Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains
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- 作者：Marta Isasa ; Christopher M. Rose ; Suzanne Elsasser ; Jos茅 Navarrete-Perea ; Joao A. Paulo ; Daniel J. Finley ; Steven P. Gygi
- 刊名：Journal of Proteome Research
- 出版年：2015
- 出版时间：December 4, 2015
- 年：2015
- 卷：14
- 期：12
- 页码：5306-5317
- 全文大小：698K
- ISSN：1535-3907
文摘
Characterizing a protein鈥檚 function often requires a description of the cellular state in its absence. Multiplexing in mass spectrometry-based proteomics has now achieved the ability to globally measure protein expression levels in yeast from 10 cell states simultaneously. We applied this approach to quantify expression differences in wild type and nine deubiquitylating enzyme (DUB) knockout strains with the goal of creating 鈥渋nformation networks鈥?that might provide deeper, mechanistic insights into a protein鈥檚 biological role. In total, more than 3700 proteins were quantified with high reproducibility across three biological replicates (30 samples in all). DUB mutants demonstrated different proteomics profiles, consistent with distinct roles for each family member. These included differences in total ubiquitin levels and specific chain linkages. Moreover, specific expression changes suggested novel functions for several DUB family members. For instance, the ubp3螖 mutant showed large expression changes for members of the cytochrome C oxidase complex, consistent with a role for Ubp3 in mitochondrial regulation. Several DUBs also showed broad expression changes for phosphate transporters as well as other components of the inorganic phosphate signaling pathway, suggesting a role for these DUBs in regulating phosphate metabolism. These data highlight the potential of multiplexed proteome-wide analyses for biological investigation and provide a framework for further study of the DUB family. Our methods are readily applicable to the entire collection of yeast deletion mutants and may help facilitate systematic analysis of yeast and other organisms.