The many paths to frameshifting: kinetic modelling and analysis of the effects of different elongation steps on programmed –1 ribosomal frameshifting

Liao, Pei-Yu; Choi, Yong Seok; Dinman, Jonathan D.; Lee, Kelvin H.

The frameshift sequence for HIV-1 is U AAU UUU UUA, where a space separates each zero frame codon and the P-site of the recoding site is underlined. The E-site tRNA GUU Asn may form one canonical base pairing with the À1 frame UAA. In the MB2UCC strain, the sequence was mutated to U CCU UUU UUA (mutations shown in bold) where the E-site tRNA GGG Pro can potentially form one G:U and two C:G interactions. In the MB2CCC strain, the sequence was mutated to C CCU UUU UUA (mutations shown in bold) where the E-site tRNA GGG Pro can form three canonical base pairings with the À1 frame CCC. Because Pathway I requires that the E-and P-site tRNAs interact with the À1 frame, UCC and CCC as the À1 frame E-site codons may enhance this reaction, i.e. these codons would promote an increase in r t . The model predicts that a larger r t should result in a higher FS% due to increased production of FS m . Consistently, 1.2-and 1.4-fold increase in FS% exp are observed for the MB2UCC and MB2CCC strains compared to the MB2 strain, respectively (Figure 9b ). In the MB2UCC strain, 76.4% of the frameshift products were FS m , and in the MB2CCC strain, 90.3% of the frameshift products were FS m . These results suggest that changing the sequence to favor incomplete translocation, i.e. to favor Pathway I, can dramatically alter the composition of the frameshift product.