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Sahu I, Mali SM, Sulkshane P, Xu C, Rozenberg A, Morag R, Sahoo MP, Singh SK, Ding Z, Wang Y, Day S, Cong Y, Kleifeld O, Brik A, Glickman MH. The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag. Nat Commun 2021; 12:6173. [PMID: 34702852 PMCID: PMC8548400 DOI: 10.1038/s41467-021-26427-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
The proteasome, the primary protease for ubiquitin-dependent proteolysis in eukaryotes, is usually found as a mixture of 30S, 26S, and 20S complexes. These complexes have common catalytic sites, which makes it challenging to determine their distinctive roles in intracellular proteolysis. Here, we chemically synthesize a panel of homogenous ubiquitinated proteins, and use them to compare 20S and 26S proteasomes with respect to substrate selection and peptide-product generation. We show that 20S proteasomes can degrade the ubiquitin tag along with the conjugated substrate. Ubiquitin remnants on branched peptide products identified by LC-MS/MS, and flexibility in the 20S gate observed by cryo-EM, reflect the ability of the 20S proteasome to proteolyze an isopeptide-linked ubiquitin-conjugate. Peptidomics identifies proteasome-trapped ubiquitin-derived peptides and peptides of potential 20S substrates in Hi20S cells, hypoxic cells, and human failing-heart. Moreover, elevated levels of 20S proteasomes appear to contribute to cell survival under stress associated with damaged proteins.
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Affiliation(s)
- Indrajit Sahu
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Sachitanand M Mali
- Schulich faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Prasad Sulkshane
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Cong Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Roni Morag
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | | | - Sumeet K Singh
- Schulich faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Zhanyu Ding
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Sharleen Day
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Ashraf Brik
- Schulich faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Michael H Glickman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
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Glynn SE, Kardon JR, Mueller-Cajar O, Cho C. AAA+ proteins: converging mechanisms, diverging functions. Nat Struct Mol Biol 2020; 27:515-518. [PMID: 32461632 DOI: 10.1038/s41594-020-0444-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.
| | - Julia R Kardon
- Department of Biochemistry, Brandeis University, Waltham, MA, USA.
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Carol Cho
- Research Center for Natural Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
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