Regulation of primate lentiviral RNA dimerization by structural entrapment

Tayyba T Baig,J Stephen Lodmell,Christy L Strong,Jean-Marc Lanchy

doi:10.1186/1742-4690-5-65

Abstract

BackgroundGenomic RNA dimerization is an important process in the formation of an infectious lentiviral particle. One of the signals involved is the stem-loop 1 (SL1) element located in the leader region of lentiviral genomic RNAs which also plays a role in encapsidation and reverse transcription. Recent studies revealed that HIV types 1 and 2 leader RNAs adopt different conformations that influence the presentation of RNA signals such as SL1. To determine whether common mechanisms of SL1 regulation exist among divergent lentiviral leader RNAs, here we compare the dimerization properties of SIVmac239, HIV-1, and HIV-2 leader RNA fragments using homologous constructs and experimental conditions. Prior studies from several groups have employed a variety of constructs and experimental conditions.ResultsAlthough some idiosyncratic differences in the dimerization details were observed, we find unifying principles in the regulation strategies of the three viral RNAs through long- and short-range base pairing interactions. Presentation and efficacy of dimerization through SL1 depends strongly upon the formation or dissolution of the lower stem of SL1 called stem B. SL1 usage may also be down-regulated by long-range interactions involving sequences between SL1 and the first codons of the gag gene.ConclusionDespite their sequence differences, all three lentiviral RNAs tested in this study showed a local regulation of dimerization through the stabilization of SL1.

Highlights

Genomic RNA dimerization is an important process in the formation of an infectious lentiviral particle
Tight dimerization characteristics of Human immunodeficiency virus (HIV)-2, Simian immunodeficiency virus (SIV), and HIV-1 leader RNAs The ability of 1–561 HIV-2, 1–550 SIV, and 1–373 HIV-1 RNAs to form tight dimers when incubated at 55°C in dimerization buffers was compared
Loose dimers are thought to correspond to a loop-loop interaction between two stem-loop 1 (SL1) motifs, whereas tight dimers are thought to represent a more extensive SL1–SL1 interaction due to the intra- to intermolecular conversion of the stems located below the SL1 loop ([2,4])

Summary

Introduction

Genomic RNA dimerization is an important process in the formation of an infectious lentiviral particle. The 5' untranslated region of the lentiviral genomic RNA is replete with RNA signals involved in different stages of the replication cycle, such as transcription transactivation, polyadenylation, tRNA primer binding, dimerization, encapsidation, splicing, and translation [1]. The RNA signals mediate viral functions through RNA-protein (genomic RNA encapsidation and reverse transcription) and RNA-RNA interactions (dimerization, tRNA hybridization to PBS) Most of these signals can be linked to a precise stage of the viral replication cycle, they overlap structurally and functionally ([2,3,4]). The stem-loop 1 (SL1) dimerization signal overlaps with the genomic RNA encapsidation signal in HIV-2 ([5,6,7,8]) Another interesting characteristic of retroviral leader RNA signals is the fact that their presentation may vary during the different stages of viral replication. The dimerization and encapsidation signals in Moloney (page number not for citation purposes)

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