1
|
Grandgenett DP, Engelman AN. Brief Histories of Retroviral Integration Research and Associated International Conferences. Viruses 2024; 16:604. [PMID: 38675945 PMCID: PMC11054761 DOI: 10.3390/v16040604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The field of retroviral integration research has a long history that started with the provirus hypothesis and subsequent discoveries of the retroviral reverse transcriptase and integrase enzymes. Because both enzymes are essential for retroviral replication, they became valued targets in the effort to discover effective compounds to inhibit HIV-1 replication. In 2007, the first integrase strand transfer inhibitor was licensed for clinical use, and subsequently approved second-generation integrase inhibitors are now commonly co-formulated with reverse transcriptase inhibitors to treat people living with HIV. International meetings specifically focused on integrase and retroviral integration research first convened in 1995, and this paper is part of the Viruses Special Issue on the 7th International Conference on Retroviral Integration, which was held in Boulder Colorado in the summer of 2023. Herein, we overview key historical developments in the field, especially as they pertain to the development of the strand transfer inhibitor drug class. Starting from the mid-1990s, research advancements are presented through the lens of the international conferences. Our overview highlights the impact that regularly scheduled, subject-specific international meetings can have on community-building and, as a result, on field-specific collaborations and scientific advancements.
Collapse
Affiliation(s)
- Duane P. Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO 63104, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
2
|
Dwivedi R, Prakash P, Kumbhar BV, Balasubramaniam M, Dash C. HIV-1 capsid and viral DNA integration. mBio 2024; 15:e0021222. [PMID: 38085100 PMCID: PMC10790781 DOI: 10.1128/mbio.00212-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE HIV-1 capsid protein (CA)-independently or by recruiting host factors-mediates several key steps of virus replication in the cytoplasm and nucleus of the target cell. Research in the recent years have established that CA is multifunctional and genetically fragile of all the HIV-1 proteins. Accordingly, CA has emerged as a validated and high priority therapeutic target, and the first CA-targeting antiviral drug was recently approved for treating multi-drug resistant HIV-1 infection. However, development of next generation CA inhibitors depends on a better understanding of CA's known roles, as well as probing of CA's novel roles, in HIV-1 replication. In this timely review, we present an updated overview of the current state of our understanding of CA's multifunctional role in HIV-1 replication-with a special emphasis on CA's newfound post-nuclear roles, highlight the pressing knowledge gaps, and discuss directions for future research.
Collapse
Affiliation(s)
- Richa Dwivedi
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed to be) University, Mumbai, Maharashtra, India
| | - Muthukumar Balasubramaniam
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| |
Collapse
|
3
|
Jang S, Engelman AN. Capsid-host interactions for HIV-1 ingress. Microbiol Mol Biol Rev 2023; 87:e0004822. [PMID: 37750702 PMCID: PMC10732038 DOI: 10.1128/mmbr.00048-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
The HIV-1 capsid, composed of approximately 1,200 copies of the capsid protein, encases genomic RNA alongside viral nucleocapsid, reverse transcriptase, and integrase proteins. After cell entry, the capsid interacts with a myriad of host factors to traverse the cell cytoplasm, pass through the nuclear pore complex (NPC), and then traffic to chromosomal sites for viral DNA integration. Integration may very well require the dissolution of the capsid, but where and when this uncoating event occurs remains hotly debated. Based on size constraints, a long-prevailing view was that uncoating preceded nuclear transport, but recent research has indicated that the capsid may remain largely intact during nuclear import, with perhaps some structural remodeling required for NPC traversal. Completion of reverse transcription in the nucleus may further aid capsid uncoating. One canonical type of host factor, typified by CPSF6, leverages a Phe-Gly (FG) motif to bind capsid. Recent research has shown these peptides reside amid prion-like domains (PrLDs), which are stretches of protein sequence devoid of charged residues. Intermolecular PrLD interactions along the exterior of the capsid shell impart avid host factor binding for productive HIV-1 infection. Herein we overview capsid-host interactions implicated in HIV-1 ingress and discuss important research questions moving forward. Highlighting clinical relevance, the long-acting ultrapotent inhibitor lenacapavir, which engages the same capsid binding pocket as FG host factors, was recently approved to treat people living with HIV.
Collapse
Affiliation(s)
- Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
4
|
Padron A, Prakash P, Pandhare J, Luban J, Aiken C, Balasubramaniam M, Dash C. Emerging role of cyclophilin A in HIV-1 infection: from producer cell to the target cell nucleus. J Virol 2023; 97:e0073223. [PMID: 37843371 PMCID: PMC10688351 DOI: 10.1128/jvi.00732-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
The HIV-1 genome encodes a small number of proteins with structural, enzymatic, regulatory, and accessory functions. These viral proteins interact with a number of host factors to promote the early and late stages of HIV-1 infection. During the early stages of infection, interactions between the viral proteins and host factors enable HIV-1 to enter the target cell, traverse the cytosol, dock at the nuclear pore, gain access to the nucleus, and integrate into the host genome. Similarly, the viral proteins recruit another set of host factors during the late stages of infection to orchestrate HIV-1 transcription, translation, assembly, and release of progeny virions. Among the host factors implicated in HIV-1 infection, Cyclophilin A (CypA) was identified as the first host factor to be packaged within HIV-1 particles. It is now well established that CypA promotes HIV-1 infection by directly binding to the viral capsid. Mechanistic models to pinpoint CypA's role have spanned from an effect in the producer cell to the early steps of infection in the target cell. In this review, we will describe our understanding of the role(s) of CypA in HIV-1 infection, highlight the current knowledge gaps, and discuss the potential role of this host factor in the post-nuclear entry steps of HIV-1 infection.
Collapse
Affiliation(s)
- Adrian Padron
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Jui Pandhare
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, USA
| | - Jeremy Luban
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Chris Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Muthukumar Balasubramaniam
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| |
Collapse
|
5
|
Sowd GA, Shi J, Fulmer A, Aiken C. HIV-1 capsid stability enables inositol phosphate-independent infection of target cells and promotes integration into genes. PLoS Pathog 2023; 19:e1011423. [PMID: 37267431 PMCID: PMC10266667 DOI: 10.1371/journal.ppat.1011423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/14/2023] [Accepted: 05/14/2023] [Indexed: 06/04/2023] Open
Abstract
The mature HIV-1 capsid is stabilized by host and viral determinants. The capsid protein CA binds to the cellular metabolites inositol hexakisphosphate (IP6) and its precursor inositol (1, 3, 4, 5, 6) pentakisphosphate (IP5) to stabilize the mature capsid. In target cells, capsid destabilization by the antiviral compounds lenacapavir and PF74 reveals a HIV-1 infectivity defect due to IP5/IP6 (IP5/6) depletion. To test whether intrinsic HIV-1 capsid stability and/or host factor binding determines HIV-1 insensitivity to IP5/6 depletion, a panel of CA mutants was assayed for infection of IP5/6-depleted T cells and wildtype cells. Four CA mutants with unstable capsids exhibited dependence on host IP5/6 for infection and reverse transcription (RTN). Adaptation of one such mutant, Q219A, by spread in culture resulted in Vpu truncation and a capsid three-fold interface mutation, T200I. T200I increased intrinsic capsid stability as determined by in vitro uncoating of purified cores and partially reversed the IP5/6-dependence in target cells for each of the four CA mutants. T200I further rescued the changes to lenacapavir sensitivity associated with the parental mutation. The premature dissolution of the capsid caused by the IP5/6-dependent mutations imparted a unique defect in integration targeting that was rescued by T200I. Collectively, these results demonstrate that T200I restored other capsid functions after RTN for the panel of mutants. Thus, the hyperstable T200I mutation stabilized the instability defects imparted by the parental IP5/6-dependent CA mutation. The contribution of Vpu truncation to mutant adaptation was linked to BST-2 antagonization, suggesting that cell-to-cell transfer promoted replication of the mutants. We conclude that interactions at the three-fold interface are adaptable, key mediators of capsid stability in target cells and are able to antagonize even severe capsid instability to promote infection.
Collapse
Affiliation(s)
- Gregory A. Sowd
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jiong Shi
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Ashley Fulmer
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| |
Collapse
|
6
|
Tough Way In, Tough Way Out: The Complex Interplay of Host and Viral Factors in Nucleocytoplasmic Trafficking during HIV-1 Infection. Viruses 2022; 14:v14112503. [PMID: 36423112 PMCID: PMC9696704 DOI: 10.3390/v14112503] [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: 08/31/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) is a retrovirus that integrates its reverse-transcribed genome as proviral DNA into the host genome to establish a successful infection. The viral genome integration requires safeguarding the subviral complexes, reverse transcription complex (RTC) and preintegration complex (PIC), in the cytosol from degradation, presumably effectively secured by the capsid surrounding these complexes. An intact capsid, however, is a large structure, which raises concerns about its translocation from cytoplasm to nucleus crossing the nuclear membrane, guarded by complex nuclear pore structures, which do not allow non-specific transport of large molecules. In addition, the generation of new virions requires the export of incompletely processed viral RNA from the nucleus to the cytoplasm, an event conventionally not permitted through mammalian nuclear membranes. HIV-1 has evolved multiple mechanisms involving redundant host pathways by liaison with the cell's nucleocytoplasmic trafficking system, failure of which would lead to the collapse of the infection cycle. This review aims to assemble the current developments in temporal and spatial events governing nucleocytoplasmic transport of HIV-1 factors. Discoveries are anticipated to serve as the foundation for devising host-directed therapies involving selective abolishment of the critical interactomes between viral proteins and their host equivalents.
Collapse
|
7
|
Allosteric Integrase Inhibitor Influences on HIV-1 Integration and Roles of LEDGF/p75 and HDGFL2 Host Factors. Viruses 2022; 14:v14091883. [PMID: 36146690 PMCID: PMC9502684 DOI: 10.3390/v14091883] [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: 07/28/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 02/01/2023] Open
Abstract
Allosteric integrase (IN) inhibitors (ALLINIs), which are promising preclinical compounds that engage the lens epithelium-derived growth factor (LEDGF)/p75 binding site on IN, can inhibit different aspects of human immunodeficiency virus 1 (HIV-1) replication. During the late phase of replication, ALLINIs induce aberrant IN hyper-multimerization, the consequences of which disrupt IN binding to genomic RNA and virus particle morphogenesis. During the early phase of infection, ALLINIs can suppress HIV-1 integration into host genes, which is also observed in LEDGF/p75-depelted cells. Despite this similarity, the roles of LEDGF/p75 and its paralog hepatoma-derived growth factor like 2 (HDGFL2) in ALLINI-mediated integration retargeting are untested. Herein, we mapped integration sites in cells knocked out for LEDGF/p75, HDGFL2, or both factors, which revealed that these two proteins in large part account for ALLINI-mediated integration retargeting during the early phase of infection. We also determined that ALLINI-treated viruses are defective during the subsequent round of infection for integration into genes associated with speckle-associated domains, which are naturally highly targeted for HIV-1 integration. Class II IN mutant viruses with alterations distal from the LEDGF/p75 binding site moreover shared this integration retargeting phenotype. Altogether, our findings help to inform the molecular bases and consequences of ALLINI action.
Collapse
|
8
|
Troyano-Hernáez P, Reinosa R, Holguín Á. HIV Capsid Protein Genetic Diversity Across HIV-1 Variants and Impact on New Capsid-Inhibitor Lenacapavir. Front Microbiol 2022; 13:854974. [PMID: 35495642 PMCID: PMC9039614 DOI: 10.3389/fmicb.2022.854974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
The HIV p24 capsid protein has an essential, structural, and functional role in the viral replication cycle, being an interesting target for vaccine design, diagnostic tests, and new antiretroviral drugs (ARVs). The HIV-1 variability poses a challenge for the accuracy and efficiency of diagnostic and treatment tools. This study analyzes p24 diversity among HIV-1 variants and within its secondary structure in HIV-1 M, O, P, and N groups. All available HIV-1 p24 nucleotide sequences were downloaded from the Los Alamos HIV Sequence Database, selecting 23,671 sequences belonging to groups O, N, P, and M (9 subtypes, 7 sub-sub types, and 109 circulating recombinant forms or CRFs). Using a bioinformatics tool developed in our laboratory (EpiMolBio program), we analyzed the amino acid conservation compared to the HXB2 subtype B reference sequence and the V-markers, or amino acid changes that were specific for each variant with at least 10 available sequences. We inferred the p24 consensus sequence for HIV-1 and for each group to analyze the overall conservation in p24 main structural regions, reporting the percentage of substitutions per variant affecting the capsid assembly and molecule-binding, including those associated with resistance to the new capsid-inhibitor lenacapavir, and the key residues involved in lenacapavir-p24 interaction, according to the bibliography. Although the overall structure of p24 was highly conserved, the conservation in the secondary structure varied between HIV-1 variants and the type of secondary structure. All HIV-1 variants presented >80% amino acid conservation vs. HXB2 reference sequence, except for group M sub-subtype F1 (69.27%). Mutants affecting the capsid assembly or lenacapavir capsid-binding were found in <1% of the p24 consensus sequence. Our study reports the HIV-1 variants carrying 14 unique single V-markers in 9/38 group M variants and the level of p24 conservation in each secondary structure region among the 4 HIV-1 groups and group M variants, revealing no natural resistance to lenacapavir in any HIV-1 variant. We present a thorough analysis of p24 variability among all HIV-1 variants circulating to date. Since p24 genetic variability can impact the viral replication cycle and the efficacy of new p24-based diagnostic, therapeutic, and vaccine strategies, conservation studies must consider all HIV-1 variants circulating worldwide.
Collapse
Affiliation(s)
- Paloma Troyano-Hernáez
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| | - Roberto Reinosa
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| |
Collapse
|
9
|
Abstract
A hallmark of retroviral replication is establishment of the proviral state, wherein a DNA copy of the viral RNA genome is stably incorporated into a host cell chromosome. Integrase is the viral enzyme responsible for the catalytic steps involved in this process, and integrase strand transfer inhibitors are widely used to treat people living with HIV. Over the past decade, a series of X-ray crystallography and cryogenic electron microscopy studies have revealed the structural basis of retroviral DNA integration. A variable number of integrase molecules congregate on viral DNA ends to assemble a conserved intasome core machine that facilitates integration. The structures additionally informed on the modes of integrase inhibitor action and the means by which HIV acquires drug resistance. Recent years have witnessed the development of allosteric integrase inhibitors, a highly promising class of small molecules that antagonize viral morphogenesis. In this Review, we explore recent insights into the organization and mechanism of the retroviral integration machinery and highlight open questions as well as new directions in the field.
Collapse
|
10
|
McFadden WM, Snyder AA, Kirby KA, Tedbury PR, Raj M, Wang Z, Sarafianos SG. Rotten to the core: antivirals targeting the HIV-1 capsid core. Retrovirology 2021; 18:41. [PMID: 34937567 PMCID: PMC8693499 DOI: 10.1186/s12977-021-00583-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
The capsid core of HIV-1 is a large macromolecular assembly that surrounds the viral genome and is an essential component of the infectious virus. In addition to its multiple roles throughout the viral life cycle, the capsid interacts with multiple host factors. Owing to its indispensable nature, the HIV-1 capsid has been the target of numerous antiretrovirals, though most capsid-targeting molecules have not had clinical success until recently. Lenacapavir, a long-acting drug that targets the HIV-1 capsid, is currently undergoing phase 2/3 clinical trials, making it the most successful capsid inhibitor to-date. In this review, we detail the role of the HIV-1 capsid protein in the virus life cycle, categorize antiviral compounds based on their targeting of five sites within the HIV-1 capsid, and discuss their molecular interactions and mechanisms of action. The diverse range of inhibition mechanisms provides insight into possible new strategies for designing novel HIV-1 drugs and furthers our understanding of HIV-1 biology. ![]()
Collapse
Affiliation(s)
- William M McFadden
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alexa A Snyder
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
| |
Collapse
|
11
|
Lau CY, Adan MA, Maldarelli F. Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection. Viruses 2021; 13:2512. [PMID: 34960781 PMCID: PMC8708047 DOI: 10.3390/v13122512] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antiretroviral therapy (ART) effectively reduces cycles of viral replication but does not target proviral populations in cells that persist for prolonged periods and that can undergo clonal expansion. Consequently, chronic human immunodeficiency virus (HIV) infection is sustained during ART by a reservoir of long-lived latently infected cells and their progeny. This proviral landscape undergoes change over time on ART. One of the forces driving change in the landscape is the clonal expansion of infected CD4 T cells, which presents a key obstacle to HIV eradication. Potential mechanisms of clonal expansion include general immune activation, antigenic stimulation, homeostatic proliferation, and provirus-driven clonal expansion, each of which likely contributes in varying, and largely unmeasured, amounts to maintaining the reservoir. The role of clinical events, such as infections or neoplasms, in driving these mechanisms remains uncertain, but characterizing these forces may shed light on approaches to effectively eradicate HIV. A limited number of individuals have been cured of HIV infection in the setting of bone marrow transplant; information from these and other studies may identify the means to eradicate or control the virus without ART. In this review, we describe the mechanisms of HIV-1 persistence and clonal expansion, along with the attempts to modify these factors as part of reservoir reduction and cure strategies.
Collapse
Affiliation(s)
- Chuen-Yen Lau
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
| | - Matthew A. Adan
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
- Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
| |
Collapse
|
12
|
Saito A, Yamashita M. HIV-1 capsid variability: viral exploitation and evasion of capsid-binding molecules. Retrovirology 2021; 18:32. [PMID: 34702294 PMCID: PMC8549334 DOI: 10.1186/s12977-021-00577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid.
Collapse
Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| |
Collapse
|
13
|
Bedwell GJ, Jang S, Li W, Singh PK, Engelman AN. rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo. Nucleic Acids Res 2021; 49:7330-7346. [PMID: 34165568 PMCID: PMC8287940 DOI: 10.1093/nar/gkab514] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/31/2021] [Accepted: 06/22/2021] [Indexed: 12/19/2022] Open
Abstract
HIV-1 integration favors recurrent integration gene (RIG) targets and genic proviruses can confer cell survival in vivo. However, the relationship between initial RIG integrants and how these evolve in patients over time are unknown. To address these shortcomings, we built phenomenological models of random integration in silico, which were used to identify 3718 RIGs as well as 2150 recurrent avoided genes from 1.7 million integration sites across 10 in vitro datasets. Despite RIGs comprising only 13% of human genes, they harbored 70% of genic HIV-1 integrations across in vitro and patient-derived datasets. Although previously reported to associate with super-enhancers, RIGs tracked more strongly with speckle-associated domains. While depletion of the integrase cofactor LEDGF/p75 significantly reduced recurrent HIV-1 integration in vitro, LEDGF/p75 primarily occupied non-speckle-associated regions of chromatin, suggesting a previously unappreciated dynamic aspect of LEDGF/p75 functionality in HIV-1 integration targeting. Finally, we identified only six genes from patient samples-BACH2, STAT5B, MKL1, MKL2, IL2RB and MDC1-that displayed enriched integration targeting frequencies and harbored proviruses that likely contributed to cell survival. Thus, despite the known preference of HIV-1 to target cancer-related genes for integration, we conclude that genic proviruses play a limited role to directly affect cell proliferation in vivo.
Collapse
Affiliation(s)
- Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
14
|
Yoder KE, Rabe AJ, Fishel R, Larue RC. Strategies for Targeting Retroviral Integration for Safer Gene Therapy: Advances and Challenges. Front Mol Biosci 2021; 8:662331. [PMID: 34055882 PMCID: PMC8149907 DOI: 10.3389/fmolb.2021.662331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Retroviruses are obligate intracellular parasites that must integrate a copy of the viral genome into the host DNA. The integration reaction is performed by the viral enzyme integrase in complex with the two ends of the viral cDNA genome and yields an integrated provirus. Retroviral vector particles are attractive gene therapy delivery tools due to their stable integration. However, some retroviral integration events may dysregulate host oncogenes leading to cancer in gene therapy patients. Multiple strategies to target retroviral integration, particularly to genetic safe harbors, have been tested with limited success. Attempts to target integration may be limited by the multimerization of integrase or the presence of host co-factors for integration. Several retroviral integration complexes have evolved a mechanism of tethering to chromatin via a host protein. Integration host co-factors bind chromatin, anchoring the complex and allowing integration. The tethering factor allows for both close proximity to the target DNA and specificity of targeting. Each retrovirus appears to have distinct preferences for DNA sequence and chromatin features at the integration site. Tethering factors determine the preference for chromatin features, but do not affect the subtle sequence preference at the integration site. The sequence preference is likely intrinsic to the integrase protein. New developments may uncouple the requirement for a tethering factor and increase the ability to redirect retroviral integration.
Collapse
Affiliation(s)
- Kristine E Yoder
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Anthony J Rabe
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Richard Fishel
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Ross C Larue
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
15
|
Toccafondi E, Lener D, Negroni M. HIV-1 Capsid Core: A Bullet to the Heart of the Target Cell. Front Microbiol 2021; 12:652486. [PMID: 33868211 PMCID: PMC8046902 DOI: 10.3389/fmicb.2021.652486] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
The first step of the intracellular phase of retroviral infection is the release of the viral capsid core in the cytoplasm. This structure contains the viral genetic material that will be reverse transcribed and integrated into the genome of infected cells. Up to recent times, the role of the capsid core was considered essentially to protect this genetic material during the earlier phases of this process. However, increasing evidence demonstrates that the permanence inside the cell of the capsid as an intact, or almost intact, structure is longer than thought. This suggests its involvement in more aspects of the infectious cycle than previously foreseen, particularly in the steps of viral genomic material translocation into the nucleus and in the phases preceding integration. During the trip across the infected cell, many host factors are brought to interact with the capsid, some possessing antiviral properties, others, serving as viral cofactors. All these interactions rely on the properties of the unique component of the capsid core, the capsid protein CA. Likely, the drawback of ensuring these multiple functions is the extreme genetic fragility that has been shown to characterize this protein. Here, we recapitulate the busy agenda of an HIV-1 capsid in the infectious process, in particular in the light of the most recent findings.
Collapse
Affiliation(s)
- Elenia Toccafondi
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Daniela Lener
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Matteo Negroni
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, Strasbourg, France
| |
Collapse
|
16
|
Janssens J, Bruggemans A, Christ F, Debyser Z. Towards a Functional Cure of HIV-1: Insight Into the Chromatin Landscape of the Provirus. Front Microbiol 2021; 12:636642. [PMID: 33868195 PMCID: PMC8044952 DOI: 10.3389/fmicb.2021.636642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Despite potent combination antiretroviral therapy, HIV-1 infection persists due to irreversible integration of the virus in long-living cells of the immune system. The main focus of HIV-1 cure strategies has been on HIV-1 eradication, yet without great success so far. Therefore, HIV-1 remission or a functional cure, whereby the virus is silenced rather than eradicated, is considered as an alternative strategy. Elite controllers, individuals who spontaneously control HIV-1, may point us the way toward a functional HIV-1 cure. In order to achieve such a cure, a profound understanding of the mechanisms controlling HIV-1 expression and silencing is needed. In recent years, evidence has grown that the site of integration as well as the chromatin landscape surrounding the integration site affects the transcriptional state of the provirus. Still, at present, the impact of integration site selection on the establishment and maintenance of the HIV-1 reservoirs remains poorly understood. The discovery of LEDGF/p75 as a binding partner of HIV-1 integrase has led to a better understanding of integration site selection. LEDGF/p75 is one of the important determinants of integration site selection and targets integration toward active genes. In this review, we will provide an overview of the most important determinants of integration site selection. Secondly, we will discuss the chromatin landscape at the integration site and its implications on HIV-1 gene expression and silencing. Finally, we will discuss how interventions that affect integration site selection or modifications of the chromatin could yield a functional cure of HIV-1 infection.
Collapse
Affiliation(s)
- Julie Janssens
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Anne Bruggemans
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| |
Collapse
|
17
|
Scoca V, Di Nunzio F. The HIV-1 Capsid: From Structural Component to Key Factor for Host Nuclear Invasion. Viruses 2021; 13:273. [PMID: 33578999 PMCID: PMC7916756 DOI: 10.3390/v13020273] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of HIV-1, the viral capsid has been recognized to have an important role as a structural protein that holds the viral genome, together with viral proteins essential for viral life cycle, such as the reverse transcriptase (RT) and the integrase (IN). The reverse transcription process takes place between the cytoplasm and the nucleus of the host cell, thus the Reverse Transcription Complexes (RTCs)/Pre-integration Complexes (PICs) are hosted in intact or partial cores. Early biochemical assays failed to identify the viral CA associated to the RTC/PIC, possibly due to the stringent detergent conditions used to fractionate the cells or to isolate the viral complexes. More recently, it has been observed that some host partners of capsid, such as Nup153 and CPSF6, can only bind multimeric CA proteins organized in hexamers. Those host factors are mainly located in the nuclear compartment, suggesting the entrance of the viral CA as multimeric structure inside the nucleus. Recent data show CA complexes within the nucleus having a different morphology from the cytoplasmic ones, clearly highlighting the remodeling of the viral cores during nuclear translocation. Thus, the multimeric CA complexes lead the viral genome into the host nuclear compartment, piloting the intranuclear journey of HIV-1 in order to successfully replicate. The aim of this review is to discuss and analyze the main discoveries to date that uncover the viral capsid as a key player in the reverse transcription and PIC maturation until the viral DNA integration into the host genome.
Collapse
Affiliation(s)
- Viviana Scoca
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology Pasteur Institute, 75015 Paris, France;
- BioSPC Doctoral School, Universitè de Paris, 75015 Paris, France
| | - Francesca Di Nunzio
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology Pasteur Institute, 75015 Paris, France;
| |
Collapse
|
18
|
Bedwell GJ, Engelman AN. Factors that mold the nuclear landscape of HIV-1 integration. Nucleic Acids Res 2021; 49:621-635. [PMID: 33337475 PMCID: PMC7826272 DOI: 10.1093/nar/gkaa1207] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/26/2020] [Indexed: 12/17/2022] Open
Abstract
The integration of retroviral reverse transcripts into the chromatin of the cells that they infect is required for virus replication. Retroviral integration has far-reaching consequences, from perpetuating deadly human diseases to molding metazoan evolution. The lentivirus human immunodeficiency virus 1 (HIV-1), which is the causative agent of the AIDS pandemic, efficiently infects interphase cells due to the active nuclear import of its preintegration complex (PIC). To enable integration, the PIC must navigate the densely-packed nuclear environment where the genome is organized into different chromatin states of varying accessibility in accordance with cellular needs. The HIV-1 capsid protein interacts with specific host factors to facilitate PIC nuclear import, while additional interactions of viral integrase, the enzyme responsible for viral DNA integration, with cellular nuclear proteins and nucleobases guide integration to specific chromosomal sites. HIV-1 integration favors transcriptionally active chromatin such as speckle-associated domains and disfavors heterochromatin including lamina-associated domains. In this review, we describe virus-host interactions that facilitate HIV-1 PIC nuclear import and integration site targeting, highlighting commonalities among factors that participate in both of these steps. We moreover discuss how the nuclear landscape influences HIV-1 integration site selection as well as the establishment of active versus latent virus infection.
Collapse
Affiliation(s)
- Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
19
|
Engelman AN. HIV Capsid and Integration Targeting. Viruses 2021; 13:125. [PMID: 33477441 PMCID: PMC7830116 DOI: 10.3390/v13010125] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/20/2022] Open
Abstract
Integration of retroviral reverse transcripts into the chromosomes of the cells that they infect is required for efficient viral gene expression and the inheritance of viral genomes to daughter cells. Before integration can occur, retroviral reverse transcription complexes (RTCs) must access the nuclear environment where the chromosomes reside. Retroviral integration is non-random, with different types of virus-host interactions impacting where in the host chromatin integration takes place. Lentiviruses such as HIV efficiently infect interphase cells because their RTCs have evolved to usurp cellular nuclear import transport mechanisms, and research over the past decade has revealed specific interactions between the HIV capsid protein and nucleoporin (Nup) proteins such as Nup358 and Nup153. The interaction of HIV capsid with cleavage and polyadenylation specificity factor 6 (CPSF6), which is a component of the cellular cleavage and polyadenylation complex, helps to dictate nuclear import as well as post-nuclear RTC invasion. In the absence of the capsid-CPSF6 interaction, RTCs are precluded from reaching nuclear speckles and gene-rich regions of chromatin known as speckle-associated domains, and instead mis-target lamina-associated domains out at the nuclear periphery. Highlighting this area of research, small molecules that inhibit capsid-host interactions important for integration site targeting are highly potent antiviral compounds.
Collapse
Affiliation(s)
- Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; ; Tel.: +1-617-632-4361
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
20
|
Capsid Lattice Destabilization Leads to Premature Loss of the Viral Genome and Integrase Enzyme during HIV-1 Infection. J Virol 2020; 95:JVI.00984-20. [PMID: 33115869 DOI: 10.1128/jvi.00984-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/24/2020] [Indexed: 01/28/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein forms a conical lattice around the viral ribonucleoprotein complex (vRNP) consisting of a dimeric viral genome and associated proteins, together constituting the viral core. Upon entry into target cells, the viral core undergoes a process termed uncoating, during which CA molecules are shed from the lattice. Although the timing and degree of uncoating are important for reverse transcription and integration, the molecular basis of this phenomenon remains unclear. Using complementary approaches, we assessed the impact of core destabilization on the intrinsic stability of the CA lattice in vitro and fates of viral core components in infected cells. We found that substitutions in CA can impact the intrinsic stability of the CA lattice in vitro in the absence of vRNPs, which mirrored findings from an assessment of CA stability in virions. Altering CA stability tended to increase the propensity to form morphologically aberrant particles, in which the vRNPs were mislocalized between the CA lattice and the viral lipid envelope. Importantly, destabilization of the CA lattice led to premature dissociation of CA from vRNPs in target cells, which was accompanied by proteasomal-independent losses of the viral genome and integrase enzyme. Overall, our studies show that the CA lattice protects the vRNP from untimely degradation in target cells and provide the mechanistic basis of how CA stability influences reverse transcription.IMPORTANCE The human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein forms a conical lattice around the viral RNA genome and the associated viral enzymes and proteins, together constituting the viral core. Upon infection of a new cell, viral cores are released into the cytoplasm where they undergo a process termed "uncoating," i.e., shedding of CA molecules from the conical lattice. Although proper and timely uncoating has been shown to be important for reverse transcription, the molecular mechanisms that link these two events remain poorly understood. In this study, we show that destabilization of the CA lattice leads to premature dissociation of CA from viral cores, which exposes the viral genome and the integrase enzyme for degradation in target cells. Thus, our studies demonstrate that the CA lattice protects the viral ribonucleoprotein complexes from untimely degradation in target cells and provide the first causal link between how CA stability affects reverse transcription.
Collapse
|
21
|
Li W, Singh PK, Sowd GA, Bedwell GJ, Jang S, Achuthan V, Oleru AV, Wong D, Fadel HJ, Lee K, KewalRamani VN, Poeschla EM, Herschhorn A, Engelman AN. CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration. mBio 2020; 11:e02254-20. [PMID: 32994325 PMCID: PMC7527728 DOI: 10.1128/mbio.02254-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
Lentiviral DNA integration favors transcriptionally active chromatin. We previously showed that the interaction of human immunodeficiency virus type 1 (HIV-1) capsid with cleavage and polyadenylation specificity factor 6 (CPSF6) localizes viral preintegration complexes (PICs) to nuclear speckles for integration into transcriptionally active speckle-associated domains (SPADs). In the absence of the capsid-CPSF6 interaction, PICs uncharacteristically accumulate at the nuclear periphery and target heterochromatic lamina-associated domains (LADs) for integration. The integrase-binding protein lens epithelium-derived growth factor (LEDGF)/p75 in contrast to CPSF6 predominantly functions to direct HIV-1 integration to interior regions of transcription units. Though CPSF6 and LEDGF/p75 can reportedly interact with the capsid and integrase proteins of both primate and nonprimate lentiviruses, the extents to which these different viruses target SPADs versus LADs, as well as their dependencies on CPSF6 and LEDGF/p75 for integration targeting, are largely unknown. Here, we mapped 5,489,157 primate and nonprimate lentiviral integration sites in HEK293T and Jurkat T cells as well as derivative cells that were knocked out or knocked down for host factor expression. Despite marked preferences of all lentiviruses to target genes for integration, nonprimate lentiviruses only marginally favored SPADs, with corresponding upticks in LAD-proximal integration. While LEDGF/p75 knockout disrupted the intragenic integration profiles of all lentiviruses similarly, CPSF6 depletion specifically counteracted SPAD integration targeting by primate lentiviruses. CPSF6 correspondingly failed to appreciably interact with nonprimate lentiviral capsids. We conclude that primate lentiviral capsid proteins evolved to interact with CPSF6 to optimize PIC localization for integration into transcriptionally active SPADs.IMPORTANCE Integration is the defining step of the retroviral life cycle and underlies the inability to cure HIV/AIDS through the use of intensified antiviral therapy. The reservoir of latent, replication-competent proviruses that forms early during HIV infection reseeds viremia when patients discontinue medication. HIV cure research is accordingly focused on the factors that guide provirus formation and associated chromatin environments that regulate transcriptional reactivation, and studies of orthologous infectious agents such as nonprimate lentiviruses can inform basic principles of HIV biology. HIV-1 utilizes the integrase-binding protein LEDGF/p75 and the capsid interactor CPSF6 to target speckle-associated domains (SPADs) for integration. However, the extent to which these two host proteins regulate integration of other lentiviruses is largely unknown. Here, we mapped millions of retroviral integration sites in cell lines that were depleted for LEDGF/p75 and/or CPSF6. Our results reveal that primate lentiviruses uniquely target SPADs for integration in a CPSF6-dependent manner.
Collapse
Affiliation(s)
- Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory A Sowd
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Amarachi V Oleru
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Doris Wong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Hind J Fadel
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - KyeongEun Lee
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Alon Herschhorn
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
22
|
Santos da Silva E, Shanmugapriya S, Malikov V, Gu F, Delaney MK, Naghavi MH. HIV-1 capsids mimic a microtubule regulator to coordinate early stages of infection. EMBO J 2020; 39:e104870. [PMID: 32896909 DOI: 10.15252/embj.2020104870] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 01/09/2023] Open
Abstract
While the microtubule end-binding protein, EB1 facilitates early stages of HIV-1 infection, how it does so remains unclear. Here, we show that beyond its effects on microtubule acetylation, EB1 also indirectly contributes to infection by delivering the plus-end tracking protein (+TIP), cytoplasmic linker protein 170 (CLIP170) to the cell periphery. CLIP170 bound to intact HIV-1 cores or in vitro assembled capsid-nucleocapsid complexes, while EB1 did not. Moreover, unlike EB1 and several other +TIPs, CLIP170 enhanced infection independently of effects on microtubule acetylation. Capsid mutants and imaging revealed that CLIP170 bound HIV-1 cores in a manner distinct from currently known capsid cofactors, influenced by pentamer composition or curvature. Structural analyses revealed an EB-like +TIP-binding motif within the capsid major homology region (MHR) that binds SxIP motifs found in several +TIPs, and variability across this MHR sequence correlated with the extent to which different retroviruses engage CLIP170 to facilitate infection. Our findings provide mechanistic insights into the complex roles of +TIPs in mediating early stages of retroviral infection, and reveal divergent capsid-based EB1 mimicry across retroviral species.
Collapse
Affiliation(s)
- Eveline Santos da Silva
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Shanmugapriya Shanmugapriya
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Viacheslav Malikov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Feng Gu
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - M Keegan Delaney
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mojgan H Naghavi
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
23
|
How HIV-1 Gag Manipulates Its Host Cell Proteins: A Focus on Interactors of the Nucleocapsid Domain. Viruses 2020; 12:v12080888. [PMID: 32823718 PMCID: PMC7471995 DOI: 10.3390/v12080888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/27/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) polyprotein Gag (Group-specific antigen) plays a central role in controlling the late phase of the viral lifecycle. Considered to be only a scaffolding protein for a long time, the structural protein Gag plays determinate and specific roles in HIV-1 replication. Indeed, via its different domains, Gag orchestrates the specific encapsidation of the genomic RNA, drives the formation of the viral particle by its auto-assembly (multimerization), binds multiple viral proteins, and interacts with a large number of cellular proteins that are needed for its functions from its translation location to the plasma membrane, where newly formed virions are released. Here, we review the interactions between HIV-1 Gag and 66 cellular proteins. Notably, we describe the techniques used to evidence these interactions, the different domains of Gag involved, and the implications of these interactions in the HIV-1 replication cycle. In the final part, we focus on the interactions involving the highly conserved nucleocapsid (NC) domain of Gag and detail the functions of the NC interactants along the viral lifecycle.
Collapse
|
24
|
Francis AC, Marin M, Singh PK, Achuthan V, Prellberg MJ, Palermino-Rowland K, Lan S, Tedbury PR, Sarafianos SG, Engelman AN, Melikyan GB. HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains. Nat Commun 2020; 11:3505. [PMID: 32665593 PMCID: PMC7360574 DOI: 10.1038/s41467-020-17256-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
The early steps of HIV-1 infection, such as uncoating, reverse transcription, nuclear import, and transport to integration sites are incompletely understood. Here, we imaged nuclear entry and transport of HIV-1 replication complexes in cell lines, primary monocyte-derived macrophages (MDMs) and CD4+ T cells. We show that viral replication complexes traffic to and accumulate within nuclear speckles and that these steps precede the completion of viral DNA synthesis. HIV-1 transport to nuclear speckles is dependent on the interaction of the capsid proteins with host cleavage and polyadenylation specificity factor 6 (CPSF6), which is also required to stabilize the association of the viral replication complexes with nuclear speckles. Importantly, integration site analyses reveal a strong preference for HIV-1 to integrate into speckle-associated genomic domains. Collectively, our results demonstrate that nuclear speckles provide an architectural basis for nuclear homing of HIV-1 replication complexes and subsequent integration into associated genomic loci. Early steps of HIV infection of primary human cells remain poorly understood. Here, Francis et al. show that early viral replication complexes accumulate within nuclear speckles, in reliance on viral capsid/host CPSF6 interactions, and preferentially integrate in speckle-associated genomic domains.
Collapse
Affiliation(s)
- Ashwanth C Francis
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Mariana Marin
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Mathew J Prellberg
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Kristina Palermino-Rowland
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Shuiyun Lan
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Gregory B Melikyan
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
| |
Collapse
|
25
|
Chaudhuri E, Dash S, Balasubramaniam M, Padron A, Holland J, Sowd GA, Villalta F, Engelman AN, Pandhare J, Dash C. The HIV-1 capsid-binding host factor CPSF6 is post-transcriptionally regulated by the cellular microRNA miR-125b. J Biol Chem 2020; 295:5081-5094. [PMID: 32152226 DOI: 10.1074/jbc.ra119.010534] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/27/2020] [Indexed: 12/15/2022] Open
Abstract
Cleavage and polyadenylation specificity factor 6 (CPSF6) is a cellular protein involved in mRNA processing. Emerging evidence suggests that CPSF6 also plays key roles in HIV-1 infection, specifically during nuclear import and integration targeting. However, the cellular and molecular mechanisms that regulate CPSF6 expression are largely unknown. In this study, we report a post-transcriptional mechanism that regulates CPSF6 via the cellular microRNA miR-125b. An in silico analysis revealed that the 3'UTR of CPSF6 contains a miR-125b-binding site that is conserved across several mammalian species. Because miRNAs repress protein expression, we tested the effects of miR-125b expression on CPSF6 levels in miR-125b knockdown and over-expression experiments, revealing that miR-125b and CPSF6 levels are inversely correlated. To determine whether miR-125b post-transcriptionally regulates CPSF6, we introduced the 3'UTR of CPSF6 mRNA into a luciferase reporter and found that miR-125b negatively regulates CPSF6 3'UTR-driven luciferase activity. Accordingly, mutations in the miR-125b seed sequence abrogated the regulatory effect of the miRNA on the CPSF6 3'UTR. Finally, pulldown experiments demonstrated that miR-125b physically interacts with CPSF6 3'UTR. Interestingly, HIV-1 infection down-regulated miR-125b expression concurrent with up-regulation of CPSF6. Notably, miR-125b down-regulation in infected cells was not due to reduced pri-miRNA or pre-miRNA levels. However, miR-125b down-regulation depended on HIV-1 reverse transcription but not viral DNA integration. These findings establish a post-transcriptional mechanism that controls CPSF6 expression and highlight a novel function of miR-125b during HIV-host interaction.
Collapse
Affiliation(s)
- Evan Chaudhuri
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee 37208.,Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee 37208
| | - Sabyasachi Dash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee 37208.,Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee 37208.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10065
| | - Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee 37208.,Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee 37208
| | - Adrian Padron
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee 37208.,Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee 37208.,School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee 37208
| | - Joseph Holland
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee 37208.,Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee 37208
| | - Gregory A Sowd
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
| | - Fernando Villalta
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee 37208.,Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee 37208
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee 37208.,Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee 37208.,School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee 37208
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee 37208 .,Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee 37208.,School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee 37208
| |
Collapse
|
26
|
Ingram Z, Taylor M, Okland G, Martin R, Hulme AE. Characterization of HIV-1 uncoating in human microglial cell lines. Virol J 2020; 17:31. [PMID: 32143686 PMCID: PMC7060623 DOI: 10.1186/s12985-020-01301-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Background After viral fusion with the cell membrane, the conical capsid of HIV-1 disassembles by a process called uncoating. Previously we have utilized the CsA washout assay, in which TRIM-CypA mediated restriction of viral replication is used to detect the state of the viral capsid, to study the kinetics of HIV-1 uncoating in owl monkey kidney (OMK) and HeLa cells. Here we have extended this analysis to the human microglial cell lines CHME3 and C20 to characterize uncoating in a cell type that is a natural target of HIV infection. Methods The CsA washout was used to characterize uncoating of wildtype and capsid mutant viruses in CHME3 and C20 cells. Viral fusion assays and nevirapine addition assays were performed to relate the kinetics of viral fusion and reverse transcription to uncoating. Results We found that uncoating initiated within the first hour after viral fusion and was facilitated by reverse transcription in CHME3 and C20 cells. The capsid mutation A92E did not significantly alter uncoating kinetics. Viruses with capsid mutations N74D and E45A decreased the rate of uncoating in CHME3 cells, but did not alter reverse transcription. Interestingly, the second site suppressor capsid mutation R132T was able to rescue the uncoating kinetics of the E45A mutation, despite having a hyperstable capsid. Conclusions These results are most similar to previously observed characteristics of uncoating in HeLa cells and support the model in which uncoating is initiated by early steps of reverse transcription in the cytoplasm. A comparison of the uncoating kinetics of CA mutant viruses in OMK and CHME3 cells reveals the importance of cellular factors in the process of uncoating. The E45A/R132T mutant virus specifically suggests that disrupted interactions with cellular factors, rather than capsid stability, is responsible for the delayed uncoating kinetics seen in E45A mutant virus. Future studies aimed at identifying these factors will be important for understanding the process of uncoating and the development of interventions to disrupt this process.
Collapse
Affiliation(s)
- Zachary Ingram
- Department of Biomedical Sciences, Missouri State University, Springfield, MO, USA
| | - Melanie Taylor
- Department of Biomedical Sciences, Missouri State University, Springfield, MO, USA
| | - Glister Okland
- Department of Biomedical Sciences, Missouri State University, Springfield, MO, USA
| | - Richard Martin
- Department of Biomedical Sciences, Missouri State University, Springfield, MO, USA
| | - Amy E Hulme
- Department of Biomedical Sciences, Missouri State University, Springfield, MO, USA.
| |
Collapse
|
27
|
Dominant Negative MA-CA Fusion Protein Is Incorporated into HIV-1 Cores and Inhibits Nuclear Entry of Viral Preintegration Complexes. J Virol 2019; 93:JVI.01118-19. [PMID: 31413124 DOI: 10.1128/jvi.01118-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 08/03/2019] [Indexed: 11/20/2022] Open
Abstract
Particle maturation is a critical step in the HIV-1 replication cycle that requires proteolytic cleavage of the Gag polyprotein into its constitutive proteins: the matrix (MA), capsid (CA), nucleocapsid (NC), and p6 proteins. The accurate and efficient cleavage of Gag is essential for virion infectivity; inhibitors of the viral protease are potent antivirals, and substitutions in Gag that prevent its cleavage result in reduced HIV-1 infectivity. In a previous study, a mutation inhibiting cleavage at the MA-CA junction was observed to potently inhibit virus infection: incorporation of small amounts of uncleaved MA-CA protein into HIV-1 particles inhibited infectivity by ∼95%, and the resulting viral particles exhibited aberrant capsids. Here we report a detailed mechanistic analysis of HIV-1 particles bearing uncleaved MA-CA protein. We show that the particles contain stable cores and can efficiently saturate host restriction by TRIMCyp in target cells. We further show that MA-CA associates with CA in particles without detectably affecting the formation of intermolecular CA interfaces. Incorporation of MA-CA did not markedly affect reverse transcription in infected cells, but nuclear entry was impaired and integration targeting was altered. Additionally, results from mutational analysis of Gag revealed that membrane-binding elements of MA contribute to the antiviral activity of uncleaved MA-CA protein. Our results suggest that small amounts of partially processed Gag subunits coassemble with CA during virion maturation, resulting in impaired capsid functions.IMPORTANCE To become infectious, newly formed HIV-1 particles undergo a process of maturation in which the viral polyproteins are cleaved into smaller components. A previous study demonstrated that inclusion of even small quantities of an uncleavable mutant Gag polyprotein results in a strong reduction in virus infectivity. Here we show that the mechanism of transdominant inhibition by uncleavable Gag involves inhibition of nuclear entry and alteration of viral integration sites. Additionally, the results of mutational analysis suggest that the membrane-binding activity of Gag is a major requirement for the antiviral activity. These results further define the antiviral mechanism of uncleavable Gag, which may be useful for exploiting this effect to develop new antivirals.
Collapse
|
28
|
Interferon-Inducible MicroRNA miR-128 Modulates HIV-1 Replication by Targeting TNPO3 mRNA. J Virol 2019; 93:JVI.00364-19. [PMID: 31341054 DOI: 10.1128/jvi.00364-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
The HIV/AIDS pandemic remains an important threat to human health. We have recently demonstrated that a novel microRNA (miR), miR-128, represses retrotransposon long interspaced element 1 (L1) by a dual mechanism, namely, by directly targeting the coding region of the L1 RNA and by repressing a required nuclear import factor (TNPO1). We have further determined that miR-128 represses the expression of all three TNPO proteins (transportins TNPO1, TNPO2, and TNPO3). Here, we establish that miR-128 also influences HIV-1 replication by repressing TNPO3, a factor that regulates HIV-1 nuclear import and viral; replication of TNPO3 is well established to regulate HIV-1 nuclear import and viral replication. Here, we report that type I interferon (IFN)-inducible miR-128 directly targets two sites in the TNPO3 mRNA, significantly downregulating TNPO3 mRNA and protein expression levels. Challenging miR-modulated Jurkat cells or primary CD4+ T-cells with wild-type (WT), replication-competent HIV-1 demonstrated that miR-128 reduces viral replication and delays spreading of infection. Manipulation of miR-128 levels in HIV-1 target cell lines and in primary CD4+ T-cells by overexpression or knockdown showed that reduction of TNPO3 levels by miR-128 significantly affects HIV-1 replication but not murine leukemia virus (MLV) infection and that miR-128 modulation of HIV-1 replication is reduced with TNPO3-independent HIV-1 virus, suggesting that miR-128-indued TNPO3 repression contributes to the inhibition of HIV-1 replication. Finally, we determine that anti-miR-128 partly neutralizes the IFN-mediated block of HIV-1. Thus, we have established a novel role of miR-128 in antiviral defense in human cells, namely inhibiting HIV-1 replication by altering the cellular milieu through targeting factors that include TNPO3.IMPORTANCE HIV-1 is the causative agent of AIDS. During HIV-1 infection, type I interferons (IFNs) are induced, and their effectors limit HIV-1 replication at multiple steps in its life cycle. However, the cellular targets of INFs are still largely unknown. In this study, we identified the interferon-inducible microRNA (miR) miR-128, a novel antiviral mediator that suppresses the expression of the host gene TNPO3, which is known to modulate HIV-1 replication. Notably, we observe that anti-miR-128 partly neutralizes the IFN-mediated block of HIV-1. Elucidation of the mechanisms through which miR-128 impairs HIV-1 replication may provide novel candidates for the development of therapeutic interventions.
Collapse
|
29
|
Shukla E, Chauhan R. Host-HIV-1 Interactome: A Quest for Novel Therapeutic Intervention. Cells 2019; 8:cells8101155. [PMID: 31569640 PMCID: PMC6830350 DOI: 10.3390/cells8101155] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
The complex nature and structure of the human immunodeficiency virus has rendered the cure for HIV infections elusive. The advances in antiretroviral treatment regimes and the development of highly advanced anti-retroviral therapy, which primarily targets the HIV enzymes, have dramatically changed the face of the HIV epidemic worldwide. Despite this remarkable progress, patients treated with these drugs often witness inadequate efficacy, compound toxicity and non-HIV complications. Considering the limited inventory of druggable HIV proteins and their susceptibility to develop drug resistance, recent attempts are focussed on targeting HIV-host interactomes that are essential for viral reproduction. Noticeably, unlike other viruses, HIV subverts the host nuclear pore complex to enter into and exit through the nucleus. Emerging evidence suggests a crucial role of interactions between HIV-1 proteins and host nucleoporins that underlie the import of the pre-integration complex into the nucleus and export of viral RNAs into the cytoplasm during viral replication. Nevertheless, the interaction of HIV-1 with nucleoporins has been poorly described and the role of nucleoporins during nucleocytoplasmic transport of HIV-1 still remains unclear. In this review, we highlight the advances and challenges in developing a more effective antiviral arsenal by exploring critical host-HIV interactions with a special focus on nuclear pore complex (NPC) and nucleoporins.
Collapse
Affiliation(s)
- Ekta Shukla
- National Center for Cell Science, S.P Pune University, Pune-411007, Maharashtra, India.
| | - Radha Chauhan
- National Center for Cell Science, S.P Pune University, Pune-411007, Maharashtra, India.
| |
Collapse
|
30
|
Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration. Nat Commun 2019; 10:4059. [PMID: 31492853 PMCID: PMC6731298 DOI: 10.1038/s41467-019-12046-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
HIV-1 recurrently targets active genes and integrates in the proximity of the nuclear pore compartment in CD4+ T cells. However, the genomic features of these genes and the relevance of their transcriptional activity for HIV-1 integration have so far remained unclear. Here we show that recurrently targeted genes are proximal to super-enhancer genomic elements and that they cluster in specific spatial compartments of the T cell nucleus. We further show that these gene clusters acquire their location during the activation of T cells. The clustering of these genes along with their transcriptional activity are the major determinants of HIV-1 integration in T cells. Our results provide evidence of the relevance of the spatial compartmentalization of the genome for HIV-1 integration, thus further strengthening the role of nuclear architecture in viral infection.
Collapse
|
31
|
A Novel Phenotype Links HIV-1 Capsid Stability to cGAS-Mediated DNA Sensing. J Virol 2019; 93:JVI.00706-19. [PMID: 31167922 DOI: 10.1128/jvi.00706-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/19/2019] [Indexed: 01/27/2023] Open
Abstract
The HIV-1 capsid executes essential functions that are regulated by capsid stability and host factors. In contrast to increasing knowledge on functional roles of capsid-interacting host proteins during postentry steps, less is known about capsid stability and its impact on intracellular events. Here, using the antiviral compound PF-3450074 (PF74) as a probe for capsid function, we uncovered a novel phenotype of capsid stability that has a profound effect on innate sensing of viral DNA by the DNA sensor cGAS. A single mutation, R143A, in the capsid protein conferred resistance to high concentrations of PF74, without affecting capsid binding to PF74. A cell-free assay showed that the R143A mutant partially counteracted the capsid-destabilizing activity of PF74, pointing to capsid stabilization as a resistance mechanism for the R143A mutant. In monocytic THP-1 cells, the R143A virus, but not the wild-type virus, suppressed cGAS-dependent innate immune activation. These results suggest that capsid stabilization improves the shielding of viral DNA from innate sensing. We found that a naturally occurring transmitted founder (T/F) variant shares the same properties as the R143A mutant with respect to PF74 resistance and DNA sensing. Imaging assays revealed delayed uncoating kinetics of this T/F variant and the R143A mutant. All these phenotypes of this T/F variant were controlled by a genetic polymorphism located at the trimeric interface between capsid hexamers, thus linking these capsid-dependent properties. Overall, this work functionally connects capsid stability to innate sensing of viral DNA and reveals naturally occurring phenotypic variation in HIV-1 capsid stability.IMPORTANCE The HIV-1 capsid, which is made from individual viral capsid proteins (CA), is a target for a number of antiviral compounds, including the small-molecule inhibitor PF74. In the present study, we utilized PF74 to identify a transmitted/founder (T/F) strain that shows increased capsid stability. Interestingly, PF74-resistant variants prevented cGAS-dependent innate immune activation under a condition where the other T/F strains induced type I interferon. These observations thus reveal a new CA-specific phenotype that couples capsid stability to viral DNA recognition by cytosolic DNA sensors.
Collapse
|
32
|
Jang S, Cook NJ, Pye VE, Bedwell GJ, Dudek AM, Singh PK, Cherepanov P, Engelman AN. Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6. Nucleic Acids Res 2019; 47:4663-4683. [PMID: 30916345 PMCID: PMC6511849 DOI: 10.1093/nar/gkz206] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 02/12/2019] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
Cleavage factor I mammalian (CFIm) complex, composed of cleavage and polyadenylation specificity factor 5 (CPSF5) and serine/arginine-like protein CPSF6, regulates alternative polyadenylation (APA). Loss of CFIm function results in proximal polyadenylation site usage, shortening mRNA 3' untranslated regions (UTRs). Although CPSF6 plays additional roles in human disease, its nuclear translocation mechanism remains unresolved. Two β-karyopherins, transportin (TNPO) 1 and TNPO3, can bind CPSF6 in vitro, and we demonstrate here that while the TNPO1 binding site is dispensable for CPSF6 nuclear import, the arginine/serine (RS)-like domain (RSLD) that mediates TNPO3 binding is critical. The crystal structure of the RSLD-TNPO3 complex revealed potential CPSF6 interaction residues, which were confirmed to mediate TNPO3 binding and CPSF6 nuclear import. Both binding and nuclear import were independent of RSLD phosphorylation, though a hyperphosphorylated mimetic mutant failed to bind TNPO3 and mislocalized to the cell cytoplasm. Although hypophosphorylated CPSF6 largely supported normal polyadenylation site usage, a significant number of mRNAs harbored unnaturally extended 3' UTRs, similar to what is observed when other APA regulators, such as CFIIm component proteins, are depleted. Our results clarify the mechanism of CPSF6 nuclear import and highlight differential roles for RSLD phosphorylation in nuclear translocation versus regulation of APA.
Collapse
Affiliation(s)
- Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nicola J Cook
- Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK
| | - Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda M Dudek
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Medicine, Imperial College London, St-Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
33
|
D Urbano V, De Crignis E, Re MC. Host Restriction Factors and Human Immunodeficiency Virus (HIV-1): A Dynamic Interplay Involving All Phases of the Viral Life Cycle. Curr HIV Res 2019; 16:184-207. [PMID: 30117396 DOI: 10.2174/1570162x16666180817115830] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/31/2018] [Accepted: 08/09/2018] [Indexed: 02/08/2023]
Abstract
Mammalian cells have evolved several mechanisms to prevent or block lentiviral infection and spread. Among the innate immune mechanisms, the signaling cascade triggered by type I interferon (IFN) plays a pivotal role in limiting the burden of HIV-1. In the presence of IFN, human cells upregulate the expression of a number of genes, referred to as IFN-stimulated genes (ISGs), many of them acting as antiviral restriction factors (RFs). RFs are dominant proteins that target different essential steps of the viral cycle, thereby providing an early line of defense against the virus. The identification and characterization of RFs have provided unique insights into the molecular biology of HIV-1, further revealing the complex host-pathogen interplay that characterizes the infection. The presence of RFs drove viral evolution, forcing the virus to develop specific proteins to counteract their activity. The knowledge of the mechanisms that prevent viral infection and their viral counterparts may offer new insights to improve current antiviral strategies. This review provides an overview of the RFs targeting HIV-1 replication and the mechanisms that regulate their expression as well as their impact on viral replication and the clinical course of the disease.
Collapse
Affiliation(s)
- Vanessa D Urbano
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Elisa De Crignis
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Carla Re
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| |
Collapse
|
34
|
Novikova M, Zhang Y, Freed EO, Peng K. Multiple Roles of HIV-1 Capsid during the Virus Replication Cycle. Virol Sin 2019; 34:119-134. [PMID: 31028522 PMCID: PMC6513821 DOI: 10.1007/s12250-019-00095-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/16/2019] [Indexed: 11/29/2022] Open
Abstract
Human immunodeficiency virus-1 capsid (HIV-1 CA) is involved in different stages of the viral replication cycle. During virion assembly, CA drives the formation of the hexameric lattice in immature viral particles, while in mature virions CA monomers assemble in cone-shaped cores surrounding the viral RNA genome and associated proteins. In addition to its functions in late stages of the viral replication cycle, CA plays key roles in a number of processes during early phases of HIV-1 infection including trafficking, uncoating, recognition by host cellular proteins and nuclear import of the viral pre-integration complex. As a result of efficient cooperation of CA with other viral and cellular proteins, integration of the viral genetic material into the host genome, which is an essential step for productive viral infection, successfully occurs. In this review, we will summarize available data on CA functions in HIV-1 replication, describing in detail its roles in late and early phases of the viral replication cycle.
Collapse
Affiliation(s)
- Mariia Novikova
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Yulan Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Ke Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
35
|
Peng W, Shi J, Márquez CL, Lau D, Walsh J, Faysal KMR, Byeon CH, Byeon IJL, Aiken C, Böcking T. Functional analysis of the secondary HIV-1 capsid binding site in the host protein cyclophilin A. Retrovirology 2019; 16:10. [PMID: 30947724 PMCID: PMC6449974 DOI: 10.1186/s12977-019-0471-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Efficient HIV-1 replication depends on interaction of the viral capsid with the host protein cyclophilin A (CypA). CypA, a peptidylprolyl isomerase, binds to an exposed loop in the viral CA protein via the enzyme's active site. Recent structural analysis of CypA in complex with CA tubes in conjunction with molecular dynamics simulations identified a secondary CA binding site on CypA that allows a bridging interaction with two hexameric subunits of the assembled CA lattice, leading to capsid stabilization (Liu et al. in Nat Commun 7:10714, 2016). RESULTS We performed mutational analysis of residues that have been proposed to mediate CA binding at the secondary binding site on CypA (A25, K27, P29 and K30) and tested the effects of the amino acid substitutions using interaction assays and HIV-1 infection assays in cells. The binding of recombinant CypA to self-assembled CA tubes or native HIV-1 capsids was measured in vitro using a quantitative fluorescence microscopy binding assay revealing that affinity and stoichiometry of CypA to the CA lattice was not affected by the substitutions. To test for functionality of the CypA secondary CA-binding site in HIV-1 infection, mutant CypA proteins were expressed in cells in which endogenous CypA was deleted, and the effects on HIV-1 infection were assayed. In normal HeLa-P4 cells, infection with HIV-1 bearing the A92E substitution in CA is inhibited by endogenous CypA and was inhibited to the same extent by expression of CypA mutants in CypA-null HeLa-P4 cells. Expression of the mutant CypA proteins in CypA-null Jurkat cells restored their permissiveness to infection by wild type HIV-1. CONCLUSIONS The amino acid changes at A25, K27, P29 and K30 did not affect the affinity of CypA for the CA lattice and did not impair CypA function in infection assays suggesting that these residues are not part of a secondary CA binding site on CypA.
Collapse
Affiliation(s)
- Wang Peng
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW, Sydney, NSW 2052 Australia
| | - Jiong Shi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Chantal L. Márquez
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW, Sydney, NSW 2052 Australia
| | - Derrick Lau
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW, Sydney, NSW 2052 Australia
| | - James Walsh
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW, Sydney, NSW 2052 Australia
| | - K. M. Rifat Faysal
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW, Sydney, NSW 2052 Australia
| | - Chang H. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - In-Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW, Sydney, NSW 2052 Australia
| |
Collapse
|
36
|
Balasubramaniam M, Zhou J, Addai A, Martinez P, Pandhare J, Aiken C, Dash C. PF74 Inhibits HIV-1 Integration by Altering the Composition of the Preintegration Complex. J Virol 2019; 93:e01741-18. [PMID: 30567984 PMCID: PMC6401427 DOI: 10.1128/jvi.01741-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/06/2018] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 capsid protein (CA) facilitates reverse transcription and nuclear entry of the virus. However, CA's role in post-nuclear entry steps remains speculative. We describe a direct link between CA and integration by employing the capsid inhibitor PF74 as a probe coupled with the biochemical analysis of HIV-1 preintegration complexes (PICs) isolated from acutely infected cells. At a low micromolar concentration, PF74 potently inhibited HIV-1 infection without affecting reverse transcription. Surprisingly, PF74 markedly reduced proviral integration owing to inhibition of nuclear entry and/or integration. However, a 2-fold reduction in nuclear entry by PF74 did not quantitatively correlate with the level of antiviral activity. Titration of PF74 against the integrase inhibitor raltegravir showed an additive antiviral effect that is dependent on a block at the post-nuclear entry step. PF74's inhibitory effect was not due to the formation of defective viral DNA ends or a delay in integration, suggesting that the compound inhibits PIC-associated integration activity. Unexpectedly, PICs recovered from cells infected in the presence of PF74 exhibited elevated integration activity. PF74's effect on PIC activity is CA specific since the compound did not increase the integration activity of PICs of a PF74-resistant HIV-1 CA mutant. Sucrose gradient-based fractionation studies revealed that PICs assembled in the presence of PF74 contained lower levels of CA, suggesting a negative association between CA and PIC-associated integration activity. Finally, the addition of a CA-specific antibody or PF74 inhibited PIC-associated integration activity. Collectively, our results demonstrate that PF74's targeting of PIC-associated CA results in impaired HIV-1 integration.IMPORTANCE Antiretroviral therapy (ART) that uses various combinations of small molecule inhibitors has been highly effective in controlling HIV. However, the drugs used in the ART regimen are expensive, cause side effects, and face viral resistance. The HIV-1 CA plays critical roles in the virus life cycle and is an attractive therapeutic target. While currently there is no CA-based therapy, highly potent CA-specific inhibitors are being developed as a new class of antivirals. Efforts to develop a CA-targeted therapy can be aided through a clear understanding of the role of CA in HIV-1 infection. CA is well established to coordinate reverse transcription and nuclear entry of the virus. However, the role of CA in post-nuclear entry steps of HIV-1 infection is poorly understood. We show that a CA-specific drug PF74 inhibits HIV-1 integration revealing a novel role of this multifunctional viral protein in a post-nuclear entry step of HIV-1 infection.
Collapse
Affiliation(s)
- Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Jing Zhou
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Amma Addai
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Phillip Martinez
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| |
Collapse
|
37
|
Achuthan V, Perreira JM, Sowd GA, Puray-Chavez M, McDougall WM, Paulucci-Holthauzen A, Wu X, Fadel HJ, Poeschla EM, Multani AS, Hughes SH, Sarafianos SG, Brass AL, Engelman AN. Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration. Cell Host Microbe 2018; 24:392-404.e8. [PMID: 30173955 PMCID: PMC6368089 DOI: 10.1016/j.chom.2018.08.002] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/22/2018] [Accepted: 08/01/2018] [Indexed: 10/28/2022]
Abstract
HIV-1 integration into the host genome favors actively transcribed genes. Prior work indicated that the nuclear periphery provides the architectural basis for integration site selection, with viral capsid-binding host cofactor CPSF6 and viral integrase-binding cofactor LEDGF/p75 contributing to selection of individual sites. Here, by investigating the early phase of infection, we determine that HIV-1 traffics throughout the nucleus for integration. CPSF6-capsid interactions allow the virus to bypass peripheral heterochromatin and penetrate the nuclear structure for integration. Loss of interaction with CPSF6 dramatically alters virus localization toward the nuclear periphery and integration into transcriptionally repressed lamina-associated heterochromatin, while loss of LEDGF/p75 does not significantly affect intranuclear HIV-1 localization. Thus, CPSF6 serves as a master regulator of HIV-1 intranuclear localization by trafficking viral preintegration complexes away from heterochromatin at the periphery toward gene-dense chromosomal regions within the nuclear interior.
Collapse
Affiliation(s)
- Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jill M Perreira
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Gregory A Sowd
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - William M McDougall
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Hind J Fadel
- Division of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - Asha S Multani
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Stefan G Sarafianos
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Abraham L Brass
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA; Gastroenterology Division, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
38
|
Nup153 Unlocks the Nuclear Pore Complex for HIV-1 Nuclear Translocation in Nondividing Cells. J Virol 2018; 92:JVI.00648-18. [PMID: 29997211 DOI: 10.1128/jvi.00648-18] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) displays the unique ability to infect nondividing cells. The capsid of HIV-1 is the viral determinant for viral nuclear import. To understand the cellular factors involved in the ability of HIV-1 to infect nondividing cells, we sought to find capsid mutations that allow the virus to infect dividing but not nondividing cells. Because the interaction of capsid with the nucleoporin protein 153 (Nup153) is important for nuclear import of HIV-1, we solved new crystal structures of hexameric HIV-1 capsid in complex with a Nup153-derived peptide containing a phenylalanine-glycine repeat (FG repeat), which we used to guide structure-based mutagenesis of the capsid-binding interface. HIV-1 viruses with mutations in these capsid residues were tested for their ability to infect dividing and nondividing cells. HIV-1 viruses with capsid N57 substitutions infected dividing but not nondividing cells. Interestingly, HIV-1 viruses with N57 mutations underwent reverse transcription but not nuclear translocation. The mutant capsids also lost the ability to interact with Nup153 and CPSF6. The use of small molecules PF74 and BI-2 prevented the interaction of FG-containing nucleoporins (Nups), such as Nup153, with the HIV-1 core. Analysis of integration sites in HIV-1 viruses with N57 mutations revealed diminished integration into transcriptionally active genes in a manner resembling that of HIV-1 in CPSF6 knockout cells or that of HIV-1-N74D. The integration pattern of the N57 mutant HIV-1 can be explained by loss of capsid interaction with CPSF6, whereas capsid interaction with Nup153 is required for HIV-1 to infect nondividing cells. Additionally, the observed viral integration profiles suggested that integration site selection is a multiparameter process that depends upon nuclear factors and the state of the cellular chromatin.IMPORTANCE One of the key advantages that distinguish lentiviruses, such as HIV-1, from all other retroviruses is its ability to infect nondividing cells. Interaction of the HIV-1 capsid with Nup153 and CPSF6 is important for nuclear entry and integration; however, the contribution of each of these proteins to nuclear import and integration is not clear. Using genetics, we demonstrated that these proteins contribute to different processes: Nup153 is essential for the HIV-1 nuclear import in nondividing cells, and CPSF6 is important for HIV-1 integration. In addition, nuclear factors such as CPSF6 and the state of the chromatin are known to be important for integration site selection; nevertheless, the preferential determinant influencing integration site selection is not known. This work demonstrates that integration site selection is a multiparameter process that depends upon nuclear factors and the state of the cellular chromatin.
Collapse
|
39
|
Kane M, Rebensburg SV, Takata MA, Zang TM, Yamashita M, Kvaratskhelia M, Bieniasz PD. Nuclear pore heterogeneity influences HIV-1 infection and the antiviral activity of MX2. eLife 2018; 7:e35738. [PMID: 30084827 PMCID: PMC6101944 DOI: 10.7554/elife.35738] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
HIV-1 accesses the nuclear DNA of interphase cells via a poorly defined process involving functional interactions between the capsid protein (CA) and nucleoporins (Nups). Here, we show that HIV-1 CA can bind multiple Nups, and that both natural and manipulated variation in Nup levels impacts HIV-1 infection in a manner that is strikingly dependent on cell-type, cell-cycle, and cyclophilin A (CypA). We also show that Nups mediate the function of the antiviral protein MX2, and that MX2 can variably inhibit non-viral NLS function. Remarkably, both enhancing and inhibiting effects of cyclophilin A and MX2 on various HIV-1 CA mutants could be induced or abolished by manipulating levels of the Nup93 subcomplex, the Nup62 subcomplex, NUP88, NUP214, RANBP2, or NUP153. Our findings suggest that several Nup-dependent 'pathways' are variably exploited by HIV-1 to target host DNA in a cell-type, cell-cycle, CypA and CA-sequence dependent manner, and are differentially inhibited by MX2.
Collapse
Affiliation(s)
- Melissa Kane
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
| | - Stephanie V Rebensburg
- Division of Infectious DiseasesUniversity of Colorado School of MedicineAuroraUnited States
| | - Matthew A Takata
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
| | - Trinity M Zang
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | | | - Mamuka Kvaratskhelia
- Division of Infectious DiseasesUniversity of Colorado School of MedicineAuroraUnited States
| | - Paul D Bieniasz
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| |
Collapse
|
40
|
Engelman AN, Singh PK. Cellular and molecular mechanisms of HIV-1 integration targeting. Cell Mol Life Sci 2018; 75:2491-2507. [PMID: 29417178 PMCID: PMC6004233 DOI: 10.1007/s00018-018-2772-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 12/21/2022]
Abstract
Integration is central to HIV-1 replication and helps mold the reservoir of cells that persists in AIDS patients. HIV-1 interacts with specific cellular factors to target integration to interior regions of transcriptionally active genes within gene-dense regions of chromatin. The viral capsid interacts with several proteins that are additionally implicated in virus nuclear import, including cleavage and polyadenylation specificity factor 6, to suppress integration into heterochromatin. The viral integrase protein interacts with transcriptional co-activator lens epithelium-derived growth factor p75 to principally position integration within gene bodies. The integrase additionally senses target DNA distortion and nucleotide sequence to help fine-tune the specific phosphodiester bonds that are cleaved at integration sites. Research into virus-host interactions that underlie HIV-1 integration targeting has aided the development of a novel class of integrase inhibitors and may help to improve the safety of viral-based gene therapy vectors.
Collapse
Affiliation(s)
- Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA, 02215, USA.
- Department of Medicine, Harvard Medical School, A-111, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, A-111, 25 Shattuck Street, Boston, MA, 02115, USA
| |
Collapse
|
41
|
Localized Phosphorylation of a Kinesin-1 Adaptor by a Capsid-Associated Kinase Regulates HIV-1 Motility and Uncoating. Cell Rep 2018; 20:2792-2799. [PMID: 28930676 DOI: 10.1016/j.celrep.2017.08.076] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/08/2017] [Accepted: 08/23/2017] [Indexed: 12/28/2022] Open
Abstract
Although microtubule motors mediate intracellular virus transport, the underlying interactions and control mechanisms remain poorly defined. This is particularly true for HIV-1 cores, which undergo complex, interconnected processes of cytosolic transport, reverse transcription, and uncoating of the capsid shell. Although kinesins have been implicated in regulating these events, curiously, there are no direct kinesin-core interactions. We recently showed that the capsid-associated kinesin-1 adaptor protein, fasciculation and elongation protein zeta-1 (FEZ1), regulates HIV-1 trafficking. Here, we show that FEZ1 and kinesin-1 heavy, but not light, chains regulate not only HIV-1 transport but also uncoating. This required FEZ1 phosphorylation, which controls its interaction with kinesin-1. HIV-1 did not stimulate widespread FEZ1 phosphorylation but, instead, bound microtubule (MT) affinity-regulating kinase 2 (MARK2) to stimulate FEZ1 phosphorylation on viral cores. Our findings reveal that HIV-1 binds a regulatory kinase to locally control kinesin-1 adaptor function on viral cores, thereby regulating both particle motility and uncoating.
Collapse
|
42
|
Abstract
Replication-defective retroviral vectors have been used for more than 25 years as a tool for efficient and stable insertion of therapeutic transgenes in human cells. Patients suffering from severe genetic diseases have been successfully treated by transplantation of autologous hematopoietic stem-progenitor cells (HSPCs) transduced with retroviral vectors, and the first of this class of therapies, Strimvelis, has recently received market authorization in Europe. Some clinical trials, however, resulted in severe adverse events caused by vector-induced proto-oncogene activation, which showed that retroviral vectors may retain a genotoxic potential associated to proviral integration in the human genome. The adverse events sparked a renewed interest in the biology of retroviruses, which led in a few years to a remarkable understanding of the molecular mechanisms underlying retroviral integration site selection within mammalian genomes. This review summarizes the current knowledge on retrovirus-host interactions at the genomic level, and the peculiar mechanisms by which different retroviruses, and their related gene transfer vectors, integrate in, and interact with, the human genome. This knowledge provides the basis for the development of safer and more efficacious retroviral vectors for human gene therapy.
Collapse
Affiliation(s)
| | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| |
Collapse
|
43
|
Abstract
Advances in technology have made it possible to analyze integration sites in cells from HIV-infected patients. A significant fraction of infected cells in patients on long-term therapy are clonally expanded; in some cases the integrated viral DNA contributes to the clonal expansion of the infected cells. Although the large majority (>95%) of the HIV proviruses in treated patients are defective, expanded clones can carry replication-competent proviruses, and cells from these clones can release infectious virus. As discussed in this Perspective, it is likely that cells that produce virus are strongly selected against in vivo, and cells with replication competent proviruses expand and survive because only a small fraction of the cells produce virus. These findings have implications for strategies that are intended to eliminate the reservoir of infected cells that has made it almost impossible to cure HIV-infected patients.
Collapse
Affiliation(s)
- Stephen H Hughes
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA.
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| |
Collapse
|
44
|
Alvarez FJD, He S, Perilla JR, Jang S, Schulten K, Engelman AN, Scheres SHW, Zhang P. CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction. SCIENCE ADVANCES 2017; 3:e1701264. [PMID: 28929138 PMCID: PMC5600524 DOI: 10.1126/sciadv.1701264] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/17/2017] [Indexed: 06/01/2023]
Abstract
Human dynamin-like, interferon-induced myxovirus resistance 2 (Mx2 or MxB) is a potent HIV-1 inhibitor. Antiviral activity requires both the amino-terminal region of MxB and protein oligomerization, each of which has eluded structural determination due to difficulties in protein preparation. We report that maltose binding protein-fused, full-length wild-type MxB purifies as oligomers and further self-assembles into helical arrays in physiological salt. Guanosine triphosphate (GTP), but not guanosine diphosphate, binding results in array disassembly, whereas subsequent GTP hydrolysis allows its reformation. Using cryo-electron microscopy (cryoEM), we determined the MxB assembly structure at 4.6 Å resolution, representing the first near-atomic resolution structure in the mammalian dynamin superfamily. The structure revealed previously described and novel MxB assembly interfaces. Mutational analyses demonstrated a critical role for one of the novel interfaces in HIV-1 restriction.
Collapse
Affiliation(s)
- Frances J. D. Alvarez
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Shaoda He
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Juan R. Perilla
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sooin Jang
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alan N. Engelman
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sjors H. W. Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Headington, Oxford OX3 7BN, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| |
Collapse
|
45
|
Distinct functions of diaphanous-related formins regulate HIV-1 uncoating and transport. Proc Natl Acad Sci U S A 2017; 114:E6932-E6941. [PMID: 28760985 DOI: 10.1073/pnas.1700247114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Diaphanous (Dia)-related formins (DRFs) coordinate cytoskeletal remodeling by controlling actin nucleation and microtubule (MT) stabilization to facilitate processes such as cell polarization and migration; yet the full extent of their activities remains unknown. Here, we uncover two discrete roles and functions of DRFs during early human immunodeficiency virus type 1 (HIV-1) infection. Independent of their actin regulatory activities, Dia1 and Dia2 facilitated HIV-1-induced MT stabilization and the intracellular motility of virus particles. However, DRFs also bound in vitro assembled capsid-nucleocapsid complexes and promoted the disassembly of HIV-1 capsid (CA) shell. This process, also known as "uncoating," is among the most poorly understood stages in the viral lifecycle. Domain analysis and structure modeling revealed that regions of Dia2 that bound viral CA and mediated uncoating as well as early infection contained coiled-coil domains, and that these activities were genetically separable from effects on MT stabilization. Our findings reveal that HIV-1 exploits discrete functions of DRFs to coordinate critical steps in early infection and identifies Dia family members as regulators of the poorly understood process of HIV-1 uncoating.
Collapse
|
46
|
Capsid-Dependent Host Factors in HIV-1 Infection. Trends Microbiol 2017; 25:741-755. [PMID: 28528781 DOI: 10.1016/j.tim.2017.04.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/31/2017] [Accepted: 04/18/2017] [Indexed: 11/20/2022]
Abstract
After invasion of a susceptible target cell, HIV-1 completes the early phase of its life cycle upon integration of reverse-transcribed viral DNA into host chromatin. The viral capsid, a conical shell encasing the viral ribonucleoprotein complex, along with its constitutive capsid protein, plays essential roles at virtually every step in the early phase of the viral life cycle. Recent work has begun to reveal how the viral capsid interacts with specific cellular proteins to promote these processes. At the same time, cellular restriction factors target the viral capsid to thwart infection. Comprehensive understanding of capsid-host interactions that promote or impede HIV-1 infection may provide unique insight to exploit for novel therapeutic interventions.
Collapse
|
47
|
Abstract
The interactions between a retrovirus and host cell chromatin that underlie integration and provirus expression are poorly understood. The prototype foamy virus (PFV) structural protein GAG associates with chromosomes via a chromatin-binding sequence (CBS) located within its C-terminal region. Here, we show that the PFV CBS is essential and sufficient for a direct interaction with nucleosomes and present a crystal structure of the CBS bound to a mononucleosome. The CBS interacts with the histone octamer, engaging the H2A-H2B acidic patch in a manner similar to other acidic patch-binding proteins such as herpesvirus latency-associated nuclear antigen (LANA). Substitutions of the invariant arginine anchor residue in GAG result in global redistribution of PFV and macaque simian foamy virus (SFVmac) integration sites toward centromeres, dampening the resulting proviral expression without affecting the overall efficiency of integration. Our findings underscore the importance of retroviral structural proteins for integration site selection and the avoidance of genomic junkyards.
Collapse
|
48
|
Imaging HIV-1 Genomic DNA from Entry through Productive Infection. J Virol 2017; 91:JVI.00034-17. [PMID: 28250118 DOI: 10.1128/jvi.00034-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/17/2017] [Indexed: 02/07/2023] Open
Abstract
In order to track the fate of HIV-1 particles from early entry events through productive infection, we developed a method to visualize HIV-1 DNA reverse transcription complexes by the incorporation and fluorescent labeling of the thymidine analog 5-ethynyl-2'-deoxyuridine (EdU) into nascent viral DNA during cellular entry. Monocyte-derived macrophages were chosen as natural targets of HIV-1, as they do not divide and therefore do not incorporate EdU into chromosomal DNA, which would obscure the detection of intranuclear HIV-1 genomes. Using this approach, we observed distinct EdU puncta in the cytoplasm of infected cells within 12 h postinfection and subsequent accumulation of puncta in the nucleus, which remained stable through 5 days. The depletion of the restriction factor SAMHD1 resulted in a markedly increased number of EdU puncta, allowing efficient quantification of HIV-1 reverse transcription events. Analysis of HIV-1 isolates bearing defined mutations in the capsid protein revealed differences in their cytoplasmic and nuclear accumulation, and data from quantitative PCR analysis closely recapitulated the EdU results. RNA fluorescence in situ hybridization identified actively transcribing, EdU-labeled HIV-1 genomes in productively infected cells, and immunofluorescence analysis confirmed that CDK9, phosphorylated at serine 175, was recruited to RNA-positive HIV-1 DNA, providing a means to directly observe transcriptionally active HIV-1 genomes in productively infected cells. Overall, this system allows stable labeling and monitoring of HIV genomic DNA within infected cells during cytoplasmic transit, nuclear import, and mRNA synthesis.IMPORTANCE The fates of HIV-1 reverse transcription products within infected cells are not well understood. Although previous imaging approaches identified HIV-1 intermediates during early stages of infection, few have connected these events with the later stages that ultimately lead to proviral transcription and the production of progeny virus. Here we developed a technique to label HIV-1 genomes using modified nucleosides, allowing subsequent imaging of cytoplasmic and nuclear HIV-1 DNA in infected monocyte-derived macrophages. We used this technique to track the efficiency of nuclear entry as well as the fates of HIV-1 genomes in productively and nonproductively infected macrophages. We visualized transcriptionally active HIV-1 DNA, revealing that transcription occurs in a subset of HIV-1 genomes in productively infected cells. Collectively, this approach provides new insights into the nature of transcribing HIV-1 genomes and allows us to track the entire course of infection in macrophages, a key target of HIV-1 in infected individuals.
Collapse
|
49
|
Integration site selection by retroviruses and transposable elements in eukaryotes. Nat Rev Genet 2017; 18:292-308. [PMID: 28286338 DOI: 10.1038/nrg.2017.7] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transposable elements and retroviruses are found in most genomes, can be pathogenic and are widely used as gene-delivery and functional genomics tools. Exploring whether these genetic elements target specific genomic sites for integration and how this preference is achieved is crucial to our understanding of genome evolution, somatic genome plasticity in cancer and ageing, host-parasite interactions and genome engineering applications. High-throughput profiling of integration sites by next-generation sequencing, combined with large-scale genomic data mining and cellular or biochemical approaches, has revealed that the insertions are usually non-random. The DNA sequence, chromatin and nuclear context, and cellular proteins cooperate in guiding integration in eukaryotic genomes, leading to a remarkable diversity of insertion site distribution and evolutionary strategies.
Collapse
|
50
|
The benefits of integration. Clin Microbiol Infect 2017; 22:324-332. [PMID: 27107301 DOI: 10.1016/j.cmi.2016.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 01/06/2023]
Abstract
Retroviruses, including the human immunodeficiency virus (HIV), are notorious for two essential steps of their viral replication: reverse transcription and integration. This latter property is considered to be essential for productive replication and ensures the stable long-term insertion of the viral genome sequence in the host chromatin, thereby leading to the life-long association of the virus with the infected cell. Using HIV as a prototypic example, the present review aims to provide an overview of how and where integration occurs, as well as presenting general consequences for both the virus and the infected host.
Collapse
|