Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication

Abstract

Mosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5′ and 3′ untranslated regions (UTRs). The 3′ UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs) that regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we used x-ray crystallography and structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.

Information Encoded by the Flavivirus Genomes beyond the Nucleotide Sequence

“…The PK elements within domain II involve sequences located at the apical loops (named TLs) of the DB and the corresponding downstream complementary motifs. Since sequences interacting with the TLs overlap conserved sequences (CS) required for genomic cyclization ( Figure 2 ) [ 19 , 24 , 33 ], it is likely that these PK structures compete for elements that are essential in genomic cyclization, preventing the latter from occurring (see below; [ 20 , 25 , 34 ]). This competition may provide a means of regulating switching between different steps of the viral cycle.…”