Capsid-host interactions for HIV-1 ingress

Abstract

The HIV-1 capsid, composed of approximately 1,200 copies of the capsid protein, encases genomic RNA alongside viral nucleocapsid, reverse transcriptase, and integrase proteins. After cell entry, the capsid interacts with a myriad of host factors to traverse the cell cytoplasm, pass through the nuclear pore complex (NPC), and then traffic to chromosomal sites for viral DNA integration. Integration may very well require the dissolution of the capsid, but where and when this uncoating event occurs remains hotly debated. Based on size constraints, a long-prevailing view was that uncoating preceded nuclear transport, but recent research has indicated that the capsid may remain largely intact during nuclear import, with perhaps some structural remodeling required for NPC traversal. Completion of reverse transcription in the nucleus may further aid capsid uncoating. One canonical type of host factor, typified by CPSF6, leverages a Phe-Gly (FG) motif to bind capsid. Recent research has shown these peptides reside amid prion-like domains (PrLDs), which are stretches of protein sequence devoid of charged residues. Intermolecular PrLD interactions along the exterior of the capsid shell impart avid host factor binding for productive HIV-1 infection. Herein we overview capsid-host interactions implicated in HIV-1 ingress and discuss important research questions moving forward. Highlighting clinical relevance, the long-acting ultrapotent inhibitor lenacapavir, which engages the same capsid binding pocket as FG host factors, was recently approved to treat people living with HIV.

Keywords: CPSF6; FG domain; HIV; NUP153; capsid; lenacapavir; liquid-liquid phase separation; mixed-charge domain; nuclear import; prion-like domain; speckle-associated domain; trafficking.

Fig 1

The HIV-1 core, CA, and capsomeres. (A) The drawing depicts the core with luminal components noted in text. IN, integrase. The approximate width of the wide end of the core is indicated. (B) Structure of the CA monomer (based on Protein Data Bank (PDB) accession code 4XFY) (9). The NTD, short interdomain linker, and CTD are colored forest green, magenta, and pale green, respectively. CYP-binding loop and FG pocket locations within the NTD are noted. N57 and N74 sidechains, which form part of the FG pocket, are drawn as sticks. (C) All-atom model of the capsid shell built from 186 hexamers and 12 pentamers (PDB accession code 3J3Y) (10) alongside resected CA hexamer [PDB code 4U0D (11)], pentamer [PDB code 3P05 (12)], and hexamer-2 [PDB code 6ECO (13)] structures. Hexamer and hexamer-2 colorings are the same as in panel B; pentamer-specific NTDs and CTDs are colored navy and light blue, respectively. Arg18 sidechains within the hexamer, which surround the R18 pore label, are shown as sticks. Coalesced NTD Glu75 and CTD Glu212 and Glu 213 residues are shown in space-fill at the tri-hexamer interface, where a single copy of each residue is labeled.

Fig 2

Schematic of HIV-1 ingress. Following virus-cell membrane fusion (step 1), the viral core in association with motor complex adapter proteins such as BICD2 and FEZ1 travels along microtubules (step 2) toward the microtubule organizing complex (MTOC)/nuclear membrane. The interaction of the core with cell proteins such as CPSF6, NUP358, and NUP153 facilitates transport through the nuclear pore complex (NPC) (step 3). The CA-CPSF6 interaction further licenses core incursion into the nucleoplasm (step 4) toward speckle-associated domain (SPAD) regions of chromatin for integration (step 5). The leftward flow depicts steady-state condition in the absence of HIV-1 infection whereby the β-karyopherin transportin 3 (TNPO3) engages pre-mRNA splicing factors in the cytoplasm to affect their nuclear transport and subsequent downstream targeting of nuclear speckles (43, 44). LAD, lamina-associated domain; LEDGF, lens epithelium-derived growth factor; PIC, preintegration complex; Pol II, RNA polymerase II.

Fig 3

Host factor binding sequences and regions. (A) Domain arrangements of FG host factors NUP153, SEC24C, and CPSF6. Short vertical lines mark positions of FG peptides, with green arrows highlighting specific FGs for capsid binding. Yellow shade demarcates PrLDs as predicted from the PLAAC server (124). The red ticks at the NUP153 C-terminus demarcate the terminal RRRK_COOH sequence (triple-Arg binding motif underlined). The CPSF6 PrLD lies amid a larger Pro-rich domain (PRD), which is denoted as orange rectangle. ZnF, zinc-finger domain; RRM, RNA recognition motif; RSLD, arginine-serine like domain [a.k.a. Arg-mixed charge domain or R-MCD (125)]. (B) Sequence alignment of similar stretches of FEZ1 (top) and PQBP1 (bottom) proteins. Numbers refer to amino acid positions within the respective proteins. Asterisks demarcate FEZ1 residues shown by MD to bind CA Arg18 at >87.8% occupancy, with E182 and E183 showing near complete occupancy (>99.5%). Black and gray backgrounds indicate identical residues and physiochemically conserved side chains, respectively.

Fig 4

Roles for the CA-CPSF6 interaction in HIV-1 intranuclear trafficking and integration targeting. (A) In the absence of its interaction with CA, CPSF6 localization remains largely pan-nuclear, HIV-1 trafficking arrests at the nuclear pore complex (NPC), and integration occurs at proximal chromosomal locations including lamina-associated domains (LADs). (B) The CA-CPSF6 interaction is critical for nuclear evasion of the HIV-1 core, CPSF6 puncta formation, and SPAD-integration targeting. Recent work has raised the intriguing possibility that CPSF6 LLPS activity underlies HIV-induced puncta formation (240), which will require additional experiments to formally prove or disprove. NS, nuclear speckles; SPAD, speckle-associated domain.