An Unusual Topological Structure of the HIV-1 Rev Response Element

Nuclear export of unspliced and singly spliced viral mRNA is a critical step in the HIV life cycle. The structural basis by which the virus selects its own mRNA among more abundant host cellular RNAs for export has been a mystery for more than 25 years. Here, we describe an unusual topological structure that the virus uses to recognize its own mRNA. The viral Rev response element (RRE) adopts an “A”-like structure in which the two legs constitute two tracks of binding sites for the viral Rev protein and position the two primary known Rev-binding sites ∼55 Å apart, matching the distance between the two RNA-binding motifs in the Rev dimer. Both the legs of the “A” and the separation between them are required for optimal RRE function. This structure accounts for the specificity of Rev for the RRE and thus the specific recognition of the viral RNA. [Display omitted] •The 233 nucleotide RRE of HIV-1 folds into an “A”-like structure•The two “legs” of the “A” consist of two main segments of the RRE structure•The two known Rev primary binding sites are about 55 Å apart•Both segments must be present for Rev oligomerization and HIV export function A unique “A” shaped structure found in RNA’s from HIV explains how they are selectively chosen for nuclear export by the viral protein Rev.