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Vijay N, Chande A. A hypothetical new role for single-stranded DNA binding proteins in the immune system. Immunobiology 2018; 223:671-676. [DOI: 10.1016/j.imbio.2018.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/25/2018] [Accepted: 07/05/2018] [Indexed: 12/21/2022]
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2
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Leal FE, Menezes SM, Costa EAS, Brailey PM, Gama L, Segurado AC, Kallas EG, Nixon DF, Dierckx T, Khouri R, Vercauteren J, Galvão-Castro B, Saraiva Raposo RA, Van Weyenbergh J. Comprehensive Antiretroviral Restriction Factor Profiling Reveals the Evolutionary Imprint of the ex Vivo and in Vivo IFN-β Response in HTLV-1-Associated Neuroinflammation. Front Microbiol 2018; 9:985. [PMID: 29872426 PMCID: PMC5972197 DOI: 10.3389/fmicb.2018.00985] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022] Open
Abstract
HTLV-1-Associated Myelopathy (HAM/TSP) is a progressive neuroinflammatory disorder for which no disease-modifying treatment exists. Modest clinical benefit from type I interferons (IFN-α/β) in HAM/TSP contrasts with its recently identified IFN-inducible gene signature. In addition, IFN-α treatment in vivo decreases proviral load and immune activation in HAM/TSP, whereas IFN-β therapy decreases tax mRNA and lymphoproliferation. We hypothesize this "IFN paradox" in HAM/TSP might be explained by both cell type- and gene-specific effects of type I IFN in HTLV-1-associated pathogenesis. Therefore, we analyzed ex vivo transcriptomes of CD4+ T cells, PBMCs and whole blood in healthy controls, HTLV-1-infected individuals, and HAM/TSP patients. First, we used a targeted approach, simultaneously quantifying HTLV-1 mRNA (HBZ, Tax), proviral load and 42 host genes with known antiretroviral (anti-HIV) activity in purified CD4+ T cells. This revealed two major clusters ("antiviral/protective" vs. "proviral/deleterious"), as evidenced by significant negative (TRIM5/TRIM22/BST2) vs. positive correlation (ISG15/PAF1/CDKN1A) with HTLV-1 viral markers and clinical status. Surprisingly, we found a significant inversion of antiretroviral activity of host restriction factors, as evidenced by opposite correlation to in vivo HIV-1 vs. HTLV-1 RNA levels. The anti-HTLV-1 effect of antiviral cluster genes was significantly correlated to their adaptive chimp/human evolution score, for both Tax mRNA and PVL. Six genes of the proposed antiviral cluster underwent lentivirus-driven purifying selection during primate evolution (TRIM5/TRIM22/BST2/APOBEC3F-G-H), underscoring the cross-retroviral evolutionary imprint. Secondly, we examined the genome-wide type I IFN response in HAM/TSP patients, following short-term ex vivo culture of PBMCs with either IFN-α or IFN-β. Microarray analysis evidenced 12 antiretroviral genes (including TRIM5α/TRIM22/BST2) were significantly up-regulated by IFN-β, but not IFN-α, in HAM/TSP. This was paralleled by a significant decrease in lymphoproliferation by IFN-β, but not IFN-α treatment. Finally, using published ex vivo whole blood transcriptomic data of independent cohorts, we validated the significant positive correlation between TRIM5, TRIM22, and BST2 in HTLV-1-infected individuals and HAM/TSP patients, which was independent of the HAM/TSP disease signature. In conclusion, our results provide ex vivo mechanistic evidence for the observed immunovirological effect of in vivo IFN-β treatment in HAM/TSP, reconcile an apparent IFN paradox in HTLV-1 research and identify biomarkers/targets for a precision medicine approach.
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Affiliation(s)
- Fabio E Leal
- Oncovirology Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Microbiology Immunology and Tropical Medicine, George Washington University, Washington, DC, United States
| | - Soraya Maria Menezes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Emanuela A S Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Phillip M Brailey
- Oncovirology Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Lucio Gama
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aluisio C Segurado
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Esper G Kallas
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Douglas F Nixon
- Oncovirology Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Tim Dierckx
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Ricardo Khouri
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Fundação Oswaldo Cruz, Instituto Gonçalo Moniz (IGM), Salvador-Bahia, Brazil
| | - Jurgen Vercauteren
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | | | - Johan Van Weyenbergh
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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Bhat J, Sosna J, Fritsch J, Quabius ES, Schütze S, Zeissig S, Ammerpohl O, Adam D, Kabelitz D. Expression of non-secreted IL-4 is associated with HDAC inhibitor-induced cell death, histone acetylation and c-Jun regulation in human gamma/delta T-cells. Oncotarget 2018; 7:64743-64756. [PMID: 27556516 PMCID: PMC5323112 DOI: 10.18632/oncotarget.11462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/11/2016] [Indexed: 01/24/2023] Open
Abstract
Previously, the expression of a non-secreted IL-4 variant (IL-4δ13) has been described in association with apoptosis and age-dependent Th2 T-cell polarization. Signaling pathways involved in this process have so far not been studied. Here we report the induction of IL-4δ13 expression in human γδ T-cells upon treatment with a sublethal dose of histone deacetylase (HDACi) inhibitor valproic acid (VPA). Induction of IL-4δ13 was associated with increased cytoplasmic IL-4Rα and decreased IL-4 expression, while mRNA for mature IL-4 was concomitantly down-regulated. Importantly, only the simultaneous combination of apoptosis and necroptosis inhibitors prevented IL-4δ13 expression and completely abrogated VPA-induced global histone H3K9 acetylation mark. Further, our work reveals a novel involvement of transcription factor c-Jun in the signaling network of IL-4, HDAC1, caspase-3 and mixed lineage kinase domain-like protein (MLKL). This study provides novel insights into the effects of epigenetic modulator VPA on human γδ T-cell differentiation.
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Affiliation(s)
- Jaydeep Bhat
- Institute of Immunology, Christian-Albrechts-University, Kiel, Germany
| | - Justyna Sosna
- Institute of Immunology, Christian-Albrechts-University, Kiel, Germany.,Current address: Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA, USA
| | - Jürgen Fritsch
- Institute of Immunology, Christian-Albrechts-University, Kiel, Germany
| | - Elgar Susanne Quabius
- Institute of Immunology, Christian-Albrechts-University, Kiel, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, Kiel, Germany
| | - Stefan Schütze
- Institute of Immunology, Christian-Albrechts-University, Kiel, Germany
| | - Sebastian Zeissig
- Department of Internal Medicine I, Christian-Albrechts-University, Kiel, Germany.,Current address: Department of Medicine I, University Medical Center Dresden, Technical University Dresden, Dresden, Germany.,Current address: Center for Regenerative Therapies Dresden (CRTD), Technical University Dresden, Dresden, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, University Medical Center Schleswig-Holstein Kiel, Christian-Albrechts-University, Kiel, Germany
| | - Dieter Adam
- Institute of Immunology, Christian-Albrechts-University, Kiel, Germany
| | - Dieter Kabelitz
- Institute of Immunology, Christian-Albrechts-University, Kiel, Germany
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4
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van der Lee R, Wiel L, van Dam TJP, Huynen MA. Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. Nucleic Acids Res 2017; 45:10634-10648. [PMID: 28977405 PMCID: PMC5737536 DOI: 10.1093/nar/gkx704] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/02/2017] [Indexed: 12/17/2022] Open
Abstract
Hotspots of rapid genome evolution hold clues about human adaptation. We present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection in 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%). Our new procedure is stringent and reveals substantial artefacts (20% of initial predictions) that have inflated previous estimates. The final 331 positively selected genes (PSG) are strongly enriched for innate and adaptive immunity, secreted and cell membrane proteins (e.g. pattern recognition, complement, cytokines, immune receptors, MHC, Siglecs). We also find evidence for positive selection in reproduction and chromosome segregation (e.g. centromere-associated CENPO, CENPT), apolipoproteins, smell/taste receptors and mitochondrial proteins. Focusing on the virus–host interaction, we retrieve most evolutionary conflicts known to influence antiviral activity (e.g. TRIM5, MAVS, SAMHD1, tetherin) and predict 70 novel cases through integration with virus–human interaction data. Protein structure analysis further identifies positive selection in the interaction interfaces between viruses and their cellular receptors (CD4-HIV; CD46-measles, adenoviruses; CD55-picornaviruses). Finally, primate PSG consistently show high sequence variation in human exomes, suggesting ongoing evolution. Our curated dataset of positive selection is a rich source for studying the genetics underlying human (antiviral) phenotypes. Procedures and data are available at https://github.com/robinvanderlee/positive-selection.
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Affiliation(s)
- Robin van der Lee
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laurens Wiel
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Teunis J P van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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5
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Evans AL, Blackburn JWD, Taruc K, Kipp A, Dirk BS, Hunt NR, Barr SD, Dikeakos JD, Heit B. Antagonistic Coevolution of MER Tyrosine Kinase Expression and Function. Mol Biol Evol 2017; 34:1613-1628. [PMID: 28369510 DOI: 10.1093/molbev/msx102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TYRO3, AXL, and MERTK (TAM) receptors are a family of receptor tyrosine kinases that maintain homeostasis through the clearance of apoptotic cells, and when defective, contribute to chronic inflammatory and autoimmune diseases such as atherosclerosis, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and Crohn's disease. In addition, certain enveloped viruses utilize TAM receptors for immune evasion and entry into host cells, with several viruses preferentially hijacking MERTK for these purposes. Despite the biological importance of TAM receptors, little is understood of their recent evolution and its impact on their function. Using evolutionary analysis of primate TAM receptor sequences, we identified strong, recent positive selection in MERTK's signal peptide and transmembrane domain that was absent from TYRO3 and AXL. Reconstruction of hominid and primate ancestral MERTK sequences revealed three nonsynonymous single nucleotide polymorphisms in the human MERTK signal peptide, with a G14C mutation resulting in a predicted non-B DNA cruciform motif, producing a significant decrease in MERTK expression with no significant effect on MERTK trafficking or half-life. Reconstruction of MERTK's transmembrane domain identified three amino acid substitutions and four amino acid insertions in humans, which led to significantly higher levels of self-clustering through the creation of a new interaction motif. This clustering counteracted the effect of the signal peptide mutations through enhancing MERTK avidity, whereas the lower MERTK expression led to reduced binding of Ebola virus-like particles. The decreased MERTK expression counterbalanced by increased avidity is consistent with antagonistic coevolution to evade viral hijacking of MERTK.
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Affiliation(s)
- Amanda L Evans
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Jack W D Blackburn
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Kyle Taruc
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Angela Kipp
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Brennan S Dirk
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Nina R Hunt
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Stephen D Barr
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
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6
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Schott K, Riess M, König R. Role of Innate Genes in HIV Replication. Curr Top Microbiol Immunol 2017; 419:69-111. [PMID: 28685292 DOI: 10.1007/82_2017_29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cells use an elaborate innate immune surveillance and defense system against virus infections. Here, we discuss recent studies that reveal how HIV-1 is sensed by the innate immune system. Furthermore, we present mechanisms on the counteraction of HIV-1. We will provide an overview how HIV-1 actively utilizes host cellular factors to avoid sensing. Additionally, we will summarize effectors of the innate response that provide an antiviral cellular state. HIV-1 has evolved passive mechanism to avoid restriction and to regulate the innate response. We review in detail two prominent examples of these cellular factors: (i) NLRX1, a negative regulator of the innate response that HIV-1 actively usurps to block cytosolic innate sensing; (ii) SAMHD1, a restriction factor blocking the virus at the reverse transcription step that HIV-1 passively avoids to escape sensing.
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Affiliation(s)
- Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany
| | - Maximilian Riess
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany. .,Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA. .,German Center for Infection Research (DZIF), 63225, Langen, Germany.
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7
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Wang Y, Wang Z, Pramanik A, Santiago ML, Qiu J, Stephens EB. A chimeric human APOBEC3A protein with a three amino acid insertion confers differential HIV-1 and adeno-associated virus restriction. Virology 2016; 498:149-163. [PMID: 27584592 DOI: 10.1016/j.virol.2016.08.001] [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: 05/11/2016] [Revised: 07/27/2016] [Accepted: 08/01/2016] [Indexed: 12/22/2022]
Abstract
Old World monkey (OWM) and hominid APOBEC3Aproteins exhibit differential restriction activities against lentiviruses and DNA viruses. Human APOBEC3A(hA3A)has weak restriction activity against HIV-1Δvifbut is efficiently restricted by an artificially generated chimeric from mandrills (mndA3A/G). We show that a chimeric hA3Acontaining the "WVS" insertion (hA3A[(27)WVS(29)]) conferred potent HIV-1restriction activity. Analysis of each amino acid of the "WVS" motif show that the length and not necessarily the charge or hydrophobicity of the amino acids accounted for restriction activity. Our results suggest that hA3A[(27)WVS(29)]restricts HIV-1at the level of reverse transcription in target cells. Finally, our results suggest that insertion of "WVS" into hA3Amodestly reduces restriction of adeno-associated virus 2(AAV-2)while insertion of the AC Loop1region of the mndA3A/G into hA3A abolished AAV-2 restriction, strengthening the role of this molecular interface in the functional evolution of primate A3A.
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Affiliation(s)
- Yaqiong Wang
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 2000 Hixon Hall, 3901 Rainbow Blvd., Kansas City, KS 66160, United States
| | - Zekun Wang
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 2000 Hixon Hall, 3901 Rainbow Blvd., Kansas City, KS 66160, United States
| | - Ankita Pramanik
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 2000 Hixon Hall, 3901 Rainbow Blvd., Kansas City, KS 66160, United States
| | - Mario L Santiago
- Departments of Medicine, Microbiology and Immunology, University of Colorado, Denver Aurora, CO 80045, United States
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 2000 Hixon Hall, 3901 Rainbow Blvd., Kansas City, KS 66160, United States
| | - Edward B Stephens
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 2000 Hixon Hall, 3901 Rainbow Blvd., Kansas City, KS 66160, United States.
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Enard D, Cai L, Gwennap C, Petrov DA. Viruses are a dominant driver of protein adaptation in mammals. eLife 2016; 5. [PMID: 27187613 PMCID: PMC4869911 DOI: 10.7554/elife.12469] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/04/2016] [Indexed: 12/12/2022] Open
Abstract
Viruses interact with hundreds to thousands of proteins in mammals, yet adaptation against viruses has only been studied in a few proteins specialized in antiviral defense. Whether adaptation to viruses typically involves only specialized antiviral proteins or affects a broad array of virus-interacting proteins is unknown. Here, we analyze adaptation in ~1300 virus-interacting proteins manually curated from a set of 9900 proteins conserved in all sequenced mammalian genomes. We show that viruses (i) use the more evolutionarily constrained proteins within the cellular functions they interact with and that (ii) despite this high constraint, virus-interacting proteins account for a high proportion of all protein adaptation in humans and other mammals. Adaptation is elevated in virus-interacting proteins across all functional categories, including both immune and non-immune functions. We conservatively estimate that viruses have driven close to 30% of all adaptive amino acid changes in the part of the human proteome conserved within mammals. Our results suggest that viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes.
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Affiliation(s)
- David Enard
- Department of Biology, Stanford University, Stanford, United States
| | - Le Cai
- Department of Biology, Stanford University, Stanford, United States
| | - Carina Gwennap
- Department of Biology, Stanford University, Stanford, United States
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, United States
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9
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Wang Y, Schmitt K, Guo K, Santiago ML, Stephens EB. Role of the single deaminase domain APOBEC3A in virus restriction, retrotransposition, DNA damage and cancer. J Gen Virol 2015; 97:1-17. [PMID: 26489798 DOI: 10.1099/jgv.0.000320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The apolipoprotein mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) proteins are a family of seven cytidine deaminases (A3A, A3B, A3C, A3D, A3F, A3G and A3H) that restrict certain viral infections. These innate defence factors are best known for their ability to restrict the replication of human immunodeficiency virus type 1 (HIV-1) lacking a functional Vif protein (HIV-1Δvif) through the deamination of cytidine residues to uridines during reverse transcription, ultimately leading to lethal G → A changes in the viral genome. The best studied of the A3 proteins has been APOBEC3G because of its potent activity against HIV-1Δvif. However, one member of this family, A3A, has biological properties that make it unique among the A3 proteins. In this review, we will focus on the structural and phylogenetic features of the human and non-human primate A3A proteins, their role in the restriction of retroviruses and other viruses, and current findings on other biological properties affected by this protein.
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Affiliation(s)
- Yaqiong Wang
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Kimberly Schmitt
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Kejun Guo
- Departments of Medicine, Microbiology and Immunology, University of Colorado Denver Medical School, Aurora, CO 80045, USA
| | - Mario L Santiago
- Departments of Medicine, Microbiology and Immunology, University of Colorado Denver Medical School, Aurora, CO 80045, USA
| | - Edward B Stephens
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
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Identification of Owl Monkey CD4 Receptors Broadly Compatible with Early-Stage HIV-1 Isolates. J Virol 2015; 89:8611-22. [PMID: 26063421 DOI: 10.1128/jvi.00890-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/02/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Most HIV-1 variants isolated from early-stage human infections do not use nonhuman primate versions of the CD4 receptor for cellular entry, or they do so poorly. We and others have previously shown that CD4 has experienced strong natural selection over the course of primate speciation, but it is unclear whether this selection has influenced the functional characteristics of CD4 as an HIV-1 receptor. Surprisingly, we find that selection on CD4 has been most intense in the New World monkeys, animals that have never been found to harbor lentiviruses related to HIV-1. Based on this, we sampled CD4 genetic diversity within populations of individuals from seven different species, including five species of New World monkeys. We found that some, but not all, CD4 alleles found in Spix's owl monkeys (Aotus vociferans) encode functional receptors for early-stage human HIV-1 isolates representing all of the major group M clades (A, B, C, and D). However, only some isolates of HIV-1 subtype C can use the CD4 receptor encoded by permissive Spix's owl monkey alleles. We characterized the prevalence of functional CD4 alleles in a colony of captive Spix's owl monkeys and found that 88% of surveyed individuals are homozygous for permissive CD4 alleles, which encode an asparagine at position 39 of the receptor. We found that the CD4 receptors encoded by two other species of owl monkeys (Aotus azarae and Aotus nancymaae) also serve as functional entry receptors for early-stage isolates of HIV-1. IMPORTANCE Nonhuman primates, particularly macaques, are used for preclinical evaluation of HIV-1 vaccine candidates. However, a significant limitation of the macaque model is the fact that most circulating HIV-1 variants cannot use the macaque CD4 receptor to enter cells and have to be adapted to these species. This is particularly true for viral variants from early stages of infection, which represent the most relevant vaccine targets. In this study, we found that some individuals from captive owl monkey populations harbor CD4 alleles that are compatible with a broad collection of HIV-1 isolates, including those isolated from early in infection in highly affected populations and representing diverse subtypes.
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11
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McLaren PJ, Gawanbacht A, Pyndiah N, Krapp C, Hotter D, Kluge SF, Götz N, Heilmann J, Mack K, Sauter D, Thompson D, Perreaud J, Rausell A, Munoz M, Ciuffi A, Kirchhoff F, Telenti A. Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses. Retrovirology 2015; 12:41. [PMID: 25980612 PMCID: PMC4434878 DOI: 10.1186/s12977-015-0165-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/24/2015] [Indexed: 02/07/2023] Open
Abstract
Background Known antiretroviral restriction factors are encoded by genes that are under positive selection pressure, induced during HIV-1 infection, up-regulated by interferons, and/or interact with viral proteins. To identify potential novel restriction factors, we performed genome-wide scans for human genes sharing molecular and evolutionary signatures of known restriction factors and tested the anti-HIV-1 activity of the most promising candidates. Results Our analyses identified 30 human genes that share characteristics of known restriction factors. Functional analyses of 27 of these candidates showed that over-expression of a strikingly high proportion of them significantly inhibited HIV-1 without causing cytotoxic effects. Five factors (APOL1, APOL6, CD164, TNFRSF10A, TNFRSF10D) suppressed infectious HIV-1 production in transfected 293T cells by >90% and six additional candidates (FCGR3A, CD3E, OAS1, GBP5, SPN, IFI16) achieved this when the virus was lacking intact accessory vpr, vpu and nef genes. Unexpectedly, over-expression of two factors (IL1A, SP110) significantly increased infectious HIV-1 production. Mechanistic studies suggest that the newly identified potential restriction factors act at different steps of the viral replication cycle, including proviral transcription and production of viral proteins. Finally, we confirmed that mRNA expression of most of these candidate restriction factors in primary CD4+ T cells is significantly increased by type I interferons. Conclusions A limited number of human genes share multiple characteristics of genes encoding for known restriction factors. Most of them display anti-retroviral activity in transient transfection assays and are expressed in primary CD4+ T cells. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0165-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul J McLaren
- École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, 1005, Lausanne, Switzerland.
| | - Ali Gawanbacht
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Nitisha Pyndiah
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Christian Krapp
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Silvia F Kluge
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Nicola Götz
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Jessica Heilmann
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Katharina Mack
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Danielle Thompson
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Jérémie Perreaud
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Antonio Rausell
- Swiss Institute of Bioinformatics, 1005, Lausanne, Switzerland. .,Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Miguel Munoz
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Angela Ciuffi
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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12
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Ross CT, Roodgar M, Smith DG. Evolutionary distance of amino acid sequence orthologs across macaque subspecies: identifying candidate genes for SIV resistance in Chinese rhesus macaques. PLoS One 2015; 10:e0123624. [PMID: 25884674 PMCID: PMC4401517 DOI: 10.1371/journal.pone.0123624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 02/20/2015] [Indexed: 11/18/2022] Open
Abstract
We use the Reciprocal Smallest Distance (RSD) algorithm to identify amino acid sequence orthologs in the Chinese and Indian rhesus macaque draft sequences and estimate the evolutionary distance between such orthologs. We then use GOanna to map gene function annotations and human gene identifiers to the rhesus macaque amino acid sequences. We conclude methodologically by cross-tabulating a list of amino acid orthologs with large divergence scores with a list of genes known to be involved in SIV or HIV pathogenesis. We find that many of the amino acid sequences with large evolutionary divergence scores, as calculated by the RSD algorithm, have been shown to be related to HIV pathogenesis in previous laboratory studies. Four of the strongest candidate genes for SIVmac resistance in Chinese rhesus macaques identified in this study are CDK9, CXCL12, TRIM21, and TRIM32. Additionally, ANKRD30A, CTSZ, GORASP2, GTF2H1, IL13RA1, MUC16, NMDAR1, Notch1, NT5M, PDCD5, RAD50, and TM9SF2 were identified as possible candidates, among others. We failed to find many laboratory experiments contrasting the effects of Indian and Chinese orthologs at these sites on SIVmac pathogenesis, but future comparative studies might hold fertile ground for research into the biological mechanisms underlying innate resistance to SIVmac in Chinese rhesus macaques.
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Affiliation(s)
- Cody T. Ross
- Department of Anthropology, University of California, Davis. Davis, United States of America
- Molecular Anthropology Laboratory, University of California, Davis. Davis, United States of America
| | - Morteza Roodgar
- Molecular Anthropology Laboratory, University of California, Davis. Davis, United States of America
- California National Primate Research Center, University of California, Davis. Davis, United States of America
- Graduate Group of Comparative Pathology, University of California, Davis. Davis, United States of America
| | - David Glenn Smith
- Department of Anthropology, University of California, Davis. Davis, United States of America
- Molecular Anthropology Laboratory, University of California, Davis. Davis, United States of America
- California National Primate Research Center, University of California, Davis. Davis, United States of America
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13
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McBee RM, Rozmiarek SA, Meyerson NR, Rowley PA, Sawyer SL. The effect of species representation on the detection of positive selection in primate gene data sets. Mol Biol Evol 2015; 32:1091-6. [PMID: 25556235 PMCID: PMC4379402 DOI: 10.1093/molbev/msu399] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Over evolutionary time, both host- and virus-encoded genes have been continually selected to modify their interactions with one another. This has resulted in the rapid evolution of the specific codons that govern the physical interactions between host and virus proteins. Virologists have discovered that these evolutionary signatures, acquired in nature, can provide a shortcut in the functional dissection of host-virus interactions in the laboratory. However, the use of evolution studies in this way is complicated by the fact that many nonhuman primate species are endangered, and biomaterials are often difficult to acquire. Here, we assess how the species representation in primate gene data sets affects the detection of positive natural selection. Our results demonstrate how targeted primate sequencing projects could greatly enhance research in immunology, virology, and beyond.
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Affiliation(s)
- Ross M McBee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | | | - Nicholas R Meyerson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | - Paul A Rowley
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | - Sara L Sawyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
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14
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Petrov P, Syrjänen R, Smith J, Gutowska MW, Uchida T, Vainio O, Burt DW. Characterization of the avian Trojan gene family reveals contrasting evolutionary constraints. PLoS One 2015; 10:e0121672. [PMID: 25803627 PMCID: PMC4372362 DOI: 10.1371/journal.pone.0121672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/03/2015] [Indexed: 12/12/2022] Open
Abstract
"Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.
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Affiliation(s)
- Petar Petrov
- Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
- Nordlab Oulu, Oulu University Hospital, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Riikka Syrjänen
- Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
- Nordlab Oulu, Oulu University Hospital, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jacqueline Smith
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, United Kingdom
| | - Maria Weronika Gutowska
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, United Kingdom
| | - Tatsuya Uchida
- Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Olli Vainio
- Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
- Nordlab Oulu, Oulu University Hospital, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - David W Burt
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, United Kingdom
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15
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Viral interference with functions of the cellular receptor tyrosine phosphatase CD45. Viruses 2015; 7:1540-57. [PMID: 25807057 PMCID: PMC4379584 DOI: 10.3390/v7031540] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/24/2022] Open
Abstract
The receptor tyrosine phosphatase CD45 is expressed on the surface of almost all cells of hematopoietic origin. CD45 functions are central to the development of T cells and determine the threshold at which T and B lymphocytes can become activated. Given this pivotal role of CD45 in the immune system, it is probably not surprising that viruses interfere with the activity of CD45 in lymphocytes to dampen the immune response and that they also utilize this molecule to accomplish their replication cycle. Here we report what is known about the interaction of viral proteins with CD45. Moreover, we debate putative interactions of viruses with CD45 in myeloid cells and the resulting consequences-subjects that remain to be investigated. Finally, we summarize the evidence that pathogens were the driving force for the evolution of CD45.
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16
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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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17
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Ooms M, Brayton B, Letko M, Maio SM, Pilcher CD, Hecht FM, Barbour JD, Simon V. HIV-1 Vif adaptation to human APOBEC3H haplotypes. Cell Host Microbe 2014; 14:411-21. [PMID: 24139399 DOI: 10.1016/j.chom.2013.09.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/02/2013] [Accepted: 08/30/2013] [Indexed: 11/16/2022]
Abstract
Several human APOBEC3 deaminases can inhibit HIV-1 replication in vitro. HIV-1 Vif counteracts this restriction by targeting APOBEC3 for proteasomal degradation. Human APOBEC3H (A3H) is highly polymorphic, with natural variants differing considerably in anti-HIV-1 activity in vitro. To examine HIV-1 adaptation to variation in A3H activity in a natural infection context, we determined the A3H haplotypes and Vif sequences from 76 recently infected HIV-1 patients. We detected A3H-specific Vif changes suggesting viral adaptation. The patient-derived Vif sequences were used to engineer viruses that specifically differed in their ability to counteract A3H. Replication of these Vif-variant viruses in primary T cells naturally expressing active or inactive A3H haplotypes showed that endogenously expressed A3H restricts HIV-1 replication. Proviral DNA from A3H-restricted viruses showed high levels of G-to-A mutations in an A3H-specific GA dinucleotide context. Taken together, our data validate A3H expressed at endogenous levels as a bona fide HIV-1 restriction factor.
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Affiliation(s)
- Marcel Ooms
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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18
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Woods MW, Tong JG, Tom SK, Szabo PA, Cavanagh PC, Dikeakos JD, Haeryfar SMM, Barr SD. Interferon-induced HERC5 is evolving under positive selection and inhibits HIV-1 particle production by a novel mechanism targeting Rev/RRE-dependent RNA nuclear export. Retrovirology 2014; 11:27. [PMID: 24693865 PMCID: PMC4021598 DOI: 10.1186/1742-4690-11-27] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 03/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Type I interferon (IFN) inhibits virus replication by activating multiple antiviral mechanisms and pathways. It has long been recognized that type I IFNs can potently block HIV-1 replication in vitro; as such, HIV-1 has been used as a system to identify and characterize IFN-induced antiviral proteins responsible for this block. IFN-induced HERC5 contains an amino-terminal Regulator of Chromosome Condensation 1 (RCC1)-like domain and a carboxyl-terminal Homologous to the E6-AP Carboxyl Terminus (HECT) domain. HERC5 is the main cellular E3 ligase that conjugates the IFN-induced protein ISG15 to proteins. This E3 ligase activity was previously shown to inhibit the replication of evolutionarily diverse viruses, including HIV-1. The contribution of the RCC1-like domain to the antiviral activity of HERC5 was previously unknown. RESULTS In this study, we showed that HERC5 inhibits HIV-1 particle production by a second distinct mechanism that targets the nuclear export of Rev/RRE-dependent RNA. Unexpectedly, the E3 ligase activity of HERC5 was not required for this inhibition. Instead, this activity required the amino-terminal RCC1-like domain of HERC5. Inhibition correlated with a reduction in intracellular RanGTP protein levels and/or the ability of RanGTP to interact with RanBP1. Inhibition also correlated with altered subcellular localization of HIV-1 Rev. In addition, we demonstrated that positive evolutionary selection is operating on HERC5. We identified a region in the RCC1-like domain that exhibits an exceptionally high probability of having evolved under positive selection and showed that this region is required for HERC5-mediated inhibition of nuclear export. CONCLUSIONS We have identified a second distinct mechanism by which HERC5 inhibits HIV-1 replication and demonstrate that HERC5 is evolving under strong positive selection. Together, our findings contribute to a growing body of evidence suggesting that HERC5 is a novel host restriction factor.
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Affiliation(s)
| | | | | | | | | | | | | | - Stephen Dominic Barr
- Department of Microbiology and Immunology, Dental Sciences Building Room 3006b, The University of Western Ontario, Schulich School of Medicine and Dentistry, Center for Human Immunology, London, Ontario, Canada.
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19
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Meyerson NR, Rowley PA, Swan CH, Le DT, Wilkerson GK, Sawyer SL. Positive selection of primate genes that promote HIV-1 replication. Virology 2014; 454-455:291-8. [PMID: 24725956 DOI: 10.1016/j.virol.2014.02.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 02/19/2014] [Accepted: 02/28/2014] [Indexed: 12/22/2022]
Abstract
Evolutionary analyses have revealed that most host-encoded restriction factors against HIV have experienced virus-driven selection during primate evolution. However, HIV also depends on the function of many human proteins, called host factors, for its replication. It is not clear whether virus-driven selection shapes the evolution of host factor genes to the extent that it is known to shape restriction factor genes. We show that five out of 40 HIV host factor genes (13%) analyzed do bear strong signatures of positive selection. Some of these genes (CD4, NUP153, RANBP2/NUP358) have been characterized with respect to the HIV lifecycle, while others (ANKRD30A/NY-BR-1 and MAP4) remain relatively uncharacterized. One of these, ANKRD30A, shows the most rapid evolution within this set of genes and is induced by interferon stimulation. We discuss how evolutionary analysis can aid the study of host factors for viral replication, just as it has the study of host immunity systems.
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Affiliation(s)
- Nicholas R Meyerson
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Paul A Rowley
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Christina H Swan
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA; Regents School of Austin, 3230 Travis Country Circle, Austin, TX, USA
| | - Dona T Le
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Sara L Sawyer
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA.
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20
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Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW, Martinez-Picado J, Dalmau J, López-Galíndez C, Casado C, Rauch A, Günthard HF, Bernasconi E, Vernazza P, Klimkait T, Yerly S, O'Brien SJ, Listgarten J, Pfeifer N, Lippert C, Fusi N, Kutalik Z, Allen TM, Müller V, Harrigan PR, Heckerman D, Telenti A, Fellay J. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. eLife 2013; 2:e01123. [PMID: 24171102 PMCID: PMC3807812 DOI: 10.7554/elife.01123] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/26/2013] [Indexed: 12/31/2022] Open
Abstract
HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10(-12)). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the 'intermediate phenotype' nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction. DOI:http://dx.doi.org/10.7554/eLife.01123.001.
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Affiliation(s)
- István Bartha
- School of Life Sciences , École Polytechnique Fédérale de Lausanne , Lausanne , Switzerland ; Institute of Microbiology , University Hospital and University of Lausanne , Lausanne , Switzerland ; Research Group of Theoretical Biology and Evolutionary Ecology , Eötvös Loránd University and the Hungarian Academy of Sciences , Budapest , Hungary ; Swiss Institute of Bioinformatics , Lausanne , Switzerland
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21
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Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD. Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). PLoS One 2013; 8:e77175. [PMID: 24194868 PMCID: PMC3806739 DOI: 10.1371/journal.pone.0077175] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 08/30/2013] [Indexed: 12/04/2022] Open
Abstract
To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.
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Affiliation(s)
- Xin Ma
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Joanna L. Kelley
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Kirsten Eilertson
- Bioinformatics Core, Gladstone Institutes, San Francisco, California, United States of America
| | - Shaila Musharoff
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jeremiah D. Degenhardt
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - André L. Martins
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Tomas Vinar
- Department of Applied Informatics, Comenius University, Bratislava, Slovakia
| | - Carolin Kosiol
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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22
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Abstract
Acquired immunodeficiency syndrome (AIDS) of humans is caused by two lentiviruses, human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2). Here, we describe the origins and evolution of these viruses, and the circumstances that led to the AIDS pandemic. Both HIVs are the result of multiple cross-species transmissions of simian immunodeficiency viruses (SIVs) naturally infecting African primates. Most of these transfers resulted in viruses that spread in humans to only a limited extent. However, one transmission event, involving SIVcpz from chimpanzees in southeastern Cameroon, gave rise to HIV-1 group M-the principal cause of the AIDS pandemic. We discuss how host restriction factors have shaped the emergence of new SIV zoonoses by imposing adaptive hurdles to cross-species transmission and/or secondary spread. We also show that AIDS has likely afflicted chimpanzees long before the emergence of HIV. Tracing the genetic changes that occurred as SIVs crossed from monkeys to apes and from apes to humans provides a new framework to examine the requirements of successful host switches and to gauge future zoonotic risk.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
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23
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Darc M, Schrago CG, Soares EA, Pissinatti A, Menezes AN, Soares MA, Seuánez HN. Molecular evolution of α4 integrin binding site to lentiviral envelope proteins in new world primates. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2012; 12:1501-7. [PMID: 22691367 DOI: 10.1016/j.meegid.2012.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/02/2012] [Accepted: 05/25/2012] [Indexed: 01/09/2023]
Abstract
Integrin epitopes encoded by ITGA4 exons 5 and 6 encompass the α4β7 binding site to natural ligands and HIV-1 gp120. Functional assays of α4 variants of new world primates (NWP) showed reduced binding of several ligands, including the HIV-1 envelope, probably accounting for restriction phenotypes conferring resistance to lentiviral infection (Darc et al., 2011). In this paper, we have analyzed, by cloning and sequencing, the α4 domain polymorphisms present in 10 NWP species and four old world primates (including human). Analyses of differential selection at codon sites and along evolutionary lineages were carried out. We identified codons under positive selection, including polymorphic variations at codon 201, presumably convergent during NWP radiation and significant positive selection leading to a single allele (SagVar2).
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Affiliation(s)
- Mirela Darc
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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24
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The role of tripartite motif family members in mediating susceptibility to HIV-1 infection. Curr Opin HIV AIDS 2012; 7:180-6. [PMID: 22258502 DOI: 10.1097/coh.0b013e32835048e1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW This review highlights new roles of the large family of tripartite motif (TRIM) proteins in antiviral defense. RECENT FINDINGS Recent research explores the participation of several TRIM family members in regulating the innate immune response. A large number of TRIM genes are upregulated upon treatment by interferon and are directly involved in signaling (TRIM5, 13, 16, 20, 21, 22, 23, 25, 27, 30, 32 and 38). Notably, TRIM5α has been identified as a 'pattern recognition receptor' triggering a cascade of signals upon viral recognition, and contributing to the establishment of the antiviral state. SUMMARY The identification of new roles for TRIM5α and other family members contributes to an emerging paradigm of host antiretroviral factors as mediators of the innate immune response and of the antiviral state. This leads both to direct therapeutic applications, such as gene therapy, and to the possibility of immune modulation.
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Patel MR, Loo YM, Horner SM, Gale M, Malik HS. Convergent evolution of escape from hepaciviral antagonism in primates. PLoS Biol 2012; 10:e1001282. [PMID: 22427742 PMCID: PMC3302847 DOI: 10.1371/journal.pbio.1001282] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/30/2012] [Indexed: 12/30/2022] Open
Abstract
Escape from antagonism by hepatitis C and related viruses has repeatedly evolved in antiviral factor MAVS via convergent evolution, revealing an ancient history of previous viral encounters in primates. The ability to mount an interferon response on sensing viral infection is a critical component of mammalian innate immunity. Several viruses directly antagonize viral sensing pathways to block activation of the host immune response. Here, we show that recurrent viral antagonism has shaped the evolution of the host protein MAVS—a crucial component of the viral-sensing pathway in primates. From sequencing and phylogenetic analyses of MAVS from 21 simian primates, we found that MAVS has evolved under strong positive selection. We focused on how this positive selection has shaped MAVS' susceptibility to Hepatitis C virus (HCV). We functionally tested MAVS proteins from diverse primate species for their ability to resist antagonism by HCV, which uses its protease NS3/4A to cleave human MAVS. We found that MAVS from multiple primates are resistant to inhibition by the HCV protease. This resistance maps to single changes within the protease cleavage site in MAVS, which protect MAVS from getting cleaved by the HCV protease. Remarkably, most of these changes have been independently acquired at a single residue 506 that evolved under positive selection. We show that “escape” mutations lower affinity of the NS3 protease for MAVS and allow it to better restrict HCV replication. We further show that NS3 proteases from all other primate hepaciviruses, including the highly divergent GBV-A and GBV-C viruses, are functionally similar to HCV. We conclude that convergent evolution at residue 506 in multiple primates has resulted in escape from antagonism by hepaciviruses. Our study provides a model whereby insights into the ancient history of viral infections in primates can be gained using extant host and virus genes. Our analyses also provide a means by which primates might clear infections by extant hepaciviruses like HCV. Hepatitis C virus (HCV) causes chronic liver disease and is estimated to infect 170 million people worldwide. HCV is able to establish a persistent infection in part by inhibiting the innate immune response. It does so by using its protease, NS3, to cleave the host's antiviral factor MAVS, which normally activates the interferon response. Using an assay that measures MAVS activity, we found that multiple primate species contain a version of MAVS that is resistant to HCV antagonism. Surprisingly, most of these primates have independently converged on changes in the same amino acid residue of MAVS to escape cleavage by the HCV protease. We found that the HCV protease has lower binding affinity for these resistant MAVS variants, which consequently are more effective at restricting HCV infection. Using a combination of phylogenetic and functional analyses of proteases from other HCV-related viruses, we infer that ancestral primates were likely exposed to and adapted to HCV-like viruses. One consequence of this adaptation is that changes that have given rise to extant MAVS variants may now provide protection from modern-day viruses.
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Affiliation(s)
- Maulik R. Patel
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Yueh-Ming Loo
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Stacy M. Horner
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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Laguette N, Rahm N, Sobhian B, Chable-Bessia C, Münch J, Snoeck J, Sauter D, Switzer WM, Heneine W, Kirchhoff F, Delsuc F, Telenti A, Benkirane M. Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe 2012; 11:205-17. [PMID: 22305291 DOI: 10.1016/j.chom.2012.01.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 12/08/2011] [Accepted: 01/12/2012] [Indexed: 12/21/2022]
Abstract
SAMHD1 has recently been identified as an HIV-1 restriction factor operating in myeloid cells. As a countermeasure, the Vpx accessory protein from HIV-2 and certain lineages of SIV have evolved to antagonize SAMHD1 by inducing its ubiquitin-proteasome-dependent degradation. Here, we show that SAMHD1 experienced strong positive selection episodes during primate evolution that occurred in the Catarrhini ancestral branch prior to the separation between hominoids (gibbons and great apes) and Old World monkeys. The identification of SAMHD1 residues under positive selection led to mapping the Vpx-interaction domain of SAMHD1 to its C-terminal region. Importantly, we found that while SAMHD1 restriction activity toward HIV-1 is evolutionarily maintained, antagonism of SAMHD1 by Vpx is species-specific. The distinct evolutionary signature of SAMHD1 sheds light on the development of its antiviral specificity.
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Affiliation(s)
- Nadine Laguette
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Laboratoires de Virologie Moléculaire, 34000 Montpellier, France
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How SAMHD1 changes our view of viral restriction. Trends Immunol 2011; 33:26-33. [PMID: 22177690 DOI: 10.1016/j.it.2011.11.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 10/31/2011] [Accepted: 11/02/2011] [Indexed: 01/21/2023]
Abstract
Recent studies have uncovered sterile alpha motif and HD domain 1 (SAMHD1) as the restriction factor that blocks HIV-1 replication in myeloid cells. In contrast to previously identified HIV-1 restriction factors, SAMHD1 does not meet a countermeasure developed by HIV-1. However, HIV-2 and certain simian immunodeficiency virus (SIV) strains express the auxiliary protein Vpx that potently blocks SAMHD1. It is therefore perplexing why this function has been lost or not acquired during the course of lentiviral evolution. This article summarizes the similarities and differences between SAMHD1 and other HIV-1 restriction factors, while highlighting the new questions that are emerging about the crosstalk between restriction factors and innate immune responses.
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Siddiqui RA, Krawczak M, Platzer M, Sauermann U. Association of TLR7 variants with AIDS-like disease and AIDS vaccine efficacy in rhesus macaques. PLoS One 2011; 6:e25474. [PMID: 22022401 PMCID: PMC3192768 DOI: 10.1371/journal.pone.0025474] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 09/05/2011] [Indexed: 02/07/2023] Open
Abstract
In HIV infection, TLR7-triggered IFN-α production exerts a direct antiviral effect through the inhibition of viral replication, but may also be involved in immune pathogenesis leading to AIDS. TLR7 could also be an important mediator of vaccine efficacy. In this study, we analyzed polymorphisms in the X-linked TLR7 gene in the rhesus macaque model of AIDS. Upon resequencing of the TLR7 gene in 36 rhesus macaques of Indian origin, 12 polymorphic sites were detected. Next, we identified three tightly linked single nucleotide polymorphisms (SNP) as being associated with survival time. Genotyping of 119 untreated, simian immunodeficiency virus (SIV)-infected male rhesus macaques, including an 'MHC adjusted' subset, revealed that the three TLR7 SNPs are also significantly associated with set-point viral load. Surprisingly, this effect was not observed in 72 immunized SIV-infected male monkeys. We hypothesize (i) that SNP c.13G>A in the leader peptide is causative for the observed genotype-phenotype association and that (ii) the underlying mechanism is related to RNA secondary structure formation. Therefore, we investigated a fourth SNP (c.-17C>T), located 17 bp upstream of the ATG translation initiation codon, that is also potentially capable of influencing RNA structure. In c.13A carriers, neither set-point viral load nor survival time were related to the c.-17C>T genotype. In c.13G carriers, by contrast, the c.-17C allele was significantly associated with prolonged survival. Again, no such association was detected among immunized SIV-infected macaques. Our results highlight the dual role of TLR7 in immunodeficiency virus infection and vaccination and imply that it may be important to control human AIDS vaccine trials, not only for MHC genotype, but also for TLR7 genotype.
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Affiliation(s)
- Roman A. Siddiqui
- German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian–Albrechts University, Kiel, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany
| | - Ulrike Sauermann
- German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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Cagliani R, Riva S, Fumagalli M, Biasin M, Caputo SL, Mazzotta F, Piacentini L, Pozzoli U, Bresolin N, Clerici M, Sironi M. A positively selected APOBEC3H haplotype is associated with natural resistance to HIV-1 infection. Evolution 2011; 65:3311-22. [PMID: 22023594 DOI: 10.1111/j.1558-5646.2011.01368.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
APOBEC3 genes encode cytidine deaminases endowed with the ability to inhibit retroviruses and retrotransposons. These genes have been targets of natural selection throughout primate evolutionary history. We analyzed their selection pattern in human populations observing that APOBEC3F and 3G are neutrally evolving. Conversely, nucleotide diversity was extremely high for APOBEC3H, and most tests rejected the hypothesis of selective neutrality in Eurasian populations. Haplotype analysis and the derived intraallelic nucleotide diversity test indicated that positive selection has driven the increase in frequency of one haplotype (Hap I) outside Africa. Consistently, population genetic differentiation between African and non-African populations was higher than expected under neutrality. A case-control association analysis indicated that Hap I is associated with protection from sexually transmitted HIV-1 infection. Hap I carries a protein-destabilizing variant and a residue conferring resistance to Vif-mediated degradation. Data herein suggest that lower protein stability might have been traded-off with a higher ability to circumvent Vif-mediated hijacking. Alternatively, transcription regulatory variants might represent the selection target. Our data represent an example of how the selective pressures exerted by extinct or unknown viral agents can be exploited to provide valuable information on the allelic determinants of susceptibility to modern infections.
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Affiliation(s)
- Rachele Cagliani
- Scientific Institute IRCCS E. Medea, Via don L. Monza 20, Bosisio Parini (LC), Italy
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Klimentidis YC, Aissani B, Shriver MD, Allison DB, Shrestha S. Natural selection among Eurasians at genomic regions associated with HIV-1 control. BMC Evol Biol 2011; 11:173. [PMID: 21689440 PMCID: PMC3141432 DOI: 10.1186/1471-2148-11-173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 06/20/2011] [Indexed: 12/11/2022] Open
Abstract
Background HIV susceptibility and pathogenicity exhibit both interindividual and intergroup variability. The etiology of intergroup variability is still poorly understood, and could be partly linked to genetic differences among racial/ethnic groups. These genetic differences may be traceable to different regimes of natural selection in the 60,000 years since the human radiation out of Africa. Here, we examine population differentiation and haplotype patterns at several loci identified through genome-wide association studies on HIV-1 control, as determined by viral-load setpoint, in European and African-American populations. We use genome-wide data from the Human Genome Diversity Project, consisting of 53 world-wide populations, to compare measures of FST and relative extended haplotype homozygosity (REHH) at these candidate loci to the rest of the respective chromosome. Results We find that the Europe-Middle East and Europe-South Asia pairwise FST in the most strongly associated region are elevated compared to most pairwise comparisons with the sub-Saharan African group, which exhibit very low FST. We also find genetic signatures of recent positive selection (higher REHH) at these associated regions among all groups except for sub-Saharan Africans and Native Americans. This pattern is consistent with one in which genetic differentiation, possibly due to diversifying/positive selection, occurred at these loci among Eurasians. Conclusions These findings are concordant with those from earlier studies suggesting recent evolutionary change at immunity-related genomic regions among Europeans, and shed light on the potential genetic and evolutionary origin of population differences in HIV-1 control.
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Affiliation(s)
- Yann C Klimentidis
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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31
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Meyerson NR, Sawyer SL. Two-stepping through time: mammals and viruses. Trends Microbiol 2011; 19:286-94. [PMID: 21531564 DOI: 10.1016/j.tim.2011.03.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 03/08/2011] [Accepted: 03/16/2011] [Indexed: 12/14/2022]
Abstract
Recent studies have identified ancient virus genomes preserved as fossils within diverse animal genomes. These fossils have led to the revelation that a broad range of mammalian virus families are older and more ubiquitous than previously appreciated. Long-term interactions between viruses and their hosts often develop into genetic arms races where both parties continually jockey for evolutionary dominance. It is difficult to imagine how mammalian hosts have kept pace in the evolutionary race against rapidly evolving viruses over large expanses of time, given their much slower evolutionary rates. However, recent data has begun to reveal the evolutionary strategy of slowly-evolving hosts. We review these data and suggest a modified arms race model where the evolutionary possibilities of viruses are relatively constrained. Such a model could allow more accurate forecasting of virus evolution.
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Affiliation(s)
- Nicholas R Meyerson
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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32
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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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33
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Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses. J Virol 2011; 85:4173-83. [PMID: 21345948 DOI: 10.1128/jvi.00075-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lentiviruses, the genus of retrovirus that includes HIV-1, rarely endogenize. Some lemurs uniquely possess an endogenous lentivirus called PSIV ("prosimian immunodeficiency virus"). Thus, lemurs provide the opportunity to study the activity of host defense factors, such as TRIM5α, in the setting of germ line invasion. We characterized the activities of TRIM5α proteins from two distant lemurs against exogenous retroviruses and a chimeric PSIV. TRIM5α from gray mouse lemur, which carries PSIV in its genome, exhibited the narrowest restriction activity. One allelic variant of gray mouse lemur TRIM5α restricted only N-tropic murine leukemia virus (N-MLV), while a second variant restricted N-MLV and, uniquely, B-tropic MLV (B-MLV); both variants poorly blocked PSIV. In contrast, TRIM5α from ring-tailed lemur, which does not contain PSIV in its genome, revealed one of the broadest antiviral activities reported to date against lentiviruses, including PSIV. Investigation into the antiviral specificity of ring-tailed lemur TRIM5α demonstrated a major contribution of a 32-amino-acid expansion in variable region 2 (v2) of the B30.2/SPRY domain to the breadth of restriction. Data on lemur TRIM5α and the prediction of ancestral simian sequences hint at an evolutionary scenario where antiretroviral specificity is prominently defined by the lineage-specific expansion of the variable loops of B30.2/SPRY.
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CD4 intragenic SNPs associate with HIV-2 plasma viral load and CD4 count in a community-based study from Guinea-Bissau, West Africa. J Acquir Immune Defic Syndr 2011; 56:1-8. [PMID: 20924289 DOI: 10.1097/qai.0b013e3181f638ed] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVES The human genetics of HIV-2 infection and disease progression is understudied. Therefore, we studied the effect of variation in 2 genes that encode products critical to HIV pathogenesis and disease progression: CD4 and CD209. DESIGN This cross-sectional study consisted of 143 HIV-2, 30 HIV-1 + HIV-2 and 29 HIV-1-infected subjects and 194 uninfected controls recruited from rural Guinea-Bissau. METHODS We genotyped 14 CD4 and 4 CD209 single nucleotide polymorphisms (SNPs) that were tested for association with HIV infection, HIV-2 plasma viral load (high vs. low), and CD4 T-cell count (high vs. low). RESULTS The most significant association was between a CD4 haplotype rs11575097-rs10849523 and high viral load [odds ratio (OR): = 2.37, 95% confidence interval (CI): 1.35 to 4.19, P = 0.001, corrected for multiple testing], suggesting increased genetic susceptibility to HIV-2 disease progression for individuals carrying the high-risk haplotype. Significant associations were also observed at a CD4 SNP (rs2255301) with HIV-2 infection (OR: = 2.36, 95% CI: 1.19 to 4.65, P = 0.01) and any HIV infection (OR: = 2.50, 95% CI: 1.34 to 4.69, P = 0.004). CONCLUSIONS Our results support a role of CD4 polymorphisms in HIV-2 infection, in agreement with recent data showing that CD4 gene variants increase risk to HIV-1 in Kenyan female sex workers. These findings indicate at least some commonality in HIV-1 and HIV-2 susceptibility.
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35
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Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. Functional comparison of innate immune signaling pathways in primates. PLoS Genet 2010; 6:e1001249. [PMID: 21187902 PMCID: PMC3002988 DOI: 10.1371/journal.pgen.1001249] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 11/16/2010] [Indexed: 01/08/2023] Open
Abstract
Humans respond differently than other primates to a large number of infections. Differences in susceptibility to infectious agents between humans and other primates are probably due to inter-species differences in immune response to infection. Consistent with that notion, genes involved in immunity-related processes are strongly enriched among recent targets of positive selection in primates, suggesting that immune responses evolve rapidly, yet providing only indirect evidence for possible inter-species functional differences. To directly compare immune responses among primates, we stimulated primary monocytes from humans, chimpanzees, and rhesus macaques with lipopolysaccharide (LPS) and studied the ensuing time-course regulatory responses. We find that, while the universal Toll-like receptor response is mostly conserved across primates, the regulatory response associated with viral infections is often lineage-specific, probably reflecting rapid host–virus mutual adaptation cycles. Additionally, human-specific immune responses are enriched for genes involved in apoptosis, as well as for genes associated with cancer and with susceptibility to infectious diseases or immune-related disorders. Finally, we find that chimpanzee-specific immune signaling pathways are enriched for HIV–interacting genes. Put together, our observations lend strong support to the notion that lineage-specific immune responses may help explain known inter-species differences in susceptibility to infectious diseases. We know of a large number of diseases or medical conditions that affect humans more severely than non-human primates, such as AIDS, malaria, hepatitis B, and cancer. These differences likely arise from different immune responses to infection among species. However, due to the lack of comparative functional data across species, it remains unclear how the immune system of humans and other primates differ. In this work, we present the first genome-wide characterization of functional differences in innate immune responses between humans and our closest evolutionary relatives. Our results indicate that “core” immune responses, those that are critical to fight any invading pathogen, are the most conserved across primates and that much of the divergence in immune responses is observed in genes that are involved in response to specific microbial and viral agents. In addition, we show that human-specific immune responses are enriched for genes involved in apoptosis and cancer biology, as well as with genes previously associated with susceptibility to infectious diseases or immune-related disorders. Finally, we find that chimpanzee-specific immune signaling pathways are enriched for HIV–interacting genes. Our observations may therefore help explain known inter-species differences in susceptibility to infectious diseases.
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Affiliation(s)
- Luis B. Barreiro
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (LBB); (YG)
| | - John C. Marioni
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Ran Blekhman
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (LBB); (YG)
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Abstract
This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.
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Affiliation(s)
- Jacques Fellay
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America.
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37
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BST-2/tetherin: a new component of the innate immune response to enveloped viruses. Trends Microbiol 2010; 18:388-96. [PMID: 20688520 DOI: 10.1016/j.tim.2010.06.010] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 06/28/2010] [Accepted: 06/29/2010] [Indexed: 11/23/2022]
Abstract
The interferon-inducible, transmembrane protein BST-2 (CD317, tetherin) directly holds fully formed enveloped virus particles to the cells that produce them, inhibiting their spread. BST-2 inhibits members of the retrovirus, filovirus, arenavirus and herpesvirus families. These viruses encode a variety of proteins to degrade BST-2 and/or direct it away from its site of action at the cell surface. Viral antagonism has subjected BST-2 to positive selection, leading to species-specific differences that presented a barrier to the transmission of simian immunodeficiency viruses (SIVs) to humans. This barrier was crossed by HIV-1 when its Vpu protein acquired activity as a BST-2 antagonist. Here, we review this new host-pathogen relationship and discuss its impact on the evolution of primate lentiviruses and the origins of the HIV pandemic.
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38
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Liu J, Chen K, Wang JH, Zhang C. Molecular evolution of the primate antiviral restriction factor tetherin. PLoS One 2010; 5:e11904. [PMID: 20689591 PMCID: PMC2912774 DOI: 10.1371/journal.pone.0011904] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 07/09/2010] [Indexed: 01/27/2023] Open
Abstract
Background Tetherin is a recently identified antiviral restriction factor that restricts HIV-1 particle release in the absence of the HIV-1 viral protein U (Vpu). It is reminiscent of APOBEC3G and TRIM5a that also antagonize HIV. APOBEC3G and TRIM5a have been demonstrated to evolve under pervasive positive selection throughout primate evolution, supporting the red-queen hypothesis. Therefore, one naturally presumes that Tetherin also evolves under pervasive positive selection throughout primate evolution and supports the red-queen hypothesis. Here, we performed a detailed evolutionary analysis to address this presumption. Methodology/Principal Findings Results of non-synonymous and synonymous substitution rates reveal that Tetherin as a whole experiences neutral evolution rather than pervasive positive selection throughout primate evolution, as well as in non-primate mammal evolution. Sliding-window analyses show that the regions of the primate Tetherin that interact with viral proteins are under positive selection or relaxed purifying selection. In particular, the sites identified under positive selection generally focus on these regions, indicating that the main selective pressure acting on the primate Tetherin comes from virus infection. The branch-site model detected positive selection acting on the ancestral branch of the New World Monkey lineage, suggesting an episodic adaptive evolution. The positive selection was also found in duplicated Tetherins in ruminants. Moreover, there is no bias in the alterations of amino acids in the evolution of the primate Tetherin, implying that the primate Tetherin may retain broad spectrum of antiviral activity by maintaining structure stability. Conclusions/Significance These results conclude that the molecular evolution of Tetherin may be attributed to the host–virus arms race, supporting the Red Queen hypothesis, and Tetherin may be in an intermediate stage in transition from neutral to pervasive adaptive evolution.
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Affiliation(s)
- Jun Liu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jian-Hua Wang
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Chiyu Zhang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
- * E-mail:
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Koyanagi M, Kerns JA, Chung L, Zhang Y, Brown S, Moldoveanu T, Malik HS, Bix M. Diversifying selection and functional analysis of interleukin-4 suggests antagonism-driven evolution at receptor-binding interfaces. BMC Evol Biol 2010; 10:223. [PMID: 20649995 PMCID: PMC3017759 DOI: 10.1186/1471-2148-10-223] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 07/22/2010] [Indexed: 12/30/2022] Open
Abstract
Background Interleukin-4 (IL4) is a secreted immunoregulatory cytokine critically involved in host protection from parasitic helminths [1]. Reasoning that helminths may have evolved mechanisms to antagonize IL4 to maximize their dispersal, we explored mammalian IL4 evolution. Results This analysis revealed evidence of diversifying selection at 15 residues, clustered in epitopes responsible for IL4 binding to its Type I and Type II receptors. Such a striking signature of selective pressure suggested either recurrent episodes of pathogen antagonism or ligand/receptor co-evolution. To test the latter possibility, we performed detailed functional analysis of IL4 allotypes expressed by Mus musculus musculus and Mus musculus castaneus, which happen to differ at 5 residues (including three at positively selected sites) in and adjacent to the site 1 epitope that binds the IL4Rα subunit shared by the Type I and Type II IL4 receptors. We show that this intra-species variation affects the ability of IL4 neither to bind IL4 receptor alpha (IL4Rα) nor to signal biological responses through its Type I receptor. Conclusions Our results -- reminiscent of clustered positively selected sites revealing functionally important residues at host-virus interaction interfaces -- are consistent with IL4 having evolved to avoid recurrent pathogen antagonism, while maintaining the capacity to bind and signal through its cognate receptor. This work exposes what may be a general feature of evolutionary conflicts fought by pathogen antagonists at host protein-protein interaction interfaces involved in immune signaling: the emergence of receptor-binding ligand epitopes capable of buffering amino acid variation.
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Affiliation(s)
- Madoka Koyanagi
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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Bożek K, Lengauer T. Positive selection of HIV host factors and the evolution of lentivirus genes. BMC Evol Biol 2010; 10:186. [PMID: 20565842 PMCID: PMC2906474 DOI: 10.1186/1471-2148-10-186] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 06/18/2010] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Positive selection of host proteins that interact with pathogens can indicate factors relevant for infection and potentially be a measure of pathogen driven evolution. RESULTS Our analysis of 1439 primate genes and 175 lentivirus genomes points to specific host factors of high genetic variability that could account for differences in susceptibility to disease and indicate specific mechanisms of host defense and pathogen adaptation. We find that the largest amount of genetic change occurs in genes coding for cellular membrane proteins of the host as well as in the viral envelope genes suggesting cell entry and immune evasion as the primary evolutionary interface between host and pathogen. We additionally detect the innate immune response as a gene functional group harboring large differences among primates that could potentially account for the different levels of immune activation in the HIV/SIV primate infection. We find a significant correlation between the evolutionary rates of interacting host and viral proteins pointing to processes of the host-pathogen biology that are relatively conserved among species and to those undergoing accelerated genetic evolution. CONCLUSIONS These results indicate specific host factors and their functional groups experiencing pathogen driven evolutionary selection pressures. Individual host factors pointed to by our analysis might merit further study as potential targets of antiretroviral therapies.
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Affiliation(s)
- Katarzyna Bożek
- Max Planck Institute for Informatics Computational Biology and Applied Algorithmics Campus E1 4 66123 Saarbrücken, Germany
| | - Thomas Lengauer
- Max Planck Institute for Informatics Computational Biology and Applied Algorithmics Campus E1 4 66123 Saarbrücken, Germany
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Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. J Virol 2010; 84:7124-34. [PMID: 20444900 DOI: 10.1128/jvi.00468-10] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Tetherin/BST-2 is a host-encoded protein that restricts a wide diversity of viruses at the stage of virion release. However, viruses have evolved antagonists of Tetherin, including the Vpu and Nef proteins of primate lentiviruses. Like other host genes subject to viral antagonism, primate Tetherin genes have evolved under positive selection. We show here that viral antagonists acting at three independent sites of selection have driven the evolution of Tetherin, with the strongest selective pressure on the cytoplasmic tail domain. Human Tetherin is unique among the Tetherins of simian primates in that it has a 5-amino-acid deletion that results in the loss of the residue under the strongest positive selection. We show that this residue at amino acid 17 is the site of the functional interaction of Tetherin with Nef, since single amino acid substitutions at this single position can determine the susceptibility of Tetherin to Nef antagonism. While the simian immunodeficiency viruses SIVcpz and SIVgor are able to antagonize their hosts' Tetherin with Nef, human immunodeficiency virus type 1 (HIV-1) Vpu has evolved to counteract Tetherin in humans. We mapped the adaptations in the N-terminal transmembrane domain of Vpu that allow it to counteract human Tetherin. Our combined evolutionary and functional studies have allowed us to reconstruct the host-pathogen interactions that have shaped Tetherin and its lentivirus-encoded antagonists.
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The specificity of TRIM5 alpha-mediated restriction is influenced by its coiled-coil domain. J Virol 2010; 84:5790-801. [PMID: 20219908 DOI: 10.1128/jvi.02413-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Retroviruses are both powerful evolutionary forces and dangerous threats to genome integrity. As such, they have imposed strong selective pressure on their hosts, notably triggering the emergence of restriction factors, such as TRIM5 alpha, that act as potent barriers to their cross-species transmission. TRIM5 alpha orthologues from different primates have distinct retroviral restriction patterns, largely dictated by the sequence of their C-terminal PRYSPRY domain, which binds the capsid protein of incoming virions. Here, by combining genetic and functional analyses of human and squirrel monkey TRIM5 alpha, we demonstrate that the coiled-coil domain of this protein, thus far essentially known for mediating oligomerization, also conditions the spectrum of antiretroviral activity. Furthermore, we identify three coiled-coil residues responsible for this effect, one of which has been under positive selection during primate evolution, notably in New World monkeys. These results indicate that the PRYSPRY and coiled-coil domains cooperate to determine the specificity of TRIM5 alpha-mediated capture of retroviral capsids, shedding new light on this complex event.
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Rotger M, Dang KK, Fellay J, Heinzen EL, Feng S, Descombes P, Shianna KV, Ge D, Günthard HF, Goldstein DB, Telenti A. Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals. PLoS Pathog 2010; 6:e1000781. [PMID: 20195503 PMCID: PMC2829051 DOI: 10.1371/journal.ppat.1000781] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 01/20/2010] [Indexed: 12/17/2022] Open
Abstract
There is great interindividual variability in HIV-1 viral setpoint after seroconversion, some of which is known to be due to genetic differences among infected individuals. Here, our focus is on determining, genome-wide, the contribution of variable gene expression to viral control, and to relate it to genomic DNA polymorphism. RNA was extracted from purified CD4+ T-cells from 137 HIV-1 seroconverters, 16 elite controllers, and 3 healthy blood donors. Expression levels of more than 48,000 mRNA transcripts were assessed by the Human-6 v3 Expression BeadChips (Illumina). Genome-wide SNP data was generated from genomic DNA using the HumanHap550 Genotyping BeadChip (Illumina). We observed two distinct profiles with 260 genes differentially expressed depending on HIV-1 viral load. There was significant upregulation of expression of interferon stimulated genes with increasing viral load, including genes of the intrinsic antiretroviral defense. Upon successful antiretroviral treatment, the transcriptome profile of previously viremic individuals reverted to a pattern comparable to that of elite controllers and of uninfected individuals. Genome-wide evaluation of cis-acting SNPs identified genetic variants modulating expression of 190 genes. Those were compared to the genes whose expression was found associated with viral load: expression of one interferon stimulated gene, OAS1, was found to be regulated by a SNP (rs3177979, p = 4.9E-12); however, we could not detect an independent association of the SNP with viral setpoint. Thus, this study represents an attempt to integrate genome-wide SNP signals with genome-wide expression profiles in the search for biological correlates of HIV-1 control. It underscores the paradox of the association between increasing levels of viral load and greater expression of antiviral defense pathways. It also shows that elite controllers do not have a fully distinctive mRNA expression pattern in CD4+ T cells. Overall, changes in global RNA expression reflect responses to viral replication rather than a mechanism that might explain viral control.
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Affiliation(s)
- Margalida Rotger
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kristen K. Dang
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Jacques Fellay
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Erin L. Heinzen
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Sheng Feng
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | | | - Kevin V. Shianna
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Dongliang Ge
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Huldrych F. Günthard
- Division of Infectious Diseases, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - David B. Goldstein
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Amalio Telenti
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
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