HIV-1 capsid and viral DNA integration

Abstract

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.

Keywords: HIV; capsid; integration; nuclear entry; reverse transcription.

FIG 1

A cartoon depiction of the HIV-1 particle and a schematic representation of the viral genomic map. The mature particle contains two genomic RNA molecules (shown here as black curved lines inside the green-colored capsid) that encode nine open reading frames and contain long terminal repeats (LTRs) at both the 5′ and 3′ ends. The RNA genome encodes viral polyprotein precursors (Gag, Gag-Pol) or, after splicing, viral envelope (gp160), regulatory (Tat, Rev), and accessory proteins (Nef, Vpr, Vpu, Vif). The HIV-1 proteins are generated after the integration of the reverse-transcribed viral DNA, followed by transcription into viral mRNAs. The HIV-1 PR-mediated processing of the Gag into MA, CA, NC, and p6, and the processing of Gag-Pol into RT and IN proteins within the released immature virus particle trigger the assembly of the fullerene cone-shaped capsid and the generation of the mature infectious HIV-1 particle (virion). The capsid contains RT, IN, PR, Vif, Vpr, Vpu, Nef, and HIV-1 genomic RNA dimers coated with NC. The host cell protease-mediated processing of the viral envelope polyprotein gp160 in the producer cell yields trimeric complexes of heterodimers of gp120 and gp41 that are embedded in the host cell membrane enclosing the virus.

FIG 2

HIV-1 CA oligomerization into a conical lattice of hexamers and pentamers. (A) Ribbon diagram of the CA monomer (PDB ID: 4XFY) with the N-terminal domain (NTD, purple), a linker region, the C-terminal domain (CTD, cyan), and the unstructured cyclophilin A (CypA)-binding loop (red). (B) A zoomed-in view of the CA hexamers and pentamers that constitute the HIV-1 capsid fullerene cone. In the upper inset, the top view of the CA hexamer (PDB ID: 4XFY) is depicted with the NTD (purple) oriented toward the anterior and the CTD (cyan) positioned toward the posterior. In the lower inset, the top view of the CA pentamer (PDB ID: 3P05) is shown with the NTD (yellow) oriented toward the anterior and the CTD (cyan) oriented toward the posterior. (C) The entire HIV-1 capsid cone (PDB ID: 3J3Y) is composed of CA hexamers (purple) and CA pentamers (yellow). A 180° rotation view depicts the positioning of the pentamers on the capsid surface.

FIG 3

Illustration of the canonical and emerging models of the early events of HIV-1 replication culminating in viral integration. Sequential binding of the HIV-1 envelope glycoprotein gp120 to the CD4+ receptor and to one of the co-receptors (CCR5 or CXCR4) leads to the fusion of the viral and cellular membranes and the release of the capsid into the cytoplasm. The capsid contains two copies of the linear ssRNA viral genome as well as certain viral and cellular factors, and it is trafficked by the host microtubule machinery through the cytoplasm toward the nucleus. While the canonical and emerging models of the early events of HIV-1 replication concur that the reverse transcription begins within the confines of the capsid, the models differ on the spatiotemporal staging of the reverse transcription and the subsequent steps. In the canonical sequence of events (A), reverse transcription occurring within the capsid in the cytoplasm leads to two concurrent outcomes: the generation of the PIC and the uncoating of the capsid. The PIC contains the viral dsDNA complexed with multimers of the viral IN, as well as other viral and cellular factors. The PIC is then imported via the NPC into the nucleus, wherein the IN inserts the viral DNA into the chromosomal DNA (integration). An alternate version of early events proposes that (B) reverse transcription is ongoing or completed within the capsid during its cytoplasmic trafficking to the NPC, and the intact or partially intact capsid is imported into the nucleus, where further loss of the capsid’s structural integrity during its intranuclear trafficking enables viral DNA integration into the chromosomal DNA. In another emerging version of early events (C), reverse transcription is initiated only upon nuclear import of the intact capsid and is completed during intranuclear trafficking, which coincides with the loss of the capsid’s structural integrity that enables viral DNA integration.