Abstract

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 contain homologous functional and structural RNA elements in their 5'-untranslated 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-nucleotide self-complementary sequence in the loop, flanked by unpaired purines. In HIV-1, 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 SIVsm RNA. Surprisingly, we found that SL1 is neither required nor involved in the dimerization of HIV-2 and SIV RNA. We identified the NarI sequence located in the PBS as the main site of HIV-2 RNA dimerization. cis and trans complementation of point mutations indicated that this self-complementary sequence forms symmetrical intermolecular interactions in the RNA dimer and suggested that HIV-2 and SIV RNA dimerization proceeds through a kissing loop mechanism, as previously shown for HIV-1. Furthermore, annealing of tRNA(3)(Lys) to the PBS strongly inhibited in vitro RNA dimerization, indicating that, in vivo, the intermolecular interaction involving the NarI sequence must be dissociated to allow annealing of the primer tRNA.

Highlights

  • IntroductionThe HIV-1/SIVcpz and the HIV-2/SIVsm primate viruses belong to the same lentivirus genus of the retrovirus family [1]

  • Based on phylogenetic analysis, the HIV-1/SIVcpz and the HIV-2/SIVsm primate viruses belong to the same lentivirus genus of the retrovirus family [1]

  • We identified the NarI sequence located in the primer binding site (PBS) as the main site of HIV-2 RNA dimerization. cis and trans complementation of point mutations indicated that this self-complementary sequence forms symmetrical intermolecular interactions in the RNA dimer and suggested that HIV-2 and SIV RNA dimerization proceeds through a kissing loop mechanism, as previously shown for HIV-1

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Summary

Introduction

The HIV-1/SIVcpz and the HIV-2/SIVsm primate viruses belong to the same lentivirus genus of the retrovirus family [1] They cause similar diseases characterized by long and variable incubation periods, persistent viral replication, neurological manifestations, and destruction of specific hematologic and immunologic cells (for a review see Ref. 2). A similar situation prevails in HIV-2 and SIVsm genomic RNAs (Fig. 1B) In those viruses, six short hairpins follow the first three structural domains. The first of the short HIV-2/SIVsm stem-loops (SL1) contains a loop with a six-nucleotide self-complementary sequence flanked by one or more purines, as does the HIV-1/ SIVcpz DIS loop (see Fig. 1) [3, 4]. As dimerization of genomic RNA is ubiquitous among retroviruses (29 – 42), and the location and structural features of the HIV-1 DIS and the HIV-2/SIVsm SL1 are conserved

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