1
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Huang HJ, Li YY, Ye ZX, Li LL, Hu QL, He YJ, Qi YH, Zhang Y, Li T, Lu G, Mao QZ, Zhuo JC, Lu JB, Xu ZT, Sun ZT, Yan F, Chen JP, Zhang CX, Li JM. Co-option of a non-retroviral endogenous viral element in planthoppers. Nat Commun 2023; 14:7264. [PMID: 37945658 PMCID: PMC10636211 DOI: 10.1038/s41467-023-43186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
Non-retroviral endogenous viral elements (nrEVEs) are widely dispersed throughout the genomes of eukaryotes. Although nrEVEs are known to be involved in host antiviral immunity, it remains an open question whether they can be domesticated as functional proteins to serve cellular innovations in arthropods. In this study, we found that endogenous toti-like viral elements (ToEVEs) are ubiquitously integrated into the genomes of three planthopper species, with highly variable distributions and polymorphism levels in planthopper populations. Three ToEVEs display exon‒intron structures and active transcription, suggesting that they might have been domesticated by planthoppers. CRISPR/Cas9 experiments revealed that one ToEVE in Nilaparvata lugens, NlToEVE14, has been co-opted by its host and plays essential roles in planthopper development and fecundity. Large-scale analysis of ToEVEs in arthropod genomes indicated that the number of arthropod nrEVEs is currently underestimated and that they may contribute to the functional diversity of arthropod genes.
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Affiliation(s)
- Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yi-Yuan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Li-Li Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Qing-Ling Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yu-Juan He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yu-Hua Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Ting Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Gang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Qian-Zhuo Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jia-Bao Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhong-Tian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zong-Tao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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2
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Srinivasachar Badarinarayan S, Sauter D. Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections. J Virol 2021; 95:e02299-20. [PMID: 33883223 PMCID: PMC8315955 DOI: 10.1128/jvi.02299-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/30/2021] [Indexed: 01/15/2023] Open
Abstract
Long disregarded as junk DNA or genomic dark matter, endogenous retroviruses (ERVs) have turned out to represent important components of the antiviral immune response. These remnants of once-infectious retroviruses not only regulate cellular immune activation, but may even directly target invading viral pathogens. In this Gem, we summarize mechanisms by which retroviral fossils protect us from viral infections. One focus will be on recent advances in the role of ERVs as regulators of antiviral gene expression.
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MESH Headings
- Animals
- Endogenous Retroviruses/genetics
- Endogenous Retroviruses/physiology
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Humans
- Immunity, Cellular
- Promoter Regions, Genetic
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Pattern Recognition/metabolism
- Receptors, Virus/antagonists & inhibitors
- Receptors, Virus/metabolism
- Retroelements
- Viral Proteins/metabolism
- Virion/metabolism
- Virus Diseases/genetics
- Virus Diseases/immunology
- Virus Diseases/virology
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Affiliation(s)
- Smitha Srinivasachar Badarinarayan
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Germany
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3
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Retroviral Restriction Factors and Their Viral Targets: Restriction Strategies and Evolutionary Adaptations. Microorganisms 2020; 8:microorganisms8121965. [PMID: 33322320 PMCID: PMC7764263 DOI: 10.3390/microorganisms8121965] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
The evolutionary conflict between retroviruses and their vertebrate hosts over millions of years has led to the emergence of cellular innate immune proteins termed restriction factors as well as their viral antagonists. Evidence accumulated in the last two decades has substantially increased our understanding of the elaborate mechanisms utilized by these restriction factors to inhibit retroviral replication, mechanisms that either directly block viral proteins or interfere with the cellular pathways hijacked by the viruses. Analyses of these complex interactions describe patterns of accelerated evolution for these restriction factors as well as the acquisition and evolution of their virus-encoded antagonists. Evidence is also mounting that many restriction factors identified for their inhibition of specific retroviruses have broader antiviral activity against additional retroviruses as well as against other viruses, and that exposure to these multiple virus challenges has shaped their adaptive evolution. In this review, we provide an overview of the restriction factors that interfere with different steps of the retroviral life cycle, describing their mechanisms of action, adaptive evolution, viral targets and the viral antagonists that evolved to counter these factors.
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4
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Rajpoot K. Lipid-based Nanoplatforms in Cancer Therapy: Recent Advances and Applications. Curr Cancer Drug Targets 2020; 20:271-287. [PMID: 31951180 DOI: 10.2174/1568009620666200115160805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022]
Abstract
Though modern available cancer therapies are effective, they possess major adverse effects, causing non-compliance to patients. Furthermore, the majority of the polymeric-based medication platforms are certainly not universally acceptable, due to their several restrictions. With this juxtaposition, lipid-based medication delivery systems have appeared as promising drug nanocarriers to replace the majority of the polymer-based products because they are in a position to reverse polymer as well as, drug-associated restrictions. Furthermore, the amalgamation of the basic principle of nanotechnology in designing lipid nanocarriers, which are the latest form of lipid carriers, has tremendous chemotherapeutic possibilities as tumor-targeted drug-delivery pertaining to tumor therapy. Apart from this, it is reported that nearly 40% of the modern medication entities are lipophilic. Moreover, research continues to be efficient in attaining a significant understanding of the absorption and bioavailability of the developed lipids systems.
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Affiliation(s)
- Kuldeep Rajpoot
- Institute of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh- 495009, India
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5
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Xue B, Sechi LA, Kelvin DJ. Human Endogenous Retrovirus K (HML-2) in Health and Disease. Front Microbiol 2020; 11:1690. [PMID: 32765477 PMCID: PMC7380069 DOI: 10.3389/fmicb.2020.01690] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/29/2020] [Indexed: 02/05/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are derived from exogenous retrovirus infections in the evolution of primates and account for about 8% of the human genome. They were considered as silent passengers within our genomes for a long time, however, reactivation of HERVs has been associated with tumors and autoimmune diseases, especially the HERV-K (HML-2) family, the most recent integration groups with the least number of mutations and the most biologically active to encode functional retroviral proteins and produce retrovirus-like particles. Increasing studies are committed to determining the potential role of HERV-K (HML-2) in pathogenicity. Although there is still no evidence for HERV-K (HML-2) as a direct cause of diseases, aberrant expression profiles of the HERV-K (HML-2) transcripts and their regulatory function to their proximal host-genes were identified in different diseases. In this review, we summarized the advances between HERV-K (HML-2) and diseases to provide basis for further studies on the causal relationship between HERV-K (HML-2) and diseases. We recommended more attention to polymorphic integrated HERV-K (HML-2) loci which could be genetic causative factors and be associated with inter-individual differences in tumorigenesis and autoimmune diseases.
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Affiliation(s)
- Bei Xue
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Mediterranean Center for Disease Control, University of Sassari, Sassari, Italy
| | - David J. Kelvin
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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6
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Young GR, Yap MW, Michaux JR, Steppan SJ, Stoye JP. Evolutionary journey of the retroviral restriction gene Fv1. Proc Natl Acad Sci U S A 2018; 115:10130-10135. [PMID: 30224488 PMCID: PMC6176592 DOI: 10.1073/pnas.1808516115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Both exogenous and endogenous retroviruses have long been studied in mice, and some of the earliest mouse studies focused on the heritability of genetic factors influencing permissivity and resistance to infection. The prototypic retroviral restriction factor, Fv1, is now understood to exhibit a degree of control across multiple retroviral genera and is highly diverse within Mus To better understand the age and evolutionary history of Fv1, a comprehensive survey of the Muroidea was conducted, allowing the progenitor integration to be dated to ∼45 million years. Intact coding potential is visible beyond Mus, and sequence analysis reveals strong signatures of positive selection also within field mice, ApodemusFv1's survival for such a period implies a recurring and shifting retroviral burden imparting the necessary selective pressures-an influence likely also common to analogous factors. Regions of Fv1 adapt cooperatively, highlighting its preference for repeated structures and suggesting that this functionally constrained aspect of the retroviral capsid lattice presents a common target in the evolution of intrinsic immunity.
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Affiliation(s)
- George R Young
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Melvyn W Yap
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Johan R Michaux
- Laboratoire de Génétique de la Conservation, Université de Liège, 4000 Liège, Belgium
- UMR Animal, Santé, Territoires, Risques et Ecosystèmes (ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Campus International de Baillarguet, Université de Montpellier, 34398 Montpellier, France
| | - Scott J Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32304
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom;
- Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
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7
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Boso G, Buckler-White A, Kozak CA. Ancient Evolutionary Origin and Positive Selection of the Retroviral Restriction Factor Fv1 in Muroid Rodents. J Virol 2018; 92:e00850-18. [PMID: 29976659 PMCID: PMC6146698 DOI: 10.1128/jvi.00850-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/23/2018] [Indexed: 12/16/2022] Open
Abstract
The laboratory mouse Fv1 gene encodes a retroviral restriction factor that mediates resistance to murine leukemia viruses (MLVs). Sequence similarity between Fv1 and the gag protein of the murine endogenous retrovirus L (MuERV-L) family of ERVs suggests that Fv1 was coopted from an ancient provirus. Previous evolutionary studies found Fv1 orthologs only in the genus Mus Here, we describe identification of orthologous Fv1 sequences in several species belonging to multiple families of rodents outside the genus Mus We show that these Fv1 orthologs are in the same region of conserved synteny, between the genes Miip and Mfn2, suggesting a minimum insertion time of 45 million years for the ancient progenitor of Fv1 Our analysis also revealed that Fv1 was not detectable or heavily mutated in some lineages in the superfamily Muroidea, while, in concert with previous findings in the genus Mus, we found strong evidence of positive selection of Fv1 in the African clade in the subfamily Muridae Residues identified as evolving under positive selection include those that have been previously found to be important for restriction of multiple retroviral lineages. Taken together, these findings suggest that the evolutionary origin of Fv1 substantially predates Mus evolution, that the rodent Fv1 has been shaped by lineage-specific differential selection pressures, and that Fv1 has long been evolving under positive selection in the rodent family Muridae, supporting a defensive role that significantly antedates exposure to MLVs.IMPORTANCE Retroviruses have adapted to living in concert with their hosts throughout vertebrate evolution. Over the years, the study of these relationships revealed the presence of host proteins called restriction factors that inhibit retroviral replication in host cells. The first of these restriction factors to be identified, encoded by the Fv1 gene found in mice, was thought to have originated in the genus Mus In this study, we utilized genome database searches and DNA sequencing to identify Fv1 copies in multiple rodent lineages. Our findings suggest a minimum time of insertion into the genome of rodents of 45 million years for the ancestral progenitor of Fv1 While Fv1 is not detectable in some lineages, we also identified full-length orthologs showing signatures of a molecular "arms race" in a family of rodent species indigenous to Africa. This finding suggests that Fv1 in these species has been coevolving with unidentified retroviruses for millions of years.
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Affiliation(s)
- Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Alicia Buckler-White
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Christine A Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
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8
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Wanaguru M, Barry DJ, Benton DJ, O’Reilly NJ, Bishop KN. Murine leukemia virus p12 tethers the capsid-containing pre-integration complex to chromatin by binding directly to host nucleosomes in mitosis. PLoS Pathog 2018; 14:e1007117. [PMID: 29906285 PMCID: PMC6021111 DOI: 10.1371/journal.ppat.1007117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/27/2018] [Accepted: 05/22/2018] [Indexed: 12/31/2022] Open
Abstract
The murine leukaemia virus (MLV) Gag cleavage product, p12, is essential for both early and late steps in viral replication. The N-terminal domain of p12 binds directly to capsid (CA) and stabilises the mature viral core, whereas defects in the C-terminal domain (CTD) of p12 can be rescued by addition of heterologous chromatin binding sequences (CBSs). We and others hypothesised that p12 tethers the pre-integration complex (PIC) to host chromatin ready for integration. Using confocal microscopy, we have observed for the first time that CA localises to mitotic chromatin in infected cells in a p12-dependent manner. GST-tagged p12 alone, however, did not localise to chromatin and mass-spectrometry analysis of its interactions identified only proteins known to bind the p12 region of Gag. Surprisingly, the ability to interact with chromatin was conferred by a single amino acid change, M63I, in the p12 CTD. Interestingly, GST-p12_M63I showed increased phosphorylation in mitosis relative to interphase, which correlated with an increased interaction with mitotic chromatin. Mass-spectrometry analysis of GST-p12_M63I revealed nucleosomal histones as primary interactants. Direct binding of MLV p12_M63I peptides to histones was confirmed by biolayer-interferometry (BLI) assays using highly-avid recombinant poly-nucleosomal arrays. Excitingly, using this method, we also observed binding between MLV p12_WT and nucleosomes. Nucleosome binding was additionally detected with p12 orthologs from feline and gibbon ape leukemia viruses using both pull-down and BLI assays, indicating that this a common feature of gammaretroviral p12 proteins. Importantly, p12 peptides were able to block the binding of the prototypic foamy virus CBS to nucleosomes and vice versa, implying that their docking sites overlap and suggesting a conserved mode of chromatin tethering for different retroviral genera. We propose that p12 is acting in a similar capacity to CPSF6 in HIV-1 infection by facilitating initial chromatin targeting of CA-containing PICs prior to integration.
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Affiliation(s)
- Madushi Wanaguru
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David J. Barry
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, United Kingdom
| | - Donald J. Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Kate N. Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
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9
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Frank JA, Feschotte C. Co-option of endogenous viral sequences for host cell function. Curr Opin Virol 2017; 25:81-89. [PMID: 28818736 DOI: 10.1016/j.coviro.2017.07.021] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/13/2017] [Accepted: 07/23/2017] [Indexed: 01/26/2023]
Abstract
Eukaryotic genomes are littered with sequences of diverse viral origins, termed endogenous viral elements (EVEs). Here we used examples primarily drawn from mammalian endogenous retroviruses to document how the influx of EVEs has provided a source of prefabricated coding and regulatory sequences that were formerly utilized for viral infection and replication, but have been occasionally repurposed for cellular function. While EVE co-option has benefited a variety of host biological functions, there appears to be a disproportionate contribution to immunity and antiviral defense. The mammalian embryo and placenta offer opportunistic routes of viral transmission to the next host generation and as such they represent hotbeds for EVE cooption. Based on these observations, we propose that EVE cooption is initially driven as a mean to mitigate conflicts between host and viruses, which in turn acts as a stepping-stone toward the evolution of cellular innovations serving host physiology and development.
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Affiliation(s)
- John A Frank
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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10
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Ball NJ, Nicastro G, Dutta M, Pollard DJ, Goldstone DC, Sanz-Ramos M, Ramos A, Müllers E, Stirnnagel K, Stanke N, Lindemann D, Stoye JP, Taylor WR, Rosenthal PB, Taylor IA. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid. PLoS Pathog 2016; 12:e1005981. [PMID: 27829070 PMCID: PMC5102385 DOI: 10.1371/journal.ppat.1005981] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 10/06/2016] [Indexed: 12/26/2022] Open
Abstract
The Spumaretrovirinae, or foamy viruses (FVs) are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV). The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA) and C-terminal domains (CtDCA) of archetypal orthoretroviral capsid protein (CA). Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN—CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold. Foamyviruses (FVs) or Spuma-retroviruses derive their name from the cytopathic effects they cause in cell culture. However, infection in humans is benign and FVs have entered the human population through zoonosis from apes resulting in the emergence of Prototype FV (PFV). Like all retroviruses, FVs contain gag, pol and env structural genes and replicate through reverse-transcription and host genome integration. Gag, the major structural protein, is required for genome packaging, virion assembly, trafficking and egress. However, although functionally equivalent, FV and orthoretroviral Gag share little sequence homology and it is unclear how they perform the same function. Therefore, to understand more about relationship between FV and orthoretroviral replication we have carried out structural studies of PFV-Gag. Here we present the structure of CA domains from a central region PFV-Gag and show that despite little sequence similarity they share the same fold as the CA domains of orthoretroviral Gag. These data provide the first information relating the Spuma and Orthoretrovirinae Gag proteins. We discuss our findings in terms of evolutionary divergence of spuma and orthoretroviral lineages.
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Affiliation(s)
- Neil J. Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Moumita Dutta
- Structural Biology of Cells and Viruses, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Dominic J. Pollard
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - David C. Goldstone
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Marta Sanz-Ramos
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Andres Ramos
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Erik Müllers
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | | | - Nicole Stanke
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - William R. Taylor
- Computational Cell and Molecular Biology Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
- * E-mail:
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11
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Li W, Yap MW, Voss V, Stoye JP. Expression levels of Fv1: effects on retroviral restriction specificities. Retrovirology 2016; 13:42. [PMID: 27342974 PMCID: PMC4921018 DOI: 10.1186/s12977-016-0276-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mouse protein Fv1 is a factor that can confer resistance to retroviral infection. The two major Fv1 alleles from laboratory mice, Fv1 (n) and Fv1 (b) , restrict infection by different murine leukaemia viruses (MLVs). Fv1(n) restricts B-tropic MLV, but not N-tropic MLV or NB-tropic MLV. In cells expressing Fv1(b) at natural levels, only N-MLV is restricted, however restriction of NB-MLV and partial restriction of B-MLV were observed when recombinant Fv1(b) was expressed from an MLV promoter in Fv1 null Mus dunni tail fibroblast cells. To investigate the relationship between expression level and restriction specificity we have developed new retroviral delivery vectors which allow inducible expression of Fv1, and yet allow sufficient production of fluorescent reporter proteins for analysis in our FACS-based restriction assay. RESULTS We demonstrated that at concentrations close to the endogenous expression level, Fv1(b) specifically restricts only N-MLV, but restriction of NB-MLV, and to a lesser extent B-MLV, could be gained by increasing the protein level of Fv1(b). By contrast, we found that even when Fv1(n) is expressed at very high levels, no significant inhibition of N-MLV or NB-MLV could be observed. Study of Fv1 mutants using this assay led to the identification of determinants for N/B tropism at an expression level close to that of endogenous Fv1(n) and Fv1(b). We also compared the recently described restriction activities of wild mice Fv1 proteins directed against non-MLV retroviruses when expressed at different levels. Fv1 from M. spretus restricted N-MLV, B-MLV and equine infectious anaemia virus equally even at low concentrations, while Fv1 from M. macedonicus showed even stronger restriction against equine infectious anaemia virus than to N-MLV. Restriction of feline foamy virus by Fv1 of M. caroli occurred at levels equivalent to MLV restriction. CONCLUSIONS Our data indicate that for some but not all Fv1 proteins, gain of restriction activities could be achieved by increasing the expression level of Fv1. However such a concentration dependent effect is not seen with most Fv1s and cannot explain the recently reported activities against non-MLVs. It will be interesting to examine whether overexpression of other capsid binding restriction factors such as TRIM5α or Mx2 result in novel restriction specificities.
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Affiliation(s)
- Wilson Li
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Melvyn W Yap
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Vicky Voss
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK. .,Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK.
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12
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Honda T, Tomonaga K. Endogenous non-retroviral RNA virus elements evidence a novel type of antiviral immunity. Mob Genet Elements 2016; 6:e1165785. [PMID: 27510928 PMCID: PMC4964890 DOI: 10.1080/2159256x.2016.1165785] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/10/2016] [Indexed: 10/25/2022] Open
Abstract
Vertebrate genomes contain many virus-related sequences derived from both retroviruses and non-retroviral RNA and DNA viruses. Such non-retroviral RNA sequences are possibly produced by reverse-transcription and integration of viral mRNAs of ancient RNA viruses using retrotransposon machineries. We refer to this process as transcript reversion. During an ancient bornavirus infection, transcript reversion may have left bornavirus-related sequences, known as endogenous bornavirus-like nucleoproteins (EBLNs), in the genome. We have recently demonstrated that all Homo sapiens EBLNs are expressed in at least one tissue. Because species with EBLNs appear relatively protected against infection by a current bornavirus, Borna disease virus, it is speculated that EBLNs play some roles in antiviral immunity, as seen with some endogenous retroviruses. EBLNs can function as dominant negative forms of viral proteins, small RNAs targeting viral sequences, or DNA or RNA elements modulating the gene expression. Growing evidence reveals that various RNA viruses are reverse-transcribed and integrated into the genome of infected cells, suggesting transcript reversion generally occurs during ongoing infection. Considering this, transcript reversion-mediated interference with related viruses may be a novel type of antiviral immunity in vertebrates. Understanding the biological significance of transcript reversion will provide novel insights into host defenses against viral infections.
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Affiliation(s)
- Tomoyuki Honda
- Department of Viral Oncology, Institute for Virus Research, Kyoto University , Kyoto, Japan
| | - Keizo Tomonaga
- Department of Viral Oncology, Institute for Virus Research, Kyoto University , Kyoto, Japan
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13
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Tucker JM, Garfinkel DJ. Ty1 escapes restriction by the self-encoded factor p22 through mutations in capsid. Mob Genet Elements 2016; 6:e1154639. [PMID: 27141327 DOI: 10.1080/2159256x.2016.1154639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/04/2016] [Accepted: 02/11/2016] [Indexed: 12/26/2022] Open
Abstract
Ty1 is a long terminal repeat (LTR) retrotransposon belonging to the Ty1/copia family and is present in up to 32 full-length copies in Saccharomyces. Like retroviruses, Ty1 contains GAG and POL genes, LTRs, and replicates via an RNA intermediate within a virus-like particle (VLP). Although Ty1 retrotransposition is not infectious, uncontrolled replication can lead to detrimental effects on the host genome, including insertional mutagenesis and chromosomal rearrangements. Ty1 copy number control (CNC) limits replication and is mediated through a self-encoded protein called p22. p22 is translated from a subgenomic Ty1 RNA and encodes an amino-truncated version of the Gag protein. We highlight a recent study identifying Ty1 Gag, which comprises the VLP capsid and provides nucleic acid chaperone functions, as a direct target of p22-mediated inhibition. CNC-resistant (CNCR) mutations map within predicted helical domains of Gag, including those in the Ty1/copia pfam domain Retrotran_gag_2 (formerly UBN2) and a central region we refer to as the CNCR domain. CNCR Gag forms VLPs that exclude p22, thus restoring Ty1 replication. We discuss possible mechanisms for p22 inclusion in Ty1 VLPs and compare Ty1 CNC with retroviral restriction factors targeting capsid (CA).
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Affiliation(s)
- Jessica M Tucker
- Department of Biochemistry & Molecular Biology, University of Georgia , Athens, GA, USA
| | - David J Garfinkel
- Department of Biochemistry & Molecular Biology, University of Georgia , Athens, GA, USA
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14
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Abstract
Endogenous bornavirus-like elements (EBLs) are ancient bornavirus-derived sequence in the genomes of eukaryotes. Expression profile of EBLs suggests that, although most of the EBLs in mammalian genomes have lost their coding potential, many of them are transcribed in a cell-type specific or ubiquitous manner. This observation leads us to speculate that EBLs may have functions in their host cells. Here we describe possible functions of EBLs and their evolutionary significance. Our recent studies revealed that EBLs in some mammals, including humans, play critical roles in viral infection as either RNAs or proteins in previously undescribed mechanisms. Considering that species having EBLs in their genomes appear to be relatively resistance to BDV-mediated pathogenesis, endogenization of RNA viruses might be an evolutionarily inevitable event in the adaptation of hosts to the viruses.
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Affiliation(s)
- Tomoyuki Honda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine
- Department of Viral Oncology, Institute for Virus Research, Kyoto University
| | - Keizo Tomonaga
- Department of Viral Oncology, Institute for Virus Research, Kyoto University
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15
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Garfinkel DJ, Tucker JM, Saha A, Nishida Y, Pachulska-Wieczorek K, Błaszczyk L, Purzycka KJ. A self-encoded capsid derivative restricts Ty1 retrotransposition in Saccharomyces. Curr Genet 2015; 62:321-9. [PMID: 26650614 DOI: 10.1007/s00294-015-0550-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
Retrotransposons and retroviral insertions have molded the genomes of many eukaryotes. Since retroelements transpose via an RNA intermediate, the additive nature of the replication cycle can result in massive increases in copy number if left unchecked. Host organisms have countered with several defense systems, including domestication of retroelement genes that now act as restriction factors to minimize propagation. We discovered a novel truncated form of the Saccharomyces Ty1 retrotransposon capsid protein, dubbed p22 that inhibits virus-like particle (VLP) assembly and function. The p22 restriction factor expands the repertoire of defense proteins targeting the capsid and highlights a novel host-parasite strategy. Instead of inhibiting all transposition by domesticating the restriction gene as a distinct locus, Ty1 and budding yeast may have coevolved a relationship that allows high levels of transposition when Ty1 copy numbers are low and progressively less transposition as copy numbers rise. Here, we offer a perspective on p22 restriction, including its mode of expression, effect on VLP functions, interactions with its target, properties as a nucleic acid chaperone, similarities to other restriction factors, and future directions.
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Affiliation(s)
- David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA.
| | - Jessica M Tucker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Agniva Saha
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Yuri Nishida
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Leszek Błaszczyk
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Katarzyna J Purzycka
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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16
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The Ty1 Retrotransposon Restriction Factor p22 Targets Gag. PLoS Genet 2015; 11:e1005571. [PMID: 26451601 PMCID: PMC4599808 DOI: 10.1371/journal.pgen.1005571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/15/2015] [Indexed: 01/09/2023] Open
Abstract
A novel form of copy number control (CNC) helps maintain a low number of Ty1 retrovirus-like transposons in the Saccharomyces genome. Ty1 produces an alternative transcript that encodes p22, a trans-dominant negative inhibitor of Ty1 retrotransposition whose sequence is identical to the C-terminal half of Gag. The level of p22 increases with copy number and inhibits normal Ty1 virus-like particle (VLP) assembly and maturation through interactions with full length Gag. A forward genetic screen for CNC-resistant (CNCR) mutations in Ty1 identified missense mutations in GAG that restore retrotransposition in the presence of p22. Some of these mutations map within a predicted UBN2 domain found throughout the Ty1/copia family of long terminal repeat retrotransposons, and others cluster within a central region of Gag that is referred to as the CNCR domain. We generated multiple alignments of yeast Ty1-like Gag proteins and found that some Gag proteins, including those of the related Ty2 elements, contain non-Ty1 residues at multiple CNCR sites. Interestingly, the Ty2-917 element is resistant to p22 and does not undergo a Ty1-like form of CNC. Substitutions conferring CNCR map within predicted helices in Ty1 Gag that overlap with conserved sequence in Ty1/copia, suggesting that p22 disturbs a central function of the capsid during VLP assembly. When hydrophobic residues within predicted helices in Gag are mutated, Gag level remains unaffected in most cases yet VLP assembly and maturation is abnormal. Gag CNCR mutations do not alter binding to p22 as determined by co-immunoprecipitation analyses, but instead, exclude p22 from Ty1 VLPs. These findings suggest that the CNCR alleles enhance retrotransposition in the presence of p22 by allowing productive Gag-Gag interactions during VLP assembly. Our work also expands the strategies used by retroviruses for developing resistance to Gag-like restriction factors to now include retrotransposons. The presence of transposable elements in the eukaryotic genome threatens genomic stability and normal gene function, thus various defense mechanisms exist to silence element expression and target integration to benign locations in the genome. Even though the budding yeast Saccharomyces lacks many of the defense systems present in other eukaryotes, including RNAi, DNA methylation, and APOBEC3 proteins, they maintain low numbers of mobile elements in their genome. In the case of the Saccharomyces retrotransposon Ty1, a system called copy number control (CNC) helps determine the number of elements in the genome. Recently, we demonstrated that the mechanism of CNC relies on a trans-acting protein inhibitor of Ty1 expressed from the element itself. This protein inhibitor, called p22, impacts the replication of Ty1 as its copy number increases. To identify a molecular target of p22, mutagenized Ty1 was subjected to a forward genetic screen for CNC-resistance. Mutations in specific domains of Gag, including the UBN2 Gag motif and a novel region we have named the CNCR domain, confer CNCR by preventing the incorporation of p22 into assembling virus-like particles (VLPs), which restores maturation and completion of the Ty1 life cycle. The mechanism of Ty1 inhibition by p22 is conceptually similar to Gag-like restriction factors in mammals since they inhibit normal particle function. In particular, resistance to p22 and the enJS56A1 restriction factor of sheep involves exclusion of the restriction factor during particle assembly, although Ty1 CNCR achieves this in a way that is distinct from the Jaagsiekte retrovirus escape mutants. Our work introduces an intriguing variation on resistance mechanisms to retroviral restriction factors.
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17
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Saha A, Mitchell JA, Nishida Y, Hildreth JE, Ariberre JA, Gilbert WV, Garfinkel DJ. A trans-dominant form of Gag restricts Ty1 retrotransposition and mediates copy number control. J Virol 2015; 89:3922-38. [PMID: 25609815 PMCID: PMC4403431 DOI: 10.1128/jvi.03060-14] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/15/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Saccharomyces cerevisiae and Saccharomyces paradoxus lack the conserved RNA interference pathway and utilize a novel form of copy number control (CNC) to inhibit Ty1 retrotransposition. Although noncoding transcripts have been implicated in CNC, here we present evidence that a truncated form of the Gag capsid protein (p22) or its processed form (p18) is necessary and sufficient for CNC and likely encoded by Ty1 internal transcripts. Coexpression of p22/p18 and Ty1 decreases mobility more than 30,000-fold. p22/p18 cofractionates with Ty1 virus-like particles (VLPs) and affects VLP yield, protein composition, and morphology. Although p22/p18 and Gag colocalize in the cytoplasm, p22/p18 disrupts sites used for VLP assembly. Glutathione S-transferase (GST) affinity pulldowns also suggest that p18 and Gag interact. Therefore, this intrinsic Gag-like restriction factor confers CNC by interfering with VLP assembly and function and expands the strategies used to limit retroelement propagation. IMPORTANCE Retrotransposons dominate the chromosomal landscape in many eukaryotes, can cause mutations by insertion or genome rearrangement, and are evolutionarily related to retroviruses such as HIV. Thus, understanding factors that limit transposition and retroviral replication is fundamentally important. The present work describes a retrotransposon-encoded restriction protein derived from the capsid gene of the yeast Ty1 element that disrupts virus-like particle assembly in a dose-dependent manner. This form of copy number control acts as a molecular rheostat, allowing high levels of retrotransposition when few Ty1 elements are present and inhibiting transposition as copy number increases. Thus, yeast and Ty1 have coevolved a form of copy number control that is beneficial to both "host and parasite." To our knowledge, this is the first Gag-like retrotransposon restriction factor described in the literature and expands the ways in which restriction proteins modulate retroelement replication.
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Affiliation(s)
- Agniva Saha
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Jessica A Mitchell
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Yuri Nishida
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Jonathan E Hildreth
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Joshua A Ariberre
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wendy V Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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18
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The N-terminus of murine leukaemia virus p12 protein is required for mature core stability. PLoS Pathog 2014; 10:e1004474. [PMID: 25356837 PMCID: PMC4214797 DOI: 10.1371/journal.ppat.1004474] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/15/2014] [Indexed: 12/02/2022] Open
Abstract
The murine leukaemia virus (MLV) gag gene encodes a small protein called p12 that is essential for the early steps of viral replication. The N- and C-terminal regions of p12 are sequentially acting domains, both required for p12 function. Defects in the C-terminal domain can be overcome by introducing a chromatin binding motif into the protein. However, the function of the N-terminal domain remains unknown. Here, we undertook a detailed analysis of the effects of p12 mutation on incoming viral cores. We found that both reverse transcription complexes and isolated mature cores from N-terminal p12 mutants have altered capsid complexes compared to wild type virions. Electron microscopy revealed that mature N-terminal p12 mutant cores have different morphologies, although immature cores appear normal. Moreover, in immunofluorescent studies, both p12 and capsid proteins were lost rapidly from N-terminal p12 mutant viral cores after entry into target cells. Importantly, we determined that p12 binds directly to the MLV capsid lattice. However, we could not detect binding of an N-terminally altered p12 to capsid. Altogether, our data imply that p12 stabilises the mature MLV core, preventing premature loss of capsid, and that this is mediated by direct binding of p12 to the capsid shell. In this manner, p12 is also retained in the pre-integration complex where it facilitates tethering to mitotic chromosomes. These data also explain our previous observations that modifications to the N-terminus of p12 alter the ability of particles to abrogate restriction by TRIM5alpha and Fv1, factors that recognise viral capsid lattices. All retroviral genomes contain a gag gene that codes for the Gag polyprotein. Gag is cleaved upon viral maturation to release individual proteins, including matrix, capsid and nucleocapsid, providing the structural components of the virion. In murine leukaemia virus (MLV), Gag cleavage releases an additional protein, named p12, required for both early and late stages of the viral life cycle. The role of p12 during early events is poorly understood, and it is the only MLV protein without a function-associated name. Here, we show that p12 binds to the capsid shell of the viral core and stabilises it. Mutations that give rise to N-terminally altered p12 proteins result in a rapid loss of both p12 and capsid from viral cores, leading to abnormal core morphologies and abolishing the ability of particles to abrogate restriction by cellular factors that target viral capsid lattices. Understanding how the mature retroviral core forms and how it disassembles during infection is important as this determines the infectivity of all retroviruses, including HIV-1. Furthermore, altering core stability has recently become a novel target for HIV-1 therapeutics.
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19
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Inhibition of Borna disease virus replication by an endogenous bornavirus-like element in the ground squirrel genome. Proc Natl Acad Sci U S A 2014; 111:13175-80. [PMID: 25157155 DOI: 10.1073/pnas.1407046111] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Animal genomes contain endogenous viral sequences, such as endogenous retroviruses and retrotransposons. Recently, we and others discovered that nonretroviral viruses also have been endogenized in many vertebrate genomes. Bornaviruses belong to the Mononegavirales and have left endogenous fragments, called "endogenous bornavirus-like elements" (EBLs), in the genomes of many mammals. The striking features of EBLs are that they contain relatively long ORFs which have high sequence homology to the extant bornavirus proteins. Furthermore, some EBLs derived from bornavirus nucleoprotein (EBLNs) have been shown to be transcribed as mRNA and probably are translated into proteins. These features lead us to speculate that EBLs may function as cellular coopted genes. An EBLN element in the genome of the thirteen-lined ground squirrel (Ictidomys tridecemlineatus), itEBLN, encodes an ORF with 77% amino acid sequence identity to the current bornavirus nucleoprotein. In this study, we cloned itEBLN from the ground squirrel genome and investigated its involvement in Borna disease virus (BDV) replication. Interestingly, itEBLN, but not a human EBLN, colocalized with the viral factory in the nucleus and appeared to affect BDV polymerase activity by being incorporated into the viral ribonucleoprotein. Our data show that, as do certain endogenous retroviruses, itEBLN potentially may inhibit infection by related exogenous viruses in vivo.
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20
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Antiretroviral restriction factors in mice. Virus Res 2014; 193:130-4. [PMID: 25018022 DOI: 10.1016/j.virusres.2014.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 12/31/2022]
Abstract
One of the most exciting areas in contemporary retrovirus research is the discovery of "restriction factors". These are cellular proteins that act after virus entry to inhibit infection by or replication of retroviruses (and other viruses and intracellular pathogens). We briefly discuss here three antiretroviral restriction factors in mice: Fv1, APOBEC3, and tetherin, touching on both biological and molecular aspects of these restriction systems.
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21
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Structural studies of postentry restriction factors reveal antiparallel dimers that enable avid binding to the HIV-1 capsid lattice. Proc Natl Acad Sci U S A 2014; 111:9609-14. [PMID: 24979782 DOI: 10.1073/pnas.1402448111] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Restriction factors (RFs) form important components of host defenses to retroviral infection. The Fv1, Trim5α, and TrimCyp RFs contain N-terminal dimerization and C-terminal specificity domains that target assembled retroviral capsid (CA) proteins enclosing the viral core. However, the molecular detail of the interaction between RFs and their CA targets is unknown. Therefore, we have determined the crystal structure of the B-box and coiled-coil (BCC) region from Trim5α and used small-angle X-ray scattering to examine the solution structure of Trim5α BCC, the dimerization domain of Fv1 (Fv1Ntd), and the hybrid restriction factor Fv1Cyp comprising Fv1NtD fused to the HIV-1 binding protein Cyclophilin A (CypA). These data reveal that coiled-coil regions of Fv1 and Trim5α form extended antiparallel dimers. In Fv1Cyp, two CypA moieties are located at opposing ends, creating a molecule with a dumbbell appearance. In Trim5α, the B-boxes are located at either end of the coiled-coil, held in place by interactions with a helical motif from the L2 region of the opposing monomer. A comparative analysis of Fv1Cyp and CypA binding to a preformed HIV-1 CA lattice reveals how RF dimerization enhances the affinity of interaction through avidity effects. We conclude that the antiparallel organization of the NtD regions of Fv1 and Trim5α dimers correctly positions C-terminal specificity and N-terminal effector domains and facilitates stable binding to adjacent CA hexamers in viral cores.
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22
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Yap MW, Colbeck E, Ellis SA, Stoye JP. Evolution of the retroviral restriction gene Fv1: inhibition of non-MLV retroviruses. PLoS Pathog 2014; 10:e1003968. [PMID: 24603659 PMCID: PMC3948346 DOI: 10.1371/journal.ppat.1003968] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/16/2014] [Indexed: 11/18/2022] Open
Abstract
Fv1 is the prototypic restriction factor that protects against infection by the murine leukemia virus (MLV). It was first identified in cells that were derived from laboratory mice and was found to be homologous to the gag gene of an endogenous retrovirus (ERV). To understand the evolution of the host restriction gene from its retroviral origins, Fv1s from wild mice were isolated and characterized. Most of these possess intact open reading frames but not all restricted N-, B-, NR-or NB-tropic MLVs, suggesting that other viruses could have played a role in the selection of the gene. The Fv1s from Mus spretus and Mus caroli were found to restrict equine infectious anemia virus (EIAV) and feline foamy virus (FFV) respectively, indicating that Fv1 could have a broader target range than previously thought, including activity against lentiviruses and spumaviruses. Analyses of the Fv1 sequences revealed a number of residues in the C-terminal region that had evolved under positive selection. Four of these selected residues were found to be involved in the novel restriction by mapping studies. These results strengthen the similarities between the two capsid binding restriction factors, Fv1 and TRIM5α, which support the hypothesis that Fv1 defended mice against waves of retroviral infection possibly including non-MLVs as well as MLVs. We have followed the evolution of the retroviral restriction gene, Fv1, by functional analysis. We show that Fv1 can recognize and restrict a wider range of retroviruses than previously thought including examples from the gammaretrovirus, lentivirus and foamy virus genera. Nearly every Fv1 tested showed a different pattern of restriction activity. We also identify several hypervariable regions in the coding sequence containing positively selected amino acids that we show to be directly involved in determining restriction specificity. Our results strengthen the analogy between Fv1 and another capsid-binding, retrovirus restriction factor, TRIM5α. Although they share no sequence identity they appear to share a similar design and appear likely to recognise different targets by a mechanism involving multiple weak interactions between a virus-binding domain containing several variable regions and the surface of the viral capsid. We also describe a pattern of constant genetic change, implying that different species of Mus have evolved in the face of ever-changing retroviral threats by viruses of different kinds.
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Affiliation(s)
- Melvyn W. Yap
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Emily Colbeck
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Scott A. Ellis
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Jonathan P. Stoye
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
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23
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Viral and cellular requirements for the nuclear entry of retroviral preintegration nucleoprotein complexes. Viruses 2013; 5:2483-511. [PMID: 24103892 PMCID: PMC3814599 DOI: 10.3390/v5102483] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/26/2013] [Accepted: 10/03/2013] [Indexed: 02/07/2023] Open
Abstract
Retroviruses integrate their reverse transcribed genomes into host cell chromosomes as an obligate step in virus replication. The nuclear envelope separates the chromosomes from the cell cytoplasm during interphase, and different retroviral groups deal with this physical barrier in different ways. Gammaretroviruses are dependent on the passage of target cells through mitosis, where they are believed to access chromosomes when the nuclear envelope dissolves for cell division. Contrastingly, lentiviruses such as HIV-1 infect non-dividing cells, and are believed to enter the nucleus by passing through the nuclear pore complex. While numerous virally encoded elements have been proposed to be involved in HIV-1 nuclear import, recent evidence has highlighted the importance of HIV-1 capsid. Furthermore, capsid was found to be responsible for the viral requirement of various nuclear transport proteins, including transportin 3 and nucleoporins NUP153 and NUP358, during infection. In this review, we describe our current understanding of retroviral nuclear import, with emphasis on recent developments on the role of the HIV-1 capsid protein.
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Nexø BA, Hansen B, Nissen KK, Gundestrup L, Terkelsen T, Villesen P, Bahrami S, Petersen T, Pedersen FS, Laska MJ. Restriction genes for retroviruses influence the risk of multiple sclerosis. PLoS One 2013; 8:e74063. [PMID: 24066097 PMCID: PMC3774660 DOI: 10.1371/journal.pone.0074063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/26/2013] [Indexed: 11/18/2022] Open
Abstract
We recently described that the autoimmune, central nervous system disease, multiple sclerosis (MS), is genetically associated with the human endogenous retroviral locus, HERV-Fc1, in Scandinavians. A number of dominant human genes encoding factors that restrict retrovirus replication have been known for a long time. Today human restriction genes for retroviruses include amongst others TRIMs, APOBEC3s, BST2 and TREXs. We have therefore looked for a role of these retroviral restriction genes in MS using genetic epidemiology. We here report that markers in two TRIMs, TRIM5 and TRIM22 and a marker in BST2, associated statistically with the risk of getting MS, while markers in or near APOBEC3s and TREXs showed little or no effect. This indicates that the two TRIMs and BST2 influence the risk of disease and thus supports the hypothesis of a viral involvement.
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Affiliation(s)
- Bjørn A. Nexø
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Bettina Hansen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Kari K. Nissen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Lisa Gundestrup
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | | | - Palle Villesen
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | | | - Thor Petersen
- Department of Neurology, Aarhus University Hospital, Aarhus C, Denmark
| | - Finn S. Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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Sanz-Ramos M, Stoye JP. Capsid-binding retrovirus restriction factors: discovery, restriction specificity and implications for the development of novel therapeutics. J Gen Virol 2013; 94:2587-2598. [PMID: 24026671 DOI: 10.1099/vir.0.058180-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The development of drugs against human immunodeficiency virus type 1 infection has been highly successful, and numerous combinational treatments are currently available. However, the risk of the emergence of resistance and the toxic effects associated with prolonged use of antiretroviral therapies have emphasized the need to consider alternative approaches. One possible area of investigation is provided by the properties of restriction factors, cellular proteins that protect organisms against retroviral infection. Many show potent viral inhibition. Here, we describe the discovery, properties and possible therapeutic uses of the group of restriction factors known to interact with the capsid core of incoming retroviruses. This group comprises Fv1, TRIM5α and TRIMCypA: proteins that all act shortly after virus entry into the target cell and block virus replication at different stages prior to integration of viral DNA into the host chromosome. They have different origins and specificities, but share general structural features required for restriction, with an N-terminal multimerization domain and a C-terminal capsid-binding domain. Their overall efficacy makes it reasonable to ask whether they might provide a framework for developing novel antiretroviral strategies.
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Affiliation(s)
- Marta Sanz-Ramos
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Jonathan P Stoye
- Department of Medicine, Imperial College London, London W2 1PG, UK.,Division of Virology, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
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Halemano K, Barrett BS, Li SX, Harper MS, Smith DS, Heilman KJ, Santiago ML. Fv1 restriction and retrovirus vaccine immunity in Apobec3-deficient 129P2 mice. PLoS One 2013; 8:e60500. [PMID: 23533681 PMCID: PMC3606284 DOI: 10.1371/journal.pone.0060500] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 02/27/2013] [Indexed: 11/18/2022] Open
Abstract
Understanding the host genetics of the immune response in retrovirus infection models could provide insights for basic HIV vaccine discovery. In Friend retrovirus (FV) infection of mice, Fv1 differentially inhibits N-tropic versus B-tropic FV infection by mediating a capsid-dependent post-entry block, Fv2 susceptibility governs splenomegaly induction, and Rfv3 resistance primes a stronger neutralizing antibody response due to more potent Apobec3 activity. Apobec3 polymorphisms in inbred mouse strains correlate with Rfv3 resistance and susceptibility, with one unresolved exception. The 129/OlaHsd (129P2) mouse strain is Fv2 and Rfv3 susceptible based on genotyping, but infection of 129P2 mice with B-tropic FV resulted in strong neutralizing antibody responses and no splenomegaly. Here we confirm that 129P2 mice are Fv1nr/nr, explaining its resistance to B-tropic FV. Infection of 129P2 mice with NB-tropic FV, which can efficiently infect mice independent of Fv1 genotype, resulted in severe splenomegaly, high levels of viremia and weak neutralizing antibody responses regardless of Apobec3 status. Notably, high-dose B-tropic FV infection of 129P2 Apobec3-deficient mice induced significant adaptive immune responses and conferred high levels of protection following challenge with pathogenic NB-tropic FV. This immunological protection complemented previous studies that N-tropic FV can act as a live-attenuated vaccine in Fv1b/b mice. Altogether, the results obtained in 129P2 mice strengthen the conclusion that Rfv3 is encoded by Apobec3, and highlight Fv1 incompatibility as a retroviral vaccine paradigm in mice. Due to its susceptibility to disease that allows for pathogenic challenge studies, B-tropic FV infection of 129P2 mice may be a useful model to study the immunological pathways induced by retroviral capsid restriction.
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Affiliation(s)
- Kalani Halemano
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Microbiology, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Bradley S. Barrett
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Sam X. Li
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Microbiology, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Michael S. Harper
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Integrated Department of Immunology, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Diana S. Smith
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Karl J. Heilman
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Mario L. Santiago
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Microbiology, University of Colorado Denver, Aurora, Colorado, United States of America
- Integrated Department of Immunology, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail:
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Abstract
Retroviral replication involves the formation of a DNA provirus integrated into the host genome. Through this process, retroviruses can colonize the germ line to form endogenous retroviruses (ERVs). ERV inheritance can have multiple adverse consequences for the host, some resembling those resulting from exogenous retrovirus infection but others arising by mechanisms unique to ERVs. Inherited retroviruses can also confer benefits on the host. To meet the different threats posed by endogenous and exogenous retroviruses, various host defences have arisen during evolution, acting at various stages on the retrovirus life cycle. In this Review, I describe our current understanding of the distribution and architecture of ERVs, the consequences of their acquisition for the host and the emerging details of the intimate evolutionary relationship between virus and vertebrate host.
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Lee K, Mulky A, Yuen W, Martin TD, Meyerson NR, Choi L, Yu H, Sawyer SL, KewalRamani VN. HIV-1 capsid-targeting domain of cleavage and polyadenylation specificity factor 6. J Virol 2012; 86:3851-60. [PMID: 22301135 PMCID: PMC3302544 DOI: 10.1128/jvi.06607-11] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 01/19/2012] [Indexed: 12/27/2022] Open
Abstract
The antiviral factor CPSF6-358 restricts human immunodeficiency virus type 1 (HIV-1) infection through an interaction with capsid (CA), preventing virus nuclear entry and integration. HIV-1 acquires resistance to CPSF6-358 through an N74D mutation of CA that impairs binding of the antiviral factor. Here we examined the determinants within CPSF6-358 that are necessary for CA-specific interaction. Residues 314 to 322 include amino acids that are essential for CPSF6-358 restriction of HIV-1. Fusion of CPSF6 residues 301 to 358 to rhesus TRIM5α is also sufficient to restrict wild-type but not N74D HIV-1. Restriction is lost if CPSF6 residues in the amino acid 314 to 322 interaction motif are mutated. Examination of the CA targeting motif in CPSF6-358 did not reveal evidence of positive selection. Given the sensitivity of different primate lentiviruses to CPSF6-358 and apparent conservation of this interaction, our data suggest that CPSF6-358-mediated targeting of HIV-1 could provide a broadly effective antiviral strategy.
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Affiliation(s)
- KyeongEun Lee
- HIV Drug Resistance Program, National Cancer Institute
| | - Alok Mulky
- HIV Drug Resistance Program, National Cancer Institute
| | - Wendy Yuen
- HIV Drug Resistance Program, National Cancer Institute
- SAIC-Frederick, Basic Science Program, Frederick, Maryland, USA
| | | | - Nicholas R. Meyerson
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Laura Choi
- HIV Drug Resistance Program, National Cancer Institute
| | - Hyun Yu
- HIV Drug Resistance Program, National Cancer Institute
| | - Sara L. Sawyer
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
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29
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Feschotte C, Gilbert C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 2012; 13:283-96. [PMID: 22421730 DOI: 10.1038/nrg3199] [Citation(s) in RCA: 490] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent studies have uncovered myriad viral sequences that are integrated or 'endogenized' in the genomes of various eukaryotes. Surprisingly, it appears that not just retroviruses but almost all types of viruses can become endogenous. We review how these genomic 'fossils' offer fresh insights into the origin, evolutionary dynamics and structural evolution of viruses, which are giving rise to the burgeoning field of palaeovirology. We also examine the multitude of ways through which endogenous viruses have influenced, for better or worse, the biology of their hosts. We argue that the conflict between hosts and viruses has led to the invention and diversification of molecular arsenals, which, in turn, promote the cellular co-option of endogenous viruses.
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Affiliation(s)
- Cédric Feschotte
- Department of Biology, University of Texas, Arlington, Texas 76016, USA.
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30
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Nakayama EE, Shioda T. Role of Human TRIM5α in Intrinsic Immunity. Front Microbiol 2012; 3:97. [PMID: 22435067 PMCID: PMC3304089 DOI: 10.3389/fmicb.2012.00097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 02/28/2012] [Indexed: 12/14/2022] Open
Abstract
Human immunodeficiency virus (HIV) has a very narrow host range. HIV type 1 (HIV-1) does not infect Old World monkeys, such as the rhesus monkey (Rh). Rh TRIM5α was identified as a factor that confers resistance, intrinsic immunity, to HIV-1 infection. Unfortunately, human TRIM5α is almost powerless to restrict HIV-1. However, human TRIM5α potently restricts N-tropic murine leukemia viruses (MLV) but not B-tropic MLV, indicating that human TRIM5α represents the restriction factor previously designated as Ref1. African green monkey TRIM5α represents another restriction factor previously designated as Lv1, which restricts both HIV-1 and simian immunodeficiency virus isolated from macaque (SIVmac) infection. TRIM5 is a member of the tripartite motif family containing RING, B-box2, and coiled-coil domains. The RING domain is frequently found in E3 ubiquitin ligase, and TRIM5α is thought to degrade viral core via ubiquitin–proteasome-dependent and -independent pathways. The alpha isoform of TRIM5 has an additional C-terminal PRYSPRY domain, which is a determinant of species-specific retrovirus restriction by TRIM5α. On the other hand, the target regions of viral capsid protein (CA) are scattered on the surface of core. A single amino acid difference in the surface-exposed loop between α-helices 6 and 7 (L6/7) of HIV type 2 (HIV-2) CA affects viral sensitivity to human TRIM5α and was also shown to be associated with viral load in West African HIV-2 patients, indicating that human TRIM5α is a critical modulator of HIV-2 replication in vivo. Interestingly, L6/7 of CA corresponds to the MLV determinant of sensitivity to mouse factor Fv1, which potently restricts N-tropic MLV. In addition, human genetic polymorphisms also affect antiviral activity of human TRIM5α. Recently, human TRIM5α was shown to activate signaling pathways that lead to activation of NF-κB and AP-1 by interacting with TAK1 complex. TRIM5α is thus involved in control of viral infection in multiple ways.
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Affiliation(s)
- Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University Suita, Osaka, Japan
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31
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In vitro assembly of virus-like particles of a gammaretrovirus, the murine leukemia virus XMRV. J Virol 2011; 86:1297-306. [PMID: 22090120 DOI: 10.1128/jvi.05564-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Immature retroviral particles are assembled by self-association of the structural polyprotein precursor Gag. During maturation the Gag polyprotein is proteolytically cleaved, yielding mature structural proteins, matrix (MA), capsid (CA), and nucleocapsid (NC), that reassemble into a mature viral particle. Proteolytic cleavage causes the N terminus of CA to fold back to form a β-hairpin, anchored by an internal salt bridge between the N-terminal proline and the inner aspartate. Using an in vitro assembly system of capsid-nucleocapsid protein (CANC), we studied the formation of virus-like particles (VLP) of a gammaretrovirus, the xenotropic murine leukemia virus (MLV)-related virus (XMRV). We show here that, unlike other retroviruses, XMRV CA and CANC do not assemble tubular particles characteristic of mature assembly. The prevention of β-hairpin formation by the deletion of either the N-terminal proline or 10 initial amino acids enabled the assembly of ΔProCANC or Δ10CANC into immature-like spherical particles. Detailed three-dimensional (3D) structural analysis of these particles revealed that below a disordered N-terminal CA layer, the C terminus of CA assembles a typical immature lattice, which is linked by rod-like densities with the RNP.
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32
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Murine leukemia viruses: objects and organisms. Adv Virol 2011; 2011:403419. [PMID: 22312342 PMCID: PMC3265304 DOI: 10.1155/2011/403419] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 07/25/2011] [Indexed: 01/12/2023] Open
Abstract
Murine leukemia viruses (MLVs) are among the simplest retroviruses. Prototypical gammaretroviruses encode only the three polyproteins that will be used in the assembly of progeny virus particles. These are the Gag polyprotein, which is the structural protein of a retrovirus particle, the Pol protein, comprising the three retroviral enzymes—protease, which catalyzes the maturation of the particle, reverse transcriptase, which copies the viral RNA into DNA upon infection of a new host cell, and integrase, which inserts the DNA into the chromosomal DNA of the host cell, and the Env polyprotein, which induces the fusion of the viral membrane with that of the new host cell, initiating infection. In general, a productive MLV infection has no obvious effect upon host cells. Although gammaretroviral structure and replication follow the same broad outlines as those of other retroviruses, we point out a number of significant differences between different retroviral genera.
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