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      The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation

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          Abstract

          ISG20 is a broad spectrum antiviral protein thought to directly degrade viral RNA. However, this mechanism of inhibition remains controversial. Using the Vesicular Stomatitis Virus (VSV) as a model RNA virus, we show here that ISG20 interferes with viral replication by decreasing protein synthesis in the absence of RNA degradation. Importantly, we demonstrate that ISG20 exerts a translational control over a large panel of non-self RNA substrates including those originating from transfected DNA, while sparing endogenous transcripts. This activity correlates with the protein’s ability to localize in cytoplasmic processing bodies. Finally, these functions are conserved in the ISG20 murine ortholog, whose genetic ablation results in mice with increased susceptibility to viral infection. Overall, our results posit ISG20 as an important defense factor able to discriminate the self/ non-self origins of the RNA through translation modulation.

          Author summary

          The interferon-induced protein 20 (ISG20) is an RNA exonuclease endowed with broad antiviral properties. The prevailing mechanism of inhibition described for ISG20 indicates that this enzyme is capable of directly degrading viral RNA in the absence of apparent sequence specificity. This mode of action has been however challenged by recent studies that revealed that ISG20 could target specific structures on the hepatitis B virus, as well as by others that suggested inhibition in the absence of viral RNA degradation. We now demonstrate that ISG20 interferes with viral replication not by degrading viral RNA, but by impairing its translation. This mechanism of translational control targets all RNAs originated from ectopically introduced genetic material (through viral infection or transient transfection) that we define here collectively as non-self, independently from their viral/non-viral origins. However, ISG20 bears no effect on the translation of endogenous mRNAs transcripts, suggesting that ISG20 can discriminate between the cell’s own genetic material ( self) and foreign one. By taking profit of their mode of replication through integration, or EBV-like episomal maintenance certain pathogens seemingly escape ISG20 by what can be defined as self-mimicry. Lastly, this mechanism of action is conserved in the ISG20 murine ortholog, whose genetic ablation results in mice with increased susceptibility to viral infection. Overall, our study reveals a novel role of ISG20 as a translational modulator of foreign genetic material playing important functions during viral infection in vivo.

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          P bodies and the control of mRNA translation and degradation.

          Recent results indicate that many untranslating mRNAs in somatic eukaryotic cells assemble into related mRNPs that accumulate in specific cytoplasmic foci referred to as P bodies. Transcripts associated with P body components can either be degraded or return to translation. Moreover, P bodies are also biochemically and functionally related to some maternal and neuronal mRNA granules. This suggests an emerging model of cytoplasmic mRNA function in which the rates of translation and degradation of mRNAs are influenced by a dynamic equilibrium between polysomes and the mRNPs seen in P bodies. Moreover, some mRNA-specific regulatory factors, including miRNAs and RISC, appear to repress translation and promote decay by recruiting P body components to individual mRNAs.
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            Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide.

            Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether ribosome heterogeneity at the level of core ribosomal proteins (RPs) exists and enables ribosomes to preferentially translate specific mRNAs genome-wide. Here, we measured the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or depleted from select subsets of ribosomes within embryonic stem cells. We find that heterogeneity in RP composition endows ribosomes with differential selectivity for translating subpools of transcripts, including those controlling metabolism, cell cycle, and development. As an example, mRNAs enriched in binding to RPL10A/uL1-containing ribosomes are shown to require RPL10A/uL1 for their efficient translation. Within several of these transcripts, this level of regulation is mediated, at least in part, by internal ribosome entry sites. Together, these results reveal a critical functional link between ribosome heterogeneity and the post-transcriptional circuitry of gene expression.
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              Processing bodies require RNA for assembly and contain nontranslating mRNAs.

              Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), wherein mRNA decay factors are concentrated and where mRNA decay can occur. However, the physical nature of P-bodies, their relationship to translation, and possible roles of P-bodies in cellular responses remain unclear. We describe four properties of yeast P-bodies that indicate that P-bodies are dynamic structures that contain nontranslating mRNAs and function during cellular responses to stress. First, in vivo and in vitro analysis indicates that P-bodies are dependent on RNA for their formation. Second, the number and size of P-bodies vary in response to glucose deprivation, osmotic stress, exposure to ultraviolet light, and the stage of cell growth. Third, P-bodies vary with the status of the cellular translation machinery. Inhibition of translation initiation by mutations, or cellular stress, results in increased P-bodies. In contrast, inhibition of translation elongation, thereby trapping the mRNA in polysomes, leads to dissociation of P-bodies. Fourth, multiple translation factors and ribosomal proteins are lacking from P-bodies. These results suggest additional biological roles of P-bodies in addition to being sites of mRNA degradation.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: Methodology
                Role: Formal analysisRole: Methodology
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysisRole: Methodology
                Role: ConceptualizationRole: Methodology
                Role: ConceptualizationRole: Methodology
                Role: Methodology
                Role: Data curationRole: InvestigationRole: Supervision
                Role: ConceptualizationRole: Data curationRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                10 October 2019
                October 2019
                : 15
                : 10
                : e1008093
                Affiliations
                [1 ] CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
                [2 ] Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
                [3 ] Shanghai Emerging and Reemerging Infectious Disease Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
                [4 ] Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
                NYU School of Medicine, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                ‡ These authors are joint second authors.

                Author information
                http://orcid.org/0000-0002-4735-6894
                http://orcid.org/0000-0002-0973-0777
                http://orcid.org/0000-0001-8255-9091
                http://orcid.org/0000-0002-5129-6804
                http://orcid.org/0000-0002-2001-8916
                http://orcid.org/0000-0003-0892-0488
                Article
                PPATHOGENS-D-19-01291
                10.1371/journal.ppat.1008093
                6805002
                31600344
                6cf4f3d3-0013-45b6-ae0d-a69c4eccc7df
                © 2019 Wu et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 15 July 2019
                : 18 September 2019
                Page count
                Figures: 7, Tables: 0, Pages: 27
                Funding
                The laboratory of AC is funded by grants from the Agence Nationale de Recherche sur le SIDA (ANRS) and from Sidaction. This project was funded by grants from the Joint Research Institute for Science and Society (JoRISS) and by the Project CMIRA Cooperation of the Region RHONE-ALPES AUVERGNE. RM and CJ have the label Equipe Fondation pour la Recherche Médicale, FRM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
                Categories
                Research Article
                Biology and life sciences
                Biochemistry
                Nucleic acids
                RNA
                Messenger RNA
                Biology and Life Sciences
                Genetics
                Gene Expression
                Protein Translation
                Computer and Information Sciences
                Data Visualization
                Infographics
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                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Transfection
                Research and Analysis Methods
                Molecular Biology Techniques
                Transfection
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzymes
                Oxidoreductases
                Luciferase
                Biology and Life Sciences
                Biochemistry
                Proteins
                Enzymes
                Oxidoreductases
                Luciferase
                Biology and Life Sciences
                Biochemistry
                Proteins
                Interferons
                Biology and Life Sciences
                Microbiology
                Virology
                Viral Replication
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Custom metadata
                vor-update-to-uncorrected-proof
                2019-10-22
                All relevant data are within the paper and its Supporting Information files

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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