Multiple Roles of HIV-1 Capsid during the Virus Replication Cycle

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.

Keywords: Assembly; Capsid (CA); Human immunodeficiency virus-1 (HIV-1); Inhibitor; Post entry; Uncoating and nuclear import.

Fig. 1

Structure of the HIV-1 virion and its components. A HIV-1 Gag domain organization. The HIV-1 Gag consists of four domains—matrix (MA), capsid (CA), nucleocapsid (NC) and p6—and two short peptides, SP1 and SP2, that are cleaved into distinct proteins by the viral protease during maturation. B Immature and mature HIV-1 virions. In the immature virion (left) Gag molecules are radially organized in the hexameric lattice (Gag domains are shown in the same colors as in A). Two molecules of viral genomic RNA (magenta) per virion are packaged. Trimers of Env protein are embedded in the viral membrane. Gag-Pol molecules that produce viral enzymes—protease (PR) (purple), reverse transcriptase (RT) (orange) and integrase (IN) (brown)—are present in 1:20 ratio to Gag. In the mature virion (right), MA retains bound to the viral membrane, released CA forms a characteristic cone-shaped core, NC is bound to the viral genomic RNA (reprinted from Freed 2015). Electron microscopy images of the immature (left) and mature (right) virions are shown (Novikova and Freed, unpublished data). Scale bar, 100 nm. C Structure of the mature capsid (Pornillos et al.2011), reprinted with permission from Nature Publishing Group. Capsid is formed by a hexameric CA lattice (CA-NTDs in orange, CA-CTDs in blue) with 12 embedded CA pentamers (yellow) allowing for the closing off of both ends of the conical structure.

Fig. 2

Arrangement of CA in immature and mature HIV-1 virions. A Structure of the CA monomer. CA consists of two α-helical domains—CA-NTD and CA-CTD—that are connected by a short linker. The CypA-binding loop and β-hairpin are indicated. Helices of CA-NTD: helix 1 (ruby), helix 2 (cyan), helix 3 (orange), helix 4 (blue), helix 5 (magenta), helix 6 (light green) and helix 7 (yellow). Helices of CA-CTD: 3₁₀ helix (brown), helix 8 (wheat), helix 9 (green), helix 10 (purple) and helix 11 (red) [PDB ID: 5MCX (Mattei et al.2016a)]. B Structural arrangement of the CA layer in intact immature (left) and mature (right) HIV-1 virions. CA-NTDs and CA-CTDs of two CA monomers from neighbouring hexamers are colored in blue and red, respectively. All other CA-NTDs and CA-CTDs are in cyan and in orange, respectively. Some important interfaces involved in the formation of the two structures are shown. Hexagons indicate a sixfold interface in the individual hexamer in both structures. In the immature lattice (left) homo-dimeric (ovals) and homo-trimeric (triangles) interfaces important for connecting neighboring hexamers are formed by helices 1 and 2 of CA-NTDs, respectively [PDB ID: 4USN (Schur et al.2015)]. In the mature virion (right), inter-hexamer interactions are formed by helices 10 and 11 residing at threefold interfaces (triangles) and by residues from helix 9 at twofold interfaces (ovals) [PDB ID: 5MCX (Mattei et al.2016a)]. C CA-CTD and the N-terminal seven residues of SP1 (side view—left; top view—right) in the six-helix bundle. Residues of SP1 (light green), CA-CTD (orange), MHR loop (red), loop connecting helices 9 and 10 (cyan), and a β-turn (yellow) are key elements for the formation of the CA-SP1 bundle in the immature Gag lattice [PDB ID: 5I4T (Wagner et al.2016)]. The arrow indicates the cleavage site between CA and SP1.

Fig. 3

A proposed model for post-entry events of HIV-1 infection mediated by CA-interacting host factors. Microtubule-associated proteins MAP1, kinesin-1 adaptor protein FEZ1, and dynein adaptor protein BICD2 bind to CA protein and facilitate the inward trafficking of HIV-1 reverse transcription complex (RTC) and pre-integration complex (PIC) towards the nuclear membrane. Upon arrival at the nuclear pore complex (NPC), Nup358 mediates docking of RTC/PIC through interacting with CA. Nup153 then mediates PIC translocation through the NPC by interacting with CA, and potentially facilitates nuclear PIC (n-PIC) release from the nuclear basket in concert with CPSF6. Afterwards, CPSF6, together with LEDGF, associate with the n-PIC to facilitate HIV-1 integration. TNPO3 might indirectly facilitate these processes through mediating proper CPSF6 nuclear localization. Several restriction factors also interfere with these post-entry infection events through interacting with CA. TRIM5 binds to the CA of RTC/PIC causing premature uncoating and inhibits reverse transcription. MxB restricts RTC/PIC nuclear entry by interacting with CA. Nuclear factor NONO binds to the CA on n-PIC and promotes cGAS sensing of HIV viral DNA genome in the nucleus. CA in the incoming viral capsid, RTC, and PIC is indicated in green. Viral nucleic acid (RNA or DNA) is shown inside the CA-containing complexes. Host dependency factors are shown in pink and host restriction factors in blue.