Fig. 3: Environment-specific effects of P_TDH3 mutations on gene expression and fitness.

a, Mean YFP expression with 95% confidence intervals from 4–8 replicates of each genotype in each environment for the 47 mutant P_TDH3 alleles driving expression of YFP in glucose (blue), galactose (green), glycerol (purple) and ethanol (orange). Mutant strains are grouped by whether they had one mutation (1 mut.), two mutations (2 mut.), more than two mutations (>2 mut.) or two copies of P_TDH3 with mutations (2 copies + mut.). YFP expression of each strain was normalized by the expression level of the strain carrying an unmutated P_TDH3 grown in glucose. b, Pairwise comparisons for expression effects of mutant P_TDH3 alleles in glucose, galactose, glycerol and ethanol. The mean expression levels (±s.d.) of the 47 P_TDH3-YFP mutant genotypes relative to the reference strain were estimated from 4–8 replicates. Panels I and II show comparisons of genotypes between the two fermentable and two non-fermentable environments, respectively. Panels III–VI show comparisons between fermentable and non-fermentable environments. Relative expression levels of each mutant genotype in each environment were estimated from four to eight replicates. Genotypes with significantly different effects between the environments compared are shown in red. Significance was determined by two-sided t-tests, with P < 0.008 following Bonferroni correction for the six comparisons between pairs of environments. Pearson correlation coefficients (r) are also shown in each panel. c, Mean relative activity of P_TDH3 (normalized to expression of the reference in glucose) is plotted against the relative fitness of the strain carrying the same P_TDH3 allele at the native locus, with fitness normalized to the fitness of the unmutated reference strain in each environment. A LOESS regression line inferred from these points is shown for each environment (span = 0.75). d, The fitness functions shown in c are overlaid to show similarities and differences between environments. The coloured dots represent relative expression and fitness of the unmutated P_TDH3 reference allele in glucose (blue), galactose (green), glycerol (purple) and ethanol (orange). The inset shows a higher magnification of the region of relative expression to better show expression plasticity of the reference allele. The lighter shaded areas in each environment indicate the inferred 95% confidence intervals in c and d.