1
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Filippopoulou C, Thomé CC, Perdikari S, Ntini E, Simos G, Bohnsack KE, Chachami G. Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile. Cell Mol Life Sci 2024; 81:58. [PMID: 38279024 PMCID: PMC10817850 DOI: 10.1007/s00018-023-05035-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 01/28/2024]
Abstract
Reduced oxygen availability (hypoxia) triggers adaptive cellular responses via hypoxia-inducible factor (HIF)-dependent transcriptional activation. Adaptation to hypoxia also involves transcription-independent processes like post-translational modifications; however, these mechanisms are poorly characterized. Investigating the involvement of protein SUMOylation in response to hypoxia, we discovered that hypoxia strongly decreases the SUMOylation of Exosome subunit 10 (EXOSC10), the catalytic subunit of the RNA exosome, in an HIF-independent manner. EXOSC10 is a multifunctional exoribonuclease enriched in the nucleolus that mediates the processing and degradation of various RNA species. We demonstrate that the ubiquitin-specific protease 36 (USP36) SUMOylates EXOSC10 and we reveal SUMO1/sentrin-specific peptidase 3 (SENP3) as the enzyme-mediating deSUMOylation of EXOSC10. Under hypoxia, EXOSC10 dissociates from USP36 and translocates from the nucleolus to the nucleoplasm concomitant with its deSUMOylation. Loss of EXOSC10 SUMOylation does not detectably affect rRNA maturation but affects the mRNA transcriptome by modulating the expression levels of hypoxia-related genes. Our data suggest that dynamic modulation of EXOSC10 SUMOylation and localization under hypoxia regulates the RNA degradation machinery to facilitate cellular adaptation to low oxygen conditions.
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Affiliation(s)
- Chrysa Filippopoulou
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Chairini C Thomé
- Department of Molecular Biology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Sofia Perdikari
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (FORTH), 70013, Heraklion, Greece
| | - Evgenia Ntini
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (FORTH), 70013, Heraklion, Greece
| | - George Simos
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, 41500, Larissa, Greece
- Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, Canada
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Georgia Chachami
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, 41500, Larissa, Greece.
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2
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 12/14/2022] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea,Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea,Corresponding author. Tel: +82-53-950-6352; Fax: +82-53-955-5522; E-mail:
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3
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707 DOI: 10.5483/bmbrep.2022.55.11.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2023] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea
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4
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Yasuhara T, Xing YH, Bauer NC, Lee L, Dong R, Yadav T, Soberman RJ, Rivera MN, Zou L. Condensates induced by transcription inhibition localize active chromatin to nucleoli. Mol Cell 2022; 82:2738-2753.e6. [PMID: 35662392 PMCID: PMC9357099 DOI: 10.1016/j.molcel.2022.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/25/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
The proper function of the genome relies on spatial organization of DNA, RNA, and proteins, but how transcription contributes to the organization is unclear. Here, we show that condensates induced by transcription inhibition (CITIs) drastically alter genome spatial organization. CITIs are formed by SFPQ, NONO, FUS, and TAF15 in nucleoli upon inhibition of RNA polymerase II (RNAPII). Mechanistically, RNAPII inhibition perturbs ribosomal RNA (rRNA) processing, releases rRNA-processing factors from nucleoli, and enables SFPQ to bind rRNA. While accumulating in CITIs, SFPQ/TAF15 remain associated with active genes and tether active chromatin to nucleoli. In the presence of DNA double-strand breaks (DSBs), the altered chromatin compartmentalization induced by RNAPII inhibition increases gene fusions in CITIs and stimulates the formation of fusion oncogenes. Thus, proper RNAPII transcription and rRNA processing prevent the altered compartmentalization of active chromatin in CITIs, suppressing the generation of gene fusions from DSBs.
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Affiliation(s)
- Takaaki Yasuhara
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, the University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yu-Hang Xing
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Nicholas C Bauer
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lukuo Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Rui Dong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Roy J Soberman
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Miguel N Rivera
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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5
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Petit FG, Jamin SP, Kernanec PY, Becker E, Halet G, Primig M. EXOSC10/Rrp6 is essential for the eight-cell embryo/morula transition. Dev Biol 2021; 483:58-65. [PMID: 34965385 DOI: 10.1016/j.ydbio.2021.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 11/03/2022]
Abstract
The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 is required for gametogenesis, brain development, erythropoiesis and blood cell enhancer function. The human ortholog is essential for mitosis in cultured cancer cells. Little is known, however, about the role of Exosc10 during embryo development and organogenesis. We generated an Exosc10 knockout model and find that Exosc10-/- mice show an embryonic lethal phenotype. We demonstrate that Exosc10 maternal wild type mRNA is present in mutant oocytes and that the gene is expressed during all stages of early embryogenesis. Furthermore, we observe that EXOSC10 early on localizes to the periphery of nucleolus precursor bodies in blastomeres, which is in keeping with the protein's role in rRNA processing and may indicate a function in the establishment of chromatin domains during initial stages of embryogenesis. Finally, we infer from genotyping data for embryonic days e7.5, e6.5 and e4.5 and embryos cultured in vitro that Exosc10-/- mutants arrest at the eight-cell embryo/morula transition. Our results demonstrate a novel essential role for Exosc10 during early embryogenesis, and they are consistent with earlier work showing that impaired ribosome biogenesis causes a developmental arrest at the morula stage.
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Affiliation(s)
- Fabrice G Petit
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France.
| | - Soazik P Jamin
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Pierre-Yves Kernanec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | | | - Guillaume Halet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France.
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6
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Peng T, Phasouk K, Sodroski CN, Sun S, Hwangbo Y, Layton ED, Jin L, Klock A, Diem K, Magaret AS, Jing L, Laing K, Li A, Huang ML, Mertens M, Johnston C, Jerome KR, Koelle DM, Wald A, Knipe DM, Corey L, Zhu J. Tissue-Resident-Memory CD8 + T Cells Bridge Innate Immune Responses in Neighboring Epithelial Cells to Control Human Genital Herpes. Front Immunol 2021; 12:735643. [PMID: 34552595 PMCID: PMC8450389 DOI: 10.3389/fimmu.2021.735643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/11/2021] [Indexed: 12/02/2022] Open
Abstract
Tissue-resident-memory T cells (TRM) populate the body's barrier surfaces, functioning as frontline responders against reencountered pathogens. Understanding of the mechanisms by which CD8TRM achieve effective immune protection remains incomplete in a naturally recurring human disease. Using laser capture microdissection and transcriptional profiling, we investigate the impact of CD8TRM on the tissue microenvironment in skin biopsies sequentially obtained from a clinical cohort of diverse disease expression during herpes simplex virus 2 (HSV-2) reactivation. Epithelial cells neighboring CD8TRM display elevated and widespread innate and cell-intrinsic antiviral signature expression, largely related to IFNG expression. Detailed evaluation via T-cell receptor reconstruction confirms that CD8TRM recognize viral-infected cells at the specific HSV-2 peptide/HLA level. The hierarchical pattern of core IFN-γ signature expression is well-conserved in normal human skin across various anatomic sites, while elevation of IFI16, TRIM 22, IFITM2, IFITM3, MX1, MX2, STAT1, IRF7, ISG15, IFI44, CXCL10 and CCL5 expression is associated with HSV-2-affected asymptomatic tissue. In primary human cells, IFN-γ pretreatment reduces gene transcription at the immediate-early stage of virus lifecycle, enhances IFI16 restriction of wild-type HSV-2 replication and renders favorable kinetics for host protection. Thus, the adaptive immune response through antigen-specific recognition instructs innate and cell-intrinsic antiviral machinery to control herpes reactivation, a reversal of the canonical thinking of innate activating adaptive immunity in primary infection. Communication from CD8TRM to surrounding epithelial cells to activate broad innate resistance might be critical in restraining various viral diseases.
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Affiliation(s)
- Tao Peng
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Khamsone Phasouk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Catherine N. Sodroski
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Sijie Sun
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Yon Hwangbo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Erik D. Layton
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Lei Jin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Alexis Klock
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Kurt Diem
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Amalia S. Magaret
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Lichen Jing
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Kerry Laing
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Alvason Li
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Max Mertens
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Christine Johnston
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - David M. Koelle
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
- Benaroya Research Institute, Seattle, WA, United States
| | - Anna Wald
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - David M. Knipe
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Lawrence Corey
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Jia Zhu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, United States
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7
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Stuparević I, Novačić A, Rahmouni AR, Fernandez A, Lamb N, Primig M. Regulation of the conserved 3'-5' exoribonuclease EXOSC10/Rrp6 during cell division, development and cancer. Biol Rev Camb Philos Soc 2021; 96:1092-1113. [PMID: 33599082 DOI: 10.1111/brv.12693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 processes and degrades RNA, regulates gene expression and participates in DNA double-strand break repair and control of telomere maintenance via degradation of the telomerase RNA component. EXOSC10/Rrp6 is part of the multimeric nuclear RNA exosome and interacts with numerous proteins. Previous clinical, genetic, biochemical and genomic studies revealed the protein's essential functions in cell division and differentiation, its RNA substrates and its relevance to autoimmune disorders and oncology. However, little is known about the regulatory mechanisms that control the transcription, translation and stability of EXOSC10/Rrp6 during cell growth, development and disease and how these mechanisms evolved from yeast to human. Herein, we provide an overview of the RNA- and protein expression profiles of EXOSC10/Rrp6 during cell division, development and nutritional stress, and we summarize interaction networks and post-translational modifications across species. Additionally, we discuss how known and predicted protein interactions and post-translational modifications influence the stability of EXOSC10/Rrp6. Finally, we explore the idea that different EXOSC10/Rrp6 alleles, which potentially alter cellular protein levels or affect protein function, might influence human development and disease progression. In this review we interpret information from the literature together with genomic data from knowledgebases to inspire future work on the regulation of this essential protein's stability in normal and malignant cells.
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Affiliation(s)
- Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - A Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR4301 du CNRS, Orléans, 45071, France
| | - Anne Fernandez
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Ned Lamb
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, 35000, France
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8
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Peretti D, Smith HL, Verity N, Humoud I, de Weerd L, Swinden DP, Hayes J, Mallucci GR. TrkB signaling regulates the cold-shock protein RBM3-mediated neuroprotection. Life Sci Alliance 2021; 4:4/4/e202000884. [PMID: 33563652 PMCID: PMC7893816 DOI: 10.26508/lsa.202000884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 02/02/2023] Open
Abstract
Increasing levels of the cold-shock protein, RNA-binding motif 3 (RBM3), either through cooling or by ectopic over-expression, prevents synapse and neuronal loss in mouse models of neurodegeneration. To exploit this process therapeutically requires an understanding of mechanisms controlling cold-induced RBM3 expression. Here, we show that cooling increases RBM3 through activation of TrkB via PLCγ1 and pCREB signaling. RBM3, in turn, has a hitherto unrecognized negative feedback on TrkB-induced ERK activation through induction of its specific phosphatase, DUSP6. Thus, RBM3 mediates structural plasticity through a distinct, non-canonical activation of TrkB signaling, which is abolished in RBM3-null neurons. Both genetic reduction and pharmacological antagonism of TrkB and its downstream mediators abrogate cooling-induced RBM3 induction and prevent structural plasticity, whereas TrkB inhibition similarly prevents RBM3 induction and the neuroprotective effects of cooling in prion-diseased mice. Conversely, TrkB agonism induces RBM3 without cooling, preventing synapse loss and neurodegeneration. TrkB signaling is, therefore, necessary for the induction of RBM3 and related neuroprotective effects and provides a target by which RBM3-mediated synapse-regenerative therapies in neurodegenerative disorders can be used therapeutically without the need for inducing hypothermia.
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Affiliation(s)
- Diego Peretti
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Heather L Smith
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Nicholas Verity
- MRC Toxicology Unit at the University of Cambridge, Leicester, UK
| | - Ibrahim Humoud
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Lis de Weerd
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Dean P Swinden
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Joseph Hayes
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Giovanna R Mallucci
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
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9
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Ulmke PA, Xie Y, Sokpor G, Pham L, Shomroni O, Berulava T, Rosenbusch J, Basu U, Fischer A, Nguyen HP, Staiger JF, Tuoc T. Post-transcriptional regulation by the exosome complex is required for cell survival and forebrain development via repression of P53 signaling. Development 2021; 148:dev.188276. [PMID: 33462115 DOI: 10.1242/dev.188276] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
Fine-tuned gene expression is crucial for neurodevelopment. The gene expression program is tightly controlled at different levels, including RNA decay. N6-methyladenosine (m6A) methylation-mediated degradation of RNA is essential for brain development. However, m6A methylation impacts not only RNA stability, but also other RNA metabolism processes. How RNA decay contributes to brain development is largely unknown. Here, we show that Exosc10, a RNA exonuclease subunit of the RNA exosome complex, is indispensable for forebrain development. We report that cortical cells undergo overt apoptosis, culminating in cortical agenesis upon conditional deletion of Exosc10 in mouse cortex. Mechanistically, Exosc10 directly binds and degrades transcripts of the P53 signaling-related genes, such as Aen and Bbc3. Overall, our findings suggest a crucial role for Exosc10 in suppressing the P53 pathway, in which the rapid turnover of the apoptosis effectors Aen and Bbc3 mRNAs is essential for cell survival and normal cortical histogenesis.
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Affiliation(s)
- Pauline Antonie Ulmke
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Yuanbin Xie
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Gannan Medical University, 341000 Ganzhou, The People's Republic of China
| | - Godwin Sokpor
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Linh Pham
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Orr Shomroni
- Microarray and Deep-Sequencing Core Facility, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Tea Berulava
- German Center for Neurodegenerative Diseases, Goettingen 37075, Germany
| | - Joachim Rosenbusch
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Andre Fischer
- German Center for Neurodegenerative Diseases, Goettingen 37075, Germany.,Department for Psychiatry and Psychotherapy, University Medical Center, Georg-August-University Goettingen, Goettingen 37075, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen 37075, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Jochen F Staiger
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Tran Tuoc
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany .,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
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10
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Wermuth PJ, Jimenez SA. Molecular characteristics and functional differences of anti-PM/Scl autoantibodies and two other distinct and unique supramolecular structures known as "EXOSOMES". Autoimmun Rev 2020; 19:102644. [PMID: 32801042 DOI: 10.1016/j.autrev.2020.102644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023]
Abstract
The term "exosome" has been applied to three distinct supramolecular entities, namely the PM/Scl autoantibodies or "RNA exosomes", transforming DNA fragments termed "DNA exosomes", and small size extracellular vesicles knows as "exosomes". Some of the molecular components of the "PM/Scl exosome complex" or "RNA exosome" are recognized by specific autoantibodies present in the serum from some Systemic Sclerosis (SSc), polymyositis (PM) and polymyositis SSc (PM/Scl) overlap syndrome patients. On the other hand, one of the most active focuses of laboratory investigation in the last decade has been the biogenesis and role of extracellular vesicles known as "exosomes". The remarkable ability of these "exosome" vesicles to alter the cellular phenotype following fusion with target cells and the release of their macromolecular cargo has revealed a possible role in the pathogenesis of numerous diseases, including malignant, inflammatory, and autoimmune disorders and may allow them to serve as theranostic agents for personalized and precision medicine. The indiscriminate use of the term "exosome" to refer to these three distinct molecular entities has engendered great confusion in the scientific literature. Here, we review the molecular characteristics and functional differences between the three molecular structures identified as "exosomes". Given the rapidly growing scientific interest in extravesicular exosomes, unless a solution is found the confusion in the literature resulting from the use of the term "exosomes" will markedly increase.
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Affiliation(s)
- Peter J Wermuth
- Jefferson Institute of Molecular Medicine and Scleroderma Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Sergio A Jimenez
- Jefferson Institute of Molecular Medicine and Scleroderma Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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11
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Wu D, Dean J. EXOSC10 sculpts the transcriptome during the growth-to-maturation transition in mouse oocytes. Nucleic Acids Res 2020; 48:5349-5365. [PMID: 32313933 DOI: 10.1093/nar/gkaa249] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/28/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Growing mammalian oocytes accumulate substantial amounts of RNA, most of which is degraded during subsequent meiotic maturation. The growth-to-maturation transition begins with germinal vesicle or nuclear envelope breakdown (GVBD) and is critical for oocyte quality and early development. The molecular machinery responsible for the oocyte transcriptome transition remains unclear. Here, we report that an exosome-associated RNase, EXOSC10, sculpts the transcriptome to facilitate the growth-to-maturation transition of mouse oocytes. We establish an oocyte-specific conditional knockout of Exosc10 in mice using CRISPR/Cas9 which results in female subfertility due to delayed GVBD. By performing multiple single oocyte RNA-seq, we document dysregulation of several types of RNA, and the mRNAs that encode proteins important for endomembrane trafficking and meiotic cell cycle. As expected, EXOSC10-depleted oocytes have impaired endomembrane components including endosomes, lysosomes, endoplasmic reticulum and Golgi. In addition, CDK1 fails to activate, possibly due to persistent WEE1 activity, which blocks lamina phosphorylation and disassembly. Moreover, we identified rRNA processing defects that cause higher percentage of developmentally incompetent oocytes after EXOSC10 depletion. Collectively, we propose that EXOSC10 promotes normal growth-to-maturation transition in mouse oocytes by sculpting the transcriptome to degrade RNAs encoding growth-phase factors and, thus, support the maturation phase of oogenesis.
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Affiliation(s)
- Di Wu
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Boschen KE, Ptacek TS, Simon JM, Parnell SE. Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. Alcohol Clin Exp Res 2020; 44:1540-1550. [PMID: 32557641 DOI: 10.1111/acer.14389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/02/2020] [Accepted: 05/31/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Early gestational alcohol exposure is associated with severe craniofacial and CNS dysmorphologies and behavioral abnormalities during adolescence and adulthood. Alcohol exposure during the formation of the neural tube (gestational day [GD] 8 to 10 in mice; equivalent to4th week of human pregnancy) disrupts development of ventral midline brain structures such as the pituitary, septum, and ventricles. This study identifies transcriptomic changes in the rostroventral neural tube (RVNT), the region of the neural tube that gives rise to the midline structures sensitive to alcohol exposure during neurulation. METHODS Female C57BL/6J mice were administered 2 doses of alcohol (2.9 g/kg) or vehicle 4 hours apart on GD 9.0. The RVNTs of embryos were collected 6 or 24 hours after the first dose and processed for RNA-seq. RESULTS Six hours following GD 9.0 alcohol exposure (GD 9.25), over 2,300 genes in the RVNT were determined to be differentially regulated by alcohol. Enrichment analysis determined that PAE affected pathways related to cell proliferation, p53 signaling, ribosome biogenesis, and immune activation. In addition, over 100 genes involved in primary cilia formation and function and regulation of morphogenic pathways were altered 6 hours after alcohol exposure. The changes to gene expression were largely transient, as only 91 genes identified as differentially regulated by prenatal alcohol at GD 10 (24 hours postexposure). Functionally, the differentially regulated genes at GD 10 were related to organogenesis and cell migration. CONCLUSIONS These data give a comprehensive view of the changing landscape of the embryonic transcriptome networks in regions of the neural tube that give rise to brain structures impacted by a neurulation-stage alcohol exposure. Identification of gene networks dysregulated by alcohol will help elucidate the pathogenic mechanisms of alcohol's actions.
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Affiliation(s)
- Karen E Boschen
- From the Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Travis S Ptacek
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeremy M Simon
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Scott E Parnell
- From the Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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13
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Zhu X, Zhang W, Guo J, Zhang X, Li L, Wang T, Yan J, Zhang F, Hou B, Gao N, Gao GF, Zhou X. Noc4L-Mediated Ribosome Biogenesis Controls Activation of Regulatory and Conventional T Cells. Cell Rep 2020; 27:1205-1220.e4. [PMID: 31018134 DOI: 10.1016/j.celrep.2019.03.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 02/12/2019] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
Regulatory T cell (Treg) activation is crucial for maintaining self-tolerance, but the translational regulation of this process is still poorly understood. Although ribosome biogenesis is considered a housekeeping process, emerging evidence supports the hypothesis that ribosome biogenesis can selectively regulate protein synthesis by tuning translation. Here, we focused on the ribosome biogenesis factor Noc4L, based on the observations that Noc4L is highly expressed in activated Tregs. Conditional Noc4L knockout in Tregs resulted in a lethal autoimmune phenotype resembling Treg-deficient scurfy mice. Interestingly, the Noc4L defect did not globally affect overall protein translation in Tregs but was selectively detrimental to the expression of mRNAs related to Treg activation. These results demonstrate the critical role of Noc4L-mediated ribosome biogenesis in controlling the activation of Tregs and maintaining immune tolerance.
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Affiliation(s)
- Xueping Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jie Guo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Xuejie Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Fuping Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baidong Hou
- University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ning Gao
- School of Life Sciences, Peking University, Beijing 100871, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Weick EM, Zinder JC, Lima CD. Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts. Methods Mol Biol 2020; 2062:417-425. [PMID: 31768988 PMCID: PMC8565498 DOI: 10.1007/978-1-4939-9822-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The eukaryotic RNA exosome is a conserved and ubiquitous multiprotein complex that possesses multiple RNase activities and is involved in a diverse array of RNA degradation and processing events. While much of our current understanding of RNA exosome function has been elucidated using genetics and cell biology based studies of protein functions, in particular in S. cerevisiae, many important contributions in the field have been enabled through use of in vitro reconstituted complexes. Here, we present an overview of our approach to purify exosome components from recombinant sources and reconstitute them into functional complexes. Three chapters following this overview provide detailed protocols for reconstituting exosome complexes from S. cerevisiae, S. pombe, and H. sapiens. We additionally provide insight on some of the drawbacks of these methods and highlight several important discoveries that have been achieved using reconstituted complexes.
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Affiliation(s)
- Eva-Maria Weick
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John C Zinder
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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15
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Telekawa C, Boisvert FM, Bachand F. Proteomic profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome. Nucleic Acids Res 2019; 46:11169-11183. [PMID: 30321377 PMCID: PMC6265454 DOI: 10.1093/nar/gky915] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
The RNA exosome is a conserved multi-subunit complex essential for processing and degradation of several types of RNAs. Although many of the functions of the RNA exosome are well established, whether the activity of this complex is regulated remains unclear. Here we performed a proteomic analysis of the RNA exosome complex purified from Schizosaccharomyces pombe and identified 39 post-translational modifications (PTMs), including phosphorylation, methylation, and acetylation sites. Interestingly, most of the modifications were identified in Dis3, a catalytic subunit of the RNA exosome, as well as in the exosome-associated RNA helicase, Mtr4. Functional analysis of selected PTM sites using modification-deficient and -mimetic versions of exosome subunits revealed substitutions that affected cell growth and exosome functions. Notably, our results suggest that site-specific phosphorylation in the catalytic center of Dis3 and in the helical bundle domain of Mtr4 control their activity. Our findings support a view in which post-translational modifications fine-tune exosome activity and add a layer of regulation to RNA degradation.
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Affiliation(s)
- Caroline Telekawa
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - François Bachand
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
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16
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Tu X, Qin B, Zhang Y, Zhang C, Kahila M, Nowsheen S, Yin P, Yuan J, Pei H, Li H, Yu J, Song Z, Zhou Q, Zhao F, Liu J, Zhang C, Dong H, Mutter RW, Lou Z. PD-L1 (B7-H1) Competes with the RNA Exosome to Regulate the DNA Damage Response and Can Be Targeted to Sensitize to Radiation or Chemotherapy. Mol Cell 2019; 74:1215-1226.e4. [PMID: 31053471 DOI: 10.1016/j.molcel.2019.04.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 02/20/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
Programmed death ligand 1 (PD-L1, also called B7-H1) is an immune checkpoint protein that inhibits immune function through its binding of the programmed cell death protein 1 (PD-1) receptor. Clinically approved antibodies block extracellular PD-1 and PD-L1 binding, yet the role of intracellular PD-L1 in cancer remains poorly understood. Here, we discovered that intracellular PD-L1 acts as an RNA binding protein that regulates the mRNA stability of NBS1, BRCA1, and other DNA damage-related genes. Through competition with the RNA exosome, intracellular PD-L1 protects targeted RNAs from degradation, thereby increasing cellular resistance to DNA damage. RNA immunoprecipitation and RNA-seq experiments demonstrated that PD-L1 regulates RNA stability genome-wide. Furthermore, we developed a PD-L1 antibody, H1A, which abrogates the interaction of PD-L1 with CMTM6, thereby promoting PD-L1 degradation. Intracellular PD-L1 may be a potential therapeutic target to enhance the efficacy of radiotherapy and chemotherapy in cancer through the inhibition of DNA damage response and repair.
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Affiliation(s)
- Xinyi Tu
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN 55905, USA; Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yong Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Mohamed Kahila
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Yuan
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Huadong Pei
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Science, 2300 Eye Street, NW, Washington, DC 20037, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiwang Song
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jiaqi Liu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chao Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Haidong Dong
- Department of Urology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
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17
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Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. Cell 2019; 173:1663-1677.e21. [PMID: 29906447 DOI: 10.1016/j.cell.2018.05.041] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/26/2018] [Accepted: 05/17/2018] [Indexed: 01/08/2023]
Abstract
The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.
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18
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Piñeiro D, Stoneley M, Ramakrishna M, Alexandrova J, Dezi V, Juke-Jones R, Lilley KS, Cain K, Willis AE. Identification of the RNA polymerase I-RNA interactome. Nucleic Acids Res 2018; 46:11002-11013. [PMID: 30169671 PMCID: PMC6237751 DOI: 10.1093/nar/gky779] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/27/2018] [Accepted: 08/29/2018] [Indexed: 12/13/2022] Open
Abstract
Ribosome biogenesis is a complex process orchestrated by a host of ribosome assembly factors. Although it is known that many of the proteins involved in this process have RNA binding activity, the full repertoire of proteins that interact with the precursor ribosomal RNA is currently unknown. To gain a greater understanding of the extent to which RNA-protein interactions have the potential to control ribosome biogenesis, we used RNA affinity isolation coupled with proteomics to measure the changes in RNA-protein interactions that occur when rRNA transcription is blocked. Our analysis identified 211 out of 457 nuclear RNA binding proteins with a >3-fold decrease in RNA-protein interaction after inhibition of RNA polymerase I (RNAPI). We have designated these 211 RNA binding proteins as the RNAPI RNA interactome. As expected, the RNAPI RNA interactome is highly enriched for nucleolar proteins and proteins associated with ribosome biogenesis. Selected proteins from the interactome were shown to be nucleolar in location and to have RNA binding activity that was dependent on RNAPI activity. Furthermore, our data show that two proteins, which are required for rRNA maturation, AATF and NGDN, and which form part of the RNA interactome, both lack canonical RNA binding domains and yet are novel pre-rRNA binding proteins.
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Affiliation(s)
- David Piñeiro
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK
| | - Mark Stoneley
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK
| | - Manasa Ramakrishna
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK
| | - Jana Alexandrova
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK
| | - Veronica Dezi
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK
| | - Rebekha Juke-Jones
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Kelvin Cain
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK
| | - Anne E Willis
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester LE1 9HN, UK
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19
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Beta RAA, Balatsos NAA. Tales around the clock: Poly(A) tails in circadian gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1484. [PMID: 29911349 DOI: 10.1002/wrna.1484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 04/15/2018] [Accepted: 04/20/2018] [Indexed: 11/07/2022]
Abstract
Circadian rhythms are ubiquitous time-keeping processes in eukaryotes with a period of ~24 hr. Light is perhaps the main environmental cue (zeitgeber) that affects several aspects of physiology and behaviour, such as sleep/wake cycles, orientation of birds and bees, and leaf movements in plants. Temperature can serve as the main zeitgeber in the absence of light cycles, even though it does not lead to rhythmicity through the same mechanism as light. Additional cues include feeding patterns, humidity, and social rhythms. At the molecular level, a master oscillator orchestrates circadian rhythms and organizes molecular clocks located in most cells. The generation of the 24 hr molecular clock is based on transcriptional regulation, as it drives intrinsic rhythmic changes based on interlocked transcription/translation feedback loops that synchronize expression of genes. Thus, processes and factors that determine rhythmic gene expression are important to understand circadian rhythms. Among these, the poly(A) tails of RNAs play key roles in their stability, translational efficiency and degradation. In this article, we summarize current knowledge and discuss perspectives on the role and significance of poly(A) tails and associating factors in the context of the circadian clock. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > 3' End Processing.
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Affiliation(s)
- Rafailia A A Beta
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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20
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Marini A, Rotblat B, Sbarrato T, Niklison-Chirou MV, Knight JRP, Dudek K, Jones C, Bushell M, Knight RA, Amelio I, Willis AE, Melino G. TAp73 contributes to the oxidative stress response by regulating protein synthesis. Proc Natl Acad Sci U S A 2018; 115:6219-6224. [PMID: 29844156 PMCID: PMC6004440 DOI: 10.1073/pnas.1718531115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TAp73 is a transcription factor that plays key roles in brain development, aging, and cancer. At the cellular level, TAp73 is a critical homeostasis-maintaining factor, particularly following oxidative stress. Although major studies focused on TAp73 transcriptional activities have indicated a contribution of TAp73 to cellular metabolism, the mechanisms underlying its role in redox homeostasis have not been completely elucidated. Here we show that TAp73 contributes to the oxidative stress response by participating in the control of protein synthesis. Regulation of mRNA translation occupies a central position in cellular homeostasis during the stress response, often by reducing global rates of protein synthesis and promoting translation of specific mRNAs. TAp73 depletion results in aberrant ribosomal RNA (rRNA) processing and impaired protein synthesis. In particular, polysomal profiles show that TAp73 promotes the integration of mRNAs that encode rRNA-processing factors in polysomes, supporting their translation. Concurrently, TAp73 depletion causes increased sensitivity to oxidative stress that correlates with reduced ATP levels, hyperactivation of AMPK, and translational defects. TAp73 is important for maintaining active translation of mitochondrial transcripts in response to oxidative stress, thus promoting mitochondrial activity. Our results indicate that TAp73 contributes to redox homeostasis by affecting the translational machinery, facilitating the translation of specific mitochondrial transcripts. This study identifies a mechanism by which TAp73 contributes to the oxidative stress response and describes a completely unexpected role for TAp73 in regulating protein synthesis.
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Affiliation(s)
- Alberto Marini
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Barak Rotblat
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Thomas Sbarrato
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Maria Victoria Niklison-Chirou
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom
| | - John R P Knight
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Kate Dudek
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Carolyn Jones
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Martin Bushell
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Richard A Knight
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Ivano Amelio
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom
| | - Anne E Willis
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom;
| | - Gerry Melino
- Medical Research Council, Toxicology Unit, University of Cambridge, Leicester LE1 9HN, United Kingdom;
- Department of Experimental Medicine and Surgery, IDI-IRCCS (Istituto Dermopatico dell'Immacolata-Istituto di Ricovero e Cura a Carattere Scientifico), University of Rome Tor Vergata, 00133 Rome, Italy
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21
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El-Naggar AM, Sorensen PH. Translational control of aberrant stress responses as a hallmark of cancer. J Pathol 2018; 244:650-666. [PMID: 29293271 DOI: 10.1002/path.5030] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022]
Abstract
Altered mRNA translational control is emerging as a critical factor in cancer development and progression. Targeting specific elements of the translational machinery, such as mTORC1 or eIF4E, is emerging as a new strategy for innovative cancer therapy. While translation of most mRNAs takes place through cap-dependent mechanisms, a sub-population of cellular mRNA species, particularly stress-inducible mRNAs with highly structured 5'-UTR regions, are primarily translated through cap-independent mechanisms. Intriguingly, many of these mRNAs encode proteins that are involved in tumour cell adaptation to microenvironmental stress, and thus linked to aggressive behaviour including tumour invasion and metastasis. This necessitates a rigorous search for links between microenvironmental stress and aggressive tumour phenotypes. Under stress, cells block global protein synthesis to preserve energy while maintaining selective synthesis of proteins that support cell survival. One highly conserved mechanism to regulate protein synthesis under cell stress is to sequester mRNAs into cytosolic aggregates called stress granules (SGs), where their translation is silenced. SGs confer survival advantages and chemotherapeutic resistance to tumour cells under stress. Recently, it has been shown that genetically blocking SG formation dramatically reduces tumour invasive and metastatic capacity in vivo. Therefore, targeting SG formation might represent a potential treatment strategy to block cancer metastasis. Here, we present the critical link between selective mRNA translation, stress adaptation, SGs, and tumour progression. Further, we also explain how deciphering mechanisms of selective mRNA translation occurs under cell stress holds great promise for the identification of new targets in the treatment of cancer. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Egypt
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
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22
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Jamin SP, Petit FG, Kervarrec C, Smagulova F, Illner D, Scherthan H, Primig M. EXOSC10/Rrp6 is post-translationally regulated in male germ cells and controls the onset of spermatogenesis. Sci Rep 2017; 7:15065. [PMID: 29118343 PMCID: PMC5678167 DOI: 10.1038/s41598-017-14643-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/10/2017] [Indexed: 12/31/2022] Open
Abstract
EXOSC10 is a catalytic subunit of the exosome that processes biologically active transcripts, degrades aberrant mRNAs and targets certain long non-coding RNAs (lncRNAs). The yeast orthologue Rrp6 is required for efficient growth and gametogenesis, and becomes unstable during meiosis. However, nothing is known about the localization, stability and function of EXOSC10 in the rodent male germline. We detect the protein in nucleoli and the cytoplasm of mitotic and meiotic germ cells, and find that it transiently associates with the XY body, a structure targeted by meiotic sex chromosome inactivation (MSCI). Finally, EXOSC10 becomes unstable at later stages of gamete development. To determine Exosc10’s meiotic function, we inactivated the gene specifically in male germ cells using cre recombinase controlled by Stra8 or Ddx4/Vasa promoters. Mutant mice have small testes, show impaired germ cell differentiation and are subfertile. Our results demonstrate that EXOSC10 is post-translationally regulated in germ cells, associate the protein with epigenetic chromosome silencing, and reveal its essential role in germ cell growth and development.
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Affiliation(s)
- Soazik P Jamin
- Inserm U1085 IRSET, Université de Rennes 1, 35000, Rennes, France.
| | - Fabrice G Petit
- Inserm U1085 IRSET, Université de Rennes 1, 35000, Rennes, France
| | | | - Fatima Smagulova
- Inserm U1085 IRSET, Université de Rennes 1, 35000, Rennes, France
| | - Doris Illner
- Institut für Radiobiologie der Bundeswehr in Verb. mit der Universität Ulm, 80937, Munich, Germany.,PAN-Biotech, 94501, Aidenbach, Germany
| | - Harry Scherthan
- Institut für Radiobiologie der Bundeswehr in Verb. mit der Universität Ulm, 80937, Munich, Germany
| | - Michael Primig
- Inserm U1085 IRSET, Université de Rennes 1, 35000, Rennes, France.
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23
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Tan TCJ, Knight J, Sbarrato T, Dudek K, Willis AE, Zamoyska R. Suboptimal T-cell receptor signaling compromises protein translation, ribosome biogenesis, and proliferation of mouse CD8 T cells. Proc Natl Acad Sci U S A 2017; 114:E6117-E6126. [PMID: 28696283 PMCID: PMC5544288 DOI: 10.1073/pnas.1700939114] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Global transcriptomic and proteomic analyses of T cells have been rich sources of unbiased data for understanding T-cell activation. Lack of full concordance of these datasets has illustrated that important facets of T-cell activation are controlled at the level of translation. We undertook translatome analysis of CD8 T-cell activation, combining polysome profiling and microarray analysis. We revealed that altering T-cell receptor stimulation influenced recruitment of mRNAs to heavy polysomes and translation of subsets of genes. A major pathway that was compromised, when TCR signaling was suboptimal, was linked to ribosome biogenesis, a rate-limiting factor in both cell growth and proliferation. Defective TCR signaling affected transcription and processing of ribosomal RNA precursors, as well as the translation of specific ribosomal proteins and translation factors. Mechanistically, IL-2 production was compromised in weakly stimulated T cells, affecting the abundance of Myc protein, a known regulator of ribosome biogenesis. Consequently, weakly activated T cells showed impaired production of ribosomes and a failure to maintain proliferative capacity after stimulation. We demonstrate that primary T cells respond to various environmental cues by regulating ribosome biogenesis and mRNA translation at multiple levels to sustain proliferation and differentiation.
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Affiliation(s)
- Thomas C J Tan
- Institute of Immunology and Infection Research, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - John Knight
- Medical Research Council Toxicology Unit, Leicester LE1 9HN, United Kingdom
| | - Thomas Sbarrato
- Medical Research Council Toxicology Unit, Leicester LE1 9HN, United Kingdom
| | - Kate Dudek
- Medical Research Council Toxicology Unit, Leicester LE1 9HN, United Kingdom
| | - Anne E Willis
- Medical Research Council Toxicology Unit, Leicester LE1 9HN, United Kingdom
| | - Rose Zamoyska
- Institute of Immunology and Infection Research, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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24
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RTN3 Is a Novel Cold-Induced Protein and Mediates Neuroprotective Effects of RBM3. Curr Biol 2017; 27:638-650. [PMID: 28238655 PMCID: PMC5344685 DOI: 10.1016/j.cub.2017.01.047] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/21/2016] [Accepted: 01/23/2017] [Indexed: 11/28/2022]
Abstract
Cooling and hypothermia are profoundly neuroprotective, mediated, at least in part, by the cold shock protein, RBM3. However, the neuroprotective effector proteins induced by RBM3 and the mechanisms by which mRNAs encoding cold shock proteins escape cooling-induced translational repression are unknown. Here, we show that cooling induces reprogramming of the translatome, including the upregulation of a new cold shock protein, RTN3, a reticulon protein implicated in synapse formation. We report that this has two mechanistic components. Thus, RTN3 both evades cooling-induced translational elongation repression and is also bound by RBM3, which drives the increased expression of RTN3. In mice, knockdown of RTN3 expression eliminated cooling-induced neuroprotection. However, lentivirally mediated RTN3 overexpression prevented synaptic loss and cognitive deficits in a mouse model of neurodegeneration, downstream and independently of RBM3. We conclude that RTN3 expression is a mediator of RBM3-induced neuroprotection, controlled by novel mechanisms of escape from translational inhibition on cooling. Cooling-induced reprogramming of the translatome increases synthesis of RTN3 The neuroprotective protein RBM3 binds RTN3 mRNA and drives its expression RTN3 overexpression prevents synaptic loss in mice with prion disease RTN3 expression is a mediator of RBM3-induced neuroprotection
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