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Delviks-Frankenberry KA, Ojha CR, Hermann KJ, Hu WS, Torbett BE, Pathak VK. Potent dual block to HIV-1 infection using lentiviral vectors expressing fusion inhibitor peptide mC46- and Vif-resistant APOBEC3G. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:794-809. [PMID: 37662965 PMCID: PMC10470399 DOI: 10.1016/j.omtn.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023]
Abstract
Gene therapy strategies that effectively inhibit HIV-1 replication are needed to reduce the requirement for lifelong antiviral therapy and potentially achieve a functional cure. We previously designed self-activating lentiviral vectors that efficiently delivered and expressed a Vif-resistant mutant of APOBEC3G (A3G-D128K) to T cells, which potently inhibited HIV-1 replication and spread with no detectable virus. Here, we developed vectors that express A3G-D128K, membrane-associated fusion inhibitor peptide mC46, and O6-methylguanine-DNA-methyltransferase (MGMT) selectable marker for in vivo selection of transduced CD34+ hematopoietic stem and progenitor cells. MGMT-selected T cell lines MT4, CEM, and PM1 expressing A3G-D128K (with or without mC46) potently inhibited NL4-3 infection up to 45 days post infection with no detectable viral replication. Expression of mC46 was sufficient to block infection >80% in a single-cycle assay. Importantly, expression of mC46 provided a selective advantage to the A3G-D128K-modified T cells in the presence of replication competent virus. This combinational approach to first block HIV-1 entry with mC46, and then block any breakthrough infection with A3G-D128K, could provide an effective gene therapy treatment and a potential functional cure for HIV-1 infection.
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Affiliation(s)
- Krista A. Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Chet R. Ojha
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Kip J. Hermann
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Bruce E. Torbett
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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2
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Yang H, Kim K, Li S, Pacheco J, Chen XS. Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G. Nat Commun 2022; 13:7498. [PMID: 36470880 PMCID: PMC9722718 DOI: 10.1038/s41467-022-35201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
An essential step in restricting HIV infectivity by the antiviral factor APOBEC3G is its incorporation into progeny virions via binding to HIV RNA. However, the mechanism of APOBEC3G capturing viral RNA is unknown. Here, we report crystal structures of a primate APOBEC3G bound to different types of RNAs, revealing that APOBEC3G specifically recognizes unpaired 5'-AA-3' dinucleotides, and to a lesser extent, 5'-GA-3' dinucleotides. APOBEC3G binds to the common 3'A in the AA/GA motifs using an aromatic/hydrophobic pocket in the non-catalytic domain. It binds to the 5'A or 5'G in the AA/GA motifs using an aromatic/hydrophobic groove conformed between the non-catalytic and catalytic domains. APOBEC3G RNA binding property is distinct from that of the HIV nucleocapsid protein recognizing unpaired guanosines. Our findings suggest that the sequence-specific RNA recognition is critical for APOBEC3G virion packaging and restricting HIV infectivity.
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Affiliation(s)
- Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Shuxing Li
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089 USA
| | - Josue Pacheco
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA
| | - Xiaojiang S. Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089 USA ,grid.42505.360000 0001 2156 6853Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, Los Angeles, CA 90033 USA ,grid.42505.360000 0001 2156 6853Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033 USA
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3
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Genomic instability genes in lung and colon adenocarcinoma indicate organ specificity of transcriptomic impact on Copy Number Alterations. Sci Rep 2022; 12:11739. [PMID: 35817785 PMCID: PMC9273645 DOI: 10.1038/s41598-022-15692-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
Genomic instability (GI) in cancer facilitates cancer evolution and is an exploitable target for therapy purposes. However, specific genes involved in cancer GI remain elusive. Causal genes for GI via expressions have not been comprehensively identified in colorectal cancers (CRCs). To fill the gap in knowledge, we developed a data mining strategy (Gene Expression to Copy Number Alterations; "GE-CNA"). Here we applied the GE-CNA approach to 592 TCGA CRC datasets, and identified 500 genes whose expression levels associate with CNA. Among these, 18 were survival-critical (i.e., expression levels correlate with significant differences in patients' survival). Comparison with previous results indicated striking differences between lung adenocarcinoma and CRC: (a) less involvement of overexpression of mitotic genes in generating genomic instability in the colon and (b) the presence of CNA-suppressing pathways, including immune-surveillance, was only partly similar to those in the lung. Following 13 genes (TIGD6, TMED6, APOBEC3D, EP400NL, B3GNT4, ZNF683, FOXD4, FOXD4L1, PKIB, DDB2, MT1G, CLCN3, CAPS) were evaluated as potential drug development targets (hazard ratio [> 1.3 or < 0.5]). Identification of specific CRC genomic instability genes enables researchers to develop GI targeting approach. The new results suggest that the "targeting genomic instability and/or aneuploidy" approach must be tailored for specific organs.
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McDaniel YZ, Wang D, Love RP, Adolph MB, Mohammadzadeh N, Chelico L, Mansky LM. Deamination hotspots among APOBEC3 family members are defined by both target site sequence context and ssDNA secondary structure. Nucleic Acids Res 2020; 48:1353-1371. [PMID: 31943071 PMCID: PMC7026630 DOI: 10.1093/nar/gkz1164] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022] Open
Abstract
The human apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3, A3) family member proteins can deaminate cytosines in single-strand (ss) DNA, which restricts human immunodeficiency virus type 1 (HIV-1), retrotransposons, and other viruses such as hepatitis B virus, but can cause a mutator phenotype in many cancers. While structural information exists for several A3 proteins, the precise details regarding deamination target selection are not fully understood. Here, we report the first parallel, comparative analysis of site selection of A3 deamination using six of the seven purified A3 member enzymes, oligonucleotides having 5'TC3' or 5'CT3' dinucleotide target sites, and different flanking bases within diverse DNA secondary structures. A3A, A3F and A3H were observed to have strong preferences toward the TC target flanked by A or T, while all examined A3 proteins did not show a preference for a TC target flanked by a G. We observed that the TC target was strongly preferred in ssDNA regions rather than dsDNA, loop or bulge regions, with flanking bases influencing the degree of preference. CT was also shown to be a potential deamination target. Taken together, our observations provide new insights into A3 enzyme target site selection and how A3 mutagenesis impacts mutation rates.
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Affiliation(s)
- Yumeng Z McDaniel
- Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
| | - Dake Wang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
- Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
| | - Robin P Love
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Madison B Adolph
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Nazanin Mohammadzadeh
- 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
| | - Louis M Mansky
- Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455 USA
- Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN 55455 USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455 USA
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN 55455 USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
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5
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Timilsina U, Ghimire D, Sharma S, Gaur R. Role of APOBEC3 proteins in proteasome inhibitor-mediated reactivation of latent HIV-1 viruses. J Gen Virol 2019; 100:523-532. [PMID: 30566069 DOI: 10.1099/jgv.0.001205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteasome inhibitors (PIs) have been identified as an emerging class of HIV-1 latency-reversing agents (LRAs). These inhibitors can reactivate latent HIV-1 to produce non-infectious viruses. The mechanism underlying reduced infectivity of reactivated viruses is unknown. In this study, we analysed PI-reactivated viruses using biochemical and virological assays and demonstrated that these PIs stabilized the cellular expression of HIV-1 restriction factor, APOBEC3G, facilitating its packaging in the released viruses. Using infectivity assay and immunoblotting, we observed that the reduction in viral infectivity was due to enhanced levels of functionally active APOBEC3 proteins packaged in the virions. Sequencing of the proviral genome in the target cells revealed the presence of APOBEC3 signature hypermutations. Our study strengthens the role of PIs as bifunctional LRAs and demonstrates that the loss of infectivity of reactivated HIV-1 virions may be due to the increased packaging of APOBEC3 proteins in the virus.
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Affiliation(s)
- Uddhav Timilsina
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi-110021, Delhi
| | - Dibya Ghimire
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi-110021, Delhi
| | - Shilpa Sharma
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi-110021, Delhi
| | - Ritu Gaur
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi-110021, Delhi
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6
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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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7
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Iqbal K, Imran M, Ullah S, Jamal M, Waheed Y, Ali Q. Correlation of Apolipoprotein B mRNA-editing Enzyme, Catalytic Polypeptide- like 3G Genetic Variant rs8177832 with HIV-1 Predisposition in Pakistani Population. Curr HIV Res 2018; 16:297-301. [PMID: 30338740 PMCID: PMC6416456 DOI: 10.2174/1570162x16666181018155827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Human immunodeficiency virus (HIV) infection is a global health burden which ultimately results in acquired immune deficiency syndrome (AIDS). There are multiple host factors which are capable of limiting HIV-1 replication. One of the most important host factors which inhibit HIV-1 DNA synthesis is the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide- like 3G (APOBEC3G). Any genetic variation of this important host factor may influence the host susceptibility to viral infection. OBJECTIVE The aim of the current study was to evaluate any correlation of APOBEC3G genetic variation rs8177832 with HIV-1 infection. METHODS The study involved 142 healthy control and 100 HIV-1 infected subjects. The genetic variation rs8177832 of all studied subjects was determined by allele-specific polymerase chain reaction (AS-PCR). RESULTS The results showed that the distribution of rs8177832 genotypes AA, AG and GG in healthy subjects and HIV-1 subjects was; 42.253%, 42.957%, 14.788% and 66%, 27%, 7% respectively. Statistical analyses of data showed that there was a significant variation in rs8177832 genotype AA in healthy control and HIV-1 infected subjects (42.257% vs 66%; p-value<0.001). CONCLUSION Thus it was concluded that APOBEC3G rs8177832 AA genotype contributes in genetic predisposition to HIV-1 infection in Pakistani population.
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Affiliation(s)
- Khurshid Iqbal
- Address correspondence to this author at the Department of Medical Laboratory Sciences, Imperial College of Business Studies, Lahore, Pakistan; Tel: 00923028051657; E-mail:
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Okada A, Iwatani Y. APOBEC3G-Mediated G-to-A Hypermutation of the HIV-1 Genome: The Missing Link in Antiviral Molecular Mechanisms. Front Microbiol 2016; 7:2027. [PMID: 28066353 PMCID: PMC5165236 DOI: 10.3389/fmicb.2016.02027] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/02/2016] [Indexed: 12/20/2022] Open
Abstract
APOBEC3G (A3G) is a member of the cellular polynucleotide cytidine deaminases, which catalyze the deamination of cytosine (dC) to uracil (dU) in single-stranded DNA. These enzymes potently inhibit the replication of a variety of retroviruses and retrotransposons, including HIV-1. A3G is incorporated into vif-deficient HIV-1 virions and targets viral reverse transcripts, particularly minus-stranded DNA products, in newly infected cells. It is well established that the enzymatic activity of A3G is closely correlated with the potential to greatly inhibit HIV-1 replication in the absence of Vif. However, the details of the underlying molecular mechanisms are not fully understood. One potential mechanism of A3G antiviral activity is that the A3G-dependent deamination may trigger degradation of the dU-containing reverse transcripts by cellular uracil DNA glycosylases (UDGs). More recently, another mechanism has been suggested, in which the virion-incorporated A3G generates lethal levels of the G-to-A hypermutation in the viral DNA genome, thus potentially driving the viruses into “error catastrophe” mode. In this mini review article, we summarize the deaminase-dependent and deaminase-independent molecular mechanisms of A3G and discuss how A3G-mediated deamination is linked to antiviral mechanisms.
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Affiliation(s)
- Ayaka Okada
- Department of Microbiology and Immunology, Laboratory of Infectious Diseases, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yasumasa Iwatani
- Department of Microbiology and Immunology, Laboratory of Infectious Diseases, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of AIDS Research, Nagoya University Graduate School of MedicineNagoya, Japan
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Li Q, Qiao Y, Zhang G, He N, Zhang X, Jia X, Sun H, Wang C, Xu L. Association of single nucleotide polymorphisms of APOBEC3G with susceptibility to HIV-1 infection and disease progression among men engaging in homosexual activity in northern China. Arch Virol 2016; 162:259-268. [PMID: 27730383 DOI: 10.1007/s00705-016-3080-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 11/27/2022]
Abstract
Men who have sex with men (MSM) are at high risk of HIV infection. The APOBEC3G (apolipoprotein B mRNA editing catalytic polypeptide 3G) protein is a component of innate antiviral immunity that inhibits HIV-1 replication. In the present study, a total of 483 HIV-1 seropositive men and 493 HIV-1 seronegative men were selected to investigate the association between single nucleotide polymorphisms (SNPs) of the APOBEC3G gene and susceptibility to HIV-1 infection and AIDS progression among MSM residing in northern China. Genotyping of four SNPs (rs5757465, rs3736685, rs8177832, and rs2899313) of the APOBEC3G was performed using the SNPscan™ Kit, while the rs2294367 polymorphism was genotyped using the SNaPshot multiplex system. Our results disclosed no association between the SNPs of APOBEC3G and susceptibility to HIV-1, or effects of these polymorphisms on the CD4+ T cell count or clinical phase of disease. A meta-analysis of 1624 men with HIV-1 infection and 1523 controls suggested that the association between rs8177832 and susceptibility was not significant. However, we observed a trend towards association with HIV-1 infection for haplotype TTACA (p = 0.082). The potential role of variants of APOBEC3G in HIV-1/AIDS warrants further investigation.
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Affiliation(s)
- Qiuyan Li
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Yuandong Qiao
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Guangfa Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Ning He
- Department of Clinical Laboratory, Qiqihar Traditional Chinese Medicine Hospital, Qiqihar, 161000, People's Republic of China
| | - Xuelong Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Chuntao Wang
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, Baojian Road 157, Nangang District, Harbin, 150081, People's Republic of China.
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Czubala MA, Finsterbusch K, Ivory MO, Mitchell JP, Ahmed Z, Shimauchi T, Karoo ROS, Coulman SA, Gateley C, Birchall JC, Blanchet FP, Piguet V. TGFβ Induces a SAMHD1-Independent Post-Entry Restriction to HIV-1 Infection of Human Epithelial Langerhans Cells. J Invest Dermatol 2016; 136:1981-1989. [PMID: 27375111 DOI: 10.1016/j.jid.2016.05.123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/13/2016] [Accepted: 05/31/2016] [Indexed: 11/24/2022]
Abstract
Sterile alpha motif (SAM) and histidine-aspartic (HD) domains protein 1 (SAMHD1) was previously identified as a critical post-entry restriction factor to HIV-1 infection in myeloid dendritic cells. Here we show that SAMHD1 is also expressed in epidermis-isolated Langerhans cells (LC), but degradation of SAMHD1 does not rescue HIV-1 or vesicular stomatitis virus G-pseudotyped lentivectors infection in LC. Strikingly, using Langerhans cells model systems (mutz-3-derived LC, monocyte-derived LC [MDLC], and freshly isolated epidermal LC), we characterize previously unreported post-entry restriction activity to HIV-1 in these cells, which acts at HIV-1 reverse transcription, but remains independent of restriction factors SAMHD1 and myxovirus resistance 2 (MX2). We demonstrate that transforming growth factor-β signaling confers this potent HIV-1 restriction in MDLC during their differentiation and blocking of mothers against decapentaplegic homolog 2 (SMAD2) signaling in MDLC restores cells' infectivity. Interestingly, maturation of MDLC with a toll-like receptor 2 agonist or transforming growth factor-α significantly increases cells' susceptibility to HIV-1 infection, which may explain why HIV-1 acquisition is increased during coinfection with sexually transmitted infections. In conclusion, we report a SAMHD1-independent post-entry restriction in MDLC and LC isolated from epidermis, which inhibits HIV-1 replication. A better understanding of HIV-1 restriction and propagation from LC to CD4(+) T cells may help in the development of new microbicides or vaccines to curb HIV-1 infection at its earliest stages during mucosal transmission.
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Affiliation(s)
- Magdalena A Czubala
- Department of Dermatology and Academic Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Katja Finsterbusch
- Department of Dermatology and Academic Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Matthew O Ivory
- Department of Dermatology and Academic Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK; Cardiff University School of Pharmacy and Pharmaceutical Sciences, Cardiff CF10 3NB, UK
| | - J Paul Mitchell
- Department of Dermatology and Academic Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Zahra Ahmed
- Department of Dermatology and Academic Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Takatoshi Shimauchi
- Department of Dermatology and Academic Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | | | - Sion A Coulman
- Cardiff University School of Pharmacy and Pharmaceutical Sciences, Cardiff CF10 3NB, UK
| | - Christopher Gateley
- Aneurin Bevan University Health Board Royal Gwent Hospital, Newport NP20 2UB, UK
| | - James C Birchall
- Cardiff University School of Pharmacy and Pharmaceutical Sciences, Cardiff CF10 3NB, UK
| | - Fabien P Blanchet
- Department of Dermatology and Academic Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Vincent Piguet
- Department of Dermatology and Academic Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK.
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11
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Delviks-Frankenberry KA, Nikolaitchik OA, Burdick RC, Gorelick RJ, Keele BF, Hu WS, Pathak VK. Minimal Contribution of APOBEC3-Induced G-to-A Hypermutation to HIV-1 Recombination and Genetic Variation. PLoS Pathog 2016; 12:e1005646. [PMID: 27186986 PMCID: PMC4871359 DOI: 10.1371/journal.ppat.1005646] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/28/2016] [Indexed: 11/19/2022] Open
Abstract
Although the predominant effect of host restriction APOBEC3 proteins on HIV-1 infection is to block viral replication, they might inadvertently increase retroviral genetic variation by inducing G-to-A hypermutation. Numerous studies have disagreed on the contribution of hypermutation to viral genetic diversity and evolution. Confounding factors contributing to the debate include the extent of lethal (stop codon) and sublethal hypermutation induced by different APOBEC3 proteins, the inability to distinguish between G-to-A mutations induced by APOBEC3 proteins and error-prone viral replication, the potential impact of hypermutation on the frequency of retroviral recombination, and the extent to which viral recombination occurs in vivo, which can reassort mutations in hypermutated genomes. Here, we determined the effects of hypermutation on the HIV-1 recombination rate and its contribution to genetic variation through recombination to generate progeny genomes containing portions of hypermutated genomes without lethal mutations. We found that hypermutation did not significantly affect the rate of recombination, and recombination between hypermutated and wild-type genomes only increased the viral mutation rate by 3.9 × 10-5 mutations/bp/replication cycle in heterozygous virions, which is similar to the HIV-1 mutation rate. Since copackaging of hypermutated and wild-type genomes occurs very rarely in vivo, recombination between hypermutated and wild-type genomes does not significantly contribute to the genetic variation of replicating HIV-1. We also analyzed previously reported hypermutated sequences from infected patients and determined that the frequency of sublethal mutagenesis for A3G and A3F is negligible (4 × 10-21 and1 × 10-11, respectively) and its contribution to viral mutations is far below mutations generated during error-prone reverse transcription. Taken together, we conclude that the contribution of APOBEC3-induced hypermutation to HIV-1 genetic variation is substantially lower than that from mutations during error-prone replication.
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Affiliation(s)
- Krista A. Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Olga A. Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, Maryland, United States of America
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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12
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Bai R, Zhang XJ, Li YL, Liu JP, Zhang HB, Xiao WL, Pu JX, Sun HD, Zheng YT, Liu LX. SJP-L-5, a novel small-molecule compound, inhibits HIV-1 infection by blocking viral DNA nuclear entry. BMC Microbiol 2015; 15:274. [PMID: 26630969 PMCID: PMC4667461 DOI: 10.1186/s12866-015-0605-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 11/24/2015] [Indexed: 11/15/2022] Open
Abstract
Background Small-molecule compounds that inhibit human immunodeficiency virus type 1 (HIV-1) infection can be used not only as drug candidates, but also as reagents to dissect the life cycle of the virus. Thus, it is desirable to have an arsenal of such compounds that inhibit HIV-1 infection by various mechanisms. Until now, only a few small-molecule compounds that inhibit nuclear entry of viral DNA have been documented. Results We identified a novel, small-molecule compound, SJP-L-5, that inhibits HIV-1 infection. SJP-L-5 is a nitrogen-containing, biphenyl compound whose synthesis was based on the dibenzocyclooctadiene lignan gomisin M2, an anti-HIV bioactive compound isolated from Schisandra micrantha A. C. Smith. SJP-L-5 displayed relatively low cytotoxicity (50 % cytoxicity concentrations were greater than 200 μg/ml) and high antiviral activity against a variety of HIV strains (50 % effective concentrations (EC50)) of HIV-1 laboratory-adapted strains ranged from 0.16–0.97 μg/ml; EC50s of primary isolates ranged from 1.96–5.33 μg/ml). Analyses of the viral DNA synthesis indicated that SJP-L-5 specifically blocks the entry of the HIV-1 pre-integration complex (PIC) into the nucleus. Further results implicated that SJP-L-5 inhibits the disassembly of HIV-1 particulate capsid in the cytoplasm of the infected cells. Conclusions SJP-L-5 is a novel small-molecule compound that inhibits HIV-1 nuclear entry by blocking the disassembly of the viral core. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0605-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ru Bai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
| | - Xing-Jie Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and the Kunming Institute of Zoology of the Chinese Academy of Sciences, Kunming, 650223, P. R. China.
| | - Yan-Li Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
| | - Jing-Ping Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, P. R. China.
| | - Hong-Bin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China.
| | - Wei-Lie Xiao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, P. R. China.
| | - Jian-Xin Pu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, P. R. China.
| | - Han-Dong Sun
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, P. R. China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and the Kunming Institute of Zoology of the Chinese Academy of Sciences, Kunming, 650223, P. R. China.
| | - Li-Xin Liu
- Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
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13
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Willems L, Gillet NA. APOBEC3 Interference during Replication of Viral Genomes. Viruses 2015; 7:2999-3018. [PMID: 26110583 PMCID: PMC4488724 DOI: 10.3390/v7062757] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/26/2015] [Accepted: 06/04/2015] [Indexed: 01/05/2023] Open
Abstract
Co-evolution of viruses and their hosts has reached a fragile and dynamic equilibrium that allows viral persistence, replication and transmission. In response, infected hosts have developed strategies of defense that counteract the deleterious effects of viral infections. In particular, single-strand DNA editing by Apolipoprotein B Editing Catalytic subunits proteins 3 (APOBEC3s) is a well-conserved mechanism of mammalian innate immunity that mutates and inactivates viral genomes. In this review, we describe the mechanisms of APOBEC3 editing during viral replication, the viral strategies that prevent APOBEC3 activity and the consequences of APOBEC3 modulation on viral fitness and host genome integrity. Understanding the mechanisms involved reveals new prospects for therapeutic intervention.
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Affiliation(s)
- Luc Willems
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) of University of Liège (ULg), B34, 1 avenue de L'Hôpital, Sart-Tilman Liège 4000, Belgium.
- Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège (ULg), 13 avenue Maréchal Juin, Gembloux 5030, Belgium.
| | - Nicolas Albert Gillet
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) of University of Liège (ULg), B34, 1 avenue de L'Hôpital, Sart-Tilman Liège 4000, Belgium.
- Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège (ULg), 13 avenue Maréchal Juin, Gembloux 5030, Belgium.
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14
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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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15
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Desimmie BA, Delviks-Frankenberrry KA, Burdick RC, Qi D, Izumi T, Pathak VK. Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all. J Mol Biol 2014; 426:1220-45. [PMID: 24189052 PMCID: PMC3943811 DOI: 10.1016/j.jmb.2013.10.033] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 12/11/2022]
Abstract
Several members of the APOBEC3 family of cellular restriction factors provide intrinsic immunity to the host against viral infection. Specifically, APOBEC3DE, APOBEC3F, APOBEC3G, and APOBEC3H haplotypes II, V, and VII provide protection against HIV-1Δvif through hypermutation of the viral genome, inhibition of reverse transcription, and inhibition of viral DNA integration into the host genome. HIV-1 counteracts APOBEC3 proteins by encoding the viral protein Vif, which contains distinct domains that specifically interact with these APOBEC3 proteins to ensure their proteasomal degradation, allowing virus replication to proceed. Here, we review our current understanding of APOBEC3 structure, editing and non-editing mechanisms of APOBEC3-mediated restriction, Vif-APOBEC3 interactions that trigger APOBEC3 degradation, and the contribution of APOBEC3 proteins to restriction and control of HIV-1 replication in infected patients.
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Affiliation(s)
- Belete A Desimmie
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | | | - Ryan C Burdick
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - DongFei Qi
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
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16
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Santa-Marta M, de Brito PM, Godinho-Santos A, Goncalves J. Host Factors and HIV-1 Replication: Clinical Evidence and Potential Therapeutic Approaches. Front Immunol 2013; 4:343. [PMID: 24167505 PMCID: PMC3807056 DOI: 10.3389/fimmu.2013.00343] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 10/06/2013] [Indexed: 12/17/2022] Open
Abstract
HIV and human defense mechanisms have co-evolved to counteract each other. In the process of infection, HIV takes advantage of cellular machinery and blocks the action of the host restriction factors (RF). A small subset of HIV+ individuals control HIV infection and progression to AIDS in the absence of treatment. These individuals known as long-term non-progressors (LNTPs) exhibit genetic and immunological characteristics that confer upon them an efficient resistance to infection and/or disease progression. The identification of some of these host factors led to the development of therapeutic approaches that attempted to mimic the natural control of HIV infection. Some of these approaches are currently being tested in clinical trials. While there are many genes which carry mutations and polymorphisms associated with non-progression, this review will be specifically focused on HIV host RF including both the main chemokine receptors and chemokines as well as intracellular RF including, APOBEC, TRIM, tetherin, and SAMHD1. The understanding of molecular profiles and mechanisms present in LTNPs should provide new insights to control HIV infection and contribute to the development of novel therapies against AIDS.
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Affiliation(s)
- Mariana Santa-Marta
- URIA-Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa , Lisboa , Portugal ; Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa , Lisboa , Portugal
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17
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De Pasquale M, Kourteva Y, Allos T, D'Aquila RT. Lower HIV provirus levels are associated with more APOBEC3G protein in blood resting memory CD4+ T lymphocytes of controllers in vivo. PLoS One 2013; 8:e76002. [PMID: 24146808 PMCID: PMC3797809 DOI: 10.1371/journal.pone.0076002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/21/2013] [Indexed: 12/22/2022] Open
Abstract
Immunodeficiency does not progress for prolonged periods in some HLA B57- and/or B27-positive subjects with human immunodeficiency virus type 1 (HIV) infection, even in the absence of antiretroviral therapy (ART). These "controllers" have fewer HIV provirus-containing peripheral blood mononuclear cells than "non-controller" subjects, but lymphocytes that harbor latent proviruses were not specifically examined in studies to date. Provirus levels in resting memory cells that can serve as latent reservoirs of HIV in blood were compared here between controllers and ART-suppressed non-controllers. APOBEC3G (A3G), a cellular factor that blocks provirus formation at multiple steps if not antagonized by HIV virion infectivity factor (Vif), was also studied. HLA-linked HIV control was associated with less provirus and more A3G protein in resting CD4+ T central memory (Tcm) and effector memory (Tem) lymphocytes (provirus: p = 0.01 for Tcm and p = 0.02 for Tem; A3G: p = 0.02 for Tcm and p = 0.02 for Tem). Resting memory T cells with the highest A3G protein levels (>0.5 RLU per unit of actin) had the lowest levels of provirus (<1,000 copies of DNA per million cells) in vivo (p = 0.03, Fisher's exact test). Using two different experimental approaches, Vif-positive viruses with more A3G were found to have decreased virion infectivity ex vivo. These results raise the hypothesis that HIV control is associated with increased cellular A3G that may be packaged into Vif-positive virions to add that mode of inhibition of provirus formation to previously described adaptive immune mechanisms for HIV control.
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Affiliation(s)
- MariaPia De Pasquale
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Yordanka Kourteva
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Tara Allos
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Richard T. D'Aquila
- Division of Infectious Diseases and Northwestern HIV Translational Research Center, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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18
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Vieira VC, Soares MA. The role of cytidine deaminases on innate immune responses against human viral infections. BIOMED RESEARCH INTERNATIONAL 2013; 2013:683095. [PMID: 23865062 PMCID: PMC3707226 DOI: 10.1155/2013/683095] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 05/29/2013] [Accepted: 05/31/2013] [Indexed: 02/06/2023]
Abstract
The APOBEC family of proteins comprises deaminase enzymes that edit DNA and/or RNA sequences. The APOBEC3 subgroup plays an important role on the innate immune system, acting on host defense against exogenous viruses and endogenous retroelements. The role of APOBEC3 proteins in the inhibition of viral infection was firstly described for HIV-1. However, in the past few years many studies have also shown evidence of APOBEC3 action on other viruses associated with human diseases, including HTLV, HCV, HBV, HPV, HSV-1, and EBV. APOBEC3 inhibits these viruses through a series of editing-dependent and independent mechanisms. Many viruses have evolved mechanisms to counteract APOBEC effects, and strategies that enhance APOBEC3 activity constitute a new approach for antiviral drug development. On the other hand, novel evidence that editing by APOBEC3 constitutes a source for viral genetic diversification and evolution has emerged. Furthermore, a possible role in cancer development has been shown for these host enzymes. Therefore, understanding the role of deaminases on the immune response against infectious agents, as well as their role in human disease, has become pivotal. This review summarizes the state-of-the-art knowledge of the impact of APOBEC enzymes on human viruses of distinct families and harboring disparate replication strategies.
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Affiliation(s)
- Valdimara C. Vieira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua André Cavalcanti, No. 37–4 Andar, Bairro de Fátima, 20231-050 Rio de Janeiro, RJ, Brazil
| | - Marcelo A. Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua André Cavalcanti, No. 37–4 Andar, Bairro de Fátima, 20231-050 Rio de Janeiro, RJ, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, 21949-570 Rio de Janeiro, RJ, Brazil
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19
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Suppression of HIV-1 infection by APOBEC3 proteins in primary human CD4(+) T cells is associated with inhibition of processive reverse transcription as well as excessive cytidine deamination. J Virol 2012; 87:1508-17. [PMID: 23152537 DOI: 10.1128/jvi.02587-12] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Vif protein of human immunodeficiency virus type 1 (HIV-1) promotes viral replication by downregulation of the cell-encoded, antiviral APOBEC3 proteins. These proteins exert their suppressive effects through the inhibition of viral reverse transcription as well as the induction of cytidine deamination within nascent viral cDNA. Importantly, these two effects have not been characterized in detail in human CD4(+) T cells, leading to controversies over their possible contributions to viral inhibition in the natural cell targets of HIV-1 replication. Here we use wild-type and Vif-deficient viruses derived from the CD4(+) T cells of multiple donors to examine the consequences of APOBEC3 protein function at natural levels of expression. We demonstrate that APOBEC3 proteins impart a profound deficiency to reverse transcription from the initial stages of cDNA synthesis, as well as excessive cytidine deamination (hypermutation) of the DNAs that are synthesized. Experiments using viruses from transfected cells and a novel method for mapping the 3' termini of cDNAs indicate that the inhibition of reverse transcription is not limited to a few specific sites, arguing that APOBEC3 proteins impede enzymatic processivity. Detailed analyses of mutation spectra in viral cDNA strongly imply that one particular APOBEC3 protein, APOBEC3G, provides the bulk of the antiviral phenotype in CD4(+) T cells, with the effects of APOBEC3F and APOBEC3D being less significant. Taken together, we conclude that the dual mechanisms of action of APOBEC3 proteins combine to deliver more effective restriction of HIV-1 than either function would by itself.
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20
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Imahashi M, Nakashima M, Iwatani Y. Antiviral Mechanism and Biochemical Basis of the Human APOBEC3 Family. Front Microbiol 2012; 3:250. [PMID: 22787460 PMCID: PMC3391693 DOI: 10.3389/fmicb.2012.00250] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 06/21/2012] [Indexed: 12/24/2022] Open
Abstract
The human APOBEC3 (A3) family (A, B, C, DE, F, G, and H) comprises host defense factors that potently inhibit the replication of diverse retroviruses, retrotransposons, and the other viral pathogens. HIV-1 has a counterstrategy that includes expressing the Vif protein to abrogate A3 antiviral function. Without Vif, A3 proteins, particularly APOBEC3G (A3G) and APOBEC3F (A3F), inhibit HIV-1 replication by blocking reverse transcription and/or integration and hypermutating nascent viral cDNA. The molecular mechanisms of this antiviral activity have been primarily attributed to two biochemical characteristics common to A3 proteins: catalyzing cytidine deamination in single-stranded DNA (ssDNA) and a nucleic acid-binding capability that is specific to ssDNA or ssRNA. Recent advances suggest that unique property of A3G dimer/oligomer formations, is also important for the modification of antiviral activity. In this review article we summarize how A3 proteins, particularly A3G, inhibit viral replication based on the biochemical and structural characteristics of the A3G protein.
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Affiliation(s)
- Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
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21
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Chang MO, Suzuki T, Yamamoto N, Watanabe M, Takaku H. HIV-1 Gag-virus-like particles inhibit HIV-1 replication in dendritic cells and T cells through IFN-α-dependent upregulation of APOBEC3G and 3F. J Innate Immun 2012; 4:579-90. [PMID: 22739040 DOI: 10.1159/000339402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 05/10/2012] [Indexed: 12/17/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) infection and the acquired immune deficiency syndrome (AIDS) pandemic remain global threats in the absence of a protective or a therapeutic vaccine. HIV-1 replication is reportedly inhibited by some cellular factors, including APOBEC3G (A3G) and APOBEC3F (A3F), which are well known inhibitors of HIV-1. Recently, HIV-1 Gag-virus-like particles (Gag-VLPs) have been shown to be safe and potent HIV-1 vaccine candidates that can elicit strong cellular and humoral immunity without need of any adjuvant. In this report, we stimulated human monocyte-derived dendritic cells (DCs) with Gag-VLPs and we demonstrated that Gag-VLP-treated DCs (VLP-DCs) produced interferon alpha (IFN-α), along with an increase in mRNA and protein expression of A3G and A3F. Gag-VLPs inhibited HIV-1 replication not only in DCs themselves, but also in cocultured T cells in an IFN-α-dependent manner. In addition, A3G/3F content in HIV virions released from VLP-DCs increased. Both the increase in A3G/3F expression and the inhibition of HIV-1 replication were reversed by anti-IFN-α or anti-IFNAR antibodies. Our findings in this study provide insight into the mechanism of Gag-VLP-induced inhibition of HIV-1 replication in DCs and T cells.
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Affiliation(s)
- Myint Oo Chang
- Department of Life and Environmental Sciences, Chiba Institute of Technology, Chiba, Japan.
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22
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Batisse J, Guerrero S, Bernacchi S, Sleiman D, Gabus C, Darlix JL, Marquet R, Tisné C, Paillart JC. The role of Vif oligomerization and RNA chaperone activity in HIV-1 replication. Virus Res 2012; 169:361-76. [PMID: 22728817 DOI: 10.1016/j.virusres.2012.06.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 06/04/2012] [Accepted: 06/12/2012] [Indexed: 11/28/2022]
Abstract
The viral infectivity factor (Vif) is essential for the productive infection and dissemination of HIV-1 in non-permissive cells that involve most natural HIV-1 target cells. Vif counteracts the packaging of two cellular cytidine deaminases named APOBEC3G (A3G) and A3F by diverse mechanisms including the recruitment of an E3 ubiquitin ligase complex and the proteasomal degradation of A3G/A3F, the inhibition of A3G mRNA translation or by a direct competition mechanism. In addition, Vif appears to be an active partner of the late steps of viral replication by participating in virus assembly and Gag processing, thus regulating the final stage of virion formation notably genomic RNA dimerization and by inhibiting the initiation of reverse transcription. Vif is a small pleiotropic protein with multiple domains, and recent studies highlighted the importance of Vif conformation and flexibility in counteracting A3G and in binding RNA. In this review, we will focus on the oligomerization and RNA chaperone properties of Vif and show that the intrinsic disordered nature of some Vif domains could play an important role in virus assembly and replication. Experimental evidence demonstrating the RNA chaperone activity of Vif will be presented.
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Affiliation(s)
- Julien Batisse
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France
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23
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Monajemi M, Woodworth CF, Benkaroun J, Grant M, Larijani M. Emerging complexities of APOBEC3G action on immunity and viral fitness during HIV infection and treatment. Retrovirology 2012; 9:35. [PMID: 22546055 PMCID: PMC3416701 DOI: 10.1186/1742-4690-9-35] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/30/2012] [Indexed: 12/31/2022] Open
Abstract
The enzyme APOBEC3G (A3G) mutates the human immunodeficiency virus (HIV) genome by converting deoxycytidine (dC) to deoxyuridine (dU) on minus strand viral DNA during reverse transcription. A3G restricts viral propagation by degrading or incapacitating the coding ability of the HIV genome. Thus, this enzyme has been perceived as an innate immune barrier to viral replication whilst adaptive immunity responses escalate to effective levels. The discovery of A3G less than a decade ago led to the promise of new anti-viral therapies based on manipulation of its cellular expression and/or activity. The rationale for therapeutic approaches has been solidified by demonstration of the effectiveness of A3G in diminishing viral replication in cell culture systems of HIV infection, reports of its mutational footprint in virions from patients, and recognition of its unusually robust enzymatic potential in biochemical studies in vitro. Despite its effectiveness in various experimental systems, numerous recent studies have shown that the ability of A3G to combat HIV in the physiological setting is severely limited. In fact, it has become apparent that its mutational activity may actually enhance viral fitness by accelerating HIV evolution towards the evasion of both anti-viral drugs and the immune system. This body of work suggests that the role of A3G in HIV infection is more complex than heretofore appreciated and supports the hypothesis that HIV has evolved to exploit the action of this host factor. Here we present an overview of recent data that bring to light historical overestimation of A3G's standing as a strictly anti-viral agent. We discuss the limitations of experimental systems used to assess its activities as well as caveats in data interpretation.
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Affiliation(s)
- Mahdis Monajemi
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, Newfoundland, Canada
| | - Claire F Woodworth
- Mani Larijani, Division of Biomedical Sciences, Faculty of Medicine, Health Sciences Center, MUN, 300 Prince Phillip Dr., St. John’s, NL, A1B 3V6, Canada
| | - Jessica Benkaroun
- Mani Larijani, Division of Biomedical Sciences, Faculty of Medicine, Health Sciences Center, MUN, 300 Prince Phillip Dr., St. John’s, NL, A1B 3V6, Canada
| | - Michael Grant
- Division of Biomedical Sciences, Faculty of Medicine, Health Sciences Center, MUN, 300 Prince Phillip Dr., St. John’s, NL, A1B 3V6, Canada
| | - Mani Larijani
- Division of Biomedical Sciences, Faculty of Medicine, Health Sciences Center, MUN, 300 Prince Phillip Dr., St. John’s, NL, A1B 3V6, Canada
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N-terminal hemagglutinin tag renders lysine-deficient APOBEC3G resistant to HIV-1 Vif-induced degradation by reduced polyubiquitination. J Virol 2011; 85:4510-9. [PMID: 21345952 DOI: 10.1128/jvi.01925-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
APOBEC3G, a potent HIV-1 host restriction factor, is overcome by HIV-1 viral infectivity factor (Vif), which induces its polyubiquitination and proteasomal degradation. Here we show that lysine-deficient APOBEC3G with an N-terminal hemagglutinin (HA) tag fusion (HA-A3G20K/R) was resistant to HIV-1 Vif-induced proteasomal degradation. HA-A3G20K/R molecules were packaged into wild-type HIV-1 particles, and HA-A3G20K/R drastically decreased wild-type HIV-1 reverse transcription products and infectivity. We also showed that the N terminus of A3G was a target of polyubiquitination induced by HIV-1 Vif. Thus, fusion of the HA tag to the N terminus of A3G20K/R reduced its polyubiquitination, the likely mechanism for the resistance of this protein to HIV-1 Vif-induced proteasomal degradation. Finding such ways to induce resistance of A3G to Vif may provide new approaches to anti-HIV/AIDS therapy.
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25
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Smith JL, Pathak VK. Identification of specific determinants of human APOBEC3F, APOBEC3C, and APOBEC3DE and African green monkey APOBEC3F that interact with HIV-1 Vif. J Virol 2010; 84:12599-608. [PMID: 20943965 PMCID: PMC3004357 DOI: 10.1128/jvi.01437-10] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 10/04/2010] [Indexed: 11/20/2022] Open
Abstract
Human APOBEC3F (hA3F) and human APOBEC3G (hA3G) are potent anti-human immunodeficiency virus (anti-HIV) host factors that suppress viral replication by hypermutating the viral genome, inhibiting reverse transcription, and hindering integration. To overcome hA3F and hA3G, HIV-1 encodes Vif, which binds and targets these host proteins for proteasomal degradation. Previously, we reported that the hA3F-Vif interactions that lead to hA3F degradation are located in the region comprising amino acids 283 to 300. We have now performed mutational analysis of this region and found that the (289)EFLARH(294) amino acids contribute to hA3F-Vif binding and are critical for A3F's sensitivity to Vif. Mutants in which E289 is mutated significantly increase hA3F's ability to inhibit viral infectivity in the presence of Vif, and coimmunoprecipitation assays show that binding of Vif to the E289K mutant is decreased. We examined the role of the EFLARH sequence in other A3 proteins, including human A3C (hA3C), human A3DE (hA3DE), African green monkey A3F (agmA3F), and rhesus macaque A3F (rhA3F). hA3C, hA3DE, and agmA3F were all susceptible to degradation induced by HIV-1 Vif, while rhA3F was not. Mutagenesis of the glutamate in the EFLARH sites of hA3C, hA3DE, and agmA3F decreases the susceptibilities of these proteins to Vif-induced degradation. Together, these results indicate that the EFLARH region in hA3F, hA3C, hA3DE, and agmA3F interacts with HIV-1 Vif and that this interaction plays a role in the Vif-mediated proteasomal degradation of these A3 proteins. These studies identify a conserved region in 3 of 7 human A3 proteins that is critical for degradation mediated by HIV-1 Vif and provide structural insights into the hA3F-Vif interactions that could facilitate the development of a novel class of anti-HIV agents.
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Affiliation(s)
- Jessica L. Smith
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702
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26
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Towards Inhibition of Vif-APOBEC3G Interaction: Which Protein to Target? Adv Virol 2010; 2010:649315. [PMID: 22347227 PMCID: PMC3275931 DOI: 10.1155/2010/649315] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Revised: 07/31/2010] [Accepted: 08/14/2010] [Indexed: 11/17/2022] Open
Abstract
APOBEC proteins appeared in the cellular battle against HIV-1 as part of intrinsic cellular immunity. The antiretroviral activity of some of these proteins is overtaken by the action of HIV-1 Viral Infectivity Factor (Vif) protein. Since the discovery of APOBEC3G (A3G) as an antiviral factor, many advances have been made to understand its mechanism of action in the cell and how Vif acts in order to counteract its activity. The mainstream concept is that Vif overcomes the innate antiviral activity of A3G by direct protein binding and promoting its degradation via the cellular ubiquitin/proteasomal pathway. Vif may also inhibit A3G through mechanisms independent of proteasomal degradation. Binding of Vif to A3G is essential for its degradation since disruption of this interaction is predicted to stimulate intracellular antiviral immunity. In this paper we will discuss the different binding partners between both proteins as one of the major challenges for the development of new antiviral drugs.
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27
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Thielen BK, McNevin JP, McElrath MJ, Hunt BVS, Klein KC, Lingappa JR. Innate immune signaling induces high levels of TC-specific deaminase activity in primary monocyte-derived cells through expression of APOBEC3A isoforms. J Biol Chem 2010; 285:27753-66. [PMID: 20615867 PMCID: PMC2934643 DOI: 10.1074/jbc.m110.102822] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 07/05/2010] [Indexed: 01/06/2023] Open
Abstract
In HIV-1-infected individuals, G-to-A hypermutation is found in HIV-1 DNA isolated from peripheral blood mononuclear cells (PBMCs). These mutations are thought to result from editing by one or more host enzymes in the APOBEC3 (A3) family of cytidine deaminases, which act on CC (APOBEC3G) and TC (other A3 proteins) dinucleotide motifs in DNA (edited cytidine underlined). Although many A3 proteins display high levels of deaminase activity in model systems, only low levels of A3 deaminase activity have been found in primary cells examined to date. In contrast, here we report high levels of deaminase activity at TC motifs when whole PBMCs or isolated primary monocyte-derived cells were treated with interferon-alpha (IFNalpha) or IFNalpha-inducing toll-like receptor ligands. Induction of TC-specific deaminase activity required new transcription and translation and correlated with the appearance of two APOBEC3A (A3A) isoforms. Knockdown of A3A in monocytes with siRNA abolished TC-specific deaminase activity, confirming that A3A isoforms are responsible for all TC-specific deaminase activity observed. Both A3A isoforms appear to be enzymatically active; moreover, our mutational studies raise the possibility that the smaller isoform results from internal translational initiation. In contrast to the high levels of TC-specific activity observed in IFNalpha-treated monocytes, CC-specific activity remained low in PBMCs, suggesting that A3G deaminase activity is relatively inhibited, unlike that of A3A. Together, these findings suggest that deaminase activity of A3A isoforms in monocytes and macrophages may play an important role in host defense against viruses.
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Affiliation(s)
- Beth K. Thielen
- From the Department of Global Health, University of Washington, Seattle, Washington 98102
| | - John P. McNevin
- the Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, and
| | - M. Juliana McElrath
- the Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, and
- the Department of Medicine, University of Washington, Seattle, Washington 98195
| | | | - Kevin C. Klein
- From the Department of Global Health, University of Washington, Seattle, Washington 98102
| | - Jaisri R. Lingappa
- From the Department of Global Health, University of Washington, Seattle, Washington 98102
- the Department of Medicine, University of Washington, Seattle, Washington 98195
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28
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Wissing S, Galloway NLK, Greene WC. HIV-1 Vif versus the APOBEC3 cytidine deaminases: an intracellular duel between pathogen and host restriction factors. Mol Aspects Med 2010; 31:383-97. [PMID: 20538015 DOI: 10.1016/j.mam.2010.06.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Revised: 06/03/2010] [Accepted: 06/03/2010] [Indexed: 10/19/2022]
Abstract
The Vif protein of HIV is essential for the effective propagation of this pathogenic retrovirus in vivo. Vif acts by preventing virion encapsidation of two potent antiviral factors, the APOBEC3G and APOBEC3F cytidine deaminases. Decreased encapsidation in part involves Vif-mediated recruitment of a ubiquitin E3 ligase complex that promotes polyubiquitylation and proteasome-mediated degradation of APOBEC3G/F. The resultant decline in intracellular levels of these enzymes leads to decreased encapsidation of APOBECG/F into budding virions. This review discusses recent advances in our understanding of the dynamic interplay of Vif with the antiviral APOBEC3 enzymes.
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Affiliation(s)
- Silke Wissing
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94158, USA
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29
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Mbisa JL, Bu W, Pathak VK. APOBEC3F and APOBEC3G inhibit HIV-1 DNA integration by different mechanisms. J Virol 2010; 84:5250-9. [PMID: 20219927 PMCID: PMC2863843 DOI: 10.1128/jvi.02358-09] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 03/02/2010] [Indexed: 12/25/2022] Open
Abstract
APOBEC3F (A3F) and APBOBEC3G (A3G) both are host restriction factors that can potently inhibit human immunodeficiency virus type 1 (HIV-1) replication. Their antiviral activities are at least partially mediated by cytidine deamination, which causes lethal mutations of the viral genome. We recently showed that A3G blocks viral plus-strand DNA transfer and inhibits provirus establishment in the host genome (J. L. Mbisa, R. Barr, J. A. Thomas, N. Vandegraaff, I. J. Dorweiler, E. S. Svarovskaia, W. L. Brown, L. M. Mansky, R. J. Gorelick, R. S. Harris, A. Engelman, and V. K. Pathak, J. Virol. 81:7099-7110, 2007). Here, we investigated whether A3F similarly interferes with HIV-1 provirus formation. We observed that both A3F and A3G inhibit viral DNA synthesis and integration, but A3F is more potent than A3G in preventing viral DNA integration. We further investigated the mechanisms by which A3F and A3G block viral DNA integration by analyzing their effects on viral cDNA processing using Southern blot analysis. A3G generates a 6-bp extension at the viral U5 end of the 3' long terminal repeat (3'-LTR), which is a poor substrate for integration; in contrast, A3F inhibits viral DNA integration by reducing the 3' processing of viral DNA at both the U5 and U3 ends. Furthermore, we demonstrated that a functional C-terminal catalytic domain is more critical for A3G than A3F function in blocking HIV-1 provirus formation. Finally, we showed that A3F has a greater binding affinity for a viral 3'-LTR double-stranded DNA (dsDNA) oligonucleotide template than A3G. Taking these results together, we demonstrated that mechanisms utilized by A3F to prevent HIV-1 viral DNA integration were different from those of A3G, and that their target specificities and/or their affinities for dsDNA may contribute to their distinct mechanisms.
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Affiliation(s)
- Jean L. Mbisa
- HIV Drug Resistance Program, National Cancer Institute—Frederick, Center for Cancer Research, SAIC—Frederick, Inc., Frederick, Maryland 21702-1021
| | - Wei Bu
- HIV Drug Resistance Program, National Cancer Institute—Frederick, Center for Cancer Research, SAIC—Frederick, Inc., Frederick, Maryland 21702-1021
| | - Vinay K. Pathak
- HIV Drug Resistance Program, National Cancer Institute—Frederick, Center for Cancer Research, SAIC—Frederick, Inc., Frederick, Maryland 21702-1021
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30
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Smith JL, Bu W, Burdick RC, Pathak VK. Multiple ways of targeting APOBEC3-virion infectivity factor interactions for anti-HIV-1 drug development. Trends Pharmacol Sci 2009; 30:638-46. [PMID: 19837465 PMCID: PMC2787722 DOI: 10.1016/j.tips.2009.09.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 09/12/2009] [Accepted: 09/14/2009] [Indexed: 01/31/2023]
Abstract
HIV-1 infections and the resulting AIDS pandemic remain a global challenge in the absence of a protective vaccine and because of rapid selection of drug-resistant viral variants in response to all currently available antiviral therapies. The development of new and highly active antiviral agents would greatly facilitate effective clinical management of HIV-1 infections and delay the onset of AIDS. Recent advances in our understanding of intracellular immunity conferred by host cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) and the mechanism by which the virally encoded virion infectivity factor (Vif) protein induces their proteasomal degradation provide fresh opportunities for the development of novel antiviral treatments. Interestingly, the Vif-A3G and Vif-A3F interactions that overcome this host defense mechanism are structurally distinct and provide two potential targets for antiviral drug development. This review provides an overview of current knowledge of APOBEC3-Vif interactions and recent efforts to target these interactions for antiviral drug development.
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Affiliation(s)
- Jessica L. Smith
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Maryland 21702, USA
| | - Wei Bu
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Maryland 21702, USA
- SAIC-Frederick, Frederick, Maryland 21702, USA
| | - Ryan C. Burdick
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Maryland 21702, USA
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Maryland 21702, USA
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31
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Defining APOBEC3 expression patterns in human tissues and hematopoietic cell subsets. J Virol 2009; 83:9474-85. [PMID: 19587057 DOI: 10.1128/jvi.01089-09] [Citation(s) in RCA: 266] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human APOBEC3 enzymes are cellular DNA cytidine deaminases that inhibit and/or mutate a variety of retroviruses, retrotransposons, and DNA viruses. Here, we report a detailed examination of human APOBEC3 gene expression, focusing on APOBEC3G (A3G) and APOBEC3F (A3F), which are potent inhibitors of human immunodeficiency virus type 1 (HIV-1) infection but are suppressed by HIV-1 Vif. A3G and A3F are expressed widely in hematopoietic cell populations, including T cells, B cells, and myeloid cells, as well as in tissues where mRNA levels broadly correlate with the lymphoid cell content (gonadal tissues are exceptions). By measuring mRNA copy numbers, we find that A3G mRNA is approximately 10-fold more abundant than A3F mRNA, implying that A3G is the more significant anti-HIV-1 factor in vivo. A3G and A3F levels also vary between donors, and these differences are sustained over 12 months. Responses to T-cell activation or cytokines reveal that A3G and A3F mRNA levels are induced approximately 10-fold in macrophages and dendritic cells (DCs) by alpha interferon (IFN-alpha) and approximately 4-fold in naïve CD4(+) T cells. However, immunoblotting revealed that A3G protein levels are induced by IFN-alpha in macrophages and DCs but not in T cells. In contrast, T-cell activation and IFN-gamma had a minimal impact on A3G or A3F expression. Finally, we noted that A3A mRNA expression and protein expression are exquisitely sensitive to IFN-alpha induction in CD4(+) T cells, macrophages, and DCs but not to T-cell activation or other cytokines. Given that A3A does not affect HIV-1 infection, these observations imply that this protein may participate in early antiviral innate immune responses.
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32
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Tumultuous relationship between the human immunodeficiency virus type 1 viral infectivity factor (Vif) and the human APOBEC-3G and APOBEC-3F restriction factors. Microbiol Mol Biol Rev 2009; 73:211-32. [PMID: 19487726 DOI: 10.1128/mmbr.00040-08] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The viral infectivity factor (Vif) is dispensable for human immunodeficiency virus type 1 (HIV-1) replication in so-called permissive cells but is required for replication in nonpermissive cell lines and for pathogenesis. Virions produced in the absence of Vif have an aberrant morphology and an unstable core and are unable to complete reverse transcription. Recent studies demonstrated that human APOBEC-3G (hA3G) and APOBEC-3F (hA3F), which are selectively expressed in nonpermissive cells, possess strong anti-HIV-1 activity and are sufficient to confer a nonpermissive phenotype. Vif induces the degradation of hA3G and hA3F, suggesting that its main function is to counteract these cellular factors. Most studies focused on the hypermutation induced by the cytidine deaminase activity of hA3G and hA3F and on their Vif-induced degradation by the proteasome. However, recent studies suggested that several mechanisms are involved both in the antiviral activity of hA3G and hA3F and in the way Vif counteracts these antiviral factors. Attempts to reconcile the studies involving Vif in virus assembly and stability with these recent findings suggest that hA3G and hA3F partially exert their antiviral activity independently of their catalytic activity by destabilizing the viral core and the reverse transcription complex, possibly by interfering with the assembly and/or maturation of the viral particles. Vif could then counteract hA3G and hA3F by excluding them from the viral assembly intermediates through competition for the viral genomic RNA, by regulating the proteolytic processing of Pr55(Gag), by enhancing the efficiency of the reverse transcription process, and by inhibiting the enzymatic activities of hA3G and hA3F.
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33
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Cytoplasmic APOBEC3G restricts incoming Vif-positive human immunodeficiency virus type 1 and increases two-long terminal repeat circle formation in activated T-helper-subtype cells. J Virol 2009; 83:8646-54. [PMID: 19535442 DOI: 10.1128/jvi.00020-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytoplasmic APOBEC3G has been reported to block wild-type human immunodeficiency virus type 1 (HIV-1) infection in some primary cells. It is not known whether cytoplasmic APOBEC3G has residual activity in activated T cells, even though virion-packaged APOBEC3G does restrict HIV-1 in activated T cells. Because we found that APOBEC3G expression is greater in activated CD4(+) T-helper type 1 (Th1) lymphocytes than in T-helper type 2 (Th2) lymphocytes, we hypothesized that residual target cell restriction of incoming Vif-positive virions that lack APOBEC3G, if present, would be greater in Th1 than Th2 lymphocytes. Infection of activated Th1 cells with APOBEC3-negative virions did result in decreased amounts of early and late reverse transcription products and integrated virus relative to infection of activated Th2 cells. Two-long terminal repeat (2-LTR) circles, which are formed in the nucleus when reverse transcripts do not integrate, were increased after APOBEC3-negative virus infection of activated Th1 cells relative to infection of activated Th2 cells. In contrast, 2-LTR circle forms were decreased after infection of APOBEC3G-negative cells with APOBEC3G-containing virions relative to APOBEC3G-negative virions and with Th1 cell-produced virions relative to Th2 cell-produced virions. Increasing APOBEC3G in Th2 cells and decreasing APOBEC3G in Th1 cells modulated the target cell phenotypes, indicating causation by APOBEC3G. The comparison between activated Th1 and Th2 cells indicates that cytoplasmic APOBEC3G in activated Th1 cells partially restricts reverse transcription and integration of incoming Vif-positive, APOBEC3G-negative HIV-1. The differing effects of cytoplasmic and virion-packaged APOBEC3G on 2-LTR circle formation indicate a difference in their antiviral mechanisms.
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34
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Malim MH. APOBEC proteins and intrinsic resistance to HIV-1 infection. Philos Trans R Soc Lond B Biol Sci 2009; 364:675-87. [PMID: 19038776 DOI: 10.1098/rstb.2008.0185] [Citation(s) in RCA: 202] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Members of the APOBEC family of cellular polynucleotide cytidine deaminases, most notably APOBEC3G and APOBEC3F, are potent inhibitors of HIV-1 infection. Wild type HIV-1 infections are largely spared from APOBEC3G/F function through the action of the essential viral protein, Vif. In the absence of Vif, APOBEC3G/F are encapsidated by budding virus particles leading to excessive cytidine (C) to uridine (U) editing of negative sense reverse transcripts in newly infected cells. This registers as guanosine (G) to adenosine (A) hypermutations in plus-stranded cDNA. In addition to this profoundly debilitating effect on genetic integrity, APOBEC3G/F also appear to inhibit viral DNA synthesis by impeding the translocation of reverse transcriptase along template RNA. Because the functions of Vif and APOBEC3G/F proteins oppose each other, it is likely that fluctuations in the Vif-APOBEC balance may influence the natural history of HIV-1 infection, as well as viral sequence diversification and evolution. Given Vif's critical role in suppressing APOBEC3G/F function, it can be argued that pharmacologic strategies aimed at restoring the activity of these intrinsic anti-viral factors in the context of infected cells in vivo have clear therapeutic merit, and therefore deserve aggressive pursuit.
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Affiliation(s)
- Michael H Malim
- Department of Infectious Diseases, King's College London School of Medicine, 2nd Floor, Borough Wing, Guy's Hospital, London Bridge, London SE1 9RT, UK.
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35
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Niewiadomska AM, Yu XF. Host restriction of HIV-1 by APOBEC3 and viral evasion through Vif. Curr Top Microbiol Immunol 2009; 339:1-25. [PMID: 20012521 DOI: 10.1007/978-3-642-02175-6_1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The arms race between virus and host is a constant battle. APOBEC3 proteins are known to be potent innate cellular defenses against both endogenous retroelements and diverse retroviruses. However, retroviruses have developed their own methods to launch counter-strikes. Most primate lentiviruses encode a protein called the viral infectivity factor (Vif). Vif induces targeted destruction of APOBEC3 proteins by hijacking the cellular ubiquitin-proteasome pathway. Here we review the research that led up to the identification of A3G, the mechanisms by which APOBEC3 proteins can inhibit retroelements, and the counter-mechanisms that HIV-1 Vif has developed to evade its antiviral activities.
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Affiliation(s)
- Anna Maria Niewiadomska
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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36
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APOBEC3G inhibits elongation of HIV-1 reverse transcripts. PLoS Pathog 2008; 4:e1000231. [PMID: 19057663 PMCID: PMC2584787 DOI: 10.1371/journal.ppat.1000231] [Citation(s) in RCA: 248] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 11/05/2008] [Indexed: 12/21/2022] Open
Abstract
APOBEC3G (A3G) is a host cytidine deaminase that, in the absence of Vif, restricts HIV-1 replication and reduces the amount of viral DNA that accumulates in cells. Initial studies determined that A3G induces extensive mutation of nascent HIV-1 cDNA during reverse transcription. It has been proposed that this triggers the degradation of the viral DNA, but there is now mounting evidence that this mechanism may not be correct. Here, we use a natural endogenous reverse transcriptase assay to show that, in cell-free virus particles, A3G is able to inhibit HIV-1 cDNA accumulation not only in the absence of hypermutation but also without the apparent need for any target cell factors. We find that although reverse transcription initiates in the presence of A3G, elongation of the cDNA product is impeded. These data support the model that A3G reduces HIV-1 cDNA levels by inhibiting synthesis rather than by inducing degradation.
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37
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Huthoff H, Towers GJ. Restriction of retroviral replication by APOBEC3G/F and TRIM5alpha. Trends Microbiol 2008; 16:612-9. [PMID: 18976920 PMCID: PMC3556578 DOI: 10.1016/j.tim.2008.08.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 08/21/2008] [Accepted: 08/26/2008] [Indexed: 12/24/2022]
Abstract
Pathogenic viral infections have exerted selection pressure on their hosts to evolve cellular antiviral inhibitors referred to as restriction factors. Examples of such molecules are APOBEC3G, APOBEC3F and TRIM5alpha. APOBEC3G and APOBEC3F are cytidine deaminases that are able to strongly inhibit retroviral replication by at least two mechanisms. They are counteracted by the lentiviral Vif protein. TRIM5alpha binds to sensitive, incoming retroviruses via its C-terminal PRY/SPRY domain and rapidly recruits them to the proteasome before significant viral DNA synthesis can occur. Both of these proteins robustly block retroviral replication in a species-specific way. It remains an open but important question as to whether innate restriction factors such as these can be harnessed to inhibit HIV-1 replication in humans.
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Affiliation(s)
- Hendrik Huthoff
- Department of Infectious Diseases, Guy's, King's and St Thomas' School of Medicine, London SE1 9RT, UK
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38
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Human immunodeficiency virus type 1 replication and regulation of APOBEC3G by peptidyl prolyl isomerase Pin1. J Virol 2008; 82:9928-36. [PMID: 18684817 DOI: 10.1128/jvi.01017-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
APOBEC3G (A3G) is a cytidine deaminase that restricts human immunodeficiency virus type 1 (HIV-1) replication. HIV-1 synthesizes a viral infectivity factor (Vif) to counter A3G restriction. Currently, it is poorly understood how A3G expression/activity is regulated by cellular factors. Here, we show that the prolyl isomerase Pin1 protein modulates A3G expression. Pin1 was found to be an A3G-interacting protein that reduces A3G expression and its incorporation into HIV-1 virion, thereby limiting A3G-mediated restriction of HIV-1. Intriguingly, HIV-1 infection modulates the phosphorylation state of Pin1, enhancing its ability to moderate A3G activity. These new findings suggest a potential Vif-independent way for HIV-1 to moderate the cellular action of A3G.
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