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.

To examine the model predictions, À1 PRF efficiency was monitored in vivo using a dual fluorescence reporter system. In addition, compositions of the frameshift protein products were analysed by mass spectrometry. Analysis of the frameshift products revealed that the ratio of FS z to FS m was $4:1 in MB2 cells (Figure 9 ), thus indicating that the vast majority of À1 PRF events naturally occur through Pathways II and/or III. The model predicts that a smaller k pt should cause higher FS% and a lower fraction of FS m (Figure 8) . A prior study using yeast demonstrated that inhibition of peptidyltransfer promoted increased rates of À1 PRF, but did not differentiate between FS m and FS z products (36) . The model predicts that addition of chloramphenicol, a potent peptidyltransferase inhibitor in bacteria (37), should promote increased FS%. Consistent with the model, a 2.1-fold increase in FS% exp was observed in the E. coli culture containing 0.75 mg/ml chloramphenicol compared to the culture without the drug. The fractions of FS m for the culture with and without chloramphenicol were 17.3 and 20.4%, respectively (Figure 9a) . Although a slight decrease in the fraction of FS m was observed in the presence of the drug, the difference was not statistically significant (P > 0.05).