HIV-1 Integrase Binds the Viral RNA Genome and Is Essential during Virion Morphogenesis

Abstract

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.

Allosteric HIV-1 Integrase Inhibitors Lead to Premature Degradation of the Viral RNA Genome and Integrase in Target Cells

“…We next extended these experiments to the R269A/K273A class II IN mutant, which specifically inhibits IN binding to the viral RNA genome without affecting the catalytic activity of IN and leads to formation of particles with the eccentric morphology (4). Although the nearby K264A/K266A mutation similarly inhibits IN-RNA interactions and generates eccentric particles, this mutation is pleiotropic and interferes with the catalytic activity of IN.…”

“…It is important to note that comparison of ALLINIs with the R269A/K273A IN mutation is particularly informative for delineating whether premature degradation of vRNA and IN is a consequence of the aberrant IN multimerization or the inability of IN to bind vRNA. While ALLINIs both induce aberrant IN multimerization (9,17,(24)(25)(26) and block IN-RNA interactions (4), the R269A/K273A substitutions impair the ability of IN to bind to vRNA in virions without altering its multimeric state in vitro (4).…”

“…A remarkably similar morphological defect is observed in particles generated in the presence of allosteric integrase inhibitors (ALLINIs) (also known as LEDGINs, NCINIs, or INLAIs) (18)(19)(20)(21)(22)(23). Proposed mechanisms that underlie this morphogenesis defect include ALLINI-induced aberrant IN multimerization (9,17,(24)(25)(26)(27) and inhibition of IN binding to the viral RNA genome (4).…”

“…Importantly, RNA (viral or cellular) has been shown to play a structural role in viral particles (2,3). Although the proposed models of virion maturation have been largely centered on proteolytic cleavage events of Gag, recent studies have revealed an active role of integrase (IN) in encapsidation of the viral RNA genome within the mature conical CA lattice (4).…”

“…While a large fraction of eccentric particles contain irregularly shaped nonconical CA assemblies (9,17,24), they appear to retain all of the components necessary for reverse transcription, i.e., a dimeric viral RNA genome primed with tRNA-Lys, functional reverse transcriptase (RT) (23), and normal levels of NC-RNA complexes (4,17). Nevertheless, these particles are blocked at an early reverse transcription stage in target cells (9,11,13,24), the basis of which remains unknown.…”