Figure 5. Predicted vs. measured YFP synthesis rates during Leu starvation upon variation in number of stall sites.
yfp reporters having one to four CTA codons at the five Leu positions in yfp are shown in the schematic. X axis – location of CTA codons in each of the yfp variants. Y axis – Predicted and measured YFP synthesis rates during Leu starvation are shown relative to a yfp mRNA without CTA codon. The Leu positions are labeled by their order of occurrence along yfp relative to the start codon (22 Leu codons total), and correspond to the following codon positions along yfp: 2: 15, 6: 46, 10: 68, 14: 141, 18: 201. Error bars indicate standard error over triplicate cultures. Simulation parameters are shown in Supplementary file 3. RMS error % is the root mean square error between predictions from each model and measured YFP synthesis rate, normalized by the average measured value. RMS error was calculated only for mutants with multiple CTA codons.
Figure 5—figure supplement 1. Predicted and measured YFP synthesis rates during Leu starvation (A-B) or Ser starvation (C) from yfp reporters having stall-inducing codons CTC (A), CTT (B), or TCG (C) at one or two among either five Leu positions shown in the upper schematic or six Ser positions in yfp in the lower schematic.
