PMC

(a) codon usage (tRNA adaptation index and (b) average base pairing probability at the 5′ UTR mRNA structure for different noise differential levels. The nonribosomal genes were subdivided into three groups: low, medium and high noise genes, according to their noise differential levels in YEPD and SD media.

(a) Histograms of tRNA adaptation index (tAI) scores of budding yeast genes shows a long tail of high tAI values that is highly enriched in ribosomal genes (98 out of 153 genes with tAI>0.55, binomial test p-value<e-74). Inset: Spearman correlation between tAI and DM increases at a wide range of high tAI cut-off values. (b,c) Ribosomal and nonribosomal genes have different distributions of noise differentials (DM) in both YEPD and SD media – the ribosomal genes are significantly less noisy. For graphing purpose the DM values are shifted by constant c = 5 prior taking the logarithm. (d) Spearman correlation between tAI and noise differential (DM) for the whole dataset, including nonribosomal and ribosomal proteins in YEPD and SD media.

(a) The trend lines for the relation between protein abundance and noise strength (YEPD medium) in three groups of genes: TATA genes with high tAI (red), non-TATA genes with high tAI (blue) and non-TATA genes with low tAI (cyan). High and low tAI mean upper and lower tertile of tAI distribution, respectively. The abundance region where all three trend lines overlap is enlarged. The shift between TATA and non-TATA genes, both with high tAI, represents an amplification associated with the TATA box (transcription feature), β = 1.27±0.07, while the shift between non-TATA genes with high and low tAI represents an amplification associated with high codon usage (translation feature), α = 1.19±0.02. (b) The trend for the noise strength (YEPD medium) as a function of codon usage efficiency (tAI) for TATA genes (red) and non-TATA genes (blue). The shift between these two trend lines provides an alternative estimate of , representing the impact of the TATA box on noise strength.