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Burdick RC, Morse M, Rouzina I, Williams MC, Hu WS, Pathak VK. HIV-1 uncoating requires long double-stranded reverse transcription products. Sci Adv 2024; 10:eadn7033. [PMID: 38657061 PMCID: PMC11042746 DOI: 10.1126/sciadv.adn7033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
HIV-1 cores, which contain the viral genome and replication machinery, must disassemble (uncoat) during viral replication. However, the viral and host factors that trigger uncoating remain unidentified. Recent studies show that infectious cores enter the nucleus and uncoat near the site of integration. Here, we show that efficient uncoating of nuclear cores requires synthesis of a double-stranded DNA (dsDNA) genome >3.5 kb and that the efficiency of uncoating correlates with genome size. Core disruption by capsid inhibitors releases viral DNA, some of which integrates. However, most of the viral DNA is degraded, indicating that the intact core safeguards viral DNA. Atomic force microscopy and core content estimation reveal that synthesis of full-length genomic dsDNA induces substantial internal strain on the core to promote uncoating. We conclude that HIV-1 cores protect viral DNA from degradation by host factors and that synthesis of long double-stranded reverse transcription products is required to trigger efficient HIV-1 uncoating.
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Affiliation(s)
- Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
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2
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Duchon A, Burdick RC, Pathak VK, Hu WS. Single-Virion Analysis: A Method to Visualize HIV-1 Particle Content Using Fluorescence Microscopy. Methods Mol Biol 2024; 2807:77-91. [PMID: 38743222 DOI: 10.1007/978-1-0716-3862-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
HIV-1 virions incorporate viral RNA, cellular RNAs, and proteins during the assembly process. Some of these components, such as the viral RNA genome and viral proteins, are essential for viral replication, whereas others, such as host innate immune proteins, can inhibit virus replication. Therefore, analyzing the virion content is an integral part of studying HIV-1 replication. Traditionally, virion contents have been examined using biochemical assays, which can provide information on the presence or absence of the molecule of interest but not its distribution in the virion population. Here, we describe a method, single-virion analysis, that directly examines the presence of molecules of interest in individual viral particles using fluorescence microscopy. Thus, this method can detect both the presence and the distribution of molecules of interest in the virion population. Single-virion analysis was first developed to study HIV-1 RNA genome packaging. In this assay, HIV-1 unspliced RNA is labeled with a fluorescently tagged RNA-binding protein (protein A) and some of the Gag proteins are labeled with a different fluorescent protein (protein B). Using fluorescence microscopy, HIV-1 particles can be identified by the fluorescent protein B signal and the presence of unspliced HIV-1 RNA can be identified by the fluorescent protein A signal. Therefore, the proportions of particles that contain unspliced RNA can be determined by the fraction of Gag particles that also have a colocalized RNA signal. By tagging the molecule of interest with fluorescent proteins, single-virion analysis can be easily adapted to study the incorporation of other viral or host cell molecules into particles. Indeed, this method has been adapted to examine the proportion of HIV-1 particles that contain APOBEC3 proteins and the fraction of particles that contain a modified Gag protein. Therefore, single-virion analysis is a flexible method to study the nucleic acid and protein content of HIV-1 particles.
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Affiliation(s)
- Alice Duchon
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA
| | - Ryan C Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA.
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3
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Burdick RC, Duchon A, Hu WS, Pathak VK. Imaging HIV-1 Nuclear Import, Uncoating, and Proviral Transcription. Methods Mol Biol 2024; 2807:15-30. [PMID: 38743218 DOI: 10.1007/978-1-0716-3862-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Live-cell imaging has become a powerful tool for dissecting the behavior of viral complexes during HIV-1 infection with high temporal and spatial resolution. Very few HIV-1 particles in a viral population are infectious and successfully complete replication (~1/50). Single-particle live-cell imaging enables the study of these rare infectious viral particles, which cannot be accomplished in biochemical assays that measure the average property of the entire viral population, most of which are not infectious. The timing and location of many events in the early stage of the HIV-1 life cycle, including nuclear import, uncoating, and integration, have only recently been elucidated. Live-cell imaging also provides a valuable approach to study interactions of viral and host factors in distinct cellular compartments and at specific stages of viral replication. Successful live-cell imaging experiments require careful consideration of the fluorescent labeling method used and avoid or minimize its potential impact on normal viral replication and produce misleading results. Ideally, it is beneficial to utilize multiple virus labeling strategies and compare the results to ensure that the virion labeling did not adversely influence the viral replication step that is under investigation. Another potential benefit of using different labeling strategies is that they can provide information about the state of the viral complexes. Here, we describe our methods that utilize multiple fluorescent protein labeling approaches to visualize and quantify important events in the HIV-1 life cycle, including docking HIV-1 particles with the nuclear envelope (NE) and their nuclear import, uncoating, and proviral transcription.
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Affiliation(s)
- Ryan C Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Alice Duchon
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.
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4
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Shen Q, Kumari S, Xu C, Jang S, Shi J, Burdick RC, Levintov L, Xiong Q, Wu C, Devarkar SC, Tian T, Tripler TN, Hu Y, Yuan S, Temple J, Feng Q, Lusk CP, Aiken C, Engelman AN, Perilla JR, Pathak VK, Lin C, Xiong Y. The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores. Proc Natl Acad Sci U S A 2023; 120:e2202815120. [PMID: 36943880 PMCID: PMC10068764 DOI: 10.1073/pnas.2202815120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/30/2023] [Indexed: 03/23/2023] Open
Abstract
Increasing evidence has suggested that the HIV-1 capsid enters the nucleus in a largely assembled, intact form. However, not much is known about how the cone-shaped capsid interacts with the nucleoporins (NUPs) in the nuclear pore for crossing the nuclear pore complex. Here, we elucidate how NUP153 binds HIV-1 capsid by engaging the assembled capsid protein (CA) lattice. A bipartite motif containing both canonical and noncanonical interaction modules was identified at the C-terminal tail region of NUP153. The canonical cargo-targeting phenylalanine-glycine (FG) motif engaged the CA hexamer. By contrast, a previously unidentified triple-arginine (RRR) motif in NUP153 targeted HIV-1 capsid at the CA tri-hexamer interface in the capsid. HIV-1 infection studies indicated that both FG- and RRR-motifs were important for the nuclear import of HIV-1 cores. Moreover, the presence of NUP153 stabilized tubular CA assemblies in vitro. Our results provide molecular-level mechanistic evidence that NUP153 contributes to the entry of the intact capsid into the nucleus.
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Affiliation(s)
- Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Sushila Kumari
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Jiong Shi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Ryan C. Burdick
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Qiancheng Xiong
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Swapnil C. Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Taoran Tian
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Therese N. Tripler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Vinay K. Pathak
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
- Department of Biomedical Engineering, Yale University, New Haven, CT06511
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
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5
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Ziegler SJ, Liu C, Landau M, Buzovetsky O, Desimmie BA, Zhao Q, Sasaki T, Burdick RC, Pathak VK, Anderson KS, Xiong Y. Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies. PLoS One 2018; 13:e0195048. [PMID: 29596531 PMCID: PMC5875850 DOI: 10.1371/journal.pone.0195048] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/15/2018] [Indexed: 01/27/2023] Open
Abstract
Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of deoxycytidine (dC) to deoxyuridine (dU) in single-stranded DNA (ssDNA). A3 proteins act in the innate immune response to viral infection by mutating the viral ssDNA. One of the most well-studied human A3 family members is A3G, which is a potent inhibitor of HIV-1. Each A3 protein prefers a specific substrate sequence for catalysis-for example, A3G deaminates the third dC in the CCCA sequence motif. However, the interaction between A3G and ssDNA is difficult to characterize due to poor solution behavior of the full-length protein and loss of DNA affinity of the truncated protein. Here, we present a novel DNA-anchoring fusion strategy using the protection of telomeres protein 1 (Pot1) which has nanomolar affinity for ssDNA, with which we captured an A3G-ssDNA interaction. We crystallized a non-preferred adenine in the -1 nucleotide-binding pocket of A3G. The structure reveals a unique conformation of the catalytic site loops that sheds light onto how the enzyme scans substrate in the -1 pocket. Furthermore, our biochemistry and virology studies provide evidence that the nucleotide-binding pockets on A3G influence each other in selecting the preferred DNA substrate. Together, the results provide insights into the mechanism by which A3G selects and deaminates its preferred substrates and help define how A3 proteins are tailored to recognize specific DNA sequences. This knowledge contributes to a better understanding of the mechanism of DNA substrate selection by A3G, as well as A3G antiviral activity against HIV-1.
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Affiliation(s)
- Samantha J. Ziegler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Chang Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Mark Landau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Olga Buzovetsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Belete A. Desimmie
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Qi Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Tomoaki Sasaki
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Karen S. Anderson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
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6
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Desimmie BA, Burdick RC, Izumi T, Doi H, Shao W, Alvord WG, Sato K, Koyanagi Y, Jones S, Wilson E, Hill S, Maldarelli F, Hu WS, Pathak VK. APOBEC3 proteins can copackage and comutate HIV-1 genomes. Nucleic Acids Res 2016; 44:7848-65. [PMID: 27439715 PMCID: PMC5027510 DOI: 10.1093/nar/gkw653] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/31/2023] Open
Abstract
Although APOBEC3 cytidine deaminases A3G, A3F, A3D and A3H are packaged into virions and inhibit viral replication by inducing G-to-A hypermutation, it is not known whether they are copackaged and whether they can act additively or synergistically to inhibit HIV-1 replication. Here, we showed that APOBEC3 proteins can be copackaged by visualization of fluorescently-tagged APOBEC3 proteins using single-virion fluorescence microscopy. We further determined that viruses produced in the presence of A3G + A3F and A3G + A3H, exhibited extensive comutation of viral cDNA, as determined by the frequency of G-to-A mutations in the proviral genomes in the contexts of A3G (GG-to-AG) and A3D, A3F or A3H (GA-to-AA) edited sites. The copackaging of A3G + A3F and A3G + A3H resulted in an additive increase and a modest synergistic increase (1.8-fold) in the frequency of GA-to-AA mutations, respectively. We also identified distinct editing site trinucleotide sequence contexts for each APOBEC3 protein and used them to show that hypermutation of proviral DNAs from seven patients was induced by A3G, A3F (or A3H), A3D and A3G + A3F (or A3H). These results indicate that APOBEC3 proteins can be copackaged and can comutate the same genomes, and can cooperate to inhibit HIV replication.
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Affiliation(s)
- Belete A Desimmie
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ryan C Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hibiki Doi
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei Shao
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Gregory Alvord
- Statistical Consulting, Data Management Services, Inc., Frederick, MD 21702, USA
| | - Kei Sato
- Institute of Virus Research, Kyoto University, Kyoto, 606-8057, Japan CREST, Japan Science and Technology Agency, Saitama, 332-0012, Japan
| | - Yoshio Koyanagi
- Institute of Virus Research, Kyoto University, Kyoto, 606-8057, Japan
| | - Sara Jones
- Leidos Biomedical Research, Inc., Bethesda, MD 20892, USA
| | - Eleanor Wilson
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Shawn Hill
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Frank Maldarelli
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Chikaev AN, Bakulina AY, Burdick RC, Karpenko LI, Pathak VK, Ilyichev AA. Selection of peptide mimics of HIV-1 epitope recognized by neutralizing antibody VRC01. PLoS One 2015; 10:e0120847. [PMID: 25785734 PMCID: PMC4364665 DOI: 10.1371/journal.pone.0120847] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 01/26/2015] [Indexed: 12/24/2022] Open
Abstract
The ability to induce anti-HIV-1 antibodies that can neutralize a broad spectrum of viral isolates from different subtypes seems to be a key requirement for development of an effective HIV-1 vaccine. The epitopes recognized by the most potent broadly neutralizing antibodies that have been characterized are largely discontinuous. Mimetics of such conformational epitopes could be potentially used as components of a synthetic immunogen that can elicit neutralizing antibodies. Here we used phage display technology to identify peptide motifs that mimic the epitope recognized by monoclonal antibody VRC01, which is able to neutralize up to 91% of circulating primary isolates. Three rounds of biopanning were performed against 2 different phage peptide libraries for this purpose. The binding specificity of selected phage clones to monoclonal antibody VRC01 was estimated using dot blot analysis. The putative peptide mimics exposed on the surface of selected phages were analyzed for conformational and linear homology to the surface of HIV-1 gp120 fragment using computational analysis. Corresponding peptides were synthesized and checked for their ability to interfere with neutralization activity of VRC01 in a competitive inhibition assay. One of the most common peptides selected from 12-mer phage library was found to partially mimic a CD4-binding loop fragment, whereas none of the circular C7C-mer peptides was able to mimic any HIV-1 domains. However, peptides identified from both the 12-mer and C7C-mer peptide libraries showed rescue of HIV-1 infectivity in the competitive inhibition assay. The identification of epitope mimics may lead to novel immunogens capable of inducing broadly reactive neutralizing antibodies.
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Affiliation(s)
- Anton N. Chikaev
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk region, 630559, Russia
- * E-mail:
| | - Anastasiya Yu. Bakulina
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk region, 630559, Russia
| | - Ryan C. Burdick
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Viral Mutation Section, Frederick, Maryland, 21702, United States of America
| | - Larisa I. Karpenko
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk region, 630559, Russia
| | - Vinay K. Pathak
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Viral Mutation Section, Frederick, Maryland, 21702, United States of America
| | - Alexander A. Ilyichev
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk region, 630559, Russia
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Mertens JA, Burdick RC, Rooney AP. Identification, biochemical characterization, and evolution of the Rhizopus oryzae 99–880 polygalacturonase gene family. Fungal Genet Biol 2008; 45:1616-24. [DOI: 10.1016/j.fgb.2008.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 09/22/2008] [Accepted: 09/30/2008] [Indexed: 11/25/2022]
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