Identification of the in vitro HIV-2/SIV RNA dimerization site reveals striking differences with HIV-1

Although their genomes cannot be aligned at the nucleotide level, the HIV-1 /SIVcpz and the HIV-2/SIVsm viruses are closely related lentiviruses that c ontain homologous functional and structural RNA elements in their 5'-untran slated regions. In both groups, the domains containing the trans-activating region, the 5'-copy of the polyadenylation signal, and the primer binding site (PBS) are followed by a short stem-loop (SL1) containing a six-nucleot ide self-complementary sequence in the loop, flanked by unpaired purines. I n HIV-I, SL1 is involved in the dimerization of the viral RNA, in vitro and in vivo. Here, we tested whether SL1 has the same function in HIV-2 and SI Vsm RNA. Surprisingly, we found that SL1 is neither required nor involved i n the dimerization of HIV-2 and SIV RNA We identified the NarI sequence loc ated in the PBS as the main site of HIV-2 RNA dimerization. cis and trans c omplementation of point mutations indicated that this self-complementary se quence forms symmetrical inter-molecular interactions in the RNA dimer and suggested that HIV-2 and SIV RNA dimerization proceeds through a kissing lo op mechanism, as previously shown for HIV-1. Furthermore, annealing of tRNA (3)(Lys) to the PBS strongly inhibited in vitro RNA dimerization, indicatin g that, in vivo, the intermolecular interaction involving the NarI sequence must be dissociated to allow annealing of the primer tRNA.