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Moreira DA, Lamarca AP, Soares RF, Coelho AMA, Furtado C, Scherer NM, Moreira MAM, Seuánez HN, Boroni M. Transcriptome of the Southern Muriqui Brachyteles arachnoides (Primates:Platyrrhini), a Critically Endangered New World Monkey: Evidence of Adaptive Evolution. Front Genet 2020; 11:831. [PMID: 32849820 PMCID: PMC7412869 DOI: 10.3389/fgene.2020.00831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/09/2020] [Indexed: 12/03/2022] Open
Abstract
The southern muriqui (Brachyteles arachnoides) is the largest neotropical primate. This species is endemic to Brazil and is currently critically endangered due to its habitat destruction. The genetic basis underlying adaptive traits of New World monkeys has been a subject of interest to several investigators, with significant concern about genes related to the immune system. In the absence of a reference genome, RNA-seq and de novo transcriptome assembly have proved to be valuable genetic procedures for accessing gene sequences and testing evolutionary hypotheses. We present here a first report on the sequencing, assembly, annotation and adaptive selection analysis for thousands of transcripts of B. arachnoides from two different samples, corresponding to 13 different blood cells and fibroblasts. We assembled 284,283 transcripts with N50 of 2,940 bp, with a high rate of complete transcripts, with a median high scoring pair coverage of 88.2%, including low expressed transcripts, accounting for 72.3% of complete BUSCOs. We could predict and extract 81,400 coding sequences with 79.8% of significant BLAST hit against the Euarchontoglires SwissProt dataset. Of these 64,929 sequences, 34,084 were considered homologous to Supraprimate proteins, and of the remaining sequences (30,845), 94% were associated with a protein domain or a KEGG Orthology group, indicating potentially novel or specific protein-coding genes of B. arachnoides. We use the predicted protein sequences to perform a comparative analysis with 10 other primates. This analysis revealed, for the first time in an Atelid species, an expansion of APOBEC3G, extending this knowledge to all NWM families. Using a branch-site model, we searched for evidence of positive selection in 4,533 orthologous sets. This evolutionary analysis revealed 132 amino acid sites in 30 genes potentially evolving under positive selection, shedding light on primate genome evolution. These genes belonged to a wide variety of categories, including those encoding the innate immune system proteins (APOBEC3G, OAS2, and CEACAM1) among others related to the immune response. This work generated a set of thousands of complete sequences that can be used in other studies on molecular evolution and may help to unveil the evolution of primate genes. Still, further functional studies are required to provide an understanding of the underlying evolutionary forces modeling the primate genome.
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Affiliation(s)
- Daniel A Moreira
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Alessandra P Lamarca
- Laboratory of Bioinformatics and Molecular Evolution, Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Rafael Ferreira Soares
- Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Ana M A Coelho
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carolina Furtado
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Nicole M Scherer
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Miguel A M Moreira
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Hector N Seuánez
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Mariana Boroni
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
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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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Muniz CP, Troncoso LL, Moreira MA, Soares EA, Pissinatti A, Bonvicino CR, Seuánez HN, Sharma B, Jia H, Shankar A, Switzer WM, Santos AF, Soares MA. Identification and characterization of highly divergent simian foamy viruses in a wide range of new world primates from Brazil. PLoS One 2013; 8:e67568. [PMID: 23844033 PMCID: PMC3701081 DOI: 10.1371/journal.pone.0067568] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/18/2013] [Indexed: 01/08/2023] Open
Abstract
Foamy viruses naturally infect a wide range of mammals, including Old World (OWP) and New World primates (NWP), which are collectively called simian foamy viruses (SFV). While NWP species in Central and South America are highly diverse, only SFV from captive marmoset, spider monkey, and squirrel monkey have been genetically characterized and the molecular epidemiology of SFV infection in NWPs remains unknown. We tested a large collection of genomic DNA (n = 332) comprising 14 genera of NWP species for the presence of SFV polymerase (pol) sequences using generic PCR primers. Further molecular characterization of positive samples was carried out by LTR-gag and larger pol sequence analysis. We identified novel SFVs infecting nine NWP genera. Prevalence rates varied between 14-30% in different species for which at least 10 specimens were tested. High SFV genetic diversity among NWP up to 50% in LTR-gag and 40% in pol was revealed by intragenus and intrafamilial comparisons. Two different SFV strains infecting two captive yellow-breasted capuchins did not group in species-specific lineages but rather clustered with SFVs from marmoset and spider monkeys, indicating independent cross-species transmission events. We describe the first SFV epidemiology study of NWP, and the first evidence of SFV infection in wild NWPs. We also document a wide distribution of distinct SFVs in 14 NWP genera, including two novel co-speciating SFVs in capuchins and howler monkeys, suggestive of an ancient evolutionary history in NWPs for at least 28 million years. A high SFV genetic diversity was seen among NWP, yet these viruses seem able to jump between NWP species and even genera. Our results raise concerns for the risk of zoonotic transmission of NWP SFV to humans as these primates are regularly hunted for food or kept as pets in forest regions of South America.
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Affiliation(s)
- Cláudia P. Muniz
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lian L. Troncoso
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Miguel A. Moreira
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Esmeralda A. Soares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cibele R. Bonvicino
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Héctor N. Seuánez
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bechan Sharma
- Department of Biochemistry, University of Allahabad, Allahabad, India
| | - Hongwei Jia
- Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Anupama Shankar
- Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - William M. Switzer
- Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - André F. Santos
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo A. Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
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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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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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Darc M, Hait SH, Soares EA, Cicala C, Seuanez HN, Machado ES, Arthos JA, Soares MA. Polymorphisms in the α4 integrin of neotropical primates: insights for binding of natural ligands and HIV-1 gp120 to the human α4β7. PLoS One 2011; 6:e24461. [PMID: 21912696 PMCID: PMC3166318 DOI: 10.1371/journal.pone.0024461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 08/10/2011] [Indexed: 11/30/2022] Open
Abstract
The α4 integrin subunit associates with β7 and β1 and plays important roles in immune function and cell trafficking. The gut-homing receptor α4β7 has been recently described as a new receptor for HIV. Here, we describe polymorphisms of ITGA4 gene in New World primates (NWP), and tested their impact on the binding to monoclonal antibodies, natural ligands (MAdCAM and VCAM), and several gp120 HIV-1 envelope proteins. Genomic DNA of NWP specimens comprising all genera of the group had their exons 5 and 6 (encoding the region of binding to the ligands studied) analyzed. The polymorphisms found were introduced into an ITGA4 cDNA clone encoding the human α4 subunit. Mutant α4 proteins were co-expressed with β7 and were tested for binding of mAbs, MAdCAM, VCAM and gp120 of HIV-1, which was compared to the wild-type (human) α4. Mutant α4 proteins harboring the K201E/I/N substitution had reduced binding of all ligands tested, including HIV-1 gp120 envelopes. The mAbs found with reduced biding included one from which a clinically-approved drug for the treatment of neurological disorders has been derived. α4 polymorphisms in other primate species may influence outcomes in the development and treatment of infectious and autoimmune diseases in humans and in non-human primates.
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Affiliation(s)
- Mirela Darc
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Sabrina H. Hait
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Claudia Cicala
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hector N. Seuanez
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Elizabeth S. Machado
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - James A. Arthos
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marcelo A. Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- * E-mail:
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Kar AK, Mao Y, Bird G, Walensky L, Sodroski J. Characterization of a core fragment of the rhesus monkey TRIM5α protein. BMC BIOCHEMISTRY 2011; 12:1. [PMID: 21205312 PMCID: PMC3025952 DOI: 10.1186/1471-2091-12-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 01/04/2011] [Indexed: 11/13/2022]
Abstract
Background Like all tripartite motif (TRIM) proteins, the retroviral restriction factor TRIM5α consists of RING, B-box 2 and coiled-coil domains, with a C-terminal B30.2(SPRY) domain. Although structures have been determined for some individual TRIM domains, the structure of an intact TRIM protein is unknown. Results Here, we express and characterize a protease-resistant 29-kD core fragment containing the B-box 2, coiled coil and adjacent linker (L2) region of TRIM5α. This BCCL2 protein formed dimers and higher-order oligomers in solution. Approximately 40% of the BCCL2 secondary structure consisted of alpha helices. Partial loss of alpha-helical content and dissociation of dimers occurred at 42°C, with the residual alpha helices remaining stable up to 80°C. Conclusions These results indicate that the B-box 2, coiled-coil and linker 2 regions of TRIM5α form a core dimerization motif that exhibits a high level of alpha-helical content.
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Affiliation(s)
- Alak K Kar
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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Hare TRIM5α restricts divergent retroviruses and exhibits significant sequence variation from closely related lagomorpha TRIM5 genes. J Virol 2010; 84:12463-8. [PMID: 20861252 DOI: 10.1128/jvi.01514-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TRIM5α proteins recruit and restrict incoming cytoplasmic retroviruses. Primate TRIM5α sequence diversity underlies species-specific restriction and is likely caused by selective pressure from ancient pathogenic infections. Here we show that TRIM5α from the European brown hare restricts diverse retroviruses. Furthermore, it differs significantly in sequence from TRIM5α from the closely related rabbit, suggesting evolutionary changes in the last 12 million years since these species diverged. We propose that, like primates, lagomorphs have been subject to selective pressure from TRIM5-sensitive viruses, possibly related to the endogenous lentivirus RELIK found in both rabbits and hares.
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Ylinen LMJ, Price AJ, Rasaiyaah J, Hué S, Rose NJ, Marzetta F, James LC, Towers GJ. Conformational adaptation of Asian macaque TRIMCyp directs lineage specific antiviral activity. PLoS Pathog 2010; 6:e1001062. [PMID: 20808866 PMCID: PMC2924388 DOI: 10.1371/journal.ppat.1001062] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 07/22/2010] [Indexed: 12/24/2022] Open
Abstract
TRIMCyps are anti-retroviral proteins that have arisen independently in New World and Old World primates. All TRIMCyps comprise a CypA domain fused to the tripartite domains of TRIM5α but they have distinct lentiviral specificities, conferring HIV-1 restriction in New World owl monkeys and HIV-2 restriction in Old World rhesus macaques. Here we provide evidence that Asian macaque TRIMCyps have acquired changes that switch restriction specificity between different lentiviral lineages, resulting in species-specific alleles that target different viruses. Structural, thermodynamic and viral restriction analysis suggests that a single mutation in the Cyp domain, R69H, occurred early in macaque TRIMCyp evolution, expanding restriction specificity to the lentiviral lineages found in African green monkeys, sooty mangabeys and chimpanzees. Subsequent mutations have enhanced restriction to particular viruses but at the cost of broad specificity. We reveal how specificity is altered by a scaffold mutation, E143K, that modifies surface electrostatics and propagates conformational changes into the active site. Our results suggest that lentiviruses may have been important pathogens in Asian macaques despite the fact that there are no reported lentiviral infections in current macaque populations. Retroviruses have constantly been infecting mammals throughout their evolution, causing them to evolve defensive mechanisms to protect themselves. One of these mechanisms utilises intracellular antiviral molecules referred to as restriction factors. Restriction factor sequences have changed through primate evolution, suggesting an ongoing battle between retroviruses and their hosts as described by the Red Queen hypothesis. TRIM5 is an important restriction factor able to protect some monkeys, but not humans, from HIV infection. Certain monkeys have modified their TRIM5 genes by swapping the virus binding B30.2 domain with a cyclophilin A domain inserted into the TRIM5 locus by retrotransposition. This leads to expression of a TRIMCyp protein with antiviral activity against viruses, such as HIV-1, that recruit cyclophilins. It appears that cyclophilin makes a particularly flexible virus-binding domain able to restrict divergent lentiviruses from primates as well as cats. Here we characterise the molecular details of Cyclophilin-Capsid interactions focusing on TRIMCyp proteins from Macaca Fascicularis. Using a structure/function approach we can show the molecular details of how adaptive changes in the TRIMCyp sequence switch specificity between members of different primate lentiviral lineages. Mapping these changes onto the macaque phylogeny reveals a history of TRIMCyp evolution that directs restriction to a variety of diverse lentiviruses.
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Affiliation(s)
- Laura M. J. Ylinen
- University College London Medical Research Council Centre for Medical Molecular Virology, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Amanda J. Price
- Medical Research Council Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge, United Kingdom
| | - Jane Rasaiyaah
- University College London Medical Research Council Centre for Medical Molecular Virology, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Stéphane Hué
- University College London Medical Research Council Centre for Medical Molecular Virology, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Nicola J. Rose
- The National Institute for Biological Standards and Control, A Centre of the Health Protection Agency, Potters Bar, Hertfordshire, United Kingdom
| | - Flavia Marzetta
- University College London Medical Research Council Centre for Medical Molecular Virology, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Leo C. James
- Medical Research Council Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge, United Kingdom
- * E-mail: (LCJ); (GJT)
| | - Greg J. Towers
- University College London Medical Research Council Centre for Medical Molecular Virology, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
- * E-mail: (LCJ); (GJT)
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