Limits...
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.

Show MeSH

Related in: MedlinePlus

GO term analysis of attenuated proteins not found in complexes.(A) Comparison of the protein levels of attenuated proteins, not known to be part of complexes, when present in a duplicated chromosome in disomic cells grown in YEPD vs synthetic medium. Pairwise comparison show a Pearson correlation coefficient (r) = 0.45. (B) Log2 ratios of subunits of complexes when encoded in a duplicated chromosome relative to wild-type. Complexes that show significant attenuation (mean of their subunits < 0.6, dashed red line) are shown in red.DOI:http://dx.doi.org/10.7554/eLife.03023.022
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4129440&req=5

fig5s2: GO term analysis of attenuated proteins not found in complexes.(A) Comparison of the protein levels of attenuated proteins, not known to be part of complexes, when present in a duplicated chromosome in disomic cells grown in YEPD vs synthetic medium. Pairwise comparison show a Pearson correlation coefficient (r) = 0.45. (B) Log2 ratios of subunits of complexes when encoded in a duplicated chromosome relative to wild-type. Complexes that show significant attenuation (mean of their subunits < 0.6, dashed red line) are shown in red.DOI:http://dx.doi.org/10.7554/eLife.03023.022

Mentions: To determine which multi-subunit complexes were subject to subunit dosage compensation, we used a manually curated set of yeast protein complexes to assign complex status to all duplicated gene products (Pu et al., 2009). We found that more than half of the proteins designated as members of macromolecular complexes were significantly attenuated in the disomes grown in rich medium (469 of 923 showed log2 ratios ≤ 0.6). Nonlinear regression analysis of the distribution of the log2 ratios of their levels relative to wild-type cells showed two populations, one of which encompassed the majority with a mean ratio of 0.46 (1.4-fold), a value significantly lower than the predicted increase of twofold that would be expected if protein levels scaled with gene copy number (Figure 5A). Similar results were obtained with cells analyzed by SILAC (Figure 5—figure supplement 1A). In contrast, proteins encoded by duplicated genes that are not found in complexes showed little attenuation (Figure 5B, Figure 5—figure supplement 1B). Nonetheless, levels of a small number of uncomplexed proteins were attenuated. To assess how these proteins contribute to the total attenuation, we analyzed their identity and the reproducibility of their attenuation in selective and rich media. We identified 88 proteins not known to function in complexes that were attenuated in both growth conditions. Gene ontology analysis did not reveal any significant enrichment for a particular function, cellular process or component. In fact, the biological function of 15 of 88 proteins is unknown (Figure 5—figure supplement 2A). Our analysis not only indicates that most of the proteome attenuation observed in aneuploid cells is caused by the attenuation of components of protein complexes but also leads us to estimate that about half of all cellular proteins found in complexes (469 of 923 detected proteins) are unstable and rapidly degraded unless they find their binding partners.10.7554/eLife.03023.019Figure 5.Subunits of macromolecular complexes accounts for most of the attenuation.


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)

GO term analysis of attenuated proteins not found in complexes.(A) Comparison of the protein levels of attenuated proteins, not known to be part of complexes, when present in a duplicated chromosome in disomic cells grown in YEPD vs synthetic medium. Pairwise comparison show a Pearson correlation coefficient (r) = 0.45. (B) Log2 ratios of subunits of complexes when encoded in a duplicated chromosome relative to wild-type. Complexes that show significant attenuation (mean of their subunits < 0.6, dashed red line) are shown in red.DOI:http://dx.doi.org/10.7554/eLife.03023.022
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4129440&req=5

fig5s2: GO term analysis of attenuated proteins not found in complexes.(A) Comparison of the protein levels of attenuated proteins, not known to be part of complexes, when present in a duplicated chromosome in disomic cells grown in YEPD vs synthetic medium. Pairwise comparison show a Pearson correlation coefficient (r) = 0.45. (B) Log2 ratios of subunits of complexes when encoded in a duplicated chromosome relative to wild-type. Complexes that show significant attenuation (mean of their subunits < 0.6, dashed red line) are shown in red.DOI:http://dx.doi.org/10.7554/eLife.03023.022
Mentions: To determine which multi-subunit complexes were subject to subunit dosage compensation, we used a manually curated set of yeast protein complexes to assign complex status to all duplicated gene products (Pu et al., 2009). We found that more than half of the proteins designated as members of macromolecular complexes were significantly attenuated in the disomes grown in rich medium (469 of 923 showed log2 ratios ≤ 0.6). Nonlinear regression analysis of the distribution of the log2 ratios of their levels relative to wild-type cells showed two populations, one of which encompassed the majority with a mean ratio of 0.46 (1.4-fold), a value significantly lower than the predicted increase of twofold that would be expected if protein levels scaled with gene copy number (Figure 5A). Similar results were obtained with cells analyzed by SILAC (Figure 5—figure supplement 1A). In contrast, proteins encoded by duplicated genes that are not found in complexes showed little attenuation (Figure 5B, Figure 5—figure supplement 1B). Nonetheless, levels of a small number of uncomplexed proteins were attenuated. To assess how these proteins contribute to the total attenuation, we analyzed their identity and the reproducibility of their attenuation in selective and rich media. We identified 88 proteins not known to function in complexes that were attenuated in both growth conditions. Gene ontology analysis did not reveal any significant enrichment for a particular function, cellular process or component. In fact, the biological function of 15 of 88 proteins is unknown (Figure 5—figure supplement 2A). Our analysis not only indicates that most of the proteome attenuation observed in aneuploid cells is caused by the attenuation of components of protein complexes but also leads us to estimate that about half of all cellular proteins found in complexes (469 of 923 detected proteins) are unstable and rapidly degraded unless they find their binding partners.10.7554/eLife.03023.019Figure 5.Subunits of macromolecular complexes accounts for most of the attenuation.

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