HIV-1 replication can be inhibited by type-I interferon (IFN), and the expression of a number of gene products with anti HIV-1 activity is induced by type-I IFN1,2. However, none of the known antiretroviral proteins can account for the ability of type-I IFN to inhibit early, preintegration, phases of the HIV-1 replication cycle in human cells3,4. By comparing gene expression profiles in cell lines that differ in their ability to support the inhibitory action of IFNα on early steps of the HIV-1 replication cycle, we identified Myxovirus resistance-2 (Mx2) as an interferon-induced inhibitor of HIV-1 infection. Expression of Mx2 reduced permissiveness to a variety of lentiviruses, while depletion of Mx2 using RNA interference reduced the anti-HIV-1 potency of IFNα. HIV-1 reverse transcription proceeded normally in Mx2-expressing cells, but 2-LTR circular forms of HIV-1 DNA were less abundant, suggesting that Mx2 inhibits HIV-1 nuclear import, or destabilizes nuclear HIV-1 DNA. Consistent with this notion, mutations in the HIV-1 capsid protein that are known, or suspected to alter the nuclear import pathways used by HIV-1 conferred resistance to Mx2, while preventing cell division increased Mx2 potency. Overall, these findings indicate that Mx2 is an effector of the anti-HIV-1 activity of type-I IFN, and suggest that Mx2 inhibits HIV-1 infection by inhibiting capsid-dependent nuclear import of subviral complexes.

Summary The HIV-1 Gag protein orchestrates all steps of virion genesis, including membrane targeting and RNA recruitment into virions. Using crosslinking-immunoprecipitation (CLIP) sequencing, we uncover several dramatic changes in the RNA binding properties of Gag that occur during virion genesis, coincident with membrane binding, multimerization and proteolytic maturation. Prior to assembly, and after virion assembly and maturation, the nucleocapsid domain of Gag preferentially binds to psi and Rev Response elements in the viral genome, and GU-rich mRNA sequences. However, during virion genesis, this specificity transiently changes in a manner that facilitates genome packaging; nucleocapsid binds to many sites on the HIV-1 genome and to mRNA sequences with a HIV-1-like, A-rich nucleotide composition. Additionally, we find that the matrix domain of Gag binds almost exclusively to specific tRNAs in the cytosol, and this association regulates Gag binding to cellular membranes.

SUMMARY While an essential role of HIV-1 integrase (IN) for integration of viral cDNA into human chromosome is established, studies with IN mutants and allosteric IN inhibitors (ALLINIs) have suggested that IN can also influence viral particle maturation. However, it has remained enigmatic as to how IN contributes to virion morphogenesis. Here we demonstrate that IN directly binds the viral RNA genome in virions. These interactions have specificity as IN exhibits distinct preference for select viral RNA structural elements. We show that IN substitutions that selectively impair its binding to viral RNA result in eccentric, non-infectious virions without affecting nucleocapsid-RNA interactions. Likewise, ALLINIs impair IN binding to viral RNA in virions of wild type but not escape mutant virus. These results reveal an unexpected biological role of IN binding to the viral RNA genome during virion morphogenesis and elucidate the mode of action of ALLINIs.