Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome

Sztuba-Solinska, Joanna; Teramoto, Tadahisa; Rausch, Jason W.; Shapiro, Bruce A.; Padmanabhan, Radhakrishnan; Le Grice, Stuart F. J.

It has been proposed that the 3 0 -localized elements, including the terminal stem-loop (3 0 SL) together with cyclization sequence (3 0 CS), the upstream of AUG region (3 0 UAR) and the downstream of AUG region (3 0 DAR), are crucial for the initiation of (À) strand, RNAdependent RNA synthesis (2, 5) . These motifs are proposed to interact with their complementary elements positioned at the 5 0 terminus, the 5 0 CS, the 5 0 UAR and the 5 0 DAR, resulting in long-range RNA-RNAmediated genome circularization (5, 6, 11) . Following hybridization of the 5 0 and 3 0 termini, the DENV genome has been proposed to endure extensive rearrangements of both UTRs, opening of the 3 0 SL to form an extended duplex with the 5 0 UAR and formation of a doublestranded region via 5 0 and 3 0 CS interactions (12) . As a result, the viral NS5 polymerase initially docked at the 5 0 stem-loop A (SLA) would be relocated to the structurally reorganized 3 0 terminus, allowing launch of (À) strand synthesis (6, 11) . Additional structural motifs of the 3 0 -UTR have also been shown to modulate DENV molecular processes. Phylogenetic comparisons have suggested that the tandem, almost identical dumbbell structures, designated 3 0 and 5 0 DB, might participate in regulation of RNA synthesis and translation (13) (14) (15) . The leftmost hairpins of both DBs contain a set of identical five nucleotide motifs, referred to as TL1 and TL2 (5 0 -GCUGU-3 0 ). The top loop (TL) regions have been suggested to pair with complementary motifs (PK2 and PK1, respectively) nested within A-rich sequences flanking both DBs (13, 16) . The TL1/PK2 and TL2/PK1 interactions would promote formation of two pseudoknots, which have been proposed to modulate both viral replication (15) and translation (8) .