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

Previously, a ribosomal E site adjacent duplex formed between an internal SD-like element upstream of the slippery site and the anti-SD sequence of 16S rRNA was shown to attenuate prokaryotic −1 frameshifting efficiency in E. coli (18) . By contrast, internal SD can promote release factor 2 (RF2)-dependent +1 frameshifting when placed adjacent to the ribosomal E site (20) . Such an opposite role in −1 and +1 frameshifting regulation led to the suggestion of a tension-mediated mechanism in frameshifting stimulation (19) . Alternatively, such effects could be caused by the elongation pausing mediated by an internal SD·anti-SD interaction during the elongation of 70S ribosome (50) . Interestingly, we have previously shown that an upstream hairpin can stimulate +1 frameshifting in yeast in addition to attenuating −1 PRF in an in vitro 80S translation system (29) . The mechanism of in-cis refolding hairpin as well as trans-formed upstream duplex in eukaryotic frameshifting regulation may thus be relevant to that of the duplex formed between internal SD and 16S rRNA in prokaryotic frameshifting regulation, given that formation of a duplex upstream of the slippery site is involved in all these cases. However, moving the attenuator hairpin 5 further (29) did not enhance −1 PRF efficiency in the same manner as SD-like stimulator element did (18) . A possible reason for this difference is that the internal SD-mediated duplex involves the 16S ribosomal RNA component of 70S ribosome and is part of the translational machinery, whereas the eukaryotic ribosome lacks an anti-SD sequence. Due to such a difference between 70S and 80S translation systems, the antisense-mediated upstream duplex identified in this work could simply act as a wheel chock to block −1 ribosome movement triggered by downstream −1 PRF stimulator mediated tension effect (14) (15) (16) .