A general strategy to inhibiting viral -1 frameshifting based on upstream attenuation duplex formation

Hu, Hao-Teng; Cho, Che-Pei; Lin, Ya-Hui; Chang, Kung-Yao

Efficient eukaryotic −1 PRF requires two cis-acting elements in mRNA, a slippery sequence (where frameshifting occurs) and an optimally placed downstream stimulator structure. An X XXY YYZ sequence in the slippery site facilitates −1 frameshifting by paving codon-anticodon disruption in the P and A sites of the 0-frame (XXY and YYZ codons) and codon-anticodon repairing in the −1 frame (XXX and YYY codons). This transition is further enhanced by resistance from the downstream stimulator (usually a pseudoknot or a hairpin) to the duplex unwinding activity of ribosome, leading to interference in the translocation step of an elongation cycle (9) (10) (11) (12) (13) . Additionally, the spacing nucleotide number between the slippery site and downstream stimulator affects −1 PRF efficiency because it helps positioning the slippery site in the A and P sites of an elongating ribosome while the downstream stimulator approaches the mRNA entry channel of the ribosome (14) . It has been proposed that tension is created between the unwinding stimulator and the codon-anticodon interaction network anchored around the ribosomal P and A sites, and the shift to −1 frame relieves the tension and overcomes the ribosomal pause imposed by the stimulator (14) (15) (16) . Interestingly, base-pairing interaction between an internal Shine-Dalgarno (SD)-like sequence upstream of the frameshifting site and anti-SD sequence in 16S ribosomal RNA also acts as a frameshifting regulator in 70S ribosome (17, 18) . This could be due to the tension or a translation pause mediated by the upstream SD·anti-SD mediated duplex (19) .