Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity
Autophagy and the ubiquitin proteasome system are the two major processes for the clearance and recycling of proteins and organelles in eukaryotic cells. Evidence is accumulating that there is extensive crosstalk between the two pathways, but the underlying mechanisms are still unclear. We previousl...
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MDPI AG
2023-05-01
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| author | Qiuhong Xiong Rong Feng Sarah Fischer Malte Karow Maria Stumpf Susanne Meßling Leonie Nitz Stefan Müller Christoph S. Clemen Ning Song Ping Li Changxin Wu Ludwig Eichinger |
| author_facet | Qiuhong Xiong Rong Feng Sarah Fischer Malte Karow Maria Stumpf Susanne Meßling Leonie Nitz Stefan Müller Christoph S. Clemen Ning Song Ping Li Changxin Wu Ludwig Eichinger |
| author_sort | Qiuhong Xiong |
| collection | DOAJ |
| description | Autophagy and the ubiquitin proteasome system are the two major processes for the clearance and recycling of proteins and organelles in eukaryotic cells. Evidence is accumulating that there is extensive crosstalk between the two pathways, but the underlying mechanisms are still unclear. We previously found that autophagy 9 (ATG9) and 16 (ATG16) proteins are crucial for full proteasomal activity in the unicellular amoeba <i>Dictyostelium discoideum</i>. In comparison to AX2 wild-type cells, ATG9<sup>−</sup>and ATG16<sup>−</sup> cells displayed a 60%, and ATG9<sup>−</sup>/16<sup>−</sup> cells a 90%, decrease in proteasomal activity. Mutant cells also showed a significant increase in poly-ubiquitinated proteins and contained large ubiquitin-positive protein aggregates. Here, we focus on possible reasons for these results. Reanalysis of published tandem mass tag-based quantitative proteomic results of AX2, ATG9<sup>−</sup>, ATG16<sup>−</sup>, and ATG9<sup>−</sup>/16<sup>−</sup> cells revealed no change in the abundance of proteasomal subunits. To identify possible differences in proteasome-associated proteins, we generated AX2 wild-type and ATG16<sup>−</sup> cells expressing the 20S proteasomal subunit PSMA4 as GFP-tagged fusion protein, and performed co-immunoprecipitation experiments followed by mass spectrometric analysis. The results revealed no significant differences in the abundance of proteasomes between the two strains. However, we found enrichment as well as depletion of proteasomal regulators and differences in the ubiquitination of associated proteins for ATG16<sup>−</sup>, as compared to AX2 cells. Recently, proteaphagy has been described as a means to replace non-functional proteasomes. We propose that autophagy-deficient <i>D. discoideum</i> mutants suffer from inefficient proteaphagy, which results in the accumulation of modified, less-active, and also of inactive, proteasomes. As a consequence, these cells exhibit a dramatic decrease in proteasomal activity and deranged protein homeostasis. |
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| institution | Directory Open Access Journal |
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| spelling | doaj.art-b91cdcd1cd9e420688ca1b8b2fca18382023-11-18T07:41:08ZengMDPI AGCells2073-44092023-05-011211151410.3390/cells12111514Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in ActivityQiuhong Xiong0Rong Feng1Sarah Fischer2Malte Karow3Maria Stumpf4Susanne Meßling5Leonie Nitz6Stefan Müller7Christoph S. Clemen8Ning Song9Ping Li10Changxin Wu11Ludwig Eichinger12Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, ChinaShanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, ChinaCenter for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, GermanyCenter for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, GermanyCenter for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, GermanyCenter for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, GermanyCenter for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, GermanyCECAD Proteomics Facility, Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, GermanyInstitute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, GermanyShanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, ChinaShanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, ChinaShanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institutes of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, ChinaCenter for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, GermanyAutophagy and the ubiquitin proteasome system are the two major processes for the clearance and recycling of proteins and organelles in eukaryotic cells. Evidence is accumulating that there is extensive crosstalk between the two pathways, but the underlying mechanisms are still unclear. We previously found that autophagy 9 (ATG9) and 16 (ATG16) proteins are crucial for full proteasomal activity in the unicellular amoeba <i>Dictyostelium discoideum</i>. In comparison to AX2 wild-type cells, ATG9<sup>−</sup>and ATG16<sup>−</sup> cells displayed a 60%, and ATG9<sup>−</sup>/16<sup>−</sup> cells a 90%, decrease in proteasomal activity. Mutant cells also showed a significant increase in poly-ubiquitinated proteins and contained large ubiquitin-positive protein aggregates. Here, we focus on possible reasons for these results. Reanalysis of published tandem mass tag-based quantitative proteomic results of AX2, ATG9<sup>−</sup>, ATG16<sup>−</sup>, and ATG9<sup>−</sup>/16<sup>−</sup> cells revealed no change in the abundance of proteasomal subunits. To identify possible differences in proteasome-associated proteins, we generated AX2 wild-type and ATG16<sup>−</sup> cells expressing the 20S proteasomal subunit PSMA4 as GFP-tagged fusion protein, and performed co-immunoprecipitation experiments followed by mass spectrometric analysis. The results revealed no significant differences in the abundance of proteasomes between the two strains. However, we found enrichment as well as depletion of proteasomal regulators and differences in the ubiquitination of associated proteins for ATG16<sup>−</sup>, as compared to AX2 cells. Recently, proteaphagy has been described as a means to replace non-functional proteasomes. We propose that autophagy-deficient <i>D. discoideum</i> mutants suffer from inefficient proteaphagy, which results in the accumulation of modified, less-active, and also of inactive, proteasomes. As a consequence, these cells exhibit a dramatic decrease in proteasomal activity and deranged protein homeostasis.https://www.mdpi.com/2073-4409/12/11/1514autophagyubiquitin proteasome system (UPS)<i>Dictyostelium</i>ATG9ATG16 |
| spellingShingle | Qiuhong Xiong Rong Feng Sarah Fischer Malte Karow Maria Stumpf Susanne Meßling Leonie Nitz Stefan Müller Christoph S. Clemen Ning Song Ping Li Changxin Wu Ludwig Eichinger Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity Cells autophagy ubiquitin proteasome system (UPS) <i>Dictyostelium</i> ATG9 ATG16 |
| title | Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity |
| title_full | Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity |
| title_fullStr | Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity |
| title_full_unstemmed | Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity |
| title_short | Proteasomes of Autophagy-Deficient Cells Exhibit Alterations in Regulatory Proteins and a Marked Reduction in Activity |
| title_sort | proteasomes of autophagy deficient cells exhibit alterations in regulatory proteins and a marked reduction in activity |
| topic | autophagy ubiquitin proteasome system (UPS) <i>Dictyostelium</i> ATG9 ATG16 |
| url | https://www.mdpi.com/2073-4409/12/11/1514 |
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