Integrase-RNA interactions underscore the critical role of integrase in HIV-1 virion morphogenesis

Abstract

A number of human immunodeficiency virus 1 integrase (IN) alterations, referred to as class II substitutions, exhibit pleotropic effects during virus replication. However, the underlying mechanism for the class II phenotype is not known. Here we demonstrate that all tested class II IN substitutions compromised IN-RNA binding in virions by one of three distinct mechanisms: i) markedly reducing IN levels thus precluding formation of IN complexes with viral RNA; ii) adversely affecting functional IN multimerization and consequently impairing IN binding to viral RNA; iii) directly compromising IN-RNA interactions without substantially affecting IN levels or functional IN multimerization. Inhibition of IN-RNA interactions resulted in mislocalization of the viral ribonucleoprotein complexes outside the capsid lattice, which led to premature degradation of the viral genome and IN in target cells. Collectively, our studies uncover causal mechanisms for the class II phenotype and highlight an essential role of IN-RNA interactions for accurate virion maturation.

Optimized binding of substituted quinoline ALLINIs within the HIV-1 integrase oligomer

“…This mislocalization of the RNP to a position located between the low density empty capsid (CA) core and the particle membrane in mature virions has been observed using electron microscopy ( 17 , 31 , 32 ). The buoyant sucrose gradient technique that measure the relative density of the viral core of mature virions has also been validated as an effective approach to characterize this mislocalization of the RNP ( 17 , 33 , 34 ). Here, to confirm the effect of JDH2110 on virus particle maturation, we subjected cell-free and detergent-lysed progeny virions to a linear 20 to 70% (wt/vol) sucrose gradient fractionation.…”

Mutations altering acetylated residues in the CTD of HIV-1 integrase cause defects in proviral transcription at early times after integration of viral DNA

“…Residues in the CTD of IN have also previously been identified as class II mutants that are defective for viral RNA binding and particle morphogenesis, and as a consequence the virions are defective in early steps of infection such as reverse transcription and nuclear import [ 7 ]. To determine if our mutations might display a similar phenotype we assayed the early steps of the viral life cycle.…”

“…Various residues in the CTD of IN, including some of the residues mutated in this study, have been implicated as responsible for the phenotypes of class II IN mutants [ 7 ]. When these residues were mutated, IN binding to viral RNA was disturbed leading to the formation of non-infectious viral particles.…”

“…Class II IN mutants are defective for viral RNA binding which leads to the formation of eccentric virion particles with mislocalized viral RNA genomes [ 5 , 6 ]. As a consequence of this abnormal particle morphogenesis, virions are defective for early steps of the viral life cycle including reverse transcription and nuclear import [ 7 ].…”

How to package the RNA of HIV-1

“…Multiple studies have suggested that these class II mutants have defects in reverse transcription, possibly because they have lost their vRNA, or because reverse transcriptase becomes physically separated from the genetic information upon infection of a target cell ( Koneru et al, 2019 ; Madison et al, 2017 ). Now, in eLife, Sebla Kutluay of Washington University in St. Louis and colleagues – including Jennifer Elliot as first author – report how class II integrase substitutions impair the maturation of HIV-1 particles ( Elliott et al, 2020 ).…”