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Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast.

Dephoure N, Hwang S, O'Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM - Elife (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, Harvard Medical School, Boston, United States.

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Related in: MedlinePlus

Attenuation of proteins encoded on duplicated chromosomes.(A) Histogram of the log2 ratios of the relative mRNA levels of duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to a normal distribution is shown (black line). (B) Histogram of the log2 ratios of the relative protein levels of duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to the sum of two normal distributions is shown (black line). Fit of individual distributions are shown in dashed-line. (C) Histogram of the log2 ratios of the relative mRNA levels of non-duplicated genes of 12 disomes relative to wild-type grown in grown in synthetic medium. Fit to a normal distribution is shown (black line). (D) Histogram of the log2 ratios of the relative protein levels of non-duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to a normal distribution is shown (black line).DOI:http://dx.doi.org/10.7554/eLife.03023.010
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fig2s1: Attenuation of proteins encoded on duplicated chromosomes.(A) Histogram of the log2 ratios of the relative mRNA levels of duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to a normal distribution is shown (black line). (B) Histogram of the log2 ratios of the relative protein levels of duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to the sum of two normal distributions is shown (black line). Fit of individual distributions are shown in dashed-line. (C) Histogram of the log2 ratios of the relative mRNA levels of non-duplicated genes of 12 disomes relative to wild-type grown in grown in synthetic medium. Fit to a normal distribution is shown (black line). (D) Histogram of the log2 ratios of the relative protein levels of non-duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to a normal distribution is shown (black line).DOI:http://dx.doi.org/10.7554/eLife.03023.010

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.


Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast.

Dephoure N, Hwang S, O'Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM - Elife (2014)

Attenuation of proteins encoded on duplicated chromosomes.(A) Histogram of the log2 ratios of the relative mRNA levels of duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to a normal distribution is shown (black line). (B) Histogram of the log2 ratios of the relative protein levels of duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to the sum of two normal distributions is shown (black line). Fit of individual distributions are shown in dashed-line. (C) Histogram of the log2 ratios of the relative mRNA levels of non-duplicated genes of 12 disomes relative to wild-type grown in grown in synthetic medium. Fit to a normal distribution is shown (black line). (D) Histogram of the log2 ratios of the relative protein levels of non-duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to a normal distribution is shown (black line).DOI:http://dx.doi.org/10.7554/eLife.03023.010
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig2s1: Attenuation of proteins encoded on duplicated chromosomes.(A) Histogram of the log2 ratios of the relative mRNA levels of duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to a normal distribution is shown (black line). (B) Histogram of the log2 ratios of the relative protein levels of duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to the sum of two normal distributions is shown (black line). Fit of individual distributions are shown in dashed-line. (C) Histogram of the log2 ratios of the relative mRNA levels of non-duplicated genes of 12 disomes relative to wild-type grown in grown in synthetic medium. Fit to a normal distribution is shown (black line). (D) Histogram of the log2 ratios of the relative protein levels of non-duplicated genes of 12 disomes relative to wild-type grown in synthetic medium. Fit to a normal distribution is shown (black line).DOI:http://dx.doi.org/10.7554/eLife.03023.010
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, Harvard Medical School, Boston, United States.

Show MeSH
Related in: MedlinePlus