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

Here we scrutinize features of the third stem of the SARS-CoV frameshift-stimulating pseudoknot that are important for RNA structure and frameshifting efficiency. We demonstrate the importance of the capping loop sequence in promoting Stem 3 stability and maintaining near-wild-type levels of frameshifting. Specifically, a hexanucleotide, self-complementary sequence in the loop capping Stem 3 raises the possibility that dimerization of the pseudoknot may play a role in viral lifecycle. While the palindromic sequence embedded in the SARS-CoV Stem 3 is not strictly conserved among severe acute respiratory syndrome-related coronaviruses (SARSr-CoV), genomic sequences from Rhinolophus Chinese horseshoe bats (SARSr-Rh-BatCoV) (8) that were previously identified as a natural reservoir of SARS-CoV-related CoV (9) also encode the hexanucleotide palindrome.