1
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Dupont M, Krischuns T, Gianetto QG, Paisant S, Bonazza S, Brault JB, Douché T, Arragain B, Florez-Prada A, Perez-Perri J, Hentze M, Cusack S, Matondo M, Isel C, Courtney D, Naffakh N. The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication. Nucleic Acids Res 2024; 52:7188-7210. [PMID: 38686810 PMCID: PMC11229366 DOI: 10.1093/nar/gkae291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Genome-wide approaches have significantly advanced our knowledge of the repertoire of RNA-binding proteins (RBPs) that associate with cellular polyadenylated mRNAs within eukaryotic cells. Recent studies focusing on the RBP interactomes of viral mRNAs, notably SARS-Cov-2, have revealed both similarities and differences between the RBP profiles of viral and cellular mRNAs. However, the RBPome of influenza virus mRNAs remains unexplored. Herein, we identify RBPs that associate with the viral mRNA encoding the nucleoprotein (NP) of an influenza A virus. Focusing on TDP-43, we show that it binds several influenza mRNAs beyond the NP-mRNA, and that its depletion results in lower levels of viral mRNAs and proteins within infected cells, and a decreased yield of infectious viral particles. We provide evidence that the viral polymerase recruits TDP-43 onto viral mRNAs through a direct interaction with the disordered C-terminal domain of TDP-43. Notably, other RBPs found to be associated with influenza virus mRNAs also interact with the viral polymerase, which points to a role of the polymerase in orchestrating the assembly of viral messenger ribonucleoproteins.
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Affiliation(s)
- Maud Dupont
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Stefano Bonazza
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Jean-Baptiste Brault
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Benoît Arragain
- European Molecular Biology Laboratory, 38042Grenoble, France
| | | | | | | | - Stephen Cusack
- European Molecular Biology Laboratory, 38042Grenoble, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - David G Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
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2
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Bernabéu-Herrero ME, Patel D, Bielowka A, Zhu J, Jain K, Mackay IS, Chaves Guerrero P, Emanuelli G, Jovine L, Noseda M, Marciniak SJ, Aldred MA, Shovlin CL. Mutations causing premature termination codons discriminate and generate cellular and clinical variability in HHT. Blood 2024; 143:2314-2331. [PMID: 38457357 PMCID: PMC11181359 DOI: 10.1182/blood.2023021777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 03/10/2024] Open
Abstract
ABSTRACT For monogenic diseases caused by pathogenic loss-of-function DNA variants, attention focuses on dysregulated gene-specific pathways, usually considering molecular subtypes together within causal genes. To better understand phenotypic variability in hereditary hemorrhagic telangiectasia (HHT), we subcategorized pathogenic DNA variants in ENG/endoglin, ACVRL1/ALK1, and SMAD4 if they generated premature termination codons (PTCs) subject to nonsense-mediated decay. In 3 patient cohorts, a PTC-based classification system explained some previously puzzling hemorrhage variability. In blood outgrowth endothelial cells (BOECs) derived from patients with ACVRL1+/PTC, ENG+/PTC, and SMAD4+/PTC genotypes, PTC-containing RNA transcripts persisted at low levels (8%-23% expected, varying between replicate cultures); genes differentially expressed to Bonferroni P < .05 in HHT+/PTC BOECs clustered significantly only to generic protein terms (isopeptide-bond/ubiquitin-like conjugation) and pulse-chase experiments detected subtle protein maturation differences but no evidence for PTC-truncated protein. BOECs displaying highest PTC persistence were discriminated in unsupervised hierarchical clustering of near-invariant housekeeper genes, with patterns compatible with higher cellular stress in BOECs with >11% PTC persistence. To test directionality, we used a HeLa reporter system to detect induction of activating transcription factor 4 (ATF4), which controls expression of stress-adaptive genes, and showed that ENG Q436X but not ENG R93X directly induced ATF4. AlphaFold accurately modeled relevant ENG domains, with AlphaMissense suggesting that readthrough substitutions would be benign for ENG R93X and other less rare ENG nonsense variants but more damaging for Q436X. We conclude that PTCs should be distinguished from other loss-of-function variants, PTC transcript levels increase in stressed cells, and readthrough proteins and mechanisms provide promising research avenues.
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Affiliation(s)
- Maria E. Bernabéu-Herrero
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Dilipkumar Patel
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Adrianna Bielowka
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - JiaYi Zhu
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Kinshuk Jain
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Ian S. Mackay
- Ear, Nose and Throat Surgery, Charing Cross and Royal Brompton Hospitals, London, United Kingdom
| | | | - Giulia Emanuelli
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Stefan J. Marciniak
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Micheala A. Aldred
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Claire L. Shovlin
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
- Specialist Medicine, Imperial College Healthcare NHS Trust, London, United Kingdom
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3
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Kern C, Radon C, Wende W, Leitner A, Sträßer K. Cross-linking mass spectrometric analysis of the endogenous TREX complex from Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2023; 29:1870-1880. [PMID: 37699651 PMCID: PMC10653388 DOI: 10.1261/rna.079758.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023]
Abstract
The conserved TREX complex has multiple functions in gene expression such as transcription elongation, 3' end processing, mRNP assembly and nuclear mRNA export as well as the maintenance of genomic stability. In Saccharomyces cerevisiae, TREX is composed of the pentameric THO complex, the DEAD-box RNA helicase Sub2, the nuclear mRNA export adaptor Yra1, and the SR-like proteins Gbp2 and Hrb1. Here, we present the structural analysis of the endogenous TREX complex of S. cerevisiae purified from its native environment. To this end, we used cross-linking mass spectrometry to gain structural information on regions of the complex that are not accessible to classical structural biology techniques. We also used negative-stain electron microscopy to investigate the organization of the cross-linked complex used for XL-MS by comparing our endogenous TREX complex with recently published structural models of recombinant THO-Sub2 complexes. According to our analysis, the endogenous yeast TREX complex preferentially assembles into a dimer.
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Affiliation(s)
- Carina Kern
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Christin Radon
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Wolfgang Wende
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
- Cardio-Pulmonary Institute (CPI), EXC 2026, 35392 Giessen, Germany
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4
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Asada R, Dominguez A, Montpetit B. Single-molecule quantitation of RNA-binding protein occupancy and stoichiometry defines a role for Yra1 (Aly/REF) in nuclear mRNP organization. Cell Rep 2023; 42:113415. [PMID: 37963019 PMCID: PMC10841842 DOI: 10.1016/j.celrep.2023.113415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/09/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
RNA-binding proteins (RBPs) interact with mRNA to form supramolecular complexes called messenger ribonucleoprotein (mRNP) particles. These dynamic assemblies direct and regulate individual steps of gene expression; however, their composition and functional importance remain largely unknown. Here, we develop a total internal reflection fluorescence-based single-molecule imaging assay to investigate stoichiometry and co-occupancy of 15 RBPs within mRNPs from Saccharomyces cerevisiae. We show compositional heterogeneity of single mRNPs and plasticity across different growth conditions, with major co-occupants of mRNPs containing the nuclear cap-binding complex identified as Yra1 (1-10 copies), Nab2 (1-6 copies), and Npl3 (1-6 copies). Multicopy Yra1-bound mRNPs are specifically co-occupied by the THO complex and assembled on mRNAs biased by transcript length and RNA secondary structure. Yra1 depletion results in decreased compaction of nuclear mRNPs demonstrating a packaging function. Together, we provide a quantitative framework for gene- and condition-dependent RBP occupancy and stoichiometry in individual nuclear mRNPs.
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Affiliation(s)
- Ryuta Asada
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Andrew Dominguez
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA.
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5
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Xie Y, Gao S, Zhang K, Bhat P, Clarke BP, Batten K, Mei M, Gazzara M, Shay JW, Lynch KW, Angelos AE, Hill PS, Ivey AL, Fontoura BMA, Ren Y. Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly. Cell Rep 2023; 42:112988. [PMID: 37578863 PMCID: PMC10508174 DOI: 10.1016/j.celrep.2023.112988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/10/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
mRNA in eukaryotic cells is packaged into highly compacted ribonucleoprotein particles (mRNPs) in the nucleus and exported to the cytoplasm for translation. mRNP packaging and export require the evolutionarily conserved transcription-export (TREX) complex. TREX facilitates loading of various RNA-binding proteins on mRNA through the action of its DDX39B subunit. SARNP (Tho1 [transcriptional defect of Hpr1 by overexpression 1] in yeast) is shown to interact with DDX39B and affect mRNA export. The molecular mechanism of how SARNP recognizes DDX39B and functions in mRNP assembly is unclear. Here, we determine the crystal structure of a Tho1/DDX39B/RNA complex, revealing a multivalent interaction mediated by tandem DDX39B interacting motifs in SARNP/Tho1. The high-order complex of SARNP and DDX39B is evolutionarily conserved, and human SARNP can engage with five DDX39B molecules. RNA sequencing (RNA-seq) from SARNP knockdown cells shows the most affected RNAs in export are GC rich. Our work suggests the role of the high-order SARNP/DDX39B/RNA complex in mRNP assembly and export.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Menghan Mei
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexia E Angelos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Pate S Hill
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Austin L Ivey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA.
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
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6
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Kurshakova MM, Georgieva SG, Kopytova DV. The Xmas-2 Protein of Drosophila melanogaster Undergoes Cleavage into Two Fragments. DOKL BIOCHEM BIOPHYS 2023; 509:37-40. [PMID: 37340289 DOI: 10.1134/s1607672923700163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 06/22/2023]
Abstract
The TREX-2 complex integrates several stages of gene expression, such as transcriptional activation and mRNA export. In D. melanogaster, TREX-2 consists of four major proteins: Xmas-2, ENY2, PCID2, and Sem1p. The Xmas-2 protein is the core subunit of the complex, with which other TREX-2 subunits interact. Xmas-2 homologues were found in all higher eukaryotes. Previously, it was shown that the human Xmas-2 homologue, GANP protein, can undergo cleavage into two parts, probably during apoptosis. We showed that the Xmas-2 protein of D. melanogaster can also split into two fragments. The resulting fragments of the protein correspond to the two large Xmas-2 domains. Protein splitting is observed both in vivo and in vitro. However, Xmas-2 cleavage in D. melanogaster is observed under normal conditions and is probably a part of the mechanism of transcription and mRNA export regulation in D. melanogaster.
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Affiliation(s)
- M M Kurshakova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - S G Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D V Kopytova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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7
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Keil P, Wulf A, Kachariya N, Reuscher S, Hühn K, Silbern I, Altmüller J, Keller M, Stehle R, Zarnack K, Sattler M, Urlaub H, Sträßer K. Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA. Nucleic Acids Res 2022; 51:831-851. [PMID: 36583366 PMCID: PMC9881175 DOI: 10.1093/nar/gkac1206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/25/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate multiple functions at once and likely impact the structural integrity of the large ribonucleoprotein particles (RNPs) these proteins function in. Using UV-induced RNA-protein crosslinking of entire cells, protein complex purification and mass spectrometric analysis, we identified >100 in vivo RNA crosslinks in 16 nuclear mRNP components in Saccharomyces cerevisiae. For functional analysis, we chose Npl3, which displayed crosslinks in its two RNA recognition motifs (RRMs) and in the connecting flexible linker region. Both RRM domains and the linker uniquely contribute to RNA recognition as revealed by NMR and structural analyses. Interestingly, mutations in these regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains. Notably, an npl3-Linker mutation strongly impairs recruitment of several mRNP components to chromatin and incorporation of other mRNP components into nuclear mRNPs, establishing a so far unknown function of Npl3 in nuclear mRNP assembly. Taken together, our integrative analysis uncovers a specific function of the RNA-binding activity of the nuclear mRNP component Npl3. This approach can be readily applied to RBPs in any RNA metabolic process.
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Affiliation(s)
| | | | | | - Samira Reuscher
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany
| | - Kristin Hühn
- Institute of Biochemistry, FB08, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Ivan Silbern
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Goettingen, University Medical Center Goettingen, Institute of Clinical Chemistry, Robert-Koch-Strasse 40, 37075 Goettingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931 Cologne, Germany,Technology platform genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Mario Keller
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany
| | - Ralf Stehle
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany,Institute of Structural Biology, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt a.M., Germany,Cardio-Pulmonary Institute (CPI), EXC 2026, 35392 Giessen, Germany
| | | | | | - Katja Sträßer
- To whom correspondence should be addressed. Tel: +49 641 99 35400; Fax: +49 641 99 35409;
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8
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Bensidoun P, Reiter T, Montpetit B, Zenklusen D, Oeffinger M. Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast. Mol Cell 2022; 82:3856-3871.e6. [PMID: 36220102 PMCID: PMC10300651 DOI: 10.1016/j.molcel.2022.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/24/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022]
Abstract
To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that basket formation is dependent on RNA polymerase II transcription and subsequent mRNP processing. We further show that while all NPCs can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing NPCs associate a distinct protein and RNA interactome. Taken together, our data point toward NPC heterogeneity and an RNA-dependent mechanism for functionalization of NPCs in budding yeast through nuclear basket assembly.
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Affiliation(s)
- Pierre Bensidoun
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Taylor Reiter
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Daniel Zenklusen
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada.
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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9
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Abstract
RNA-binding proteins (RBPs) are of fundamental importance for post-transcriptional gene regulation and protein synthesis. They are required for pre-mRNA processing and for RNA transport, degradation and translation into protein, and can regulate every step in the life cycle of their RNA targets. In addition, RBP function can be modulated by RNA binding. RBPs also participate in the formation of ribonucleoprotein complexes that build up macromolecular machineries such as the ribosome and spliceosome. Although most research has focused on mRNA-binding proteins, non-coding RNAs are also regulated and sequestered by RBPs. Functional defects and changes in the expression levels of RBPs have been implicated in numerous diseases, including neurological disorders, muscular atrophy and cancers. RBPs also contribute to a wide spectrum of kidney disorders. For example, human antigen R has been reported to have a renoprotective function in acute kidney injury (AKI) but might also contribute to the development of glomerulosclerosis, tubulointerstitial fibrosis and diabetic kidney disease (DKD), loss of bicaudal C is associated with cystic kidney diseases and Y-box binding protein 1 has been implicated in the pathogenesis of AKI, DKD and glomerular disorders. Increasing data suggest that the modulation of RBPs and their interactions with RNA targets could be promising therapeutic strategies for kidney diseases.
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10
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Banerjee P, Markande S, Kalarikkal M, Joseph J. SUMOylation modulates the function of DDX19 in mRNA export. J Cell Sci 2022; 135:274424. [PMID: 35080244 DOI: 10.1242/jcs.259449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
Abstract
Nuclear export of mRNAs is a critical regulatory step in eukaryotic gene expression. The mRNA transcript undergoes extensive processing, and is loaded with a set of RNA-binding proteins (RBPs) to form export-competent messenger ribonucleoprotein particles (mRNPs) in the nucleus. During the transit of mRNPs through the nuclear pore complex (NPC), the DEAD-box ATPase - DDX19 - remodels mRNPs at the cytoplasmic side of the NPC, by removing a subset of RNA-binding proteins to terminate mRNP export. This requires the RNA-dependent ATPase activity of DDX19 and its dynamic interactions with Gle1 and Nup214. However, the regulatory mechanisms underlying these interactions are unclear. We find that DDX19 gets covalently attached with a small ubiquitin-like modifier (SUMO) at lysine 26, which enhances its interaction with Gle1. Furthermore, a SUMOylation-defective mutant of human DDX19B, K26R, failed to provide a complete rescue of the mRNA export defect caused by DDX19 depletion. Collectively, our results suggest that SUMOylation fine-tunes the function of DDX19 in mRNA export by regulating its interaction with Gle1. This study identifies SUMOylation of DDX19 as a modulatory mechanism during the mRNA export process.
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Affiliation(s)
- Poulomi Banerjee
- National Centre for Cell Science, S. P. Pune University Campus, Pune - 411007, Maharashtra State, India
| | - Shubha Markande
- National Centre for Cell Science, S. P. Pune University Campus, Pune - 411007, Maharashtra State, India
| | - Misha Kalarikkal
- National Centre for Cell Science, S. P. Pune University Campus, Pune - 411007, Maharashtra State, India
| | - Jomon Joseph
- National Centre for Cell Science, S. P. Pune University Campus, Pune - 411007, Maharashtra State, India
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11
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Qin T, Cheng Y, Wang X. RNA-binding proteins as drivers of AML and novel therapeutic targets. Leuk Lymphoma 2022; 63:1045-1057. [PMID: 35075986 DOI: 10.1080/10428194.2021.2008381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Acute myeloid leukemia (AML) is a group of genetically complex and heterogeneous invasive hematological malignancies with a low 5-year overall survival rate of 30%, which highlights the urgent need for improved treatment measures. RNA-binding proteins (RBPs) regulate the abundance of isoforms of related proteins by regulating RNA splicing, translation, stability, and localization, thereby affecting cell differentiation and self-renewal. It is increasingly believed that RBPs are essential for normal hematopoiesis, and RBPs play a key role in hematological tumors, especially AML, by acting as oncogenes or tumor suppressors. In addition, targeting an RBP that is significantly related to AML can trigger the apoptosis of leukemic stem cells or promote the proliferation of stem and progenitor cells by modulating the expression of important pathway regulatory factors such as HOXA9, MYC, and CDKN1A. Accordingly, RBPs involved in normal myeloid differentiation and the occurrence of AML may represent promising therapeutic targets.
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Affiliation(s)
- Tingyu Qin
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ying Cheng
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaozhong Wang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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12
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Sun R, Pan Y, Mu L, Ma Y, Shen H, Long Y. Development of a 3 RNA Binding Protein Signature for Predicting Prognosis and Treatment Response for Glioblastoma Multiforme. Front Genet 2021; 12:768930. [PMID: 34733320 PMCID: PMC8558313 DOI: 10.3389/fgene.2021.768930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose: Glioblastoma multiforme (GBM) is the most widely occurring brain malignancy. It is modulated by a variety of genes, and patients with GBM have a low survival ratio and an unsatisfactory treatment effect. The irregular regulation of RNA binding proteins (RBPs) is implicated in several malignant neoplasms and reported to exhibit an association with the occurrence and development of carcinoma. Thus, it is necessary to build a stable, multi-RBPs signature-originated model for GBM prognosis and treatment response prediction. Methods: Differentially expressed RBPs (DERBPs) were screened out based on the RBPs data of GBM and normal brain tissues from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression Program (GTEx) datasets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses on DERBPs were performed, followed by an analysis of the Protein-Protein Interaction network. Survival analysis of the DERBPs was conducted by univariate and multivariate Cox regression. Then, a risk score model was created on the basis of the gene signatures in various survival-associated RBPs, and its prognostic and predictive values were evaluated through Kaplan-Meier analysis and log-rank test. A nomogram on the basis of the hub RBPs signature was applied to estimate GBM patients’ survival rates. Moreover, western blot was for the detection of the proteins. Results: BICC1, GNL3L, and KHDRBS2 were considered as prognosis-associated hub RBPs and then were applied in the construction of a prognostic model. Poor survival results appeared in GBM patients with a high-risk score. The area under the time-dependent ROC curve of the prognostic model was 0.723 in TCGA and 0.707 in Chinese Glioma Genome Atlas (CGGA) cohorts, indicating a good prognostic model. What was more, the survival duration of the high-risk group receiving radiotherapy or temozolomide chemotherapy was shorter than that of the low-risk group. The nomogram showed a great discriminating capacity for GBM, and western blot experiments demonstrated that the proteins of these 3 RBPs had different expressions in GBM cells. Conclusion: The identified 3 hub RBPs-derived risk score is effective in the prediction of GBM prognosis and treatment response, and benefits to the treatment of GBM patients.
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Affiliation(s)
- Ruohan Sun
- Department of Neurology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yujun Pan
- Department of Neurology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Long Mu
- Department of Neurosurgery, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yaguang Ma
- Department of Neurosurgery, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hong Shen
- Department of Neurosurgery, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Long
- Department of Neurosurgery, the First Affiliated Hospital of Harbin Medical University, Harbin, China
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13
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Lu YY, Krebber H. Nuclear mRNA Quality Control and Cytoplasmic NMD Are Linked by the Guard Proteins Gbp2 and Hrb1. Int J Mol Sci 2021; 22:ijms222011275. [PMID: 34681934 PMCID: PMC8541090 DOI: 10.3390/ijms222011275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/13/2021] [Accepted: 10/17/2021] [Indexed: 12/23/2022] Open
Abstract
Pre-mRNA splicing is critical for cells, as defects in this process can lead to altered open reading frames and defective proteins, potentially causing neurodegenerative diseases and cancer. Introns are removed in the nucleus and splicing is documented by the addition of exon-junction-complexes (EJCs) at exon-exon boundaries. This “memory” of splicing events is important for the ribosome, which translates the RNAs in the cytoplasm. In case a stop codon was detected before an EJC, translation is blocked and the RNA is eliminated by the nonsense-mediated decay (NMD). In the model organism Saccharomyces cerevisiae, two guard proteins, Gbp2 and Hrb1, have been identified as nuclear quality control factors for splicing. In their absence, intron-containing mRNAs leak into the cytoplasm. Their presence retains transcripts until the process is completed and they release the mRNAs by recruitment of the export factor Mex67. On transcripts that experience splicing problems, these guard proteins recruit the nuclear RNA degradation machinery. Interestingly, they continue their quality control function on exported transcripts. They support NMD by inhibiting translation and recruiting the cytoplasmic degradation factors. In this way, they link the nuclear and cytoplasmic quality control systems. These discoveries are also intriguing for humans, as homologues of these guard proteins are present also in multicellular organisms. Here, we provide an overview of the quality control mechanisms of pre-mRNA splicing, and present Gbp2 and Hrb1, as well as their human counterparts, as important players in these pathways.
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14
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Basyuk E, Rage F, Bertrand E. RNA transport from transcription to localized translation: a single molecule perspective. RNA Biol 2021; 18:1221-1237. [PMID: 33111627 PMCID: PMC8354613 DOI: 10.1080/15476286.2020.1842631] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transport of mRNAs is an important step of gene expression, which brings the genetic message from the DNA in the nucleus to a precise cytoplasmic location in a regulated fashion. Perturbation of this process can lead to pathologies such as developmental and neurological disorders. In this review, we discuss recent advances in the field of mRNA transport made using single molecule fluorescent imaging approaches. We present an overview of these approaches in fixed and live cells and their input in understanding the key steps of mRNA journey: transport across the nucleoplasm, export through the nuclear pores and delivery to its final cytoplasmic location. This review puts a particular emphasis on the coupling of mRNA transport with translation, such as localization-dependent translational regulation and translation-dependent mRNA localization. We also highlight the recently discovered translation factories, and how cellular and viral RNAs can hijack membrane transport systems to travel in the cytoplasm.
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Affiliation(s)
- Eugenia Basyuk
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS-UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Florence Rage
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
- Equipe Labélisée Ligue Nationale Contre Le Cancer, Montpellier, France
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15
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Bensidoun P, Zenklusen D, Oeffinger M. Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1660. [PMID: 33938148 DOI: 10.1002/wrna.1660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022]
Abstract
The nuclear pore complex (NPC) serves as a central gate for mRNAs to transit from the nucleus to the cytoplasm. The ability for mRNAs to get exported is linked to various upstream nuclear processes including co-transcriptional RNP assembly and processing, and only export competent mRNPs are thought to get access to the NPC. While the nuclear pore is generally viewed as a monolithic structure that serves as a mediator of transport driven by transport receptors, more recent evidence suggests that the NPC might be more heterogenous than previously believed, both in its composition or in the selective treatment of cargo that seek access to the pore, providing functional plasticity to mRNA export. In this review, we consider the interconnected processes of nuclear mRNA metabolism that contribute and mediate export competence. Furthermore, we examine different aspects of NPC heterogeneity, including the role of the nuclear basket and its associated complexes in regulating selective and/or efficient binding to and transport through the pore. This article is categorized under: RNA Export and Localization > Nuclear Export/Import RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Pierre Bensidoun
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Marlene Oeffinger
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada
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16
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Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export.
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17
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Guha S, Bhaumik SR. Viral regulation of mRNA export with potentials for targeted therapy. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194655. [PMID: 33246183 DOI: 10.1016/j.bbagrm.2020.194655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Eukaryotic gene expression begins with transcription in the nucleus to synthesize mRNA (messenger RNA), which is subsequently exported to the cytoplasm for translation to protein. Like transcription and translation, mRNA export is an important regulatory step of eukaryotic gene expression. Various factors are involved in regulating mRNA export, and thus gene expression. Intriguingly, some of these factors interact with viral proteins, and such interactions interfere with mRNA export of the host cell, favoring viral RNA export. Hence, viruses hijack host mRNA export machinery for export of their own RNAs from nucleus to cytoplasm for translation to proteins for viral life cycle, suppressing host mRNA export (and thus host gene expression and immune/antiviral response). Therefore, the molecules that can impair the interactions of these mRNA export factors with viral proteins could emerge as antiviral therapeutic agents to suppress viral RNA transport and enhance host mRNA export, thereby promoting host gene expression and immune response. Thus, there has been a number of studies to understand how virus hijacks mRNA export machinery in suppressing host gene expression and promoting its own RNA export to the cytoplasm for translation to proteins required for viral replication/assembly/life cycle towards developing targeted antiviral therapies, as concisely described here.
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Affiliation(s)
- Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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18
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Eyboulet F, Jeronimo C, Côté J, Robert F. The deubiquitylase Ubp15 couples transcription to mRNA export. eLife 2020; 9:e61264. [PMID: 33226341 PMCID: PMC7682988 DOI: 10.7554/elife.61264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
Nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed, and exported. The role of ubiquitylation in this process is increasingly recognized but, while a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here we identified deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts with both RNA polymerase II and the nuclear pore complex, and its deletion reverts the nuclear export defect of E3 ligase Rsp5 mutants. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.
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Affiliation(s)
- Fanny Eyboulet
- Institut de recherches cliniques de MontréalMontréalCanada
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - Célia Jeronimo
- Institut de recherches cliniques de MontréalMontréalCanada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - François Robert
- Institut de recherches cliniques de MontréalMontréalCanada
- Département de Médecine, Faculté de Médecine, Université de MontréalMontréalCanada
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19
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Schuller SK, Schuller JM, Prabu JR, Baumgärtner M, Bonneau F, Basquin J, Conti E. Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex. eLife 2020; 9:e61467. [PMID: 33191913 PMCID: PMC7744097 DOI: 10.7554/elife.61467] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/13/2020] [Indexed: 12/15/2022] Open
Abstract
The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containing structures. How THO-containing complexes function at the mechanistic level is unclear. Here, we elucidated a 3.4 Å resolution structure of Saccharomyces cerevisiae THO-Sub2 by cryo-electron microscopy. THO subunits Tho2 and Hpr1 intertwine to form a platform that is bound by Mft1, Thp2, and Tex1. The resulting complex homodimerizes in an asymmetric fashion, with a Sub2 molecule attached to each protomer. The homodimerization interfaces serve as a fulcrum for a seesaw-like movement concomitant with conformational changes of the Sub2 ATPase. The overall structural architecture and topology suggest the molecular mechanisms of nucleic acid remodeling during mRNA biogenesis.
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Affiliation(s)
- Sandra K Schuller
- Department of Structural Cell Biology, Max Planck Institute of BiochemistryMunichGermany
| | - Jan M Schuller
- Department of Structural Cell Biology, Max Planck Institute of BiochemistryMunichGermany
| | - J Rajan Prabu
- Department of Structural Cell Biology, Max Planck Institute of BiochemistryMunichGermany
| | - Marc Baumgärtner
- Department of Structural Cell Biology, Max Planck Institute of BiochemistryMunichGermany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of BiochemistryMunichGermany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of BiochemistryMunichGermany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of BiochemistryMunichGermany
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20
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Vasianovich Y, Bajon E, Wellinger RJ. Telomerase biogenesis requires a novel Mex67 function and a cytoplasmic association with the Sm 7 complex. eLife 2020; 9:60000. [PMID: 33095156 PMCID: PMC7644208 DOI: 10.7554/elife.60000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/22/2020] [Indexed: 12/15/2022] Open
Abstract
The templating RNA is the core of the telomerase reverse transcriptase. In Saccharomyces cerevisiae, the complex life cycle and maturation of telomerase includes a cytoplasmic stage. However, timing and reason for this cytoplasmic passage are poorly understood. Here, we use inducible RNA tagging experiments to show that immediately after transcription, newly synthesized telomerase RNAs undergo one round of nucleo-cytoplasmic shuttling. Their export depends entirely on Crm1/Xpo1, whereas re-import is mediated by Kap122 plus redundant, kinetically less efficient import pathways. Strikingly, Mex67 is essential to stabilize newly transcribed RNA before Xpo1-mediated nuclear export. The results further show that the Sm7 complex associates with and stabilizes the telomerase RNA in the cytoplasm and promotes its nuclear re-import. Remarkably, after this cytoplasmic passage, the nuclear stability of telomerase RNA no longer depends on Mex67. These results underscore the utility of inducible RNA tagging and challenge current models of telomerase maturation.
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Affiliation(s)
- Yulia Vasianovich
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Emmanuel Bajon
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
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21
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Zarnack K, Balasubramanian S, Gantier MP, Kunetsky V, Kracht M, Schmitz ML, Sträßer K. Dynamic mRNP Remodeling in Response to Internal and External Stimuli. Biomolecules 2020; 10:biom10091310. [PMID: 32932892 PMCID: PMC7565591 DOI: 10.3390/biom10091310] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Signal transduction and the regulation of gene expression are fundamental processes in every cell. RNA-binding proteins (RBPs) play a key role in the post-transcriptional modulation of gene expression in response to both internal and external stimuli. However, how signaling pathways regulate the assembly of RBPs with mRNAs remains largely unknown. Here, we summarize observations showing that the formation and composition of messenger ribonucleoprotein particles (mRNPs) is dynamically remodeled in space and time by specific signaling cascades and the resulting post-translational modifications. The integration of signaling events with gene expression is key to the rapid adaptation of cells to environmental changes and stress. Only a combined approach analyzing the signal transduction pathways and the changes in post-transcriptional gene expression they cause will unravel the mechanisms coordinating these important cellular processes.
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Affiliation(s)
- Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt a.M., Germany;
| | | | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia;
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Vladislav Kunetsky
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
- Correspondence:
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