bRNA helicase A (RHA) promotes multiple steps of HIV-1 RNA metabolism during viral replication, including transcription, translation, and the annealing of primer tRNA 3 Lys to the viral RNA. RHA is a member of the DExH subclass of RNA helicases that uniquely contains two double-stranded RNA binding domains (dsRBDs) at its N terminus. Here, we performed a genome-wide analysis of the interaction of RHA with HIV-1 RNA both in vitro, using fluorescence polarization, and during viral replication, using an RNA-protein coprecipitation assay. In vitro, RHA binds to all the isolated regions of the HIV-1 RNA genome tested, with K d (equilibrium dissociation constant) values ranging from 44 to 178 nM. In contrast, during viral replication, RNA-protein coprecipitation assays detected only a major interaction of RHA with the 5=-untranslated region (5=-UTR) and a minor interaction with the Rev response element (RRE) of HIV-1 RNA. Since RHA does not associate well with all the highly structured regions of HIV-1 RNA tested in vivo, the results suggest that other viral or cellular factors not present in vitro may modulate the direct interaction of RHA with HIV-1 RNA during virus replication. Nevertheless, a role for duplex RNA as a target for RHA binding in vivo is suggested by the fact that the deletion of either one or both dsRBDs eliminates the in vivo interaction of RHA with HIV-1 RNA. Furthermore, these mutant RHAs do not promote the in vivo annealing of tRNA 3Lys to viral RNA, nor are they packaged into virions, demonstrating that the dsRBDs are essential for the role of RHA in HIV-1 replication.
RNA helicases are ubiquitous in nature and have been shown to be involved in all aspects of RNA metabolism. They are classified into five different superfamilies, of which superfamily 2 (SF2) is the largest (7). RNA helicase A (RHA), also known as DHX9, is an SF2 DExH box protein that can unwind both doublestranded RNA (dsRNA) and double-stranded DNA (dsDNA) by utilizing any of the four ribo-or deoxyribonucleotide triphosphates (31, 57). RHA contains 7 domains (depicted in Fig. 3A). The core helicase domain is located at the center and is composed of two subdomains, the DExH subdomain (named after a signature amino acid sequence in RNA helicases, which is DEIH in RHA) and the HELICc subdomain (35). The core helicase domain can bind and hydrolyze nucleotide triphosphates (NTPs) and is composed of 8 motifs that are conserved in all members of the DExD/H box helicases (14). The residues N terminal to the core helicase domain contain two dsRNA binding domains (dsRBDs). The C terminus of RHA is characterized by a stretch of repeated arginine and glycine-glycine (RGG) residues that have a higher binding affinity for single-stranded RNA (ssRNA) than for dsRNA (10,45,57). Between the core helicase and the RGG domains are the helicase-associated domain (HA2) and the oligonucleotide/ oligosaccharide binding (OB-fold) that was defined by its homology with the Saccharomyces cerevisiae protein Prp43p (51).RHA was reported to participate in a d...