Human H4 tail stimulates HIV-1 integration through binding to the carboxy-terminal domain of integrase

Abstract

The integration of the retroviral genome into the chromatin of the infected cell is catalysed by the integrase (IN)•viral DNA complex (intasome). This process requires functional association between the integration complex and the nucleosomes. Direct intasome/histone contacts have been reported to modulate the interaction between the integration complex and the target DNA (tDNA). Both prototype foamy virus (PFV) and HIV-1 integrases can directly bind histone amino-terminal tails. We have further investigated this final association by studying the effect of isolated histone tails on HIV-1 integration. We show here that the binding of HIV-1 IN to a peptide derived from the H4 tail strongly stimulates integration catalysis in vitro . This stimulation was not observed with peptide tails from other variants or with alpha-retroviral (RAV) and spuma-retroviral PFV integrases. Biochemical analyses show that the peptide tail induces both an increase in the IN oligomerization state and affinity for the target DNA, which are associated with substantial structural rearrangements in the IN carboxy-terminal domain (CTD) observed by NMR. Our data indicate that the H4 peptide tail promotes the formation of active strand transfer complexes (STCs) and support an activation step of the incoming intasome at the contact of the histone tail.

Analysis of the intrinsic chromatin binding property of HIV-1 integrase and its regulation by LEDGF/p75 using human chromosomes spreads

“…These data make histone tails good candidates for potential receptors of incoming intasomes. This idea is further supported by findings showing that retroviral IN can bind, via its CTD directly to histone tails (Benleulmi et al 2017;Mauro et al 2019;Maskell et al 2015). HIV-1 IN mutagenesis studies have shown that amino acid substitutions that affect IN binding to nucleosomes and histone tails also affect viral infectivity (Benleulmi et al 2017).…”

“…To further investigate the effect of LEDGF/p75 on functional integration complexes and determine whether the LEDGF/p75-mediated increase in IN chromatin-binding was related to the nucleosomal features of chromosomes, we performed typical in vitro integration assays using biotinylated mononucleosomes (MNs) immobilized on streptavidin beads as previously performed (Benleulmi et al 2017;Mauro et al 2019). As shown in Figure 3A, LEDGF/p75 strongly stimulated HIV-1 IN activity on MNs, while integration onto naked DNA was only slightly improved in the presence of the cofactor.…”

“…Since IN alone shows affinity for chromatin, we also investigated the molecular determinants of this interaction and their roles in tethering the viral enzyme in the presence of LEDGF/p75 to chromatin. Target DNA and histone-binding properties have been described for the CTD of several retroviral INs, including HIV-1 IN (Maskell et al 2015;Benleulmi et al 2017;Mauro et al 2019). Thus, we analyzed the importance of this domain in binding to chromosomes.…”

“…Thus, we analyzed the importance of this domain in binding to chromosomes. Several amino acids have been identified in HIV-1 IN as important for the interaction to both the target DNA and histone tail (Benleulmi et al 2017;Mauro et al 2019;Serrao et al 2014;Demeulemeester et al 2014). These positions include the R231 and D253 residues.…”

Structural Insights on Retroviral DNA Integration: Learning from Foamy Viruses

“…Indeed, HIV-1 virion packages around 250 molecules of integrase, which is far more than needed from the recent structures of lentiviral intasomes. Also, although the structure of the PFV intasome bound to a nucleosome afforded important information on the chromatin capture by retroviral intasomes, the requirement for histones might differs from genus to genus [83,84], highlighting the need for additional structures of intasomes bound to nucleosomes. Additionally, early chromatinisation of retroviral pre-integration complexes has emerged as a feature of two retroviral genera [85,86].…”