HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome

Mouzakis, Kathryn D.; Lang, Andrew L.; Vander Meulen, Kirk A.; Easterday, Preston D.; Butcher, Samuel E.

Here, we investigate the role of the HIV-1 RNA structure in frameshifting, focusing on elucidating the relationships between frameshift efficiency and (i) the downstream RNA stem-loop thermodynamic stability, (ii) spacer length and (iii) surrounding genomic secondary structure. By systematically altering the base pair composition of the stem-loop, we dissect the contributions of global and local thermodynamic stability on frameshifting. These data reveal that the thermodynamic stability of the first 3-4 bp in the stem-loop is a primary determinant of frameshift efficiency. Our data further indicate that the base pairs important for frameshifting are located at a distance of 8 nt from the slippery site, which corresponds to the length of the spacer and is consistent with a structural model of the ribosome paused at the frameshift site. Finally, we find that the conserved genomic RNA secondary structure serves to attenuate the frameshift efficiency, likely by affecting the overall rate of translation. Importantly, our study describes the first quantitative and predictive model for frameshift inducing stem-loops, which can be generally applied to many À1 PRF viral systems.