Cellular Targets of HIV-1 Protease: Just the Tip of the Iceberg?

Abstract

Human immunodeficiency virus 1 (HIV-1) viral protease (PR) is one of the most studied viral enzymes and a crucial antiviral target. Despite its well-characterized role in virion maturation, an increasing body of research is starting to focus on its ability to cleave host cell proteins. Such findings are apparently in contrast with the dogma of HIV-1 PR activity being restricted to the interior of nascent virions and suggest catalytic activity within the host cell environment. Given the limited amount of PR present in the virion at the time of infection, such events mainly occur during late viral gene expression, mediated by newly synthesized Gag-Pol polyprotein precursors, rather than before proviral integration. HIV-1 PR mainly targets proteins involved in three different processes: those involved in translation, those controlling cell survival, and restriction factors responsible for innate/intrinsic antiviral responses. Indeed, by cleaving host cell translation initiation factors, HIV-1 PR can impair cap-dependent translation, thus promoting IRES-mediated translation of late viral transcripts and viral production. By targeting several apoptotic factors, it modulates cell survival, thus promoting immune evasion and viral dissemination. Additionally, HIV-1 PR counteracts restriction factors incorporated in the virion that would otherwise interfere with nascent virus vitality. Thus, HIV-1 PR appears to modulate host cell function at different times and locations during its life cycle, thereby ensuring efficient viral persistency and propagation. However, we are far from having a complete picture of PR-mediated host cell modulation, which is emerging as a field that needs further investigation.

Keywords: HIV-1 PR; antiviral therapy; apoptosis; cell death; host cell shut-off; host factors; protease.

Figure 1

Schematic representation of IRES locations in the HIV-1 genome and transcripts.

Figure 2

HIV-1 replication cycle with targets cleaved by HIV-1 protease. The exact timing and location of the activity of HIV-1 PR are still not completely characterized. It is speculated that due to its possible anti-RT activity, eIF3D may be an early target of PR, and inactivating this factor may serve as a way to escape antiviral defenses of the cell and hinder cap-dependent translation. The other intracellular targets are most likely cleaved by post-integration synthetized PR, among these targets there are several proteins involved in protein synthesis that are responsible for either cap-dependent translation initiation (eIF4G, PABP) or translation regulation (GCN2). The other major protein cluster that is targeted by the viral enzyme represents proteins involved in cell death and the innate defenses of the cell (Bcl2, Procaspase8, NF-κB1, NDR1/2, RIPK1, TBK1). Lastly, HIV-1 PR was shown to cleave host proteins that are incorporated into the nascent virion, two of which exert antiviral activity (A3H SV200, YTHDF3) while the specific function of the other two (NDR1/2, Lyric) remain unknown.

Figure 3

3D structure of HIV-1 PR (PDB ID 6O48) visualized as a ribbon diagram with functional domains highlighted in different colors [34]: protease flaps in green, flap elbows in turquoise, fulcrum in orange, cantilever in yellow, dimer interface in pale magenta, and active site in red.

Figure 4

Processing of HIV-1 polyproteins by the viral protease. (a) Ordered processing of Gag-Pol by the poorly-active protease (PR) precursor still embedded in the polyprotein context. The first cleavage events aim at separating PR from the polyprotein at its N-terminus (separating the PR from the transframe domain p6*), later events finally free the protease from the rest of the precursor. (b) Processing of Gag by the mature PR. Maturation occurs in a precise and ordered manner (events order is numbered 1–3), with the first cleavage occurring between the nucleocapsid (NC) and spacer peptide (Sp)1, then between the matrix (MA)/capsid (CA) and SP2/p6, and lastly, the CA and NC are separated from the spacer peptides. (c) Schematic representation of virion maturation.

Figure 5

Graph of identified HIV-1 PR interactors from Jäger et al. represented by STRING [54].

Figure 6

Schematic representation of eukaryotic 43S pre-initiation complex with HIV-1 PR cleavage targets.

Figure 7

HIV-1 PR modulation of apoptosis via cleavage or interaction with cellular factors. The viral protease is able to cleave several proteins involved in apoptosis regulation. By cleaving procaspase 8 into its cas8p41 fragment, the viral enzyme is able to promote programmed cell death. Likewise, cleavage and consequent inhibition of Bcl-2 also contributes to apoptosis activation. Interestingly, the non-proteolytic interaction between PR and BCA3 was also shown to increase apoptosis. Furthermore, HIV-1 PR cleaves several other proteins involved in the activation and regulation of apoptosis. In these cases, the consequences of their cleavage are not as clear but they fit into the complex scheme of HIV-1-dependent regulation of programmed cell death.