Interactions between HIV-1 and the Cell-Autonomous Innate Immune System
Authors: Greg J. Towers, Mahdad Noursadeghi
Journal: Cell Host & Microbe (2014)

HIV-1 was recognized as the cause of AIDS in humans in 1984. Despite 30 years of intensive research, we are still unraveling the molecular details of the host-pathogen interactions that enable this virus to escape immune clearance and cause immunodeficiency. Here we explore a series of recent studies that consider how HIV-1 interacts with the cell-autonomous innate immune system as it navigates its way in and out of host cells. We discuss how these studies improve our knowledge of HIV-1 and host biology as well as increase our understanding of transmission, persistence, and immunodeficiency and the potential for therapeutic or prophylactic interventions. HIV-1 was recognized as the cause of AIDS in humans in 1984. Despite 30 years of intensive research, we are still unraveling the molecular details of the host-pathogen interactions that enable this virus to escape immune clearance and cause immunodeficiency. Here we explore a series of recent studies that consider how HIV-1 interacts with the cell-autonomous innate immune system as it navigates its way in and out of host cells. We discuss how these studies improve our knowledge of HIV-1 and host biology as well as increase our understanding of transmission, persistence, and immunodeficiency and the potential for therapeutic or prophylactic interventions. Like all viruses, lentiviruses parasitize their hosts and rely on a complex interaction with host intracellular functions to complete their life cycles. HIV-1 has evolved to recruit host dependency factors, or cofactors, as well as evade or manipulate the cell-autonomous innate immune system that has evolved over millions of years to defend the host from infection. This defensive system provides a mechanism by which cells can detect the presence of a pathogen and also deploy a series of local and systemic defensive measures that enhance and mediate antiviral defenses. Importantly, the cell-autonomous innate immune system also influences the adaptive immune system, providing information on the nature of the pathogen and thus the appropriate adaptive response. The molecular tripwires of the cell-autonomous innate immune system are pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPS) within the specific compartments that they patrol. In this respect, principal cellular PRRs can be broadly classified as transmembrane receptors of the Toll-like receptor (TLR) family that sense extracellular or endosomal compartments. There is also an increasing repertoire of cytoplasmic receptors, mainly with specificity for pathogen nucleic acids as well as nonmicrobial danger-associated molecular patterns. The canonical response to PRR stimulation leads to activation of signaling cascades and, typically, nuclear translocation of cytoplasmic transcription factors exemplified by NF-κB RelA and IRF3 with consequent transactivation of innate immune response genes. In the antiviral response, this is dominated by induction and secretion of soluble type 1 interferon (IFN). This leads to autocrine, paracrine, or endocrine activation of cell surface IFN receptors and downstream intracellular JAK/STAT signaling cascade activation (Stark and Darnell, 2012Stark G.R. Darnell Jr., J.E. The JAK-STAT pathway at twenty.Immunity. 2012; 36: 503-514Abstract Full Text Full Text PDF PubMed Scopus (961) Google Scholar), resulting in a second line of gene expression changes that lead to development of the so-called antiviral state. The antiviral state is mediated by the combination of all the genes induced by the IFN response and can comprise hundreds of proteins whose expression is increased by exposure to IFN. In this way both infected and nearby uninfected cells become nonpermissive to viral replication through expression of a host of diverse antiviral activities that lead to the suppression of replication of most viruses as well as other pathogens. In fact, the ability to antagonize or evade this response is probably the most important determinant for viral replication, or tropism, in a particular host. Importantly, PRRs also lie upstream of the inflammasome, in which caspase activation can unleash the function of inflammatory procytokines and initiate apoptosis or pyroptosis pathways, thereby coupling innate immune sensing of pathogens to host cell death (Figure 1). Although this robust IFN response is initiated, until recently the suppression of HIV-1 replication by IFN and the characterization of how HIV-1 avoids triggering IFN responses have been understudied. This is partly because IFN induces the expression of many effector genes, making the system rather complicated to dissect. However, studies examining the mechanisms underlying species-specific replication of lentiviruses as well as the role of lentiviral accessory proteins have led to excellent progress in this field. This work uncovered IFN-stimulated factors that restrict HIV, notably APOBEC3G (Sheehy et al., 2002Sheehy A.M. Gaddis N.C. Choi J.D. Malim M.H. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein.Nature. 2002; 418: 646-650Crossref PubMed Scopus (1912) Google Scholar), TRIM5α (Stremlau et al., 2004Stremlau M. Owens C.M. Perron M.J. Kiessling M. Autissier P. Sodroski J. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys.Nature. 2004; 427: 848-853Crossref PubMed Scopus (1504) Google Scholar), tetherin (Neil et al., 2008Neil S.J. Zang T. Bieniasz P.D. Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu.Nature. 2008; 451: 425-430Crossref PubMed Scopus (1422) Google Scholar, Van Damme et al., 2008Van Damme N. Goff D. Katsura C. Jorgenson R.L. Mitchell R. Johnson M.C. Stephens E.B. Guatelli J. The interferon-induced protein BST-2 restricts HIV-1 release and is downregulated from the cell surface by the viral Vpu protein.Cell Host Microbe. 2008; 3: 245-252Abstract Full Text Full Text PDF PubMed Scopus (841) Google Scholar), SAMHD1 (Hrecka et al., 2011Hrecka K. Hao C. Gierszewska M. Swanson S.K. Kesik-Brodacka M. Srivastava S. Florens L. Washburn M.P. Skowronski J. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein.Nature. 2011; 474: 658-661Crossref PubMed Scopus (914) Google Scholar, Laguette et al., 2011Laguette N. Sobhian B. Casartelli N. Ringeard M. Chable-Bessia C. Ségéral E. Yatim A. Emiliani S. Schwartz O. Benkirane M. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx.Nature. 2011; 474: 654-657Crossref PubMed Scopus (1125) Google Scholar), and more recently Mx2 (Goujon et al., 2013Goujon C. Moncorgé O. Bauby H. Doyle T. Ward C.C. Schaller T. Hué S. Barclay W.S. Schulz R. Malim M.H. Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection.Nature. 2013; 502: 559-562Crossref PubMed Scopus (422) Google Scholar, Kane et al., 2013Kane M. Yadav S.S. Bitzegeio J. Kutluay S.B. Zang T. Wilson S.J. Schoggins J.W. Rice C.M. Yamashita M. Hatziioannou T. Bieniasz P.D. MX2 is an interferon-induced inhibitor of HIV-1 infection.Nature. 2013; 502: 563-566Crossref PubMed Scopus (365) Google Scholar). Many studies have shown that HIV-1 is sensitive to IFN (Tsang et al., 2009Tsang J. Chain B.M. Miller R.F. Webb B.L. Barclay W. Towers G.J. Katz D.R. Noursadeghi M. HIV-1 infection of macrophages is dependent on evasion of innate immune cellular activation.AIDS. 2009; 23: 2255-2263Crossref PubMed Scopus (69) Google Scholar), but it is only now becoming possible to dissect the IFN effector systems using modern high-throughput molecular approaches. For example, comparative gene expression arrays were used to identify both tetherin (Neil et al., 2008Neil S.J. Zang T. Bieniasz P.D. Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu.Nature. 2008; 451: 425-430Crossref PubMed Scopus (1422) Google Scholar) and Mx2 (Goujon et al., 2013Goujon C. Moncorgé O. Bauby H. Doyle T. Ward C.C. Schaller T. Hué S. Barclay W.S. Schulz R. Malim M.H. Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection.Nature. 2013; 502: 559-562Crossref PubMed Scopus (422) Google Scholar, Kane et al., 2013Kane M. Yadav S.S. Bitzegeio J. Kutluay S.B. Zang T. Wilson S.J. Schoggins J.W. Rice C.M. Yamashita M. Hatziioannou T. Bieniasz P.D. MX2 is an interferon-induced inhibitor of HIV-1 infection.Nature. 2013; 502: 563-566Crossref PubMed Scopus (365) Google Scholar). Here, we discuss recent progress in understanding how HIV-1 interacts with the cell-autonomous innate immune system and how this new knowledge could lead to new therapeutic opportunities for viral infection and a better understanding of HIV disease. Because retroviruses reverse transcribe their RNA genome into double-stranded DNA in the cytoplasm of infected cells, innate DNA sensors that detect cytoplasmic DNA pose a particular problem for this family of viruses. Cytoplasmic DNA sensors have received a great deal of attention recently. As a result, we are beginning to understand the details of their sensing mechanisms and the downstream consequences of their activation. IFI16 is a cytoplasmic DNA sensor thought to have a role in detection of specific viruses, including HIV-1 (Jakobsen et al., 2013Jakobsen M.R. Bak R.O. Andersen A. Berg R.K. Jensen S.B. Tengchuan J. Laustsen A. Hansen K. Ostergaard L. Fitzgerald K.A. et al.IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication.Proc. Natl. Acad. Sci. USA. 2013; 110: E4571-E4580Crossref PubMed Scopus (233) Google Scholar, Monroe et al., 2014Monroe K.M. Yang Z. Johnson J.R. Geng X. Doitsh G. Krogan N.J. Greene W.C. IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV.Science. 2014; 343: 428-432Crossref PubMed Scopus (349) Google Scholar), whose life cycle involves DNA in the cytoplasm of infected cells (Unterholzner et al., 2010Unterholzner L. Keating S.E. Baran M. Horan K.A. Jensen S.B. Sharma S. Sirois C.M. Jin T. Latz E. Xiao T.S. et al.IFI16 is an innate immune sensor for intracellular DNA.Nat. Immunol. 2010; 11: 997-1004Crossref PubMed Scopus (1189) Google Scholar). However, the recently identified DNA sensor cGAS has generated considerable attention with regard to HIV-1 infection. This sensor synthesizes a second messenger molecule formed from cyclic AMP and cyclic GMP called cGAMP (Wu et al., 2013Wu J. Sun L. Chen X. Du F. Shi H. Chen C. Chen Z.J. Cyclic GMP-AMP is an endogenous second messenger in innate immune signaling by cytosolic DNA.Science. 2013; 339: 826-830Crossref PubMed Scopus (1353) Google Scholar), giving rise to the name cGAMP synthetase, or cGAS, for the sensor (Sun et al., 2013Sun L. Wu J. Du F. Chen X. Chen Z.J. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway.Science. 2013; 339: 786-791Crossref PubMed Scopus (2523) Google Scholar). The cGAMP produced by cGAS binds to the adaptor molecule STING, leading to dimerization of the transcription factor IRF3 and activation of IRF3-regulated genes (Figure 1). Evasion of DNA sensors is thought to be particularly important for lentiviruses, including HIV-1, not only because they synthesize DNA in the cytoplasm of infected cells, but also because they are particularly sensitive to the effects of IFN. In most cases, lentiviruses are strongly repressed in cells treated with type 1 IFN (Goujon and Malim, 2010Goujon C. Malim M.H. Characterization of the alpha interferon-induced postentry block to HIV-1 infection in primary human macrophages and T cells.J. Virol. 2010; 84: 9254-9266Crossref PubMed Scopus (111) Google Scholar, Tsang et al., 2009Tsang J. Chain B.M. Miller R.F. Webb B.L. Barclay W. Towers G.J. Katz D.R. Noursadeghi M. HIV-1 infection of macrophages is dependent on evasion of innate immune cellular activation.AIDS. 2009; 23: 2255-2263Crossref PubMed Scopus (69) Google Scholar). We therefore believe that HIV-1 is highly evolved to avoid triggering DNA sensors, using a process we have termed cloaking. In a series of studies from several labs, HIV-1 has been shown to utilize cellular cofactors that allow evasion of DNA sensor activation and thereby prevent triggering of innate responses. In the first example, the endoplasmic reticulum-associated nuclease TREX1 was shown to be a critical cofactor for HIV-1 replication (Yan et al., 2010Yan N. Regalado-Magdos A.D. Stiggelbout B. Lee-Kirsch M.A. Lieberman J. The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1.Nat. Immunol. 2010; 11: 1005-1013Crossref PubMed Scopus (402) Google Scholar) (Figure 2). At first, it seems paradoxical that a nuclease that degrades HIV-1 DNA could act as a cofactor for infection. However, in the absence of TREX1, excess cytoplasmic DNA produced by reverse transcription appears to trigger the cytoplasmic DNA sensor cGAS, leading to production of the second messenger cGAMP (Gao et al., 2013Gao D. Wu J. Wu Y.T. Du F. Aroh C. Yan N. Sun L. Chen Z.J. Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses.Science. 2013; 341: 903-906Crossref PubMed Scopus (692) Google Scholar, Sun et al., 2013Sun L. Wu J. Du F. Chen X. Chen Z.J. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway.Science. 2013; 339: 786-791Crossref PubMed Scopus (2523) Google Scholar, Yan et al., 2010Yan N. Regalado-Magdos A.D. Stiggelbout B. Lee-Kirsch M.A. Lieberman J. The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1.Nat. Immunol. 2010; 11: 1005-1013Crossref PubMed Scopus (402) Google Scholar). cGAMP production leads to type 1 IFN production, via STING activation, and suppression of replication. Thus, HIV-1 appears to have evolved to synthesize DNA in such a way that TREX1 degrades excess reverse transcription products and prevents the virus from triggering cytosolic DNA sensors. In individuals that are defective for TREX1, through genetic polymorphism, an autoinflammatory encephalitis manifests, called Aicardi-Goutieres syndrome. This debilitating disease is characterized by high levels of IFN production, thought to be due to activation of DNA sensors by endogenous viruses (Stetson et al., 2008Stetson D.B. Ko J.S. Heidmann T. Medzhitov R. Trex1 prevents cell-intrinsic initiation of autoimmunity.Cell. 2008; 134: 587-598Abstract Full Text Full Text PDF PubMed Scopus (924) Google Scholar). Thus, paradoxically, despite acting as a nuclease and degrading viral DNA, TREX1 acts as a viral cofactor, preventing HIV-1-mediated triggering of innate DNA sensors and promoting viral replication. In this way, TREX1 negatively regulates activation of cell-autonomous innate immunity, potentially to the advantage of both endogenous and exogenous retroviruses. We assume that the evolutionarily advantageous rearrangement of genes provided by retrotransposition has led to TREX1-mediated tolerance of cytoplasmic reverse transcription. Although this pathway has evolved for use by the relatively unrelated, reverse-transcribing, endogenous retroelements, exogenous retroviruses such as HIV-1 can exploit this tolerance. We recently suggested that HIV-1 can replicate in human macrophages without triggering innate sensors because, in addition to TREX1, the virus has evolved to utilize several additional cellular cofactors to cloak its presence and avoid detection by PRRs (Rasaiyaah et al., 2013Rasaiyaah J. Tan C.P. Fletcher A.J. Price A.J. Blondeau C. Hilditch L. Jacques D.A. Selwood D.L. James L.C. Noursadeghi M. Towers G.J. HIV-1 evades innate immune recognition through specific cofactor recruitment.Nature. 2013; 503: 402-405Crossref PubMed Scopus (318) Google Scholar) (Figure 2). HIV-1 recruits two particular cofactors, cyclophilin A (CypA) and CPSF6, to the incoming capsid (Franke et al., 1994Franke E.K. Yuan H.E. Luban J. Specific incorporation of cyclophilin A into HIV-1 virions.Nature. 1994; 372: 359-362Crossref PubMed Scopus (645) Google Scholar, Lee et al., 2010Lee K. Ambrose Z. Martin T.D. Oztop I. Mulky A. Julias J.G. Vandegraaff N. Baumann J.G. Wang R. Yuen W. et al.Flexible use of nuclear import pathways by HIV-1.Cell Host Microbe. 2010; 7: 221-233Abstract Full Text Full Text PDF PubMed Scopus (321) Google Scholar, Price et al., 2012Price A.J. Fletcher A.J. Schaller T. Elliott T. Lee K. KewalRamani V.N. Chin J.W. Towers G.J. James L.C. CPSF6 defines a conserved capsid interface that modulates HIV-1 replication.PLoS Pathog. 2012; 8: e1002896Crossref PubMed Scopus (187) Google Scholar, Towers et al., 2003Towers G.J. Hatziioannou T. Cowan S. Goff S.P. Luban J. Bieniasz P.D. Cyclophilin A modulates the sensitivity of HIV-1 to host restriction factors.Nat. Med. 2003; 9: 1138-1143Crossref PubMed Scopus (325) Google Scholar). CypA is an abundant cytoplasmic prolyl isomerase enzyme that recruits to the surface of the incoming HIV-1 capsid and isomerizes the peptide bond between capsid residues G89 and P90. CPSF6 also recruits to the HIV-1 capsid while it is in the cytoplasm. CPSF6 is a predominantly nuclear protein with a role in 3′-end mRNA processing, which may contribute to targeting HIV-1 into a particular pathway of nuclear entry (Rasaiyaah et al., 2013Rasaiyaah J. Tan C.P. Fletcher A.J. Price A.J. Blondeau C. Hilditch L. Jacques D.A. Selwood D.L. James L.C. Noursadeghi M. Towers G.J. HIV-1 evades innate immune recognition through specific cofactor recruitment.Nature. 2013; 503: 402-405Crossref PubMed Scopus (318) Google Scholar). These cofactors are critical for HIV-1 replication in primary human monocyte-derived macrophages (MDM) (Rasaiyaah et al., 2013Rasaiyaah J. Tan C.P. Fletcher A.J. Price A.J. Blondeau C. Hilditch L. Jacques D.A. Selwood D.L. James L.C. Noursadeghi M. Towers G.J. HIV-1 evades innate immune recognition through specific cofactor recruitment.Nature. 2013; 503: 402-405Crossref PubMed Scopus (318) Google Scholar). When interactions between CA and CypA or CPSF6 are prevented, such as by mutating the viral capsid, HIV-1 triggers DNA sensors and activates a type 1 IFN response, leading to suppression of replication. Specifically, the HIV-1 capsid mutant N74D cannot recruit CPSF6 and the P90A mutant capsid cannot recruit CypA. HIV-1 encoding either of these mutations cannot replicate in MDM due to simulation of type 1 IFN. The importance of IFN in suppressing replication is illustrated by the fact that blockade of IFN signaling using an IFN receptor antibody can rescue the replication defect of the mutant viruses. The DNA sensor cGAS appears to have a role in this process, as increased cGAMP was detected after infection of MDM with the P90A capsid mutant. Similar levels of IFN secretion were elicited after RNAi-mediated CPSF6 depletion and subsequent wild-type virus infection or after prevention of CypA recruitment with a nonimmunosuppressive cyclosporine, CsA-SmBz. This pharmacological uncloaking of HIV-1 suggests a new paradigm for the treatment or prevention of viral infection in which viruses are revealed to innate immune sensors by targeting cloaking cofactors (Figure 3). The observation that CPSF6 mutants with a defective nuclear localization signal become cytoplasmic and can act as dominant negatives that suppress HIV-1 reverse transcription (Hori et al., 2013Hori T. Takeuchi H. Saito H. Sakuma R. Inagaki Y. Yamaoka S. A carboxy-terminally truncated human CPSF6 lacking residues encoded by exon 6 inhibits HIV-1 cDNA synthesis and promotes capsid disassembly.J. Virol. 2013; 87: 7726-7736Crossref PubMed Scopus (40) Google Scholar, Rasaiyaah et al., 2013Rasaiyaah J. Tan C.P. Fletcher A.J. Price A.J. Blondeau C. Hilditch L. Jacques D.A. Selwood D.L. James L.C. Noursadeghi M. Towers G.J. HIV-1 evades innate immune recognition through specific cofactor recruitment.Nature. 2013; 503: 402-405Crossref PubMed Scopus (318) Google Scholar) suggested that HIV-1 utilizes CPSF6 to suppress premature DNA synthesis that would otherwise trigger cytoplasmic DNA sensors. Why TREX1 is not able to degrade the viral DNA responsible for DNA sensor triggering in this case remains unclear, but may be due to the quantity, location, or nature of the DNA products. For example, it is plausible that TREX1-dependent DNA clearance is saturated, or that the DNA products form specific immunostimulatory motifs (single- or double-stranded or even RNA/DNA hybrids), which are resistant to TREX1 degradation. The role of CypA is less clear than CPSF6, but it may have a role in camouflaging the hexameric lattice of HIV-1 capsid or an allosteric role in CPSF6 recruitment. In summary, we hypothesize that HIV-1 recruits CypA and CPSF6 to suppress premature reverse transcription and allow evasion of DNA sensors in MDM (Hilditch and Towers, 2014Hilditch L. Towers G.J. A model for cofactor use during HIV-1 reverse transcription and nuclear entry.Curr Opin Virol. 2014; 4: 32-36Crossref PubMed Scopus (70) Google Scholar). Importantly, both CypA and CPSF6 were unnecessary for HIV-1 replication in HeLa and HOS cell-based indicator cell lines. This observation suggests that some cell lines may not have intact DNA sensor pathways and may therefore be misleading when examining cofactor dependence of HIV-1 or sensitivity to innate immune sensors. Early work characterizing the behavior of HIV-1 cores upon target cell entry suggested that the viral cone-shaped capsid containing the reverse transcription complex uncoats in the cytoplasm as a prerequisite to DNA synthesis. However, recent knowledge of DNA sensors and their ability to detect cytoplasmic DNA suggests that HIV may have evolved a more sophisticated uncoating process that can evade DNA sensors, at least in certain circumstances. Microscopic analysis of HIV-1 behavior inside cells suggested that the virus might carry out reverse transcription and uncoating in a highly organized way, perhaps in complex with the nuclear pore, at least in some cells (Arhel et al., 2007Arhel N.J. Souquere-Besse S. Munier S. Souque P. Guadagnini S. Rutherford S. Prévost M.C. Allen T.D. Charneau P. HIV-1 DNA Flap formation promotes uncoating of the pre-integration complex at the nuclear pore.EMBO J. 2007; 26: 3025-3037Crossref PubMed Scopus (217) Google Scholar). More recent genetic analysis has described multiple direct interactions between the HIV-1 capsid and nuclear pore proteins that might mediate this process. Functional interactions have been described between the viral capsid and nuclear pore components Nup358 (Bichel et al., 2013Bichel K. Price A.J. Schaller T. Towers G.J. Freund S.M. James L.C. HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358.Retrovirology. 2013; 10: 81Crossref PubMed Scopus (78) Google Scholar, Schaller et al., 2011Schaller T. Ocwieja K.E. Rasaiyaah J. Price A.J. Brady T.L. Roth S.L. Hué S. Fletcher A.J. Lee K. KewalRamani V.N. et al.HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency.PLoS Pathog. 2011; 7: e1002439Crossref PubMed Scopus (333) Google Scholar) and Nup153 (Matreyek and Engelman, 2011Matreyek K.A. Engelman A. The requirement for nucleoporin NUP153 during human immunodeficiency virus type 1 infection is determined by the viral capsid.J. Virol. 2011; 85: 7818-7827Crossref PubMed Scopus (159) Google Scholar, Matreyek et al., 2013Matreyek K.A. Yücel 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. 2013; 9: e1003693Crossref PubMed Scopus (177) Google Scholar) and perhaps interaction between integrase and the karyopherin TNPO3 (Christ et al., 2008Christ F. Thys W. De Rijck J. Gijsbers R. Albanese A. Arosio D. Emiliani S. Rain J.C. Benarous R. Cereseto A. Debyser Z. Transportin-SR2 imports HIV into the nucleus.Curr. Biol. 2008; 18: 1192-1202Abstract Full Text Full Text PDF PubMed Scopus (210) Google Scholar). Intriguingly, Nup153 is largely found on the inside of the nuclear membrane and yet appears to interact with HIV-1 capsid in the same pocket as CPSF6 (Matreyek and Engelman, 2011Matreyek K.A. Engelman A. The requirement for nucleoporin NUP153 during human immunodeficiency virus type 1 infection is determined by the viral capsid.J. Virol. 2011; 85: 7818-7827Crossref PubMed Scopus (159) Google Scholar, Matreyek et al., 2013Matreyek K.A. Yücel 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. 2013; 9: e1003693Crossref PubMed Scopus (177) Google Scholar). Thus, one possibility is that Nup153 reaches through the nuclear pore complex (NPC) from the nuclear side to displace CPSF6 and uncoat the intact reverse transcribing capsid. Such a model might allow Nup153 to uncoat the viral core in the region associated with the central pore of the NPC. This could allow the DNA to be fed through the pore into the nucleus without being exposed to the cytoplasm at any point, despite being synthesized on the cytoplasmic side of the nuclear membrane. Nuclear entry of the DNA is likely to be immediately followed by integration into chromatin, with nuclear entry and integration occurring as a single coordinated event at the nuclear pore. An attractive aspect of this more complex model of coordinated DNA synthesis, uncoating, nuclear entry, and integration in complex with the NPC is that it suggests a mechanism by which HIV-1 can evade activation of the cell-autonomous innate immune system by avoiding revealing viral DNA to cytoplasmic DNA sensors or free viral DNA ends to the nuclear DNA damage machinery. In the case of lentiviruses, such as HIV-1, the IFN-induced effector proteins that are actually responsible for suppressing viral infectivity are called restriction factors. This phrase was coined in the earliest days of considering the tropism of murine leukemia viruses and their suppression by the restriction factor Fv1 (Best et al., 1996Best S. Le Tissier P. Towers G. Stoye J.P. Positional cloning of the mouse retrovirus restriction gene Fv1.Nature. 1996; 382: 826-829Crossref PubMed Scopus (401) Google Scholar). Most restriction factors are expressed at low levels, even in the absence of IFN-mediated induction. These proteins have therefore been described as mediating intrinsic innate immunity because they are intrinsically expressed (Bieniasz, 2004Bieniasz P.D. Intrinsic immunity: a front-line defense against viral attack.Nat. Immunol. 2004; 5: 1109-1115Crossref PubMed Scopus (362) Google Scholar). However, distinguishing between proteins based on their expression levels in uninduced cells may be misleading, and we prefer to think of all IFN-induced proteins as critical and integral features of the cell-autonomous innate immune system. Lentiviruses travel light, with only 9–10 genes. Because of this, they do not have the genetic capacity to globally manipulate innate immune responses as larger viruses do. For example, herpes viruses encode in excess of 200 open reading frames, the majority of which have roles in antagonizing cellular defensive processes (for review, see Amsler et al., 2013Amsler L. Verweij M.C. DeFilippis V.R. The tiers and dimensions of evasion of the type I interferon response by human cytomegalovirus.J. Mol. Biol. 2013; 425: 4857-4871Crossref PubMed Scopus (46) Google Scholar). We hypothesize that the constraints of a small genome provide selective pressure for HIV-1 to evolve evasion strategies, rather than antagonists that abrogate the effector functions of restriction factors. However, because many restriction factors are intrinsically expressed, even in the absence of IFN induction, the virus cannot simply inhibit the IFN pathway but must antagonize or avoid specific restriction factors that pose a barrier to replication. In the case of lentiviruses, accessory proteins carry the burden of restriction factor antagonism. Indeed, it appears that the major function of lentiviral accessory proteins is to act as adaptor molecules that recruit ubiquitination machinery to mark the targeted restriction factor for proteasome-mediated degradation (Schwefel et al., 2014Schwefel D. Groom H.C. Boucherit V.C. Christodoulou E. Walker P.A. Stoye J.P. Bishop K.N. Taylor I.A. Structural basis of lentiviral subversion of a cellular protein degradation pathway.Nature. 2014; 505: 234-238Crossref PubMed Scopus (89) Google Scholar). The restriction factor tetherin provides a good example of this Red Queen-style antagonistic evolution between the host and virus (Gupta et al., 2009aGupta R.K. Hué S. Schaller T. Verschoor E. Pillay D. Towers G.J. Mutation of a single residue renders human tetherin resistant to HIV-1 Vpu-mediated depletion.PLoS Pathog. 2009; 5: e1000443Crossref PubMed Scopus (164) Google Scholar). Tetherin is a transmembrane protein that forms a physical tether to prevent nascent HIV-1 virions from leaving the surface of infected cells (Neil et al., 2008Neil S.J. Zang T. Bieniasz P.D. Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu.Nature. 2008; 451: 425-430Crossref PubMed Scopus (1422) Google Scholar). HIV-1 is unable to avoid budding through membranes and therefore cannot avoid restriction by tetherin if the protein is present in the host cell plasma membrane. The importance of suppressing tetherin activity is illustrated by the fact that the pandemic HIV-1 strain, HIV-1 M group, has evolved to use the accessory Vpu protein to antagonize tetherin. The parental virus SIVcpz from chimpanzees uses its Nef protein to antagonize tetherin, and the less successful HIV-1 zoonoses, giving rise to HIV-1 groups O, N, and P, have not made this evolutionary transition as effectively and thus antagonize tetherin poorly (Sauter et al., 2009Sauter D. Schindler M. Spec