Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: Implications for viral genomic RNA packaging

Despite the vast excess of cellular RNAs, precisely two copies of viral genomic RNA (gRNA) are selectively packaged into new human immunodeficiency type 1 (HIV-1) particles via specific interactions between the HIV-1 Gag and the gRNA psi (psi) packaging signal. Gag consists of the matrix (MA), capsid, nucleocapsid (NC), and p6 domains. Binding of the Gag NC domain to psi is necessary for gRNA packaging, but the mechanism by which Gag selectively interacts with. is unclear. Here, we investigate the binding of NC and Gag variants to an RNA derived from psi (Psi RNA), as well as to a non-psi region (TARPolyA). Binding was measured as a function of salt to obtain the effective charge (Z(eff)) and nonelectrostatic (i.e., specific) component of binding, K-d(1M). Gag binds to Psi RNA with a dramatically reduced K-d(1M) and lower Z(eff) relative to TARPolyA. NC, Gag Delta MA, and a dimerization mutant of Gag bind TARPolyA with reduced Z(eff) relative to WT Gag. Mutations involving the NC zinc finger motifs of Gag or changes to the G-rich NC-binding regions of Psi RNA significantly reduce the nonelectrostatic component of binding, leading to an increase in Z(eff). These results show that Gag interacts with gRNA using different binding modes; both the NC and MA domains are bound to RNA in the case of TARPolyA, whereas binding to Psi RNA involves only the NC domain. Taken together, these results suggest a novel mechanism for selective gRNA encapsidation.