Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast.
Bottom Line: Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis.Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains.Our results show that aneuploidy causes alterations in metabolism and redox homeostasis.
Affiliation: Department of Cell Biology, Harvard Medical School, Boston, United States.Show MeSH
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Mentions: Dosage compensation, where a change in gene dosage does not lead to a corresponding change in protein levels, is common for genes located on sex chromosomes (Lee and Bartolomei, 2013). Whether dosage compensation also occurs on autosomes and if so, which genes are affected and how it is brought about are critical questions not only to understand the effects of aneuploidy but also to understand how protein homeostasis is maintained in normal cells. Our set of disomic yeast strains, which comprises duplications of 12 of the 16 chromosomes (corresponding to 73% of the yeast genome), allowed us to address this question. We grew the 12 disomic strains in rich medium, split the cultures and analyzed mRNA and protein levels. In total, we obtained quantitative information for both mRNA and protein, reported as log2 ratios, for 2,581 genes located on duplicated chromosomes (Figure 2A,B) and 39,011 paired measurements for genes on non-duplicated chromosomes (Figure 2C,D). The ratios of mRNA levels of duplicated genes fit a normal distribution with a mean increase of 1.9-fold (SD = 0.3 and R2 = 0.99, Figure 2A). Parallel analysis of the corresponding protein changes did not fit as well to a normal distribution (R2 = 0.96, Pearson's mode skewness = −0.12). Nonlinear regression analysis of the protein data best fit a sum of two normal distributions; one with a mean increase of twofold, the other with a significantly reduced mean increase of ∼1.6-fold (R2 = 1.00, Figure 2B). In contrast, analysis of both mRNA and protein changes of non-duplicated genes showed nearly perfect normal distributions (R2 = 0.99, Figure 2C,D). These analyses indicate that although acquisition of an extra chromosome leads on average to twofold increases in mRNA levels of the duplicated genes, a large and statistically significant number of proteins do not increase proportionally with copy number. Importantly, neither the growth conditions nor the quantitative approach affected the degree of attenuation, as analysis of mRNA and protein levels from cells grown in selective medium and analyzed by SILAC showed similar results (Figure 2—figure supplement 1).10.7554/eLife.03023.007Figure 2.Attenuation of proteins encoded on duplicated chromosomes.
Affiliation: Department of Cell Biology, Harvard Medical School, Boston, United States.