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Wen X, Xu H, Woolley PR, Conway OM, Yao J, Matouschek A, Lambowitz AM, Paull TT. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation. J Cell Biol 2024; 223:e202309036. [PMID: 38717338 PMCID: PMC11080644 DOI: 10.1083/jcb.202309036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 05/12/2024] Open
Abstract
Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells. We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus.
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Affiliation(s)
- Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hengyi Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Phillip R. Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Olivia M. Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Alan M. Lambowitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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2
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Arkinson C, Dong KC, Gee CL, Costello SM, Marqusee S, Martin A. Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598715. [PMID: 38915702 PMCID: PMC11195292 DOI: 10.1101/2024.06.12.598715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor Nub1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system and revealed that Nub1 utilizes FAT10's intrinsic instability to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin- and p97-independent manner. Through hydrogen-deuterium exchange, structural modeling, and site-directed mutagenesis, we identified the formation of a peculiar complex with FAT10 that activates Nub1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic Nub1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These studies thus identified a novel mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.
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Affiliation(s)
- Connor Arkinson
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Ken C. Dong
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Christine L. Gee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Shawn M. Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Susan Marqusee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Andreas Martin
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
- Lead contact
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3
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Goncalves D, Duy DL, Peffer S, Morano KA. Cytoplasmic redox imbalance in the thioredoxin system activates Hsf1 and results in hyperaccumulation of the sequestrase Hsp42 with misfolded proteins. Mol Biol Cell 2024; 35:ar53. [PMID: 38381577 PMCID: PMC11064659 DOI: 10.1091/mbc.e23-07-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Cells employ multiple systems to maintain homeostasis when experiencing environmental stress. For example, the folding of nascent polypeptides is exquisitely sensitive to proteotoxic stressors including heat, pH, and oxidative stress, and is safeguarded by a network of protein chaperones that concentrate potentially toxic misfolded proteins into transient assemblies to promote folding or degradation. The redox environment itself is buffered by both cytosolic and organellar thioredoxin and glutathione pathways. How these systems are linked is poorly understood. Here, we determine that specific disruption of the cytosolic thioredoxin system resulted in constitutive activation of the heat shock response in Saccharomyces cerevisiae and accumulation of the sequestrase Hsp42 into an exaggerated and persistent juxtanuclear quality control (JUNQ) compartment. Terminally misfolded proteins also accumulated in this compartment in thioredoxin reductase (TRR1)-deficient cells, despite apparently normal formation and dissolution of transient cytoplasmic quality control (CytoQ) bodies during heat shock. Notably, cells lacking TRR1 and HSP42 exhibited severe synthetic slow growth exacerbated by oxidative stress, signifying a critical role for Hsp42 under redox-challenged conditions. Finally, we demonstrated that Hsp42 localization patterns in trr1∆ cells mimic those observed in chronically aging and glucose-starved cells, linking nutrient depletion and redox imbalance with management of misfolded proteins via a process of long-term sequestration.
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Affiliation(s)
- Davi Goncalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
| | - Duong Long Duy
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
| | - Sara Peffer
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
- Microbiology and Infectious Disease Program, MD Anderson UTHealth Graduate School at UTHealth Houston, Houston, TX 77030
| | - Kevin A. Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth Houston, Houston, TX 77030
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4
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Suen TC, DeBruyne JP. Lysine-independent ubiquitination and degradation of REV-ERBα involves a bi-functional degradation control sequence at its N-terminus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538963. [PMID: 37205588 PMCID: PMC10187254 DOI: 10.1101/2023.05.01.538963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
REV-ERBα and REV-ERBβ proteins play crucial roles in linking the circadian system to overt daily rhythms in mammalian physiology and behavior. In most tissues, REV-ERBα protein robustly cycles such that it is detected only within a tight interval of 4-6 hours each day, suggesting both its synthesis and degradation are tightly controlled. Several ubiquitin ligases are known to drive REV-ERBα degradation, but how they interact with REV-ERBα and which lysine residues they ubiquitinate to promote degradation are unknown. In this study, we attempted to identify both ubiquitin-ligase-binding and ubiquitination sites within REV-ERBα required for its degradation. Surprisingly, mutating all lysine residues, the common sites for ubiquitin conjugation, in REV-ERBα to arginines (K20R), did very little to impair its degradation in cells. K20R were degraded much faster by co-expression of two E3 ligases, SIAH2 or SPSB4, suggesting possible N-terminal ubiquitination. To explore this, we examined if small deletions at the N-terminus of REV-ERBα would alter its degradation. Interestingly, deletion of amino acid (AA) residues 2 to 9 (delAA2-9) clearly resulted in a less stable REV-ERBα. We found that it was the length (i.e. 8 AA), and not the specific sequence, that confers stability in this region. Simultaneously, we also mapped the interaction site of the E3 ligase SPSB4 to this same region, specifically requiring AA4-9 of REV-ERBα. Thus, the first 9 AA of REV-ERBα has two opposing roles in regulating REV-ERBα turnover. Further, deleting eight additional AAs (delAA2-17) from the N-terminus strongly prevents REV-ERBα degradation. Combined, these results suggest that complex interactions within the first 25AAs potentially act as an endogenous 'switch' that allows REV-ERBα to exist in a stabilized conformation in order to accumulate at one time of day, but then rapidly shifts to a destabilized form, to enhance its removal at the end of its daily cycle.
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5
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Wellington D, Yin Z, Yu Z, Heilig R, Davis S, Fischer R, Felce SL, Antoun E, Hublitz P, Beveridge R, Dong D, Liu G, Yao X, Peng Y, Kessler BM, Dong T. SARS-CoV-2 mutations affect antigen processing by the proteasome to alter CD8 + T cell responses. Heliyon 2023; 9:e20076. [PMID: 37842619 PMCID: PMC10570596 DOI: 10.1016/j.heliyon.2023.e20076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Mutations within viral epitopes can result in escape from T cells, but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two SARS-CoV-2 nucleoprotein CD8+ epitopes, we investigated the contribution of these flanking mutations to proteasomal processing and T cell activation. We found decreased NP9-17-B*27:05 CD8+ T cell responses to the NP-Q7K mutation, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103 N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+ T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on proteasomal processing, either contributing to T cell escape or enhancement that may be exploited for future vaccine design.
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Affiliation(s)
- Dannielle Wellington
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zixi Yin
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zhanru Yu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Simon Davis
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Elie Antoun
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Ryan Beveridge
- Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Yanchun Peng
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Benedikt M. Kessler
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
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6
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Davis C, Spaller BL, Choi E, Kurrasch J, Chong H, Elsasser S, Finley D, Matouschek A. A strict requirement in proteasome substrates for spacing between ubiquitin tag and degradation initiation elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552540. [PMID: 37609285 PMCID: PMC10441315 DOI: 10.1101/2023.08.08.552540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Proteins are typically targeted to the proteasome for degradation through the attachment of ubiquitin chains and the proteasome initiates degradation at a disordered region within the target protein. Yet some proteins with ubiquitin chains and disordered regions escape degradation. Here we investigate how the position of the ubiquitin chain on the target protein relative to the disordered region modulates degradation and show that the distance between the two determines whether a protein is degraded efficiently. This distance depends on the type of the degradation tag and is likely a result of the separation on the proteasome between the receptor that binds the tag and the site that engages the disordered region.
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7
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Collins MA, Avery R, Albert FW. Substrate-specific effects of natural genetic variation on proteasome activity. PLoS Genet 2023; 19:e1010734. [PMID: 37126494 PMCID: PMC10174532 DOI: 10.1371/journal.pgen.1010734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 05/11/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Protein degradation is an essential biological process that regulates protein abundance and removes misfolded and damaged proteins from cells. In eukaryotes, most protein degradation occurs through the stepwise actions of two functionally distinct entities, the ubiquitin system and the proteasome. Ubiquitin system enzymes attach ubiquitin to cellular proteins, targeting them for degradation. The proteasome then selectively binds and degrades ubiquitinated substrate proteins. Genetic variation in ubiquitin system genes creates heritable differences in the degradation of their substrates. However, the challenges of measuring the degradative activity of the proteasome independently of the ubiquitin system in large samples have limited our understanding of genetic influences on the proteasome. Here, using the yeast Saccharomyces cerevisiae, we built and characterized reporters that provide high-throughput, ubiquitin system-independent measurements of proteasome activity. Using single-cell measurements of proteasome activity from millions of genetically diverse yeast cells, we mapped 15 loci across the genome that influence proteasomal protein degradation. Twelve of these 15 loci exerted specific effects on the degradation of two distinct proteasome substrates, revealing a high degree of substrate-specificity in the genetics of proteasome activity. Using CRISPR-Cas9-based allelic engineering, we resolved a locus to a causal variant in the promoter of RPT6, a gene that encodes a subunit of the proteasome's 19S regulatory particle. The variant increases RPT6 expression, which we show results in increased proteasome activity. Our results reveal the complex genetic architecture of proteasome activity and suggest that genetic influences on the proteasome may be an important source of variation in the many cellular and organismal traits shaped by protein degradation.
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Affiliation(s)
- Mahlon A. Collins
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Randi Avery
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Frank W. Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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8
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Grønbæk-Thygesen M, Kampmeyer C, Hofmann K, Hartmann-Petersen R. The moonlighting of RAD23 in DNA repair and protein degradation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194925. [PMID: 36863450 DOI: 10.1016/j.bbagrm.2023.194925] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
A moonlighting protein is one, which carries out multiple, often wholly unrelated, functions. The RAD23 protein is a fascinating example of this, where the same polypeptide and the embedded domains function independently in both nucleotide excision repair (NER) and protein degradation via the ubiquitin-proteasome system (UPS). Hence, through direct binding to the central NER component XPC, RAD23 stabilizes XPC and contributes to DNA damage recognition. Conversely, RAD23 also interacts directly with the 26S proteasome and ubiquitylated substrates to mediate proteasomal substrate recognition. In this function, RAD23 activates the proteolytic activity of the proteasome and engages specifically in well-characterized degradation pathways through direct interactions with E3 ubiquitin-protein ligases and other UPS components. Here, we summarize the past 40 years of research into the roles of RAD23 in NER and the UPS.
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Affiliation(s)
- Martin Grønbæk-Thygesen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark.
| | - Caroline Kampmeyer
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Germany
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark.
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9
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Zhu Y, Saribas AS, Liu J, Lin Y, Bodnar B, Zhao R, Guo Q, Ting J, Wei Z, Ellis A, Li F, Wang X, Yang X, Wang H, Ho WZ, Yang L, Hu W. Protein expression/secretion boost by a novel unique 21-mer cis-regulatory motif (Exin21) via mRNA stabilization. Mol Ther 2023; 31:1136-1158. [PMID: 36793212 PMCID: PMC9927791 DOI: 10.1016/j.ymthe.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/24/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Boosting protein production is invaluable in both industrial and academic applications. We discovered a novel expression-increasing 21-mer cis-regulatory motif (Exin21) that inserts between SARS-CoV-2 envelope (E) protein-encoding sequence and luciferase reporter gene. This unique Exin21 (CAACCGCGGTTCGCGGCCGCT), encoding a heptapeptide (QPRFAAA, designated as Qα), significantly (34-fold on average) boosted E production. Both synonymous and nonsynonymous mutations within Exin21 diminished its boosting capability, indicating the exclusive composition and order of 21 nucleotides. Further investigations demonstrated that Exin21/Qα addition could boost the production of multiple SARS-CoV-2 structural proteins (S, M, and N) and accessory proteins (NSP2, NSP16, and ORF3), and host cellular gene products such as IL-2, IFN-γ, ACE2, and NIBP. Exin21/Qα enhanced the packaging yield of S-containing pseudoviruses and standard lentivirus. Exin21/Qα addition on the heavy and light chains of human anti-SARS-CoV monoclonal antibody robustly increased antibody production. The extent of such boosting varied with protein types, cellular density/function, transfection efficiency, reporter dosage, secretion signaling, and 2A-mediated auto-cleaving efficiency. Mechanistically, Exin21/Qα increased mRNA synthesis/stability, and facilitated protein expression and secretion. These findings indicate that Exin21/Qα has the potential to be used as a universal booster for protein production, which is of importance for biomedicine research and development of bioproducts, drugs, and vaccines.
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Affiliation(s)
- Yuanjun Zhu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - A. Sami Saribas
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Jinbiao Liu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Yuan Lin
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Brittany Bodnar
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ruotong Zhao
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Qian Guo
- Department of Medical Genetics & Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Julia Ting
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Zhengyu Wei
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Aidan Ellis
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Fang Li
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA,Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ling Yang
- Department of Medical Genetics & Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Wenhui Hu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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10
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Hwang J, Peterson BG, Knupp J, Baldridge RD. The ERAD system is restricted by elevated ceramides. SCIENCE ADVANCES 2023; 9:eadd8579. [PMID: 36638172 PMCID: PMC9839339 DOI: 10.1126/sciadv.add8579] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) are removed through a process known as ER-associated degradation (ERAD). ERAD occurs through an integral membrane protein quality control system that recognizes substrates, retrotranslocates the substrates across the membrane, and ubiquitinates and extracts the substrates from the membrane for degradation at the cytosolic proteasome. While ERAD systems are known to regulate lipid biosynthetic enzymes, the regulation of ERAD systems by the lipid composition of cellular membranes remains unexplored. Here, we report that the ER membrane composition influences ERAD function by incapacitating substrate extraction. Unbiased lipidomic profiling revealed that elevation of specific very-long-chain ceramides leads to a marked increase in the level of ubiquitinated substrates in the ER membrane and concomitantly reduces extracted substrates in the cytoplasm. This work reveals a previously unrecognized mechanism in which ER membrane lipid remodeling changes the activity of ERAD.
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Affiliation(s)
- Jiwon Hwang
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Brian G. Peterson
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jeffrey Knupp
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ryan D. Baldridge
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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11
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The Role of Ubiquitin-Proteasome System in the Pathogenesis of Severe Acute Respiratory Syndrome Coronavirus-2 Disease. Int J Inflam 2023; 2023:6698069. [PMID: 36915828 PMCID: PMC10008111 DOI: 10.1155/2023/6698069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/21/2022] [Accepted: 02/22/2023] [Indexed: 03/07/2023] Open
Abstract
Different protein degradation pathways exist in cells. However, the bulk of cellular proteins are degraded by the ubiquitin-proteasome system (UPS), which is one of these pathways. The upkeep of cellular protein homeostasis is facilitated by the ubiquitin-proteasome system, which has a variety of important functions. With the emergence of eukaryotic organisms, the relationship between ubiquitylation and proteolysis by the proteasome became apparent. Severe acute respiratory syndrome coronavirus-2 (SARS-Coronavirus-2) hijacks the ubiquitin-proteasome system and causes their viral proteins to become ubiquitinated, facilitating assembly and budding. Ubiquitination of the enzyme keratin-38 (E-K38) residue gave the virion the ability to engage with at least one putative cellular receptor, T-cell immunoglobin-mucin (TIM-1), boosting virus entry, reproduction, and pathogenesis. A fraction of infectious viral particles produced during replication have been ubiquitinated. The ubiquitin system promotes viral replication. In order to replicate their viral genome after entering the host cell, viruses combine the resources of the host cell with recently generated viral proteins. Additionally, viruses have the ability to encode deubiquitinating (DUB)-active proteins that can boost viral replication through both direct and indirect means. The SARS-Coronavirus-2 papain-like protease (PLpro) protein is a DUB enzyme that is necessary for breaking down viral polyproteins to create a working replicase complex and promote viral propagation. The ubiquitin-like molecule interferon-stimulated gene 15 (ISG15), which is likewise a regulator of the innate immune response and has antiviral characteristics, can also be broken down by this enzyme. However, limiting the E1-activating enzyme's ability to suppress the ubiquitination pathway prevented virus infection but did not prevent viral RNA genome translation. Numerous investigations have revealed that the use of proteasome inhibitors has a detrimental effect on the replication of SARS-Coronavirus-2 and other viruses in the host cell. Studies have shown that the use of proteasome inhibitors is also known to deplete free cellular ubiquitin, which may have an impact on viral replication and other vital cellular functions.
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12
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Jonsson E, Htet ZM, Bard JA, Dong KC, Martin A. Ubiquitin modulates 26 S proteasome conformational dynamics and promotes substrate degradation. SCIENCE ADVANCES 2022; 8:eadd9520. [PMID: 36563145 PMCID: PMC9788759 DOI: 10.1126/sciadv.add9520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
The 26S proteasome recognizes thousands of appropriate protein substrates in eukaryotic cells through attached ubiquitin chains and uses its adenosine triphosphatase (ATPase) motor for mechanical unfolding and translocation into a proteolytic chamber. Here, we used single-molecule Förster resonance energy transfer measurements to monitor the conformational dynamics of the proteasome, observe individual substrates during their progression toward degradation, and elucidate how these processes are regulated by ubiquitin chains. Rapid transitions between engagement- and processing-competent proteasome conformations control substrate access to the ATPase motor. Ubiquitin chain binding functions as an allosteric regulator to slow these transitions, stabilize the engagement-competent state, and aid substrate capture to accelerate degradation initiation. Upon substrate engagement, the proteasome remains in processing-competent states for translocation and unfolding, except for apparent motor slips when encountering stably folded domains. Our studies revealed how ubiquitin chains allosterically regulate degradation initiation, which ensures substrate selectivity in a crowded cellular environment.
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Affiliation(s)
- Erik Jonsson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | | | - Ken C. Dong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
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13
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Handa T, Kundu D, Dubey VK. Perspectives on evolutionary and functional importance of intrinsically disordered proteins. Int J Biol Macromol 2022; 224:243-255. [DOI: 10.1016/j.ijbiomac.2022.10.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
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14
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Wang X, Simon SM, Coffino P. Single-molecule microscopy reveals diverse actions of substrate sequences that impair ClpX AAA+ ATPase function. J Biol Chem 2022; 298:102457. [PMID: 36064000 PMCID: PMC9531181 DOI: 10.1016/j.jbc.2022.102457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 10/28/2022] Open
Abstract
AAA+ (ATPases Associated with diverse cellular Activities) proteases unfold substrate proteins by pulling the substrate polypeptide through a narrow pore. To overcome the barrier to unfolding, substrates may require extended association with the ATPase. Failed unfolding attempts can lead to a slip of grip, which may result in substrate dissociation, but how substrate sequence affects slippage is unresolved. Here, we measured single-molecule dwell time using TIRF (Total Internal Reflection Fluorescence) microscopy, scoring time-dependent dissociation of engaged substrates from bacterial AAA+ ATPase unfoldase/translocase ClpX. Substrates comprising a stable domain resistant to unfolding and a C-terminal unstructured tail, tagged with a degron for initiating translocase insertion, were used to determine dwell time in relation to tail length and composition. We found greater tail length promoted substrate retention during futile unfolding. Additionally, we tested two tail compositions known to frustrate unfolding. A poly-glycine tract (polyG) promoted substrate release, but only when adjacent to the folded domain, whereas glycine-alanine repeats (GAr) did not promote release. A high-complexity motif containing polar and charged residues also promoted release. We further investigated the impact of these and related motifs on substrate degradation rates and ATP consumption, using the unfoldase-protease complex ClpXP. Here, substrate domain stability modulates the effects of substrate tail sequences. Although polyG and GAr are both inhibitory for unfolding, they act in different ways. GAr motifs only negatively affected degradation of highly stable substrates, which is accompanied by reduced ClpXP ATPase activity. Together, our results specify substrate characteristics that affect unfolding and degradation by ClpXP.
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Affiliation(s)
- Xiao Wang
- Laboratory of Cellular Biophysics, The Rockefeller University
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University
| | - Philip Coffino
- Laboratory of Cellular Biophysics, The Rockefeller University.
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15
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Rethi-Nagy Z, Abraham E, Udvardy K, Klement E, Darula Z, Pal M, Katona RL, Tubak V, Pali T, Kota Z, Sinka R, Udvardy A, Lipinszki Z. STABILON, a Novel Sequence Motif That Enhances the Expression and Accumulation of Intracellular and Secreted Proteins. Int J Mol Sci 2022; 23:ijms23158168. [PMID: 35897744 PMCID: PMC9332151 DOI: 10.3390/ijms23158168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
The dynamic balance of transcriptional and translational regulation together with degron-controlled proteolysis shapes the ever-changing cellular proteome. While a large variety of degradation signals has been characterized, our knowledge of cis-acting protein motifs that can in vivo stabilize otherwise short-lived proteins is very limited. We have identified and characterized a conserved 13-mer protein segment derived from the p54/Rpn10 ubiquitin receptor subunit of the Drosophila 26S proteasome, which fulfills all the characteristics of a protein stabilization motif (STABILON). Attachment of STABILON to various intracellular as well as medically relevant secreted model proteins resulted in a significant increase in their cellular or extracellular concentration in mammalian cells. We demonstrate that STABILON acts as a universal and dual function motif that, on the one hand, increases the concentration of the corresponding mRNAs and, on the other hand, prevents the degradation of short-lived fusion proteins. Therefore, STABILON may lead to a breakthrough in biomedical recombinant protein production.
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Affiliation(s)
- Zsuzsanna Rethi-Nagy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Edit Abraham
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | - Katalin Udvardy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | - Eva Klement
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), H-6726 Szeged, Hungary; (E.K.); (Z.D.)
- Biological Research Centre, Laboratory of Proteomics Research, ELKH, H-6726 Szeged, Hungary
| | - Zsuzsanna Darula
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), H-6726 Szeged, Hungary; (E.K.); (Z.D.)
- Biological Research Centre, Laboratory of Proteomics Research, ELKH, H-6726 Szeged, Hungary
| | - Margit Pal
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | | | - Vilmos Tubak
- Creative Laboratory Ltd., H-6726 Szeged, Hungary;
| | - Tibor Pali
- Biological Research Centre, Institute of Biophysics, ELKH, H-6726 Szeged, Hungary; (T.P.); (Z.K.)
| | - Zoltan Kota
- Biological Research Centre, Institute of Biophysics, ELKH, H-6726 Szeged, Hungary; (T.P.); (Z.K.)
| | - Rita Sinka
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Correspondence: (R.S.); (A.U.); (Z.L.)
| | - Andor Udvardy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Correspondence: (R.S.); (A.U.); (Z.L.)
| | - Zoltan Lipinszki
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Correspondence: (R.S.); (A.U.); (Z.L.)
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16
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Singh Gautam AK, Yu H, Yellman C, Elcock AH, Matouschek A. Design principles that protect the proteasome from self-destruction. Protein Sci 2022; 31:556-567. [PMID: 34878680 PMCID: PMC8862440 DOI: 10.1002/pro.4251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 11/07/2022]
Abstract
The proteasome is a powerful intracellular protease that can degrade effectively any protein, self or foreign, for regulation, quality control, or immune response. Proteins are targeted for degradation by localizing them to the proteasome, typically by ubiquitin tags. At the same time, the proteasome is built from ~33 subunits, and their assembly into the complex and activity are tuned by post-translational modifications on long disordered regions on the subunits. Molecular modeling and biochemical experiments show that some of the disordered regions of proteasomal subunits can access the substrate recognition sites. All disordered regions tested, independent of location, are constructed from amino acid sequences that escape recognition. Replacing a disordered region with a sequence that is recognized by the proteasome leads to self-degradation and, in the case of an essential subunit, cell death.
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Affiliation(s)
| | - Houqing Yu
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTexasUSA
| | - Christopher Yellman
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTexasUSA
| | - Adrian H. Elcock
- Department of Biochemistry, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Andreas Matouschek
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTexasUSA
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17
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Tomita T. Structural and biochemical elements of efficiently degradable proteasome substrates. J Biochem 2021; 171:261-268. [PMID: 34967398 DOI: 10.1093/jb/mvab157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/14/2021] [Indexed: 11/14/2022] Open
Abstract
Most regulated proteolysis in cells is conducted by the ubiquitin-proteasome system, in which proteins to be eliminated are selected through multiple steps to achieve high specificity. The large protease complex proteasome binds to ubiquitin molecules that are attached to the substrate and further interacts with a disordered region in the target to initiate unfolding for degradation. Recent studies have expanded our view of the complexity of ubiquitination as well as the details of substrate engagement by the proteasome and at the same time have suggested the characteristics of substrates that are susceptible to proteasomal degradation. Here, I review some destabilizing elements of proteasome substrates with particular attention to ubiquitination, initiation region and stability against unfolding and discuss their interplay to determine the substrate stability. A spatial perspective is important to understand the mechanism of action of proteasomal degradation, which may be critical for drug development targeting the ubiquitin-proteasome system including targeted protein degradation.
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Affiliation(s)
- Takuya Tomita
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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18
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Chen X, Htet ZM, López-Alfonzo E, Martin A, Walters KJ. Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies. FEBS J 2021; 288:5231-5251. [PMID: 33211406 PMCID: PMC8131406 DOI: 10.1111/febs.15638] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022]
Abstract
The 26S proteasome is responsible for regulated proteolysis in eukaryotic cells. Its substrates are diverse in structure, function, sequence length, and amino acid composition, and are targeted to the proteasome by post-translational modification with ubiquitin. Ubiquitination occurs through a complex enzymatic cascade and can also signal for other cellular events, unrelated to proteasome-catalyzed degradation. Like other post-translational protein modifications, ubiquitination is reversible, with ubiquitin chain hydrolysis catalyzed by the action of deubiquitinating enzymes (DUBs), ~ 90 of which exist in humans and allow for temporal events and dynamic ubiquitin-chain remodeling. DUBs have been known for decades to be an integral part of the proteasome, as deubiquitination is coupled to substrate unfolding and translocation into the internal degradation chamber. Moreover, the proteasome also binds several ubiquitinating enzymes and shuttle factors that recruit ubiquitinated substrates. The role of this intricate machinery and how ubiquitinated substrates interact with proteasomes remains an area of active investigation. Here, we review what has been learned about the mechanisms used by the proteasome to bind ubiquitinated substrates, substrate shuttle factors, ubiquitination machinery, and DUBs. We also discuss many open questions that require further study or the development of innovative approaches to be answered. Finally, we address the promise of expanded therapeutic targeting that could benefit from such new discoveries.
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Affiliation(s)
- Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
| | - Erika López-Alfonzo
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California at Berkeley, CA, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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19
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Cascarina SM, Kaplan JP, Elder MR, Brookbank L, Ross ED. Generalizable Compositional Features Influencing the Proteostatic Fates of Polar Low-Complexity Domains. Int J Mol Sci 2021; 22:ijms22168944. [PMID: 34445649 PMCID: PMC8396281 DOI: 10.3390/ijms22168944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Protein aggregation is associated with a growing list of human diseases. A substantial fraction of proteins in eukaryotic proteomes constitutes a proteostasis network—a collection of proteins that work together to maintain properly folded proteins. One of the overarching functions of the proteostasis network is the prevention or reversal of protein aggregation. How proteins aggregate in spite of the anti-aggregation activity of the proteostasis machinery is incompletely understood. Exposed hydrophobic patches can trigger degradation by the ubiquitin-proteasome system, a key branch of the proteostasis network. However, in a recent study, we found that model glycine (G)-rich or glutamine/asparagine (Q/N)-rich prion-like domains differ in their susceptibility to detection and degradation by this system. Here, we expand upon this work by examining whether the features controlling the degradation of our model prion-like domains generalize broadly to G-rich and Q/N-rich domains. Experimentally, native yeast G-rich domains in isolation are sensitive to the degradation-promoting effects of hydrophobic residues, whereas native Q/N-rich domains completely resist these effects and tend to aggregate instead. Bioinformatic analyses indicate that native G-rich domains from yeast and humans tend to avoid degradation-promoting features, suggesting that the proteostasis network may act as a form of selection at the molecular level that constrains the sequence space accessible to G-rich domains. However, the sensitivity or resistance of G-rich and Q/N-rich domains, respectively, was not always preserved in their native protein contexts, highlighting that proteins can evolve other sequence features to overcome the intrinsic sensitivity of some LCDs to degradation.
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20
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Davis C, Spaller BL, Matouschek A. Mechanisms of substrate recognition by the 26S proteasome. Curr Opin Struct Biol 2021; 67:161-169. [PMID: 33296738 PMCID: PMC8096638 DOI: 10.1016/j.sbi.2020.10.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
The majority of regulated protein degradation in eukaryotes is accomplished by the 26S proteasome, the large proteolytic complex responsible for removing regulatory proteins and damaged proteins. Proteins are targeted to the proteasome by ubiquitination, and degradation is initiated at a disordered region within the protein. The ability of the proteasome to precisely select which proteins to break down is necessary for cellular functioning. Recent studies reveal the subtle mechanisms of substrate recognition by the proteasome - diverse ubiquitin chains can act as potent proteasome targeting signals, ubiquitin receptors function uniquely and cooperatively, and modification of initiation regions modulate degradation. Here, we summarize recent findings illuminating the nature of substrate recognition by the proteasome.
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Affiliation(s)
- Caroline Davis
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brian Logan Spaller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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21
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Correa Marrero M, Barrio-Hernandez I. Toward Understanding the Biochemical Determinants of Protein Degradation Rates. ACS OMEGA 2021; 6:5091-5100. [PMID: 33681549 PMCID: PMC7931188 DOI: 10.1021/acsomega.0c05318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Protein degradation is a key component of the regulation of gene expression and is at the center of several pathogenic processes. Proteins are regularly degraded, but there is large variation in their lifetimes, and the kinetics of protein degradation are not well understood. Many different factors can influence protein degradation rates, painting a highly complex picture. This has been partially unravelled in recent years thanks to invaluable advances in proteomics techniques. In this Mini-Review, we give a global vision of the determinants of protein degradation rates with the backdrop of the current understanding of proteolytic systems to give a contemporary view of the field.
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Affiliation(s)
- Miguel Correa Marrero
- European
Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10
1SD, United Kingdom
| | - Inigo Barrio-Hernandez
- European
Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10
1SD, United Kingdom
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22
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Burris A, Waite KA, Reuter Z, Ockerhausen S, Roelofs J. Proteasome activator Blm10 levels and autophagic degradation directly impact the proteasome landscape. J Biol Chem 2021; 296:100468. [PMID: 33639167 PMCID: PMC8039559 DOI: 10.1016/j.jbc.2021.100468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/12/2021] [Accepted: 02/23/2021] [Indexed: 12/09/2022] Open
Abstract
The proteasome selectively degrades proteins. It consists of a core particle (CP), which contains proteolytic active sites that can associate with different regulators to form various complexes. How these different complexes are regulated and affected by changing physiological conditions, however, remains poorly understood. In this study, we focused on the activator Blm10 and the regulatory particle (RP). In yeast, increased expression of Blm10 outcompeted RP for CP binding, which suggests that controlling the cellular levels of Blm10 can affect the relative amounts of RP-bound CP. While strong overexpression of BLM10 almost eliminated the presence of RP-CP complexes, the phenotypes this should induce were not observed. Our results show this was due to the induction of Blm10-CP autophagy under prolonged growth in YPD. Similarly, under conditions of endogenous BLM10 expression, Blm10 was degraded through autophagy as well. This suggests that reducing the levels of Blm10 allows for more CP-binding surfaces and the formation of RP-CP complexes under nutrient stress. This work provides important insights into maintaining the proteasome landscape and how protein expression levels affect proteasome function.
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Affiliation(s)
- Alicia Burris
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kenrick A Waite
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Zachary Reuter
- Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Samuel Ockerhausen
- Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA.
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23
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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24
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Gaynor AS, Chen W. Conditional Protein Rescue by Binding-Induced Protective Shielding. ACS Synth Biol 2020; 9:2639-2647. [PMID: 33025786 DOI: 10.1021/acssynbio.0c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic protein-level circuits offer an extra layer of cellular control on top of conventional gene-level circuits. Here, we describe a technology that allows conditional protein rescue (CPR) from proteasomal degradation using different protein inputs as masking agents. A target protein is fused to a degron tag and an affinity sensor domain. The use of nanobodies as the sensor domain offers a generalizable strategy to execute a wide range of protein-level circuits with ease. The utility of this new strategy was successfully demonstrated to distinguish cancer cells out of a healthy population using the HPV-specific E7 protein as a cellular marker. Because CPR can be programmed to execute more complex Boolean logic designs using cell-specific proteomes, this platform offers a highly modular and scalable framework for a wide range of applications based on synthetic protein circuits.
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Affiliation(s)
- Andrew S. Gaynor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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25
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A masked initiation region in retinoblastoma protein regulates its proteasomal degradation. Nat Commun 2020; 11:2019. [PMID: 32332747 PMCID: PMC7181824 DOI: 10.1038/s41467-020-16003-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/01/2020] [Indexed: 12/03/2022] Open
Abstract
Retinoblastoma protein (Rb) is a tumor suppressor that binds and represses E2F transcription factors. In cervical cancer cells, human papilloma virus (HPV) protein E7 binds to Rb, releasing it from E2F to promote cell cycle progression, and inducing ubiquitination of Rb. E7-mediated proteasomal degradation of Rb requires action by another protease, calpain, which cleaves Rb after Lys 810. However, it is not clear why cleavage is required for Rb degradation. Here, we report that the proteasome cannot initiate degradation efficiently on full-length Rb. Calpain cleavage exposes a region that is recognized by the proteasome, leading to rapid proteolysis of Rb. These findings identify a mechanism for regulating protein stability by controlling initiation and provide a better understanding of the molecular mechanism underlying transformation by HPV. Human papilloma virus (HPV) E7 protein destabilizes the retinoblastoma protein (Rb) by inducing its ubiquitination in cervical cancer cells, however proteasomal degradation requires cleavage of Rb after Lys 810 and so far it has been unclear how Rb cleavage contributes to its degradation. Here, the authors combine cell based and in vitro assays and show that calpain cleavage exposes a region in Rb that is recognized by the proteasome, leading to rapid proteolysis of Rb, whereas the proteasome cannot initiate degradation efficiently on full-length Rb.
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The proteasome 19S cap and its ubiquitin receptors provide a versatile recognition platform for substrates. Nat Commun 2020; 11:477. [PMID: 31980598 PMCID: PMC6981147 DOI: 10.1038/s41467-019-13906-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/20/2019] [Indexed: 01/28/2023] Open
Abstract
Proteins are targeted to the proteasome by the attachment of ubiquitin chains, which are markedly varied in structure. Three proteasome subunits–Rpn10, Rpn13, and Rpn1–can recognize ubiquitin chains. Here we report that proteins with single chains of K48-linked ubiquitin are targeted for degradation almost exclusively through binding to Rpn10. Rpn1 can act as a co-receptor with Rpn10 for K63 chains and for certain other chain types. Differences in targeting do not correlate with chain affinity to receptors. Surprisingly, in steady-state assays Rpn13 retarded degradation of various single-chain substrates. Substrates with multiple short ubiquitin chains can be presented for degradation by any of the known receptors, whereas those targeted to the proteasome through a ubiquitin-like domain are degraded most efficiently when bound by Rpn13 or Rpn1. Thus, the proteasome provides an unexpectedly versatile binding platform that can recognize substrates targeted for degradation by ubiquitin chains differing greatly in length and topology. Ubiquitylated proteins are degraded by the proteasome and the three proteasome subunits Rpn10, Rpn13 and Rpn1 recognize ubiquitin chains. Here the authors employ biochemical and kinetic assays and characterise the ubiquitin chain type specificities of these three ubiquitin receptors.
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Finley D, Prado MA. The Proteasome and Its Network: Engineering for Adaptability. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033985. [PMID: 30833452 DOI: 10.1101/cshperspect.a033985] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteasome, the most complex protease known, degrades proteins that have been conjugated to ubiquitin. It faces the unique challenge of acting enzymatically on hundreds and perhaps thousands of structurally diverse substrates, mechanically unfolding them from their native state and translocating them vectorially from one specialized compartment of the enzyme to another. Moreover, substrates are modified by ubiquitin in myriad configurations of chains. The many unusual design features of the proteasome may have evolved in part to endow this enzyme with a robust ability to process substrates regardless of their identity. The proteasome plays a major role in preserving protein homeostasis in the cell, which requires adaptation to a wide variety of stress conditions. Modulation of proteasome function is achieved through a large network of proteins that interact with it dynamically, modify it enzymatically, or fine-tune its levels. The resulting adaptability of the proteasome, which is unique among proteases, enables cells to control the output of the ubiquitin-proteasome pathway on a global scale.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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Eldeeb MA, Siva-Piragasam R, Ragheb MA, Esmaili M, Salla M, Fahlman RP. A molecular toolbox for studying protein degradation in mammalian cells. J Neurochem 2019; 151:520-533. [PMID: 31357232 DOI: 10.1111/jnc.14838] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/14/2022]
Abstract
Protein degradation is a crucial regulatory process in maintaining cellular proteostasis. The selective degradation of intracellular proteins controls diverse cellular and biochemical processes in all kingdoms of life. Targeted protein degradation is implicated in controlling the levels of regulatory proteins as well as eliminating misfolded and any otherwise abnormal proteins. Deregulation of protein degradation is concomitant with the progression of various neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. Thus, methods of measuring metabolic half-lives of proteins greatly influence our understanding of the diverse functions of proteins in mammalian cells including neuronal cells. Historically, protein degradation rates have been studied via exploiting methods that estimate overall protein degradation or focus on few individual proteins. Notably, with the recent technical advances and developments in proteomic and imaging techniques, it is now possible to measure degradation rates of a large repertoire of defined proteins and analyze the degradation profile in a detailed spatio-temporal manner, with the aim of determining proteome-wide protein stabilities upon different physiological conditions. Herein, we discuss some of the classical and novel methods for determining protein degradation rates highlighting the crucial role of some state of art approaches in deciphering the global impact of dynamic nature of targeted degradation of cellular proteins. This article is part of the Special Issue "Proteomics".
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Affiliation(s)
- Mohamed A Eldeeb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt.,Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mohamed Salla
- Department of Biological Sciences, Lebanese International University, Bekaa, Lebanon
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Coll-Martínez B, Crosas B. How the 26S Proteasome Degrades Ubiquitinated Proteins in the Cell. Biomolecules 2019; 9:biom9090395. [PMID: 31443414 PMCID: PMC6770211 DOI: 10.3390/biom9090395] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 01/12/2023] Open
Abstract
The 26S proteasome is the central element of proteostasis regulation in eukaryotic cells, it is required for the degradation of protein factors in multiple cellular pathways and it plays a fundamental role in cell stability. The main aspects of proteasome mediated protein degradation have been highly (but not totally) described during three decades of intense cellular, molecular, structural and chemical biology research and tool development. Contributions accumulated within this time lapse allow researchers today to go beyond classical partial views of the pathway, and start generating almost complete views of how the proteasome acts inside the cell. These views have been recently reinforced by cryo-electron microscopy and mechanistic works that provide from landscapes of proteasomal populations distributed in distinct intracellular contexts, to detailed shots of each step of the process of degradation of a given substrate, of the factors that regulate it, and precise measurements of the speed of degradation. Here, we present an updated digest of the most recent developments that significantly contribute in our understanding of how the 26S proteasome degrades hundreds of ubiquitinated substrates in multiple intracellular environments.
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Affiliation(s)
- Bernat Coll-Martínez
- Department of Cell Biology, Institute of Molecular Biology of Barcelona (IBMB), Consejo Superior de investigaciones Científicas (CSIC), Baldiri i Reixac 4-10, 08028 Barcelona, Spain
- Institut Químic de Sarrià (IQS), School of Engineering, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Bernat Crosas
- Department of Cell Biology, Institute of Molecular Biology of Barcelona (IBMB), Consejo Superior de investigaciones Científicas (CSIC), Baldiri i Reixac 4-10, 08028 Barcelona, Spain.
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Proteasome Activation to Combat Proteotoxicity. Molecules 2019; 24:molecules24152841. [PMID: 31387243 PMCID: PMC6696185 DOI: 10.3390/molecules24152841] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Loss of proteome fidelity leads to the accumulation of non-native protein aggregates and oxidatively damaged species: hallmarks of an aged cell. These misfolded and aggregated species are often found, and suggested to be the culpable party, in numerous neurodegenerative diseases including Huntington's, Parkinson's, Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Diseases (AD). Many strategies for therapeutic intervention in proteotoxic pathologies have been put forth; one of the most promising is bolstering the efficacy of the proteasome to restore normal proteostasis. This strategy is ideal as monomeric precursors and oxidatively damaged proteins, so called "intrinsically disordered proteins" (IDPs), are targeted by the proteasome. This review will provide an overview of disorders in proteins, both intrinsic and acquired, with a focus on susceptibility to proteasomal degradation. We will then examine the proteasome with emphasis on newly published structural data and summarize current known small molecule proteasome activators.
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31
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Hacker K, Benke S, Agerer B, Scinicariello S, Budroni V, Versteeg GA. A repetitive acidic region contributes to the extremely rapid degradation of the cell-context essential protein TRIM52. Sci Rep 2019; 9:7901. [PMID: 31133683 PMCID: PMC6536530 DOI: 10.1038/s41598-019-44359-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022] Open
Abstract
Tripartite motif protein 52 (TRIM52) is a non-canonical TRIM family member harbouring the largest RING domain encoded in the human genome. In humans TRIM52 is conserved and has been under positive selection pressure, yet it has been lost in many non-primates. Competitive cell fitness assays demonstrated that TRIM52 ablation reduces cellular fitness in multiple different cell types. To better understand how this cell-essential factor is controlled, we investigated how expression of this non-canonical protein is regulated. Here, we show that TRIM52 mRNA is constitutively expressed from an intergenic region preceding the TRIM52 gene. Yet, TRIM52 protein is rapidly turned-over by the proteasome with a 3.5-minute half-life, one of the shortest in the human proteome. Consistent with this extremely rapid degradation rate, all three TRIM52 domains were identified to contribute to its instability. Intriguingly, a repetitive acidic loop in the RING domain was identified as one of the main destabilizing regions, which was unexpected given the prevailing notion that these sequences are poor proteasome substrates. This work indicates that the effect of such repetitive acidic regions on proteasomal degradation depends on the protein context, and it identifies TRIM52 as an attractive model protein to study what these contextual properties are.
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Affiliation(s)
- Kathrin Hacker
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Stefan Benke
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Benedikt Agerer
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT25.3, 1090, Vienna, Austria
| | - Sara Scinicariello
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Valentina Budroni
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Gijs A Versteeg
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
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32
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Tomita T, Matouschek A. Substrate selection by the proteasome through initiation regions. Protein Sci 2019; 28:1222-1232. [PMID: 31074920 DOI: 10.1002/pro.3642] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/04/2023]
Abstract
Proteins in the cell have to be eliminated once their function is no longer desired or they become damaged. Most regulated protein degradation is achieved by a large enzymatic complex called the proteasome. Many proteasome substrates are targeted for degradation by the covalent attachment of ubiquitin molecules. Ubiquitinated proteins can be bound by the proteasome, but for proteolysis to occur the proteasome needs to find a disordered tail somewhere in the target at which it initiates degradation. The initiation step contributes to the specificity of proteasomal degradation. Here, we review how the proteasome selects initiation sites within its substrates and discuss how the initiation step affects physiological processes.
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Affiliation(s)
- Takuya Tomita
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712
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Singh Gautam AK, Martinez-Fonts K, Matouschek A. Scalable In Vitro Proteasome Activity Assay. Methods Mol Biol 2019; 1844:321-341. [PMID: 30242719 DOI: 10.1007/978-1-4939-8706-1_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We developed a degradation assay based on fluorescent protein substrates that are efficiently recognized, unfolded, translocated, and hydrolyzed by the proteasome. The substrates consist of three components: a proteasome-binding tag, a folded domain, and an initiation region. All the components of the model substrate can be changed to modulate degradation, and the assay can be performed in parallel in 384-well plates. These properties allow the assay to be used to explore a wide range of experimental conditions and to screen proteasome modulators.
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Affiliation(s)
| | - Kirby Martinez-Fonts
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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35
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Sharma R, Demény M, Ambrus V, Király SB, Kurtán T, Gatti-Lafranconi P, Fuxreiter M. Specific and Fuzzy Interactions Cooperate in Modulating Protein Half-Life. J Mol Biol 2019; 431:1700-1707. [PMID: 30790629 DOI: 10.1016/j.jmb.2019.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/24/2019] [Accepted: 02/03/2019] [Indexed: 11/29/2022]
Abstract
Protein degradation is critical for maintaining cellular homeostasis. The 20S proteasome is selective for unfolded, extended polypeptide chains without ubiquitin tags. Sequestration of such segments by protein partners, however, may provide a regulatory mechanism. Here we used the AP-1 complex to study how c-Fos turnover is controlled by interactions with c-Jun. We show that heterodimerization with c-Jun increases c-Fos half-life. Mutations affecting specific contact sites (L165V, L172V) or charge separation (E175D, E189D, K190R) with c-Jun both modulate c-Fos turnover, proportionally to their impact on binding affinity. The fuzzy tail beyond the structured b-HLH/ZIP domain (~165 residues) also contributes to the stabilization of the AP-1 complex, removal of which decreases c-Fos half-life. Thus, protein turnover by 20S proteasome is fine-tuned by both specific and fuzzy interactions, consistently with the previously proposed "nanny" model.
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Affiliation(s)
- Rashmi Sharma
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Máté Demény
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Viktor Ambrus
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | | | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, Debrecen, Hungary
| | | | - Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary.
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36
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Bard JAM, Bashore C, Dong KC, Martin A. The 26S Proteasome Utilizes a Kinetic Gateway to Prioritize Substrate Degradation. Cell 2019; 177:286-298.e15. [PMID: 30929903 DOI: 10.1016/j.cell.2019.02.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/22/2018] [Accepted: 02/19/2019] [Indexed: 11/28/2022]
Abstract
The 26S proteasome is the principal macromolecular machine responsible for protein degradation in eukaryotes. However, little is known about the detailed kinetics and coordination of the underlying substrate-processing steps of the proteasome, and their correlation with observed conformational states. Here, we used reconstituted 26S proteasomes with unnatural amino-acid-attached fluorophores in a series of FRET- and anisotropy-based assays to probe substrate-proteasome interactions, the individual steps of the processing pathway, and the conformational state of the proteasome itself. We develop a complete kinetic picture of proteasomal degradation, which reveals that the engagement steps prior to substrate commitment are fast relative to subsequent deubiquitination, translocation, and unfolding. Furthermore, we find that non-ideal substrates are rapidly rejected by the proteasome, which thus employs a kinetic proofreading mechanism to ensure degradation fidelity and substrate prioritization.
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Affiliation(s)
- Jared A M Bard
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Charlene Bashore
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Ken C Dong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA.
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37
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Kim Y, Furman CM, Manhart CM, Alani E, Finkelstein I. Intrinsically disordered regions regulate both catalytic and non-catalytic activities of the MutLα mismatch repair complex. Nucleic Acids Res 2019; 47:1823-1835. [PMID: 30541127 PMCID: PMC6393296 DOI: 10.1093/nar/gky1244] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Intrinsically disordered regions (IDRs) are present in at least 30% of the eukaryotic proteome and are enriched in chromatin-associated proteins. Using a combination of genetics, biochemistry and single-molecule biophysics, we characterize how IDRs regulate the functions of the yeast MutLα (Mlh1-Pms1) mismatch repair (MMR) complex. Shortening or scrambling the IDRs in both subunits ablates MMR in vivo. Mlh1-Pms1 complexes with shorter IDRs that disrupt MMR retain wild-type DNA binding affinity but are impaired for diffusion on both naked and nucleosome-coated DNA. Moreover, the IDRs also regulate the adenosine triphosphate hydrolysis and nuclease activities that are encoded in the structured N- and C-terminal domains of the complex. This combination of phenotypes underlies the catastrophic MMR defect seen with the mutant MutLα in vivo. More broadly, this work highlights an unanticipated multi-functional role for IDRs in regulating both facilitated diffusion on chromatin and nucleolytic processing of a DNA substrate.
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Affiliation(s)
- Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Carol M Manhart
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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Kudriaeva A, Kuzina ES, Zubenko O, Smirnov IV, Belogurov A. Charge‐mediated proteasome targeting. FASEB J 2019; 33:6852-6866. [DOI: 10.1096/fj.201802237r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Ekaterina S. Kuzina
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Oleg Zubenko
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
- Kazan Federal UniversityKazanRussian Federation
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
- Department of Fundamental MedicineLomonosov Moscow State UniversityMoscowRussian Federation
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Olszewski MM, Williams C, Dong KC, Martin A. The Cdc48 unfoldase prepares well-folded protein substrates for degradation by the 26S proteasome. Commun Biol 2019; 2:29. [PMID: 30675527 PMCID: PMC6340886 DOI: 10.1038/s42003-019-0283-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/28/2018] [Indexed: 11/09/2022] Open
Abstract
Cdc48/p97 is an essential and highly conserved AAA+ ATPase that uses its protein-unfoldase activity to extract ubiquitinated polypeptides from macromolecular complexes and membranes. This motor has also been implicated in protein-degradation pathways, yet its exact role in acting upstream of the 26S proteasome remains elusive. Ubiquitinated proteins destined for degradation by the proteasome require an unstructured initiation region to engage with the proteasomal translocation machinery, and Cdc48 was proposed to generate these unfolded segments, yet direct evidence has been missing. Here, we used an in vitro reconstituted system to demonstrate the collaboration of Cdc48 and the 26S proteasome from S. cerevisiae in degrading ubiquitinated, well-folded proteins that lack unstructured segments. Our data indicate that a critical role for Cdc48 in the ubiquitin-proteasome system is to create flexible initiation regions in compact substrates that otherwise would be refractory to engagement and degradation by the proteasome.
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Affiliation(s)
- Michal M. Olszewski
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 USA
| | - Cameron Williams
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 USA
- Biophysics Graduate Group, University of California, Berkeley, CA 94720 USA
| | - Ken C. Dong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720 USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720 USA
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40
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Structure and mechanism of the ESCRT pathway AAA+ ATPase Vps4. Biochem Soc Trans 2019; 47:37-45. [PMID: 30647138 PMCID: PMC6393862 DOI: 10.1042/bst20180260] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 10/24/2018] [Accepted: 10/29/2018] [Indexed: 01/05/2023]
Abstract
The progression of ESCRT (Endosomal Sorting Complexes Required for Transport) pathways, which mediate numerous cellular membrane fission events, is driven by the enzyme Vps4. Understanding of Vps4 mechanism is, therefore, of fundamental importance in its own right and, moreover, it is highly relevant to the understanding of many related AAA+ ATPases that function in multiple facets of cell biology. Vps4 unfolds its ESCRT-III protein substrates by translocating them through its central hexameric pore, thereby driving membrane fission and recycling of ESCRT-III subunits. This mini-review focuses on recent advances in Vps4 structure and mechanism, including ideas about how Vps4 translocates and unfolds ESCRT-III subunits. Related AAA+ ATPases that share structural features with Vps4 and likely utilize an equivalent mechanism are also discussed.
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41
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Demasi M, da Cunha FM. The physiological role of the free 20S proteasome in protein degradation: A critical review. Biochim Biophys Acta Gen Subj 2018; 1862:2948-2954. [PMID: 30297324 DOI: 10.1016/j.bbagen.2018.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/27/2018] [Accepted: 09/12/2018] [Indexed: 01/26/2023]
Abstract
BACKGROUND It has been almost three decades since the removal of oxidized proteins by the free 20S catalytic unit of the proteasome (20SPT) was proposed. Since then, experimental evidence suggesting a physiological role of proteolysis mediated by the free 20SPT has being gathered. SCOPE OF REVIEW Experimental data that favors the hypothesis of free 20SPT as playing a role in proteolysis are critically reviewed. MAJOR CONCLUSIONS Protein degradation by the proteasome may proceed through multiple proteasome complexes with different requirements though the unequivocal role of the free 20SPT in cellular proteolysis towards native or oxidized proteins remains to be demonstrated. GENERAL SIGNIFICANCE The biological significance of proteolysis mediated by the free 20SPT has been elusive since its discovery. The present review critically analyzes the available experimental data supporting the proteolytic role of the free or single capped 20SPT.
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Affiliation(s)
- Marilene Demasi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, SP, Brazil.
| | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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Inobe T, Tsukamoto M, Nozaki M. Proteasome-mediated protein degradation is enhanced by fusion ubiquitin with unstructured degron. Biochem Biophys Res Commun 2018; 501:948-954. [PMID: 29777695 DOI: 10.1016/j.bbrc.2018.05.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 11/28/2022]
Abstract
Methods to induce proteasomal degradation of unwanted proteins are valuable in biomedical studies and thus receive increasing attention. For efficient degradation, the proteasome requires both a ubiquitin tag, which delivers substrates to the proteasome, and an unstructured region, where the proteasome engages the substrate for unfolding and degradation. We fused two degron components into a single molecule to create a fusion protein comprising ubiquitin and Rpn4-derived unstructured region. We demonstrated that the fusion protein retained its function to polyubiquitinate target proteins, thereby inducing more efficient proteasomal target degradation than wild-type ubiquitin in vitro and in cells. These results provide novel strategies for robust degradation enhancement of polyubiquitinated proteins.
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Affiliation(s)
- Tomonao Inobe
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan; Graduate School of Innovative Life Sciences, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan.
| | - Masayuki Tsukamoto
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
| | - Miyuki Nozaki
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
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43
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Bard JAM, Goodall EA, Greene ER, Jonsson E, Dong KC, Martin A. Structure and Function of the 26S Proteasome. Annu Rev Biochem 2018; 87:697-724. [PMID: 29652515 DOI: 10.1146/annurev-biochem-062917-011931] [Citation(s) in RCA: 437] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As the endpoint for the ubiquitin-proteasome system, the 26S proteasome is the principal proteolytic machine responsible for regulated protein degradation in eukaryotic cells. The proteasome's cellular functions range from general protein homeostasis and stress response to the control of vital processes such as cell division and signal transduction. To reliably process all the proteins presented to it in the complex cellular environment, the proteasome must combine high promiscuity with exceptional substrate selectivity. Recent structural and biochemical studies have shed new light on the many steps involved in proteasomal substrate processing, including recognition, deubiquitination, and ATP-driven translocation and unfolding. In addition, these studies revealed a complex conformational landscape that ensures proper substrate selection before the proteasome commits to processive degradation. These advances in our understanding of the proteasome's intricate machinery set the stage for future studies on how the proteasome functions as a major regulator of the eukaryotic proteome.
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Affiliation(s)
- Jared A M Bard
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Ellen A Goodall
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Eric R Greene
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Erik Jonsson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
| | - Ken C Dong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
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44
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Kandasamy G, Andréasson C. Hsp70-Hsp110 chaperones deliver ubiquitin dependent and independent substrates to the 26S proteasome for proteolysis. J Cell Sci 2018; 131:jcs.210948. [DOI: 10.1242/jcs.210948] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/14/2018] [Indexed: 02/01/2023] Open
Abstract
In protein quality control, proteotoxic misfolded proteins are recognized by molecular chaperones, ubiquitylated by dedicated quality-control ligases and delivered to 26S proteasome for degradation. The chaperone Hsp70 and its nucleotide exchange factor Hsp110 functions in the degradation of misfolded proteins by the ubiquitin-proteasome system via poorly understood mechanisms. Here we report that yeast Hsp110 (Sse1 and Sse2) functions in the degradation of Hsp70-associated ubiquitin conjugates at the post-ubiquitylation step and is required for the proteasomal degradation of ubiquitin-independent substrates. Hsp110 associates with the 19S regulatory particle of the 26S proteasome and interacts with Hsp70 to facilitate the delivery of Hsp70 substrates for proteasomal degradation. Using a highly defined ubiquitin-independent proteasome substrate we show that the mere introduction of a single Hsp70-binding site renders its degradation dependent on Hsp110. The findings define a dedicated and chaperone-dependent pathway for the efficient shuttling of cellular proteins to the proteasome with profound implications for understanding protein quality control and cellular stress management.
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Affiliation(s)
- Ganapathi Kandasamy
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
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45
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Oh JH, Chen SJ, Varshavsky A. A reference-based protein degradation assay without global translation inhibitors. J Biol Chem 2017; 292:21457-21465. [PMID: 29122887 DOI: 10.1074/jbc.m117.814236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/05/2017] [Indexed: 11/06/2022] Open
Abstract
Although it is widely appreciated that the use of global translation inhibitors, such as cycloheximide, in protein degradation assays may result in artefacts, these inhibitors continue to be employed, owing to the absence of robust alternatives. We describe here the promoter reference technique (PRT), an assay for protein degradation with two advantageous features: a reference protein and a gene-specific inhibition of translation. In PRT assays, one measures, during a chase, the ratio of a test protein to a long-lived reference protein, a dihydrofolate reductase (DHFR). The test protein and DHFR are coexpressed, in the yeast Saccharomyces cerevisiae, on a low-copy plasmid from two identical P TDH3 promoters containing additional, previously developed DNA elements. Once transcribed, these elements form 5'-RNA aptamers that bind to the added tetracycline, which represses translation of aptamer-containing mRNAs. The selectivity of repression avoids a global inhibition of translation. This selectivity is particularly important if a component of a relevant proteolytic pathway (e.g. a specific ubiquitin ligase) is itself short-lived. We applied PRT to the Pro/N-end rule pathway, whose substrates include the short-lived Mdh2 malate dehydrogenase. Mdh2 is targeted for degradation by the Gid4 subunit of the GID ubiquitin ligase. Gid4 is also a metabolically unstable protein. Through analyses of short-lived Mdh2 as a target of short-lived Gid4, we illustrate the advantages of PRT over degradation assays that lack a reference and/or involve cycloheximide. In sum, PRT avoids the use of global translation inhibitors during a chase and also provides a "built-in" reference protein.
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Affiliation(s)
- Jang-Hyun Oh
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Shun-Jia Chen
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Alexander Varshavsky
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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46
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The Logic of the 26S Proteasome. Cell 2017; 169:792-806. [PMID: 28525752 DOI: 10.1016/j.cell.2017.04.023] [Citation(s) in RCA: 562] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 12/14/2022]
Abstract
The ubiquitin proteasome pathway is responsible for most of the protein degradation in mammalian cells. Rates of degradation by this pathway have generally been assumed to be determined by rates of ubiquitylation. However, recent studies indicate that proteasome function is also tightly regulated and determines whether a ubiquitylated protein is destroyed or deubiquitylated and survives longer. This article reviews recent advances in our understanding of the proteasome's multistep ATP-dependent mechanism, its biochemical and structural features that ensure efficient proteolysis and ubiquitin recycling while preventing nonselective proteolysis, and the regulation of proteasome activity by interacting proteins and subunit modifications, especially phosphorylation.
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Mouse Mammary Tumor Virus Signal Peptide Uses a Novel p97-Dependent and Derlin-Independent Retrotranslocation Mechanism To Escape Proteasomal Degradation. mBio 2017; 8:mBio.00328-17. [PMID: 28351922 PMCID: PMC5371415 DOI: 10.1128/mbio.00328-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Multiple pathogens, including viruses and bacteria, manipulate endoplasmic reticulum-associated degradation (ERAD) to avoid the host immune response and promote their replication. The betaretrovirus mouse mammary tumor virus (MMTV) encodes Rem, which is a precursor protein that is cleaved into a 98-amino-acid signal peptide (SP) and a C-terminal protein (Rem-CT). SP uses retrotranslocation for ER membrane extraction and yet avoids ERAD by an unknown mechanism to enter the nucleus and function as a Rev-like protein. To determine how SP escapes ERAD, we used a ubiquitin-activated interaction trap (UBAIT) screen to trap and identify transient protein interactions with SP, including the ERAD-associated p97 ATPase, but not E3 ligases or Derlin proteins linked to retrotranslocation, polyubiquitylation, and proteasomal degradation of extracted proteins. A dominant negative p97 ATPase inhibited both Rem and SP function. Immunoprecipitation experiments indicated that Rem, but not SP, is polyubiquitylated. Using both yeast and mammalian expression systems, linkage of a ubiquitin-like domain (UbL) to SP or Rem induced degradation by the proteasome, whereas SP was stable in the absence of the UbL. ERAD-associated Derlin proteins were not required for SP activity. Together, these results suggested that Rem uses a novel p97-dependent, Derlin-independent retrotranslocation mechanism distinct from other pathogens to avoid SP ubiquitylation and proteasomal degradation. Bacterial and viral infections produce pathogen-specific proteins that interfere with host functions, including the immune response. Mouse mammary tumor virus (MMTV) is a model system for studies of human complex retroviruses, such as HIV-1, as well as cancer induction. We have shown that MMTV encodes a regulatory protein, Rem, which is cleaved into an N-terminal signal peptide (SP) and a C-terminal protein (Rem-CT) within the endoplasmic reticulum (ER) membrane. SP function requires ER membrane extraction by retrotranslocation, which is part of a protein quality control system known as ER-associated degradation (ERAD) that is essential to cellular health. Through poorly understood mechanisms, certain pathogen-derived proteins are retrotranslocated but not degraded. We demonstrate here that MMTV SP retrotranslocation from the ER membrane avoids degradation through a unique process involving interaction with cellular p97 ATPase and failure to acquire cellular proteasome-targeting sequences.
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48
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Abstract
The ubiquitin proteasome system controls the concentrations of regulatory proteins and removes damaged and misfolded proteins from cells. Proteins are targeted to the protease at the center of this system, the proteasome, by ubiquitin tags, but ubiquitin is also used as a signal in other cellular processes. Specificity is conferred by the size and structure of the ubiquitin tags, which are recognized by receptors associated with the different cellular processes. However, the ubiquitin code remains ambiguous, and the same ubiquitin tag can target different proteins to different fates. After binding substrate protein at the ubiquitin tag, the proteasome initiates degradation at a disordered region in the substrate. The proteasome has pronounced preferences for the initiation site, and its recognition represents a second component of the degradation signal.
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Affiliation(s)
- Houqing Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
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49
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Abstract
Determination of the general capacity of proteolytic activity of a certain cell or tissue type can be crucial for an assessment of various features of an organism's growth and development and also for the optimization of biotechnological applications. Here, we describe the use of chimeric protein stability reporters that can be detected by standard laboratory techniques such as histological staining, selection using selective media or fluorescence microscopy. Dependent on the expression of the reporters due to the promoters applied, cell- and tissue-specific questions can be addressed. Here, we concentrate on methods which can be used for large-scale screening for protein stability changes rather than for detailed protein stability studies.
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Affiliation(s)
- Pavel Reichman
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and Science Campus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and Science Campus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany.
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