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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

Analysis of proteome changes of meiotically generated aneuploid strains.(A) The plots show the log2 ratio of the relative protein abundance of five meiotically generated aneuploid strains compared to wild-type cells as reported in Pavelka et al. (2010). The duplicated chromosomes are indicated. Protein levels are shown in the order of the chromosomal location of their encoding genes. (B) Histogram of the log2 ratios of the relative protein levels of duplicated genes relative to wild-type genes from Pavelka et al. (2010). In each plot, a fit to a normal distribution or the sum of two normal distributions is shown (black line). Fit of individual distributions are shown in dashed-line. (C) Attenuation of proteins encoded on duplicated chromosomes of meiotically generated aneuploid strains. For each of the five meiotically generated aneuploid strains, the mean log2 ratio to wild-type cells for all duplicated genes is plotted separately for proteins annotated as protein complex members and those that are not. The left plot uses the set of Core Complex proteins defined in Gavin et al. (2006). The right plot uses a set of manually curated protein complexes from Pu et al. (2009). p-values were calculated using Welch's t test. (D) Attenuation of duplicated proteins in the meiotically generated set of aneuploid yeast strains. p-values were calculated using Welch's t test.DOI:http://dx.doi.org/10.7554/eLife.03023.014
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fig3s1: Analysis of proteome changes of meiotically generated aneuploid strains.(A) The plots show the log2 ratio of the relative protein abundance of five meiotically generated aneuploid strains compared to wild-type cells as reported in Pavelka et al. (2010). The duplicated chromosomes are indicated. Protein levels are shown in the order of the chromosomal location of their encoding genes. (B) Histogram of the log2 ratios of the relative protein levels of duplicated genes relative to wild-type genes from Pavelka et al. (2010). In each plot, a fit to a normal distribution or the sum of two normal distributions is shown (black line). Fit of individual distributions are shown in dashed-line. (C) Attenuation of proteins encoded on duplicated chromosomes of meiotically generated aneuploid strains. For each of the five meiotically generated aneuploid strains, the mean log2 ratio to wild-type cells for all duplicated genes is plotted separately for proteins annotated as protein complex members and those that are not. The left plot uses the set of Core Complex proteins defined in Gavin et al. (2006). The right plot uses a set of manually curated protein complexes from Pu et al. (2009). p-values were calculated using Welch's t test. (D) Attenuation of duplicated proteins in the meiotically generated set of aneuploid yeast strains. p-values were calculated using Welch's t test.DOI:http://dx.doi.org/10.7554/eLife.03023.014

Mentions: We previously quantified protein abundances in two disomic strains, disomes V and XIII, relative to wild-type cells (Torres et al., 2010). Consistent with our findings presented here, preliminary analyses indicated that subunits of macromolecular complexes were enriched among the dosage compensated genes (Torres et al., 2010). A subsequent quantitative proteomic study of five aneuploid yeasts obtained as progeny from triploid or pentaploid meioses found no evidence for the attenuation of proteins that form multi-subunit complexes (Pavelka et al., 2010). To better understand this discrepancy, we analyzed the protein measurements generated by Pavelka et al. (2010) (Figure 3—figure supplement 1A). In two strains, the ratios of protein levels of duplicated genes fit a sum of two normal distributions; one with a mean increase close to twofold, the other with significantly reduced mean close to zero (R2’s = 0.94 and 0.92, Figure 3—figure supplement 1B). In the other three strains, the ratios of protein levels of duplicated genes fit normal distributions and show average increases significantly lower than the predicted twofold change (mean log2 ratios equal to 0.79, 0.77 and 0.65) (Figure 3—figure supplement 1B). Pavelka et al. showed that attenuation of protein levels of subunits of macromolecular complexes were small but not significant compared to proteins not found in complexes. Using the same list of complexes in Pavelka et al. (2010) (Gavin et al., 2006), we obtained similar results (Figure 3—figure supplement 1C). However, when we used a more up to date and manually curated list of subunits of macromolecular complexes (Pu et al., 2009), we found that statistically significant attenuation in proteins that form part of complexes takes places in all the strains (Figure 3—figure supplement 1C). Next, we focused on the identity of the most attenuated proteins and asked whether subunits of complexes were enriched among them. We used a stringent cutoff of log2 ratio of 0.6 lower than the mean increase in protein levels of the duplicate genes in each of the five aneuploid strains and found that between 23 and 38% of duplicated proteins were significantly attenuated (Figure 3—figure supplement 1D). Importantly, the attenuated proteins are enriched for subunits of macromolecular complexes in all five strains (Figure 3—figure supplement 1D). We conclude that significant attenuation of subunits of macromolecular complexes is a general feature of aneuploid yeast strains.


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)

Analysis of proteome changes of meiotically generated aneuploid strains.(A) The plots show the log2 ratio of the relative protein abundance of five meiotically generated aneuploid strains compared to wild-type cells as reported in Pavelka et al. (2010). The duplicated chromosomes are indicated. Protein levels are shown in the order of the chromosomal location of their encoding genes. (B) Histogram of the log2 ratios of the relative protein levels of duplicated genes relative to wild-type genes from Pavelka et al. (2010). In each plot, a fit to a normal distribution or the sum of two normal distributions is shown (black line). Fit of individual distributions are shown in dashed-line. (C) Attenuation of proteins encoded on duplicated chromosomes of meiotically generated aneuploid strains. For each of the five meiotically generated aneuploid strains, the mean log2 ratio to wild-type cells for all duplicated genes is plotted separately for proteins annotated as protein complex members and those that are not. The left plot uses the set of Core Complex proteins defined in Gavin et al. (2006). The right plot uses a set of manually curated protein complexes from Pu et al. (2009). p-values were calculated using Welch's t test. (D) Attenuation of duplicated proteins in the meiotically generated set of aneuploid yeast strains. p-values were calculated using Welch's t test.DOI:http://dx.doi.org/10.7554/eLife.03023.014
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fig3s1: Analysis of proteome changes of meiotically generated aneuploid strains.(A) The plots show the log2 ratio of the relative protein abundance of five meiotically generated aneuploid strains compared to wild-type cells as reported in Pavelka et al. (2010). The duplicated chromosomes are indicated. Protein levels are shown in the order of the chromosomal location of their encoding genes. (B) Histogram of the log2 ratios of the relative protein levels of duplicated genes relative to wild-type genes from Pavelka et al. (2010). In each plot, a fit to a normal distribution or the sum of two normal distributions is shown (black line). Fit of individual distributions are shown in dashed-line. (C) Attenuation of proteins encoded on duplicated chromosomes of meiotically generated aneuploid strains. For each of the five meiotically generated aneuploid strains, the mean log2 ratio to wild-type cells for all duplicated genes is plotted separately for proteins annotated as protein complex members and those that are not. The left plot uses the set of Core Complex proteins defined in Gavin et al. (2006). The right plot uses a set of manually curated protein complexes from Pu et al. (2009). p-values were calculated using Welch's t test. (D) Attenuation of duplicated proteins in the meiotically generated set of aneuploid yeast strains. p-values were calculated using Welch's t test.DOI:http://dx.doi.org/10.7554/eLife.03023.014
Mentions: We previously quantified protein abundances in two disomic strains, disomes V and XIII, relative to wild-type cells (Torres et al., 2010). Consistent with our findings presented here, preliminary analyses indicated that subunits of macromolecular complexes were enriched among the dosage compensated genes (Torres et al., 2010). A subsequent quantitative proteomic study of five aneuploid yeasts obtained as progeny from triploid or pentaploid meioses found no evidence for the attenuation of proteins that form multi-subunit complexes (Pavelka et al., 2010). To better understand this discrepancy, we analyzed the protein measurements generated by Pavelka et al. (2010) (Figure 3—figure supplement 1A). In two strains, the ratios of protein levels of duplicated genes fit a sum of two normal distributions; one with a mean increase close to twofold, the other with significantly reduced mean close to zero (R2’s = 0.94 and 0.92, Figure 3—figure supplement 1B). In the other three strains, the ratios of protein levels of duplicated genes fit normal distributions and show average increases significantly lower than the predicted twofold change (mean log2 ratios equal to 0.79, 0.77 and 0.65) (Figure 3—figure supplement 1B). Pavelka et al. showed that attenuation of protein levels of subunits of macromolecular complexes were small but not significant compared to proteins not found in complexes. Using the same list of complexes in Pavelka et al. (2010) (Gavin et al., 2006), we obtained similar results (Figure 3—figure supplement 1C). However, when we used a more up to date and manually curated list of subunits of macromolecular complexes (Pu et al., 2009), we found that statistically significant attenuation in proteins that form part of complexes takes places in all the strains (Figure 3—figure supplement 1C). Next, we focused on the identity of the most attenuated proteins and asked whether subunits of complexes were enriched among them. We used a stringent cutoff of log2 ratio of 0.6 lower than the mean increase in protein levels of the duplicate genes in each of the five aneuploid strains and found that between 23 and 38% of duplicated proteins were significantly attenuated (Figure 3—figure supplement 1D). Importantly, the attenuated proteins are enriched for subunits of macromolecular complexes in all five strains (Figure 3—figure supplement 1D). We conclude that significant attenuation of subunits of macromolecular complexes is a general feature of aneuploid yeast strains.

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