Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity
Abstract
:1. Introduction
2. Materials and Methods
2.1. Dictyostelium Strains
2.2. Vector Construction and Transformation
2.3. Native Gel Immunoblotting of the Proteasome
2.4. SDS PAGE and Western Blotting
2.5. Co-Immunoprecipitation (IP) Assays
2.6. Mass Spectrometry
2.7. Miscellaneous Methods
3. Results
3.1. Autophagy Mutants Exhibit a Strong Decrease in Proteasomal Activity but No Quantitative Change in Proteasomal Proteins
3.2. Immunoprecipitation of Tagged Proteasomes and Mass Spectrometry Support the Finding of Similar Amounts of Proteasomes in AX2 and ATG16− Cells
3.3. Some Proteasome-Associated Proteins Were Ubiquitinated
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Strains | Summary | Reference |
---|---|---|
AX2 | Axenically growing derivate of wild isolate NC-4 | [43] |
ATG9− | ATG9 knock-out mutant | [37] |
ATG16− | ATG16 knock-out mutant | [27] |
ATG9−/16− | ATG9 and ATG16 double knock-out mutant | [27] |
AX2/RFP-PSMD1 | AX2 cells expressing RFP-tagged PSMD1 | [17] |
AX2/RFP-PSMD1/PSMA4-GFP | AX2 cells expressing RFP-tagged PSMD1 and GFP-tagged PSMA4 | This work |
ATG16−/RFP-PSMD1 | ATG16 null cells expressing RFP-tagged PSMD1 | [17] |
ATG16−/RFP-PSMD1/PSMA4-GFP | ATG16 null cells expressing RFP-tagged PSMD1 and GFP-tagged PSMA4 | This work |
UniProt ID | DDB_G ID | Description | AA | Position | Mean Intensities (log2) | ||
---|---|---|---|---|---|---|---|
AX2 | ATG16− | ||||||
Exclusive in AX2 | Q54SZ7 | DDB_G0282111 | Uncharacterized protein | K | 700 | 24.51 | 0.00 |
Q75JX9 | DDB_G0272214 | Uncharacterized protein | K | 303 | 24.20 | 0.00 | |
Q54LV8 | DDB_G0286389 | 60S ribosomal protein L34 | K | 106 | 21.81 | 0.00 | |
Ubiquitinated in AX2 and ATG16− cells | Q54VN6 | DDB_G0280229 | 60S ribosomal protein L24 | K | 70 | 26.22 | 27.42 |
Q55B20 | DDB_G0271470 | Uncharacterized protein | K | 3 | 26.21 | 28.01 | |
Q86HT3 | DDB_G0274439 | BolA-like protein | K | 19 | 25.16 | 27.28 | |
Q54KW5 | DDB_G0287061 | Uncharacterized protein | K | 927 | 24.20 | 26.19 | |
Q54QR2 | DDB_G0283679 | Proteasome subunit beta type-7 | K | 63 | 23.78 | 25.52 | |
P14794 | DDB_G0280755 | Ubiquitin-60S ribosomal protein L40 | K | 48 | 23.61 | 25.40 | |
Exclusive in ATG16− | B0G0Z1 | DDB_G0270910 | Eukaryotic translation initiation factor 4E | K | 870 | 0.00 | 30.46 |
Q54T94 | DDB_G0281913 | Uncharacterized protein | K | 146 | 0.00 | 28.58 | |
Q55BM4 | DDB_G0269190 | T-complex protein 1 subunit alpha | K | 468 | 0.00 | 26.14 | |
Q55GK4 | DDB_G0267634 | Uncharacterized protein | K | 827 | 0.00 | 26.05 | |
Q54ED9 | DDB_G0291538 | Uncharacterized protein | K | 3 | 0.00 | 25.71 | |
Q54HN5 | DDB_G0289337 | Uncharacterized protein | K | 3 | 0.00 | 25.64 | |
Q55CG3 | DDB_G0271028 | Uncharacterized protein | K | 18 | 0.00 | 25.50 | |
Q54JB0 | DDB_G0288187 | DDI1 homolog | K | 55 | 0.00 | 24.82 | |
Q54QE4 | DDB_G0283987 | Bifunctional purine synth. protein purC/E | K | 234 | 0.00 | 24.71 | |
Q8MMQ2 | DDB_G0275539 | Uncharacterized protein | K | 86 | 0.00 | 24.64 | |
Q54GS9 | DDB_G0289933 | Uncharacterized protein | K | 346 | 0.00 | 24.30 | |
Q54YL1 | DDB_G0278621 | Uncharacterized protein | K | 604 | 0.00 | 23.89 | |
Q559T1 | DDB_G0272438 | Uncharacterized protein | K | 231 | 0.00 | 23.73 | |
Q55C03 | DDB_G0270284 | Uncharacterized protein | K | 373 | 0.00 | 23.67 | |
Q54WT5 | DDB_G0279449 | Uncharacterized protein | K | 115 | 0.00 | 23.24 | |
Q54GX0 | DDB_G0289871 | Uncharacterized protein | K | 2 | 0.00 | 22.15 |
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Xiong, Q.; Feng, R.; Fischer, S.; Karow, M.; Stumpf, M.; Meßling, S.; Nitz, L.; Müller, S.; Clemen, C.S.; Song, N.; et al. Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity. Cells 2023, 12, 1514. https://doi.org/10.3390/cells12111514
Xiong Q, Feng R, Fischer S, Karow M, Stumpf M, Meßling S, Nitz L, Müller S, Clemen CS, Song N, et al. Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity. Cells. 2023; 12(11):1514. https://doi.org/10.3390/cells12111514
Chicago/Turabian StyleXiong, Qiuhong, Rong Feng, Sarah Fischer, Malte Karow, Maria Stumpf, Susanne Meßling, Leonie Nitz, Stefan Müller, Christoph S. Clemen, Ning Song, and et al. 2023. "Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity" Cells 12, no. 11: 1514. https://doi.org/10.3390/cells12111514