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Fernandes AP, OhAinle M, Esteves PJ. Patterns of Evolution of TRIM Genes Highlight the Evolutionary Plasticity of Antiviral Effectors in Mammals. Genome Biol Evol 2023; 15:evad209. [PMID: 37988574 PMCID: PMC10709114 DOI: 10.1093/gbe/evad209] [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: 09/21/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
The innate immune system of mammals is formed by a complex web of interacting proteins, which together constitute the first barrier of entry for infectious pathogens. Genes from the E3-ubiquitin ligase tripartite motif (TRIM) family have been shown to play an important role in the innate immune system by restricting the activity of different retrovirus species. For example, TRIM5 and TRIM22 have both been associated with HIV restriction and are regarded as crucial parts of the antiretroviral machinery of mammals. Our analyses of positive selection corroborate the great significance of these genes for some groups of mammals. However, we also show that many species lack TRIM5 and TRIM22 altogether. By analyzing a large number of mammalian genomes, here we provide the first comprehensive view of the evolution of these genes in eutherians, showcasing that the pattern of accumulation of TRIM genes has been dissimilar across mammalian orders. Our data suggest that these differences are caused by the evolutionary plasticity of the immune system of eutherians, which have adapted to use different strategies to combat retrovirus infections. Altogether, our results provide insights into the dissimilar evolution of a representative family of restriction factors, highlighting an example of adaptive and idiosyncratic evolution in the innate immune system.
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Affiliation(s)
- Alexandre P Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Molly OhAinle
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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2
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TLR7 and TLR8 evolution in lagomorphs: different patterns in the different lineages. Immunogenetics 2022; 74:475-485. [PMID: 35419618 DOI: 10.1007/s00251-022-01262-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2022] [Indexed: 11/05/2022]
Abstract
Toll-like receptors (TLRs) are one of the most ancient and widely studied innate immune receptors responsible for host defense against invading pathogens. Among the known TLRs, TLR7 and TLR8 sense and recognize single-stranded (ss) RNAs with a dynamic evolutionary history. While TLR8 was lost in birds and duplicated in turtles and crocodiles, TLR7 is duplicated in some birds, but in other tetrapods, there is only one copy. In mammals, with the exception of lagomorphs, TLR7 and TLR8 are highly conserved. Here, we aim to study the evolution of TLR7 and TLR8 in mammals, with a special focus in the order Lagomorpha. By searching public sequence databases, conducting evolutionary analysis, and evaluating gene expression, we were able to confirm that TLR8 is absent in hares but widely expressed in the European rabbit. In contrast, TLR7 is absent in the European rabbit and quite divergent in hares. Our results suggest that, in lagomorphs, more in particular in leporids, TLR7 and TLR8 genes have evolved faster than in any other mammalian group. The long history of interaction with viruses and their location in highly dynamic telomeric regions might explain the pattern observed.
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Águeda-Pinto A, Lemos de Matos A, Pinheiro A, Neves F, de Sousa-Pereira P, Esteves PJ. Not so unique to Primates: The independent adaptive evolution of TRIM5 in Lagomorpha lineage. PLoS One 2019; 14:e0226202. [PMID: 31830084 PMCID: PMC6907815 DOI: 10.1371/journal.pone.0226202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
The plethora of restriction factors with the ability to inhibit the replication of retroviruses have been widely studied and genetic hallmarks of evolutionary selective pressures in Primates have been well documented. One example is the tripartite motif-containing protein 5 alpha (TRIM5α), a cytoplasmic factor that restricts retroviral infection in a species-specific fashion. In Lagomorphs, similarly to what has been observed in Primates, the specificity of TRIM5 restriction has been assigned to the PRYSPRY domain. In this study, we present the first insight of an intra-genus variability within the Lagomorpha TRIM5 PRYSPRY domain. Remarkably, and considering just the 32 residue-long v1 region of this domain, the deduced amino acid sequences of Daurian pika (Ochotona dauurica) and steppe pika (O. pusilla) evidenced a high divergence when compared to the remaining Ochotona species, presenting values of 44% and 66% of amino acid differences, respectively. The same evolutionary pattern was also observed when comparing the v1 region of two Sylvilagus species members (47% divergence). However, and unexpectedly, the PRYSPRY domain of Lepus species exhibited a great conservation. Our results show a high level of variation in the PRYSPRY domain of Lagomorpha species that belong to the same genus. This suggests that, throughout evolution, the Lagomorpha TRIM5 should have been influenced by constant selective pressures, likely as a result of multiple different retroviral infections.
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Affiliation(s)
- Ana Águeda-Pinto
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Ana Lemos de Matos
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Ana Pinheiro
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Fabiana Neves
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Patrícia de Sousa-Pereira
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
| | - Pedro J. Esteves
- CIBIO/InBio—Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto,Porto, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU,Gandra, Portugal
- * E-mail:
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4
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Mage RG, Esteves PJ, Rader C. Rabbit models of human diseases for diagnostics and therapeutics development. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:99-104. [PMID: 30339876 PMCID: PMC6364550 DOI: 10.1016/j.dci.2018.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/07/2018] [Accepted: 10/11/2018] [Indexed: 05/03/2023]
Abstract
This review presents some examples of studies using the European rabbit (Oryctolagus cuniculus) that have led to, and continue to, contribute to advancement of understanding of human diseases as well as therapeutics development. In addition, we tabulate FDA-approved rabbit polyclonal and rabbit monoclonal antibodies (mAbs) that are used for diagnostic applications, as well as an overview of some "humanized" or otherwise altered rabbit mAbs that are in initial phase I, II, or advanced to phase III clinical trials. Information about endogenous retriviruses learned from studies of rabbits and other members of the order Lagomorpha are summarized as this knowledge now applies to new therapeutics being developed for several human diseases including Multiple Sclerosis, Type 1 Diabetes and Cancer.
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Affiliation(s)
- Rose G Mage
- Laboratory of Immune System Biology, NIAID, NIH, Bldg 10 11N311, 10 Center Drive, Bethesda, MD, 20892-1892, USA.
| | - Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal; Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
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5
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de Sousa-Pereira P, Abrantes J, Bauernfried S, Pierini V, Esteves PJ, Keppler OT, Pizzato M, Hornung V, Fackler OT, Baldauf HM. The antiviral activity of rodent and lagomorph SERINC3 and SERINC5 is counteracted by known viral antagonists. J Gen Virol 2018; 100:278-288. [PMID: 30566072 DOI: 10.1099/jgv.0.001201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A first step towards the development of a human immunodeficiency virus (HIV) animal model has been the identification and surmounting of species-specific barriers encountered by HIV along its replication cycle in cells from small animals. Serine incorporator proteins 3 (SERINC3) and 5 (SERINC5) were recently identified as restriction factors that reduce HIV-1 infectivity. Here, we compared the antiviral activity of SERINC3 and SERINC5 among mice, rats and rabbits, and their susceptibility to viral counteraction to their human counterparts. In the absence of viral antagonists, rodent and lagomorph SERINC3 and SERINC5 displayed anti-HIV activity in a similar range to human controls. Vesicular stomatitis virus G protein (VSV-G) pseudotyped virions were considerably less sensitive to restriction by all SERINC3/5 orthologs. Interestingly, HIV-1 Nef, murine leukemia virus (MLV) GlycoGag and equine infectious anemia virus (EIAV) S2 counteracted the antiviral activity of all SERINC3/5 orthologs with similar efficiency. Our results demonstrate that the antiviral activity of SERINC3/5 proteins is conserved in rodents and rabbits, and can be overcome by all three previously reported viral antagonists.
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Affiliation(s)
- Patrícia de Sousa-Pereira
- 3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal.,5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,2Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Joana Abrantes
- 1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal
| | - Stefan Bauernfried
- 6Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Virginia Pierini
- 7Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Pedro José Esteves
- 1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal.,2Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,8CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
| | - Oliver T Keppler
- 3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany
| | - Massimo Pizzato
- 9University of Trento, Centre for Integrative Biology, Trento, Italy
| | - Veit Hornung
- 6Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Oliver T Fackler
- 7Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hanna-Mari Baldauf
- 5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany.,3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
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de Pablo-Maiso L, Doménech A, Echeverría I, Gómez-Arrebola C, de Andrés D, Rosati S, Gómez-Lucia E, Reina R. Prospects in Innate Immune Responses as Potential Control Strategies against Non-Primate Lentiviruses. Viruses 2018; 10:v10080435. [PMID: 30126090 PMCID: PMC6116218 DOI: 10.3390/v10080435] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
Lentiviruses are infectious agents of a number of animal species, including sheep, goats, horses, monkeys, cows, and cats, in addition to humans. As in the human case, the host immune response fails to control the establishment of chronic persistent infection that finally leads to a specific disease development. Despite intensive research on the development of lentivirus vaccines, it is still not clear which immune responses can protect against infection. Viral mutations resulting in escape from T-cell or antibody-mediated responses are the basis of the immune failure to control the infection. The innate immune response provides the first line of defense against viral infections in an antigen-independent manner. Antiviral innate responses are conducted by dendritic cells, macrophages, and natural killer cells, often targeted by lentiviruses, and intrinsic antiviral mechanisms exerted by all cells. Intrinsic responses depend on the recognition of the viral pathogen-associated molecular patterns (PAMPs) by pathogen recognition receptors (PRRs), and the signaling cascades leading to an antiviral state by inducing the expression of antiviral proteins, including restriction factors. This review describes the latest advances on innate immunity related to the infection by animal lentiviruses, centered on small ruminant lentiviruses (SRLV), equine infectious anemia virus (EIAV), and feline (FIV) and bovine immunodeficiency viruses (BIV), specifically focusing on the antiviral role of the major restriction factors described thus far.
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MESH Headings
- Animals
- Cats
- Cattle
- Dendritic Cells/immunology
- Dendritic Cells/virology
- Gene Expression Regulation/immunology
- Goats
- Horses
- Immunity, Innate
- Immunodeficiency Virus, Bovine/immunology
- Immunodeficiency Virus, Bovine/pathogenicity
- Immunodeficiency Virus, Feline/immunology
- Immunodeficiency Virus, Feline/pathogenicity
- Infectious Anemia Virus, Equine/immunology
- Infectious Anemia Virus, Equine/pathogenicity
- Interferon Regulatory Factors/genetics
- Interferon Regulatory Factors/immunology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/virology
- Lentivirus Infections/genetics
- Lentivirus Infections/immunology
- Lentivirus Infections/virology
- Macrophages/immunology
- Macrophages/virology
- Pathogen-Associated Molecular Pattern Molecules/immunology
- Receptors, Pattern Recognition/genetics
- Receptors, Pattern Recognition/immunology
- Sheep
- T-Lymphocytes/immunology
- T-Lymphocytes/virology
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Affiliation(s)
- Lorena de Pablo-Maiso
- Instituto de Agrobiotecnología (IdAB), UPNA-CSIC-Gobierno de Navarra, Navarra 31192, Spain.
| | - Ana Doménech
- Dpto. Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain.
| | - Irache Echeverría
- Instituto de Agrobiotecnología (IdAB), UPNA-CSIC-Gobierno de Navarra, Navarra 31192, Spain.
| | - Carmen Gómez-Arrebola
- Instituto de Agrobiotecnología (IdAB), UPNA-CSIC-Gobierno de Navarra, Navarra 31192, Spain.
| | - Damián de Andrés
- Instituto de Agrobiotecnología (IdAB), UPNA-CSIC-Gobierno de Navarra, Navarra 31192, Spain.
| | - Sergio Rosati
- Malattie Infettive degli Animali Domestici, Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Torino 10095, Italy.
| | - Esperanza Gómez-Lucia
- Dpto. Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain.
| | - Ramsés Reina
- Instituto de Agrobiotecnología (IdAB), UPNA-CSIC-Gobierno de Navarra, Navarra 31192, Spain.
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de Sousa-Pereira P, Abrantes J, Baldauf HM, Esteves PJ. Evolutionary studies on the betaretrovirus RERV-H in the Leporidae family reveal an endogenization in the ancestor of Oryctolagus, Bunolagus and Pentalagus at 9 million years ago. Virus Res 2017; 262:24-29. [PMID: 29208424 DOI: 10.1016/j.virusres.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 01/31/2023]
Abstract
RERV-H was first identified in human tissues and mistaken for a human exogenous retrovirus. However, the integration sites carried by this virus showed that it was instead a European rabbit (Oryctolagus cuniculus) endogenous retrovirus. The first clones retrieved from European rabbit samples represented defective proviruses, although estimation of proviral copy numbers found in the European rabbit genome ranged from hundreds to thousands. Screening for the presence of RERV-H showed the absence of the virus in two other lagomorphs, pika (Ochotona) and hares (Lepus), which diverged from rabbits about 35 and 12 million years ago, respectively. Using a PCR-based approach, samples of seven different Lagomorph genera were tested for the presence of RERV-H. It was possible to amplify a proviral fragment corresponding to RNaseH from Oryctolagus, Bunolagus and Pentalagus genomic samples. The amplification of proviral DNA in species other than Oryctolagus revealed that this virus was endogenized in their common ancestor, roughly 9 million years ago. Using the European rabbit genome sequence OryCun2.0, it was possible to find multiple copies spread throughout the genome and several complete proviral genomes were retrieved. Some copies contained full open reading frames for all viral components. The lack of a complete genome in the other Lagomorph species did not allow further analyses of the provirus, although more deleterious mutations were found in Bunolagus and Pentalagus than in Oryctolagus RNaseH-amplified sequences. To what extent RERV-H and other endogenous viruses might have had an impact on the rabbit genome and its immune system remains elusive.
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Affiliation(s)
- Patricia de Sousa-Pereira
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Joana Abrantes
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
| | - Hanna-Mari Baldauf
- Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Pedro José Esteves
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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8
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Hron T, Farkašová H, Padhi A, Pačes J, Elleder D. Life History of the Oldest Lentivirus: Characterization of ELVgv Integrations in the Dermopteran Genome. Mol Biol Evol 2016; 33:2659-69. [DOI: 10.1093/molbev/msw149] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Pinheiro A, Neves F, Lemos de Matos A, Abrantes J, van der Loo W, Mage R, Esteves PJ. An overview of the lagomorph immune system and its genetic diversity. Immunogenetics 2015; 68:83-107. [PMID: 26399242 DOI: 10.1007/s00251-015-0868-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 08/31/2015] [Indexed: 01/11/2023]
Abstract
Our knowledge of the lagomorph immune system remains largely based upon studies of the European rabbit (Oryctolagus cuniculus), a major model for studies of immunology. Two important and devastating viral diseases, rabbit hemorrhagic disease and myxomatosis, are affecting European rabbit populations. In this context, we discuss the genetic diversity of the European rabbit immune system and extend to available information about other lagomorphs. Regarding innate immunity, we review the most recent advances in identifying interleukins, chemokines and chemokine receptors, Toll-like receptors, antiviral proteins (RIG-I and Trim5), and the genes encoding fucosyltransferases that are utilized by rabbit hemorrhagic disease virus as a portal for invading host respiratory and gut epithelial cells. Evolutionary studies showed that several genes of innate immunity are evolving by strong natural selection. Studies of the leporid CCR5 gene revealed a very dramatic change unique in mammals at the second extracellular loop of CCR5 resulting from a gene conversion event with the paralogous CCR2. For the adaptive immune system, we review genetic diversity at the loci encoding antibody variable and constant regions, the major histocompatibility complex (RLA) and T cells. Studies of IGHV and IGKC genes expressed in leporids are two of the few examples of trans-species polymorphism observed outside of the major histocompatibility complex. In addition, we review some endogenous viruses of lagomorph genomes, the importance of the European rabbit as a model for human disease studies, and the anticipated role of next-generation sequencing in extending knowledge of lagomorph immune systems and their evolution.
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Affiliation(s)
- Ana Pinheiro
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
- SaBio-IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - Fabiana Neves
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
- UMIB/UP-Unidade Multidisciplinar de Investigação Biomédica, Universidade do Porto, Porto, Portugal
| | - Ana Lemos de Matos
- Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joana Abrantes
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
| | - Wessel van der Loo
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
| | - Rose Mage
- NIAID, NIH, Bethesda, MD, 20892, USA
| | - Pedro José Esteves
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
- CITS-Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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10
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Azevedo L, Serrano C, Amorim A, Cooper DN. Trans-species polymorphism in humans and the great apes is generally maintained by balancing selection that modulates the host immune response. Hum Genomics 2015; 9:21. [PMID: 26337052 PMCID: PMC4559023 DOI: 10.1186/s40246-015-0043-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/20/2015] [Indexed: 12/20/2022] Open
Abstract
Known examples of ancient identical-by-descent genetic variants being shared between evolutionarily related species, known as trans-species polymorphisms (TSPs), result from counterbalancing selective forces acting on target genes to confer resistance against infectious agents. To date, putative TSPs between humans and other primate species have been identified for the highly polymorphic major histocompatibility complex (MHC), the histo-blood ABO group, two antiviral genes (ZC3HAV1 and TRIM5), an autoimmunity-related gene LAD1 and several non-coding genomic segments with a putative regulatory role. Although the number of well-characterized TSPs under long-term balancing selection is still very small, these examples are connected by a common thread, namely that they involve genes with key roles in the immune system and, in heterozygosity, appear to confer genetic resistance to pathogens. Here, we review known cases of shared polymorphism that appear to be under long-term balancing selection in humans and the great apes. Although the specific selective agent(s) responsible are still unknown, these TSPs may nevertheless be seen as constituting important adaptive events that have occurred during the evolution of the primate immune system.
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Affiliation(s)
- Luisa Azevedo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - Catarina Serrano
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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11
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Fletcher AJ, Christensen DE, Nelson C, Tan CP, Schaller T, Lehner PJ, Sundquist WI, Towers GJ. TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription. EMBO J 2015; 34:2078-95. [PMID: 26101372 PMCID: PMC4551353 DOI: 10.15252/embj.201490361] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 11/26/2022] Open
Abstract
TRIM5α is an antiviral, cytoplasmic, E3 ubiquitin (Ub) ligase that assembles on incoming retroviral capsids and induces their premature dissociation. It inhibits reverse transcription of the viral genome and can also synthesize unanchored polyubiquitin (polyUb) chains to stimulate innate immune responses. Here, we show that TRIM5α employs the E2 Ub-conjugating enzyme Ube2W to anchor the Lys63-linked polyUb chains in a process of TRIM5α auto-ubiquitination. Chain anchoring is initiated, in cells and in vitro, through Ube2W-catalyzed monoubiquitination of TRIM5α. This modification serves as a substrate for the elongation of anchored Lys63-linked polyUb chains, catalyzed by the heterodimeric E2 enzyme Ube2N/Ube2V2. Ube2W targets multiple TRIM5α internal lysines with Ub especially lysines 45 and 50, rather than modifying the N-terminal amino group, which is instead αN-acetylated in cells. E2 depletion or Ub mutation inhibits TRIM5α ubiquitination in cells and restores restricted viral reverse transcription, but not infection. Our data indicate that the stepwise formation of anchored Lys63-linked polyUb is a critical early step in the TRIM5α restriction mechanism and identify the E2 Ub-conjugating cofactors involved.
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Affiliation(s)
- Adam J Fletcher
- MRC Centre of Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
| | - Devin E Christensen
- Department of Biochemistry and HSC Core Facilities, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Chad Nelson
- Department of Biochemistry and HSC Core Facilities, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Choon Ping Tan
- MRC Centre of Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
| | - Torsten Schaller
- MRC Centre of Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
| | - Paul J Lehner
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Wesley I Sundquist
- Department of Biochemistry and HSC Core Facilities, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Greg J Towers
- MRC Centre of Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
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12
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Malfavon-Borja R, Sawyer SL, Wu LI, Emerman M, Malik HS. An evolutionary screen highlights canonical and noncanonical candidate antiviral genes within the primate TRIM gene family. Genome Biol Evol 2014; 5:2141-54. [PMID: 24158625 PMCID: PMC3845644 DOI: 10.1093/gbe/evt163] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Recurrent viral pressure has acted on host-encoded antiviral genes during primate and mammalian evolution. This selective pressure has resulted in dramatic episodes of adaptation in host antiviral genes, often detected via positive selection. These evolutionary signatures of adaptation have the potential to highlight previously unrecognized antiviral genes (also called restriction factors). Although the TRIM multigene family is recognized for encoding several bona fide restriction factors (e.g., TRIM5alpha), most members of this expansive gene family remain uncharacterized. Here, we investigated the TRIM multigene family for signatures of positive selection to identify novel candidate antiviral genes. Our analysis reveals previously undocumented signatures of positive selection in 17 TRIM genes, 10 of which represent novel candidate restriction factors. These include the unusual TRIM52 gene, which has evolved under strong positive selection despite its encoded protein lacking a putative viral recognition (B30.2) domain. We show that TRIM52 arose via gene duplication from the TRIM41 gene. Both TRIM52 and TRIM41 have dramatically expanded RING domains compared with the rest of the TRIM multigene family, yet this domain has evolved under positive selection only in primate TRIM52, suggesting that it represents a novel host–virus interaction interface. Our evolutionary-based screen not only documents positive selection in known TRIM restriction factors but also highlights candidate novel restriction factors, providing insight into the interfaces of host–pathogen interactions mediated by the TRIM multigene family.
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13
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Mu D, Yang H, Zhu JW, Liu FL, Tian RR, Zheng HY, Han JB, Shi P, Zheng YT. Independent birth of a novel TRIMCyp in Tupaia belangeri with a divergent function from its paralog TRIM5. Mol Biol Evol 2014; 31:2985-97. [PMID: 25135944 DOI: 10.1093/molbev/msu238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The origin of novel genes and their evolutionary fates are long-standing questions in evolutionary biology. These questions become more complicated for genes conserved across various lineages, such as TRIM5, an antiretroviral restriction factor and a retrovirus capsid sensor in immune signaling. TRIM5 has been subjected to numerous pathogenic challenges and undergone dynamic evolution, making it an excellent example for studying gene diversification. Previous studies among several species showed that TRIM5 gained genetic and functional novelty in a lineage-specific manner, either through gene duplication or a cyclophilin A retrotransposing into the TRIM5 locus, creating the gene fusion known as TRIM5-Cyclophilin A (TRIMCyp). To date, the general pattern of TRIM5 across the mammalian lineage remains elusive. In this study, we surveyed 36 mammalian genomes to verify a potentially novel TRIM5 pattern that uniquely seems to have occurred in tree shrews (Tupaia belangeri), and found that both gene duplication and retrotransposition worked jointly to form a specific TRIM5/TRIMCyp cluster not found among other mammals. Evolutionary analyses showed that tree shrew TRIMCyp (tsTRIMCyp) originated independently in comparison with previously reported TRIMCyps and underwent strong positive selection, whereas no signal of positive selection was detected for other tree shrew TRIM5 (tsTRIM5) genes. Functional assay results suggest a functional divergence between tsTRIMCyp and its closest paralog TRIM5-4, likely reflecting different fates under diverse evolutionary forces. These findings present a rare example of novel gene origination resulting from a combination of gene duplication, retrotransposition, and exon shuffling processes, providing a new paradigm to study genetic innovations and evolutionary fates of duplicated genes.
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Affiliation(s)
- Dan Mu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jia-Wu Zhu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Feng-Liang Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ren-Rong Tian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hong-Yi Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China University of Science and Technology of China, Hefei, China
| | - Jian-Bao Han
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China Kunming Primate Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China
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14
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Chan E, Towers GJ, Qasim W. Gene therapy strategies to exploit TRIM derived restriction factors against HIV-1. Viruses 2014; 6:243-63. [PMID: 24424502 PMCID: PMC3917441 DOI: 10.3390/v6010243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/20/2013] [Accepted: 01/06/2014] [Indexed: 02/05/2023] Open
Abstract
Restriction factors are a collection of antiviral proteins that form an important aspect of the innate immune system. Their constitutive expression allows immediate response to viral infection, ahead of other innate or adaptive immune responses. We review the molecular mechanism of restriction for four categories of restriction factors; TRIM5, tetherin, APOBEC3G and SAMHD1 and go on to consider how the TRIM5 and TRIMCyp proteins in particular, show promise for exploitation using gene therapy strategies. Such approaches could form an important alternative to current anti-HIV-1 drug regimens, especially if combined with strategies to eradicate HIV reservoirs. Autologous CD4+ T cells or their haematopoietic stem cell precursors engineered to express TRIMCyp restriction factors, and provided in a single therapeutic intervention could then be used to restore functional immunity with a pool of cells protected against HIV. We consider the challenges ahead and consider how early clinical phase testing may best be achieved.
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Affiliation(s)
- Emma Chan
- Centre for Gene Therapy, Institute of Child Health, University College London, London WC1N 1EH, UK.
| | - Greg J Towers
- Centre for Gene Therapy, Institute of Child Health, University College London, London WC1N 1EH, UK.
| | - Waseem Qasim
- Centre for Gene Therapy, Institute of Child Health, University College London, London WC1N 1EH, UK.
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15
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Yap MW, Stoye JP. Apparent effect of rabbit endogenous lentivirus type K acquisition on retrovirus restriction by lagomorph Trim5αs. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120498. [PMID: 23938750 PMCID: PMC3758185 DOI: 10.1098/rstb.2012.0498] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To test the hypothesis that rabbit endogenous lentivirus type K (RELIK) could play a role in shaping the evolution of TRIM5α, the susceptibility of viruses containing the RELIK capsid (CA) to TRIM5 restriction was evaluated. RELIK CA-containing viruses were susceptible to the TRIM5αs from Old World monkeys but were unaffected by most ape or New World monkey factors. TRIM5αs from various lagomorph species were also isolated and tested for anti-retroviral activity. The TRIM5αs from both cottontail rabbit and pika restrict a range of retroviruses, including HIV-1, HIV-2, FIV, EIAV and N-MLV. TRIM5αs from the European and cottontail rabbit, which have previously been found to contain RELIK, also restricted RELIK CA-containing viruses, whereas a weaker restriction was observed with chimeric TRIM5α containing the B30.2 domain from the pika, which lacks RELIK. Taken together, these results could suggest that the pika had not been exposed to exogenous RELIK and that endogenized RELIK might exert a selective pressure on lagomorph TRIM5α.
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Affiliation(s)
| | - Jonathan P. Stoye
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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16
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Virus-specific effects of TRIM5α(rh) RING domain functions on restriction of retroviruses. J Virol 2013; 87:7234-45. [PMID: 23637418 DOI: 10.1128/jvi.00620-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tripartite motif protein TRIM5α restricts particular retrovirus infections by binding to the incoming capsid and inhibiting the early stage of virus infection. The TRIM5α RING domain exhibits E3 ubiquitin ligase activity and assists the higher-order association of TRIM5α dimers, which promotes capsid binding. We characterized a panel of RING domain mutants of the rhesus monkey TRIM5α (TRIM5α(rh)) protein. The RING domain function that significantly contributed to retroviral restriction depended upon the restricted virus. The E3 ubiquitin ligase activity of the RING domain contributes to the potency of HIV-1 restriction. Nonetheless, TRIM5α(rh) mutants without detectable E3 ubiquitin ligase activity still blocked reverse transcription and inhibited HIV-1 infection at a moderate level. When TRIM5α(rh) capsid binding was weakened by substitution with a less efficient B30.2/SPRY domain, the promotion of higher-order association by the RING domain was more important to HIV-1 restriction than its E3 ubiquitin ligase activity. For the restriction of N-tropic murine leukemia virus (N-MLV) and equine infectious anemia virus (EIAV) infection, promotion of higher-order association represented the major contribution of the RING domain. Thus, both identity of the target virus and the B30.2/SPRY domain-mediated affinity for the viral capsid determine the relative contribution of the two known RING domain functions to TRIM5α restriction of retrovirus infection.
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17
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Jáuregui P, Crespo H, Glaria I, Luján L, Contreras A, Rosati S, de Andrés D, Amorena B, Towers GJ, Reina R. Ovine TRIM5α can restrict visna/maedi virus. J Virol 2012; 86:9504-9. [PMID: 22696640 PMCID: PMC3416128 DOI: 10.1128/jvi.00440-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 06/01/2012] [Indexed: 11/20/2022] Open
Abstract
The restrictive properties of tripartite motif-containing 5 alpha (TRIM5α) from small ruminant species have not been explored. Here, we identify highly similar TRIM5α sequences in sheep and goats. Cells transduced with ovine TRIM5α effectively restricted the lentivirus visna/maedi virus DNA synthesis. Proteasome inhibition in cells transduced with ovine TRIM5α restored restricted viral DNA synthesis, suggesting a conserved mechanism of restriction. Identification of TRIM5α active molecular species may open new prophylactic strategies against lentiviral infections.
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Affiliation(s)
- P. Jáuregui
- Instituto de Agrobiotecnología, CSIC-UPNA-Gobierno de Navarra, Mutilva Baja, Navarra, Spain
| | - H. Crespo
- Instituto de Agrobiotecnología, CSIC-UPNA-Gobierno de Navarra, Mutilva Baja, Navarra, Spain
| | - I. Glaria
- Instituto de Agrobiotecnología, CSIC-UPNA-Gobierno de Navarra, Mutilva Baja, Navarra, Spain
| | - L. Luján
- Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - A. Contreras
- Departamento de Epidemiología y Enfermedades Infecciosas, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - S. Rosati
- Dipartimento di Produzione Animali, Epidemiologia ed Ecologia, Università degli Studi di Torino, Turin, Italy
| | - D. de Andrés
- Instituto de Agrobiotecnología, CSIC-UPNA-Gobierno de Navarra, Mutilva Baja, Navarra, Spain
| | - B. Amorena
- Instituto de Agrobiotecnología, CSIC-UPNA-Gobierno de Navarra, Mutilva Baja, Navarra, Spain
| | - G. J. Towers
- MRC Centre for Medical Molecular Virology, Infection and Immunity, University College London, London, United Kingdom
| | - R. Reina
- Instituto de Agrobiotecnología, CSIC-UPNA-Gobierno de Navarra, Mutilva Baja, Navarra, Spain
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18
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Fadel HJ, Saenz DT, Poeschla EM. Construction and testing of orfA +/- FIV reporter viruses. Viruses 2012; 4:184-99. [PMID: 22355458 PMCID: PMC3280524 DOI: 10.3390/v4010184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 01/15/2012] [Accepted: 01/16/2012] [Indexed: 01/01/2023] Open
Abstract
Single cycle reporter viruses that preserve the majority of the HIV-1 genome, long terminal repeat-promoted transcription and Rev-dependent structural protein expression are useful for investigating the viral life cycle. Reporter viruses that encode the viral proteins in cis in this way have been lacking for feline immunodeficiency virus (FIV), where the field has used genetically minimized transfer vectors with viral proteins supplied in trans. Here we report construction and use of a panel of single cycle FIV reporter viruses that express fluorescent protein markers. The viruses can be produced to high titer using human cell transfection and can transduce diverse target cells. To illustrate utility, we tested versions that are (+) and (-) for OrfA, an FIV accessory protein required for replication in primary lymphocytes and previously implicated in down-regulation of the primary FIV entry receptor CD134. We observed CD134 down-regulation after infection with or without OrfA, and equivalent virion production as well. These results suggest a role for FIV proteins besides Env or OrfA in CD134 down-regulation.
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Affiliation(s)
- Hind J. Fadel
- Mayo Clinic, Department of Molecular Medicine, Guggenheim 18-11A, College of Medicine, 200 First Street SW, Rochester, MN 55905, USA;
- Mayo Clinic, Division of Infectious Diseases, Guggenheim 18-11A, College of Medicine, 200 First Street SW, Rochester, MN 55905, USA;
| | - Dyana T. Saenz
- Mayo Clinic, Department of Molecular Medicine, Guggenheim 18-11A, College of Medicine, 200 First Street SW, Rochester, MN 55905, USA;
| | - Eric M. Poeschla
- Mayo Clinic, Department of Molecular Medicine, Guggenheim 18-11A, College of Medicine, 200 First Street SW, Rochester, MN 55905, USA;
- Mayo Clinic, Division of Infectious Diseases, Guggenheim 18-11A, College of Medicine, 200 First Street SW, Rochester, MN 55905, USA;
- Author to whom correspondence should be addressed: ; Tel.: +1-507-284-5909; Fax: +1-507-266-2122
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19
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Han K, Lou DI, Sawyer SL. Identification of a genomic reservoir for new TRIM genes in primate genomes. PLoS Genet 2011; 7:e1002388. [PMID: 22144910 PMCID: PMC3228819 DOI: 10.1371/journal.pgen.1002388] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 09/29/2011] [Indexed: 11/19/2022] Open
Abstract
Tripartite Motif (TRIM) ubiquitin ligases act in the innate immune response against viruses. One of the best characterized members of this family, TRIM5α, serves as a potent retroviral restriction factor with activity against HIV. Here, we characterize what are likely to be the youngest TRIM genes in the human genome. For instance, we have identified 11 TRIM genes that are specific to humans and African apes (chimpanzees, bonobos, and gorillas) and another 7 that are human-specific. Many of these young genes have never been described, and their identification brings the total number of known human TRIM genes to approximately 100. These genes were acquired through segmental duplications, most of which originated from a single locus on chromosome 11. Another polymorphic duplication of this locus has resulted in these genes being copy number variable within the human population, with a Han Chinese woman identified as having 12 additional copies of these TRIM genes compared to other individuals screened in this study. Recently, this locus was annotated as one of 34 "hotspot" regions that are also copy number variable in the genomes of chimpanzees and rhesus macaques. Most of the young TRIM genes originating from this locus are expressed, spliced, and contain signatures of positive natural selection in regions known to determine virus recognition in TRIM5α. However, we find that they do not restrict the same retroviruses as TRIM5α, consistent with the high degree of divergence observed in the regions that control target specificity. We propose that this recombinationally volatile locus serves as a reservoir from which new TRIM genes arise through segmental duplication, allowing primates to continually acquire new antiviral genes that can be selected to target new and evolving pathogens.
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Affiliation(s)
- Kyudong Han
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Dianne I. Lou
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Sara L. Sawyer
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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20
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de Matos AL, van der Loo W, Areal H, Lanning DK, Esteves PJ. Study of Sylvilagus rabbit TRIM5α species-specific domain: how ancient endoviruses could have shaped the antiviral repertoire in Lagomorpha. BMC Evol Biol 2011; 11:294. [PMID: 21982459 PMCID: PMC3208668 DOI: 10.1186/1471-2148-11-294] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 10/08/2011] [Indexed: 12/02/2022] Open
Abstract
Background Since the first report of the antiretroviral restriction factor TRIM5α in primates, several orthologs in other mammals have been described. Recent studies suggest that leporid retroviruses like RELIK, the first reported endogenous lentivirus ever, may have imposed positive selection in TRIM5α orthologs of the European rabbit and European brown hare. Considering that RELIK must already have been present in a common ancestor of the leporid genera Lepus, Sylvilagus and Oryctolagus, we extended the study of evolutionary patterns of TRIM5α to other members of the Leporidae family, particularly to the genus Sylvilagus. Therefore, we obtained the TRIM5α nucleotide sequences of additional subspecies and species of the three leporid genera. We also compared lagomorph TRIM5α deduced protein sequences and established TRIM5α gene and TRIM5α protein phylogenies. Results The deduced protein sequence of Iberian hare TRIM5α was 89% identical to European rabbit TRIM5α, although high divergence was observed at the PRYSPRY v1 region between rabbit and the identified alleles from this hare species (allele 1: 50% divergence; allele 2: 53% divergence). A high identity was expected between the Sylvilagus and Oryctolagus TRIM5α proteins and, in fact, the Sylvilagus TRIM5α was 91% identical to the Oryctolagus protein. Nevertheless, the PRYSPRY v1 region was only 50% similar between these genera. Selection analysis of Lagomorpha TRIM5α proteins identified 25 positively-selected codons, 11 of which are located in the PRYSPRY v1 region, responsible for species specific differences in viral capsid recognition. Conclusions By extending Lagomorpha TRIM5α studies to an additional genus known to bear RELIK, we verified that the divergent species-specific pattern observed between the Oryctolagus and Lepus PRYSPRY-domains is also present in Sylvilagus TRIM5α. This work is one of the first known studies that compare the evolution of the antiretroviral restriction factor TRIM5α in different mammalian groups, Lagomorpha and Primates.
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Affiliation(s)
- Ana Lemos de Matos
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
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21
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Fadel HJ, Poeschla EM. Retroviral restriction and dependency factors in primates and carnivores. Vet Immunol Immunopathol 2011; 143:179-89. [PMID: 21715018 DOI: 10.1016/j.vetimm.2011.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recent studies have extended the rapidly developing retroviral restriction factor field to cells of carnivore species. Carnivoran genomes, and the domestic cat genome in particular, are revealing intriguing properties vis-à-vis the primate and feline lentiviruses, not only with respect to their repertoires of virus-blocking restriction factors but also replication-enabling dependency factors. Therapeutic application of restriction factors is envisioned for human immunodeficiency virus (HIV) disease and the feline immunodeficiency virus (FIV) model has promise for testing important hypotheses at the basic and translational level. Feline cell-tropic HIV-1 clones have also been generated by a strategy of restriction factor evasion. We review progress in this area in the context of what is known about retroviral restriction factors such as TRIM5α, TRIMCyp, APOBEC3 proteins and BST-2/Tetherin.
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Affiliation(s)
- Hind J Fadel
- Department of Molecular Medicine and Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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22
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Poeschla EM. Primate and feline lentiviruses in current intrinsic immunity research: the cat is back. Vet Immunol Immunopathol 2011; 143:215-20. [PMID: 21715025 DOI: 10.1016/j.vetimm.2011.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Retroviral restriction factor research is explaining long-standing lentiviral mysteries. Asking why a particular retrovirus cannot complete a critical part of its life cycle in cells of a particular species has been the starting point for numerous discoveries, including heretofore elusive functions of HIV-1 accessory genes. The potential for therapeutic application is substantial. Analyzing the feline immunodeficiency virus (FIV) life cycle has been instrumental and the source of some surprising observations in this field. FIV is restricted in cells of various primates by several restriction factors including APOBEC3 proteins and, uniquely, TRIM proteins from both Old and New World monkeys. In contrast, the feline genome does not encode functional TRIM5alpha or TRIMCyp proteins and HIV-1 is primarily blocked in feline cells by APOBEC3 proteins. These can be overcome by inserting FIV vif or even SIVmac vif into HIV-1. The domestic cat and its lentivirus are positioned to offer strategic research opportunities as the field moves forward.
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Affiliation(s)
- Eric M Poeschla
- Department of Molecular Medicine and Division of Infectious Diseases, Guggenheim 18, College of Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
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23
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Sastri J, Campbell EM. Recent insights into the mechanism and consequences of TRIM5α retroviral restriction. AIDS Res Hum Retroviruses 2011; 27:231-8. [PMID: 21247355 DOI: 10.1089/aid.2010.0367] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cellular factor TRIM5α inhibits infection by numerous retroviruses in a species-specific manner. The TRIM5α protein from rhesus macaques (rhTRIM5α) restricts infection by HIV-1 while human TRIM5α (huTRIM5α) restricts infection by murine leukemia virus (MLV). In owl monkeys a related protein TRIM-Cyp restricts HIV-1 infection. Several models have been proposed for retroviral restriction by TRIM5 proteins (TRIM5α and TRIM-Cyp). These models collectively suggest that TRIM5 proteins mediate restriction by directly binding to specific determinants in the viral capsid. Through their ability to self-associate TRIM5 proteins compartmentalize the viral capsid core and mediate its abortive disassembly via a poorly understood mechanism that is sensitive to proteasome inhibitors. In this review, we discuss TRIM5-mediated restriction in detail. We also discuss how polymorphisms within human and rhesus macaque populations have been demonstrated to affect disease progression of immunodeficiency viruses in these species.
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Affiliation(s)
- Jaya Sastri
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Edward M. Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
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