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. 2012 Mar 29;8(3):e1002603. doi: 10.1371/journal.pgen.1002603

Figure 3. Experimental evidence for the impact of codon usage imbalance on translational efficiency.

Figure 3

(A) Experimental design for examining the impact of mCherry expression on the expression of the reporter vYFP. An mCherry gene is constitutively expressed from a 2-micron plasmid in S. cerevisiae, whereas vYFP is constitutively expressed from Chromosome XII. Four different synonymous versions of mCherry are compared. (B) The codon adaptation indices (CAIs) of the four synonymous mCherry sequences (circled numbers), in comparison to CAIs of all S. cerevisiae genes. (C) Values of distance to native codon usage of yeast (D ncu) for the four mCherry sequences, in comparison to that of all S. cerevisiae genes. (D) Relationship between vYFP expression and the CAI or D ncu of mCherry, when the mCherry expression is controlled for. A finer control of mCherry expression is presented in Figure S6, where cells of the low, intermediate, and high mCherry expressions defined here are each subdivided into 5 bins. Error bars, which are barely seen, show one standard error. (E) vYFP expressions in the four strains after the removal of the plasmids that carry mCherry. Error bars show one standard error. (F) vYFP mRNA levels of the four strains relative to that of the wild-type strain, which does not carry mCherry. The mean expressions from three biological replications and the standard errors are presented.