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Xu P, Liu Y, Liu C, Guey B, Li L, Melenec P, Ricci J, Ablasser A. The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Nature 2024; 627:873-879. [PMID: 38418882 PMCID: PMC10972748 DOI: 10.1038/s41586-024-07112-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2'3'-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA demands tight regulatory mechanisms that are necessary to maintain cell and tissue homeostasis under normal conditions. Inside the cell nucleus, anchoring to nucleosomes and competition with chromatin architectural proteins jointly prohibit cGAS activation by genomic DNA8-15. However, the fate of nuclear cGAS and its role in cell physiology remains unclear. Here we show that the ubiquitin proteasomal system (UPS) degrades nuclear cGAS in cycling cells. We identify SPSB3 as the cGAS-targeting substrate receptor that associates with the cullin-RING ubiquitin ligase 5 (CRL5) complex to ligate ubiquitin onto nuclear cGAS. A cryo-electron microscopy structure of nucleosome-bound cGAS in a complex with SPSB3 reveals a highly conserved Asn-Asn (NN) minimal degron motif at the C terminus of cGAS that directs SPSB3 recruitment, ubiquitylation and cGAS protein stability. Interference with SPSB3-regulated nuclear cGAS degradation primes cells for type I interferon signalling, conferring heightened protection against infection by DNA viruses. Our research defines protein degradation as a determinant of cGAS regulation in the nucleus and provides structural insights into an element of cGAS that is amenable to therapeutic exploitation.
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Affiliation(s)
- Pengbiao Xu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Ying Liu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- School of Medicine, Jiangnan University, Wuxi, China
| | - Chong Liu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Baptiste Guey
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Lingyun Li
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Pauline Melenec
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Jonathan Ricci
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Ablasser
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Institute for Cancer Research (ISREC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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2
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Ornelas MY, Thomas AY, Johnson Rosas LI, Medina GN, Mehta AP. Characterization, Directed Evolution, and Targeting of DNA Virus-Encoded RNA Capping Enzymes Using Phenotypic Yeast Platforms. ACS Chem Biol 2023; 18:1808-1820. [PMID: 37498174 PMCID: PMC11024868 DOI: 10.1021/acschembio.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The constant and the sudden emergence of zoonotic human and animal viruses is a significant threat to human health, the world economy, and the world food supply. This has necessitated the development of broad-spectrum therapeutic strategies to combat these emerging pathogens. Mechanisms that are essential for viral replication and propagation have been successfully targeted in the past to develop broad-spectrum therapeutics that can be readily repurposed to combat new zoonotic pathogens. Because of the importance of viral RNA capping enzymes to viral replication and pathogenesis, as well as their presence in both DNA and RNA viruses, these viral proteins have been a long-standing therapeutic target. Here, we use genome sequencing information and yeast-based platforms (YeRC0M) to identify, characterize, and target viral genome-encoded essential RNA capping enzymes from emerging strains of DNA viruses, i.e., Monkeypox virus and African Swine Fever Virus, which are a significant threat to human and domestic animal health. We first identified and biochemically characterized these viral RNA capping enzymes and their necessary protein domains. We observed significant differences in functional protein domains and organization for RNA capping enzymes from emerging DNA viruses in comparison to emerging RNA viruses. We also observed several differences in the biochemical properties of these viral RNA capping enzymes using our phenotypic yeast-based approaches (YeRC0M) as compared to the previous in vitro studies. Further, using directed evolution, we were able to identify inactivation and attenuation mutations in these essential viral RNA capping enzymes; these data could have implications on virus biocontainment as well as live attenuated vaccine development. We also developed methods that would facilitate high-throughput phenotypic screening to identify broad-spectrum inhibitors that selectively target viral RNA capping enzymes over host RNA capping enzymes. As demonstrated here, our approaches to identify, characterize, and target viral genome-encoded essential RNA capping enzymes are highly modular and can be readily adapted for targeting emerging viral pathogens as well as their variants that emerge in the future.
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Affiliation(s)
- Marya Y Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, Illinois 61801, United States
| | - Angela Y Thomas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, Illinois 61801, United States
| | - L Idalee Johnson Rosas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, Illinois 61801, United States
| | - Gisselle N Medina
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, New York 11944, United States
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, Kansas 66502, United States
| | - Angad P Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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3
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Liu S, Han Y, Li WX, Ding SW. Infection Defects of RNA and DNA Viruses Induced by Antiviral RNA Interference. Microbiol Mol Biol Rev 2023; 87:e0003522. [PMID: 37052496 PMCID: PMC10304667 DOI: 10.1128/mmbr.00035-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Immune recognition of viral genome-derived double-stranded RNA (dsRNA) molecules and their subsequent processing into small interfering RNAs (siRNAs) in plants, invertebrates, and mammals trigger specific antiviral immunity known as antiviral RNA interference (RNAi). Immune sensing of viral dsRNA is sequence-independent, and most regions of viral RNAs are targeted by virus-derived siRNAs which extensively overlap in sequence. Thus, the high mutation rates of viruses do not drive immune escape from antiviral RNAi, in contrast to other mechanisms involving specific virus recognition by host immune proteins such as antibodies and resistance (R) proteins in mammals and plants, respectively. Instead, viruses actively suppress antiviral RNAi at various key steps with a group of proteins known as viral suppressors of RNAi (VSRs). Some VSRs are so effective in virus counter-defense that potent inhibition of virus infection by antiviral RNAi is undetectable unless the cognate VSR is rendered nonexpressing or nonfunctional. Since viral proteins are often multifunctional, resistance phenotypes of antiviral RNAi are accurately defined by those infection defects of VSR-deletion mutant viruses that are efficiently rescued by host deficiency in antiviral RNAi. Here, we review and discuss in vivo infection defects of VSR-deficient RNA and DNA viruses resulting from the actions of host antiviral RNAi in model systems.
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Affiliation(s)
- Si Liu
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Yanhong Han
- Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wan-Xiang Li
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Shou-Wei Ding
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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4
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Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA. Structural atlas of a human gut crassvirus. Nature 2023; 617:409-416. [PMID: 37138077 PMCID: PMC10172136 DOI: 10.1038/s41586-023-06019-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/27/2023] [Indexed: 05/05/2023]
Abstract
CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals1-4. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses4,5. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss0016, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
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Affiliation(s)
- Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Andrey N Shkoporov
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ekaterina V Khokhlova
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
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5
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Sun S, Xu Y, Qiu M, Jiang S, Cao Q, Luo J, Zhang T, Chen N, Zheng W, Meurens F, Liu Z, Zhu J. Manganese Mediates Its Antiviral Functions in a cGAS-STING Pathway Independent Manner. Viruses 2023; 15:v15030646. [PMID: 36992355 PMCID: PMC10058264 DOI: 10.3390/v15030646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The innate immune system is the first line of host defense sensing viral infection. Manganese (Mn) has recently been found to be involved in the activation of the innate immune DNA-sensing cGAS-STING pathway and subsequent anti-DNA virus function. However, it is still unclear whether Mn2+ mediates host defense against RNA viruses. In this study, we demonstrate that Mn2+ exhibited antiviral effects against various animal and human viruses, including RNA viruses such as PRRSVs and VSV, as well as DNA viruses such as HSV1, in a dose-dependent manner. Moreover, cGAS and STING were both investigated in the Mn2+ mediated antiviral roles using the knockout cells made by the CRISPR-Cas9 approach. Unexpectedly, the results revealed that neither cGAS knockout nor STING knockout had any effect on Mn2+-mediated antiviral functions. Nevertheless, we verified that Mn2+ promoted the activation of the cGAS-STING signaling pathway. These findings suggest that Mn2+ has broad-spectrum antiviral activities in a cGAS-STING pathway independent manner. This study also provides significant insights into redundant mechanisms participating in the Mn2+ antiviral functions, and also indicates a new target for Mn2+ antiviral therapeutics.
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Affiliation(s)
- Shaohua Sun
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yulin Xu
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Ming Qiu
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Sen Jiang
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Qi Cao
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jia Luo
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Tangjie Zhang
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Nanhua Chen
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Wanglong Zheng
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Francois Meurens
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, St. Hyacinthe, QC J2S 2M2, Canada
- Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Zongping Liu
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.L.); (J.Z.)
| | - Jianzhong Zhu
- College Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.L.); (J.Z.)
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6
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Wang ZZ, Ye XQ, Huang JH, Chen XX. Virus and endogenous viral element-derived small non-coding RNAs and their roles in insect-virus interaction. Curr Opin Insect Sci 2022; 49:85-92. [PMID: 34974161 DOI: 10.1016/j.cois.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
RNA interference pathways mediated by different types of small non-coding RNAs (siRNAs, miRNAs and piRNAs) are conserved biological responses to exotic stresses, including viral infection. Aside from the well-established siRNA pathway, the miRNA pathway and the piRNA pathway process viral sequences, exogenously or endogenously, into miRNAs and piRNAs, respectively. During the host-virus interaction, viral sequences, including both coding and non-coding sequences, can be integrated as endogenous viral elements (EVEs) and thereby become present within the germline of a non-viral organism. In recent years, significant progress has been made in characterizing the biogenesis and function of viruses and EVEs associated with snRNAs. Overall, the siRNA pathway acts as the primarily antiviral defense against a wide range of exogenous viruses; the miRNA pathways associated with viruses or EVEs function in antiviral response and host gene regulation; EVE derived piRNAs with a ping-pong signature have the potential to limit cognate viral infection.
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Affiliation(s)
- Zhi-Zhi Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Xi-Qian Ye
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Jian-Hua Huang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Xue-Xin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; State Key Lab of Rice Biology, Zhejiang University, Hangzhou 310058, China.
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7
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Chelico L. Special Issue "APOBECs and Virus Restriction". Viruses 2021; 13:v13081613. [PMID: 34452478 PMCID: PMC8402836 DOI: 10.3390/v13081613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada
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8
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Abstract
Encapsulins are a class of microbial protein compartments defined by the viral HK97-fold of their capsid protein, self-assembly into icosahedral shells, and dedicated cargo loading mechanism for sequestering specific enzymes. Encapsulins are often misannotated and traditional sequence-based searches yield many false positive hits in the form of phage capsids. Here, we develop an integrated search strategy to carry out a large-scale computational analysis of prokaryotic genomes with the goal of discovering an exhaustive and curated set of all HK97-fold encapsulin-like systems. We find over 6,000 encapsulin-like systems in 31 bacterial and four archaeal phyla, including two novel encapsulin families. We formulate hypotheses about their potential biological functions and biomedical relevance, which range from natural product biosynthesis and stress resistance to carbon metabolism and anaerobic hydrogen production. An evolutionary analysis of encapsulins and related HK97-type virus families shows that they share a common ancestor, and we conclude that encapsulins likely evolved from HK97-type bacteriophages.
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Affiliation(s)
- Michael P Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
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9
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Kadono T, Tomaru Y, Suzuki K, Yamada K, Adachi M. The possibility of using marine diatom-infecting viral promoters for the engineering of marine diatoms. Plant Sci 2020; 296:110475. [PMID: 32540005 DOI: 10.1016/j.plantsci.2020.110475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 02/26/2020] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
Marine diatoms constitute a major group of unicellular photosynthetic eukaryotes. Diatoms are widely applicable for both basic studies and applied studies. Molecular tools and techniques have been developed for diatom research. Among these tools, several endogenous gene promoters (e.g., the fucoxanthin chlorophyll a/c-binding protein gene promoter) have become available for expressing transgenes in diatoms. Gene promoters that drive transgene expression at a high level are very important for the metabolic engineering of diatoms. Various marine diatom-infecting viruses (DIVs), including both DNA viruses and RNA viruses, have recently been isolated, and their genome sequences have been characterized. Promoters from viruses that infect plants and mammals are widely used as constitutive promoters to achieve high expression of transgenes. Thus, we recently investigated the activity of promoters derived from marine DIVs in the marine diatom, Phaeodactylum tricornutum. We discuss novel viral promoters that will be useful for the future metabolic engineering of diatoms.
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Affiliation(s)
- Takashi Kadono
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan
| | - Kengo Suzuki
- euglena Co., Ltd., G-BASE Tamachi 2nd and 3rd Floor 5-29-11 Shiba Minato-ku, Tokyo, 108-0014, Japan
| | - Koji Yamada
- euglena Co., Ltd., G-BASE Tamachi 2nd and 3rd Floor 5-29-11 Shiba Minato-ku, Tokyo, 108-0014, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi, 783-8502, Japan.
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10
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Christensen-Quick A, Massanella M, Frick A, Rawlings SA, Spina C, Vargas-Meneses M, Schrier R, Nakazawa M, Anderson C, Gianella S. Subclinical Cytomegalovirus DNA Is Associated with CD4 T Cell Activation and Impaired CD8 T Cell CD107a Expression in People Living with HIV despite Early Antiretroviral Therapy. J Virol 2019; 93:e00179-19. [PMID: 31019052 PMCID: PMC6580967 DOI: 10.1128/jvi.00179-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/12/2019] [Indexed: 01/27/2023] Open
Abstract
Most people living with HIV (PLWH) are coinfected with cytomegalovirus (CMV). Subclinical CMV replication is associated with immune dysfunction and with increased HIV DNA in antiretroviral therapy (ART)-naive and -suppressed PLWH. To identify immunological mechanisms by which CMV could favor HIV persistence, we analyzed 181 peripheral blood mononuclear cell (PBMC) samples from 64 PLWH starting ART during early HIV infection with subsequent virologic suppression up to 58 months. In each sample, we measured levels of CMV and Epstein-Barr virus (EBV) DNA by droplet digital PCR (ddPCR). We also measured expression of immunological markers for activation (HLA-DR+ CD38+), cycling (Ki-67+), degranulation (CD107a+), and the immune checkpoint protein PD-1 on CD4+ and CD8+ T cell memory subsets. Significant differences in percentages of lymphocyte markers by CMV/EBV shedding were identified using generalized linear mixed-effects models. Overall, CMV DNA was detected at 60/181 time points. At the time of ART initiation, the presence of detectable CMV DNA was associated with increased CD4+ T cell activation and CD107a expression and with increased CD8+ T cellular cycling and reduced CD107a expression on CD8+ T cells. While some effects disappeared during ART, greater CD4+ T cell activation and reduced CD107a expression on CD8+ T cells persisted when CMV was present (P < 0.01). In contrast, EBV was not associated with any immunological differences. Among the covariates, peak HIV RNA and CD4/CD8 ratio had the most significant effect on the immune system. In conclusion, our study identified immune differences in PLWH with detectable CMV starting early ART, which may represent an additional hurdle for HIV cure efforts.IMPORTANCE Chronic viral infections such as with HIV and CMV last a lifetime and can continually antagonize the immune system. Both viruses are associated with higher expression of inflammation markers, and recent evidence suggests that CMV may complicate efforts to deplete HIV reservoirs. Our group and others have shown that CMV shedding is associated with a larger HIV reservoir. Subclinical CMV replication could favor HIV persistence via bystander effects on our immune system. In this study, we collected longitudinal PBMC samples from people starting ART and measured immune changes associated with detectable CMV. We found that when CMV was detectable, CD4+ T cell activation was higher and CD8+ T cell degranulation was lower. Both results may contribute to the slower decay of the size of the reservoir during CMV replication, since activated CD4+ T cells are more vulnerable to HIV infection, while the loss of CD8+ T cell degranulation may impede the proper killing of infected cells.
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Affiliation(s)
| | - Marta Massanella
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Canada
| | - Andrew Frick
- Department of Medicine, University of California, San Diego, California, USA
| | - Stephen A Rawlings
- Department of Medicine, University of California, San Diego, California, USA
| | - Celsa Spina
- Department of Medicine, University of California, San Diego, California, USA
| | | | - Rachel Schrier
- Department of Medicine, University of California, San Diego, California, USA
| | - Masato Nakazawa
- Department of Medicine, University of California, San Diego, California, USA
| | - Christy Anderson
- Department of Medicine, University of California, San Diego, California, USA
| | - Sara Gianella
- Department of Medicine, University of California, San Diego, California, USA
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11
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Lu Y, Stuart JH, Talbot-Cooper C, Agrawal-Singh S, Huntly B, Smid AI, Snowden JS, Dupont L, Smith GL. Histone deacetylase 4 promotes type I interferon signaling, restricts DNA viruses, and is degraded via vaccinia virus protein C6. Proc Natl Acad Sci U S A 2019; 116:11997-12006. [PMID: 31127039 PMCID: PMC6575207 DOI: 10.1073/pnas.1816399116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interferons (IFNs) represent an important host defense against viruses. Type I IFNs induce JAK-STAT signaling and expression of IFN-stimulated genes (ISGs), which mediate antiviral activity. Histone deacetylases (HDACs) perform multiple functions in regulating gene expression and some class I HDACs and the class IV HDAC, HDAC11, influence type I IFN signaling. Here, HDAC4, a class II HDAC, is shown to promote type I IFN signaling and coprecipitate with STAT2. Pharmacological inhibition of class II HDAC activity, or knockout of HDAC4 from HEK-293T and HeLa cells, caused a defective response to IFN-α. This defect in HDAC4-/- cells was rescued by reintroduction of HDAC4 or catalytically inactive HDAC4, but not HDAC1 or HDAC5. ChIP analysis showed HDAC4 was recruited to ISG promoters following IFN stimulation and was needed for binding of STAT2 to these promoters. The biological importance of HDAC4 as a virus restriction factor was illustrated by the observations that (i) the replication and spread of vaccinia virus (VACV) and herpes simplex virus type 1 (HSV-1) were enhanced in HDAC4-/- cells and inhibited by overexpression of HDAC4; and (ii) HDAC4 is targeted for proteasomal degradation during VACV infection by VACV protein C6, a multifunctional IFN antagonist that coprecipitates with HDAC4 and is necessary and sufficient for HDAC4 degradation.
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Affiliation(s)
- Yongxu Lu
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Jennifer H Stuart
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Callum Talbot-Cooper
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Shuchi Agrawal-Singh
- Cambridge Institute for Medical Research, University of Cambridge, CB2 0XY Cambridge, United Kingdom
| | - Brian Huntly
- Cambridge Institute for Medical Research, University of Cambridge, CB2 0XY Cambridge, United Kingdom
| | - Andrei I Smid
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Joseph S Snowden
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Liane Dupont
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom;
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12
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Affiliation(s)
- Sarah Duponchel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Matthias G. Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
- * E-mail:
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13
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Ziv C, Malitsky S, Othman A, Ben-Dor S, Wei Y, Zheng S, Aharoni A, Hornemann T, Vardi A. Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga. Proc Natl Acad Sci U S A 2016; 113:E1907-16. [PMID: 26984500 PMCID: PMC4822627 DOI: 10.1073/pnas.1523168113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine viruses are the most abundant biological entities in the oceans shaping community structure and nutrient cycling. The interaction between the bloom-forming alga Emiliania huxleyi and its specific large dsDNA virus (EhV) is a major factor determining the fate of carbon in the ocean, thus serving as a key host-pathogen model system. The EhV genome encodes for a set of genes involved in the de novo sphingolipid biosynthesis, not reported in any viral genome to date. We combined detailed lipidomic and biochemical analyses to characterize the functional role of this virus-encoded pathway during lytic viral infection. We identified a major metabolic shift, mediated by differential substrate specificity of virus-encoded serine palmitoyltransferase, a key enzyme of sphingolipid biosynthesis. Consequently, unique viral glycosphingolipids, composed of unusual hydroxylated C17 sphingoid bases (t17:0) were highly enriched in the infected cells, and their synthesis was found to be essential for viral assembly. These findings uncover the biochemical bases of the virus-induced metabolic rewiring of the host sphingolipid biosynthesis during the chemical "arms race" in the ocean.
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Affiliation(s)
- Carmit Ziv
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alaa Othman
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland; Institute of Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, 23562 Lübeck, Germany
| | - Shifra Ben-Dor
- Biological Services Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yu Wei
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Shuning Zheng
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
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14
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Adriaenssens EM, van Zyl LJ, Cowan DA, Trindade MI. Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses. Viruses 2016; 8:v8010014. [PMID: 26761024 PMCID: PMC4728574 DOI: 10.3390/v8010014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/26/2015] [Accepted: 12/14/2015] [Indexed: 11/26/2022] Open
Abstract
Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.
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Affiliation(s)
- Evelien M Adriaenssens
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Natural Sciences II, Lynnwood Road, 0002 Pretoria, South Africa.
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, 7535 Bellville, Cape Town, South Africa.
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Natural Sciences II, Lynnwood Road, 0002 Pretoria, South Africa.
| | - Marla I Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, 7535 Bellville, Cape Town, South Africa.
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15
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Du M, Chen M, Shen H, Wang W, Li Z, Wang W, Huang J, Chen J. CyHV-2 ORF104 activates the p38 MAPK pathway. Fish Shellfish Immunol 2015; 46:268-273. [PMID: 26072141 DOI: 10.1016/j.fsi.2015.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 06/04/2023]
Abstract
Cyprinid herpesvirus 2 (CyHV-2) is the pathogen responsible for herpesviral hematopoietic necrosis disease, which causes huge losses on aquaculture. So far the studies of CyHV-2 mainly focus on the identification and detection of this virus, but little is known about the role of specific CyHV-2 genes in the infection process. Based on the genomic information, CyHV-2 ORF104 encodes a kinase-like protein, which is highly conserved among the three CyHVs. Our study was initiated to investigate the role of kinase-like protein ORF104 during virus infection. Subcellular localization study showed that ORF104 was mainly expressed in the nucleus in both human HEK293T and fish EPC cells. However, deletion of the putative nuclear localization signal of ORF104 (ORF104M) resulted in the cytoplasmic distribution in HEK293T. We then examined whether MAPKs were involved in the ORF104-mediated signaling pathway by overexpressing ORF104 and ORF104M in HEK293T. Overexpression of ORF104 and ORF104M resulted in the up-regulation of p38 phosphorylation, but not JNK or ERK, indicating that ORF104 specifically activates p38 signaling pathway. In vivo study showed that CyHV-2 infection enhanced p38 phosphorylation in gibel carp (Carassius auratus gibelio). Interestingly, p38 inhibitor SB203580 strongly reduced fish death caused by CyHV-2 infection. Therefore, our study for the first time reveals the function of ORF104 during CyHV-2 infection, indicating that ORF104 is a potential vaccine candidate for CyHV-2.
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Affiliation(s)
- Mi Du
- School of Marine Sciences, Ningbo University, Ningbo, 315211 Zhejiang, China; State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 Fujian, China
| | - Mingliang Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 Fujian, China
| | - Haifeng Shen
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 Fujian, China
| | - Wei Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 Fujian, China
| | - Zengpeng Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 Fujian, China
| | - Weiyi Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 Fujian, China
| | - Jianhui Huang
- Putian Aquatic Products, Technical Extension Station, Putian, 351100 Fujian, China
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 Fujian, China.
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16
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Pentland I, Parish JL. Targeting CTCF to Control Virus Gene Expression: A Common Theme amongst Diverse DNA Viruses. Viruses 2015; 7:3574-85. [PMID: 26154016 PMCID: PMC4517120 DOI: 10.3390/v7072791] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 12/27/2022] Open
Abstract
All viruses target host cell factors for successful life cycle completion. Transcriptional control of DNA viruses by host cell factors is important in the temporal and spatial regulation of virus gene expression. Many of these factors are recruited to enhance virus gene expression and thereby increase virus production, but host cell factors can also restrict virus gene expression and productivity of infection. CCCTC binding factor (CTCF) is a host cell DNA binding protein important for the regulation of genomic chromatin boundaries, transcriptional control and enhancer element usage. CTCF also functions in RNA polymerase II regulation and in doing so can influence co-transcriptional splicing events. Several DNA viruses, including Kaposi's sarcoma-associated herpesvirus (KSHV), Epstein-Barr virus (EBV) and human papillomavirus (HPV) utilize CTCF to control virus gene expression and many studies have highlighted a role for CTCF in the persistence of these diverse oncogenic viruses. CTCF can both enhance and repress virus gene expression and in some cases CTCF increases the complexity of alternatively spliced transcripts. This review article will discuss the function of CTCF in the life cycle of DNA viruses in the context of known host cell CTCF functions.
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Affiliation(s)
- Ieisha Pentland
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Joanna L Parish
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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17
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Wang Y, Lian Q, Yang B, Yan S, Zhou H, He L, Lin G, Lian Z, Jiang Z, Sun B. TRIM30α Is a Negative-Feedback Regulator of the Intracellular DNA and DNA Virus-Triggered Response by Targeting STING. PLoS Pathog 2015; 11:e1005012. [PMID: 26114947 PMCID: PMC4482643 DOI: 10.1371/journal.ppat.1005012] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 06/08/2015] [Indexed: 01/09/2023] Open
Abstract
Uncontrolled immune responses to intracellular DNA have been shown to induce autoimmune diseases. Homeostasis regulation of immune responses to cytosolic DNA is critical for limiting the risk of autoimmunity and survival of the host. Here, we report that the E3 ubiquitin ligase tripartite motif protein 30α (TRIM30α) was induced by herpes simplex virus type 1 (HSV-1) infection in dendritic cells (DCs). Knockdown or genetic ablation of TRIM30α augmented the type I IFNs and interleukin-6 response to intracellular DNA and DNA viruses. Trim30α-deficient mice were more resistant to infection by DNA viruses. Biochemical analyses showed that TRIM30α interacted with the stimulator of interferon genes (STING), which is a critical regulator of the DNA-sensing response. Overexpression of TRIM30α promoted the degradation of STING via K48-linked ubiquitination at Lys275 through a proteasome-dependent pathway. These findings indicate that E3 ligase TRIM30α is an important negative-feedback regulator of innate immune responses to DNA viruses by targeting STING.
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Affiliation(s)
- Yanming Wang
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qiaoshi Lian
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bo Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shanshan Yan
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Haiyan Zhou
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lan He
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guomei Lin
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhexiong Lian
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhengfan Jiang
- State Key Laboratory of Protein and Plant Gene Research, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China; Peking University-Tsinghua University Joint Center for Life Sciences, Beijing, China
| | - Bing Sun
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Virology & Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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18
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Abstract
Nucleocytoplasmic large dsDNA viruses (NCLDVs) encompass an ever-increasing group of large eukaryotic viruses, infecting a wide variety of organisms. The set of core genes shared by all these viruses includes a major capsid protein with a double jelly-roll fold forming an icosahedral capsid, which surrounds a double layer membrane that contains the viral genome. Furthermore, some of these viruses, such as the members of the Mimiviridae and Phycodnaviridae have a unique vertex that is used during infection to transport DNA into the host.
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19
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Wen CM, Ku CC, Wang CS. Viral susceptibility, transfection and growth of SPB--a fish neural progenitor cell line from the brain of snubnose pompano, Trachinotus blochii (Lacépède). J Fish Dis 2013; 36:657-667. [PMID: 23305502 DOI: 10.1111/jfd.12067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/08/2012] [Accepted: 11/11/2012] [Indexed: 06/01/2023]
Abstract
This study investigates the susceptibilities of the SPB cell line to fish viruses including giant seaperch iridovirus (GSIV-K1), red sea bream iridovirus (RSIV-Ku), grouper nervous necrosis virus (GNNV-K1), chum salmon reovirus (CSV) and eel herpesvirus (HVA). GSIV-K1, RSIV-Ku and CSV replicated well in SPB cells, with a significant cytopathic effect and virus production. However, the cells were HVA and GNNV refractory. To examine the ability of SPB cells to stably express foreign protein, expression vectors encoding GNNV B1 and B2 fused to enhanced green fluorescent protein (EGFP) and GSIV ORF35L fused to DsRed were constructed and introduced by transfection into SPB cells. Stable transfectants displayed different morphologies compared with SPB and with each other. EGFP-B1 was predominantly localized in the nuclei, EFPF-B2 was distributed throughout the cytoplasm and nucleus, and granular 35L-DsRed was localized with secreted vesicles. The expression of EFPF-B2 in SPB cells produced blebs on the surface, but the cells showing stable expression of EGFP, EGFP-B1 or 35L-DsRed showed normal morphologies. Results show the SPB cells and the transfected cells grow well at temperatures between 20 and 35 °C and with serum-dependent growth. SPB cells are suitable for studies on foreign protein expression and virology.
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Affiliation(s)
- C-M Wen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Nan-Tzu District, Taiwan.
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20
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Fabian M, Baumer A, Steinhagen D. Do wild fish species contribute to the transmission of koi herpesvirus to carp in hatchery ponds? J Fish Dis 2013; 36:505-514. [PMID: 23121232 DOI: 10.1111/jfd.12016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 08/29/2012] [Accepted: 09/11/2012] [Indexed: 06/01/2023]
Abstract
The koi herpesvirus (KHV) has spread worldwide since its discovery in 1998 and causes disease and mortality in koi and common carp populations with a high impact on the carp production industry. Many investigations have been conducted to examine ways of distribution and to identify possible transmission vectors. The answers, however, raise many new questions. In the present study, different wild fish species taken from carp ponds with a history of KHV infection were examined for their susceptibility to the virus. In the tissue of these fish, the virus load was determined and it was tested whether a release of the virus could be induced by stress and the virus then could be transferred to naive carp. Wild fish were gathered from carp ponds during acute outbreaks of virus-induced mortality in summer and from ponds stocked with carp carrying a latent KHV infection. From these ponds, wild fish were collected during the harvesting process in autumn or spring when the ponds were drained. We found that regardless of season, temperature variation, age and infection status of the carp stock, wild fish from carp ponds and its outlets could be tested positive for the KHV genome using real-time PCR with a low prevalence and virus load. Furthermore, virus transfer to naive carp was observed after a period of cohabitation. Cyprinid and non-cyprinid wild fish can therefore be considered as an epidemiological risk for pond carp farms.
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Affiliation(s)
- M Fabian
- Fish Disease Research Unit, Centre of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
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21
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Frías-Lasserre D. Non coding RNAs and viruses in the framework of the phylogeny of the genes, epigenesis and heredity. Int J Mol Sci 2012; 13:477-490. [PMID: 22312265 PMCID: PMC3269699 DOI: 10.3390/ijms13010477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 01/21/2023] Open
Abstract
The origin of genes is one of the most enigmatic events in the origin of life. It has been suggested that noncoding (nc) RNA was probably a precursor in the formation of the first polypeptide, and also at the origin of the first manifestation of life and genes. ncRNAs are also becoming central for understanding gene expression and silencing. Indeed, before the discovery of ncRNAs, proteins were viewed as the major molecules in the regulation of gene expression and gene silencing; however, recent findings suggest that ncRNA also plays an important role in gene expression. Reverse transcription of RNA viruses and their integration into the genome of eukaryotes and also their relationship with the ncRNA suggest that their origin is basal in genome evolution, and also probably constitute the first mechanism of gene regulation. I am to review the different roles of ncRNAs in the framework of gene evolution, as well as the importance of ncRNAs and viruses in the epigenesis and in the non-Mendelian model of heredity and evolution.
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Affiliation(s)
- Daniel Frías-Lasserre
- Institute of Entomology, Metropolitan University of Educational Sciences, Avenue J.P. Alessandri 774 Ñuñoa, Código Postal 7760197, Santiago, Chile; E-Mail: ; Tel.: +56-2-2412457; Fax: +56-2-2412699
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22
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Abstract
Large DNA viruses, such as herpesvirus and poxvirus, encode proteins that target and exploit the chemokine system of their host. UL146 and UL147 in the cytomegalovirus (CMV) genome encode the two CXC chemokines vCXCL1 and vCXCL2. In this study, vCXCL1 was probed against a panel of the 18 classified human chemokine receptors. In calcium mobilization assays vCXCL1 acted as an agonist on both CXCR1 and CXCR2 but did not activate or block any of the other 16 chemokine receptors. vCXCL1 was characterized and compared with CXCL1/GROalpha, CXCL2/GRObeta, CXCL3/GROgamma, CXCL5/ENA-78, CXCL6/GCP-2, CXCL7/NAP-2 and CXCL8/IL-8 in competition binding, calcium mobilization, inositol triphosphate turnover, and chemotaxis assays using CXCR1- and CXCR2-expressing Chinese hamster ovary, 300.19, COS7, and L1.2 cells. The affinities of vCXCL1 for the CXCR1 and CXCR2 receptors were 44 and 5.6 nm, respectively, as determined in competition binding against radioactively labeled CXCL8. In calcium mobilization, phosphatidylinositol turnover, and chemotaxis assays, vCXCL1 acted as a highly efficacious activator of both receptors, with a rather low potency for the CXCR1 receptor but comparable with CXCL5 and CXCL7. It is suggested that CMV uses the UL146 gene product expressed in infected endothelial cells to attract neutrophils by activating their CXCR1 and CXCR2 receptors, whereby neutrophils can act as carriers of the virus to uninfected endothelial cells. In that way a lasting pool of CMV-infected endothelial cells could be maintained.
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Affiliation(s)
- Hans R Lüttichau
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Panum Institute, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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23
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Fernandez AF, Rosales C, Lopez-Nieva P, Graña O, Ballestar E, Ropero S, Espada J, Melo SA, Lujambio A, Fraga MF, Pino I, Javierre B, Carmona FJ, Acquadro F, Steenbergen RD, Snijders PJ, Meijer CJ, Pineau P, Dejean A, Lloveras B, Capella G, Quer J, Buti M, Esteban JI, Allende H, Rodriguez-Frias F, Castellsague X, Minarovits J, Ponce J, Capello D, Gaidano G, Cigudosa JC, Gomez-Lopez G, Pisano DG, Valencia A, Piris MA, Bosch FX, Cahir-McFarland E, Kieff E, Esteller M. The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genes Dev 2009; 19:438-51. [PMID: 19208682 PMCID: PMC2661803 DOI: 10.1101/gr.083550.108] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The natural history of cancers associated with virus exposure is intriguing, since only a minority of human tissues infected with these viruses inevitably progress to cancer. However, the molecular reasons why the infection is controlled or instead progresses to subsequent stages of tumorigenesis are largely unknown. In this article, we provide the first complete DNA methylomes of double-stranded DNA viruses associated with human cancer that might provide important clues to help us understand the described process. Using bisulfite genomic sequencing of multiple clones, we have obtained the DNA methylation status of every CpG dinucleotide in the genome of the Human Papilloma Viruses 16 and 18 and Human Hepatitis B Virus, and in all the transcription start sites of the Epstein-Barr Virus. These viruses are associated with infectious diseases (such as hepatitis B and infectious mononucleosis) and the development of human tumors (cervical, hepatic, and nasopharyngeal cancers, and lymphoma), and are responsible for 1 million deaths worldwide every year. The DNA methylomes presented provide evidence of the dynamic nature of the epigenome in contrast to the genome. We observed that the DNA methylome of these viruses evolves from an unmethylated to a highly methylated genome in association with the progression of the disease, from asymptomatic healthy carriers, through chronically infected tissues and pre-malignant lesions, to the full-blown invasive tumor. The observed DNA methylation changes have a major functional impact on the biological behavior of the viruses.
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Affiliation(s)
- Agustin F. Fernandez
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
- Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research-Catalan Institute of Oncology (IDIBELL-ICO), Barcelona, Catalonia 08907, Spain
| | - Cecilia Rosales
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Pilar Lopez-Nieva
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Osvaldo Graña
- Bioinformatics Unit and Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid E-28029, Spain
| | - Esteban Ballestar
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Santiago Ropero
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Jesus Espada
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Sonia A. Melo
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Amaia Lujambio
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Mario F. Fraga
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Irene Pino
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Biola Javierre
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Francisco J. Carmona
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
- Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research-Catalan Institute of Oncology (IDIBELL-ICO), Barcelona, Catalonia 08907, Spain
| | - Francesco Acquadro
- Molecular Cytogenetics Group and CIBERER, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid E-28029, Spain
| | - Renske D.M. Steenbergen
- Department of Pathology, Unit of Molecular Pathology, Vrije Universiteit Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Peter J.F. Snijders
- Department of Pathology, Unit of Molecular Pathology, Vrije Universiteit Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Chris J. Meijer
- Department of Pathology, Unit of Molecular Pathology, Vrije Universiteit Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Pascal Pineau
- Nuclear Organization and Oncogenesis Unit, INSERM U579, Pasteur Institute, Paris 75724, France
| | - Anne Dejean
- Nuclear Organization and Oncogenesis Unit, INSERM U579, Pasteur Institute, Paris 75724, France
| | - Belen Lloveras
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Catalonia 08907, Spain
| | - Gabriel Capella
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Catalonia 08907, Spain
| | - Josep Quer
- Liver Unit, Department of Medicine, Hospital Vall Hebron, and Universitat Autonoma Barcelona and CIBEREHD, Barcelona 08035, Spain
| | - Maria Buti
- Liver Unit, Department of Medicine, Hospital Vall Hebron, and Universitat Autonoma Barcelona and CIBEREHD, Barcelona 08035, Spain
| | - Juan-Ignacio Esteban
- Liver Unit, Department of Medicine, Hospital Vall Hebron, and Universitat Autonoma Barcelona and CIBEREHD, Barcelona 08035, Spain
| | - Helena Allende
- Pathology Department, Hospital Vall Hebron, Barcelona 08035, Spain
| | | | - Xavier Castellsague
- Service of Epidemiology and Cancer Register, Catalan Institute of Oncology (ICO), Barcelona, Catalonia 08907, Spain
| | - Janos Minarovits
- Microbiological Reseach Group, National Center for Epidemiology, Budapest 1529, Hungary
| | - Jordi Ponce
- Service of Gynecology, Hospital Universitari de Bellvitge, L'Hospitalet, Catalonia 08907, Spain
| | - Daniela Capello
- Division of Hematology, Department of Clinical and Experimental Medicine and Department of Oncology, Amedeo Avogadro University of Eastern Piedmont, Vercelli, Alessandria, Novara 13100, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Clinical and Experimental Medicine and Department of Oncology, Amedeo Avogadro University of Eastern Piedmont, Vercelli, Alessandria, Novara 13100, Italy
| | - Juan Cruz Cigudosa
- Molecular Cytogenetics Group and CIBERER, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid E-28029, Spain
| | - Gonzalo Gomez-Lopez
- Bioinformatics Unit and Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid E-28029, Spain
- Biomedical Foundation Complexo Hospitalario, Universitario de Vigo (CHUVI), Vigo 36211, Spain
| | - David G. Pisano
- Bioinformatics Unit and Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid E-28029, Spain
| | - Alfonso Valencia
- Bioinformatics Unit and Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid E-28029, Spain
| | - Miguel Angel Piris
- Lymphoma Group, Molecular Pathology Programme, Spanish National Cancer Research Centre, Madrid E-28029, Spain
| | - Francesc X. Bosch
- Service of Epidemiology and Cancer Register, Catalan Institute of Oncology (ICO), Barcelona, Catalonia 08907, Spain
| | - Ellen Cahir-McFarland
- Departments of Medicine, Microbiology, and Molecular Genetics, Harvard University, Boston, Massachusetts 02115, USA
| | - Elliott Kieff
- Departments of Medicine, Microbiology, and Molecular Genetics, Harvard University, Boston, Massachusetts 02115, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Manel Esteller
- Cancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
- Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research-Catalan Institute of Oncology (IDIBELL-ICO), Barcelona, Catalonia 08907, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
- Corresponding author.E-mail ; fax 34-91-2246923
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Kvelland I. Bromodeoxyuridine-labeled bacteriophage T4D. I. Growth parameters and frequency of markers recovered from BUdR-labeled and from non-labeled phages studied in mass lysates. Hereditas 2009; 72:223-36. [PMID: 4281767 DOI: 10.1111/j.1601-5223.1972.tb01046.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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25
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Thai V, Renesto P, Fowler CA, Brown DJ, Davis T, Gu W, Pollock DD, Kern D, Raoult D, Eisenmesser EZ. Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus. J Mol Biol 2008; 378:71-86. [PMID: 18342330 PMCID: PMC2884007 DOI: 10.1016/j.jmb.2007.08.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 08/22/2007] [Accepted: 08/23/2007] [Indexed: 12/29/2022]
Abstract
Although multiple viruses utilize host cell cyclophilins, including severe acute respiratory syndrome (SARS) and human immunodeficiency virus type-1(HIV-1), their role in infection is poorly understood. To help elucidate these roles, we have characterized the first virally encoded cyclophilin (mimicyp) derived from the largest virus discovered to date (the Mimivirus) that is also a causative agent of pneumonia in humans. Mimicyp adopts a typical cyclophilin-fold, yet it also forms trimers unlike any previously characterized homologue. Strikingly, immunofluorescence assays reveal that mimicyp localizes to the surface of the mature virion, as recently proposed for several viruses that recruit host cell cyclophilins such as SARS and HIV-1. Additionally mimicyp lacks peptidyl-prolyl isomerase activity in contrast to human cyclophilins. Thus, this study suggests that cyclophilins, whether recruited from host cells (i.e. HIV-1 and SARS) or virally encoded (i.e. Mimivirus), are localized on viral surfaces for at least a subset of viruses.
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Key Words
- fiv, feline immunodeficiency virus
- hiv-1, human immunodeficiency virus type-1
- hcypa, human cyclophilin-a
- hcypb, human cyclophilin-b
- mimicyp, mimivirus cyclophilin
- ncldv, nuclear cytoplasmic large dna viruses
- ppiase, peptidyl-prolyl isomerase
- sars, sever acute respiratory syndrome
- vv, vaccinia virus
- sv, vesicular stomatitis virus
- csa, cyclosporine-a
- trosy-hsqc, transverse relaxation optimized spectroscopy-heteronuclear single quantum coherence
- dapi, diamidino-2-phylindole
- cyclophilin
- virus
- pneumonia
- peptidyl-prolyl isomerase
- mimivirus
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Affiliation(s)
- Vu Thai
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02454, USA
| | - Patricia Renesto
- Unité des Rickettsies, Faculté de Médecine, CNRSUMR6020, Université de la Méditerranée, 13385 Marseille Cedex 05, France
| | - C. Andrew Fowler
- Department of Chemistry & Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Darin J. Brown
- Department of Biochemistry & Molecular Genetics, University of Colorado Health Science Center, School of Medicine, 12801 E 17 Ave, Aurora, CO 80045, USA
| | - Tara Davis
- Structural Genomics Consortium and the Department of Physiology, University of Toronto, 100 College St., Toronto, ON, Canada M5G1L5
| | - Wanjun Gu
- Department of Biochemistry & Molecular Genetics, University of Colorado Health Science Center, School of Medicine, 12801 E 17 Ave, Aurora, CO 80045, USA
| | - David D. Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado Health Science Center, School of Medicine, 12801 E 17 Ave, Aurora, CO 80045, USA
| | - Dorothee Kern
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02454, USA
| | - Didier Raoult
- Unité des Rickettsies, Faculté de Médecine, CNRSUMR6020, Université de la Méditerranée, 13385 Marseille Cedex 05, France
| | - Elan Z. Eisenmesser
- Department of Biochemistry & Molecular Genetics, University of Colorado Health Science Center, School of Medicine, 12801 E 17 Ave, Aurora, CO 80045, USA
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26
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Han F, Xu J, Zhang X. Characterization of an early gene (wsv477) from shrimp white spot syndrome virus (WSSV). Virus Genes 2006; 34:193-8. [PMID: 17139550 DOI: 10.1007/s11262-006-0053-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 10/16/2006] [Indexed: 10/23/2022]
Abstract
White spot syndrome virus (WSSV) is one of the most virulent pathogens causing high mortality in shrimp. The viral early genes play a key role in DNA replication and virus proliferation. In this study, a WSSV gene (wsv477) encoding 208 amino acid peptides was characterized as an early gene. The temporal analysis showed that the wsv477 gene was first transcribed at 4 h post-infection, suggesting that it was an early gene. The wsv477 gene was expressed in Escherichia coli and purified. Subsequently the specific antibody was raised using the purified fusion protein (GST-WSV477). Western blot revealed that the wsv477 gene was expressed at 6 h post-infection in vivo. As indicated by GTP-binding assay, the WSV477 protein had GTP-binding activity.
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Affiliation(s)
- Fang Han
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005, P. R. China
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27
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Renesto P, Abergel C, Decloquement P, Moinier D, Azza S, Ogata H, Fourquet P, Gorvel JP, Claverie JM. Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. J Virol 2006; 80:11678-85. [PMID: 16971431 PMCID: PMC1642625 DOI: 10.1128/jvi.00940-06] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Acanthamoeba polyphaga mimivirus is the largest known virus in both particle size and genome complexity. Its 1.2-Mb genome encodes 911 proteins, among which only 298 have predicted functions. The composition of purified isolated virions was analyzed by using a combined electrophoresis/mass spectrometry approach allowing the identification of 114 proteins. Besides the expected major structural components, the viral particle packages 12 proteins unambiguously associated with transcriptional machinery, 3 proteins associated with DNA repair, and 2 topoisomerases. Other main functional categories represented in the virion include oxidative pathways and protein modification. More than half of the identified virion-associated proteins correspond to anonymous genes of unknown function, including 45 "ORFans." As demonstrated by both Western blotting and immunogold staining, some of these "ORFans," which lack any convincing similarity in the sequence databases, are endowed with antigenic properties. Thus, anonymous and unique genes constituting the majority of the mimivirus gene complement encode bona fide proteins that are likely to participate in well-integrated processes.
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Affiliation(s)
- Patricia Renesto
- Unité des Rickettsies, CNRS UMR 6020, IFR-48, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille, France.
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28
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Abstract
MicroRNAs (miRNAs), which can be expressed in a cell-type and tissue-specific manner, can influence the activities of genes that control cell growth and differentiation. Viruses often have clear tissue tropisms, raising the possibility that cellular miRNAs might modulate their pathogenesis. In this Review, we discuss recent findings that some vertebrate viruses either encode miRNAs or subvert cellular miRNAs, and that these miRNAs participate in both the infectious and the latent phase of the viral life cycle.
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Affiliation(s)
- Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94301, USA.
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29
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Abstract
Is there a "conspiracy" at work among viral pathogens? Apparently, yes. Rabies virus, lenti- and retroviruses, and herpesviruses, the "co-conspirators", target select members of the tumor necrosis factor (TNF) receptor superfamily to invade the cells of their host. The intrigue deepens, as several reports have revealed that the viral envelope proteins interact with the cellular TNF receptor in a highly conserved region of previously unknown function. Targeting of this region by diverse pathogens suggests that a selective advantage is acquired. This advantage might involve regulation of the immune response, because recent investigations of the herpesvirus entry receptor demonstrated that this conserved region engages an inhibitory co-receptor governing T-cell activation.
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Affiliation(s)
- April Kinkade
- Division of Molecular Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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30
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Weber F, Wagner V, Rasmussen SB, Hartmann R, Paludan SR. Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses. J Virol 2006; 80:5059-64. [PMID: 16641297 PMCID: PMC1472073 DOI: 10.1128/jvi.80.10.5059-5064.2006] [Citation(s) in RCA: 711] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Double-stranded RNA (dsRNA) longer than 30 bp is a key activator of the innate immune response against viral infections. It is widely assumed that the generation of dsRNA during genome replication is a trait shared by all viruses. However, to our knowledge, no study exists in which the production of dsRNA by different viruses is systematically investigated. Here, we investigated the presence and localization of dsRNA in cells infected with a range of viruses, employing a dsRNA-specific antibody for immunofluorescence analysis. Our data revealed that, as predicted, significant amounts of dsRNA can be detected for viruses with a genome consisting of positive-strand RNA, dsRNA, or DNA. Surprisingly, however, no dsRNA signals were detected for negative-strand RNA viruses. Thus, dsRNA is indeed a general feature of most virus groups, but negative-strand RNA viruses appear to be an exception to that rule.
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Affiliation(s)
- Friedemann Weber
- Abteilung Virologie, Institut für Medizinische Mikrobiologie und Hygiene, Universität Freiburg, D-79008 Freiburg, Germany.
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31
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O'Day DH, Suhre K, Myre MA, Chatterjee-Chakraborty M, Chavez SE. Isolation, characterization, and bioinformatic analysis of calmodulin-binding protein cmbB reveals a novel tandem IP22 repeat common to many Dictyostelium and Mimivirus proteins. Biochem Biophys Res Commun 2006; 346:879-88. [PMID: 16777069 DOI: 10.1016/j.bbrc.2006.05.204] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Accepted: 05/27/2006] [Indexed: 11/20/2022]
Abstract
A novel calmodulin-binding protein cmbB from Dictyostelium discoideum is encoded in a single gene. Northern analysis reveals two cmbB transcripts first detectable at 4 h during multicellular development. Western blotting detects an approximately 46.6 kDa protein. Sequence analysis and calmodulin-agarose binding studies identified a "classic" calcium-dependent calmodulin-binding domain (179IPKSLRSLFLGKGYNQPLEF198) but structural analyses suggest binding may not involve classic alpha-helical calmodulin-binding. The cmbB protein is comprised of tandem repeats of a newly identified IP22 motif ([I,L]Pxxhxxhxhxxxhxxxhxxxx; where h = any hydrophobic amino acid) that is highly conserved and a more precise representation of the FNIP repeat. At least eight Acanthamoeba polyphaga Mimivirus proteins and over 100 Dictyostelium proteins contain tandem arrays of the IP22 motif and its variants. cmbB also shares structural homology to YopM, from the plague bacterium Yersenia pestis.
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Affiliation(s)
- Danton H O'Day
- Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6.
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32
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Abstract
RNA-mediated interference (RNAi) is a recently discovered process by which dsRNA is able to silence specific gene functions. Although initially described in plants, nematodes and Drosophila, the process is currently considered to be an evolutionarily conserved process that is present in the entire eukaryotic kingdom in which its original function was as a defense mechanism against viruses and foreign nucleic acids. Similarly to the silencing of genes by RNAi, viral functions can be also silenced by the same mechanism, through the introduction of specific dsRNA molecules into cells, where they are targeted to essential genes or directly to the viral genome in case RNA viruses, thus arresting viral replication. Since the pioneering work of Elbashir and coworkers, who identified RNAi activity in mammalian cells, many publications have described the inhibition of viruses belonging to most if not all viral families, by targeting and silencing diverse viral genes as well as cell genes that are essential for virus replication. Moreover, virus expression vectors were developed and used as vehicles with which to deliver siRNAs into cells. This review will describe the use of RNAi to inhibit virus replication directly, as well as through the silencing of the appropriate cell functions.
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Affiliation(s)
- Yehuda Stram
- Virology Division, Kimron Veterinary institute, 12, 50250, Beit-Dagan, Israel.
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33
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Langland JO, Cameron JM, Heck MC, Jancovich JK, Jacobs BL. Inhibition of PKR by RNA and DNA viruses. Virus Res 2006; 119:100-10. [PMID: 16704884 DOI: 10.1016/j.virusres.2005.10.014] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 09/28/2005] [Accepted: 10/20/2005] [Indexed: 11/28/2022]
Abstract
Interferons were the first of the anti-viral innate immune modulators to be characterized, initially characterized solely as anti-viral proteins [reviewed in Le Page, C., Genin, P., Baines, M.G., Hiscott, J., 2000. Inteferon activation and innate immunity. Rev. Immunogenet. 2, 374-386]. As we have progressed in our understanding of the interferons they have taken a more central role in our understanding of innate immunity and its interplay with the adaptive immune response. One of the key players in function of interferon is the interferon-inducible enzyme, protein kinase (PKR, activatable by RNA). The key role played by PKR in the innate response to virus infection is emphasized by the large number of viruses, DNA viruses as well as RNA viruses, whose hosts range from insects to humans, that code for PKR inhibitors. In this review we will first describe activation of PKR and then describe the myriad of ways that viruses inhibit function of PKR.
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Affiliation(s)
- Jeffrey O Langland
- Center for Infectious Disease and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5401, USA
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34
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Weber F, Wagner V, Rasmussen SB, Hartmann R, Paludan SR. Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses. J Virol 2006. [PMID: 16641297 DOI: 10.1128/jvi.80.10.5059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Double-stranded RNA (dsRNA) longer than 30 bp is a key activator of the innate immune response against viral infections. It is widely assumed that the generation of dsRNA during genome replication is a trait shared by all viruses. However, to our knowledge, no study exists in which the production of dsRNA by different viruses is systematically investigated. Here, we investigated the presence and localization of dsRNA in cells infected with a range of viruses, employing a dsRNA-specific antibody for immunofluorescence analysis. Our data revealed that, as predicted, significant amounts of dsRNA can be detected for viruses with a genome consisting of positive-strand RNA, dsRNA, or DNA. Surprisingly, however, no dsRNA signals were detected for negative-strand RNA viruses. Thus, dsRNA is indeed a general feature of most virus groups, but negative-strand RNA viruses appear to be an exception to that rule.
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Affiliation(s)
- Friedemann Weber
- Abteilung Virologie, Institut für Medizinische Mikrobiologie und Hygiene, Universität Freiburg, D-79008 Freiburg, Germany.
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35
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Gazzarrini S, Kang M, Epimashko S, Van Etten JL, Dainty J, Thiel G, Moroni A. Chlorella virus MT325 encodes water and potassium channels that interact synergistically. Proc Natl Acad Sci U S A 2006; 103:5355-60. [PMID: 16569697 PMCID: PMC1414795 DOI: 10.1073/pnas.0600848103] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fast and selective transport of water through cell membranes is facilitated by water channels. Water channels belonging to the major intrinsic proteins (MIPs) family have been found in all three domains of life, Archaea, Bacteria, and Eukarya. Here we show that Chlorella virus MT325 has a water channel gene, aqpv1, that forms a functional aquaglyceroporin in oocytes. aqpv1 is transcribed during infection together with MT325 kcv, a gene encoding a previously undescribed type of viral potassium channel. Coexpression of AQPV1 and MT325-Kcv in Xenopus oocytes synergistically increases water transport, suggesting a possible concerted action of the two channels in the infection cycle. The two channels operate by a thermodynamically coupled mechanism that simultaneously alters water conductance and driving force for water movement. Considering the universal role of osmosis, this mechanism is relevant to any cell coexpressing water and potassium channels and could have pathological as well as basic physiological relevance.
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Affiliation(s)
- Sabrina Gazzarrini
- Dipartimento di Biologia and Istituto di Biofisica–Consiglio Nazionale delle Ricerche, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Ming Kang
- Department of Plant Pathology and Nebraska Center of Virology, University of Nebraska, Lincoln, NE 68583-0722
| | - Svetlana Epimashko
- Dipartimento di Biologia and Istituto di Biofisica–Consiglio Nazionale delle Ricerche, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - James L. Van Etten
- Department of Plant Pathology and Nebraska Center of Virology, University of Nebraska, Lincoln, NE 68583-0722
- To whom correspondence should be addressed at:
Department of Plant Pathology, 406 Plant Sciences Hall, University of Nebraska, Lincoln, NE 68583-0722. E-mail:
| | - Jack Dainty
- Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2
| | - Gerhard Thiel
- Institute of Botany, Darmstadt University of Technology, 64287 Darmstadt, Germany; and
| | - Anna Moroni
- Dipartimento di Biologia and Istituto di Biofisica–Consiglio Nazionale delle Ricerche, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
- Istituto Nazionale per la Fisica della Materia, Unità di Milano-Università, Via Celoria 16, 20133 Milan, Italy
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36
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Bath C, Cukalac T, Porter K, Dyall-Smith ML. His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology 2006; 350:228-39. [PMID: 16530800 DOI: 10.1016/j.virol.2006.02.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 01/31/2006] [Accepted: 02/02/2006] [Indexed: 11/16/2022]
Abstract
Spindle-shaped viruses are a dominant morphotype in hypersaline waters but their molecular characteristics and their relationship to other archaeal viruses have not been determined. Here, we describe the isolation, characteristics and genome sequence of His2, a spindle-shaped halovirus, and compare it to the previously reported halovirus His1. Their particle dimensions, host-ranges and buoyant densities were found to be similar but they differed in their stabilities to raised temperature, low salinity and chloroform. The genomes of both viruses were linear dsDNA, of similar size (His1, 14,464 bp; His2, 16,067 bp) and mol% G+C (approximately 40%), with long, inverted terminal repeat sequences. The genomic termini of both viruses are likely to possess bound proteins. They shared little nucleotide similarity and, except for their putative DNA polymerase ORFs, no significant similarity at the predicted protein level. A few of the 35 predicted ORFs of both viruses showed significant matches to sequences in GenBank, and these were always to proteins of haloarchaea. Their DNA polymerases showed 42% aa identity, and belonged to the type B group of replicases that use protein-priming. Purified His2 particles were composed of four main proteins (62, 36, 28 and 21 kDa) and the gene for the major capsid protein was identified. Hypothetical proteins similar to His2 VP1 are present in four haloarchaeal genomes but are not part of complete prophages. This, and other evidence, suggests a high frequency of recombination between haloviruses and their hosts. His1 and His2 are unlike fuselloviruses and have been placed in a new virus group, Salterprovirus.
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Affiliation(s)
- Carolyn Bath
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia
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37
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Breitbart M, Rohwer F. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 2006; 39:729-36. [PMID: 16312220 DOI: 10.2144/000112019] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Rapid identification of viruses is needed to monitor the blood supply for emerging threats. Here we present a method that meets these criteria and allows for the shotgun sequencing of novel, uncultured DNA viruses directly from human blood. This method employs selection based on the physical properties of viruses combined with sequence-independent amplification and cloning. We show that both single- and double-stranded DNA viruses can be recovered from blood samples using this approach. In addition, we report the discovery of novel anellovirus sequences in the blood of healthy donors. PCR primers designed to amplify these novel anellovirus sequences were then used to verify the presence of these viruses in the general donor population.
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38
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Gaussier H, Yang Q, Catalano CE. Building a virus from scratch: assembly of an infectious virus using purified components in a rigorously defined biochemical assay system. J Mol Biol 2006; 357:1154-66. [PMID: 16476446 DOI: 10.1016/j.jmb.2006.01.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 12/27/2005] [Accepted: 01/03/2006] [Indexed: 10/25/2022]
Abstract
The assembly of double-stranded DNA (dsDNA) viruses such as poxvirus, the herpesviruses and many bacteriophages is a complex process that requires the coordinated activities of numerous proteins of both viral and host origin. Here, we report the assembly of an infectious wild-type lambda virus using purified proteins and commercially available DNA, and optimization of the assembly reaction in a rigorously defined biochemical system. Seven proteins, purified procapsids and tails, and mature lambda DNA are necessary and sufficient for efficient virus assembly in vitro. Analysis of the reaction suggests that (i) virus assembly in vitro is optimal under conditions that faithfully mimic the intracellular environment within an Escherichia coli cell, (ii) concatemeric DNA is required for the successful completion of virus assembly, (iii) several of the protein components oligomerize concomitant with their step-wise addition to the nascent virus particle and (iv) tail addition is the rate-limiting step in virus assembly. Importantly, the assembled virus may enter either of the developmental pathways (lytic or lysogenic) expected of a lambda virion. Thus, we demonstrate for the first time that a wild-type, complex DNA virus may be assembled from purified components under defined biochemical conditions. This system provides a powerful tool to characterize, at the molecular level, the step-by-step processes required to assemble an infectious virus particle. Given the remarkable similarities between dsDNA bacteriophage and eukaryotic dsDNA viruses, characterization of the lambda system has broad biological implications in our understanding of virus development at a global level.
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Affiliation(s)
- Hélène Gaussier
- Department of Pharmaceutical Sciences, University of Colorado Health Sciences Center, 4200 East Ninth Avenue C238, Denver, CO 80262, USA
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Affiliation(s)
- Elodie Ghedin
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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Boya P, Pauleau AL, Poncet D, Gonzalez-Polo RA, Zamzami N, Kroemer G. Viral proteins targeting mitochondria: controlling cell death. Biochim Biophys Acta 2005; 1659:178-89. [PMID: 15576050 DOI: 10.1016/j.bbabio.2004.08.007] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Revised: 07/20/2004] [Accepted: 08/16/2004] [Indexed: 01/21/2023]
Abstract
Mitochondrial membrane permeabilization (MMP) is a critical step regulating apoptosis. Viruses have evolved multiple strategies to modulate apoptosis for their own benefit. Thus, many viruses code for proteins that act on mitochondria and control apoptosis of infected cells. Viral proapoptotic proteins translocate to mitochondrial membranes and induce MMP, which is often accompanied by mitochondrial swelling and fragmentation. From a structural point of view, all the viral proapoptotic proteins discovered so far contain amphipathic alpha-helices that are necessary for the proapoptotic effects and seem to have pore-forming properties, as it has been shown for Vpr from human immunodeficiency virus-1 (HIV-1) and HBx from hepatitis B virus (HBV). In contrast, antiapoptotic viral proteins (e.g., M11L from myxoma virus, F1L from vaccinia virus and BHRF1 from Epstein-Barr virus) contain mitochondrial targeting sequences (MTS) in their C-terminus that are homologous to tail-anchoring domains. These domains are similar to those present in many proteins of the Bcl-2 family and are responsible for inserting the protein in the outer mitochondrial membrane leaving the N-terminus of the protein facing the cytosol. The antiapoptotic proteins K7 and K15 from avian encephalomyelitis virus (AEV) and viral mitochondria inhibitor of apoptosis (vMIA) from cytomegalovirus are capable of binding host-specific apoptosis-modulatory proteins such as Bax, Bcl-2, activated caspase 3, CAML, CIDE-B and HAX. In conclusion, viruses modulate apoptosis at the mitochondrial level by multiple different strategies.
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Affiliation(s)
- Patricia Boya
- Centre National de la Recherche Scientifique, UMR 8125, Institut Gustave Roussy, Pavillon de Recherche 1, 39 rue Camille-Desmoulins, F-94805 Villejuif, France
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Abstract
BACKGROUND Inteins are "protein introns" that remove themselves from their host proteins through an autocatalytic protein-splicing. After their discovery, inteins have been quickly identified in all domains of life, but only once to date in the genome of a eukaryote-infecting virus. RESULTS Here we report the identification and bioinformatics characterization of an intein in the DNA polymerase PolB gene of amoeba infecting Mimivirus, the largest known double-stranded DNA virus, the origin of which has been proposed to predate the emergence of eukaryotes. Mimivirus intein exhibits canonical sequence motifs and clearly belongs to a subclass of archaeal inteins always found in the same location of PolB genes. On the other hand, the Mimivirus PolB is most similar to eukaryotic Poldelta sequences. CONCLUSIONS The intriguing association of an extremophilic archaeal-type intein with a mesophilic eukaryotic-like PolB in Mimivirus is consistent with the hypothesis that DNA viruses might have been the central reservoir of inteins throughout the course of evolution.
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Affiliation(s)
- Hiroyuki Ogata
- Information Génomique et Structurale, UPR2589 CNRS, IBSM, IFR88, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Didier Raoult
- Unité des Rickettsies, CNRS UPRESA 6020, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Jean-Michel Claverie
- Information Génomique et Structurale, UPR2589 CNRS, IBSM, IFR88, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Strycharz M, Bartecka K, Polz-Dacewicz M. [Prophylaxis and treatment of viral infections. Part I--infections caused by DNA viruses]. Pol Merkur Lekarski 2005; 18:229-32. [PMID: 17877138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The amount of antiviral drugs have increased recently. Many viruses treated as a mild pathogens has turned out to cause different complications and severe diseaseses in elderly people and immunocomprised patients. The authors have made an attempt of presenting on the basis of scientific reports the principles of antiviral prophylaxis and treatment. The first part is focused on infections caused by DNA viruses.
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Tsai JM, Wang HC, Leu JH, Hsiao HH, Wang AHJ, Kou GH, Lo CF. Genomic and proteomic analysis of thirty-nine structural proteins of shrimp white spot syndrome virus. J Virol 2004; 78:11360-70. [PMID: 15452257 PMCID: PMC521807 DOI: 10.1128/jvi.78.20.11360-11370.2004] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
White spot syndrome virus (WSSV) virions were purified from the hemolymph of experimentally infected crayfish Procambarus clarkii, and their proteins were separated by 8 to 18% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to give a protein profile. The visible bands were then excised from the gel, and following trypsin digestion of the reduced and alkylated WSSV proteins in the bands, the peptide sequence of each fragment was determined by liquid chromatography-nano-electrospray ionization tandem mass spectrometry (LC-nanoESI-MS/MS) using a quadrupole/time-of-flight mass spectrometer. Comparison of the resulting peptide sequence data against the nonredundant database at the National Center for Biotechnology Information identified 33 WSSV structural genes, 20 of which are reported here for the first time. Since there were six other known WSSV structural proteins that could not be identified from the SDS-PAGE bands, there must therefore be a total of at least 39 (33 + 6) WSSV structural protein genes. Only 61.5% of the WSSV structural genes have a polyadenylation signal, and preliminary analysis by 3' rapid amplification of cDNA ends suggested that some structural protein genes produced mRNA without a poly(A) tail. Microarray analysis showed that gene expression started at 2, 6, 8, 12, 18, 24, and 36 hpi for 7, 1, 4, 12, 9, 5, and 1 of the genes, respectively. Based on similarities in their time course expression patterns, a clustering algorithm was used to group the WSSV structural genes into four clusters. Genes that putatively had common or similar roles in the viral infection cycle tended to appear in the same cluster.
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Affiliation(s)
- Jyh-Ming Tsai
- Graduate Institute of Zoology, National Taiwan University, Taipei 106, Taiwan R.O.C
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Abstract
We recently reported the discovery and preliminary characterization of Mimivirus, the largest known virus, with a 400-nanometer particle size comparable to mycoplasma. Mimivirus is a double-stranded DNA virus growing in amoebae. We now present its 1,181,404-base pair genome sequence, consisting of 1262 putative open reading frames, 10% of which exhibit a similarity to proteins of known functions. In addition to exceptional genome size, Mimivirus exhibits many features that distinguish it from other nucleocytoplasmic large DNA viruses. The most unexpected is the presence of numerous genes encoding central protein-translation components, including four amino-acyl transfer RNA synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation factor 1. The genome also exhibits six tRNAs. Other notable features include the presence of both type I and type II topoisomerases, components of all DNA repair pathways, many polysaccharide synthesis enzymes, and one intein-containing gene. The size and complexity of the Mimivirus genome challenge the established frontier between viruses and parasitic cellular organisms. This new sequence data might help shed a new light on the origin of DNA viruses and their role in the early evolution of eukaryotes.
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Affiliation(s)
- Didier Raoult
- Unité des Rickettsies, Faculté de Médecine, CNRS UMR6020, Université de la Méditerranée, 13385 Marseille Cedex 05, France.
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Wang YF, Hsieh YF, Lin CL, Lin JL, Chen CY, Chiou YH, Chou MC. Staurosporine-induced G2/M arrest in primary effusion lymphoma BCBL-1 cells. Ann Hematol 2004; 83:739-44. [PMID: 15452667 DOI: 10.1007/s00277-004-0949-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Accepted: 08/23/2004] [Indexed: 10/26/2022]
Abstract
Staurosporine, an inhibitor of protein kinase C, is a potential antitumor drug and its derivatives are used as anticancer drugs in clinical trials. Human herpesvirus 8 (HHV-8) is implicated in all forms of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman's disease (MCD), indicating it to be a DNA tumor virus. It is difficult to culture cell lines derived from KS patients; we therefore used a cell line derived from PEL (BCBL-1) to investigate whether staurosporine affects the HHV-8-related tumors. Our results show that staurosporine treatment reduces the cell viability of BCBL-1 cells and causes cell cycle arrest in the G2/M phase. The G2/M arrest was associated with the decrease in the expression of Cdc2 and cyclin B. Furthermore, the induction of the HHV-8 lytic cycle was not observed under the staurosporine treatment.
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Affiliation(s)
- Yi-Fen Wang
- Department of Medical Technology, Fooyin University, 151 Chin-Hsuen Road, Ta-Liao, Kaohsiung Hsien, Taiwan, Republic of China.
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Abstract
Emerging structural results confirm that the large Rolling Circle Replication initiator superfamily is composed of two classes of proteins that are circularly permutated with respect to each other, as initially suggested by sequence analysis. The two classes are united by the same endonucleolytic mechanism and a conserved Mg(2+) binding site containing multiple histidine ligands unique to this superfamily.
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Affiliation(s)
- Fred Dyda
- Laboratory of Molecular Biology, HHS/NIH/NIDDK, Building 5, Room 303, Bethesda, MD 20892, USA
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Chellappan P, Vanitharani R, Pita J, Fauquet CM. Short interfering RNA accumulation correlates with host recovery in DNA virus-infected hosts, and gene silencing targets specific viral sequences. J Virol 2004; 78:7465-77. [PMID: 15220420 PMCID: PMC434130 DOI: 10.1128/jvi.78.14.7465-7477.2004] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 03/16/2004] [Indexed: 11/20/2022] Open
Abstract
Viruses are both inducers and targets of posttranscriptional gene silencing (PTGS), a natural defense mechanism in plants. Here we report molecular evidence of the ability of single-stranded DNA (ssDNA) viruses to induce PTGS in infected plants irrespective of the severity of or recovery from the symptoms. Our results reveal that five distinct species of cassava-infecting geminiviruses were capable of triggering PTGS by producing two classes of virus-specific short interfering RNAs (siRNAs) of 21 to 26 nucleotides in two plant hosts, tobacco (Nicotiana benthamiana) and cassava (Manihot esculenta, Crantz). However, the efficacy of virus-induced PTGS varied depending on the intrinsic features of the virus and its interaction with the plant host. We found that symptom recovery over time in plants infected with the isolates of African cassava mosaic virus (ACMV-[CM]) or Sri Lankan cassava mosaic virus was associated with a much higher level of virus-derived siRNA accumulation compared to plants infected with viruses that do not show symptom recovery. Furthermore, we determined that the C terminus of AC1 that overlaps with the N terminus of AC2 early viral genes involved in virus replication were the primary targets for ACMV-[CM]-induced PTGS, whereas the C terminus of BC1 was targeted for the East African cassava mosaic Cameroon virus. In addition, our results reveal the possibility for double-stranded RNA formation during transcription in ssDNA viruses, which explains in part how these viruses can trigger PTGS in plants.
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Affiliation(s)
- Padmanabhan Chellappan
- International Laboratory for Tropical Agricultural Biotechnology, Danforth Plant Science Center, St Louis, MO 63132, USA
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Li Q, Yang F, Zhang J, Chen Y. Proteomic analysis of proteins that binds specifically to the homologous repeat regions of white spot syndrome virus. Biol Pharm Bull 2003; 26:1517-22. [PMID: 14600393 DOI: 10.1248/bpb.26.1517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
White spot syndrome virus (WSSV) is a major pathogen in the cultivated shrimp. Nine homologous repeat regions (hrrs) have been reported interspersed throughout the WSSV genome. In this investigation, the protein fraction that specifically bound to the hrrs was isolated by using DNA-affinity chromatography. A total of 9 (S1 to S9) and 5 (C1 to C5) proteins separated from the WSSV infected shrimp and the healthy shrimp, respectively, were detected by using two-dimensional polyacrylamide gel electrophoresis, and 6 proteins changed with WSSV infection were analyzed by mass spectrometry (MS). One (S4) of the 6 proteins examined was identified as WSSV ORF59 protein, and another (S3) was a shrimp arginine kinase. No homologous proteins were found with the remaining 4 proteins by searching in the WSSV ORF database and NCBI database. The specific binding site of the 6 proteins was then determined by gel mobility shift assay (GMSA). Temporal analysis revealed that ORF59 gene was transcribed at the early stage of the infection. The results we obtained provide important information to understand WSSV replication. The combination of DNA-affinity chromatography, 2D-PAGE and MS approaches should have general application to the identification of gene regulating proteins of WSSV. The results represent the first isolation of a set of proteins that bind to the hrrs, and, furthermore, lead us a new research direction for the prevention and the therapy of WSSV.
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Affiliation(s)
- Qin Li
- Department of Biochemistry and Molecular Biology, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.
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Abstract
The most unique feature of white spot syndrome virus (WSSV) is the presence of a collagen-like protein (termed as WSSV-CLP). In this report, the N-terminal fragment of WSSV-CLP (CLPn) was expressed as a fusion protein with glutathione S-transferase (GST) in Escherichia coli and purified. Specific antibody was then raised against the purified fusion protein (GST-CLPn). Temporal analysis showed that the WSSV collagen gene was an early viral gene. Immunogold localization using specific antibody revealed that the gold particles, under a transmission electron microscope, were presented along the outer envelope of WSSV virions. This experiment suggested that the collagen gene encoded an envelope protein of WSSV. Using immuno-affinity chromatography, the WSSV-CLP was purified from crudely purified WSSV virions. The WSSV-CLP was N-glycosylated, as indicated by the increased migration in SDS-PAGE after treatment with N-linked glycosidase F.
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Affiliation(s)
- Q Li
- Department of Biochemistry and Molecular Biology, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
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Abstract
Diseases caused by viruses especially by white spot syndrome virus (WSSV) are the greatest challenge to worldwide shrimp aquaculture. The innate immunity of shrimp has attracted extensive attention, but no factor involved in the virus resistance has been reported. Here we report for the first time the identification of an antiviral gene from shrimp Penaeus monodon. A differential cDNA (designated as PmAV) cloned from virus-resistant shrimp P. monodon by differential display (DD) was found to have an open reading frame (ORF) encoding a 170 amino acid peptide with a C-type lectin-like domain (CTLD). The PmAV gene was expressed in Escherichia coli and the protein was purified. Recombinant PmAV protein displayed a strong antiviral activity in inhibiting virus-induced cytopathic effect in fish cell in vitro. Moreover, native PmAV protein was isolated from shrimp hemolymph by immuno-affinity chromatography and confirmed by Western blot. No agglutination activity was observed both in recombinant and native PmAV protein. Immunohistological study showed that PmAV protein was located mainly in the cytoplasm, and not bound to the shrimp WSSV. It implies that the antiviral mechanism of PmAV protein is not by inhibiting the attachment of virus to target host cell. The discovery of PmAV gene might provide a clue to elucidate the innate immunity of marine invertebrates and would be helpful to shrimp viral disease control.
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Affiliation(s)
- Tian Luo
- School of Life Sciences, Xiamen University, 361005 Xiamen, PR China
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