(A) Protein burden changes with copy number. The bar plot shows the relative fitness of yEVenus overexpressing and control genotypes as a function of plasmid copy number, a proxy of gene expression level. From a single copy plasmid, yEVenus has no detectable fitness cost (t-test, p=not significant), while it confers around 2.5% fitness disadvantage from a high-copy plasmid (t-test, p<0.001). Absolute fitness was estimated by measuring colony size after 48 hr of growth on solid medium. Relative fitness was calculated by normalizing to the absolute fitness of the genotypes with the corresponding empty vectors, respectively. The bars indicate mean ±95% confidence interval, based on at least 12 technical and 10 biological replicates each. Source file is available as Supplementary file 5. (B) PAGE analysis of whole cell protein extracts. The figure shows the PAGE (polyacrylamide gel electrophoresis) separation of whole cell protein extracts (10 µg, 20 µg, and 30 µg) from both the control and the yEVenus overexpressing strains in denaturing conditions (4–20% gradient Tris-Glycine SDS-PAGE). To create a standard curve, a bovine serum albumin (BSA) dilution series (100–800 ng) was loaded onto the same gel. On the basis of a densitometry analysis using the standard curve, the yEVenus (band at 27 kDa) constitutes 3.7% of the total cellular proteome when expressed from a high-copy plasmid (for further details, see Materials and methods). (C) Distribution of genetic interaction scores (ε) across the haploid yeast knock-out collection. The ε value for the vast majority of the knock-out strains is approximately zero, indicating no specific genetic interaction of the corresponding gene with yEVenus overexpression. The dashed lines on the y axis represent cutoff values for ε (0.05 and −0.05, respectively). Negative/positive interactions are color-coded as magenta/green. For the calculation of genetic interaction score, see Materials and methods. Source file is available as Supplementary file 1. (D) Scatterplot of the genetic interaction scores and biomass-normalized fluorescence levels of the deletion strains from the haploid yeast knock-out collection. On the x axis, one represents the wild type fluorescence level (dashed line). The dashed lines on the y axis represent the previously defined interaction value cutoffs (0.05 and −0.05, respectively). The fluorescence level of the genotypes shows only very weak correlation with the strength of the interaction (Pearson’s correlation test, r = 0.05, p<0.001). Negative/positive interactions are color-coded as magenta/green. For the calculation of genetic interaction score and for the evaluation of fluorescence level, see Materials and methods. Source file is available as Supplementary file 1. Additional analysis of genetic interaction scores and fluorescence levels are shown in Figure 1—figure supplement 1A and B. (E) Examples on negative genetic interactions between single gene deletions and yEVenus overexpression. The bar plots show the relative fitness values (normalized to wild type) of single mutants (yEVenus overexpression or single gene deletions), and double mutants (deletion +yEVenus overexpression), based on six replicates. Negative deviation of the observed double mutant fitness from the expected value (designated as dashed line, calculated by the multiplicative model using the two single mutant fitness values) is referred to as negative interaction. Absolute fitness was estimated by measuring colony size after 48 hr of growth on solid medium. The deleted genes (Δcrp7, Δfes1, Δgim5, Δpfd1) are selected members of the chaperone system. Source file is available as Supplementary file 1. An example of positive genetic interaction is shown in Figure 1—figure supplement 1C. (F) Scatterplot of the genetic interaction scores and the fitness of the deletion strains from the haploid yeast knock-out collection. On the x axis, one represents the wild type fitness (dashed line). The dashed lines on the y axis represent the previously defined interaction value cutoffs (0.05 and −0.05, respectively). Negative/positive interactions are color-coded as magenta/green. The fitness of the deletion strains shows only a weak positive correlation with the strength of interaction (Pearson’s correlation test, r = 0.12, p<0.001). For the calculation of fitness and genetic interaction score, see Materials and methods. Source file is available as Supplementary file 1.