affiliation(s)
- Qingyang Zhang
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Juan Zhang
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.,Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, 230026, China
| | - Jin Ye
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaohui Li
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.,Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, 230026, China
| | - Hongda Liu
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaolin Ma
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Chao Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Keqiang He
- Department of Anesthesiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Wei Zhang
- Department of Anesthesiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Ji Yuan
- Department of Anesthesiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Yingjun Zhao
- The First Affiliated Hospital of Xiamen University, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Xiamen University, Xiamen, 361000, China
| | - Huaxi Xu
- The First Affiliated Hospital of Xiamen University, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Xiamen University, Xiamen, 361000, China.
| | - Qiang Liu
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China. .,Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, 230026, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China.
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6
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Marklein B, Jenning M, Konthur Z, Häupl T, Welzel F, Nonhoff U, Krobitsch S, Mulder DM, Koenders MI, Joshua V, Cope AP, Shlomchik MJ, Anders HJ, Burmester GR, Hensvold A, Catrina AI, Rönnelid J, Steiner G, Skriner K. The citrullinated/native index of autoantibodies against hnRNP-DL predicts an individual "window of treatment success" in RA patients. Arthritis Res Ther 2021; 23:239. [PMID: 34521462 PMCID: PMC8439038 DOI: 10.1186/s13075-021-02603-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a need for biomarker to identify patients "at risk" for rheumatoid arthritis (risk-RA) and to better predict the therapeutic response and in this study we tested the hypothesis that novel native and citrullinated heterogeneous nuclear ribonucleoprotein (hnRNP)-DL autoantibodies could be possible biomarkers. METHODS Using protein macroarray and ELISA, epitope recognition against hnRNP-DL was analysed in sera from different developed RA disease and diagnosed SLE patients. Toll-like receptor (TLR) 7/9 and myeloid differentiation primary response gene 88 (MyD88)-dependency were studied in sera from murine disease models. HnRNP-DL expression in cultivated cells and synovial tissue was analysed by indirect immunofluorescence, immunoblot and immunohistochemistry. RESULTS HnRNP-DL was highly expressed in stress granules, citrullinated in the rheumatoid joint and targeted by autoantibodies either as native or citrullinated proteins in patient subsets with different developed RA disease. Structural citrullination dependent epitopes (SCEs) of hnRNP-DL were detected in 58% of the SLE patients although 98% of these sera were α-CCP-2-negative. To obtain a specific citrullinated signal value, we subtracted the native antibody value from the citrullinated signal. The citrullinated/native index of autoantibodies against hnRNP-DL (CNDL-Index) was identified as a new value for an "individual window of treatment success" in early RA and for the detection of RF IgM/α-CCP-2 seronegative RA patients (24-46%). Negative CNDL-index was found in SLE patients, risk-RA and early RA cohorts such as EIRA where the majority of these patients are DAS28-responders to methotrexate (MTX) treatment (87%). High positive CNDL-values were associated with more severe RA, shared epitope and parenchymal changes in the lung. Specifically, native α-hnRNP-DL is TLR7/9-dependent, associated with pain and ROC analysis revealed an association to initial MTX or etanercept treatment response, especially in seronegative RA patients. CONCLUSION CNDL-index defines people at risk to develop RA and the "window of treatment success" thereby closing the sensitivity gap in RA.
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Affiliation(s)
- Bianka Marklein
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany
| | - Madeleine Jenning
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany
- German Rheumatism Research Centre, Leibniz Institute, 10117, Berlin, Germany
| | - Zoltán Konthur
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Analytical Chemistry (Dpt.1), Bundesanstalt für Materialforschung und-prüfung (BAM), Berlin, Germany
| | - Thomas Häupl
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany
| | | | - Ute Nonhoff
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Debbie M Mulder
- Department of Experimental Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marije I Koenders
- Department of Experimental Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vijay Joshua
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrew P Cope
- Centre for Rheumatic Diseases, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Mark J Shlomchik
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Hans-Joachim Anders
- Medical Clinic and Policlinic IV, Nephrological Center, Ludwig-Maximilian-University Hospital, Munich, Germany
| | - Gerd R Burmester
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany
| | - Aase Hensvold
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Academic Specialist Center, Center for Rheumatology, Stockholm Health Region, Stockholm, Sweden
| | - Anca I Catrina
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Günter Steiner
- Division of Rheumatology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Cluster for Arthritis and Rehabilitation, Vienna, Austria
| | - Karl Skriner
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Charite Campus Mitte, Rheumatologisches Forschungslabor - AG Skriner, Chariteplatz 1 (intern Virchowweg 11, 5.OG, R011), 10117, Berlin, Germany.
- German Rheumatism Research Centre, Leibniz Institute, 10117, Berlin, Germany.
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Batlle C, Yang P, Coughlin M, Messing J, Pesarrodona M, Szulc E, Salvatella X, Kim HJ, Taylor JP, Ventura S. hnRNPDL Phase Separation Is Regulated by Alternative Splicing and Disease-Causing Mutations Accelerate Its Aggregation. Cell Rep 2020; 30:1117-1128.e5. [PMID: 31995753 PMCID: PMC6996132 DOI: 10.1016/j.celrep.2019.12.080] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/12/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
Prion-like proteins form multivalent assemblies and phase separate into membraneless organelles. Heterogeneous ribonucleoprotein D-like (hnRNPDL) is a RNA-processing prion-like protein with three alternative splicing (AS) isoforms, which lack none, one, or both of its two disordered domains. It has been suggested that AS might regulate the assembly properties of RNA-processing proteins by controlling the incorporation of multivalent disordered regions in the isoforms. This, in turn, would modulate their activity in the downstream splicing program. Here, we demonstrate that AS controls the phase separation of hnRNPDL, as well as the size and dynamics of its nuclear complexes, its nucleus-cytoplasm shuttling, and amyloidogenicity. Mutation of the highly conserved D378 in the disordered C-terminal prion-like domain of hnRNPDL causes limb-girdle muscular dystrophy 1G. We show that D378H/N disease mutations impact hnRNPDL assembly properties, accelerating aggregation and dramatically reducing the protein solubility in the muscle of Drosophila, suggesting a genetic loss-of-function mechanism for this muscular disorder.
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Affiliation(s)
- Cristina Batlle
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
| | - Peiguo Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maura Coughlin
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 201815, USA
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 201815, USA.
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain.
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8
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Shishkin SS, Kovalev LI, Pashintseva NV, Kovaleva MA, Lisitskaya K. Heterogeneous Nuclear Ribonucleoproteins Involved in the Functioning of Telomeres in Malignant Cells. Int J Mol Sci 2019; 20:E745. [PMID: 30744200 PMCID: PMC6387250 DOI: 10.3390/ijms20030745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 12/12/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are structurally and functionally distinct proteins containing specific domains and motifs that enable the proteins to bind certain nucleotide sequences, particularly those found in human telomeres. In human malignant cells (HMCs), hnRNP-A1-the most studied hnRNP-is an abundant multifunctional protein that interacts with telomeric DNA and affects telomerase function. In addition, it is believed that other hnRNPs in HMCs may also be involved in the maintenance of telomere length. Accordingly, these proteins are considered possible participants in the processes associated with HMC immortalization. In our review, we discuss the results of studies on different hnRNPs that may be crucial to solving molecular oncological problems and relevant to further investigations of these proteins in HMCs.
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Affiliation(s)
- Sergey S Shishkin
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
| | - Leonid I Kovalev
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
| | - Natalya V Pashintseva
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
| | - Marina A Kovaleva
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
| | - Ksenia Lisitskaya
- Laboratory of Biomedical Research, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospekt, 33, bld. 2, 119071 Moscow, Russia.
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9
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Kang S, Ren D, Xiao G, Daris K, Buck L, Enyenihi AA, Zubarev R, Bondarenko PV, Deshpande R. Cell line profiling to improve monoclonal antibody production. Biotechnol Bioeng 2013; 111:748-60. [DOI: 10.1002/bit.25141] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/24/2013] [Accepted: 10/21/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Sohye Kang
- Product Attribute Sciences; Amgen, Inc.; One Amgen Center Drive Thousand Oaks California 91320
| | - Da Ren
- Product Attribute Sciences; Amgen, Inc.; One Amgen Center Drive Thousand Oaks California 91320
| | - Gang Xiao
- Product Attribute Sciences; Amgen, Inc.; One Amgen Center Drive Thousand Oaks California 91320
| | - Kristi Daris
- Drug Substance Development; Amgen, Inc.; Thousand Oaks California
| | - Lynette Buck
- Drug Substance Development; Amgen, Inc.; Thousand Oaks California
| | - Atim A. Enyenihi
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; Stockholm Sweden
| | - Roman Zubarev
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; Stockholm Sweden
- SciLifeLab; Stockholm Sweden
| | - Pavel V. Bondarenko
- Product Attribute Sciences; Amgen, Inc.; One Amgen Center Drive Thousand Oaks California 91320
| | - Rohini Deshpande
- Drug Substance Development; Amgen, Inc.; Thousand Oaks California
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Barthéléry M, Jaishankar A, Salli U, Freeman WM, Vrana KE. 2-D DIGE identification of differentially expressed heterogeneous nuclear ribonucleoproteins and transcription factors during neural differentiation of human embryonic stem cells. Proteomics Clin Appl 2012; 3:505-14. [PMID: 21136975 DOI: 10.1002/prca.200800109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Neural stem cells (NSC) are progenitors that can give rise to all neural lineages. They are found in specific niches of fetal and adult brains and grow in vitro as non-adherent colonies, the neurospheres. These cells express the intermediate filament nestin, commonly considered an NSC marker. NSC can be derived as neurospheres from human embryonic stem cells (hESC). The mechanisms of cellular programming that hESC undergo during differentiation remain obscure. To investigate the commitment process of hESC during directed neural differentiation, we compared the nuclear proteomes of hESC and hESC-derived neurospheres. We used 2-D DIGE to conduct a quantitative comparison of hESC and NSC nuclear proteins and detected 1521 protein spots matched across three gels. Statistical analysis (ANOVA n = 3 with false discovery correction) revealed that only 2.1% of the densitometric signal was significantly changed. The ranges of average ratios varied from 1.2- to 11-fold at a statistically significant p-value <0.05. MS/MS identified 15 regulated proteins previously shown to be involved in chromatin remodeling, mRNA processing and gene expression regulation. Notably, three members of the heterogeneous nuclear ribonucleoprotein family (AUF-1, and FBP-1 and FBP-2) register a 54, 70 and 99% increased expression, highlighting them as potential markers for NSC in vitro derivation. By contrast, Cpsf-6 virtually disappears with differentiation with an 11-fold drop in NSC, highlighting this protein as a novel marker for undifferentiated ESC.
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Affiliation(s)
- Miguel Barthéléry
- Pennsylvania State University College of Medicine, Department of Pharmacology, Hummelstown, PA, USA
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11
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JKTBP1 Is Involved in Stabilization and IRES-Dependent Translation of NRF mRNAs by Binding to 5′ and 3′ Untranslated Regions. J Mol Biol 2011; 407:492-504. [DOI: 10.1016/j.jmb.2011.01.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 01/26/2011] [Accepted: 01/27/2011] [Indexed: 11/15/2022]
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12
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Gratacós FM, Brewer G. The role of AUF1 in regulated mRNA decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2010; 1:457-73. [PMID: 21956942 PMCID: PMC3608466 DOI: 10.1002/wrna.26] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Messenger ribonucleic acid (mRNA) turnover is a major control point in gene expression. In mammals, many mRNAs encoding inflammatory cytokines, oncoproteins, and G-protein-coupled receptors are destabilized by the presence of AU-rich elements (AREs) in their 3'-untranslated regions. Association of ARE-binding proteins (AUBPs) with these mRNAs promotes rapid mRNA degradation. ARE/poly(U)-binding/degradation factor 1 (AUF1), one of the best-characterized AUBPs, binds to many ARE-mRNAs and assembles other factors necessary to recruit the mRNA degradation machinery. These factors include translation initiation factor eIF4G, chaperones hsp27 and hsp70, heat-shock cognate protein hsc70, lactate dehydrogenase, poly(A)-binding protein, and other unidentified proteins. Numerous signaling pathways alter the composition of this AUF1 complex of proteins to effect changes in ARE-mRNA degradation rates. This review briefly describes the roles of mRNA decay in gene expression in general and ARE-mediated decay (AMD) in particular, with a focus on AUF1 and the different modes of regulation that govern AUF1 involvement in AMD.
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Affiliation(s)
- Frances M. Gratacós
- Department of Molecular Genetics, Microbiology and Immunology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey, 08854-5635, USA
| | - Gary Brewer
- Department of Molecular Genetics, Microbiology and Immunology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey, 08854-5635, USA
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13
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Weitzdörfer R, Höger H, Burda G, Pollak A, Lubec G. Differences in Hippocampal Protein Expression at 3 Days, 3 Weeks, and 3 Months Following Induction of Perinatal Asphyxia in the Rat. J Proteome Res 2008; 7:1945-52. [DOI: 10.1021/pr700835y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Rachel Weitzdörfer
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria, and Division for Laboratory Animal Science and Genetics, Medical University of Vienna, Brauhausgasse 34, 2325 Himberg, Austria
| | - Harald Höger
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria, and Division for Laboratory Animal Science and Genetics, Medical University of Vienna, Brauhausgasse 34, 2325 Himberg, Austria
| | - Gudrun Burda
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria, and Division for Laboratory Animal Science and Genetics, Medical University of Vienna, Brauhausgasse 34, 2325 Himberg, Austria
| | - Arnold Pollak
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria, and Division for Laboratory Animal Science and Genetics, Medical University of Vienna, Brauhausgasse 34, 2325 Himberg, Austria
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria, and Division for Laboratory Animal Science and Genetics, Medical University of Vienna, Brauhausgasse 34, 2325 Himberg, Austria
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14
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Wu YY, Li H, Lv XY, Wei Q, Li X, Liu XY, Zhou Q, Wei YQ. Overexpression of JKTBP1 induces androgen-independent LNCaP cell proliferation through activation of epidermal growth factor-receptor (EGF-R). Cell Biochem Funct 2008; 26:467-77. [DOI: 10.1002/cbf.1468] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Reboll MR, Oumard A, Gazdag AC, Renger I, Ritter B, Schwarzer M, Hauser H, Wood M, Yamada M, Resch K, Nourbakhsh M. NRF IRES activity is mediated by RNA binding protein JKTBP1 and a 14-nt RNA element. RNA (NEW YORK, N.Y.) 2007; 13:1328-40. [PMID: 17592041 PMCID: PMC1924892 DOI: 10.1261/rna.545407] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The mRNA of human NF-kappaB repressing factor (NRF) contains a long 5'-untranslated region (UTR) that directs ribosomes to the downstream start codon by a cap-independent mechanism. Comparison of the nucleotide (nt) sequences of human and mouse NRF mRNAs reveals a high degree of identity throughout a fragment of 150 nt proximal to the start codon. Here, we show that this region constitutes a minimal internal ribosome entry segment (IRES) module. Enzymatic RNA structure analysis reveals a secondary structure model of the NRF IRES module. Point mutation analysis of the module determines a short, 14-nt RNA element (nt 640-653) as a mediator of IRES function. Purification of IRES binding cellular proteins and subsequent ESI/MS/MS sequence analysis led to identification of the RNA-binding protein, JKTBP1. EMSA experiments show that JKTBP1 binds upstream to the 14-nt RNA element in the NRF IRES module (nt 579-639). Over-expression of JKTBP1 significantly enhances activity of the NRF IRES module in dicistronic constructs. Moreover, siRNA experiments demonstrate that down-regulation of endogenous JKTBP1 decreases NRF IRES activity and the level of endogenous NRF protein. The data of this study show that JKTBP1 and the 14-nt element act independently to mediate NRF IRES activity.
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Affiliation(s)
- Marc René Reboll
- Institute of Pharmacology, Hannover Medical School, Hannover, Germany
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16
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Suzuki M, Iijima M, Nishimura A, Tomozoe Y, Kamei D, Yamada M. Two separate regions essential for nuclear import of the hnRNP D nucleocytoplasmic shuttling sequence. FEBS J 2005; 272:3975-87. [PMID: 16045768 DOI: 10.1111/j.1742-4658.2005.04820.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein (hnRNP) D/AUF1 functions in mRNA genesis in the nucleus and modulates mRNA decay in the cytoplasm. Although it is primarily nuclear, it shuttles between the nucleus and cytoplasm. We studied the nuclear import and export of the last exon-encoding sequence common to all its isoforms by its expression as a green fluorescent protein-fusion protein in HeLa cells and by heterokaryon assay. The C-terminal 19-residue sequence (SGYGKVSRRGGHQNSYKPY) was identified as an hnRNP D nucleocytoplasmic shuttling sequence (DNS). In vitro nuclear transport using permeabilized cells indicated that nuclear import of DNS is mediated by transportin-1 (Trn-1). DNS accumulation in the nucleus was dependent on Trn-1, Ran, and energy in multiple rounds of nuclear transport. Use of DNS with deletions, alanine scanning mutagenesis and point mutations revealed that two separate regions (the N-terminal seven residues and the C-terminal two residues) are crucial for in vivo and in vitro transport as well as for interaction with Trn-1. The N- and C-terminal motifs are conserved in the shuttling sequences of hnRNP A1 and JKTBP.
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Affiliation(s)
- Maiko Suzuki
- Graduate School of Integrated Science, Yokohama City University, Yokohama, Japan
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17
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Bandiera A, Medic N, Akindahunsi AA, Manzini G. In-vitro dual binding activity of a evolutionarily related subgroup of hnRNP proteins. Mol Cell Biochem 2005; 268:121-7. [PMID: 15724445 DOI: 10.1007/s11010-005-3700-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The wide family of heterogeneous nuclear ribonucleoproteins (hnRNPs) comprises members that interact with single-stranded nucleic acids. On the basis of their structure, some of them are characterised by a tandem RNA-binding domain (RBD) and a glycine-rich C-terminus, showing a high degree of homology. Recently, we have isolated some proteins belonging to this group that interact with single-stranded cytosine-block telomeric DNA. The aim of the present investigation is to better characterise the relationship of some structural features shared by these proteins and their in-vitro interaction with the telomeric type sequences. We analysed the in-vitro binding properties of some of these components toward both single-stranded telomeric motifs. Using deletion mutants, the relationship between cytosine-rich motif binding activity and the structural features of one of these proteins is further characterized. This binding activity appears to be related to a subgroup of the 2xRBD+Glycine rich hnRNP, suggesting functionally distinct properties of these proteins, in agreement with their evolutionary relationship.
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Affiliation(s)
- Antonella Bandiera
- Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, 34127 Trieste, Italy.
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18
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Bandiera A, Tell G, Marsich E, Scaloni A, Pocsfalvi G, Akintunde Akindahunsi A, Cesaratto L, Manzini G. Cytosine-block telomeric type DNA-binding activity of hnRNP proteins from human cell lines. Arch Biochem Biophys 2003; 409:305-14. [PMID: 12504897 DOI: 10.1016/s0003-9861(02)00413-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Following the observation of the presence in mammalian nuclear extracts of a DNA binding activity quite specific for the single-stranded C-rich telomeric motif, we have isolated from the K562 human cell line by affinity chromatography and identified by mass spectrometry a number of proteins able to bind to this sequence. All of them belong to different heterogeneous nuclear ribonucleoprotein subgroups (hnRNP). Whereas many of them, namely hnRNP K, two isoforms of hnRNP I, and the factor JKTBP, appear to bind to this sequence with limited specificity after isolation, an isoform of hnRNP D (alias AUF1) and particularly hnRNP E1 (alias PCBP-1) show a remarkable specificity for the (CCCTAA)n repeated motif. Both have been obtained also as recombinant proteins expressed in Escherichia coli and have been shown to retain their binding specificity toward the C-block repeated sequence. In the light of the current knowledge about these proteins, their possible involvement in telomere functioning is discussed.
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Affiliation(s)
- Antonella Bandiera
- Department of Biochemistry, Biophysics, and Macromolecular Chemistry, University of Trieste, via L. Giorgieri 1, 34127, Trieste, Italy
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19
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Kamei D, Yamada M. Interactions of heterogeneous nuclear ribonucleoprotein D-like protein JKTBP and its domains with high-affinity binding sites. Gene 2002; 298:49-57. [PMID: 12406575 DOI: 10.1016/s0378-1119(02)00926-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
JKTBP proteins consisting of two canonical RNA binding domains (RBDs) and a glycine-rich carboxyl domain are nucleocytoplasmic shuttling proteins. We studied in vivo and in vitro interactions between JKTBP and RNA. UV cross-linking experiments on HL-60 cells indicated that following RNA synthesis inhibition by actinomycin D, JKTBP1 accumulated in the cytoplasam is bound to poly(A)(+) RNAs. Recombinant JKTBP1 protein blots could bind poly(A)(+) RNAs, but not poly(A)(-) RNAs. For examination of RNA binding specificity of JKTBP, we enriched high binding sites from pools of 20 nt random sequence-containing RNAs by a selection/amplification method. After eight rounds of a selection and amplification, >20 sequences for each of JKTBPs 1 and 2 were identified. Their consensus high-affinity site was ACUAGC. Approximate K(d)s of JKTBPs 2 and 1 were estimated to be 6-12 nM for the selected sequences by filter binding assays. JKTBP deletion analysis indicated that not individual RBDs, both RBDs and the N-terminal 15 amino acids of the carboxyl domain are required for sequence-specific and high-affinity binding. These results indicate that JKTBP is a sequence-specific RNA binding protein differing from the related heterogeneous nuclear ribonucleoproteins A1 and D.
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Affiliation(s)
- Daisuke Kamei
- Graduate School of Integrated Science, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama 236-0027, Japan
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20
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Gururaja T, Li W, Bernstein J, Payan DG, Anderson DC. Use of MEDUSA-based data analysis and capillary HPLC-ion-trap mass spectrometry to examine complex immunoaffinity extracts of RBAp48. J Proteome Res 2002; 1:253-61. [PMID: 12645902 DOI: 10.1021/pr0255147] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To examine the Jurkat cell interaction partners of RbAp48, we digested entire immunoaffinity extracts with trypsin and identified potential interacting proteins using one- and two-dimensional microcapillary HPLC-ion-trap mass spectrometry. An Oracle-based automated data analysis system (MEDUSA) was used to compare quadruplicate anti-RbAp48 antibody affinity extracts with two sets of quadruplicate control extracts. The anti-RbAp48 extracts contained over 40 difference 1D gel bands. We identified all known proteins of the NuRD/Mi-2 complex including human p66. Three potential homologues of members of this complex were also found, suggesting that there may be more than one variant of this complex. Eleven proteins associated with RNA binding or pre-mRNA splicing were observed. Four other proteins, including a putative tumor suppressor, were identified, as were 18 ribosomal proteins. There was little overlap with RbAp48-interacting proteins defined by yeast two-hybrid methods. These results demonstrate the analysis of a complex immunoaffinity extract and suggest a more complex cellular role for RbAp48 than previously documented.
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Affiliation(s)
- Tarikere Gururaja
- Rigel, Incorporated, 240 East Grand Avenue, South San Francisco, California 94066, USA
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21
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Kawamura H, Tomozoe Y, Akagi T, Kamei D, Ochiai M, Yamada M. Identification of the nucleocytoplasmic shuttling sequence of heterogeneous nuclear ribonucleoprotein D-like protein JKTBP and its interaction with mRNA. J Biol Chem 2002; 277:2732-9. [PMID: 11705999 DOI: 10.1074/jbc.m108477200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
JKTBP proteins are related to a family of heterogeneous nuclear ribonucleoproteins (hnRNPs) that function in mRNA biogenesis and mRNA metabolism. JKTBP proteins constituted of isoforms 1, 2, and 1Delta6 are localized in the nucleus. We show that the dominant form JKTBP1 shuttles between the nucleus and the cytoplasm and interacts with mRNA. Immunofluorescence microscopy and immunoblotting of the subcellular fractions and overexpression of JKTBP tagged with green fluorescent protein indicated that JKTBP1 and JKTBP1Delta6, but not JKTBP2, accumulate in the cytoplasm upon polymerase II transcription inhibition. After release from inhibition, the return of accumulated cytoplasmic JKTBP to the nucleus was temperature-dependent. In heterokaryons, green fluorescent protein-tagged JKTBP1 and JKTBP1Delta6 migrated from the HeLa nucleus to the mouse nucleus, but JKTBP2 did not. Using various JKTBP deletion mutants, the 25-residue C-terminal tail was identified as a shuttling sequence like M9. It is conserved in the C-terminal tails of hnRNP D/AUF1 and type A/B hnRNP/ABBP-1. Analysis of its sequence-specific interacting protein indicated that JKTBP nuclear import is mediated by the receptor transportin 1/karyopherin beta2. UV cross-linking revealed the increased occurrence of JKTBP1 directly interacting with poly(A)(+) RNA in the cytoplasm following actinomycin D treatment. We discuss a role of JKTBP in mRNA nuclear export.
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MESH Headings
- 3T3 Cells
- Active Transport, Cell Nucleus
- Amino Acid Sequence
- Animals
- Cell Nucleus/metabolism
- Cloning, Molecular
- Cross-Linking Reagents/pharmacology
- Cytoplasm/metabolism
- DNA, Complementary/metabolism
- Dactinomycin/pharmacology
- Fluorescent Antibody Technique, Indirect
- Genes, Dominant
- Glutathione Transferase/metabolism
- Green Fluorescent Proteins
- HeLa Cells
- Heterogeneous-Nuclear Ribonucleoproteins
- Humans
- Immunoblotting
- Karyopherins/metabolism
- Luminescent Proteins/metabolism
- Mice
- Mice, Inbred BALB C
- Microscopy, Fluorescence
- Molecular Sequence Data
- Plasmids/metabolism
- Poly A
- Protein Binding
- Protein Isoforms
- Protein Structure, Tertiary
- Protein Synthesis Inhibitors/pharmacology
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/metabolism
- Ribonucleoproteins/metabolism
- Sequence Homology, Amino Acid
- Subcellular Fractions
- Temperature
- Ultraviolet Rays
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Affiliation(s)
- Hidenobu Kawamura
- Graduate School of Integrated Science, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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22
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Akagi T, Kamei D, Tsuchiya N, Nishina Y, Horiguchi H, Matsui M, Kamma H, Yamada M. Molecular characterization of a mouse heterogeneous nuclear ribonucleoprotein D-like protein JKTBP and its tissue-specific expression. Gene 2000; 245:267-73. [PMID: 10717477 DOI: 10.1016/s0378-1119(00)00032-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The human DNA- and RNA-binding protein JKTBP is a new member of heterogeneous nuclear ribonucleoproteins (hnRNPs) that are involved in mRNA biogenesis. We cloned and characterized a mouse homolog and studied its expression in mouse tissues. The cDNA encoded a 301-residue polypeptide. There is only a single amino acid difference between the mouse and human sequences. Northern blotting indicated ubiquitous but varied expressions of approximately 1.4 and 2.8kb mRNAs in various tissues. Immunoblotting indicated that the amounts of protein of about 38kDa were higher in the brain and testis than in other tissues. An additional protein of about 53kDa was found in the brain and testis. Germ cell-deficient W/W(v) mutant mice and aged mice had the reduced amounts of JKTBP in the testes. Immunohistochemical staining indicated cell type-specific expression of JKTBP in tissues: neurons and spermatocytes displayed strong signal intensities. The signals were confined to the nucleus. The amount of 38kDa JKTBP was estimated to be approximately 1.3x10(7) molecules per HL-60 cell. These results indicate that JKTBP is an abundant, highly conserved nuclear protein.
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Affiliation(s)
- T Akagi
- Graduate School of Integrated Science, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Japan
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