Reconstitution and visualization of HIV-1 capsid-dependent replication and integration in vitro
Open accessAbstract
During the first half of the viral life cycle, HIV-1 reverse transcribes its RNA genome and integrates the double-stranded DNA copy into a host cell chromosome. Despite progress in characterizing and inhibiting these processes, in situ mechanistic and structural studies remain challenging. This is because these operations are executed by individual viral preintegration complexes deep within cells. We therefore reconstituted and imaged the early stages of HIV-1 replication in a cell-free system. HIV-1 cores released from permeabilized virions supported efficient, capsid-dependent endogenous reverse transcription to produce double-stranded DNA genomes, which sometimes looped out from ruptured capsid walls. Concerted integration of both viral DNA ends into a target plasmid then proceeded in a cell extract-dependent reaction. This reconstituted system uncovers the role of the capsid in templating replication.
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The critical role of the capsid (CA) in HIV-1 replication has been definitively established using a cell-free system.
“The critical role of the CA in HIV-1 replication has been definitively established using a cell-free system (Christensen et al. 2020).”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Christensen et al. 2020
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ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447 · see citing works
HIV-1 uncoats in the nucleus near sites of integration
Burdick, R. C., Li, C., Munshi, M., Rawson, J. M. O., Nagashima, K., Hu, W.-S., & Pathak, V. K. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1920631117 · Cited by 313 · cited 6× · see citing works
“Integration was even strongly impaired at moderately elevated IP6 levels where appreciable levels of late ERT products were present (for example, 320 mM IP6), indicating that a final capsid “uncoating” reaction needs to occur before integration, as also occurs in the nucleus of HIV-1–infected cells (26).”
BackgroundResultInfluentialAssembly Properties of the Human Immunodeficiency Virus Type 1 CA Protein
Ganser-Pornillos, B. K., von Schwedler, U. K., Stray, K. M., Aiken, C., & Sundquist, W. I. (2004) · Journal of Virology · doi:10.1128/jvi.78.5.2545-2552.2004 · Cited by 302 · see citing works
Self-citationCarlson, L.-A., Briggs, J. A. G., Glass, B., Riches, J. D., Simon, M. N., Johnson, M. C., Müller, B., Grünewald, K., & Kräusslich, H.-G. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.10.013 · Cited by 230 · see citing works
Holman, A. G., & Coffin, J. M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0501646102 · Cited by 164 · see citing works
The Discovery of Reverse Transcriptase
Coffin, J. M., & Fan, H. (2016) · Annual Review of Virology · doi:10.1146/annurev-virology-110615-035556 · Cited by 71 · see citing works
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Research works printed but not linked: 62
- [1]Saag MS, Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2018 Recommendations of the International Antiviral Society-USA Panel. JAMA 320, 379– 396 (2018). 30043070 PMC6415748
- [2]De Clercq E, The nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and protease inhibitors in the treatment of HIV infections (AIDS). Adv Pharmacol 67, 317– 358 (2013). 23886005
- [3]Arts EJ, Hazuda DJ, HIV-1 antiretroviral drug therapy. Cold Spring Harb Perspect Med 2, a007161 (2012). 22474613 PMC3312400
- [4]Lesbats P, Engelman AN, Cherepanov P, Retroviral DNA Integration. Chem Rev 116, 12730– 12757 (2016). 27198982 PMC5084067
- [6]Sarafianos SG, Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. J Mol Biol 385, 693– 713 (2009). 19022262 PMC2881421
- [7]Pornillos O, Ganser-Pornillos BK, Maturation of retroviruses. Curr Opin Virol 36, 47– 55 (2019). 31185449 PMC6730672
- [8]Mattei S, Glass B, Hagen WJ, Krausslich HG, Briggs JA, The structure and flexibility of conical HIV-1 capsids determined within intact virions. Science 354, 1434– 1437 (2016). 27980210
- [9]Briggs JA, The stoichiometry of Gag protein in HIV-1. Nat Struct Mol Biol 11, 672– 675 (2004). 15208690
- [10]Swanson CM, Malim MH, SnapShot: HIV-1 proteins. Cell 133, 742, 742 e741 (2008). 18485880
- [12]Yong WH, Wyman S, Levy JA, Optimal conditions for synthesizing complementary DNA in the HIV-1 endogenous reverse transcriptase reaction. AIDS 4, 199– 206 (1990). 1693515
- [13]Ghosh SK, A molecular clone of HIV-1 tropic and cytopathic for human and chimpanzee lymphocytes. Virology 194, 858– 864 (1993). 8503191
- [14]Wei X, Emergence of resistant human immunodeficiency virus type 1 in patients receiving fusion inhibitor (T-20) monotherapy. Antimicrob Agents Chemother 46, 1896– 1905 (2002). 12019106 PMC127242
- [15]Wei X, Antibody neutralization and escape by HIV-1. Nature 422, 307– 312 (2003). 12646921
- [16]Boone LR, Skalka A, Two species of full-length cDNA are synthesized in high yield by melittin-treated avian retrovirus particles. Proc Natl Acad Sci USA 77, 847– 851 (1980). 6153806 PMC348378
- [17]Mallery DL, IP6 is an HIV pocket factor that prevents capsid collapse and promotes DNA synthesis. Elife 7, (2018). PMC6039178 29848441
- [18]Dick RA, Inositol phosphates are assembly co-factors for HIV-1. Nature 560, 509– 512 (2018). 30069050 PMC6242333
- [19]Jacques DA, HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis. Nature 536, 349– 353 (2016). 27509857 PMC4998957
- [20]Letcher AJ, Schell MJ, Irvine RF, Do mammals make all their own inositol hexakisphosphate? Biochem J 416, 263– 270 (2008). 18684107 PMC2605958
- [21]Diamond TL, Macrophage tropism of HIV-1 depends on efficient cellular dNTP utilization by reverse transcriptase. J Biol Chem 279, 51545– 51553 (2004). 15452123 PMC1351161
- [22]Kennedy EM, Ribonucleoside triphosphates as substrate of human immunodeficiency virus type 1 reverse transcriptase in human macrophages. J Biol Chem 285, 39380– 39391 (2010). 20924117 PMC2998149
- [23]Warrilow D, Cell factors stimulate human immunodeficiency virus type 1 reverse transcription in vitro. J Virol 82, 1425– 1437 (2008). 18045931 PMC2224456
- [24]Rawson JMO, Nikolaitchik OA, Keele BF, Pathak VK, Hu WS, Recombination is required for efficient HIV-1 replication and the maintenance of viral genome integrity. Nucleic Acids Res 46, 10535– 10545 (2018). 30307534 PMC6237782
- [25]Briggs JA, Wilk T, Welker R, Krausslich HG, Fuller SD, Structural organization of authentic, mature HIV-1 virions and cores. EMBO J 22, 1707– 1715 (2003). 12660176 PMC152888
- [27]James LC, The HIV-1 Capsid: More than Just a Delivery Package. Adv Exp Med Biol 1215, 69– 83 (2019). 31317496
- [28]Campbell EM, Hope TJ, HIV-1 capsid: the multifaceted key player in HIV-1 infection. Nat Rev Microbiol 13, 471– 483 (2015). 26179359 PMC4876022
- [29]Forshey BM, von Schwedler U, Sundquist WI, Aiken C, Formation of a human immunodeficiency virus type 1 core of optimal stability is crucial for viral replication. J Virol 76, 5667– 5677 (2002). 11991995 PMC137032
- [30]Yant SR, A highly potent long-acting small-molecule HIV-1 capsid inhibitor with efficacy in a humanized mouse model. Nature medicine 25, 1377– 1384 (2019). PMC7396128 31501601
- [31]von Schwedler UK, Stray KM, Garrus JE, Sundquist WI, Functional surfaces of the human immunodeficiency virus type 1 capsid protein. J Virol 77, 5439– 5450 (2003). 12692245 PMC153941
- [33]Link JO, Clinical targeting of HIV capsid protein with a long-acting small molecule. Nature (2020) epublication ahead of print. PMC8188729 32612233
- [34]Hooker CW, Lott WB, Harrich D, Inhibitors of human immunodeficiency virus type 1 reverse transcriptase target distinct phases of early reverse transcription. J Virol 75, 3095– 3104 (2001). 11238836 PMC114103
- [35]Pornillos O, X-ray structures of the hexameric building block of the HIV capsid. Cell 137, 1282– 1292 (2009). 19523676 PMC2840706
- [36]Pornillos O, Ganser-Pornillos BK, Yeager M, Atomic-level modelling of the HIV capsid. Nature 469, 424– 427 (2011). 21248851 PMC3075868
- [37]Zhao G, Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497, 643– 646 (2013). 23719463 PMC3729984
- [38]Marquez CL, Kinetics of HIV-1 capsid uncoating revealed by single-molecule analysis. Elife 7, (2018). PMC6039174 29877795
- [39]Novikova M, Zhang Y, Freed EO, Peng K, Multiple Roles of HIV-1 Capsid during the Virus Replication Cycle. Virol Sin 34, 119– 134 (2019). 31028522 PMC6513821
- [40]Dick RA, Mallery DL, Vogt VM, James LC, IP6 Regulation of HIV Capsid Assembly, Stability, and Uncoating. Viruses 10, (2018). PMC6267275 30445742
- [41]Ambrose Z, Aiken C, HIV-1 uncoating: connection to nuclear entry and regulation by host proteins. Virology 454-455, 371– 379 (2014). 24559861 PMC3988234
- [42]Hilditch L, Towers GJ, A model for cofactor use during HIV-1 reverse transcription and nuclear entry. Curr Opin Virol 4, 32– 36 (2014). 24525292 PMC3969716
- [43]Mamede JI, Cianci GC, Anderson MR, Hope TJ, Early cytoplasmic uncoating is associated with infectivity of HIV-1. Proc Natl Acad Sci USA 114, E7169– E7178 (2017). 28784755 PMC5576815
- [44]Rankovic S, Varadarajan J, Ramalho R, Aiken C, Rousso I, Reverse Transcription Mechanically Initiates HIV-1 Capsid Disassembly. J Virol 91, (2017). PMC5446659 28381579
- [45]Engelman A, Oztop I, Vandegraaff N, Raghavendra NK, Quantitative analysis of HIV-1 preintegration complexes. Methods 47, 283– 290 (2009). 19233280 PMC2673482
- [46]Canducci F, In vitro phenotypes to elvitegravir and dolutegravir in primary macrophages and lymphocytes of clonal recombinant viral variants selected in patients failing raltegravir. J Antimicrob Chemother 68, 2525– 2532 (2013). 23798668
- [47]Temesgen Z, Siraj DS, Raltegravir: first in class HIV integrase inhibitor. Ther Clin Risk Manag 4, 493– 500 (2008). 18728839 PMC2504063
- [49]Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD, HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res 17, 1186– 1194 (2007). 17545577 PMC1933515
- [50]Serrao E, Ballandras-Colas A, Cherepanov P, Maertens GN, Engelman AN, Key determinants of target DNA recognition by retroviral intasomes. Retrovirology 12, 39 (2015). 25924943 PMC4422553
- [51]Farnet CM, Haseltine WA, Circularization of human immunodeficiency virus type 1 DNA in vitro. J Virol 65, 6942– 6952 (1991). 1834863 PMC250802
- [52]Chen H, Engelman A, The barrier-to-autointegration protein is a host factor for HIV type 1 integration. Proc Natl Acad Sci USA 95, 15270– 15274 (1998). 9860958 PMC28032
- [53]Yan N, Cherepanov P, Daigle JE, Engelman A, Lieberman J, The SET complex acts as a barrier to autointegration of HIV-1. PLoS Pathog 5, e1000327 (2009). 19266025 PMC2644782
- [54]Keele BF, Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA 105, 7552– 7557 (2008). 18490657 PMC2387184
- [55]Rein A, RNA Packaging in HIV. Trends Microbiol 27, 715– 723 (2019). 31085095 PMC6625830
- [56]Bieniasz P, Telesnitsky A, Multiple, Switchable Protein:RNA Interactions Regulate Human Immunodeficiency Virus Type 1 Assembly. Annu Rev Virol 5, 165– 183 (2018). 30048218
- [57]Rene B, Mauffret O, Fosse P, Retroviral nucleocapsid proteins and DNA strand transfers. Biochim Open 7, 10– 25 (2018). 30109196 PMC6088434
- [58]Castano-Diez D, Kudryashev M, Arheit M, Stahlberg H, Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J Struct Biol 178, 139– 151 (2012). 22245546
- [59]Skorupka KA, Hierarchical assembly governs TRIM5alpha recognition of HIV-1 and retroviral capsids. Sci Adv 5, eaaw3631 (2019). 31807695 PMC6881174
- [60]Qu K, Structure and architecture of immature and mature murine leukemia virus capsids. Proc Natl Acad Sci USA 115, E11751– E11760 (2018). 30478053 PMC6294937
- [61]Pettersen EF, UCSF Chimera - A Visualization System for Exploratory Research and Analysis. Journal of computational chemistry 25, 1605– 1612 (2004). 15264254
- [62]Morin A, Collaboration gets the most out of software. Elife 2, e01456 (2013). 24040512 PMC3771563
- [63]Li H, Durbin R, Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754– 1760 (2009). 19451168 PMC2705234
- [64]Robinson JT, Integrative genomics viewer. Nature biotechnology 29, 24– 26 (2011). PMC3346182 21221095
- [65]Gu Z, Gu L, Eils R, Schlesner M, Brors B, circlize Implements and enhances circular visualization in R. Bioinformatics 30, 2811– 2812 (2014). 24930139
- [67]Crooks GE, Hon G, Chandonia JM, Brenner SE, WebLogo: a sequence logo generator. Genome Res 14, 1188– 1190 (2004). 15173120 PMC419797
- [68]Schneider TD, Stephens RM, Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18, 6097– 6100 (1990). 2172928 PMC332411
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Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication
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“The critical role of the CA in HIV-1 replication has been definitively established using a cell-free system (Christensen et al. 2020 ).”
- Authors
- Christensen, D. E., Ganser-Pornillos, B. K., Johnson, J. S., Pornillos, O., & Sundquist, W. I.
- Affiliations
- University of Utah (US)
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA.
- University of Virginia (US)
- Corresponding author
- Christensen, Devin E.
- Pornillos, Owen
- Sundquist, Wesley I.
- ORCID
- Venue
- Science
- Published
- 2020-10-09
- Volume
- 370
- Issue
- 6513
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC8022914
- OpenAlex
- W3092270865
- Cited by
- 150
- References
- 6
- Citations by year
- 2026: 19 · 2025: 24 · 2024: 20 · 2023: 25 · 2022: 25 · 2021: 36 · 2020: 1
- FWCI
- 11.73
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases (AI150464)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Keywords
- HIV-1, capsid, reverse transcription, viral integration, preintegration complex, cell-free reconstitution, viral DNA, in situ imaging, viral life cycle
- MeSH terms
- Capsid, Cell-Free System, Humans, Virus Replication, HIV-1, Virus Integration
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