Figure 5.

Effect of Q and m⁵C38 modification on translational efficiency. (A) Effects of Q on translational efficiency. Plots of the log₂-fold change in translational efficiency of two compared conditions are shown relative to the log₂ of the median expression of transcripts from the two conditions. Left, TE of pmt1Δ +Q/pmt1Δ; middle, TE of wt +Q/ pmt1Δ; right, TE of wt +Q/wt. Colours indicate transcripts with significantly different translational efficiency. Blue dots, P < 0.05, red dots, Benjamini–Hochberg adjusted (adj) P < 0.1. The number of genes in the respective P-value categories that are up- or down-rgeulated are given in the upper right and lower right corner of the plots, respectively. The triangle represents a data point that is outside the plotted frame and corresponds to pmt1⁺. (B) Effect of C38 methylation by Dnmt2/ Pmt1 on translational efficiency. The log₂-fold change in TE of pmt1⁺ overexpression (OE)/pmt1Δ + vector (v) (left) and wt +Q/ pmt1Δ+Q (right) is plotted against the log₂ median expression of transcripts of the two conditions. Representation as in (A). (C) Levels of Cox2 protein were decreased in pmt1Δ + Q. Protein extracts were separated by SDS-PAGE and analysed by Western blotting using an antibody against Cox2 (top) and, as a control, with an α-Tubulin antibody (Tub1). Below, quantification of Cox2 levels relative to Tub1 (mean ± SEM, n = 3, normalized to pmt1Δ value. *P = 0.11; **P = 0.002). (D) Overlap of differentially translated mRNAs between pmt1⁺ OE/ pmt1Δ +v (see Figure 4B, left) and wt +Q/ pmt1Δ +Q (Figure 4B, right) (adj. P < 0.1). (E) Overlap of mRNAs differentially translated in wt +Q/ pmt1Δ (Figure 4A, middle) and wt +Q/ pmt1Δ +Q (Figure 4B, right). (F) Translational efficiency of genes with stretches of Q codons was decreased in the absence of Q. The translational efficiency (TE) of genes with at least one stretch of 2 consecutive Asp, His, Asn or Tyr codons or three or more consecutive Q codons (size of the group of genes is given in parenthesis) was compared to that of all other genes not fulfilling this condition. The difference between the median translational efficiency of genes with the respective stretch compared to that of genes without the stretch is given. Only values that are statistically significantly different (Benjamini–Hochberg adjusted P < 0.05) are shown.