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Ruggiero E, Tassinari M, Perrone R, Nadai M, Richter SN. Stable and Conserved G-Quadruplexes in the Long Terminal Repeat Promoter of Retroviruses. ACS Infect Dis 2019; 5:1150-1159. [PMID: 31081611 PMCID: PMC6630527 DOI: 10.1021/acsinfecdis.9b00011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Retroviruses
infect almost all vertebrates, from humans to domestic and farm animals,
from primates to wild animals, where they cause severe diseases, including
immunodeficiencies, neurological disorders, and cancer. Nonhuman retroviruses
have also been recently associated with human diseases. To date, no
effective treatments are available; therefore, finding retrovirus-specific
therapeutic targets is becoming an impelling issue. G-Quadruplexes
are four-stranded nucleic acid structures that form in guanine-rich
regions. Highly conserved G-quadruplexes located in the long-terminal-repeat
(LTR) promoter of HIV-1 were shown to modulate the virus transcription
machinery; moreover, the astonishingly high degree of conservation
of G-quadruplex sequences in all primate lentiviruses corroborates
the idea that these noncanonical nucleic acid structures are crucial
elements in the lentiviral biology and thus have been selected for
during evolution. In this work, we aimed at investigating the presence
and conservation of G-quadruplexes in the Retroviridae family. Genomewide
bioinformatics analysis showed that, despite their documented high
genetic variability, most retroviruses contain highly conserved putative
G-quadruplex-forming sequences in their promoter regions. Biophysical
and biomolecular assays proved that these sequences actually fold
into G-quadruplexes in physiological concentrations of relevant cations
and that they are further stabilized by ligands. These results validate
the relevance of G-quadruplexes in retroviruses and endorse the employment
of G-quadruplex ligands as innovative antiretroviral drugs. This study
indicates new possible pathways in the management of retroviral infections
in humans and animal species. Moreover, it may shed light on the mechanism
and functions of retrovirus genomes and derived transposable elements
in the human genome.
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Affiliation(s)
- Emanuela Ruggiero
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Martina Tassinari
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Rosalba Perrone
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
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Grandi N, Pisano MP, Tramontano E. The emerging field of human endogenous retroviruses: understanding their physiological role and contribution to diseases. Future Virol 2019. [DOI: 10.2217/fvl-2019-0061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Nicole Grandi
- Department of Life & Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato (Cagliari), Italy
| | - Maria Paola Pisano
- Department of Life & Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato (Cagliari), Italy
| | - Enzo Tramontano
- Department of Life & Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato (Cagliari), Italy
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Reduced Folate Carrier: an Entry Receptor for a Novel Feline Leukemia Virus Variant. J Virol 2019; 93:JVI.00269-19. [PMID: 30996094 DOI: 10.1128/jvi.00269-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/04/2019] [Indexed: 01/08/2023] Open
Abstract
Feline leukemia virus (FeLV) is horizontally transmitted among cats and causes a variety of hematopoietic disorders. Five subgroups of FeLV, A to D and T, each with distinct receptor usages, have been described. Recently, we identified a new FeLV Env (TG35-2) gene from a pseudotyped virus that does not belong to any known subgroup. FeLV-A is the primary virus from which other subgroups have emerged via mutation or recombination of the subgroup A env gene. Retrovirus entry into cells is mediated by the interaction of envelope protein (Env) with specific cell surface receptors. Here, phenotypic screening of a human/hamster radiation hybrid panel identified SLC19A1, a feline reduced folate carrier (RFC) and potential receptor for TG35-2-phenotypic virus. RFC is a multipass transmembrane protein. Feline and human RFC cDNAs conferred susceptibility to TG35-2-pseudotyped virus when introduced into nonpermissive cells but did not render these cells permissive to other FeLV subgroups or feline endogenous retrovirus. Moreover, human cells with genomic deletion of RFC were nonpermissive for TG35-2-pseudotyped virus infection, but the introduction of feline and human cDNAs rendered them permissive. Mutation analysis of FeLV Env demonstrated that amino acid substitutions within variable region A altered the specificity of the Env-receptor interaction. We isolated and reconstructed the full-length infectious TG35-2-phenotypic provirus from a naturally FeLV-infected cat, from which the FeLV Env (TG35-2) gene was previously isolated, and compared the replication of the virus in hematopoietic cell lines with that of FeLV-A 61E by measuring the viral RNA copy numbers. These results provide a tool for further investigation of FeLV infectious disease.IMPORTANCE Feline leukemia virus (FeLV) is a member of the genus Gammaretrovirus, which causes malignant diseases in cats. The most prevalent FeLV among cats is FeLV subgroup A (FeLV-A), and specific binding of FeLV-A Env to its viral receptor, thiamine transporter feTHTR1, is the first step of infection. In infected cats, novel variants of FeLV with altered receptor specificity for viral entry have emerged by mutation or recombination of the env gene. A novel FeLV variant arose from a subtle mutation of FeLV-A Env, which altered the specific interaction of the virus with its receptor. RFC, a folate transporter, is a potential receptor for the novel FeLV variant. The perturbation of specific retrovirus-receptor interactions under selective pressure by the host results in the emergence of novel viruses.
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Raoult D, Parola P. Vaccination against the big three killers: an illusion? Clin Microbiol Infect 2019; 25:654-655. [PMID: 30898723 DOI: 10.1016/j.cmi.2019.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/26/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Affiliation(s)
- D Raoult
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
| | - P Parola
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
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55
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McMichael L, Smith C, Gordon A, Agnihotri K, Meers J, Oakey J. A novel Australian flying-fox retrovirus shares an evolutionary ancestor with Koala, Gibbon and Melomys gamma-retroviruses. Virus Genes 2019; 55:421-424. [PMID: 30877415 DOI: 10.1007/s11262-019-01653-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/04/2019] [Indexed: 01/19/2023]
Abstract
A novel gamma-retroviral sequence (7912 bp), inclusive of both partial 5' and 3' long terminal repeat regions, was identified from the brain of a black flying-fox (Pteropus alecto), Queensland, Australia. The sequence was distinct from other retroviral sequences identified in bats and showed greater identity to Koala, Gibbon ape leukaemia, Melomys burtoni and Woolly monkey retroviruses, forming their own phylogenetic clade. This finding suggests that these retroviruses may have an unknown common ancestor and that further investigation into the diversity of gamma-retroviruses in Australian Pteropus species may elucidate their evolutionary origins.
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Affiliation(s)
- L McMichael
- School of Veterinary Science, University of Queensland, Gatton Campus, Gatton, QLD, 4343, Australia.
| | - C Smith
- Department of Agriculture and Fisheries, Health and Food Science Precinct, Biosecurity Sciences Laboratory, Biosecurity Queensland, 39 Kessels Road, Coopers Plains, QLD, 4108, Australia
| | - A Gordon
- Department of Agriculture and Fisheries, Health and Food Science Precinct, Biosecurity Sciences Laboratory, Biosecurity Queensland, 39 Kessels Road, Coopers Plains, QLD, 4108, Australia
| | - K Agnihotri
- Department of Agriculture and Fisheries, Health and Food Science Precinct, Biosecurity Sciences Laboratory, Biosecurity Queensland, 39 Kessels Road, Coopers Plains, QLD, 4108, Australia
| | - J Meers
- School of Veterinary Science, University of Queensland, Gatton Campus, Gatton, QLD, 4343, Australia
| | - J Oakey
- Department of Agriculture and Fisheries, Health and Food Science Precinct, Biosecurity Sciences Laboratory, Biosecurity Queensland, 39 Kessels Road, Coopers Plains, QLD, 4108, Australia
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Identification of the Receptor Used by the Ecotropic Mouse GLN Endogenous Retrovirus. J Virol 2019; 93:JVI.01125-18. [PMID: 30541852 DOI: 10.1128/jvi.01125-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Approximately 10% of the mouse genome is composed of endogenous retroviruses belonging to different families. In contrast to the situation in the human genome, several of these families correspond to recent, still-infectious elements capable of encoding complete viral particles. The mouse GLN endogenous retrovirus is one of these active families. We previously identified one fully functional provirus from the sequenced genome of the C57BL/6 mouse strain. The GLN envelope protein gives the infectious viral particles an ecotropic host range, and we had demonstrated that the receptor was neither CAT1 nor SMIT1, the two previously identified receptors for mouse ecotropic retroviral envelope proteins. In this study, we have identified SLC19A1, the reduced folate carrier, as the cellular protein used as a receptor by the GLN retrovirus. The ecotropic tropism exhibited by this envelope is due to the presence or absence of an N-linked glycosylation site in the first extracellular loop as well as the specific amino acid sequence of the extracellular domains of the receptor. Like all the other retroviral envelope proteins from the gammaretrovirus genus whose receptors have been identified, the GLN envelope protein uses a member of the solute carrier superfamily as a receptor.IMPORTANCE Endogenous retroviruses are genomic traces of past infections present in all vertebrates. Most of these elements degenerate over time and become nonfunctional, but the mouse genome still contains several families with full infection abilities. The GLN retrovirus is one of them, and its members encode particles that are able to infect only mouse cells. Here, we identified the cellular protein used as a receptor by GLN for cell entry. It is SLC19A1, the reduced folate carrier. We show that GLN infection is limited to mouse cells due to both a mutation in the mouse gene preventing the glycosylation of SLC19A1 and also other residues conserved within the rat but not in the hamster and human proteins. Like all other gammaretroviruses whose receptors have been identified, GLN uses a member of the solute carrier superfamily for cell entry, highlighting the role of these proteins for retroviral infection in mammals.
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57
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Fuentes DR, Swigut T, Wysocka J. Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation. eLife 2018; 7:35989. [PMID: 30070637 PMCID: PMC6158008 DOI: 10.7554/elife.35989] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/01/2018] [Indexed: 12/21/2022] Open
Abstract
Recent work suggests extensive adaptation of transposable elements (TEs) for host gene regulation. However, high numbers of integrations typical of TEs, coupled with sequence divergence within families, have made systematic interrogation of the regulatory contributions of TEs challenging. Here, we employ CARGO, our recent method for CRISPR gRNA multiplexing, to facilitate targeting of LTR5HS, an ape-specific class of HERVK (HML-2) LTRs that is active during early development and present in ~700 copies throughout the human genome. We combine CARGO with CRISPR activation or interference to, respectively, induce or silence LTR5HS en masse, and demonstrate that this system robustly targets the vast majority of LTR5HS insertions. Remarkably, activation/silencing of LTR5HS is associated with reciprocal up- and down-regulation of hundreds of human genes. These effects require the presence of retroviral sequences, but occur over long genomic distances, consistent with a pervasive function of LTR5HS elements as early embryonic enhancers in apes.
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Affiliation(s)
- Daniel R Fuentes
- Cancer Biology Program, Stanford University School of Medicine, Stanford, United States.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
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58
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Koonin EV, Krupovic M. The depths of virus exaptation. Curr Opin Virol 2018; 31:1-8. [PMID: 30071360 DOI: 10.1016/j.coviro.2018.07.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/13/2018] [Accepted: 07/19/2018] [Indexed: 02/07/2023]
Abstract
Viruses are ubiquitous parasites of cellular life forms and the most abundant biological entities on earth. The relationships between viruses and their hosts involve the continuous arms race but are by no account limited to it. Growing evidence shows that, in the course of evolution, viruses and their components are repeatedly recruited (exapted) for host functions. The functions of exapted viruses typically involve either defense from other viruses or cellular competitors or transfer of nucleic acids between cells, or storage functions. Virus exaptation can reach different depths, from recruitment of a fully functional virus to exploitation of defective, partially degraded viruses, to utilization of individual virus proteins.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States.
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France.
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59
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Hron T, Farkašová H, Gifford RJ, Benda P, Hulva P, Görföl T, Pačes J, Elleder D. Remnants of an Ancient Deltaretrovirus in the Genomes of Horseshoe Bats (Rhinolophidae). Viruses 2018; 10:v10040185. [PMID: 29642581 PMCID: PMC5923479 DOI: 10.3390/v10040185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/31/2018] [Accepted: 04/07/2018] [Indexed: 12/24/2022] Open
Abstract
Endogenous retrovirus (ERV) sequences provide a rich source of information about the long-term interactions between retroviruses and their hosts. However, most ERVs are derived from a subset of retrovirus groups, while ERVs derived from certain other groups remain extremely rare. In particular, only a single ERV sequence has been identified that shows evidence of being related to an ancient Deltaretrovirus, despite the large number of vertebrate genome sequences now available. In this report, we identify a second example of an ERV sequence putatively derived from a past deltaretroviral infection, in the genomes of several species of horseshoe bats (Rhinolophidae). This sequence represents a fragment of viral genome derived from a single integration. The time of the integration was estimated to be 11-19 million years ago. This finding, together with the previously identified endogenous Deltaretrovirus in long-fingered bats (Miniopteridae), suggest a close association of bats with ancient deltaretroviruses.
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Affiliation(s)
- Tomáš Hron
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
| | - Helena Farkašová
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
| | - Robert J Gifford
- MRC-University of Glasgow, Centre for Virus Research, 464 Bearsden Road, Glasgow G12 8TA, UK.
| | - Petr Benda
- Department of Zoology, Charles University, Vinicna 7, 12844 Prague, Czech Republic.
- Department of Zoology, National Museum (Natural History), Vaclavske nam. 68, 11579 Prague, Czech Republic.
| | - Pavel Hulva
- Department of Zoology, Charles University, Vinicna 7, 12844 Prague, Czech Republic.
- Department of Biology and Ecology, University of Ostrava, Chitussiho 10, 71000 Ostrava, Czech Republic.
| | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Musem, Baross Utca 13, 1088 Budapest, Hungary.
| | - Jan Pačes
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
| | - Daniel Elleder
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
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