Quantitative Proteomics-Based Substrate Screening Revealed Cyclophilin Stabilization Regulated by Deubiquitinase Ubp7
Yonghong Wang1,2, Qiuyan Lan2, Xinyu Cheng3
1Department of Biomedicine, School of Medicine, Guizhou University, Guiyang 550025, China.
Journal of Proteome Research
|June 21, 2023
Summary
Ubiquitinomics quantitative analysis offers a more efficient method for identifying ubiquitinated substrates compared to traditional proteomics. This approach revealed novel substrates, like cyclophilin A, regulated by Ubp7, impacting cellular processes.
Area of Science:
- Biochemistry and Molecular Biology
- Proteomics and Post-Translational Modifications
Background:
- Quantitative proteomics is vital for identifying ubiquitinated substrates and understanding ubiquitination's cellular roles.
- Direct comparisons between proteome-wide and ubiquitinome-focused screening for enzyme substrates remain underexplored.
Purpose of the Study:
- To quantitatively compare the efficiency and effectiveness of substrate screening using whole proteomics versus a ubiquitinomics filter.
- To evaluate the yeast deubiquitinating enzyme Ubp7 as a model system for this comparison.
Main Methods:
- Employed quantitative proteomics and ubiquitinomics approaches to screen for Ubp7 substrates in yeast.
- Selected candidate proteins identified via ubiquitinomics for further validation.
- Investigated the ubiquitination status and regulation of selected substrates, such as cyclophilin A (Cpr1).
Main Results:
- Ubiquitinomics identified 112 potential ubiquitinated substrates, significantly more than the 27 regulated substrates found by entire proteomic screening.
- Cyclophilin A (Cpr1), missed by proteomic screening, was identified as a Ubp7-regulated substrate via ubiquitinomics.
- Cpr1 was found to possess a K48-linked ubiquitin chain regulated by Ubp7, potentially influencing its homeostasis and sensitivity to cyclosporine (CsA).
Conclusions:
- Ubiquitinomics provides a more efficient and comprehensive strategy for identifying ubiquitinated substrates compared to standard proteomic approaches.
- This study highlights Ubp7's role in regulating Cpr1 ubiquitination, suggesting implications for cellular homeostasis and drug sensitivity.
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