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Delamonica B, Davalos L, Larijani M, Anthony SJ, Liu J, MacCarthy T. Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes. Virus Evol 2023; 9:vead047. [PMID: 37577211 PMCID: PMC10422979 DOI: 10.1093/ve/vead047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/27/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023] Open
Abstract
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational 'hotspots', can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at TC motifs, suggesting recent mutations are human APOBEC3-mediated, how emerging monkeypox virus (MPXV) strains will evolve as a consequence of APOBEC3-mediated mutations remains unknown. By measuring hotspot under-representation, depletion at synonymous sites, and a combination of the two, we analyzed APOBEC3-driven evolution in human poxvirus genomes, finding varying hotspot under-representation patterns. While the native poxvirus molluscum contagiosum exhibits a signature consistent with extensive coevolution with human APOBEC3, including depletion of TC hotspots, variola virus shows an intermediate effect consistent with ongoing evolution at the time of eradication. MPXV, likely the result of recent zoonosis, showed many genes with more TC hotspots than expected by chance (over-representation) and fewer GC hotspots than expected (under-representation). These results suggest the MPXV genome: (1) may have evolved in a host with a particular APOBEC GC hotspot preference, (2) has inverted terminal repeat (ITR) regions-which may be exposed to APOBEC3 for longer during viral replication-and longer genes likely to evolve faster, and therefore (3) has a heightened potential for future human APOBEC3-meditated evolution as the virus spreads in the human population. Our predictions of MPXV mutational potential can both help guide future vaccine development and identification of putative drug targets and add urgency to the task of containing human Mpox disease transmission and uncovering the ecology of the virus in its reservoir host.
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Affiliation(s)
- Brenda Delamonica
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liliana Davalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR 72205, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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Delamonica B, Davalos L, Larijani M, Anthony SJ, Liu J, MacCarthy T. Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546779. [PMID: 37425914 PMCID: PMC10326987 DOI: 10.1101/2023.06.27.546779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational "hotspots," can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at T C motifs, suggesting recent mutations are human APOBEC3-mediated, how emerging monkeypox virus (MPXV) strains will evolve as a consequence of APOBEC3-mediated mutations remains unknown. By measuring hotspot under-representation, depletion at synonymous sites, and a combination of the two, we analyzed APOBEC3-driven evolution in human poxvirus genomes, finding varying hotspot under-representation patterns. While the native poxvirus molluscum contagiosum exhibits a signature consistent with extensive coevolution with human APOBEC3, including depletion of T C hotspots, variola virus shows an intermediate effect consistent with ongoing evolution at the time of eradication. MPXV, likely the result of recent zoonosis, showed many genes with more T C hotspots than expected by chance (over-representation) and fewer G C hotspots than expected (under-representation). These results suggest the MPXV genome: 1) may have evolved in a host with a particular APOBEC G C hotspot preference, 2) has inverted terminal repeat (ITR) regions -which may be exposed to APOBEC3 for longer during viral replication- and longer genes likely to evolve faster, and therefore 3) has a heightened potential for future human APOBEC3-meditated evolution as the virus spreads in the human population. Our predictions of MPXV mutational potential can both help guide future vaccine development and identification of putative drug targets and add urgency to the task of containing human Mpox disease transmission and uncovering the ecology of the virus in its reservoir host.
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Affiliation(s)
- Brenda Delamonica
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Liliana Davalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA; Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada; Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Jia Liu
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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Meissner ME, Talledge N, Mansky LM. Molecular Biology and Diversification of Human Retroviruses. FRONTIERS IN VIROLOGY 2022; 2:872599. [PMID: 35783361 PMCID: PMC9242851 DOI: 10.3389/fviro.2022.872599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Studies of retroviruses have led to many extraordinary discoveries that have advanced our understanding of not only human diseases, but also molecular biology as a whole. The most recognizable human retrovirus, human immunodeficiency virus type 1 (HIV-1), is the causative agent of the global AIDS epidemic and has been extensively studied. Other human retroviruses, such as human immunodeficiency virus type 2 (HIV-2) and human T-cell leukemia virus type 1 (HTLV-1), have received less attention, and many of the assumptions about the replication and biology of these viruses are based on knowledge of HIV-1. Existing comparative studies on human retroviruses, however, have revealed that key differences between these viruses exist that affect evolution, diversification, and potentially pathogenicity. In this review, we examine current insights on disparities in the replication of pathogenic human retroviruses, with a particular focus on the determinants of structural and genetic diversity amongst HIVs and HTLV.
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Affiliation(s)
- Morgan E. Meissner
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
| | - Nathaniel Talledge
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
| | - Louis M. Mansky
- Institute for Molecular Virology, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Molecular, Cellular, Developmental Biology and Genetics Graduate Program, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, MN 55455 USA
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4
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Ta TM, Malik S, Anderson EM, Jones AD, Perchik J, Freylikh M, Sardo L, Klase ZA, Izumi T. Insights Into Persistent HIV-1 Infection and Functional Cure: Novel Capabilities and Strategies. Front Microbiol 2022; 13:862270. [PMID: 35572626 PMCID: PMC9093714 DOI: 10.3389/fmicb.2022.862270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/23/2022] Open
Abstract
Although HIV-1 replication can be efficiently suppressed to undetectable levels in peripheral blood by combination antiretroviral therapy (cART), lifelong medication is still required in people living with HIV (PLWH). Life expectancies have been extended by cART, but age-related comorbidities have increased which are associated with heavy physiological and economic burdens on PLWH. The obstacle to a functional HIV cure can be ascribed to the formation of latent reservoir establishment at the time of acute infection that persists during cART. Recent studies suggest that some HIV reservoirs are established in the early acute stages of HIV infection within multiple immune cells that are gradually shaped by various host and viral mechanisms and may undergo clonal expansion. Early cART initiation has been shown to reduce the reservoir size in HIV-infected individuals. Memory CD4+ T cell subsets are regarded as the predominant cellular compartment of the HIV reservoir, but monocytes and derivative macrophages or dendritic cells also play a role in the persistent virus infection. HIV latency is regulated at multiple molecular levels in transcriptional and post-transcriptional processes. Epigenetic regulation of the proviral promoter can profoundly regulate the viral transcription. In addition, transcriptional elongation, RNA splicing, and nuclear export pathways are also involved in maintaining HIV latency. Although most proviruses contain large internal deletions, some defective proviruses may induce immune activation by expressing viral proteins or producing replication-defective viral-like particles. In this review article, we discuss the state of the art on mechanisms of virus persistence in the periphery and tissue and summarize interdisciplinary approaches toward a functional HIV cure, including novel capabilities and strategies to measure and eliminate the infected reservoirs and induce immune control.
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Affiliation(s)
- Tram M. Ta
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Sajjaf Malik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Elizabeth M. Anderson
- Office of the Assistant Secretary for Health, Region 3, U.S. Department of Health and Human Services, Washington, DC, United States
| | - Amber D. Jones
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Jocelyn Perchik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Maryann Freylikh
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Luca Sardo
- Department of Infectious Disease and Vaccines, Merck & Co., Inc., Kenilworth, NJ, United States
| | - Zackary A. Klase
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Neuroimmunology and CNS Therapeutics, Institute of Molecular Medicine and Infectious Diseases, Drexel University of Medicine, Philadelphia, PA, United States
| | - Taisuke Izumi
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,*Correspondence: Taisuke Izumi,
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Functional and Highly Cross-Linkable HIV-1 Envelope Glycoproteins Enriched in a Pretriggered Conformation. J Virol 2022; 96:e0166821. [PMID: 35343783 DOI: 10.1128/jvi.01668-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Binding to the receptor, CD4, drives the pretriggered, "closed" (state-1) conformation of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) trimer into more "open" conformations (states 2 and 3). Broadly neutralizing antibodies, which are elicited inefficiently, mostly recognize the state-1 Env conformation, whereas the more commonly elicited poorly neutralizing antibodies recognize states 2/3. HIV-1 Env metastability has created challenges for defining the state-1 structure and developing immunogens mimicking this labile conformation. The availability of functional state-1 Envs that can be efficiently cross-linked at lysine and/or acidic amino acid residues might assist these endeavors. To that end, we modified HIV-1AD8 Env, which exhibits an intermediate level of triggerability by CD4. We introduced lysine/acidic residues at positions that exhibit such polymorphisms in natural HIV-1 strains. Env changes that were tolerated with respect to gp120-gp41 processing, subunit association, and virus entry were further combined. Two common polymorphisms, Q114E and Q567K, as well as a known variant, A582T, additively rendered pseudoviruses resistant to cold, soluble CD4, and a CD4-mimetic compound, phenotypes indicative of stabilization of the pretriggered state-1 Env conformation. Combining these changes resulted in two lysine-rich HIV-1AD8 Env variants (E.2 and AE.2) with neutralization- and cold-resistant phenotypes comparable to those of natural, less triggerable tier 2/3 HIV-1 isolates. Compared with these and the parental Envs, the E.2 and AE.2 Envs were cleaved more efficiently and exhibited stronger gp120-trimer association in detergent lysates. These highly cross-linkable Envs enriched in a pretriggered conformation should assist characterization of the structure and immunogenicity of this labile state. IMPORTANCE The development of an efficient vaccine is critical for combating HIV-1 infection worldwide. However, the instability of the pretriggered shape (state 1) of the viral envelope glycoprotein (Env) makes it difficult to raise neutralizing antibodies against HIV-1. Here, by introducing multiple changes in Env, we derived two HIV-1 Env variants that are enriched in state 1 and can be efficiently cross-linked to maintain this shape. These Env complexes are more stable in detergent, assisting their purification. Thus, our study provides a path to a better characterization of the native pretriggered Env, which should assist vaccine development.
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Differential Activity of APOBEC3F, APOBEC3G, and APOBEC3H in the Restriction of HIV-2. J Mol Biol 2022; 434:167355. [PMID: 34774569 PMCID: PMC8752514 DOI: 10.1016/j.jmb.2021.167355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 02/01/2023]
Abstract
Human immunodeficiency virus (HIV) mutagenesis is driven by a variety of internal and external sources, including the host APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypetide-like 3; A3) family of mutagenesis factors, which catalyze G-to-A transition mutations during virus replication. HIV-2 replication is characterized by a relative lack of G-to-A mutations, suggesting infrequent mutagenesis by A3 proteins. To date, the activity of the A3 repertoire against HIV-2 has remained largely uncharacterized, and the mutagenic activity of these proteins against HIV-2 remains to be elucidated. In this study, we provide the first comprehensive characterization of the restrictive capacity of A3 proteins against HIV-2 in cell culture using a dual fluorescent reporter HIV-2 vector virus. We found that A3F, A3G, and A3H restricted HIV-2 infectivity in the absence of Vif and were associated with significant increases in the frequency of viral mutants. These proteins increased the frequency of G-to-A mutations within the proviruses of infected cells as well. A3G and A3H also reduced HIV-2 infectivity via inhibition of reverse transcription and the accumulation of DNA products during replication. In contrast, A3D did not exhibit any restrictive activity against HIV-2, even at higher expression levels. Taken together, these results provide evidence that A3F, A3G, and A3H, but not A3D, are capable of HIV-2 restriction. Differences in A3-mediated restriction of HIV-1 and HIV-2 may serve to provide new insights in the observed mutation profiles of these viruses.
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Hamelin DJ, Fournelle D, Grenier JC, Schockaert J, Kovalchik KA, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Syst 2021; 13:143-157.e3. [PMID: 34637888 PMCID: PMC8492600 DOI: 10.1016/j.cels.2021.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/03/2021] [Accepted: 09/23/2021] [Indexed: 02/09/2023]
Abstract
The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARS-CoV-2 genome assemblies, sampled across 143 countries and all major continents from December 2019 to December 2020 before mass vaccination or the rise of the Delta variant. We observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family; this is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7-supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+ T cell immunosurveillance during the first year of the pandemic.
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Affiliation(s)
| | - Dominique Fournelle
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jana Schockaert
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | | | - Peter Kubiniok
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Fatima Mostefai
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | | | - Frederic Saab
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | | | - Martin A Smith
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Sofie Pattijn
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | - Hugo Soudeyns
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Hélène Decaluwe
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Julie Hussin
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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Meissner ME, Julik EJ, Badalamenti JP, Arndt WG, Mills LJ, Mansky LM. Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing. Viruses 2021; 13:v13071338. [PMID: 34372543 PMCID: PMC8310143 DOI: 10.3390/v13071338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 01/23/2023] Open
Abstract
Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.
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Affiliation(s)
- Morgan E. Meissner
- Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
| | - Emily J. Julik
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonathan P. Badalamenti
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN 55455, USA;
| | - William G. Arndt
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lauren J. Mills
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (L.J.M.); (L.M.M.)
| | - Louis M. Mansky
- Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (L.J.M.); (L.M.M.)
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Gaba A, Flath B, Chelico L. Examination of the APOBEC3 Barrier to Cross Species Transmission of Primate Lentiviruses. Viruses 2021; 13:1084. [PMID: 34200141 PMCID: PMC8228377 DOI: 10.3390/v13061084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The transmission of viruses from animal hosts into humans have led to the emergence of several diseases. Usually these cross-species transmissions are blocked by host restriction factors, which are proteins that can block virus replication at a specific step. In the natural virus host, the restriction factor activity is usually suppressed by a viral antagonist protein, but this is not the case for restriction factors from an unnatural host. However, due to ongoing viral evolution, sometimes the viral antagonist can evolve to suppress restriction factors in a new host, enabling cross-species transmission. Here we examine the classical case of this paradigm by reviewing research on APOBEC3 restriction factors and how they can suppress human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). APOBEC3 enzymes are single-stranded DNA cytidine deaminases that can induce mutagenesis of proviral DNA by catalyzing the conversion of cytidine to promutagenic uridine on single-stranded viral (-)DNA if they escape the HIV/SIV antagonist protein, Vif. APOBEC3 degradation is induced by Vif through the proteasome pathway. SIV has been transmitted between Old World Monkeys and to hominids. Here we examine the adaptations that enabled such events and the ongoing impact of the APOBEC3-Vif interface on HIV in humans.
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Affiliation(s)
- Amit Gaba
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada
| | - Ben Flath
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada
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10
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Callens M, Pradier L, Finnegan M, Rose C, Bedhomme S. Read between the lines: Diversity of non-translational selection pressures on local codon usage. Genome Biol Evol 2021; 13:6263832. [PMID: 33944930 PMCID: PMC8410138 DOI: 10.1093/gbe/evab097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Protein coding genes can contain specific motifs within their nucleotide sequence that function as a signal for various biological pathways. The presence of such sequence motifs within a gene can have beneficial or detrimental effects on the phenotype and fitness of an organism, and this can lead to the enrichment or avoidance of this sequence motif. The degeneracy of the genetic code allows for the existence of alternative synonymous sequences that exclude or include these motifs, while keeping the encoded amino acid sequence intact. This implies that locally, there can be a selective pressure for preferentially using a codon over its synonymous alternative in order to avoid or enrich a specific sequence motif. This selective pressure could -in addition to mutation, drift and selection for translation efficiency and accuracy- contribute to shape the codon usage bias. In this review, we discuss patterns of avoidance of (or enrichment for) the various biological signals contained in specific nucleotide sequence motifs: transcription and translation initiation and termination signals, mRNA maturation signals, and antiviral immune system targets. Experimental data on the phenotypic or fitness effects of synonymous mutations in these sequence motifs confirm that they can be targets of local selection pressures on codon usage. We also formulate the hypothesis that transposable elements could have a similar impact on codon usage through their preferred integration sequences. Overall, selection on codon usage appears to be a combination of a global selection pressure imposed by the translation machinery, and a patchwork of local selection pressures related to biological signals contained in specific sequence motifs.
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Affiliation(s)
- Martijn Callens
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Léa Pradier
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Michael Finnegan
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Caroline Rose
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Stéphanie Bedhomme
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
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11
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Lai A, Giacomet V, Bergna A, Zuccotti GV, Zehender G, Clerici M, Trabattoni D, Fenizia C. Early-Transmitted Variants and Their Evolution in a HIV-1 Positive Couple: NGS and Phylogenetic Analyses. Viruses 2021; 13:v13030513. [PMID: 33808903 PMCID: PMC8003824 DOI: 10.3390/v13030513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 12/05/2022] Open
Abstract
We had access to both components of a couple who became infected with human immunodeficiency virus (HIV)-1 through sexual behavior during the early initial phase of infection and before initiation of therapy. We analyzed blood samples obtained at the time of diagnosis and after six months of combined antiretroviral therapy. Next-generation sequencing (NGS) and phylogenetic analyses were used to investigate the transmission and evolution of HIV-1 quasispecies. Phylogenetic analyses were conducted using Bayesian inference methods. Both partners were infected with an HIV-1 B subtype. No evidence of viral recombination was observed. The lowest intrapersonal genetic distances were observed at baseline, before initiation of therapy, and in particular in the V1V2 fragment (distances ranging from 0.102 to 0.148). One HIV-1 single variant was concluded to be dominant in all of the HIV-1 regions analyzed, although some minor variants could be observed. The same tree structure was observed both at baseline and after six months of therapy. These are the first extended phylogenetic analyses performed on both members of a therapy-naïve couple within a few weeks of infection, and in which the effect of antiretroviral therapy on viral evolution was analyzed. Understanding which HIV-1 variants are most likely to be transmitted would allow a better understanding of viral evolution, possibly playing a role in vaccine design and prevention strategies.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (A.L.); (A.B.); (G.Z.); (D.T.)
| | - Vania Giacomet
- Clinic of Pediatrics, ASST Fatebenefratelli-Sacco, Sacco Clinical Sciences Institute, Via G.B. Grassi 74, 20157 Milan, Italy; (V.G.); (G.V.Z.)
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (A.L.); (A.B.); (G.Z.); (D.T.)
| | - Gian Vincenzo Zuccotti
- Clinic of Pediatrics, ASST Fatebenefratelli-Sacco, Sacco Clinical Sciences Institute, Via G.B. Grassi 74, 20157 Milan, Italy; (V.G.); (G.V.Z.)
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (A.L.); (A.B.); (G.Z.); (D.T.)
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Via F. Sforza 35, 20122 Milan, Italy;
- IRCCS Fondazione Don Carlo Gnocchi, Via Capecelatro 66, 20148 Milan, Italy
| | - Daria Trabattoni
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (A.L.); (A.B.); (G.Z.); (D.T.)
| | - Claudio Fenizia
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (A.L.); (A.B.); (G.Z.); (D.T.)
- Department of Pathophysiology and Transplantation, University of Milan, Via F. Sforza 35, 20122 Milan, Italy;
- Correspondence: ; Tel.: +39-02-5031-9679; Fax: +39-02-5031-9677
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12
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The Role of APOBECs in Viral Replication. Microorganisms 2020; 8:microorganisms8121899. [PMID: 33266042 PMCID: PMC7760323 DOI: 10.3390/microorganisms8121899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including HIV-1 Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to APOBEC selection for viral variants that enhance replication or avoid immune elimination.
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13
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Interplay between Intrinsic and Innate Immunity during HIV Infection. Cells 2019; 8:cells8080922. [PMID: 31426525 PMCID: PMC6721663 DOI: 10.3390/cells8080922] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Restriction factors are antiviral components of intrinsic immunity which constitute a first line of defense by blocking different steps of the human immunodeficiency virus (HIV) replication cycle. In immune cells, HIV infection is also sensed by several pattern recognition receptors (PRRs), leading to type I interferon (IFN-I) and inflammatory cytokines production that upregulate antiviral interferon-stimulated genes (ISGs). Several studies suggest a link between these two types of immunity. Indeed, restriction factors, that are generally interferon-inducible, are able to modulate immune responses. This review highlights recent knowledge of the interplay between restriction factors and immunity inducing antiviral defenses. Counteraction of this intrinsic and innate immunity by HIV viral proteins will also be discussed.
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14
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Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance. Heliyon 2019; 5:e01498. [PMID: 31025011 PMCID: PMC6475876 DOI: 10.1016/j.heliyon.2019.e01498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 04/05/2019] [Indexed: 01/04/2023] Open
Abstract
The APOBEC3 enzymes can induce mutagenesis of HIV-1 proviral DNA through the deamination of cytosine. HIV-1 overcomes this restriction through the viral protein Vif that induces APOBEC3 proteasomal degradation. Within this dynamic host-pathogen relationship, the APOBEC3 enzymes have been found to be beneficial, neutral, or detrimental to HIV-1 biology. Here, we assessed the ability of co-expressed APOBEC3F and APOBEC3G to induce HIV-1 resistance to antiviral drugs. We found that co-expression of APOBEC3F and APOBEC3G enabled partial resistance of APOBEC3F to Vif-mediated degradation with a corresponding increase in APOBEC3F-induced deaminations in the presence of Vif, in addition to APOBEC3G-induced deaminations. We recovered HIV-1 drug resistant variants resulting from APOBEC3-induced mutagenesis, but these variants were less able to replicate than drug resistant viruses derived from RT-induced mutations alone. The data support a model in which APOBEC3 enzymes cooperate to restrict HIV-1, promoting viral inactivation over evolution to drug resistance.
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15
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Wan L, Kamba K, Nagata T, Katahira M. An insight into the dependence of the deamination rate of human APOBEC3F on the length of single-stranded DNA, which is affected by the concentrations of APOBEC3F and single-stranded DNA. Biochim Biophys Acta Gen Subj 2019; 1864:129346. [PMID: 30986508 DOI: 10.1016/j.bbagen.2019.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/20/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND APOBEC3F (A3F), a member of the human APOBEC3 (A3) family of cytidine deaminases, acts as an anti-HIV-1 factor by deaminating deoxycytidine in the complementary DNA of the viral genome. A full understanding of the deamination behavior of A3F awaits further investigation. METHODS The real-time NMR method and uracil-DNA glycosylase assay were used to track the activities of the C-terminal domain (CTD) of A3F at different concentrations of A3F-CTD and ssDNA. The steady-state fluorescence anisotropy measurement was used to examine the binding between A3F-CTD and ssDNA with different lengths. The use of the A3F-CTD N214H mutant, having higher activity than the wild-type, facilitated the tracking of the reactions. RESULTS A3F-CTD was found to efficiently deaminate the target deoxycytidine in long ssDNA in lower ssDNA concentration conditions ([A3F-CTD] ≫ [ssDNA]), while the target deoxycytidine in short ssDNA is deaminated efficiently in higher ssDNA concentration conditions ([A3F-CTD] ≪ [ssDNA]). This property is quite different from that of the previously studied A3 family member, A3B; the concentrations of the proteins and ssDNA had no effect. CONCLUSIONS The concentrations of A3F-CTD and ssDNA substrates affect the ssDNA-length-dependence of deamination rate of the A3F-CTD. This unique property of A3F is rationally interpreted on the basis of its binding characteristics with ssDNA. GENERAL SIGNIFICANCE The discovery of the unique property of A3F regarding the deamination rate deepens the understanding of its counteraction against HIV-1. Our strategy is applicable to investigate the other aspects of the A3 activities, such as those involved in the cancer development.
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Affiliation(s)
- Li Wan
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Keisuke Kamba
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan.
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan.
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16
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Adolph MB, Ara A, Chelico L. APOBEC3 Host Restriction Factors of HIV-1 Can Change the Template Switching Frequency of Reverse Transcriptase. J Mol Biol 2019; 431:1339-1352. [PMID: 30797859 DOI: 10.1016/j.jmb.2019.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/16/2022]
Abstract
The APOBEC3 family of deoxycytidine deaminases has the ability to restrict HIV-1 through deamination-dependent and deamination-independent mechanisms. Although the generation of mutations through deamination of cytosine to uracil in single-stranded HIV-1 (-) DNA is the dominant mechanism of restriction, the deaminase-independent mechanism additionally contributes. Previous observations indicate that APOBEC3 enzymes competitively bind the RNA template or reverse transcriptase (RT) and act as a roadblock to DNA polymerization. Here we studied how the deamination-independent inhibition of HIV-1 RT by APOBEC3C S188I, APOBEC3F, APOBEC3G, and APOBEC3H affected RT template switching. We found that APOBEC3F could promote template switching of RT, and this was dependent on the high affinity with which it bound nucleic acids, suggesting than an APOBEC3 "road-block" can force template switching. Our data demonstrate that the deamination-independent functions of APOBEC3 enzymes extend beyond only disrupting RT DNA polymerization. Since alterations to the RT template switching frequency can result in insertions or deletions, our data support a model in which APOBEC3 enzymes use multiple mechanisms to increase the probability of generating a mutated and nonfunctional virus in addition to cytosine deamination.
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Affiliation(s)
- Madison B Adolph
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Anjuman Ara
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada; Saskatchewan Cancer Agency and Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
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17
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Borzooee F, Joris KD, Grant MD, Larijani M. APOBEC3G Regulation of the Evolutionary Race Between Adaptive Immunity and Viral Immune Escape Is Deeply Imprinted in the HIV Genome. Front Immunol 2019; 9:3032. [PMID: 30687306 PMCID: PMC6338068 DOI: 10.3389/fimmu.2018.03032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022] Open
Abstract
APOBEC3G (A3G) is a host enzyme that mutates the genomes of retroviruses like HIV. Since A3G is expressed pre-infection, it has classically been considered an agent of innate immunity. We and others previously showed that the impact of A3G-induced mutations on the HIV genome extends to adaptive immunity also, by generating cytotoxic T cell (CTL) escape mutations. Accordingly, HIV genomic sequences encoding CTL epitopes often contain A3G-mutable “hotspot” sequence motifs, presumably to channel A3G action toward CTL escape. Here, we studied the depths and consequences of this apparent viral genome co-evolution with A3G. We identified all potential CTL epitopes in Gag, Pol, Env, and Nef restricted to several HLA class I alleles. We simulated A3G-induced mutations within CTL epitope-encoding sequences, and flanking regions. From the immune recognition perspective, we analyzed how A3G-driven mutations are predicted to impact CTL-epitope generation through modulating proteasomal processing and HLA class I binding. We found that A3G mutations were most often predicted to result in diminishing/abolishing HLA-binding affinity of peptide epitopes. From the viral genome evolution perspective, we evaluated enrichment of A3G hotspots at sequences encoding CTL epitopes and included control sequences in which the HIV genome was randomly shuffled. We found that sequences encoding immunogenic epitopes exhibited a selective enrichment of A3G hotspots, which were strongly biased to translate to non-synonymous amino acid substitutions. When superimposed on the known mutational gradient across the entire length of the HIV genome, we observed a gradient of A3G hotspot enrichment, and an HLA-specific pattern of the potential of A3G hotspots to lead to CTL escape mutations. These data illuminate the depths and extent of the co-evolution of the viral genome to subvert the host mutator A3G.
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Affiliation(s)
- Faezeh Borzooee
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Krista D Joris
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Michael D Grant
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
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18
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Martinez T, Shapiro M, Bhaduri-McIntosh S, MacCarthy T. Evolutionary effects of the AID/APOBEC family of mutagenic enzymes on human gamma-herpesviruses. Virus Evol 2019; 5:vey040. [PMID: 30792902 PMCID: PMC6371749 DOI: 10.1093/ve/vey040] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The human gamma-herpesviruses, Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, establish lifelong latency in B cells and are associated with multiple malignancies. Virus-host coevolution often drive changes in both host immunity and in the viral genome. We consider one host immune mechanism, the activation-induced deaminase (AID)/APOBEC family of cytidine deaminases, that induces mutations in viral DNA. AID, the ancestral gene in the family has a conserved role in somatic hypermutation, a key step in antibody affinity maturation. The APOBEC3 subfamily, of which there are seven genes in human, have evolved antiviral functions and have diversified in terms of their expression pattern, subcellular localization, and DNA mutation motifs (hotspots). In this study, we investigated how the human gamma-herpesviruses have evolved to avoid the action of the AID/APOBEC enzymes and determine if these enzymes are contributing to the ongoing evolution of the viruses. We used computational methods to evaluate observed versus expected frequency of AID/APOBEC hotspots in viral genomes and found that the viruses have evolved to limit the representation of AID and certain APOBEC3 motifs. At the same time, the remaining hotspots were highly likely to cause amino acid changes, suggesting prolonged evolutionary pressure of the enzymes on the viruses. To study current hypermutation, as opposed to historical mutation processes, we also analyzed putative mutations derived from alignments of published viral genomes and found again that AID and APOBEC3 appear to target the genome most frequently. New protein variants resulting from AID/APOBEC activity may have important consequences in health, including vaccine development (epitope evolution) and host immune evasion.
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Affiliation(s)
- Teresa Martinez
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
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19
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Colomer-Lluch M, Ruiz A, Moris A, Prado JG. Restriction Factors: From Intrinsic Viral Restriction to Shaping Cellular Immunity Against HIV-1. Front Immunol 2018; 9:2876. [PMID: 30574147 PMCID: PMC6291751 DOI: 10.3389/fimmu.2018.02876] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/22/2018] [Indexed: 01/20/2023] Open
Abstract
Antiviral restriction factors are host cellular proteins that constitute a first line of defense blocking viral replication and propagation. In addition to interfering at critical steps of the viral replication cycle, some restriction factors also act as innate sensors triggering innate responses against infections. Accumulating evidence suggests an additional role for restriction factors in promoting antiviral cellular immunity to combat viruses. Here, we review the recent progress in our understanding on how restriction factors, particularly APOBEC3G, SAMHD1, Tetherin, and TRIM5α have the cell-autonomous potential to induce cellular resistance against HIV-1 while promoting antiviral innate and adaptive immune responses. Also, we provide an overview of how these restriction factors may connect with protein degradation pathways to modulate anti-HIV-1 cellular immune responses, and we summarize the potential of restriction factors-based therapeutics. This review brings a global perspective on the influence of restrictions factors in intrinsic, innate, and also adaptive antiviral immunity opening up novel research avenues for therapeutic strategies in the fields of drug discovery, gene therapy, and vaccines to control viral infections.
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Affiliation(s)
- Marta Colomer-Lluch
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Alba Ruiz
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Arnaud Moris
- Sorbonne Université, INSERM U1135, CNRS ERL 8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Julia G Prado
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute, Universitat Autonoma de Barcelona, Badalona, Spain
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20
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Mohammadzadeh N, Follack TB, Love RP, Stewart K, Sanche S, Chelico L. Polymorphisms of the cytidine deaminase APOBEC3F have different HIV-1 restriction efficiencies. Virology 2018; 527:21-31. [PMID: 30448640 DOI: 10.1016/j.virol.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/03/2018] [Accepted: 11/04/2018] [Indexed: 12/27/2022]
Abstract
The APOBEC3 enzyme family are host restriction factors that induce mutagenesis of HIV-1 proviral genomes through the deamination of cytosine to form uracil in nascent single-stranded (-)DNA. HIV-1 suppresses APOBEC3 activity through the HIV-1 protein Vif that induces APOBEC3 degradation. Here we compared two common polymorphisms of APOBEC3F. We found that although both polymorphisms have HIV-1 restriction activity, APOBEC3F 108 A/231V can restrict HIV-1 ΔVif up to 4-fold more than APOBEC3F 108 S/231I and is partially protected from Vif-mediated degradation. This resulted from higher levels of steady state expression of APOBEC3F 108 A/231 V. Individuals are commonly heterozygous for the APOBEC3F polymorphisms and these polymorphisms formed in cells, independent of RNA, hetero-oligomers between each other and with APOBEC3G. Hetero-oligomerization with APOBEC3F 108 A/231V resulted in partial stabilization of APOBEC3F 108 S/231I and APOBEC3G in the presence of Vif. These data demonstrate functional outcomes of APOBEC3 polymorphisms and hetero-oligomerization that affect HIV-1 restriction.
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Affiliation(s)
- Nazanin Mohammadzadeh
- University of Saskatchewan, Biochemistry, Microbiology, and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada
| | - Tyson B Follack
- University of Saskatchewan, Biochemistry, Microbiology, and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada
| | - Robin P Love
- University of Saskatchewan, Biochemistry, Microbiology, and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada
| | - Kris Stewart
- University of Saskatchewan, Department of Medicine, College of Medicine, Saskatoon, Saskatchewan Canada; Saskatchewan Infectious Disease Care Network, Saskatoon, Saskatchewan, Canada; Saskatchewan HIV/AIDS Research Endeavour, Saskatoon, Saskatchewan, Canada
| | - Stephen Sanche
- University of Saskatchewan, Department of Medicine, College of Medicine, Saskatoon, Saskatchewan Canada; Saskatchewan HIV/AIDS Research Endeavour, Saskatoon, Saskatchewan, Canada
| | - Linda Chelico
- University of Saskatchewan, Biochemistry, Microbiology, and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada; Saskatchewan HIV/AIDS Research Endeavour, Saskatoon, Saskatchewan, Canada.
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21
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RNA-Mediated Dimerization of the Human Deoxycytidine Deaminase APOBEC3H Influences Enzyme Activity and Interaction with Nucleic Acids. J Mol Biol 2018; 430:4891-4907. [PMID: 30414963 DOI: 10.1016/j.jmb.2018.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/04/2018] [Accepted: 11/04/2018] [Indexed: 12/11/2022]
Abstract
Human APOBEC3H is a single-stranded (ss)DNA deoxycytidine deaminase that inhibits replication of retroelements and HIV-1 in CD4+ T cells. When aberrantly expressed in lung or breast tissue, APOBEC3H can contribute to cancer mutagenesis. These different activities are carried out by different haplotypes of APOBEC3H. Here we studied APOBEC3H haplotype II, which is able to restrict HIV-1 replication and retroelements. We determined how the dimerization mechanism, which is mediated by a double-stranded RNA molecule, influenced interactions with and activity on ssDNA. The data demonstrate that the cellular RNA bound by APOBEC3H does not completely inhibit enzyme activity, in contrast to other APOBEC family members. Despite degradation of the cellular RNA, an approximately 12-nt RNA remains bound to the enzyme, even in the presence of ssDNA. The RNA-mediated dimer is disrupted by mutating W115 on loop 7 or R175 and R176 on helix 6, but this also disrupts protein stability. In contrast, mutation of Y112 and Y113 on loop 7 also destabilizes RNA-mediated dimerization but results in a stable enzyme. Mutants unable to bind cellular RNA are unable to bind RNA oligonucleotides, oligomerize, and deaminate ssDNA in vitro, but ssDNA binding is retained. Comparison of A3H wild type and Y112A/Y113A by fluorescence polarization, single-molecule optical tweezer, and atomic force microscopy experiments demonstrates that RNA-mediated dimerization alters the interactions of A3H with ssDNA and other RNA molecules. Altogether, the biochemical analysis demonstrates that RNA binding is integral to APOBEC3H function.
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22
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Temerozo JR, de Azevedo SSD, Insuela DBR, Vieira RC, Ferreira PLC, Carvalho VF, Bello G, Bou-Habib DC. The Neuropeptides Vasoactive Intestinal Peptide and Pituitary Adenylate Cyclase-Activating Polypeptide Control HIV-1 Infection in Macrophages Through Activation of Protein Kinases A and C. Front Immunol 2018; 9:1336. [PMID: 29951068 PMCID: PMC6008521 DOI: 10.3389/fimmu.2018.01336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
Vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) are highly similar neuropeptides present in several tissues, endowed with immunoregulatory functions and other systemic effects. We previously reported that both neuropeptides reduce viral production in HIV-1-infected primary macrophages, with the participation of β-chemokines and IL-10, and now we describe molecular mechanisms engaged in this activity. Macrophages exposed to VIP or PACAP before HIV-1 infection showed resistance to viral replication, comparable to that observed when the cells were treated after infection. Also, multiple treatments with a suboptimal dose of VIP or PACAP after macrophage infection resulted in a decline of virus production similar to the inhibition promoted by a single exposure to the optimal inhibitory concentration. Cellular signaling pathways involving cAMP production and activation of protein kinases A and C were critical components of the VIP and PACAP anti-HIV-1 effects. Analysis of the transcription factors and the transcriptional/cell cycle regulators showed that VIP and PACAP induced cAMP response element-binding protein activation, inhibited NF-kB, and reduced Cyclin D1 levels in HIV-1-infected cells. Remarkably, VIP and PACAP promoted G-to-A mutations in the HIV-1 provirus, matching those derived from the activity of the APOBEC family of viral restriction factors, and reduced viral infectivity. In conclusion, our findings strengthen the antiretroviral potential of VIP and PACAP and point to new therapeutic approaches to control the progression of HIV-1 infection.
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Affiliation(s)
- Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Suwellen S D de Azevedo
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Daniella B R Insuela
- Laboratory of Inflammation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Rhaíssa C Vieira
- Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Pedro L C Ferreira
- Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Vinícius F Carvalho
- National Institute of Science and Technology on Neuroimmunomodulation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil.,Laboratory of Inflammation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
| | - Dumith Chequer Bou-Habib
- Laboratory on Thymus Research, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro, Brazil
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Borzooee F, Asgharpour M, Quinlan E, Grant MD, Larijani M. Viral subversion of APOBEC3s: Lessons for anti-tumor immunity and tumor immunotherapy. Int Rev Immunol 2018; 37:151-164. [PMID: 29211501 DOI: 10.1080/08830185.2017.1403596] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
APOBEC3s (A3) are endogenous DNA-editing enzymes that are expressed in immune cells including T lymphocytes. A3s target and mutate the genomes of retroviruses that infect immune tissues such as the human immunodeficiency virus (HIV). Therefore, A3s were classically defined as host anti-viral innate immune factors. In contrast, we and others showed that A3s can also benefit the virus by mediating escape from adaptive immune recognition and drugs. Crucially, whether A3-mediated mutations help or hinder HIV, is not up to chance. Rather, the virus has evolved multiple mechanisms to actively and maximally subvert A3 activity. More recently, extensive A3 mutational footprints in tumor genomes have been observed in many different cancers. This suggests a role for A3s in cancer initiation and progression. On the other hand, multiple anti-tumor activities of A3s have also come to light, including impact on immune checkpoint molecules and possible generation of tumor neo-antigens. Here, we review the studies that reshaped the view of A3s from anti-viral innate immune agents to host factors exploited by HIV to escape from immune recognition. Viruses and tumors share many attributes, including rapid evolution and adeptness at exploiting mutations. Given this parallel, we then discuss the pro- and anti-tumor roles of A3s, and suggest that lessons learned from studying A3s in the context of anti-viral immunity can be applied to tumor immunotherapy.
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Affiliation(s)
- Faezeh Borzooee
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mahdi Asgharpour
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Emma Quinlan
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Michael D Grant
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mani Larijani
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
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24
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Adolph MB, Love RP, Chelico L. Biochemical Basis of APOBEC3 Deoxycytidine Deaminase Activity on Diverse DNA Substrates. ACS Infect Dis 2018; 4:224-238. [PMID: 29347817 DOI: 10.1021/acsinfecdis.7b00221] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Apolipoprotein B mRNA editing complex (APOBEC) family of enzymes contains single-stranded polynucleotide cytidine deaminases. These enzymes catalyze the deamination of cytidine in RNA or single-stranded DNA, which forms uracil. From this 11 member enzyme family in humans, the deamination of single-stranded DNA by the seven APOBEC3 family members is considered here. The APOBEC3 family has many roles, such as restricting endogenous and exogenous retrovirus replication and retrotransposon insertion events and reducing DNA-induced inflammation. Similar to other APOBEC family members, the APOBEC3 enzymes are a double-edged sword that can catalyze deamination of cytosine in genomic DNA, which results in potential genomic instability due to the many mutagenic fates of uracil in DNA. Here, we discuss how these enzymes find their single-stranded DNA substrate in different biological contexts such as during human immunodeficiency virus (HIV) proviral DNA synthesis, retrotransposition of the LINE-1 element, and the "off-target" genomic DNA substrate. The enzymes must be able to efficiently deaminate transiently available single-stranded DNA during reverse transcription, replication, or transcription. Specific biochemical characteristics promote deamination in each situation to increase enzyme efficiency through processivity, rapid enzyme cycling between substrates, or oligomerization state. The use of biochemical data to clarify biological functions and alignment with cellular data is discussed. Models to bridge knowledge from biochemical, structural, and single molecule experiments are presented.
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Affiliation(s)
- Madison B Adolph
- Department of Microbiology and Immunology, College of Medicine , University of Saskatchewan , 107 Wiggins Road , Saskatoon , Saskatchewan S7N 5E5 , Canada
| | - Robin P Love
- Department of Microbiology and Immunology, College of Medicine , University of Saskatchewan , 107 Wiggins Road , Saskatoon , Saskatchewan S7N 5E5 , Canada
| | - Linda Chelico
- Department of Microbiology and Immunology, College of Medicine , University of Saskatchewan , 107 Wiggins Road , Saskatoon , Saskatchewan S7N 5E5 , Canada
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25
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Venkatesan S, Rosenthal R, Kanu N, McGranahan N, Bartek J, Quezada SA, Hare J, Harris RS, Swanton C. Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution. Ann Oncol 2018; 29:563-572. [PMID: 29324969 PMCID: PMC5888943 DOI: 10.1093/annonc/mdy003] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) mutational signature has only recently been detected in a multitude of cancers through next-generation sequencing. In contrast, APOBEC has been a focus of virology research for over a decade. Many lessons learnt regarding APOBEC within virology are likely to be applicable to cancer. In this review, we explore the parallels between the role of APOBEC enzymes in HIV and cancer evolution. We discuss data supporting the role of APOBEC mutagenesis in creating HIV genome heterogeneity, drug resistance, and immune escape variants. We hypothesize similar functions of APOBEC will also hold true in cancer.
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Affiliation(s)
- S Venkatesan
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK; Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - R Rosenthal
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - N Kanu
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - N McGranahan
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - J Bartek
- Danish Cancer Society Research Center, Copenhagen, Denmark, UK; Science for Life Laboratory, Stockholm, Sweden; Division of Genome Biology, Department of Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - S A Quezada
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK; Cancer Immunology Unit, UCL Cancer Institute, London, UK
| | - J Hare
- International AIDS Vaccine Initiative (IAVI), New York, USA
| | - R S Harris
- Masonic Cancer Center, Minneapolis, USA; Institute for Molecular Virology, Minneapolis, USA; Center for Genome Engineering, Minneapolis, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, USA.
| | - C Swanton
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK; Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK.
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26
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Grant M, Larijani M. Evasion of adaptive immunity by HIV through the action of host APOBEC3G/F enzymes. AIDS Res Ther 2017; 14:44. [PMID: 28893290 PMCID: PMC5594601 DOI: 10.1186/s12981-017-0173-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/11/2017] [Indexed: 01/11/2023] Open
Abstract
APOBEC3G (A3G) and APOBEC3F (A3F) are DNA-mutating enzymes expressed in T cells, dendritic cells and macrophages. A3G/F have been considered innate immune host factors, based on reports that they lethally mutate the HIV genome in vitro. In vivo, A3G/F effectiveness is limited by viral proteins, entrapment in inactive complexes and filtration of mutations during viral life cycle. We hypothesized that the impact of sub-lethal A3G/F action could extend beyond the realm of innate immunity confined to the cytoplasm of infected cells. We measured recognition of wild type and A3G/F-mutated epitopes by cytotoxic T lymphocytes (CTL) from HIV-infected individuals and found that A3G/F-induced mutations overwhelmingly diminished CTL recognition of HIV peptides, in a human histocompatibility-linked leukocyte antigen (HLA)-dependent manner. Furthermore, we found corresponding enrichment of A3G/F-favored motifs in CTL epitope-encoding sequences within the HIV genome. These findings illustrate that A3G/F‐mediated mutations mediate immune evasion by HIV in vivo. Therefore, we suggest that vaccine strategies target T cell or antibody epitopes that are not poised for mutation into escape variants by A3G/F action.
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27
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Chen J, MacCarthy T. The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes. PLoS Comput Biol 2017; 13:e1005471. [PMID: 28362825 PMCID: PMC5391955 DOI: 10.1371/journal.pcbi.1005471] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 04/14/2017] [Accepted: 03/21/2017] [Indexed: 12/22/2022] Open
Abstract
The AID / APOBEC genes are a family of cytidine deaminases that have evolved in vertebrates, and particularly mammals, to mutate RNA and DNA at distinct preferred nucleotide contexts (or “hotspots”) on foreign genomes such as viruses and retrotransposons. These enzymes play a pivotal role in intrinsic immunity defense mechanisms, often deleteriously mutating invading retroviruses or retrotransposons and, in the case of AID, changing antibody sequences to drive affinity maturation. We investigate the strength of various hotspots on their known biological targets by evaluating the potential impact of mutations on the DNA coding sequences of these targets, and compare these results to hypothetical hotspots that did not evolve. We find that the existing AID / APOBEC hotspots have a large impact on retrotransposons and non-mammalian viruses while having a much smaller effect on vital mammalian genes, suggesting co-evolution with AID / APOBECs may have had an impact on the genomes of the viruses we analyzed. We determine that GC content appears to be a significant, but not sole, factor in resistance to deaminase activity. We discuss possible mechanisms AID and APOBEC viral targets have adopted to escape the impacts of deamination activity, including changing the GC content of the genome. The APOBEC family of cytidine deaminases are important enzymes in most vertebrates. The ancestral member of this gene family is activation induced deaminase (AID), which mutates the Immunoglobulin loci in B Cells during antibody affinity maturation in jawed vertebrates. The APOBEC family has expanded particularly in the mammals and in primates, where they have evolved roles in restriction of viruses and retrotransposons. Biochemical studies have established that AID preferentially targets “hotspots” such as AGC and avoids “coldspots” such as CCC. Other APOBECs have evolved distinct hotspots. For example, APOBEC3G, which targets retroviruses including HIV, has evolved to target the motif CCC as a hotspot, but it is unclear why. Here we ask why the AID/APOBEC cytidine deaminases evolved their particular mutational hotspots. Our results show that a wide range of unrelated genes including mammalian LINE1 ORFs and non- mammalian (ancestral-like) viruses are highly susceptible to mutations in APOBEC hotspots and less susceptible to the hypothetical non-APOBEC hotspots. On the other hand, mammalian viruses tend to exhibit low susceptibility to the same APOBEC hotspots, suggesting these viruses have co-evolved to minimize potential damaging mutations, and that the native GC content plays a large role in this behavior.
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Affiliation(s)
- Jeffrey Chen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Book, New York, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Book, New York, United States of America
- * E-mail:
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28
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McGranahan N, Swanton C. Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future. Cell 2017; 168:613-628. [PMID: 28187284 DOI: 10.1016/j.cell.2017.01.018] [Citation(s) in RCA: 1632] [Impact Index Per Article: 233.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/03/2017] [Accepted: 01/18/2017] [Indexed: 12/12/2022]
Abstract
Intratumor heterogeneity, which fosters tumor evolution, is a key challenge in cancer medicine. Here, we review data and technologies that have revealed intra-tumor heterogeneity across cancer types and the dynamics, constraints, and contingencies inherent to tumor evolution. We emphasize the importance of macro-evolutionary leaps, often involving large-scale chromosomal alterations, in driving tumor evolution and metastasis and consider the role of the tumor microenvironment in engendering heterogeneity and drug resistance. We suggest that bold approaches to drug development, harnessing the adaptive properties of the immune-microenvironment while limiting those of the tumor, combined with advances in clinical trial-design, will improve patient outcome.
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Affiliation(s)
- Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK; Department of Medical Oncology, University College London Hospitals, 235 Euston Rd, Fitzrovia, London NW1 2BU, UK.
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29
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Sanjuán R, Domingo-Calap P. Mechanisms of viral mutation. Cell Mol Life Sci 2016; 73:4433-4448. [PMID: 27392606 PMCID: PMC5075021 DOI: 10.1007/s00018-016-2299-6] [Citation(s) in RCA: 488] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 02/08/2023]
Abstract
The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be introduced by some virus-encoded diversity-generating elements, as well as by host-encoded cytidine/adenine deaminases. Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures.
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Affiliation(s)
- Rafael Sanjuán
- Department of Genetics and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, C/Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain.
| | - Pilar Domingo-Calap
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
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30
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Chen Q, Xiao X, Wolfe A, Chen XS. The in vitro Biochemical Characterization of an HIV-1 Restriction Factor APOBEC3F: Importance of Loop 7 on Both CD1 and CD2 for DNA Binding and Deamination. J Mol Biol 2016; 428:2661-70. [PMID: 27063502 DOI: 10.1016/j.jmb.2016.03.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/27/2016] [Accepted: 03/28/2016] [Indexed: 10/22/2022]
Abstract
APOBEC3F (A3F) is a member of the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) family of proteins that can deaminate cytosine (C) to uracil (U) on nucleic acids. A3F is one of the four APOBEC members with two Zn-coordinated homologous cytosine deaminase (CD) domains, with the others being A3G, A3D, and A3B. Here we report the in vitro characterization of DNA binding and deaminase activities using purified wild-type and various mutant proteins of A3F from an Escherichia coli expression system. We show that even though CD1 is catalytically inactive and CD2 is the active deaminase domain, presence of CD1 on the N-terminus of CD2 enhances the deaminase activity by over an order of magnitude. This enhancement of CD2 catalytic activity is mainly through the increase of substrate single-stranded (ss) DNA binding by the N-terminal CD1 domain. We further show that the loop 7 of both CD1 and CD2 of A3F plays an important role for ssDNA binding for each individual domain, as well as for the deaminase activity of CD2 domain in the full-length A3F.
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Affiliation(s)
- Qihan Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiao Xiao
- Genetic, Molecular and Cellular Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron Wolfe
- Genetic, Molecular and Cellular Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center; University of Southern California, Los Angeles, CA 90089, USA.
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31
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Impact of APOBEC Mutations on CD8+ T Cell Recognition of HIV Epitopes Varies Depending on the Restricting HLA. J Acquir Immune Defic Syndr 2015; 70:172-8. [PMID: 26035050 DOI: 10.1097/qai.0000000000000689] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We previously showed that APOBEC-mediated mutations in HIV CD8 T-cell epitopes generally reduce recognition by CD8 T cells. Here, we examined this effect in the context of histocompatibility-linked leukocyte antigen (HLA) alleles differentially associated with disease progression rates. For HLA-B57-restricted epitopes, APOBEC mutations generally diminished CD8 T cell recognition. Conversely, recognition of HLA-B35-restricted epitopes was consistently enhanced. For epitopes that can be presented by either HLA-A2 or A3, the same APOBEC mutation had differential effects on CD8 T cell recognition, depending on the individual's HLA genotype. The pattern of HLA dependence provides additional evidence that APOBEC action is channeled toward cytotoxic CD8 T-cell escape.
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32
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Stavrou S, Ross SR. APOBEC3 Proteins in Viral Immunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 195:4565-70. [PMID: 26546688 PMCID: PMC4638160 DOI: 10.4049/jimmunol.1501504] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Apolipoprotein B editing complex 3 family members are cytidine deaminases that play important roles in intrinsic responses to infection by retroviruses and have been implicated in the control of other viruses, such as parvoviruses, herpesviruses, papillomaviruses, hepatitis B virus, and retrotransposons. Although their direct effect on modification of viral DNA has been clearly demonstrated, whether they play additional roles in innate and adaptive immunity to viruses is less clear. We review the data regarding the various steps in the innate and adaptive immune response to virus infection in which apolipoprotein B editing complex 3 proteins have been implicated.
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Affiliation(s)
- Spyridon Stavrou
- Department of Microbiology, Abramson Cancer Center, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6142
| | - Susan R Ross
- Department of Microbiology, Abramson Cancer Center, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6142
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33
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The external domains of the HIV-1 envelope are a mutational cold spot. Nat Commun 2015; 6:8571. [PMID: 26450412 PMCID: PMC4687473 DOI: 10.1038/ncomms9571] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/07/2015] [Indexed: 01/27/2023] Open
Abstract
In RNA viruses, mutations occur fast and have large fitness effects. While this affords remarkable adaptability, it can also endanger viral survival due to the accumulation of deleterious mutations. How RNA viruses reconcile these two opposed facets of mutation is still unknown. Here we show that, in human immunodeficiency virus (HIV-1), spontaneous mutations are not randomly located along the viral genome. We find that the viral mutation rate experiences a threefold reduction in the region encoding the most external domains of the viral envelope, which are strongly targeted by neutralizing antibodies. This contrasts with the hypermutation mechanisms deployed by other, more slowly mutating pathogens such as DNA viruses and bacteria, in response to immune pressure. We show that downregulation of the mutation rate in HIV-1 is exerted by the template RNA through changes in sequence context and secondary structure, which control the activity of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (A3)-mediated cytidine deamination and the fidelity of the viral reverse transcriptase. Mutations allow RNA virus to adapt fast but also entail fitness costs. Geller et al. show that, in HIV-1, mutations occur three times less often in the most external domains of the envelope, and that this is due to changes in RNA sequence context and structure, which control viral and host-encoded mutational mechanisms.
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Cuevas JM, Geller R, Garijo R, López-Aldeguer J, Sanjuán R. Extremely High Mutation Rate of HIV-1 In Vivo. PLoS Biol 2015; 13:e1002251. [PMID: 26375597 PMCID: PMC4574155 DOI: 10.1371/journal.pbio.1002251] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
Rates of spontaneous mutation critically determine the genetic diversity and evolution of RNA viruses. Although these rates have been characterized in vitro and in cell culture models, they have seldom been determined in vivo for human viruses. Here, we use the intrapatient frequency of premature stop codons to quantify the HIV-1 genome-wide rate of spontaneous mutation in DNA sequences from peripheral blood mononuclear cells. This reveals an extremely high mutation rate of (4.1 ± 1.7) × 10−3 per base per cell, the highest reported for any biological entity. Sequencing of plasma-derived sequences yielded a mutation frequency 44 times lower, indicating that a large fraction of viral genomes are lethally mutated and fail to reach plasma. We show that the HIV-1 reverse transcriptase contributes only 2% of mutations, whereas 98% result from editing by host cytidine deaminases of the A3 family. Hypermutated viral sequences are less abundant in patients showing rapid disease progression compared to normal progressors, highlighting the antiviral role of A3 proteins. However, the amount of A3-mediated editing varies broadly, and we find that low-edited sequences are more abundant among rapid progressors, suggesting that suboptimal A3 activity might enhance HIV-1 genetic diversity and pathogenesis. The rate of spontaneous mutation of the HIV-1 genome within its human host is exceptionally high, is mostly driven by host cytidine deaminases, and probably plays a role in disease progression. The high levels of genetic diversity of the HIV-1 virus grant it the ability to escape the immune system, to rapidly evolve drug resistance, and to circumvent vaccination strategies. However, our knowledge of HIV-1 mutation rates has been largely restricted to in vitro and cell culture studies because of the inherent complexity of measuring these rates in vivo. Here, by analyzing the frequency of premature stop codons, we show that the HIV-1 mutation rate in vivo is two orders of magnitude higher than that predicted by in vitro studies, making it the highest reported mutation rate for any biological system. A large component of this rate is from host cellular cytidine deaminases, which induce mutations in the viral DNA as a defense mechanism. While the HIV-1 genome is hypermutated in blood cells, only a very small fraction of these mutations reach the plasma, indicating that many viruses are defective as a result of the extremely high mutation load. In addition, we find that the HIV-1 mutation rate tends to be higher in patients showing normal disease progression than in those undergoing rapid progression, emphasizing the negative impact on viral fitness of hypermutation by host cytidine deaminases. However, we also observe subpopulations of weakly-mutated viral genomes whose sequence diversity may influence viral pathogenesis. Our work highlights the fine balance for HIV-1 between enough mutation to evade host responses and too much mutation that can inactivate the virus.
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Affiliation(s)
- José M. Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - Ron Geller
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - José López-Aldeguer
- Hospital Universitario La Fe, Valencia, Spain
- CoRIS and HIV Biobank, Spanish AIDS Research Network, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
- * E-mail:
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35
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Bélanger K, Langlois MA. Comparative analysis of the gene-inactivating potential of retroviral restriction factors APOBEC3F and APOBEC3G. J Gen Virol 2015; 96:2878-2887. [PMID: 26048885 DOI: 10.1099/vir.0.000214] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
APOBEC3 (A3) proteins are host-encoded restriction factors that inhibit retrovirus infection by mutagenic deamination of cytosines in minus-strand DNA replication intermediates. APOBEC3F (A3F) and APOBEC3G (A3G) are two of the most potent A3 enzymes in humans with each having a different target DNA specificity. A3G prefers to deaminate cytosines preceded by a cytosine (5'-CC), whereas A3F preferentially targets cytosines preceded by a thymine (5'-TC). Here we performed a detailed comparative analysis of retrovirus-encoded gene sequences edited by A3F and A3G, with the aim of correlating the context and intensity of the mutations with their effects on gene function. Our results revealed that, when there are few (TGG) tryptophan codons in the sequence, both enzymes alter gene function with a similar efficiency when given equal opportunities to deaminate in their preferred target DNA context. In contrast, tryptophan-rich genes are efficiently inactivated in the presence of a low mutational burden, through termination codon generation by A3G but not A3F. Overall, our results clearly demonstrated that the target DNA specificity of an A3 enzyme along with the intensity of the mutational burden and the tryptophan content of the gene being targeted are the factors that have the most forceful influence on whether A3-induced mutations will favour either terminal inactivation or genetic diversification of a retrovirus.
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Affiliation(s)
- Kasandra Bélanger
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Moris A, Murray S, Cardinaud S. AID and APOBECs span the gap between innate and adaptive immunity. Front Microbiol 2014; 5:534. [PMID: 25352838 PMCID: PMC4195361 DOI: 10.3389/fmicb.2014.00534] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/24/2014] [Indexed: 12/17/2022] Open
Abstract
The activation-induced deaminase (AID)/APOBEC cytidine deaminases participate in a diversity of biological processes from the regulation of protein expression to embryonic development and host defenses. In its classical role, AID mutates germline-encoded sequences of B cell receptors, a key aspect of adaptive immunity, and APOBEC1, mutates apoprotein B pre-mRNA, yielding two isoforms important for cellular function and plasma lipid metabolism. Investigations over the last ten years have uncovered a role of the APOBEC superfamily in intrinsic immunity against viruses and innate immunity against viral infection by deamination and mutation of viral genomes. Further, discovery in the area of human immunodeficiency virus (HIV) infection revealed that the HIV viral infectivity factor protein interacts with APOBEC3G, targeting it for proteosomal degradation, overriding its antiviral function. More recently, our and others' work have uncovered that the AID and APOBEC cytidine deaminase family members have an even more direct link between activity against viral infection and induction and shaping of adaptive immunity than previously thought, including that of antigen processing for cytotoxic T lymphocyte activity and natural killer cell activation. Newly ascribed functions of these cytodine deaminases will be discussed, including their newly identified roles in adaptive immunity, epigenetic regulation, and cell differentiation. Herein this review we discuss AID and APOBEC cytodine deaminases as a link between innate and adaptive immunity uncovered by recent studies.
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Affiliation(s)
- Arnaud Moris
- Center for Immunology and Microbial Infections, Faculty of Medicine, Université Paris-Sorbonne UPMC Univ Paris 06, Paris, France ; Center for Immunology and Microbial Infections, Institut National de la Santé et de la Recherche Médicale U1135, Paris, France ; Center for Immunology and Microbial Infections, Centre National de la Recherche Scientifique ERL 8255, Paris, France ; Department of Immunology, Hôpital Pitié-Salpêtière Paris, France
| | - Shannon Murray
- Center for Immunology and Microbial Infections, Faculty of Medicine, Université Paris-Sorbonne UPMC Univ Paris 06, Paris, France ; Center for Immunology and Microbial Infections, Institut National de la Santé et de la Recherche Médicale U1135, Paris, France ; Center for Immunology and Microbial Infections, Centre National de la Recherche Scientifique ERL 8255, Paris, France
| | - Sylvain Cardinaud
- Center for Immunology and Microbial Infections, Faculty of Medicine, Université Paris-Sorbonne UPMC Univ Paris 06, Paris, France ; Center for Immunology and Microbial Infections, Institut National de la Santé et de la Recherche Médicale U1135, Paris, France ; Center for Immunology and Microbial Infections, Centre National de la Recherche Scientifique ERL 8255, Paris, France
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Feng Y, Baig TT, Love RP, Chelico L. Suppression of APOBEC3-mediated restriction of HIV-1 by Vif. Front Microbiol 2014; 5:450. [PMID: 25206352 PMCID: PMC4144255 DOI: 10.3389/fmicb.2014.00450] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/06/2014] [Indexed: 12/21/2022] Open
Abstract
The APOBEC3 restriction factors are a family of deoxycytidine deaminases that are able to suppress replication of viruses with a single-stranded DNA intermediate by inducing mutagenesis and functional inactivation of the virus. Of the seven human APOBEC3 enzymes, only APOBEC3-D, -F, -G, and -H appear relevant to restriction of HIV-1 in CD4+ T cells and will be the focus of this review. The restriction of HIV-1 occurs most potently in the absence of HIV-1 Vif that induces polyubiquitination and degradation of APOBEC3 enzymes through the proteasome pathway. To restrict HIV-1, APOBEC3 enzymes must be encapsidated into budding virions. Upon infection of the target cell during reverse transcription of the HIV-1 RNA into (-)DNA, APOBEC3 enzymes deaminate cytosines to form uracils in single-stranded (-)DNA regions. Upon replication of the (-)DNA to (+)DNA, the HIV-1 reverse transcriptase incorporates adenines opposite to the uracils thereby inducing C/G to T/A mutations that can functionally inactivate HIV-1. APOBEC3G is the most studied APOBEC3 enzyme and it is known that Vif attempts to thwart APOBEC3 function not only by inducing its proteasomal degradation but also by several degradation-independent mechanisms, such as inhibiting APOBEC3G virion encapsidation, mRNA translation, and for those APOBEC3G molecules that still become virion encapsidated, Vif can inhibit APOBEC3G mutagenic activity. Although most Vif variants can induce efficient degradation of APOBEC3-D, -F, and -G, there appears to be differential sensitivity to Vif-mediated degradation for APOBEC3H. This review examines APOBEC3-mediated HIV restriction mechanisms, how Vif acts as a substrate receptor for a Cullin5 ubiquitin ligase complex to induce degradation of APOBEC3s, and the determinants and functional consequences of the APOBEC3 and Vif interaction from a biological and biochemical perspective.
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Affiliation(s)
- Yuqing Feng
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan Saskatoon, SK, Canada
| | - Tayyba T Baig
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan Saskatoon, SK, Canada
| | - Robin P Love
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan Saskatoon, SK, Canada
| | - Linda Chelico
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan Saskatoon, SK, Canada
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