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

Our studies of the third stem of the SARS coronavirus pseudoknot illuminate features of Stem 3 that affect RNA structure, frameshifting frequency and viral replication. Typically, G-C-rich Watson-Crick complementarity is required for stable loop-loop base pairing interactions between two RNA hairpins. Among all natural HIV isolates, two palindromic hexanucleotide sequences are most commonly found: GCGCGC and GUGCAC (49, 50) . However, mutagenesis work investigating HIV RNA dimerization also demonstrated that the GUUAAC palindrome found in SIV mnd (Simian Immunodeficiency Virus) could yield up to 20% dimers in the presence of 5 mM MgCl 2 (51) . In good agreement with those studies, we confirm that weaker palindromic sequences such as AC UAGU can readily facilitate intermolecular loop-loop kissing RNA-RNA interactions. RNA pseudoknots implicated in -1 PRF stimulation are not static and are in fact dismantled during translation (52, 53) . If a frameshift event does not occur during the first round of translation then the pseudoknot will have to refold for frameshifting to occur in subsequent rounds. Long unstructured loops between the 3 0 portion of Stem 1 and 5 0 portion of Stem 2 would be expected to reduce the chances of Stem 2 forming and reduce frameshifting efficiency. If this sequence can form a stable restricting S3L2 substructure, as is the case for the SARS-CoV pseudoknot steadied by an intermolecular kissing complex, then the rapid re-formation of Stem 2, which is required for efficient frameshifting, will be more probable.