Abstract
Nucleocytoplasmic transport of unspliced and partially spliced human immunodeficiency virus (HIV) RNA is mediated in part by the Rev response element (RRE), a ~350 nt cis-acting element located in the envelope coding region of the viral genome. Understanding the interaction of the RRE with the viral Rev protein, cellular co-factors, and its therapeutic potential has been the subject of almost three decades of structural studies, throughout which a recurring discussion theme has been RRE topology, i.e., whether it comprises 4 or 5 stem-loops (SLs) and whether this has biological significance. Moreover, while in vitro mutagenesis allows the construction of 4 SL and 5 SL RRE conformers and testing of their roles in cell culture, it has not been immediately clear if such findings can be translated to a clinical setting. Herein, we review several articles demonstrating remarkable flexibility of the HIV-1 and HIV-2 RREs following initial observations that HIV-1 resistance to trans-dominant Rev therapy was founded in structural rearrangement of its RRE. These observations can be extended not only to cell culture studies demonstrating a growth advantage for the 5 SL RRE conformer but also to evolution in RRE topology in patient isolates. Finally, RRE conformational flexibility provides a target for therapeutic intervention, and we describe high throughput screening approaches to exploit this property.
Highlights
Conformational “fluidity” of RNA allows it to mediate a variety of biological functions, examples of which include (a) catalyzing cleavage by the hammerhead ribozyme of satellite RNAs and viroids [1];(b) bacterial riboswitches [2]; (c) RNA thermometers [3]; and (d) tRNA-dependent control of specific aminoacylation and translation regulation [4]
In the case of human immunodeficiency virus (HIV), cis-acting sequences encoded in its (+)RNA genome are central to transcription of the integrated provirus, nucleocytoplasmic transport of unspliced and partially spliced RNAs, initiation of reverse transcription, genome dimerization/packaging, and ribosomal frameshifting [5]
This review summarizes several papers, including analysis of patient isolates that collectively suggest both that HIV-1 and HIV-2 Rev response element (RRE) possess sufficient flexibility to adopt alternative conformations, and that for HIV-1, at least, stabilizing these by in vitro mutagenesis confers a growth advantage for the 5 SL conformer
Summary
Conformational “fluidity” of RNA allows it to mediate a variety of biological functions, examples of which include (a) catalyzing cleavage by the hammerhead ribozyme of satellite RNAs and viroids [1];. The same study demonstrated that only two silent mutations (with respect to viral envelop protein) outside the primary Rev-binding region of the RRE, namely, G164 > A164 (at the base of SL-III/IV) and G245 > A245 (in the central loop) sufficed to confer RevM10 resistance, suggesting a conformational change in the RRE was responsible. With this in mind, RRE structures of wild-type and RevM10-resistant HIV variants containing these two RRE mutations (RRE-61) were examined by selective 20 -OH acylation monitored by primer extension (SHAPE) [47]. Modified from Reference [47]
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