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Romero MF, Krall JB, Nichols PJ, Vantreeck J, Henen MA, Dejardin E, Schulz F, Vicens Q, Vögeli B, Diallo MA. Novel Z-DNA binding domains in giant viruses. J Biol Chem 2024; 300:107504. [PMID: 38944123 DOI: 10.1016/j.jbc.2024.107504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/01/2024] Open
Abstract
Z-nucleic acid structures play vital roles in cellular processes and have implications in innate immunity due to their recognition by Zα domains containing proteins (Z-DNA/Z-RNA binding proteins, ZBPs). Although Zα domains have been identified in six proteins, including viral E3L, ORF112, and I73R, as well as, cellular ADAR1, ZBP1, and PKZ, their prevalence across living organisms remains largely unexplored. In this study, we introduce a computational approach to predict Zα domains, leading to the revelation of previously unidentified Zα domain-containing proteins in eukaryotic organisms, including non-metazoan species. Our findings encompass the discovery of new ZBPs in previously unexplored giant viruses, members of the Nucleocytoviricota phylum. Through experimental validation, we confirm the Zα functionality of select proteins, establishing their capability to induce the B-to-Z conversion. Additionally, we identify Zα-like domains within bacterial proteins. While these domains share certain features with Zα domains, they lack the ability to bind to Z-nucleic acids or facilitate the B-to-Z DNA conversion. Our findings significantly expand the ZBP family across a wide spectrum of organisms and raise intriguing questions about the evolutionary origins of Zα-containing proteins. Moreover, our study offers fresh perspectives on the functional significance of Zα domains in virus sensing and innate immunity and opens avenues for exploring hitherto undiscovered functions of ZBPs.
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Affiliation(s)
- Miguel F Romero
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jeffrey B Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, Aurora, Colorado, USA
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, Aurora, Colorado, USA
| | - Jillian Vantreeck
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, Aurora, Colorado, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, Aurora, Colorado, USA
| | - Emmanuel Dejardin
- GIGA I3 - Molecular Immunology and Signal Transduction, University of Liège, Liège, Belgium
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
| | - Quentin Vicens
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, Aurora, Colorado, USA.
| | - Mamadou Amadou Diallo
- GIGA I3 - Molecular Immunology and Signal Transduction, University of Liège, Liège, Belgium.
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2
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de Reuver R, Maelfait J. Novel insights into double-stranded RNA-mediated immunopathology. Nat Rev Immunol 2024; 24:235-249. [PMID: 37752355 DOI: 10.1038/s41577-023-00940-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 09/28/2023]
Abstract
Recent progress in human and mouse genetics has transformed our understanding of the molecular mechanisms by which recognition of self double-stranded RNA (self-dsRNA) causes immunopathology. Novel mouse models recapitulate loss-of-function mutations in the RNA editing enzyme ADAR1 that are found in patients with Aicardi-Goutières syndrome (AGS) - a monogenic inflammatory disease associated with increased levels of type I interferon. Extensive analyses of the genotype-phenotype relationships in these mice have now firmly established a causal relationship between increased intracellular concentrations of endogenous immunostimulatory dsRNA and type I interferon-driven immunopathology. Activation of the dsRNA-specific immune sensor MDA5 perpetuates the overproduction of type I interferons, and chronic engagement of the interferon-inducible innate immune receptors PKR and ZBP1 by dsRNA drives immunopathology by activating an integrated stress response or by inducing excessive cell death. Biochemical and genetic data support a role for the p150 isoform of ADAR1 in the cytosol in suppressing the spontaneous, pathological response to self-dsRNA.
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Affiliation(s)
- Richard de Reuver
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jonathan Maelfait
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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3
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Fesenko I, Sahakyan H, Shabalina SA, Koonin EV. The Cryptic Bacterial Microproteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.17.580829. [PMID: 38903115 PMCID: PMC11188072 DOI: 10.1101/2024.02.17.580829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Microproteins encoded by small open reading frames (smORFs) comprise the "dark matter" of proteomes. Although functional microproteins were identified in diverse organisms from all three domains of life, bacterial smORFs remain poorly characterized. In this comprehensive study of intergenic smORFs (ismORFs, 15-70 codons) in 5,668 bacterial genomes of the family Enterobacteriaceae, we identified 67,297 clusters of ismORFs subject to purifying selection. The ismORFs mainly code for hydrophobic, potentially transmembrane, unstructured, or minimally structured microproteins. Using AlphaFold Multimer, we predicted interactions of some of the predicted microproteins encoded by transcribed ismORFs with proteins encoded by neighboring genes, revealing the potential of microproteins to regulate the activity of various proteins, particularly, under stress. We compiled a catalog of predicted microprotein families with different levels of evidence from synteny analysis, structure prediction, and transcription and translation data. This study offers a resource for investigation of biological functions of microproteins.
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Affiliation(s)
- Igor Fesenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Harutyun Sahakyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Svetlana A. Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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4
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Williams J, Bonner J, Kibler K, Jacobs BL. Type I Interferon: Monkeypox/Mpox Viruses Achilles Heel? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1451:125-137. [PMID: 38801575 DOI: 10.1007/978-3-031-57165-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Poxviruses are notorious for having acquired/evolved numerous genes to counteract host innate immunity. Chordopoxviruses have acquired/evolved at least three different inhibitors of host necroptotic death: E3, which blocks ZBP1-dependent necroptotic cell death, and vIRD and vMLKL that inhibit necroptosis downstream of initial cell death signaling. While this suggests the importance of the necroptotic cell death pathway in inhibiting chordopoxvirus replication, several chordopoxviruses have lost one or more of these inhibitory functions. Monkeypox/mpox virus (MPXV) has lost a portion of the N-terminus of its E3 homologue. The N-terminus of the vaccinia virus E3 homologue serves to inhibit activation of the interferon-inducible antiviral protein, ZBP1. This likely makes MPXV unique among the orthopoxviruses in being sensitive to interferon (IFN) treatment in many mammals, including humans, which encode a complete necroptotic cell death pathway. Thus, IFN sensitivity may be the Achille's Heel for viruses like MPXV that cannot fully inhibit IFN-inducible, ZBP1-dependent antiviral pathways.
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Affiliation(s)
- Jacqueline Williams
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, USA
- ASU-Banner Center for Neurodegenerative Diseases, Arizona State University, Tempe, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
| | - James Bonner
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, USA
- ASU-Banner Center for Neurodegenerative Diseases, Arizona State University, Tempe, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Karen Kibler
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, USA
- ASU-Banner Center for Neurodegenerative Diseases, Arizona State University, Tempe, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
| | - Bertram L Jacobs
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, USA.
- ASU-Banner Center for Neurodegenerative Diseases, Arizona State University, Tempe, USA.
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, USA.
- School of Life Sciences, Arizona State University, Tempe, USA.
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5
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Zhong Y, Zhong X, Qiao L, Wu H, Liu C, Zhang T. Zα domain proteins mediate the immune response. Front Immunol 2023; 14:1241694. [PMID: 37771585 PMCID: PMC10523160 DOI: 10.3389/fimmu.2023.1241694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023] Open
Abstract
The Zα domain has a compact α/β architecture containing a three-helix bundle flanked on one side by a twisted antiparallel β sheet. This domain displays a specific affinity for double-stranded nucleic acids that adopt a left-handed helical conformation. Currently, only three Zα-domain proteins have been identified in eukaryotes, specifically ADAR1, ZBP1, and PKZ. ADAR1 is a double-stranded RNA (dsRNA) binding protein that catalyzes the conversion of adenosine residues to inosine, resulting in changes in RNA structure, function, and expression. In addition to its editing function, ADAR1 has been shown to play a role in antiviral defense, gene regulation, and cellular differentiation. Dysregulation of ADAR1 expression and activity has been associated with various disease states, including cancer, autoimmune disorders, and neurological disorders. As a sensing molecule, ZBP1 exhibits the ability to recognize nucleic acids with a left-handed conformation. ZBP1 harbors a RIP homotypic interaction motif (RHIM), composed of a highly charged surface region and a leucine-rich hydrophobic core, enabling the formation of homotypic interactions between proteins with similar structure. Upon activation, ZBP1 initiates a downstream signaling cascade leading to programmed cell death, a process mediated by RIPK3 via the RHIM motif. PKZ was identified in fish, and contains two Zα domains at the N-terminus. PKZ is essential for normal growth and development and may contribute to the regulation of immune system function in fish. Interestingly, some pathogenic microorganisms also encode Zα domain proteins, such as, Vaccinia virus and Cyprinid Herpesvirus. Zα domain proteins derived from pathogenic microorganisms have been demonstrated to be pivotal contributors in impeding the host immune response and promoting virus replication and spread. This review focuses on the mammalian Zα domain proteins: ADAR1 and ZBP1, and thoroughly elucidates their functions in the immune response.
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Affiliation(s)
- Yuhan Zhong
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao Zhong
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Liangjun Qiao
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Hong Wu
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Chang Liu
- Division of Liver, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Zhang
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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6
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Chaumont L, Collet B, Boudinot P. Protein kinase double-stranded RNA-dependent (PKR) in antiviral defence in fish and mammals. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 145:104732. [PMID: 37172664 DOI: 10.1016/j.dci.2023.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
The interferon-inducible double-stranded RNA-dependent protein kinase (PKR) is one of the key antiviral arms of the innate immune system. Upon binding of viral double stranded RNA, a viral Pattern Associated Molecular Pattern (PAMP), PKR gets activated and phosphorylates the eukaryotic initiation factor 2α (eIF2α) resulting in a protein shut-down that limits viral replication. Since its discovery in the mid-seventies, PKR has been shown to be involved in multiple important cellular processes including apoptosis, proinflammatory and innate immune responses. Viral subversion mechanisms of PKR underline its importance in the antiviral response of the host. PKR activation pathways and its mechanisms of action were previously identified and characterised mostly in mammalian models. However, fish Pkr and fish-specific paralogue Z-DNA-dependent protein kinase (Pkz) also play key role in antiviral defence. This review gives an update on the current knowledge on fish Pkr/Pkz, their conditions of activation and their implication in the immune responses to viruses, in comparison to their mammalian counterparts.
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Affiliation(s)
- Lise Chaumont
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, 78350, France
| | - Bertrand Collet
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, 78350, France
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, 78350, France.
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Karki R, Kanneganti TD. ADAR1 and ZBP1 in innate immunity, cell death, and disease. Trends Immunol 2023; 44:201-216. [PMID: 36710220 PMCID: PMC9974732 DOI: 10.1016/j.it.2023.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
ADAR1 and ZBP1 are the only two mammalian proteins that contain Zα domains, which are thought to bind to nucleic acids in the Z-conformation. These two molecules are crucial in regulating diverse biological processes. While ADAR1-mediated RNA editing supports host survival and development, ZBP1-mediated immune responses provide host defense against infection and disease. Recent studies have expanded our understanding of the functions of ADAR1 and ZBP1 beyond their classical roles and established their fundamental regulation of innate immune responses, including NLRP3 inflammasome activation, inflammation, and cell death. Their roles in these processes have physiological impacts across development, infectious and inflammatory diseases, and cancer. In this review, we discuss the functions of ADAR1 and ZBP1 in regulating innate immune responses in development and disease.
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Affiliation(s)
- Rajendra Karki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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8
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Boral A, Mitra D. Heterogeneity in winged helix-turn-helix and substrate DNA interactions: Insights from theory and experiments. J Cell Biochem 2023; 124:337-358. [PMID: 36715571 DOI: 10.1002/jcb.30369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/31/2023]
Abstract
Specific interactions between transcription factors (TFs) and substrate DNA constitute the fundamental basis of gene expression. Unlike in TFs like basic helix-loop-helix or basic leucine zippers, prediction of substrate DNA is extremely challenging for helix-turn-helix (HTH). Experimental techniques like chromatin immunoprecipitation combined with massively parallel DNA sequencing remains a viable option. We characterize the molecular basis of heterogeneity in HTH-DNA interaction using in silico tools and thence validate them experimentally. Given the profound functional diversity in HTH, we focus primarily on winged-HTH (wHTH). We consider 180 wHTH TFs, whose experimental three-dimensional structures are available in DNA bound/unbound conformations. Starting with PDB-wide scanning and curation of data, we construct a phylogenetic tree, which distributes 180 wHTH sequences under multiple sub-groups. Structure-sequence alignment followed by detailed intra/intergroup analysis, covariation studies and extensive network theory analysis help us to gain deep insight into heterogeneous wHTH-substrate DNA interactions. A central aim of this study is to find a consensus to predict the substrate DNA sequence for wHTH, amidst heterogeneity. The strength of our exhaustive theoretical investigations including molecular docking are successfully tested through experimental characterization of wHTH TF from Sulfurimonas denitrificans.
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Affiliation(s)
- Aparna Boral
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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9
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Abstract
Poxviruses have been long regarded as potent inhibitors of apoptotic cell death. More recently, they have been shown to inhibit necroptotic cell death through two distinct strategies. These strategies involve either blocking virus sensing by the host pattern recognition receptor, ZBP1 (also called DAI) or by influencing receptor interacting protein kinase (RIPK)3 signal transduction by inhibition of activation of the executioner of necroptosis, mixed lineage kinase-like protein (MLKL). Vaccinia virus E3 specifically blocks ZBP1 → RIPK3 → MLKL necroptosis, leaving virus-infected cells susceptible to the TNF death-receptor signaling (e.g., TNFR1 → FADD → RIPK1 → RIPK3 → MLKL), and, potentially, TLR3 → TRIF → RIPK3 → MLKL necroptosis. While E3 restriction of necroptosis appears to be common to many poxviruses that infect vertebrate hosts, another modulatory strategy not observed in vaccinia or variola virus manifests through subversion of MLKL activation. Recently described viral mimics of MLKL in other chordopoxviruses inhibit all three modes of necroptotic cell death. As with inhibition of apoptosis, the evolution of potentially redundant viral mechanisms to inhibit programmed necroptotic cell death emphasizes the importance of this pathway in the arms race between pathogens and their hosts.
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Affiliation(s)
- Heather S Koehler
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Vaccine Center, Atlanta, GA, 30322, USA
| | - Bertram L Jacobs
- Arizona State University, Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Tempe, AZ, 85287, USA.
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10
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Z-DNA and Z-RNA: Methods-Past and Future. Methods Mol Biol 2023; 2651:295-329. [PMID: 36892776 DOI: 10.1007/978-1-0716-3084-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
A quote attributed to Yogi Berra makes the observation that "It's tough to make predictions, especially about the future," highlighting the difficulties posed to an author writing a manuscript like the present. The history of Z-DNA shows that earlier postulates about its biology have failed the test of time, both those from proponents who were wildly enthusiastic in enunciating roles that till this day still remain elusive to experimental validation and those from skeptics within the larger community who considered the field a folly, presumably because of the limitations in the methods available at that time. If anything, the biological roles we now know for Z-DNA and Z-RNA were not anticipated by anyone, even when those early predictions are interpreted in the most favorable way possible. The breakthroughs in the field were made using a combination of methods, especially those based on human and mouse genetic approaches informed by the biochemical and biophysical characterization of the Zα family of proteins. The first success was with the p150 Zα isoform of ADAR1 (adenosine deaminase RNA specific), with insights into the functions of ZBP1 (Z-DNA-binding protein 1) following soon after from the cell death community. Just as the replacement of mechanical clocks by more accurate designs changed expectations about navigation, the discovery of the roles assigned by nature to alternative conformations like Z-DNA has forever altered our view of how the genome operates. These recent advances have been driven by better methodology and by better analytical approaches. This article will briefly describe the methods that were key to these discoveries and highlight areas where new method development is likely to further advance our knowledge.
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11
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Diallo MA, Pirotte S, Hu Y, Morvan L, Rakus K, Suárez NM, PoTsang L, Saneyoshi H, Xu Y, Davison A, Tompa P, Sussman J, Vanderplasschen A. A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion. Nucleic Acids Res 2022; 51:806-830. [PMID: 36130731 PMCID: PMC9881149 DOI: 10.1093/nar/gkac761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 02/06/2023] Open
Abstract
Zalpha (Zα) domains bind to left-handed Z-DNA and Z-RNA. The Zα domain protein family includes cellular (ADAR1, ZBP1 and PKZ) and viral (vaccinia virus E3 and cyprinid herpesvirus 3 (CyHV-3) ORF112) proteins. We studied CyHV-3 ORF112, which contains an intrinsically disordered region and a Zα domain. Genome editing of CyHV-3 indicated that the expression of only the Zα domain of ORF112 was sufficient for normal viral replication in cell culture and virulence in carp. In contrast, its deletion was lethal for the virus. These observations revealed the potential of the CyHV-3 model as a unique platform to compare the exchangeability of Zα domains expressed alone in living cells. Attempts to rescue the ORF112 deletion by a broad spectrum of cellular, viral, and artificial Zα domains showed that only those expressing Z-binding activity, the capacity to induce liquid-liquid phase separation (LLPS), and A-to-Z conversion, could rescue viral replication. For the first time, this study reports the ability of some Zα domains to induce LLPS and supports the biological relevance of dsRNA A-to-Z conversion mediated by Zα domains. This study expands the functional diversity of Zα domains and stimulates new hypotheses concerning the mechanisms of action of proteins containing Zα domains.
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Affiliation(s)
| | | | - Yunlong Hu
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium
| | - Léa Morvan
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium
| | - Krzysztof Rakus
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium,Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow 30387, Poland
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lee PoTsang
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium,Department of Aquaculture, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Hisao Saneyoshi
- Department of Medical Sciences, Division of Chemistry, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yan Xu
- Department of Medical Sciences, Division of Chemistry, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussel B-1050, Belgium
| | - Joel L Sussman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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12
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Thermodynamic analysis of Zα domain-nucleic acid interactions. Biochem J 2022; 479:1727-1741. [PMID: 35969150 DOI: 10.1042/bcj20220200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022]
Abstract
DNA/RNA molecules adopting the left-handed conformation (Z-form) have been attributed with immunogenic properties. However, their biological role and importance has been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Zα domains) in varied proteins that are involved in the innate immune response, such as the interferon inducible form of the RNA editing enzyme ADAR1 (p150), Z-DNA binding protein 1 (ZBP1), the fish kinase PKZ and the poxvirus inhibitor of interferon response E3L, indicates important roles of Z-DNA/RNA in immunity and self/non-self-discrimination. Such Zα domain-containing proteins recognise left-handed Z-DNA/RNA in a conformation-specific manner. Recent studies have implicated these domains in virus recognition. Given these important emerging roles for the Zα domains, it is pivotal to understand the mechanism of recognition of the Z-DNA/Z-RNA by these domains. To this end, we assessed the binding thermodynamics of Zα domain from ORF112 and ADAR1 on T(CG)3 and T(CG)6 oligonucleotides which have high propensity to adopt the Z-conformation. Our study highlights important differences in the mode of oligonucleotide binding by the two Zα domains originating from different proteins. Site-directed mutagenesis was employed together with isothermal titration calorimetry to tease apart finer details of the binding thermodynamics. Our work advances the understanding on binding thermodynamics of Zα domains to their cognate nucleic acid substrates and paves the ground for future efforts to gain a complete appreciation of this process.
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13
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Chiang DC, Li Y, Ng SK. The Role of the Z-DNA Binding Domain in Innate Immunity and Stress Granules. Front Immunol 2021; 11:625504. [PMID: 33613567 PMCID: PMC7886975 DOI: 10.3389/fimmu.2020.625504] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Both DNA and RNA can maintain left-handed double helical Z-conformation under physiological condition, but only when stabilized by Z-DNA binding domain (ZDBD). After initial discovery in RNA editing enzyme ADAR1, ZDBD has also been described in pathogen-sensing proteins ZBP1 and PKZ in host, as well as virulence proteins E3L and ORF112 in viruses. The host-virus antagonism immediately highlights the importance of ZDBD in antiviral innate immunity. Furthermore, Z-RNA binding has been shown to be responsible for the localization of these ZDBD-containing proteins to cytoplasmic stress granules that play central role in coordinating cellular response to stresses. This review sought to consolidate current understanding of Z-RNA sensing in innate immunity and implore possible roles of Z-RNA binding within cytoplasmic stress granules.
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Affiliation(s)
- De Chen Chiang
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
| | - Yan Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Siew Kit Ng
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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14
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Wu C, Zhang Y, Hu C. PKZ, a Fish-Unique eIF2α Kinase Involved in Innate Immune Response. Front Immunol 2020; 11:585. [PMID: 32296447 PMCID: PMC7137213 DOI: 10.3389/fimmu.2020.00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
PKZ is a novel and unique eIF2α protein kinase identified in fish. Although PKZ is most homologous to PKR, particularly in the C-terminal catalytic domain, it contains two N-terminal Z-DNA-binding domains (Zα1 and Zα2) instead of the dsRNA binding domains (dsRBDs) in PKR. As a novel member of eIF2α kinase family, the available data suggest that PKZ has some distinct mechanisms for recognition, binding, and B-Z DNA transition. Functionally, PKZ seems to be activated by the binding of Zα to Z-DNA and participates in innate immune responses. In this review, we summarize the recent progress on fish PKZ.
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Affiliation(s)
- Chuxin Wu
- Department of Natural Sciences, Yuzhang Normal University, Nanchang, China
| | - Yibing Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chengyu Hu
- Department of Bioscience, College of Life Sciences, Nanchang University, Nanchang, China
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15
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Ke F, Zhang QY. Aquatic animal viruses mediated immune evasion in their host. FISH & SHELLFISH IMMUNOLOGY 2019; 86:1096-1105. [PMID: 30557608 DOI: 10.1016/j.fsi.2018.12.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/09/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
Viruses are important and lethal pathogens that hamper aquatic animals. The result of the battle between host and virus would determine the occurrence of diseases. The host will fight against virus infection with various responses such as innate immunity, adaptive immunity, apoptosis, and so on. On the other hand, the virus also develops numerous strategies such as immune evasion to antagonize host antiviral responses. Here, We review the research advances on virus mediated immune evasions to host responses containing interferon response, NF-κB signaling, apoptosis, and adaptive response, which are executed by viral genes, proteins, and miRNAs from different aquatic animal viruses including Alloherpesviridae, Iridoviridae, Nimaviridae, Birnaviridae, Reoviridae, and Rhabdoviridae. Thus, it will facilitate the understanding of aquatic animal virus mediated immune evasion and potentially benefit the development of novel antiviral applications.
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Affiliation(s)
- Fei Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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16
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Kuś K, Rakus K, Boutier M, Tsigkri T, Gabriel L, Vanderplasschen A, Athanasiadis A. The Structure of the Cyprinid herpesvirus 3 ORF112-Zα·Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response. J Biol Chem 2015; 290:30713-25. [PMID: 26559969 DOI: 10.1074/jbc.m115.679407] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Indexed: 01/10/2023] Open
Abstract
In vertebrate species, the innate immune system down-regulates protein translation in response to viral infection through the action of the double-stranded RNA (dsRNA)-activated protein kinase (PKR). In some teleost species another protein kinase, Z-DNA-dependent protein kinase (PKZ), plays a similar role but instead of dsRNA binding domains, PKZ has Zα domains. These domains recognize the left-handed conformer of dsDNA and dsRNA known as Z-DNA/Z-RNA. Cyprinid herpesvirus 3 infects common and koi carp, which have PKZ, and encodes the ORF112 protein that itself bears a Zα domain, a putative competitive inhibitor of PKZ. Here we present the crystal structure of ORF112-Zα in complex with an 18-bp CpG DNA repeat, at 1.5 Å. We demonstrate that the bound DNA is in the left-handed conformation and identify key interactions for the specificity of ORF112. Localization of ORF112 protein in stress granules induced in Cyprinid herpesvirus 3-infected fish cells suggests a functional behavior similar to that of Zα domains of the interferon-regulated, nucleic acid surveillance proteins ADAR1 and DAI.
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Affiliation(s)
- Krzysztof Kuś
- From the Instituto Gulbenkian de Ciência, 2781-156, Oeiras, Portugal and
| | - Krzysztof Rakus
- the Immunology-Vaccinology Laboratory, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - Maxime Boutier
- the Immunology-Vaccinology Laboratory, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - Theokliti Tsigkri
- From the Instituto Gulbenkian de Ciência, 2781-156, Oeiras, Portugal and
| | - Luisa Gabriel
- From the Instituto Gulbenkian de Ciência, 2781-156, Oeiras, Portugal and
| | - Alain Vanderplasschen
- the Immunology-Vaccinology Laboratory, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
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17
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Boutier M, Ronsmans M, Rakus K, Jazowiecka-Rakus J, Vancsok C, Morvan L, Peñaranda MMD, Stone DM, Way K, van Beurden SJ, Davison AJ, Vanderplasschen A. Cyprinid Herpesvirus 3: An Archetype of Fish Alloherpesviruses. Adv Virus Res 2015; 93:161-256. [PMID: 26111587 DOI: 10.1016/bs.aivir.2015.03.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The order Herpesvirales encompasses viruses that share structural, genetic, and biological properties. However, members of this order infect hosts ranging from molluscs to humans. It is currently divided into three phylogenetically related families. The Alloherpesviridae family contains viruses infecting fish and amphibians. There are 12 alloherpesviruses described to date, 10 of which infect fish. Over the last decade, cyprinid herpesvirus 3 (CyHV-3) infecting common and koi carp has emerged as the archetype of fish alloherpesviruses. Since its first description in the late 1990s, this virus has induced important economic losses in common and koi carp worldwide. It has also had negative environmental implications by affecting wild carp populations. These negative impacts and the importance of the host species have stimulated studies aimed at developing diagnostic and prophylactic tools. Unexpectedly, the data generated by these applied studies have stimulated interest in CyHV-3 as a model for fundamental research. This review intends to provide a complete overview of the knowledge currently available on CyHV-3.
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Affiliation(s)
- Maxime Boutier
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Maygane Ronsmans
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Krzysztof Rakus
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Joanna Jazowiecka-Rakus
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Catherine Vancsok
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Léa Morvan
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Ma Michelle D Peñaranda
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - David M Stone
- The Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset, United Kingdom
| | - Keith Way
- The Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset, United Kingdom
| | - Steven J van Beurden
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Alain Vanderplasschen
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
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Adamek M, Steinhagen D, Irnazarow I, Hikima JI, Jung TS, Aoki T. Biology and host response to Cyprinid herpesvirus 3 infection in common carp. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 43:151-159. [PMID: 23981329 DOI: 10.1016/j.dci.2013.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 06/02/2023]
Abstract
Viruses from the family Alloherpesviridae form an aquatic clade of herpesviruses infecting fish and amphibia. Diseases caused by these herpesviruses are of increasing importance because of the high morbidity and mortality associated with the infection, and the difficulties in diagnosing latently infected carriers. Cyprinid herpesvirus 3 (CyHV-3) induces a severe disease and mortality in common carp and thus greatly affects carp aquaculture and trade. This review summarises advancements in the understanding of the infection process and the current knowledge on immune responses of carp to CyHV-3. A focus is laid on host genetics and immunity responsible for resistance/survival from the disease and on the viral mechanisms accountable for evasion of carp immune responses. As current knowledge of immune responses to CyHV-3 is still limited, perspectives for future studies are outlined. Analysing CyHV-3 fish-host interactions will be useful and thought-provoking for a basic understanding of fish immune responses.
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Affiliation(s)
- Mikołaj Adamek
- Fish Disease Research Unit, Centre of Infectious Diseases, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
| | - Dieter Steinhagen
- Fish Disease Research Unit, Centre of Infectious Diseases, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany.
| | - Ilgiz Irnazarow
- Polish Academy of Sciences, Institute of Ichthyobiology and Aquaculture in Gołysz, Kalinowa 2, 43-520 Chybie, Poland
| | - Jun-ichi Hikima
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, 900 Gajwa-dong, Jinju, Gyeongnam 660-710, South Korea
| | - Tae-Sung Jung
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, 900 Gajwa-dong, Jinju, Gyeongnam 660-710, South Korea
| | - Takashi Aoki
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, 900 Gajwa-dong, Jinju, Gyeongnam 660-710, South Korea; Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513, Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
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Kim D, Hur J, Park K, Bae S, Shin D, Ha SC, Hwang HY, Hohng S, Lee JH, Lee S, Kim YG, Kim KK. Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ). Nucleic Acids Res 2014; 42:5937-48. [PMID: 24682817 PMCID: PMC4027156 DOI: 10.1093/nar/gku189] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Double-stranded ribonucleic acid-activated protein kinase (PKR) downregulates translation as a defense mechanism against viral infection. In fish species, PKZ, a PKR-like protein kinase containing left-handed deoxyribonucleic acid (Z-DNA) binding domains, performs a similar role in the antiviral response. To understand the role of PKZ in Z-DNA recognition and innate immune response, we performed structural and functional studies of the Z-DNA binding domain (Zα) of PKZ from Carassius auratus (caZαPKZ). The 1.7-Å resolution crystal structure of caZαPKZ:Z-DNA revealed that caZαPKZ shares the overall fold with other Zα, but has discrete structural features that differentiate its DNA binding mode from others. Functional analyses of caZαPKZ and its mutants revealed that caZαPKZ mediates the fastest B-to-Z transition of DNA among Zα, and the minimal interaction for Z-DNA recognition is mediated by three backbone phosphates and six residues of caZαPKZ. Structure-based mutagenesis and B-to-Z transition assays confirmed that Lys56 located in the β-wing contributes to its fast B-to-Z transition kinetics. Investigation of the DNA binding kinetics of caZαPKZ further revealed that the B-to-Z transition rate is positively correlated with the association rate constant. Taking these results together, we conclude that the positive charge in the β-wing largely affects fast B-to-Z transition activity by enhancing the DNA binding rate.
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Affiliation(s)
- Doyoun Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Jeonghwan Hur
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Kwangsoo Park
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Sangsu Bae
- Department of Physics and Astronomy, Seoul National University, Seoul 151-747, Korea National Center for Creative Research Initiatives, Seoul National University, Seoul 151-747, Korea
| | - Donghyuk Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Sung Chul Ha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea
| | - Hye-Yeon Hwang
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, Seoul National University, Seoul 151-747, Korea National Center for Creative Research Initiatives, Seoul National University, Seoul 151-747, Korea Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-747, Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 660-701, Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Yang-Gyun Kim
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
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Thakur M, Seo EJ, Dever TE. Variola virus E3L Zα domain, but not its Z-DNA binding activity, is required for PKR inhibition. RNA (NEW YORK, N.Y.) 2014; 20:214-27. [PMID: 24335187 PMCID: PMC3895273 DOI: 10.1261/rna.042341.113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Responding to viral infection, the interferon-induced, double-stranded RNA (dsRNA)-activated protein kinase PKR phosphorylates translation initiation factor eIF2α to inhibit cellular and viral protein synthesis. To overcome this host defense mechanism, many poxviruses express the protein E3L, containing an N-terminal Z-DNA binding (Zα) domain and a C-terminal dsRNA-binding domain (dsRBD). While E3L is thought to inhibit PKR activation by sequestering dsRNA activators and by directly binding the kinase, the role of the Zα domain in PKR inhibition remains unclear. Here, we show that the E3L Zα domain is required to suppress the growth-inhibitory properties associated with expression of human PKR in yeast, to inhibit PKR kinase activity in vitro, and to reverse the inhibitory effects of PKR on reporter gene expression in mammalian cells treated with dsRNA. Whereas previous studies revealed that the Z-DNA binding activity of E3L is critical for viral pathogenesis, we identified point mutations in E3L that functionally uncouple Z-DNA binding and PKR inhibition. Thus, our studies reveal a molecular distinction between the nucleic acid binding and PKR inhibitory functions of the E3L Zα domain, and they support the notion that E3L contributes to viral pathogenesis by targeting PKR and other components of the cellular anti-viral defense pathway.
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21
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Rakus K, Ouyang P, Boutier M, Ronsmans M, Reschner A, Vancsok C, Jazowiecka-Rakus J, Vanderplasschen A. Cyprinid herpesvirus 3: an interesting virus for applied and fundamental research. Vet Res 2013; 44:85. [PMID: 24073814 PMCID: PMC3850573 DOI: 10.1186/1297-9716-44-85] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/03/2013] [Indexed: 12/28/2022] Open
Abstract
Cyprinid herpesvirus 3 (CyHV-3), a member of the family Alloherpesviridae is the causative agent of a lethal, highly contagious and notifiable disease in common and koi carp. The economic importance of common and koi carp industries together with the rapid spread of CyHV-3 worldwide, explain why this virus became soon after its isolation in the 1990s a subject of applied research. In addition to its economic importance, an increasing number of fundamental studies demonstrated that CyHV-3 is an original and interesting subject for fundamental research. In this review, we summarized recent advances in CyHV-3 research with a special interest for studies related to host-virus interactions.
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Affiliation(s)
- Krzysztof Rakus
- Immunology-Vaccinology (B43b), Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, Liège, B-4000, Belgium.
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22
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Ng SK, Weissbach R, Ronson GE, Scadden ADJ. Proteins that contain a functional Z-DNA-binding domain localize to cytoplasmic stress granules. Nucleic Acids Res 2013; 41:9786-99. [PMID: 23982513 PMCID: PMC3834823 DOI: 10.1093/nar/gkt750] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Long double-stranded RNA may undergo hyper-editing by adenosine deaminases that act on RNA (ADARs), where up to 50% of adenosine residues may be converted to inosine. However, although numerous RNAs may undergo hyper-editing, the role for inosine-containing hyper-edited double-stranded RNA in cells is poorly understood. Nevertheless, editing plays a critical role in mammalian cells, as highlighted by the analysis of ADAR-null mutants. In particular, the long form of ADAR1 (ADAR1p150) is essential for viability. Moreover, a number of studies have implicated ADAR1p150 in various stress pathways. We have previously shown that ADAR1p150 localized to cytoplasmic stress granules in HeLa cells following either oxidative or interferon-induced stress. Here, we show that the Z-DNA-binding domain (ZαADAR1) exclusively found in ADAR1p150 is required for its localization to stress granules. Moreover, we show that fusion of ZαADAR1 to either green fluorescent protein (GFP) or polypyrimidine binding protein 4 (PTB4) also results in their localization to stress granules. We additionally show that the Zα domain from other Z-DNA-binding proteins (ZBP1, E3L) is likewise sufficient for localization to stress granules. Finally, we show that Z-RNA or Z-DNA binding is important for stress granule localization. We have thus identified a novel role for Z-DNA-binding domains in mammalian cells.
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Affiliation(s)
- Siew Kit Ng
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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23
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de Rosa M, Zacarias S, Athanasiadis A. Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ. Nucleic Acids Res 2013; 41:9924-33. [PMID: 23975196 PMCID: PMC3834819 DOI: 10.1093/nar/gkt743] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The RNA-dependent protein kinase PKR plays a central role in the antiviral defense of vertebrates by shutting down protein translation upon detection of viral dsRNA in the cytoplasm. In some teleost fish, PKZ, a homolog of PKR, performs the same function, but surprisingly, instead of dsRNA binding domains, it harbors two Z-DNA/Z-RNA-binding domains belonging to the Zalpha domain family. Zalpha domains have also been found in other proteins, which have key roles in the regulation of interferon responses such as ADAR1 and DNA-dependent activator of IFN-regulatory factors (DAI) and in viral proteins involved in immune response evasion such as the poxviral E3L and the Cyprinid Herpesvirus 3 ORF112. The underlying mechanism of nucleic acids binding and stabilization by Zalpha domains is still unclear. Here, we present two crystal structures of the zebrafish PKZ Zalpha domain (DrZalphaPKZ) in alternatively organized complexes with a (CG)6 DNA oligonucleotide at 2 and 1.8 Å resolution. These structures reveal novel aspects of the Zalpha interaction with DNA, and they give insights on the arrangement of multiple Zalpha domains on DNA helices longer than the minimal binding site.
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Affiliation(s)
| | | | - Alekos Athanasiadis
- *To whom correspondence should be addressed. Tel: +351 21 4464648; Fax: +351 21 4407970;
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