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.
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Poiesz, B. J. et al. Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma. Proc. Natl Acad. Sci. USA 77, 7415–7419 (1980).
Coffin, J. M. The discovery of HTLV-1, the first pathogenic human retrovirus. Proc. Natl Acad. Sci. USA 112, 15525–15529 (2015).
Barre-Sinoussi, F. et al. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science 220, 868–871 (1983).
Gallo, R. C. et al. Isolation of human T-cell leukemia virus in acquired immune deficiency syndrome (AIDS). Science 220, 865–867 (1983).
Baltimore, D. RNA-dependent DNA polymerase in virions of RNA tumour viruses. Nature 226, 1209–1211 (1970).
Temin, H. M. & Mizutani, S. RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Nature 226, 1211–1213 (1970).
Schiff, R. D. & Grandgenett, D. P. Virus-coded origin of a 32,000-dalton protein from avian retrovirus cores: structural relatedness of p32 and the beta polypeptide of the avian retrovirus DNA polymerase. J. Virol. 28, 279–291 (1978).
Jacks, T. et al. Characterization of ribosomal frameshifting in HIV-1 gag-pol expression. Nature 331, 280–283 (1988).
Carlson, L. A. et al. Three-dimensional analysis of budding sites and released virus suggests a revised model for HIV-1 morphogenesis. Cell Host Microbe 4, 592–599 (2008).
Chen, N. Y. et al. HIV-1 capsid is involved in post-nuclear entry steps. Retrovirology 13, 28 (2016).
Burdick, R. C. et al. HIV-1 uncoats in the nucleus near sites of integration. Proc. Natl Acad. Sci. USA 117, 5486–5493 (2020).
Zila, V. et al. Cone-shaped HIV-1 capsids are transported through intact nuclear pores. Cell 184, 1032–1046.e18 (2021). This study provides visible evidence that intact viral cores pass through cellular nuclear pore complexes during HIV-1 nuclear entry.
Li, C., Burdick, R. C., Nagashima, K., Hu, W. S. & Pathak, V. K. HIV-1 cores retain their integrity until minutes before uncoating in the nucleus. Proc. Natl Acad. Sci. USA 118, e2019467118 (2021). Together with Burdick et al. (2020), imaging of HIV-1 infection reveals that viral cores remain largely intact until uncoating in the nucleus near sites of integration.
Lee, M. S. & Craigie, R. A previously unidentified host protein protects retroviral DNA from autointegration. Proc. Natl Acad. Sci. USA 95, 1528–1533 (1998).
Lin, C. W. & Engelman, A. The barrier-to-autointegration factor is a component of functional human immunodeficiency virus type 1 preintegration complexes. J. Virol. 77, 5030–5036 (2003).
Farnet, C. M. & Bushman, F. D. HIV-1 cDNA integration: requirement of HMG I(Y) protein for function of preintegration complexes in vitro. Cell 88, 483–492 (1997).
Llano, M. et al. LEDGF/p75 determines cellular trafficking of diverse lentiviral but not murine oncoretroviral integrase proteins and is a component of functional lentiviral preintegration complexes. J. Virol. 78, 9524–9537 (2004).
Machida, S. et al. Exploring histone loading on HIV DNA reveals a dynamic nucleosome positioning between unintegrated and integrated viral genome. Proc. Natl Acad. Sci. USA 117, 6822–6830 (2020).
Winans, S. & Goff, S. P. Mutations altering acetylated residues in the CTD of HIV-1 integrase cause defects in proviral transcription at early times after integration of viral DNA. PLoS Pathog. 16, e1009147 (2020).
Yoder, K. E. & Bushman, F. D. Repair of gaps in retroviral DNA integration intermediates. J. Virol. 74, 11191–11200 (2000).
Knyazhanskaya, E. et al. NHEJ pathway is involved in post-integrational DNA repair due to Ku70 binding to HIV-1 integrase. Retrovirology 16, 30 (2019).
Cai, M. et al. Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. Nat. Struct. Biol. 4, 567–577 (1997).
Dyda, F. et al. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266, 1981–1986 (1994). The first high-resolution structure of a retroviral IN CCD reveals similarity to other polynucleotidyltransferases, including DNA transposases and RNase H.
Eijkelenboom, A. P. et al. The DNA-binding domain of HIV-1 integrase has an SH3-like fold. Nat. Struct. Biol. 2, 807–810 (1995).
Hare, S., Gupta, S. S., Valkov, E., Engelman, A. & Cherepanov, P. Retroviral intasome assembly and inhibition of DNA strand transfer. Nature 464, 232–236 (2010). The first high-resolution structure of a retroviral intasome reveals the IN–viral DNA architecture underlying DNA recombination as well as the mechanism of clinical INSTI action.
Guan, R. et al. X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition. Proteins 85, 647–656 (2017).
Harshey, R. M. The Mu story: how a maverick phage moved the field forward. Mob. DNA 3, 21 (2012).
Hare, S., Maertens, G. N. & Cherepanov, P. 3′-processing and strand transfer catalysed by retroviral integrase in crystallo. EMBO J. 31, 3020–3028 (2012). This study visualizes the 3′-processing and strand transfer reactions in crystals of PFV intasomes, which defined the roles of chemical nucleophiles and divalent metal ions in catalysis, and reveals substrate mimicry by INSTIs.
Maertens, G. N., Hare, S. & Cherepanov, P. The mechanism of retroviral integration from X-ray structures of its key intermediates. Nature 468, 326–329 (2010). The first high-resolution structures of retroviral target capture and strand transfer intasome complexes reveal the requirement for target DNA distortion during integration.
Yin, Z. et al. Crystal structure of the Rous sarcoma virus intasome. Nature 530, 362–366 (2016). Together with Ballandras-Colas et al. (2016), these intasome structures first reveal the requirement for more than four IN protomers for functional integration.
Ballandras-Colas, A. et al. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. Nature 530, 358–361 (2016).
Ballandras-Colas, A. et al. A supramolecular assembly mediates lentiviral DNA integration. Science 355, 93–95 (2017). Cryo-EM structures of intasomes derived from the sheep lentivirus MVV reveal a higher-order macromolecular machine composed of 16 IN protomers and define the conserved intasome core shared by all retroviral intasome structures.
Passos, D. O. et al. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science 355, 89–92 (2017). Initial cryo-EM structures of HIV-1 strand transfer complex intasomes reveal a higher-order IN dodecamer architecture.
Li, M. et al. A peptide derived from lens epithelium-derived growth factor stimulates HIV-1 DNA integration and facilitates intasome structural studies. J. Mol. Biol. 432, 2055–2066 (2020).
Cook, N. J. et al. Structural basis of second-generation HIV integrase inhibitor action and viral resistance. Science 367, 806 (2020). High-resolution cryo-EM structures of simian immunodeficiency virus intasomes reveal the mechanism of INSTI resistance.
Passos, D. O. et al. Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science 367, 810 (2020). This study provides high-resolution cryo-EM structures of HIV-1 intasomes with several advanced INSTIs.
Bhatt, V. et al. Structural basis of host protein hijacking in human T-cell leukemia virus integration. Nat. Commun. 11, 3121 (2020). Together with Barski et al. (2020), cryo-EM studies reveal that deltaretrovirus intasomes are composed of IN tetramers and visualize details of the IN–PP2A interface.
Barski, M. S. et al. Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56γ. Nat. Commun. 11, 5043 (2020).
Pandey, K. K. et al. Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome. Commun. Biol. 4, 330 (2021).
McCord, M. et al. Purification of recombinant Rous sarcoma virus integrase possessing physical and catalytic properties similar to virion-derived integrase. Protein Expr. Purif. 14, 167–177 (1998).
Ballandras-Colas, A., Naraharisetty, H., Li, X., Serrao, E. & Engelman, A. Biochemical characterization of novel retroviral integrase proteins. PLoS ONE 8, e76638 (2013).
Hare, S. et al. Structural basis for functional tetramerization of lentiviral integrase. PLoS Pathog. 5, e1000515 (2009).
Cherepanov, P. et al. HIV-1 integrase forms stable tetramers and associates with LEDGF/p75 protein in human cells. J. Biol. Chem. 278, 372–381 (2003).
Lodi, P. J. et al. Solution structure of the DNA binding domain of HIV-1 integrase. Biochemistry 34, 9826–9833 (1995).
Wei, S. Q., Mizuuchi, K. & Craigie, R. A large nucleoprotein assembly at the ends of the viral DNA mediates retroviral DNA integration. EMBO J. 16, 7511–7520 (1997).
Chen, H., Wei, S. Q. & Engelman, A. Multiple integrase functions are required to form the native structure of the human immunodeficiency virus type I intasome. J. Biol. Chem. 274, 17358–17364 (1999).
Yang, W., Lee, J. Y. & Nowotny, M. Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol. Cell 22, 5–13 (2006).
Nowotny, M. & Yang, W. Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. EMBO J. 25, 1924–1933 (2006).
Engelman, A., Mizuuchi, K. & Craigie, R. HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67, 1211–1221 (1991).
Chow, S. A. & Brown, P. O. Juxtaposition of two viral DNA ends in a bimolecular disintegration reaction mediated by multimers of human immunodeficiency virus type 1 or murine leukemia virus integrase. J. Virol. 68, 7869–7878 (1994).
Richardson, J. M., Colloms, S. D., Finnegan, D. J. & Walkinshaw, M. D. Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote. Cell 138, 1096–1108 (2009).
Montano, S. P., Pigli, Y. Z. & Rice, P. A. The mu transpososome structure sheds light on DDE recombinase evolution. Nature 491, 413–417 (2012).
Morris, E. R., Grey, H., McKenzie, G., Jones, A. C. & Richardson, J. M. A bend, flip and trap mechanism for transposon integration. eLife 5, e15537 (2016).
Ghanim, G. E., Kellogg, E. H., Nogales, E. & Rio, D. C. Structure of a P element transposase-DNA complex reveals unusual DNA structures and GTP-DNA contacts. Nat. Struct. Mol. Biol. 26, 1013–1022 (2019).
Aiyer, S. et al. Structural and sequencing analysis of local target DNA recognition by MLV integrase. Nucleic Acids Res. 43, 5647–5663 (2015).
Serrao, E. et al. Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding. Nucleic Acids Res. 42, 5164–5176 (2014).
Demeulemeester, J. et al. HIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort. Cell Host Microbe 16, 651–662 (2014).
Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997).
Pryciak, P. M. & Varmus, H. E. Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection. Cell 69, 769–780 (1992).
Pruss, D., Bushman, F. D. & Wolffe, A. P. Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc. Natl Acad. Sci. USA 91, 5913–5917 (1994).
Wang, G. P., Ciuffi, A., Leipzig, J., Berry, C. C. & Bushman, F. D. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 17, 1186–1194 (2007).
Roth, S. L., Malani, N. & Bushman, F. D. Gammaretroviral integration into nucleosomal target DNA in vivo. J. Virol. 85, 7393–7401 (2011).
Baller, J. A., Gao, J., Stamenova, R., Curcio, M. J. & Voytas, D. F. A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon. Genome Res. 22, 704–713 (2012).
Maskell, D. P. et al. Structural basis for retroviral integration into nucleosomes. Nature 523, 366–369 (2015). Together with Wilson et al. (2019), cryo-EM studies elucidate how the PFV intasome engages and locally remodels a nucleosome for integration.
Wilson, M. D. et al. Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer. Nat. Commun. 10, 4189 (2019).
Benleulmi, M. S. et al. Intasome architecture and chromatin density modulate retroviral integration into nucleosome. Retrovirology 12, 13 (2015).
Serrao, E., Ballandras-Colas, A., Cherepanov, P., Maertens, G. N. & Engelman, A. N. Key determinants of target DNA recognition by retroviral intasomes. Retrovirology 12, 39 (2015).
Engelman, A. N., Maertens, G. N. in Retrovirus-Cell Interactions (ed. Parent, L. J.) Ch. 4, 163–199 (Elsevier Inc., 2018).
Bukrinsky, M. I. et al. Active nuclear import of human immunodeficiency virus type 1 preintegration complexes. Proc. Natl Acad. Sci. USA 89, 6580–6584 (1992).
Roe, T., Reynolds, T. C., Yu, G. & Brown, P. O. Integration of murine leukemia virus DNA depends on mitosis. EMBO J. 12, 2099–2108 (1993).
Bieniasz, P. D., Weiss, R. A. & McClure, M. O. Cell cycle dependence of foamy retrovirus infection. J. Virol. 69, 7295–7299 (1995).
Schroder, A. R. et al. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110, 521–529 (2002). Enabled by the release of the human genome sequence, this study convincingly demonstrates that HIV-1 integration strongly favours active transcription units within gene-dense regions of chromatin.
Wu, X., Li, Y., Crise, B. & Burgess, S. M. Transcription start regions in the human genome are favored targets for MLV integration. Science 300, 1749–1751 (2003). This is the first study to reveal that the gammaretrovirus Moloney murine leukaemia virus favours gene promoter regions for integration.
De Ravin, S. S. et al. Enhancers are major targets for murine leukemia virus vector integration. J. Virol. 88, 4504–4513 (2014).
LaFave, M. C. et al. MLV integration site selection is driven by strong enhancers and active promoters. Nucleic Acids Res. 42, 4257–4269 (2014).
Yamashita, M. & Emerman, M. Capsid is a dominant determinant of retrovirus infectivity in nondividing cells. J. Virol. 78, 5670–5678 (2004).
Schaller, T. et al. HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog. 7, e1002439 (2011).
Matreyek, K. A., Yucel, S. S., Li, X. & Engelman, A. Nucleoporin NUP153 phenylalanine-glycine motifs engage a common binding pocket within the HIV-1 capsid protein to mediate lentiviral infectivity. PLoS Pathog. 9, e1003693 (2013).
Rüegsegger, U., Beyer, K. & Keller, W. Purification and characterization of human cleavage factor Im involved in the 3’ end processing of messenger RNA precursors. J. Biol. Chem. 271, 6107–6113 (1996).
Price, A. J. et al. Host cofactors and pharmacologic ligands share an essential interface in HIV-1 capsid that is lost upon disassembly. PLoS Pathog. 10, e1004459 (2014).
Bejarano, D. A. et al. HIV-1 nuclear import in macrophages is regulated by CPSF6-capsid interactions at the nuclear pore complex. eLife 8, e41800 (2019).
Bizhanova, A. & Kaufman, P. D. Close to the edge: heterochromatin at the nucleolar and nuclear peripheries. Biochim. Biophys. Acta Gene Regul. Mech. 1864, 194666 (2021).
Chen, Y. et al. Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. J. Cell Biol. 217, 4025–4048 (2018).
Francis, A. C. et al. HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains. Nat. Commun. 11, 3505 (2020). This study demonstrates that HIV-1 integration favours regions of chromatin that are located close to nuclear speckles.
Achuthan, V. et al. Capsid-CPSF6 interaction licenses nuclear HIV-1 trafficking to sites of viral DNA integration. Cell Host Microbe 24, 392–404.e398 (2018).
Greig, J. A. et al. Arginine-enriched mixed-charge domains provide cohesion for nuclear speckle condensation. Mol. Cell 77, 1237–1250.e1234 (2020).
Li, W. et al. CPSF6-dependent targeting of speckle-associated domains distinguishes primate from nonprimate lentiviral integration. mBio 11, e02254-20 (2020).
Koh, Y. et al. Differential effects of human immunodeficiency virus type 1 capsid and cellular factors nucleoporin 153 and LEDGF/p75 on the efficiency and specificity of viral DNA integration. J. Virol. 87, 648–658 (2013).
Ocwieja, K. E. et al. HIV integration targeting: a pathway involving transportin-3 and the nuclear pore protein RanBP2. PLoS Pathog. 7, e1001313 (2011).
Müllers, E. The foamy virus Gag proteins: what makes them different? Viruses 5, 1023–1041 (2013).
Tobaly-Tapiero, J. et al. Chromatin tethering of incoming foamy virus by the structural Gag protein. Traffic 9, 1717–1727 (2008).
Lesbats, P. et al. Structural basis for spumavirus GAG tethering to chromatin. Proc. Natl Acad. Sci. USA 114, 5509–5514 (2017).
Elis, E., Ehrlich, M., Prizan-Ravid, A., Laham-Karam, N. & Bacharach, E. p12 tethers the murine leukemia virus pre-integration complex to mitotic chromosomes. PLoS Pathog. 8, e1003103 (2012).
Schneider, W. M. et al. Viral DNA tethering domains complement replication-defective mutations in the p12 protein of MuLV Gag. Proc. Natl Acad. Sci. USA 110, 9487–9492 (2013).
Wanaguru, M., Barry, D. J., Benton, D. J., O’Reilly, N. J. & Bishop, K. N. Murine leukemia virus p12 tethers the capsid-containing pre-integration complex to chromatin by binding directly to host nucleosomes in mitosis. PLoS Pathog. 14, e1007117 (2018).
Busschots, K. et al. The interaction of LEDGF/p75 with integrase is lentivirus-specific and promotes DNA binding. J. Biol. Chem. 280, 17841–17847 (2005).
Cherepanov, P. LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro. Nucleic Acids Res. 35, 113–124 (2007).
Marshall, H. M. et al. Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting. PLoS ONE 2, e1340 (2007).
Shun, M. C. et al. LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration. Genes Dev. 21, 1767–1778 (2007).
Singh, P. K. et al. LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes. Genes Dev. 29, 2287–2297 (2015).
Sowd, G. A. et al. A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin. Proc. Natl Acad. Sci. USA 113, E1054–E1063 (2016).
LeRoy, G. et al. LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription in differentiated cells. Sci. Adv. 5, eaay3068 (2019).
Llano, M. et al. Identification and characterization of the chromatin-binding domains of the HIV-1 integrase interactor LEDGF/p75. J. Mol. Biol. 360, 760–773 (2006).
Turlure, F., Maertens, G., Rahman, S., Cherepanov, P. & Engelman, A. A tripartite DNA-binding element, comprised of the nuclear localization signal and two AT-hook motifs, mediates the association of LEDGF/p75 with chromatin in vivo. Nucleic Acids Res. 34, 1653–1665 (2006).
Cherepanov, P., Devroe, E., Silver, P. A. & Engelman, A. Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase. J. Biol. Chem. 279, 48883–48892 (2004).
Maertens, G. et al. LEDGF/p75 is essential for nuclear and chromosomal targeting of HIV-1 integrase in human cells. J. Biol. Chem. 278, 33528–33539 (2003).
Hare, S. et al. A novel co-crystal structure affords the design of gain-of-function lentiviral integrase mutants in the presence of modified PSIP1/LEDGF/p75. PLoS Pathog. 5, e1000259 (2009).
Cherepanov, P. et al. Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75. Nat. Struct. Mol. Biol. 12, 526–532 (2005).
Cherepanov, P., Ambrosio, A. L., Rahman, S., Ellenberger, T. & Engelman, A. Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Proc. Natl Acad. Sci. USA 102, 17308–17313 (2005).
Eidahl, J. O. et al. Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res. 41, 3924–3936 (2013).
Wang, H., Farnung, L., Dienemann, C. & Cramer, P. Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding. Nat. Struct. Mol. Biol. 27, 8–13 (2020).
Shun, M. C. et al. Identification and characterization of PWWP domain residues critical for LEDGF/p75 chromatin binding and human immunodeficiency virus type 1 infectivity. J. Virol. 82, 11555–11567 (2008).
Tesina, P. et al. Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif. Nat. Commun. 6, 7968 (2015).
De Rijck, J. et al. The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites. Cell Rep. 5, 886–894 (2013).
Gupta, S. S. et al. Bromo- and extraterminal domain chromatin regulators serve as cofactors for murine leukemia virus integration. J. Virol. 87, 12721–12736 (2013).
Sharma, A. et al. BET proteins promote efficient murine leukemia virus integration at transcription start sites. Proc. Natl Acad. Sci. USA 110, 12036–12041 (2013).
Larue, R. C. et al. Bimodal high-affinity association of Brd4 with murine leukemia virus integrase and mononucleosomes. Nucleic Acids Res. 42, 4868–4881 (2014).
LeRoy, G. et al. Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins. Genome Biol. 13, R68 (2012).
Morinière, J. et al. Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature 461, 664–668 (2009).
Rahman, S. et al. The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3. Mol. Cell Biol. 31, 2641–2652 (2011).
Aiyer, S. et al. Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction. Nucleic Acids Res. 42, 5917–5928 (2014).
Crowe, B. L. et al. Structure of the Brd4 ET domain bound to a C-terminal motif from γ-retroviral integrases reveals a conserved mechanism of interaction. Proc. Natl Acad. Sci. USA 113, 2086–2091 (2016).
Aiyer, S. et al. A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins. Structure https://doi.org/10.1016/j.str.2021.01.010 (2021).
Maertens, G. N. B′-protein phosphatase 2A is a functional binding partner of delta-retroviral integrase. Nucleic Acids Res. 44, 364–376 (2016).
Winans, S. et al. The FACT complex promotes avian leukosis virus DNA integration. J. Virol. 91, e00082–17 (2017).
Hertz, E. P. T. et al. A conserved motif provides binding specificity to the PP2A-B56 phosphatase. Mol. Cell 63, 686–695 (2016).
Mitchell, R. S. et al. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2, E234 (2004).
Gillet, N. A. et al. The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood 117, 3113–3122 (2011).
Christensen, D. E., Ganser-Pornillos, B. K., Johnson, J. S., Pornillos, O. & Sundquist, W. I. Reconstitution and visualization of HIV-1 capsid-dependent replication and integration in vitro. Science 370, eabc8420 (2020). This study reports reconstitution of HIV-1 reverse transcription and integration in vitro from permeabilized virus particles.
Bukovsky, A. & Gottlinger, H. Lack of integrase can markedly affect human immunodeficiency virus type 1 particle production in the presence of an active viral protease. J. Virol. 70, 6820–6825 (1996).
Engelman, A., Englund, G., Orenstein, J. M., Martin, M. A. & Craigie, R. Multiple effects of mutations in human immunodeficiency virus type 1 integrase on viral replication. J. Virol. 69, 2729–2736 (1995).
Elliott, J. L. et al. Integrase-RNA interactions underscore the critical role of integrase in HIV-1 virion morphogenesis. eLife 9, e543111 (2020).
Engelman, A. In vivo analysis of retroviral integrase structure and function. Adv. Virus Res. 52, 411–426 (1999).
Leavitt, A. D., Robles, G., Alesandro, N. & Varmus, H. E. Human immunodeficiency virus type 1 integrase mutants retain in vitro integrase activity yet fail to integrate viral DNA efficiently during infection. J. Virol. 70, 721–728 (1996).
Mohammed, K. D., Topper, M. B. & Muesing, M. A. Sequential deletion of the integrase (Gag-Pol) carboxyl terminus reveals distinct phenotypic classes of defective HIV-1. J. Virol. 85, 4654–4666 (2011).
Hoyte, A. C. et al. Resistance to pyridine-based inhibitor KF116 reveals an unexpected role of integrase in HIV-1 Gag-Pol polyprotein proteolytic processing. J. Biol. Chem. 292, 19814–19825 (2017).
Dobard, C. W., Briones, M. S. & Chow, S. A. Molecular mechanisms by which human immunodeficiency virus type 1 integrase stimulates the early steps of reverse transcription. J. Virol. 81, 10037–10046 (2007).
Tekeste, S. S. et al. Interaction between reverse transcriptase and integrase is required for reverse transcription during HIV-1 replication. J. Virol. 89, 12058–12069 (2015).
Fontana, J. et al. Distribution and redistribution of HIV-1 nucleocapsid protein in immature, mature, and integrase-inhibited virions: a role for integrase in maturation. J. Virol. 89, 9765–9780 (2015).
Jurado, K. A. et al. Allosteric integrase inhibitor potency is determined through the inhibition of HIV-1 particle maturation. Proc. Natl Acad. Sci. USA 110, 8690–8695 (2013). This is the first study to reveal that ALLINIs potently inhibit HIV-1 maturation.
Kessl, J. J. et al. HIV-1 integrase binds the viral RNA genome and is essential during virion morphogenesis. Cell 166, 1257–1268 e1212 (2016). This study provides evidence that IN binding to viral RNA has a crucial role in RNA encapsidation, virus particle maturation and HIV-1 infection.
Balakrishnan, M. et al. Non-catalytic site HIV-1 integrase inhibitors disrupt core maturation and induce a reverse transcription block in target cells. PLoS ONE 8, e74163 (2013).
Steinrigl, A. et al. Mutations in the catalytic core or the C-terminus of murine leukemia virus (MLV) integrase disrupt virion infectivity and exert diverse effects on reverse transcription. Virology 362, 50–59 (2007).
Wlodawer, A. & Vondrasek, J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 27, 249–284 (1998).
Pattishall, K. H. in The Search for Antiviral Drugs: Case Histories from Concept to Clinic (eds Adams, J. & Merluzzi, V. J.) 23–43 (Birkhäuser, 1993).
Murray, J. M. et al. Antiretroviral therapy with the integrase inhibitor raltegravir alters decay kinetics of HIV, significantly reducing the second phase. AIDS 21, 2315–2321 (2007).
Sato, M. et al. Novel HIV-1 integrase inhibitors derived from quinolone antibiotics. J. Med. Chem. 49, 1506–1508 (2006).
DeJesus, E. et al. Antiviral activity, pharmacokinetics, and dose response of the HIV-1 integrase inhibitor GS-9137 (JTK-303) in treatment-naive and treatment-experienced patients. J. Acquir. Immune Defic. Syndr. 43, 1–5 (2006).
Tsiang, M. et al. Antiviral activity of bictegravir (GS-9883), a novel potent HIV-1 integrase strand transfer inhibitor with an improved resistance profile. Antimicrob. Agents Chemother. 60, 7086–7097 (2016).
Markham, A. Cabotegravir plus rilpivirine: first approval. Drugs 80, 915–922 (2020).
Hassounah, S. A. et al. Antiviral activity of bictegravir and cabotegravir against integrase inhibitor-resistant SIVmac239 and HIV-1. Antimicrob. Agents Chemother. 61, e01695–17 (2017).
Smith, S. J., Zhao, X. Z., Burke, T. R. Jr. & Hughes, S. H. Efficacies of cabotegravir and bictegravir against drug-resistant HIV-1 integrase mutants. Retrovirology 15, 37 (2018).
Zhang, W. W. et al. Accumulation of multiple mutations in vivo confers cross-resistance to new and existing integrase inhibitors. J. Infect. Dis. 218, 1773–1776 (2018).
WHO. Update of recommendations on first- and second-line antiretroviral regimens. WHO Policy Brief 1–16 (WHO, 2019).
Hazuda, D. J. et al. Inhibitors of strand transfer that prevent integration and inhibit HIV-1 replication in cells. Science 287, 646–650 (2000). This study reports the initial discovery and characterization of INSTIs.
Grobler, J. A. et al. Diketo acid inhibitor mechanism and HIV-1 integrase: implications for metal binding in the active site of phosphotransferase enzymes. Proc. Natl Acad. Sci. USA 99, 6661–6666 (2002).
Espeseth, A. S. et al. HIV-1 integrase inhibitors that compete with the target DNA substrate define a unique strand transfer conformation for integrase. Proc. Natl Acad. Sci. USA 97, 11244–11249 (2000).
Valkov, E. et al. Functional and structural characterization of the integrase from the prototype foamy virus. Nucleic Acids Res. 37, 243–255 (2009).
Barski, M. S., Minnell, J. J. & Maertens, G. N. Inhibition of HTLV-1 infection by HIV-1 first- and second-generation integrase strand transfer inhibitors. Front. Microbiol. 10, 1877 (2019).
Koh, Y., Matreyek, K. A. & Engelman, A. Differential sensitivities of retroviruses to integrase strand transfer inhibitors. J. Virol. 85, 3677–3682 (2011).
Hare, S. et al. Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Proc. Natl Acad. Sci. USA 107, 20057–20062 (2010).
Hare, S. et al. Structural and functional analyses of the second-generation integrase strand transfer inhibitor dolutegravir (S/GSK1349572). Mol. Pharmacol. 80, 565–572 (2011).
Langley, D. R. et al. The terminal (catalytic) adenosine of the HIV LTR controls the kinetics of binding and dissociation of HIV integrase strand transfer inhibitors. Biochemistry 47, 13481–13488 (2008).
Hightower, K. E. et al. Dolutegravir (S/GSK1349572) exhibits significantly slower dissociation than raltegravir and elvitegravir from wild-type and integrase inhibitor-resistant HIV-1 integrase-DNA complexes. Antimicrob. Agents Chemother. 55, 4552–4559 (2011).
White, K. L. et al. Long dissociation of bictegravir from HIV-1 integrase-DNA complexes. Antimicrob. Agents Chemother. 65, e02406–e02420 (2021).
Grobler, J. A. & Hazuda, D. J. Resistance to HIV integrase strand transfer inhibitors: in vitro findings and clinical consequences. Curr. Opin. Virol. 8, 98–103 (2014).
Santoro, M. M. et al. Susceptibility to HIV-1 integrase strand transfer inhibitors (INSTIs) in highly treatment-experienced patients who failed an INSTI-based regimen. Int. J. Antimicrob. Agents 56, 106027 (2020).
Ndashimye, E. et al. Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda. J. Antimicrob. Chemother. 75, 3525–3533 (2020).
Rhee, S. Y. et al. A systematic review of the genetic mechanisms of dolutegravir resistance. J. Antimicrob. Chemother. 74, 3135–3149 (2019).
Engone-Ondo, J. D. et al. High rate of virological failure and HIV drug resistance in semi-rural Gabon and implications for dolutegravir-based regimen efficacy. J. Antimicrob. Chemother. 76, 1051–1056 (2020).
Christ, F. et al. Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nat. Chem. Biol. 6, 442–448 (2010).
Fader, L. D. et al. Discovery of BI 224436, a noncatalytic site integrase inhibitor (NCINI) of HIV-1. ACS Med. Chem. Lett. 5, 422–427 (2014).
Tsiang, M. et al. New class of HIV-1 integrase (IN) inhibitors with a dual mode of action. J. Biol. Chem. 287, 21189–21203 (2012).
Le Rouzic, E. et al. Dual inhibition of HIV-1 replication by integrase-LEDGF allosteric inhibitors is predominant at the post-integration stage. Retrovirology 10, 144 (2013).
Gupta, K. et al. Allosteric inhibition of human immunodeficiency virus integrase: late block during viral replication and abnormal multimerization involving specific protein domains. J. Biol. Chem. 289, 20477–20488 (2014).
Desimmie, B. A. et al. LEDGINs inhibit late stage HIV-1 replication by modulating integrase multimerization in the virions. Retrovirology 10, 57 (2013).
Sharma, A. et al. A new class of multimerization selective inhibitors of HIV-1 integrase. PLoS Pathog. 10, e1004171 (2014).
Deng, N. et al. Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: structural and thermodynamic modeling studies. Protein Sci. 25, 1911–1917 (2016).
Gupta, K. et al. Structural basis for inhibitor-induced aggregation of HIV Integrase. PLoS Biol. 14, e1002584 (2016).
Koneru, P. C. et al. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. eLife 8, e46344 (2019).
Gupta, K. et al. Allosteric HIV integrase inhibitors promote formation of inactive branched polymers via homomeric carboxy-terminal domain interactions. Structure 29, 213–225.e5 (2021).
Amadori, C. et al. The HIV-1 integrase-LEDGF allosteric inhibitor MUT-A: resistance profile, impairment of virus maturation and infectivity but without influence on RNA packaging or virus immunoreactivity. Retrovirology 14, 50 (2017).
Bruggemans, A. et al. GS-9822, a preclinical LEDGIN candidate, displays a block-and-lock phenotype in cell culture. Antimicrob. Agents Chemother. 65, e02328–20 (2021).
Feng, L. et al. The competitive interplay between allosteric HIV-1 integrase inhibitor BI/D and LEDGF/p75 during the early stage of HIV-1 replication adversely affects inhibitor potency. ACS Chem. Biol. 11, 1313–1321 (2016).
Vranckx, L. S. et al. LEDGIN-mediated inhibition of integrase-LEDGF/p75 interaction reduces reactivation of residual latent HIV. EBioMedicine 8, 248–264 (2016).
Bonnard, D. et al. Structure-function analyses unravel distinct effects of allosteric inhibitors of HIV-1 integrase on viral maturation and integration. J. Biol. Chem. 293, 6172–6186 (2018).
Peese, K. M. et al. 5,6,7,8-Tetrahydro-1,6-naphthyridine derivatives as potent HIV-1-integrase-allosteric-site inhibitors. J. Med. Chem. 62, 1348–1361 (2019).
Fenwick, C. et al. Preclinical profile of BI 224436, a novel HIV-1 non-catalytic-site integrase inhibitor. Antimicrob. Agents Chemother. 58, 3233–3244 (2014).
Shkriabai, N. et al. A critical role of the C-terminal segment for allosteric inhibitor-induced aberrant multimerization of HIV-1 integrase. J. Biol. Chem. 289, 26430–26440 (2014).
Sutton, G. et al. Assembly intermediates of orthoreovirus captured in the cell. Nat. Commun. 11, 4445 (2020).
Hoffman, D. P. et al. Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science 367, 1–12 (2020).
The authors apologize to colleagues whose work they were unable to cite due to space constraints. This work was supported by US National Institutes of Health grants P50 AI150481 (P.C. and A.N.E.) and R01 AI070042 (A.N.E.), Wellcome Trust Investigator Award 107005/Z/15Z (G.N.M.) and the Francis Crick Institute (P.C), which receives its core funding from Cancer Research UK (FC001061), the UK Medical Research Council (FC001061) and the Wellcome Trust (FC001061).
A.N.E. consults for ViiV Healthcare Co. The other authors declare no competing interests.
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Maertens, G.N., Engelman, A.N. & Cherepanov, P. Structure and function of retroviral integrase. Nat Rev Microbiol (2021). https://doi.org/10.1038/s41579-021-00586-9