Structural Characterization of the Minimal HIV-1 Psi-RNA Packaging Signal and Potential Psi-Site Interactions Within the 5'-Utr (Paperback)

The 5'-untranslated region (5'-UTR) of the human immunodeficiency virus type-1 (HIV-1) genome regulates multiple RNA-dependent functions during viral replication and has been proposed to adopt multiple secondary structures. HIV-1 was thought to package its genome by specific interactions between the nucleocapsid (NC) domain of Gag and a ∼120 nucleotide region of the unspliced viral RNA located within the 5'-UTR, known as the Psi(psi) site. Extensive site-directed mutagenesis, chemical modification, nuclease accessibility mapping, and free energy computational studies indicate that the HIV-1 Psi-site contains four stemloop structures designated SL1 through SL4, connected by relatively short linkers. All four stemloops are important to achieve wildtype packaging levels. We have completed NMR assignments for the intact HIV-1 Psi-site and no long-range inter-stem NOE's were observed that would indicate an overall tertiary structure or fold that differs from the individual stemloop structures. Therefore, some other interaction must exist to explain the dimer dependent packaging of the HIV-1 genome. Recent phylogenetic studies identified base pair complementarity between residues of the unique 5' (U5) element and those near the gag start codon (gagAUG) that is conserved among evolutionarily distant retroviruses, suggesting a potential long-range RNA-RNA interaction. However, nucleotide accessibility studies led to conflicting conclusions about the presence of such interactions in virions and in infected cells. Here we show that an 11-nucleotide oligo-RNA containing residues 105-115 of U5 (U5LINK) readily binds to oligoribonucleotides containing the gag start codon (AUG), disrupting a pre-existing stemloop and forming a heteroduplex stabilized by 11 Watson-Crick base pairs. Addition of the HIV-1 nucleocapsid protein, the trans-acting viral factor required for genome packaging, disrupts the heteroduplex by binding tightly to U5LINK (Kd = 122 +/- 10nM at NaCl] =100mM). The structure of the NC: U5LINK complex, determined by NMR, exhibits features similar to those observed in NC complexes with HIV-1 stemloop RNAs, including the insertion of guanosine nucleobases to hydrophobic clefts on the surface of the zinc fingers and a 3'-to-5' orientation of the RNA relative to protein. Our findings indicate that previously proposed long-range U5- gagAUG interactions are feasible, and suggest a potential NC-dependent mechanism for modulating the structure of the 5'-UTR.