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Smart A, Gilmer O, Caliskan N. Translation Inhibition Mediated by Interferon-Stimulated Genes during Viral Infections. Viruses 2024; 16:1097. [PMID: 39066259 PMCID: PMC11281336 DOI: 10.3390/v16071097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Viruses often pose a significant threat to the host through the exploitation of cellular machineries for their own benefit. In the context of immune responses, myriad host factors are deployed to target viral RNAs and inhibit viral protein translation, ultimately hampering viral replication. Understanding how "non-self" RNAs interact with the host translation machinery and trigger immune responses would help in the development of treatment strategies for viral infections. In this review, we explore how interferon-stimulated gene products interact with viral RNA and the translation machinery in order to induce either global or targeted translation inhibition.
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Affiliation(s)
- Alexandria Smart
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Orian Gilmer
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Neva Caliskan
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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Huntzinger E, Sinteff J, Morlet B, Séraphin B. HELZ2: a new, interferon-regulated, human 3'-5' exoribonuclease of the RNB family is expressed from a non-canonical initiation codon. Nucleic Acids Res 2023; 51:9279-9293. [PMID: 37602378 PMCID: PMC10516660 DOI: 10.1093/nar/gkad673] [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: 03/21/2023] [Revised: 07/27/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
Proteins containing a RNB domain, originally identified in Escherichia coli RNase II, are widely present throughout the tree of life. Many RNB proteins have 3'-5' exoribonucleolytic activity but some have lost catalytic activity during evolution. Database searches identified a new RNB domain-containing protein in human: HELZ2. Analysis of genomic and expression data combined with evolutionary information suggested that the human HELZ2 protein is produced from an unforeseen non-canonical initiation codon in Hominidae. This unusual property was confirmed experimentally, extending the human protein by 247 residues. Human HELZ2 was further shown to be an active ribonuclease despite the substitution of a key residue in its catalytic center. HELZ2 RNase activity is lost in cells from some cancer patients as a result of somatic mutations. HELZ2 harbors also two RNA helicase domains and several zinc fingers and its expression is induced by interferon treatment. We demonstrate that HELZ2 is able to degrade structured RNAs through the coordinated ATP-dependent displacement of duplex RNA mediated by its RNA helicase domains and its 3'-5' ribonucleolytic action. The expression characteristics and biochemical properties of HELZ2 support a role for this factor in response to viruses and/or mobile elements.
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Affiliation(s)
- Eric Huntzinger
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Jordan Sinteff
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
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Goodier JL, Wan H, Soares AO, Sanchez L, Selser JM, Pereira GC, Karma S, García-Pérez JL, Kazazian HH, García Cañadas MM. ZCCHC3 is a stress granule zinc knuckle protein that strongly suppresses LINE-1 retrotransposition. PLoS Genet 2023; 19:e1010795. [PMID: 37405998 DOI: 10.1371/journal.pgen.1010795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 05/23/2023] [Indexed: 07/07/2023] Open
Abstract
Retrotransposons have generated about half of the human genome and LINE-1s (L1s) are the only autonomously active retrotransposons. The cell has evolved an arsenal of defense mechanisms to protect against retrotransposition with factors we are only beginning to understand. In this study, we investigate Zinc Finger CCHC-Type Containing 3 (ZCCHC3), a gag-like zinc knuckle protein recently reported to function in the innate immune response to infecting viruses. We show that ZCCHC3 also severely restricts human retrotransposons and associates with the L1 ORF1p ribonucleoprotein particle. We identify ZCCHC3 as a bona fide stress granule protein, and its association with LINE-1 is further supported by colocalization with L1 ORF1 protein in stress granules, dense cytoplasmic aggregations of proteins and RNAs that contain stalled translation pre-initiation complexes and form when the cell is under stress. Our work also draws links between ZCCHC3 and the anti-viral and retrotransposon restriction factors Mov10 RISC Complex RNA Helicase (MOV10) and Zinc Finger CCCH-Type, Antiviral 1 (ZC3HAV1, also called ZAP). Furthermore, collective evidence from subcellular localization, co-immunoprecipitation, and velocity gradient centrifugation connects ZCCHC3 with the RNA exosome, a multi-subunit ribonuclease complex capable of degrading various species of RNA molecules and that has previously been linked with retrotransposon control.
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Affiliation(s)
- John L Goodier
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Han Wan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alisha O Soares
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Laura Sanchez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - John Michael Selser
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gavin C Pereira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sadik Karma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jose Luis García-Pérez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Haig H Kazazian
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marta M García Cañadas
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
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Suzuki Y, Murakawa T. Restriction of Flaviviruses by an Interferon-Stimulated Gene SHFL/C19orf66. Int J Mol Sci 2022; 23:12619. [PMID: 36293480 PMCID: PMC9604422 DOI: 10.3390/ijms232012619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Flaviviruses (the genus Flavivirus of the Flaviviridae family) include many arthropod-borne viruses, often causing life-threatening diseases in humans, such as hemorrhaging and encephalitis. Although the flaviviruses have a significant clinical impact, it has become apparent that flavivirus replication is restricted by cellular factors induced by the interferon (IFN) response, which are called IFN-stimulated genes (ISGs). SHFL (shiftless antiviral inhibitor of ribosomal frameshifting) is a novel ISG that inhibits dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) infections. Interestingly, SHFL functions as a broad-spectrum antiviral factor exhibiting suppressive activity against various types of RNA and DNA viruses. In this review, we summarize the current understanding of the molecular mechanisms by which SHFL inhibits flavivirus infection and discuss the molecular basis of the inhibitory mechanism using a predicted tertiary structure of SHFL generated by the program AlphaFold2.
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Affiliation(s)
- Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Japan
| | - Takeshi Murakawa
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Japan
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Yang S, Zhang X, Li X, Yin X, Teng L, Ji G, Li H. Evolutionary and Expression Analysis of MOV10 and MOV10L1 Reveals Their Origin, Duplication and Divergence. Int J Mol Sci 2022; 23:ijms23147523. [PMID: 35886872 PMCID: PMC9319325 DOI: 10.3390/ijms23147523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 12/04/2022] Open
Abstract
MOV10 and MOV10L1 both encode ATP-dependent RNA helicases. In mammals, MOV10 and MOV10L1 participate in various kinds of biological contexts, such as defense of RNA virus invasion, neuron system, germ cell and early development. However, mov10 and mov10l1 in zebrafish are obscure and the evolutionary relationships of mov10 among different species remain unclear. In this study, we found MOV10 and MOV10L1 had some variations despite they possessed the conserved feature of RNA helicase, however, they may originate from a single ancestor although they shared limited homology. A single MOV10L1 gene existed among all species, while MOV10 gene experienced lineage-specific intra-chromosomal gene duplication in several species. Interestingly, the mov10 gene expanded to three in zebrafish, which originating from a duplication by whole genome specific duplication of teleost lineage followed by a specific intra-chromosome tandem duplication. The mov10 and mov10l1 showed distinct expression profiles in early stages, however, in adult zebrafish, three mov10 genes exhibited similar diverse expression patterns in almost all tissues. We also demonstrated mov10 genes were upregulated upon virus challenge, highlighting they had redundant conserved roles in virus infection. These results provide valuable data for the evolution of MOV10 and MOV10L1 and they are important to the further functional exploration.
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Affiliation(s)
- Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
| | - Xiangmin Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
| | - Xianpeng Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
| | - Xiu Yin
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
| | - Lei Teng
- School of Basic Medicine, Qingdao University, Qingdao 266071, China;
| | - Guangdong Ji
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
- Correspondence: (G.J.); (H.L.); Tel.: +86-0532-82032092 (H.L.)
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
- Correspondence: (G.J.); (H.L.); Tel.: +86-0532-82032092 (H.L.)
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Rodriguez W, Muller M. Shiftless, a Critical Piece of the Innate Immune Response to Viral Infection. Viruses 2022; 14:1338. [PMID: 35746809 PMCID: PMC9230503 DOI: 10.3390/v14061338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/08/2022] [Accepted: 06/16/2022] [Indexed: 12/14/2022] Open
Abstract
Since its initial characterization in 2016, the interferon stimulated gene Shiftless (SHFL) has proven to be a critical piece of the innate immune response to viral infection. SHFL expression stringently restricts the replication of multiple DNA, RNA, and retroviruses with an extraordinary diversity of mechanisms that differ from one virus to the next. These inhibitory strategies include the negative regulation of viral RNA stability, translation, and even the manipulation of RNA granule formation during viral infection. Even more surprisingly, SHFL is the first human protein found to directly inhibit the activity of the -1 programmed ribosomal frameshift, a translation recoding strategy utilized across nearly all domains of life and several human viruses. Recent literature has shown that SHFL expression also significantly impacts viral pathogenesis in mouse models, highlighting its in vivo efficacy. To help reconcile the many mechanisms by which SHFL restricts viral replication, we provide here a comprehensive review of this complex ISG, its influence over viral RNA fate, and the implications of its functions on the virus-host arms race for control of the cell.
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Affiliation(s)
| | - Mandy Muller
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003, USA;
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Nawaz A, Shilikbay T, Skariah G, Ceman S. Unwinding the roles of RNA helicase MOV10. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1682. [PMID: 34327836 PMCID: PMC8799784 DOI: 10.1002/wrna.1682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022]
Abstract
MOV10 is an RNA helicase that associates with the RNA‐induced silencing complex component Argonaute (AGO), likely resolving RNA secondary structures. MOV10 also binds the Fragile X mental retardation protein to block AGO2 binding at some sites and associates with UPF1, a principal component of the nonsense‐mediated RNA decay pathway. MOV10 is widely expressed and has a key role in the cellular response to viral infection and in suppressing retrotransposition. Posttranslational modifications of MOV10 include ubiquitination, which leads to stimulation‐dependent degradation, and phosphorylation, which has an unknown function. MOV10 localizes to the nucleus and/or cytoplasm in a cell type‐specific and developmental stage‐specific manner. Knockout of Mov10 leads to embryonic lethality, underscoring an important role in development where it is required for the completion of gastrulation. MOV10 is expressed throughout the organism; however, most studies have focused on germline cells and neurons. In the testes, the knockdown of Mov10 disrupts proliferation of spermatogonial progenitor cells. In brain, MOV10 is significantly elevated postnatally and binds mRNAs encoding cytoskeleton and neuron projection proteins, suggesting an important role in neuronal architecture. Heterozygous Mov10 mutant mice are hyperactive and anxious and their cultured hippocampal neurons have reduced dendritic arborization. Zygotic knockdown of Mov10 in Xenopus laevis causes abnormal head and eye development and mislocalization of neuronal precursors in the brain. Thus, MOV10 plays a vital role during development, defense against viral infection and in neuronal development and function: its many roles and regulation are only beginning to be unraveled. This article is categorized under:RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications
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Affiliation(s)
- Aatiqa Nawaz
- Department of Cell and Developmental Biology, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
| | - Temirlan Shilikbay
- Department of Cell and Developmental Biology, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
| | - Geena Skariah
- Neuroscience Program, University of Illinois-Urbana Champaign, Champaign, Illinois, USA.,Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephanie Ceman
- Department of Cell and Developmental Biology, Neuroscience Program, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
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