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.

In Pathway I, À1 PRF occurs during translocation while the pre-translocational complex is aligned with deX XXY. Two parameters play important roles in Pathway I in the kinetic model. Here, r t represents the rate constant for incomplete translocation. An increase in r t while other parameters in the model remain constant leads to an increase in FS% (blue line in Figure 4a ). Both the levels of FS m and FS z increase when r t increases (green and red lines in Figure 4a ). Because the rise in the FS m level is larger, increasing r t results in a larger FS m fraction (Figure 4b ). It is also interesting to note that the majority of FS z comes from Pathway III when r t is <2 s À1 , while the majority of FS z is from pathway II when r t is >2 s À1 (Figure 4b) . The rate constant r 45 accounts for the relocking step during translocation. A decrease in r 45 while other parameters in the model remain constant results in an increase in FS% (blue line in Figure 5a ). Both the levels of FS m and FS z increase when r 45 decreases (green and red lines in Figure 5a ). However, in this case the increase in the FS m level is larger, leading to a larger FS m fraction with a decrease in r 45 (Figure 5b) . Here, the majority of FS z is from Pathway III when r 45 is <22 s À1 , but the majority of FS z results from pathway II when r 45 becomes >22 s À1 ( Figure 5b) . These results suggest that translocation perturbations by either a downstream mRNA secondary structure, by mutations, or by chemical inhibitors may result in production of a higher FS%, primarily due to production of a larger amount of FS m . Notably, manipulating r t values causes larger changes in FS% and in the FS m fraction compared to the effect of r 45 , suggesting a dominant role by r t on À1 PRF in Pathway I. Consistent with our model, experimental studies demonstrated that mutating the E-site codon in the recoding site, or the use of a translocation inhibitor altered FS% (22) .