STRUCTURES AND FUNCTIONS OF THE HIV-1 RNA GENOME

Abstract

The function and fate of the HIV-1 RNA genome is decided by its monomer-dimer equilibrium, which is regulated by the highly conserved 5' leader region. Recently, it was found that all lentiviral genomes are transcribed in infected cells from an integrated proviral DNA that contains a stretch of three sequential guanosines, any of which could potentially serve as the transcription start site. The 5�-capped genomes beginning with one guanosine (1G) favored dimerization and were selected efficiently for packaging. The 5�-capped 2G and 3G genomes favored the monomeric conformation and were enriched on polysomes, apparently preferred for translation and possibly for splicing. Using a nuclear magnetic resonance (NMR) approach and a variety of unique 2H-labeling schemes, we analyzed the start site region of the native 5' leader in its dimeric and previously elusive monomeric conformation. The additional guanosine(s) enables the disruption of the lower stem of the adjacent polyA stem loop, freeing up residues to base pair with and sequester the palindromic loop of the dimer-promoting DIS hairpin, thereby stabilizing the monomeric form of the RNA. We have confirmed multiple secondary structures within the native 5�-L monomeric structure and discovered an end-to-end hairpin stacking structure in the dimeric conformation that sequesters the cap and may attenuate translation due to its inability to bind to the translation promoting protein, eIF4E. We have also solved the three-dimensional structure of a 42 kDa HIV-1 capped RNA representing the start site of the dimeric 5�-L.