TRIM5 and Retroviruses

Restriction factors are multiple innate immune proteins expressed in mammalian cells that protect against invading retroviruses, such as HIV-1. Two members of the tripartite motif protein family-TRIM5α and TRIMCyp were identified in 2004 as restriction factors that recognize and intercept incoming retroviruses by binding to the capsid that surrounds and protects the viral core. Here, we summarize how TRIM5 proteins recognize incoming retroviral cores and inhibit virus replication.

Mechanism of capsid recognition

All retroviral capsids are organized as fullerene structures with hexagonal lattice symmetry, and it is this shared architecture that underlies the mechanism of capsid recognition by TRIM5. Capsid recognition is described by a model in which the SPRY and CypA domains each bind to some epitope on CA.

Fig 2. Mechanism of core recognition by TRIM5
(Source: Nat Rev Microbiol. July 2019)

Avid capsid recognition by TRΙM5α Early studies established that TRIM5α does not bind the isolated CA subunit, and that binding can be detected in vitro only when the CA proteins are assembled as capsid-like tubes, other studies showed that the self-association properties of the TRIM5α coiled-coil and B-box 2 domains are critical for restriction activity. In addition, the biochemical analysis of TRIM5α proteins found those proteins assemble spontaneously into hexagonal lattices in vitro. This finding led to the realization that TRIM5α can match both the symmetry and the spacing of the capsid lattice and generate powerful avidity effects. An important unanswered question is precisely how the SPRY domain contacts the CA subunits, and several related studies suggest that the SPRY domain has a β-sandwich fold that displays all four loops on one side, where they can act independently or in concert to bind CA in multiple ways.

Capsid recognition by TRIMCyp The capsid-binding domain of TRIMCyp is homologous to the cellular pep-tidylprolyl isomerase CypA. In HIV-1, CypA binds to the cyclophilin-binding loop that is prominently exposed on the NTD of HIV-1 CA. A key proline residue (Pro90) in this loop binds to the enzyme’s active site. When bound to the assembled CA lattice, CypA has a secondary contact with another NTD in the adjacent CA hexamer. meaning that the TRIMCyp dimer can potentially contact at least four CA subunits simultaneously. Unlike the SPRY domains, the two CypA domains are more flexibly tethered to the coiled-coil domain, and so each TRIMCyp dimer presumably has a wider reach than a SPRY dimer and can sample a larger area to optimize local binding. TRIMCyp might have dispensed with the need for higher-order assembly to efficiently recognize retroviral capsids, consistent with the significantly higher affinity of the CypA domain for the CA subunit.

Ubiquitin-dependent non-productive uncoating

TRIM5 cytoplasmic bodies (both in the presence and in the absence of viral cores) are linked with ubiquitylation and ubiquitin-dependent cellular degradation machinery such as proteasomes. In the context of restriction, in the presence of proteasome inhibitors, the levels of particulate CA and core components resemble those observed under non-restricting conditions. TRIM5α undergoes self-ubiquitylation, and inhibiting this modification abrogates accelerated uncoating and restores reverse transcription. TRIM5 and HIV-1 cores initially form stable complexes, and that the ubiquitin–proteasome system is required to non-productively accelerate disassembly of the capsid coat. The ubiquitin–proteasome system is not required to inhibit virus replication, and even under conditions where reverse transcription is restored by proteasome inhibitors or RING domain mutations, infectivity is not restored. Thus, either TRIM5 imposes sequential blocks to the post-entry pathway or TRIM5 binding diverts the core into an ‘off-pathway’ trajectory that can-not be corrected by inhibiting the proteasome or disrupting TRIM5 self-ubiquitylation.

TRIM5 is a selective autophagy receptor that directs degradation of the retroviral core through a mechanism termed ‘virophagy’. TRIM5α binds and activates key autophagy effectors. TRIM5 also directly binds LC3 and other Atg8 homologues, which are ubiquitin-like proteins that are conjugated to phosphatidylethanolamine and are well-established markers of autophagosomal membranes. However, autophagy is not required for TRIM5-mediated inhibition of virus infectivity, which parallels observations on the proteasome. It might be that the proteasome and autophagy pathways are redundant or cell type-dependent mechanisms of virus clearance that operate after the core has already been disabled.

TRIM5 Antibodies