RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Ishimaru, Daniella; Plant, Ewan P.; Sims, Amy C.; Yount, Boyd L.; Roth, Braden M.; Eldho, Nadukkudy V.; Pérez-Alvarado, Gabriela C.; Armbruster, David W.; Baric, Ralph S.; Dinman, Jonathan D.; Taylor, Deborah R.; Hennig, Mirko

Several studies have demonstrated that facile formation of the H-type skeleton involving Stem 1 and 2 of a frameshift-stimulating pseudoknot structure is critical for efficient frameshifting (56, 57) . Intriguingly, several long-distance intramolecular loop-loop kissing has also been implicated in -1 PRF stimulation. Specifically, the Group 1 Human CoV 229 E has been shown to use a kissing stem loop to promote frameshifting rather than a compact H-type pseudoknot (58) . Based on sequence alignments, such 'elaborated' pseudoknots could be used by Human CoV NL63, porcine epidemic diarrhea virus and transmissible gastroenteritis virus (6) . Similarly, the P1-P2 pseudoknot from the luteovirus barley yellow dwarf virus can be considered a variation on the 'elaborated' CoV pseudoknot structure. It contains a loop L2 of nearly 4 kb, with S2 formed by long-range kissing interactions with nucleotides near the 3 0 end of the genome (59) . Such a long-distance RNA-RNA kissing interaction is also implicated in -1 PRF of red clover necrotic mosaic virus (60) . Thus, an intermolecular dimerization in SARS-CoV may simply represent a variation of the 'elaborated' pseudoknot.