PMC

a Network architecture built by the GAL2, GAL3, GAL4, and GAL80 regulatory genes. The red lines denote the four-stage signaling cascade. The galactose-bound state of Gal3p is denoted by Gal3p*. Pointed and blunt red arrows reflect activation and inhibition, respectively. The dashed blue arrows denote feedback loops established by Gal2p, Gal3p and Gal80p. The dashed red arrow represents the constitutive expression of the Gal4 proteins. The double red arrows denote translocation of Gal80p and Gal3p* between cytoplasm and nucleus. b Illustration of the fitness metric. The strain under investigation is mixed with a reference strain, allowed to equilibrate and then grown for 48 h. The fitness value is calculated from the population ratio of the two strains at the beginning and end of the growth period as shown

Results of the competition experiment in Environment A (0.03% galactose, 0.1% mannose). a Final expression level distributions of the 16 strains. b Average P_GAL1-YFP expression level of the 16 strains. Expression levels are normalized to the expression level of the reference strain in the same sample. Error bars indicate s.e.m. (N = 9). Stars indicate statistically significant differences from wild-type strain as determined by a two-tailed Student’s t-test (Bonferroni-corrected p-value: ****: p < 0.0001; ***: p < 0.001; **: p < 0.01; *: p < 0.05). c Average fitness value of the 16 strains, normalized to the average fitness value of the wild-type strain. Error bars indicate s.e.m. (N = 9). Stars indicate statistically significant differences from wild-type strain as determined by a two-tailed Student’s t-test (Bonferroni-corrected p-value: ****: p < 0.0001; ***: p < 0.001; **: p < 0.01; *: p < 0.05). d Plot of expression vs. fitness for the 16 strains. Error bars indicate s.e.m. (N = 9). e Average effect of copy number reduction on fitness for the four genes in this environment. Error bars indicate uncertainty calculated from the s.e.m. of the fitness measurements

Results of the competition experiment in Environment B (0.1% galactose, 0.03% mannose). a Final expression level distributions of the 16 strains. b Average P_GAL1-YFP expression level of the 16 strains. Expression levels are normalized to the expression level of the reference strain in the same sample. Error bars indicate s.e.m. (N = 9). Stars indicate statistically significant differences from wild-type strain as determined by a two-tailed Student’s t-test (Bonferroni-corrected p-value: ****: p < 0.0001; ***: p < 0.001; **: p < 0.01; *: p < 0.05). c Average fitness value of the 16 strains, normalized to the average fitness value of the wild-type strain. Error bars indicate s.e.m. (N = 9). Stars indicate statistically significant differences from wild-type strain as determined by a two-tailed Student’s t-test (Bonferroni-corrected p-value: ****: p < 0.0001; ***: p < 0.001; **: p < 0.01; *: p < 0.05). d Plot of expression vs. fitness for the 16 strains. e Average effect of copy number reduction on fitness for the four genes in this environment. Error bars indicate uncertainty calculated from the s.e.m. of the fitness measurements

Results of the competition experiment in Environment C (0.1% galactose). a Final expression level distributions of the 16 strains. b Average P_GAL1-YFP expression level of the 16 strains. Expression levels are normalized to the expression level of the reference strain in the same sample. Error bars indicate s.e.m. (N = 9). Stars indicate statistically significant differences from wild-type strain as determined by a two-tailed Student’s t-test (Bonferroni-corrected p-value: ****: p < 0.0001; ***: p < 0.001; **: p < 0.01; *: p < 0.05). c Average fitness value of the 16 strains, normalized to the average fitness value of the wild-type strain. Error bars indicate s.e.m. (N = 9). Stars indicate statistically significant differences from wild-type strain as determined by a two-tailed Student’s t-test (Bonferroni-corrected p-value: ****: p < 0.0001; ***: p < 0.001; **: p < 0.01; *: p < 0.05). d Plot of expression vs. fitness for the 16 strains. Solid line is the prediction of the fitted linear model. Error bars indicate s.e.m. (N = 9). e Average effect of copy number reduction on fitness for the four genes in this environment. Error bars indicate uncertainty calculated from the s.e.m. of the fitness measurements

Results of the competition experiment in Environment D (1% galactose). a Final expression level distributions of the 16 strains. b Average P_GAL1-YFP expression level of the 16 strains. Expression levels are normalized to the expression level of the reference strain in the same sample. Error bars indicate s.e.m. (N = 9). Stars indicate statistically significant differences from wild-type strain as determined by a two-tailed Student’s t-test (Bonferroni-corrected p-value: ****: p < 0.0001; ***: p < 0.001; **: p < 0.01; *: p < 0.05). c Average fitness value of the 16 strains, normalized to the average fitness value of the wild-type strain. Error bars indicate s.e.m. (N = 9). Stars indicate statistically significant differences from wild-type strain as determined by a two-tailed Student’s t-test (Bonferroni-corrected p-value: ****: p < 0.0001; ***: p < 0.001; **: p < 0.01; *: p < 0.05). d Plot of expression vs. fitness for the 16 strains. Solid line is the prediction of the fitted linear model. The dotted, dashed, and dotted-dashed lines show the prediction of the model at 0.1%, 0.3% and 2% galactose, respectively. Error bars indicate s.e.m. (N = 9). e Average effect of copy number reduction on fitness for the four genes in this environment. Error bars indicate uncertainty calculated from the s.e.m. of the fitness measurements