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Zheng JX, Du TY, Shao GC, Ma ZH, Jiang ZD, Hu W, Suo F, He W, Dong MQ, Du LL. Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers. Nat Commun 2023; 14:8334. [PMID: 38097609 PMCID: PMC10721834 DOI: 10.1038/s41467-023-44151-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. In several fission yeast species, single-gene KMDs belonging to the wtf gene family exert selfish killing by expressing a toxin and an antidote through alternative transcription initiation. Here we investigate how the toxin and antidote products of a wtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs PY motifs (Leu/Pro-Pro-X-Tyr) in its N-terminal cytosolic tail to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
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Affiliation(s)
- Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, 102206, China
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tong-Yang Du
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guang-Can Shao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhu-Hui Ma
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wen Hu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Wanzhong He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
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2
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Stanton DA, Ellis EA, Cruse MR, Jedlinski R, Kraut DA. The importance of proteasome grip depends on substrate stability. Biochem Biophys Res Commun 2023; 677:162-167. [PMID: 37591185 DOI: 10.1016/j.bbrc.2023.08.025] [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: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023]
Abstract
The 26S proteasome is responsible for the unfolding and degradation of intracellular proteins in eukaryotes. A hexameric ring of ATPases (Rpt1-Rpt6) grabs onto substrates and unfolds them by pulling them through a central pore and translocating them into the 20S degradation chamber. A set of pore loops containing a so-called aromatic paddle motif in each Rpt subunit is believed to be important for the proteasome's ability to unfold and translocate substrates. Based on structural and mechanistic experiments, paddles from adjacent Rpt subunits, which are arrayed in a spiral staircase conformation, grip and pull on the substrate in a hand-over-hand type mechanism, disengaging at the bottom of the staircase and re-engaging at the top. We tested the contribution of the aromatic paddles to unfolding substrates of differing stabilities by mutating the paddles singly or in combination. For an easy-to-unfold substrate (a circular permutant of green fluorescent protein; GFP), mutations had little effect on degradation rates. For a substrate with moderate stability (enhanced GFP), there were modest effects of individual mutations on GFP unfolding rates, and alternating aromatic paddle mutants had a larger detrimental effect on unfolding than sequential mutants. For a more stable substrate (superfolder GFP), unfolding is overall slower, and multiple simultaneous mutations essentially prevent unfolding. Our results highlight the context-dependent need for grip during unfolding, support the hand-over-hand model for substrate unfolding and translocation, and suggest that for hard-to-unfold substrates, it is important to have simultaneous strong contacts to the substrate for unfolding to occur. The results also suggest a kinetic proofreading model, where substrates that cannot be easily unfolded are instead clipped, removing the initiation region and preventing futile unfolding attempts.
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Affiliation(s)
- Destini A Stanton
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Emily A Ellis
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Mariah R Cruse
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Rafael Jedlinski
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Daniel A Kraut
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.
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3
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The 26S Proteasome Switches between ATP-Dependent and -Independent Mechanisms in Response to Substrate Ubiquitination. Biomolecules 2022; 12:biom12060750. [PMID: 35740875 PMCID: PMC9220805 DOI: 10.3390/biom12060750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The ubiquitin–proteasome system is responsible for the bulk of protein degradation in eukaryotic cells. Proteins are generally targeted to the 26S proteasome through the attachment of polyubiquitin chains. Several proteins also contain ubiquitin-independent degrons (UbIDs) that allow for proteasomal targeting without the need for ubiquitination. Our laboratory previously showed that UbID substrates are less processively degraded than ubiquitinated substrates, but the mechanism underlying this difference remains unclear. We therefore designed two model substrates containing both a ubiquitination site and a UbID for a more direct comparison. We found UbID degradation to be overall less robust, with complete degradation only occurring with loosely folded substrates. UbID degradation was unaffected by the nonhydrolyzable ATP analog ATPγS, indicating that UbID degradation proceeds in an ATP-independent manner. Stabilizing substrates halted UbID degradation, indicating that the proteasome can only capture UbID substrates if they are already at least transiently unfolded, as confirmed using native-state proteolysis. The 26S proteasome therefore switches between ATP-independent weak degradation and ATP-dependent robust unfolding and degradation depending on whether or not the substrate is ubiquitinated.
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4
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An Arsenite Relay between PSMD14 and AIRAP Enables Revival of Proteasomal DUB Activity. Biomolecules 2021; 11:biom11091317. [PMID: 34572530 PMCID: PMC8465394 DOI: 10.3390/biom11091317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 01/21/2023] Open
Abstract
Maintaining 26S proteasome activity under diverse physiological conditions is a fundamental requirement in order to maintain cellular proteostasis. Several quantitative and qualitative mechanisms have evolved to ensure that ubiquitin–proteasome system (UPS) substrates do not accumulate and lead to promiscuous protein–protein interactions that, in turn, lead to cellular malfunction. In this report, we demonstrate that Arsenite Inducible Regulatory Particle-Associate Protein (AIRAP), previously reported as a proteasomal adaptor required for maintaining proteasomal flux during arsenite exposure, can directly bind arsenite molecules. We further show that arsenite inhibits Psmd14/Rpn11 metalloprotease deubiquitination activity by substituting zinc binding to the MPN/JAMM domain. The proteasomal adaptor AIRAP is able to directly relieve PSMD14/Rpn11 inhibition. A possible metal relay between arsenylated PSMD14/Rpn11 and AIRAP may serve as a cellular mechanism that senses proteasomal inhibition to restore Psmd14/Rpn11 activity.
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5
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Determination of Proteasomal Unfolding Ability. Methods Mol Biol 2021. [PMID: 34432247 DOI: 10.1007/978-1-0716-1665-9_12] [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: 08/19/2023]
Abstract
We use an in vitro degradation assay with a model substrate to assess proteasomal unfolding ability. Our substrate has an unstructured region that is the site of ubiquitination, followed by an easy-to-unfold domain and a difficult-to-unfold domain. Degradation proceeds through the unstructured and easy-to-unfold domains, but the difficult-to-unfold domain can be degraded completely or, if the proteasome stalls, can be released as a partially degraded fragment. The ratio between these two possible outcomes allows us to quantify the unfolding ability and determine how processively the proteasome degrades its substrates.
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6
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Abstract
The 26S proteasome is the macromolecular machine responsible for the bulk of protein degradation in eukaryotic cells. As it degrades a ubiquitinated protein, the proteasome transitions from a substrate-accepting conformation (s1) to a set of substrate-processing conformations (s3 like), each stabilized by different intramolecular contacts. Tools to study these conformational changes remain limited, and although several interactions have been proposed to be important for stabilizing the proteasome's various conformations, it has been difficult to test these directly under equilibrium conditions. Here, we describe a conformationally sensitive Förster resonance energy transfer assay, in which fluorescent proteins are fused to Sem1 and Rpn6, which are nearer each other in substrate-processing conformations than in the substrate-accepting conformation. Using this assay, we find that two sets of interactions, one involving Rpn5 and another involving Rpn2, are both important for stabilizing substrate-processing conformations. Mutations that disrupt these interactions both destabilize substrate-processing conformations relative to the substrate-accepting conformation and diminish the proteasome's ability to successfully unfold and degrade hard-to-unfold substrates, providing a link between the proteasome's conformational state and its unfolding ability.
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7
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Suzuki G, Imura S, Hosokawa M, Katsumata R, Nonaka T, Hisanaga SI, Saeki Y, Hasegawa M. α-synuclein strains that cause distinct pathologies differentially inhibit proteasome. eLife 2020; 9:56825. [PMID: 32697196 PMCID: PMC7406352 DOI: 10.7554/elife.56825] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Abnormal α-synuclein aggregation has been implicated in several diseases and is known to spread in a prion-like manner. There is a relationship between protein aggregate structure (strain) and clinical phenotype in prion diseases, however, whether differences in the strains of α-synuclein aggregates account for the different pathologies remained unclear. Here, we generated two types of α-synuclein fibrils from identical monomer and investigated their seeding and propagation ability in mice and primary-cultured neurons. One α-synuclein fibril induced marked accumulation of phosphorylated α-synuclein and ubiquitinated protein aggregates, while the other did not, indicating the formation of α-synuclein two strains. Notably, the former α-synuclein strain inhibited proteasome activity and co-precipitated with 26S proteasome complex. Further examination indicated that structural differences in the C-terminal region of α-synuclein strains lead to different effects on proteasome activity. These results provide a possible molecular mechanism to account for the different pathologies induced by different α-synuclein strains.
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Affiliation(s)
- Genjiro Suzuki
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Sei Imura
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Laboratory of Molecular Neuroscience, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Masato Hosokawa
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Ryu Katsumata
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takashi Nonaka
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shin-Ichi Hisanaga
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Yasushi Saeki
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masato Hasegawa
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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8
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Unraveling proteasome engagement. Nat Chem Biol 2020; 16:813-815. [PMID: 32541967 DOI: 10.1038/s41589-020-0573-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Site-specific ubiquitination affects protein energetics and proteasomal degradation. Nat Chem Biol 2020; 16:866-875. [PMID: 32483380 DOI: 10.1038/s41589-020-0556-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/05/2020] [Accepted: 04/26/2020] [Indexed: 11/09/2022]
Abstract
Changes in the cellular environment modulate protein energy landscapes to drive important biology, with consequences for signaling, allostery and other vital processes. The effects of ubiquitination are particularly important because of their potential influence on degradation by the 26S proteasome. Moreover, proteasomal engagement requires unstructured initiation regions that many known proteasome substrates lack. To assess the energetic effects of ubiquitination and how these manifest at the proteasome, we developed a generalizable strategy to produce isopeptide-linked ubiquitin within structured regions of a protein. The effects on the energy landscape vary from negligible to dramatic, depending on the protein and site of ubiquitination. Ubiquitination at sensitive sites destabilizes the native structure and increases the rate of proteasomal degradation. In well-folded proteins, ubiquitination can even induce the requisite unstructured regions needed for proteasomal engagement. Our results indicate a biophysical role of site-specific ubiquitination as a potential regulatory mechanism for energy-dependent substrate degradation.
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10
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Abstract
Many proteins in the cell are tagged with a polyubiquitin chain, which serves as a recognition signal for degradation by the proteasome. Some tagged substrates bind directly to the proteasome, but others are delivered through shuttling factors. Yeast Ddi1 and its homologs in other eukaryotic cells have protein domains typical of shuttling factors, but they also contain a predicted protease domain that is related to those in retroviral proteases. This paper shows that Ddi1 is a ubiquitin-dependent protease, which cleaves substrate proteins only when they are tagged with long ubiquitin chains. Ddi1 is the only known endoprotease besides the proteasome that cleaves polyubiquitinated substrates. Ddi1 might prevent the excessive accumulation of polyubiquitinated proteins in cells. The Saccharomyces cerevisiae protein Ddi1 and its homologs in higher eukaryotes have been proposed to serve as shuttling factors that deliver ubiquitinated substrates to the proteasome. Although Ddi1 contains both ubiquitin-interacting UBA and proteasome-interacting UBL domains, the UBL domain is atypical, as it binds ubiquitin. Furthermore, unlike other shuttling factors, Ddi1 and its homologs contain a conserved helical domain (helical domain of Ddi1, HDD) and a retroviral-like protease (RVP) domain. The RVP domain is probably responsible for cleavage of the precursor of the transcription factor Nrf1 in higher eukaryotes, which results in the up-regulation of proteasomal subunit genes. However, enzymatic activity of the RVP domain has not yet been demonstrated, and the function of Ddi1 remains poorly understood. Here, we show that Ddi1 is a ubiquitin-dependent protease, which cleaves substrate proteins only when they are tagged with long ubiquitin chains (longer than about eight ubiquitins). The RVP domain is inactive in isolation, in contrast to its retroviral counterpart. Proteolytic activity of Ddi1 requires the HDD domain and is stimulated by the UBL domain, which mediates high-affinity interaction with the polyubiquitin chain. Compromising the activity of Ddi1 in yeast cells results in the accumulation of polyubiquitinated proteins. Aside from the proteasome, Ddi1 is the only known endoprotease that acts on polyubiquitinated substrates. Ddi1 and its homologs likely cleave polyubiquitinated substrates under conditions where proteasome function is compromised.
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11
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Sui X, Li YM. Development of Ubiquitin Tools for Studies of Complex Ubiquitin Processing Protein Machines. CURR ORG CHEM 2020. [DOI: 10.2174/1385272823666191113161511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Ubiquitination is one of the most extensive post-translational modifications in
eukaryotes and is involved in various physiological processes such as protein degradation,
autophagy, protein interaction, and protein localization. The ubiquitin (Ub)-related protein
machines include Ub-activating enzymes (E1s), Ub-conjugating enzymes (E2s), Ub ligases
(E3s), deubiquitinating enzymes (DUBs), p97, and the proteasomes. In recent years,
the role of DUBs has been extensively studied and relatively well understood. On the
other hand, the functional mechanisms of the other more complex ubiquitin-processing
protein machines (e.g., E3, p97, and proteasomes) are still to be sufficiently well explored
due to their intricate nature. One of the hurdles facing the studies of these complex protein
machines is the challenge of developing tailor-designed structurally defined model substrates,
which unfortunately cannot be directly obtained using recombinant technology. Consequently, the acquisition
and synthesis of the ubiquitin tool molecules are essential for the elucidation of the functions and
structures of the complex ubiquitin-processing protein machines. This paper aims to highlight recent studies on
these protein machines based on the synthetic ubiquitin tool molecules.
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Affiliation(s)
- Xin Sui
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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12
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Eisele MR, Reed RG, Rudack T, Schweitzer A, Beck F, Nagy I, Pfeifer G, Plitzko JM, Baumeister W, Tomko RJ, Sakata E. Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating. Cell Rep 2019; 24:1301-1315.e5. [PMID: 30067984 PMCID: PMC6140342 DOI: 10.1016/j.celrep.2018.07.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/08/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022] Open
Abstract
The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive the unfolding and translocation of substrates into the proteolytic 20S core particle for degradation. Here, we combine genetic and biochemical approaches with cryo-electron microscopy and integrative modeling to dissect the relationship between individual nucleotide binding events and proteasome conformational dynamics. We demonstrate unique impacts of ATP binding by individual ATPases on the proteasome conformational distribution and report two conformational states of the proteasome suggestive of a rotary ATP hydrolysis mechanism. These structures, coupled with functional analyses, reveal key roles for the ATPases Rpt1 and Rpt6 in gating substrate entry into the core particle. This deepened knowledge of proteasome conformational dynamics reveals key elements of intersubunit communication within the proteasome and clarifies the regulation of substrate entry into the proteolytic chamber.
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Affiliation(s)
- Markus R Eisele
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Randi G Reed
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306-4300, USA
| | - Till Rudack
- Department of Biophysics, Ruhr University Bochum, 44801 Bochum, Germany
| | - Andreas Schweitzer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Beck
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Istvan Nagy
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Günter Pfeifer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Robert J Tomko
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306-4300, USA.
| | - Eri Sakata
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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13
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Cundiff MD, Hurley CM, Wong JD, Boscia JA, Bashyal A, Rosenberg J, Reichard EL, Nassif ND, Brodbelt JS, Kraut DA. Ubiquitin receptors are required for substrate-mediated activation of the proteasome's unfolding ability. Sci Rep 2019; 9:14506. [PMID: 31601863 PMCID: PMC6787058 DOI: 10.1038/s41598-019-50857-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/20/2019] [Indexed: 12/05/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is responsible for the bulk of protein degradation in eukaryotic cells, but the factors that cause different substrates to be unfolded and degraded to different extents are still poorly understood. We previously showed that polyubiquitinated substrates were degraded with greater processivity (with a higher tendency to be unfolded and degraded than released) than ubiquitin-independent substrates. Thus, even though ubiquitin chains are removed before unfolding and degradation occur, they affect the unfolding of a protein domain. How do ubiquitin chains activate the proteasome’s unfolding ability? We investigated the roles of the three intrinsic proteasomal ubiquitin receptors - Rpn1, Rpn10 and Rpn13 - in this activation. We find that these receptors are required for substrate-mediated activation of the proteasome’s unfolding ability. Rpn13 plays the largest role, but there is also partial redundancy between receptors. The architecture of substrate ubiquitination determines which receptors are needed for maximal unfolding ability, and, in some cases, simultaneous engagement of ubiquitin by multiple receptors may be required. Our results suggest physical models for how ubiquitin receptors communicate with the proteasomal motor proteins.
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Affiliation(s)
- Mary D Cundiff
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.,Department of Biological Sciences, Carnegie Mellon University, Mellon Institute of Industrial Research, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
| | - Christina M Hurley
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Jeremy D Wong
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Joseph A Boscia
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA
| | - Aarti Bashyal
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jake Rosenberg
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Eden L Reichard
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.,Department of Chemistry, Lehigh University, 6 E. Packer Ave., Bethlehem, PA, 18015, USA
| | - Nicholas D Nassif
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.,Bronx-Lebanon Hospital Center, 1650 Grand Concourse, Bronx, NY, 10457, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Daniel A Kraut
- Department of Chemistry, Villanova University, Villanova, PA, 19085, USA.
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14
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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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15
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Kudriaeva AA, Belogurov AA. Proteasome: a Nanomachinery of Creative Destruction. BIOCHEMISTRY (MOSCOW) 2019; 84:S159-S192. [PMID: 31213201 DOI: 10.1134/s0006297919140104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the middle of the 20th century, it was postulated that degradation of intracellular proteins is a stochastic process. More than fifty years of intense studies have finally proven that protein degradation is a very complex and tightly regulated in time and space process that plays an incredibly important role in the vast majority of metabolic pathways. Degradation of more than a half of intracellular proteins is controlled by a hierarchically aligned and evolutionarily perfect system consisting of many components, the main ones being ubiquitin ligases and proteasomes, together referred to as the ubiquitin-proteasome system (UPS). The UPS includes more than 1000 individual components, and most of them are critical for the cell functioning and survival. In addition to the well-known signaling functions of ubiquitination, such as modification of substrates for proteasomal degradation and DNA repair, polyubiquitin (polyUb) chains are involved in other important cellular processes, e.g., cell cycle regulation, immunity, protein degradation in mitochondria, and even mRNA stability. This incredible variety of ubiquitination functions is related to the ubiquitin ability to form branching chains through the ε-amino group of any of seven lysine residues in its sequence. Deubiquitination is accomplished by proteins of the deubiquitinating enzyme family. The second main component of the UPS is proteasome, a multisubunit proteinase complex that, in addition to the degradation of functionally exhausted and damaged proteins, regulates many important cellular processes through controlled degradation of substrates, for example, transcription factors and cyclins. In addition to the ubiquitin-dependent-mediated degradation, there is also ubiquitin-independent degradation, when the proteolytic signal is either an intrinsic protein sequence or shuttle molecule. Protein hydrolysis is a critically important cellular function; therefore, any abnormalities in this process lead to systemic impairments further transforming into serious diseases, such as diabetes, malignant transformation, and neurodegenerative disorders (multiple sclerosis, Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease and Huntington's disease). In this review, we discuss the mechanisms that orchestrate all components of the UPS, as well as the plurality of the fine-tuning pathways of proteasomal degradation.
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Affiliation(s)
- A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia. .,Lomonosov Moscow State University, Moscow, 119991, Russia
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16
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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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17
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Kim HT, Collins GA, Goldberg AL. Measurement of the Multiple Activities of 26S Proteasomes. Methods Mol Biol 2019; 1844:289-308. [PMID: 30242717 DOI: 10.1007/978-1-4939-8706-1_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because proteasomes catalyze most of the protein degradation in mammalian cells, and their functioning is essential for cellular homeostasis, proteasome structure, biochemical mechanisms, and regulation in normal and disease states are now widely studied and are of major importance. In addition, inhibitors of the proteasome's peptidase activity have proven to be very valuable as research tools and in the treatment of hematologic malignancies, and a number of newer pharmacological agents that alter proteasome function are being developed. The rapid degradation of ubiquitinated proteins by the 26S proteasome involves multiple enzymatic and non-enzymatic steps, including the binding of ubiquitinated substrates to the 19S particle (Subheading 3.2), opening the gated substrate entry channel into the 20S particle (Subheading 3.3), disassembly of the Ub chain (Subheading 3.4), ATP hydrolysis (Subheading 3.5), substrate unfolding and translocation, and proteolysis within the 20S particle (Subheadings 3.3 and 3.7). Assaying each of these processes is important if we are to fully understand the physiological regulation of proteasome function and the effects of disease or drugs. Here, we describe several methods that we have found useful to measure many of these individual activities using purified proteasomes. Studies using these approaches have already provided valuable new insights into the effects of post-synthetic modifications to 26S subunits, the physiological regulation of the ubiquitin-proteasome system, and the impairment of proteasome activity in neurodegenerative disease. These advances would not have been possible if only the standard assays of peptidase activity were used.
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Affiliation(s)
- Hyoung Tae Kim
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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18
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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: 83] [Impact Index Per Article: 16.6] [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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19
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Muniyappan S, Lee BH. In vitro analysis of proteasome-associated USP14 activity for substrate degradation and deubiquitylation. Methods Enzymol 2019; 619:249-268. [PMID: 30910023 DOI: 10.1016/bs.mie.2018.12.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ubiquitin-proteasome pathway plays an essential role in maintaining protein homeostasis and regulates almost every aspect of cellular processes in eukaryotes. Emerging evidence indicates that the proteasome does not work as a simple unidirectional molecular machinery for substrate proteolysis. In fact, proteasome activity should be tightly regulated, and the proteasome itself can be dynamically engaged in the degradation cycle. Proteasome-mediated degradation can occur through multistep mechanisms such as ubiquitin-dependent substrate recognition, deubiquitination, and ATP-driven unfolding and translocation of the substrate into 20S chamber for proteolytic cleavage. Deubiquitination is particularly interesting because this reaction may impose a critical checkpoint for substrate turnover on the proteasome. Notably, there are three major deubiquitinating enzymes (DUBs) on human proteasomes: USP14, UCH37, and RPN11. USP14 can spare the substrate from degradation prior to the proteasome's commitment step, suggesting that USP14 inhibition may stimulate proteasomal degradation of undesirable proteins under certain proteotoxic conditions. Furthermore, USP14 deubiquitinates multichain conjugates, the first among ~100 DUBs found to have this striking specificity. In this chapter, we describe in vitro methods to test proteasome-associated USP14 activity for substrate degradation and deubiquitylation.
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Affiliation(s)
| | - Byung-Hoon Lee
- Department of New Biology, DGIST, Daegu, Republic of Korea.
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20
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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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21
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UBL domain of Usp14 and other proteins stimulates proteasome activities and protein degradation in cells. Proc Natl Acad Sci U S A 2018; 115:E11642-E11650. [PMID: 30487212 DOI: 10.1073/pnas.1808731115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The best-known function of ubiquitin-like (UBL) domains in proteins is to enable their binding to 26S proteasomes. The proteasome-associated deubiquitinating enzyme Usp14/UBP6 contains an N-terminal UBL domain and is an important regulator of proteasomal activity. Usp14 by itself represses multiple proteasomal activities but, upon binding a ubiquitin chain, Usp14 stimulates these activities and promotes ubiquitin-conjugate degradation. Here, we demonstrate that Usp14's UBL domain alone mimics this activation of proteasomes by ubiquitin chains. Addition of this UBL domain to purified 26S proteasomes stimulated the same activities inhibited by Usp14: peptide entry and hydrolysis, protein-dependent ATP hydrolysis, deubiquitination by Rpn11, and the degradation of ubiquitinated and nonubiquitinated proteins. Thus, the binding of Usp14's UBL (apparently to Rpn1's T2 site) seems to mediate the activation of proteasomes by ubiquitinated substrates. However, the stimulation of these various activities was greater in proteasomes lacking Usp14 than in wild-type particles and thus is a general response that does not involve some displacement of Usp14. Furthermore, the UBL domains from hHR23 and hPLIC1/UBQLN1 also stimulated peptide hydrolysis, and the expression of hHR23A's UBL domain in HeLa cells stimulated overall protein degradation. Therefore, many UBL-containing proteins that bind to proteasomes may also enhance allosterically its proteolytic activity.
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22
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Dong Y, Zhang S, Wu Z, Li X, Wang WL, Zhu Y, Stoilova-McPhie S, Lu Y, Finley D, Mao Y. Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Nature 2018; 565:49-55. [PMID: 30479383 PMCID: PMC6370054 DOI: 10.1038/s41586-018-0736-4] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/02/2018] [Indexed: 11/15/2022]
Abstract
The proteasome is an ATP-dependent, 2.5-megadalton machine responsible for selective protein degradation in eukaryotic cells. Here we present cryo-EM structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures visualize a continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. Three principal modes of coordinated hydrolysis are observed, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases, and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, translocation initiation and processive unfolding of substrates, respectively. ATP hydrolysis powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate.
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Affiliation(s)
- Yuanchen Dong
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Shuwen Zhang
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - Zhaolong Wu
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Xuemei Li
- Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, China
| | - Wei Li Wang
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Yanan Zhu
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | | | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Youdong Mao
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China. .,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA. .,Center for Quantitative Biology, Peking University, Beijing, China. .,Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, China.
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23
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Abstract
Access to well-defined ubiquitin conjugates has been key to elucidating the biochemical functions of proteins in the ubiquitin signaling network. Yet, we have a poor understanding of how deubiquitinases and ubiquitin-binding proteins respond to ubiquitin modifications when anchored to a protein other than ubiquitin or a ubiquitin-like protein. This is due to the difficulty of synthesizing ubiquitinated proteins comprised of native isopeptide bonds. Here we report on the evolution of a deubiquitinase capable of site-specifically modifying itself with defined ubiquitin chains. Following mutagenesis and yeast display screening, we identify a variant of the yeast ubiquitin C-terminal hydrolase Yuh1 that has a 28-fold improvement in the transamidation to hydrolysis ratio relative to the wild type enzyme. The switch in activity enables robust autoubiquitination of a lysine in the crossover loop to form an isopeptide bond. We demonstrate the utility of autoubiquitinating the evolved Yuh1 variant by investigating the consequences of ubiquitin chain anchoring on the activities of other deubiquitinases. Much to our surprise, we find that certain deubiquitinases are exquisitely sensitive to chain anchoring. These results highlight the importance of investigating the biochemical activities of deubiquitinases with both substrate-anchored and unanchored ubiquitin chains.
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24
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Tsuchiya H, Burana D, Ohtake F, Arai N, Kaiho A, Komada M, Tanaka K, Saeki Y. Ub-ProT reveals global length and composition of protein ubiquitylation in cells. Nat Commun 2018; 9:524. [PMID: 29410401 PMCID: PMC5802829 DOI: 10.1038/s41467-018-02869-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 01/02/2018] [Indexed: 01/09/2023] Open
Abstract
Protein ubiquitylation regulates diverse cellular processes via distinct ubiquitin chains that differ by linkage type and length. However, a comprehensive method for measuring these properties has not been developed. Here we describe a method for assessing the length of substrate-attached polyubiquitin chains, "ubiquitin chain protection from trypsinization (Ub-ProT)." Using Ub-ProT, we found that most ubiquitylated substrates in yeast-soluble lysate are attached to chains of up to seven ubiquitin molecules. Inactivation of the ubiquitin-selective chaperone Cdc48 caused a dramatic increase in chain lengths on substrate proteins, suggesting that Cdc48 complex terminates chain elongation by substrate extraction. In mammalian cells, we found that ligand-activated epidermal growth factor receptor (EGFR) is rapidly modified with K63-linked tetra- to hexa-ubiquitin chains following EGF treatment in human cells. Thus, the Ub-ProT method can contribute to our understanding of mechanisms regulating physiological ubiquitin chain lengths and composition.
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Affiliation(s)
- Hikaru Tsuchiya
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Daocharad Burana
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-B16 Nagatsuta, Midori, Yokohama, 226-8501, Japan
| | - Fumiaki Ohtake
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Naoko Arai
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Ai Kaiho
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Masayuki Komada
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-B16 Nagatsuta, Midori, Yokohama, 226-8501, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
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25
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Abstract
Rapid, gentle isolation of 26S proteasomes from cells or tissues is an essential step for studies of the changes in proteasome activity and composition that can occur under different physiological or pathological conditions and in response to pharmacological agents. We present here three different approaches to affinity purify or to prepare proteasome-rich cell fractions. The first method uses affinity tags fused to proteasome subunits and has been useful in several cell lines for studies of proteasome structure by cryo-electron microscopy and composition by mass spectrometry. A second method uses the proteasome's affinity for a ubiquitin-like (UBL) domain and can be used to purify these particles from any cell or tissue. This method does not require expression of a tagged subunit and has proven to be very useful to investigate how proteasomal activity changes in different physiological states (e.g., fasting or aging), with neurodegenerative diseases, and with drugs or hormones that cause subunit phosphorylation. A third, simple method that is based on the 26S proteasome's high molecular weight (about 2.5 MDa) concentrates these particles greatly by differential centrifugation. This method maintains the association of proteasomes with ubiquitin (Ub) conjugates and many other loosely associated regulatory proteins and is useful to study changes in proteasome composition under different conditions.
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26
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Boselli M, Lee BH, Robert J, Prado MA, Min SW, Cheng C, Silva MC, Seong C, Elsasser S, Hatle KM, Gahman TC, Gygi SP, Haggarty SJ, Gan L, King RW, Finley D. An inhibitor of the proteasomal deubiquitinating enzyme USP14 induces tau elimination in cultured neurons. J Biol Chem 2017; 292:19209-19225. [PMID: 28972160 DOI: 10.1074/jbc.m117.815126] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is responsible for most selective protein degradation in eukaryotes and regulates numerous cellular processes, including cell cycle control and protein quality control. A component of this system, the deubiquitinating enzyme USP14, associates with the proteasome where it can rescue substrates from degradation by removal of the ubiquitin tag. We previously found that a small-molecule inhibitor of USP14, known as IU1, can increase the rate of degradation of a subset of proteasome substrates. We report here the synthesis and characterization of 87 variants of IU1, which resulted in the identification of a 10-fold more potent USP14 inhibitor that retains specificity for USP14. The capacity of this compound, IU1-47, to enhance protein degradation in cells was tested using as a reporter the microtubule-associated protein tau, which has been implicated in many neurodegenerative diseases. Using primary neuronal cultures, IU1-47 was found to accelerate the rate of degradation of wild-type tau, the pathological tau mutants P301L and P301S, and the A152T tau variant. We also report that a specific residue in tau, lysine 174, is critical for the IU1-47-mediated tau degradation by the proteasome. Finally, we show that IU1-47 stimulates autophagic flux in primary neurons. In summary, these findings provide a powerful research tool for investigating the complex biology of USP14.
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Affiliation(s)
- Monica Boselli
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Byung-Hoon Lee
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,the Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, 42988 Daegu, Korea
| | - Jessica Robert
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Sang-Won Min
- the Department of Neurology, Gladstone Institute of Neurological Diseases, University of California, San Francisco, California 94158
| | - Chialin Cheng
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - M Catarina Silva
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Changhyun Seong
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,Regeneron Pharmaceuticals, Tarrytown, New York 10591, and
| | - Suzanne Elsasser
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Ketki M Hatle
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Timothy C Gahman
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, California 92093
| | - Steven P Gygi
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Li Gan
- the Department of Neurology, Gladstone Institute of Neurological Diseases, University of California, San Francisco, California 94158
| | - Randall W King
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115,
| | - Daniel Finley
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115,
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27
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Saeki Y. Ubiquitin recognition by the proteasome. J Biochem 2017; 161:113-124. [PMID: 28069863 DOI: 10.1093/jb/mvw091] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/21/2016] [Indexed: 12/14/2022] Open
Abstract
The 26S proteasome is a 2.5-MDa complex responsible for the selective, ATP-dependent degradation of ubiquitylated proteins in eukaryotic cells. Substrates in hundreds cellular pathways are timely ubiquitylated and converged to the proteasome by direct recognition or by multiple shuttle factors. Engagement of substrate protein triggers conformational changes of the proteasome, which drive substrate unfolding, deubiquitylation and translocation of substrates to proteolytic sites. Recent studies have challenged the previous paradigm that Lys48-linked tetraubiquitin is a minimal degradation signal: in addition, monoubiquitylation or multiple short ubiquitylations can serve as the targeting signal for proteasomal degradation. In this review, I highlight recent advances in our understanding of the proteasome structure, the ubiquitin topology in proteasome targeting, and the cellular factors that regulate proteasomal degradation.
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Affiliation(s)
- Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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28
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Kim HT, Goldberg AL. The deubiquitinating enzyme Usp14 allosterically inhibits multiple proteasomal activities and ubiquitin-independent proteolysis. J Biol Chem 2017; 292:9830-9839. [PMID: 28416611 DOI: 10.1074/jbc.m116.763128] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
The proteasome-associated deubiquitinating enzyme Usp14/Ubp6 inhibits protein degradation by catalyzing substrate deubiquitination and by poorly understood allosteric actions. However, upon binding a ubiquitin chain, Usp14 enhances proteasomal degradation by stimulating ATP and peptide degradation. These studies were undertaken to clarify these seemingly opposite regulatory roles of Usp14 and their importance. To learn how the presence of Usp14 on 26S proteasomes influences its different activities, we compared enzymatic and regulatory properties of 26S proteasomes purified from wild-type mouse embryonic fibroblast cells and those lacking Usp14. The proteasomes lacking Usp14 had higher basal peptidase activity than WT 26S, and this activity was stimulated to a greater extent by adenosine 5'-O-(thiotriphosphate) (ATPγS) than with WT particles. These differences were clear even though Usp14 is present on only a minor fraction (30-40%) of the 26S in WT mouse embryonic fibroblast cells. Addition of purified Usp14 to the WT and Usp14-defficient proteasomes reduced both their basal peptidase activity and the stimulation by ATPγS. Usp14 inhibits these processes allosterically because a catalytically inactive Usp14 mutant also inhibited them. Proteasomes lacking Usp14 also exhibited greater deubiquitinating activity by Rpn11 and greater basal ATPase activity than WT particles. ATP hydrolysis by WT proteasomes is activated if they bind a ubiquitinated protein, which is loosely folded. Surprisingly, proteasomes lacking Usp14 could be activated by such proteins even without a ubiquitin chain present. Furthermore, proteasomes lacking Usp14 are much more active in degrading non-ubiquitinated proteins (e.g. Sic1) than WT particles. Thus, without a ubiquitinated substrate present, Usp14 suppresses multiple proteasomal activities, especially basal ATP consumption and degradation of non-ubiquitinated proteins. These allosteric effects thus reduce ATP hydrolysis by inactive proteasomes and nonspecific proteolysis and enhance proteasomal specificity for ubiquitinated proteins.
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Affiliation(s)
- Hyoung Tae Kim
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Alfred L Goldberg
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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29
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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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30
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Deubiquitinase activity is required for the proteasomal degradation of misfolded cytosolic proteins upon heat-stress. Nat Commun 2016; 7:12907. [PMID: 27698423 PMCID: PMC5059457 DOI: 10.1038/ncomms12907] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 08/12/2016] [Indexed: 12/25/2022] Open
Abstract
Elimination of misfolded proteins is crucial for proteostasis and to prevent proteinopathies. Nedd4/Rsp5 emerged as a major E3-ligase involved in multiple quality control pathways that target misfolded plasma membrane proteins, aggregated polypeptides and cytosolic heat-induced misfolded proteins for degradation. It remained unclear how in one case cytosolic heat-induced Rsp5 substrates are destined for proteasomal degradation, whereas other Rsp5 quality control substrates are otherwise directed to lysosomal degradation. Here we find that Ubp2 and Ubp3 deubiquitinases are required for the proteasomal degradation of cytosolic misfolded proteins targeted by Rsp5 after heat-shock (HS). The two deubiquitinases associate more with Rsp5 upon heat-stress to prevent the assembly of K63-linked ubiquitin on Rsp5 heat-induced substrates. This activity was required to promote the K48-mediated proteasomal degradation of Rsp5 HS-induced substrates. Our results indicate that ubiquitin chain editing is key to the cytosolic protein quality control under stress conditions. Ubiquitination of misfolded proteins usually results in protein degradation. Here, the authors show that two deubiquitinases—enzymes that remove ubiquitin—are required for the proteasomal degradation of misfolded proteins in response to heat-shock in yeast.
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31
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Reichard EL, Chirico GG, Dewey WJ, Nassif ND, Bard KE, Millas NE, Kraut DA. Substrate Ubiquitination Controls the Unfolding Ability of the Proteasome. J Biol Chem 2016; 291:18547-61. [PMID: 27405762 DOI: 10.1074/jbc.m116.720151] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Indexed: 12/21/2022] Open
Abstract
In eukaryotic cells, proteins are targeted to the proteasome for degradation by polyubiquitination. These proteins bind to ubiquitin receptors, are engaged and unfolded by proteasomal ATPases, and are processively degraded. The factors determining to what extent the proteasome can successfully unfold and degrade a substrate are still poorly understood. We find that the architecture of polyubiquitin chains attached to a substrate affects the ability of the proteasome to unfold and degrade the substrate, with K48- or mixed-linkage chains leading to greater processivity than K63-linked chains. Ubiquitin-independent targeting of substrates to the proteasome gave substantially lower processivity of degradation than ubiquitin-dependent targeting. Thus, even though ubiquitin chains are removed early in degradation, during substrate engagement, remarkably they dramatically affect the later unfolding of a protein domain. Our work supports a model in which a polyubiquitin chain associated with a substrate switches the proteasome into an activated state that persists throughout the degradation process.
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Affiliation(s)
- Eden L Reichard
- From the Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085
| | - Giavanna G Chirico
- From the Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085
| | - William J Dewey
- From the Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085
| | - Nicholas D Nassif
- From the Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085
| | - Katelyn E Bard
- From the Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085
| | - Nickolas E Millas
- From the Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085
| | - Daniel A Kraut
- From the Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085
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32
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Bhattacharyya S, Renn JP, Yu H, Marko JF, Matouschek A. An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates. Anal Biochem 2016; 509:50-59. [PMID: 27296635 DOI: 10.1016/j.ab.2016.05.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/13/2016] [Accepted: 05/31/2016] [Indexed: 12/12/2022]
Abstract
The 26S proteasome is the molecular machine at the center of the ubiquitin proteasome system and is responsible for adjusting the concentrations of many cellular proteins. It is a drug target in several human diseases, and assays for the characterization of modulators of its activity are valuable. The 26S proteasome consists of two components: a core particle, which contains the proteolytic sites, and regulatory caps, which contain substrate receptors and substrate processing enzymes, including six ATPases. Current high-throughput assays of proteasome activity use synthetic fluorogenic peptide substrates that report directly on the proteolytic activity of the proteasome, but not on the activities of the proteasome caps that are responsible for protein recognition and unfolding. Here, we describe a simple and robust assay for the activity of the entire 26S proteasome using fluorescence anisotropy to follow the degradation of fluorescently labeled protein substrates. We describe two implementations of the assay in a high-throughput format and show that it meets the expected requirement of ATP hydrolysis and the presence of a canonical degradation signal or degron in the target protein.
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Affiliation(s)
| | - Jonathan P Renn
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Houqing Yu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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33
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Yu H, Kago G, Yellman CM, Matouschek A. Ubiquitin-like domains can target to the proteasome but proteolysis requires a disordered region. EMBO J 2016; 35:1522-36. [PMID: 27234297 DOI: 10.15252/embj.201593147] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 04/27/2016] [Indexed: 11/09/2022] Open
Abstract
Ubiquitin and some of its homologues target proteins to the proteasome for degradation. Other ubiquitin-like domains are involved in cellular processes unrelated to the proteasome, and proteins containing these domains remain stable in the cell. We find that the 10 yeast ubiquitin-like domains tested bind to the proteasome, and that all 11 identified domains can target proteins for degradation. Their apparent proteasome affinities are not directly related to their stabilities or functions. That is, ubiquitin-like domains in proteins not part of the ubiquitin proteasome system may bind the proteasome more tightly than domains in proteins that are bona fide components. We propose that proteins with ubiquitin-like domains have properties other than proteasome binding that confer stability. We show that one of these properties is the absence of accessible disordered regions that allow the proteasome to initiate degradation. In support of this model, we find that Mdy2 is degraded in yeast when a disordered region in the protein becomes exposed and that the attachment of a disordered region to Ubp6 leads to its degradation.
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Affiliation(s)
- Houqing Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Grace Kago
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christopher M Yellman
- 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 Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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34
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Yu H, Singh Gautam AK, Wilmington SR, Wylie D, Martinez-Fonts K, Kago G, Warburton M, Chavali S, Inobe T, Finkelstein IJ, Babu MM, Matouschek A. Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome. J Biol Chem 2016; 291:14526-39. [PMID: 27226608 PMCID: PMC4938175 DOI: 10.1074/jbc.m116.727578] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 11/23/2022] Open
Abstract
The proteasome has pronounced preferences for the amino acid sequence of its substrates at the site where it initiates degradation. Here, we report that modulating these sequences can tune the steady-state abundance of proteins over 2 orders of magnitude in cells. This is the same dynamic range as seen for inducing ubiquitination through a classic N-end rule degron. The stability and abundance of His3 constructs dictated by the initiation site affect survival of yeast cells and show that variation in proteasomal initiation can affect fitness. The proteasome's sequence preferences are linked directly to the affinity of the initiation sites to their receptor on the proteasome and are conserved between Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human cells. These findings establish that the sequence composition of unstructured initiation sites influences protein abundance in vivo in an evolutionarily conserved manner and can affect phenotype and fitness.
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Affiliation(s)
- Houqing Yu
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | | | - Shameika R Wilmington
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Dennis Wylie
- the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712
| | - Kirby Martinez-Fonts
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Grace Kago
- From the Department of Molecular Biosciences and
| | | | - Sreenivas Chavali
- the Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Tomonao Inobe
- Frontier Research Core for Life Sciences, University of Toyama, 3190 Gofuku, Toyama-shi, Toyama 930-8555, Japan
| | | | - M Madan Babu
- the Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Andreas Matouschek
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208,
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35
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Martinez-Fonts K, Matouschek A. A Rapid and Versatile Method for Generating Proteins with Defined Ubiquitin Chains. Biochemistry 2016; 55:1898-908. [PMID: 26943792 DOI: 10.1021/acs.biochem.5b01310] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ubiquitin and polyubiquitin chains target proteins for a wide variety of cellular processes. Ubiquitin-mediated targeting is regulated by the lysine through which the ubiquitins are linked as well as the broader ubiquitin landscape on the protein. The mechanisms of this regulation are not fully understood. For example, the canonical proteasome targeting signal is a lysine 48-linked polyubiquitin chain, and the canonical endocytosis signal is a lysine 63-linked polyubiquitin chain. However, lysine 63-linked polyubiquitin chains can also target substrates for degradation. Biochemical studies of ubiquitinated proteins have been limited by the difficulty of building proteins with well-defined polyubiquitin chains. Here we describe an efficient and versatile method for synthesizing ubiquitin chains of defined linkage and length. The synthesized ubiquitin chains are then attached to any protein containing a ubiquitin moiety. These proteins can be used to study ubiquitin targeting in in vitro assays in the tightly controlled manner required for biochemical studies.
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Affiliation(s)
- Kirby Martinez-Fonts
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
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36
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Open-gate mutants of the mammalian proteasome show enhanced ubiquitin-conjugate degradation. Nat Commun 2016; 7:10963. [PMID: 26957043 PMCID: PMC4786872 DOI: 10.1038/ncomms10963] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/04/2016] [Indexed: 12/20/2022] Open
Abstract
When in the closed form, the substrate translocation channel of the proteasome core
particle (CP) is blocked by the convergent N termini of α-subunits. To
probe the role of channel gating in mammalian proteasomes, we deleted the N-terminal
tail of α3; the resulting α3ΔN proteasomes are intact
but hyperactive in the hydrolysis of fluorogenic peptide substrates and the
degradation of polyubiquitinated proteins. Cells expressing the hyperactive
proteasomes show markedly elevated degradation of many established proteasome
substrates and resistance to oxidative stress. Multiplexed quantitative proteomics
revealed ∼200 proteins with reduced levels in the mutant cells. Potentially
toxic proteins such as tau exhibit reduced accumulation and aggregate formation.
These data demonstrate that the CP gate is a key negative regulator of proteasome
function in mammals, and that opening the CP gate may be an effective strategy to
increase proteasome activity and reduce levels of toxic proteins in cells. The proteasome plays a key role in proteostasis by mediating the
degradation of ubiquitinated substrates. Here the authors show that an open-gate mutant
of the proteasome is hyperactive towards a subset of substrates and can effectively
delay the accumulation of toxic protein aggregates.
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37
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Shi Y, Chen X, Elsasser S, Stocks BB, Tian G, Lee BH, Shi Y, Zhang N, de Poot SAH, Tuebing F, Sun S, Vannoy J, Tarasov SG, Engen JR, Finley D, Walters KJ. Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Science 2016; 351:351/6275/aad9421. [PMID: 26912900 DOI: 10.1126/science.aad9421] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hundreds of pathways for degradation converge at ubiquitin recognition by a proteasome. Here, we found that the five known proteasomal ubiquitin receptors in yeast are collectively nonessential for ubiquitin recognition and identified a sixth receptor, Rpn1. A site ( T1: ) in the Rpn1 toroid recognized ubiquitin and ubiquitin-like ( UBL: ) domains of substrate shuttling factors. T1 structures with monoubiquitin or lysine 48 diubiquitin show three neighboring outer helices engaging two ubiquitins. T1 contributes a distinct substrate-binding pathway with preference for lysine 48-linked chains. Proximal to T1 within the Rpn1 toroid is a second UBL-binding site ( T2: ) that assists in ubiquitin chain disassembly, by binding the UBL of deubiquitinating enzyme Ubp6. Thus, a two-site recognition domain intrinsic to the proteasome uses distinct ubiquitin-fold ligands to assemble substrates, shuttling factors, and a deubiquitinating enzyme.
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Affiliation(s)
- Yuan Shi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Suzanne Elsasser
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Bradley B Stocks
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Byung-Hoon Lee
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Yanhong Shi
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Naixia Zhang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Stefanie A H de Poot
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Fabian Tuebing
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Shuangwu Sun
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jacob Vannoy
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Linganore High School, Frederick, MD 21701, USA
| | - Sergey G Tarasov
- Biophysics Resource, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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38
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Kalinowska K, Nagel MK, Isono E. Measuring the Enzyme Activity of Arabidopsis Deubiquitylating Enzymes. Methods Mol Biol 2016; 1450:35-44. [PMID: 27424744 DOI: 10.1007/978-1-4939-3759-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Deubiquitylating enzymes, or DUBs, are important regulators of ubiquitin homeostasis and substrate stability, though the molecular mechanisms of most of the DUBs in plants are not yet understood. As different ubiquitin chain types are implicated in different biological pathways, it is important to analyze the enzyme characteristic for studying a DUB. Quantitative analysis of DUB activity is also important to determine enzyme kinetics and the influence of DUB binding proteins on the enzyme activity. Here, we show methods to analyze DUB activity using immunodetection, Coomassie Brilliant Blue staining, and fluorescence measurement that can be useful for understanding the basic characteristic of DUBs.
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Affiliation(s)
- Kamila Kalinowska
- Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Marie-Kristin Nagel
- Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Erika Isono
- Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany.
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39
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Tau-driven 26S proteasome impairment and cognitive dysfunction can be prevented early in disease by activating cAMP-PKA signaling. Nat Med 2015; 22:46-53. [PMID: 26692334 DOI: 10.1038/nm.4011] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/17/2015] [Indexed: 12/12/2022]
Abstract
The ubiquitin proteasome system (UPS) degrades misfolded proteins including those implicated in neurodegenerative diseases. We investigated the effects of tau accumulation on proteasome function in a mouse model of tauopathy and in a cross to a UPS reporter mouse (line Ub-G76V-GFP). Accumulation of insoluble tau was associated with a decrease in the peptidase activity of brain 26S proteasomes, higher levels of ubiquitinated proteins and undegraded Ub-G76V-GFP. 26S proteasomes from mice with tauopathy were physically associated with tau and were less active in hydrolyzing ubiquitinated proteins, small peptides and ATP. 26S proteasomes from normal mice incubated with recombinant oligomers or fibrils also showed lower hydrolyzing capacity in the same assays, implicating tau as a proteotoxin. Administration of an agent that activates cAMP-protein kinase A (PKA) signaling led to attenuation of proteasome dysfunction, probably through proteasome subunit phosphorylation. In vivo, this led to lower levels of aggregated tau and improvements in cognitive performance.
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40
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Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome. Nat Struct Mol Biol 2015; 22:712-9. [PMID: 26301997 PMCID: PMC4560640 DOI: 10.1038/nsmb.3075] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/27/2015] [Indexed: 12/18/2022]
Abstract
Substrates are targeted for proteasomal degradation through the attachment of ubiquitin chains that need to be removed by proteasomal deubiquitinases prior to substrate processing. In budding yeast, the deubiquitinase Ubp6 trims ubiquitin chains and affects substrate processing by the proteasome, but the underlying mechanisms and its location within the holoenzyme remained elusive. Here we show that Ubp6 activity strongly responds to interactions with the base ATPase and the conformational state of the proteasome. Electron-microscopy analyses reveal that ubiquitin-bound Ubp6 contacts the N-ring and AAA+ ring of the ATPase hexamer, in close proximity to the deubiquitinase Rpn11. Ubiquitin-bound Ubp6 inhibits substrate deubiquitination by Rpn11, stabilizes the substrate-engaged conformation of the proteasome, and allosterically interferes with the engagement of a subsequent substrate. Ubp6 may thus act as an ubiquitin-dependent timer to coordinate individual processing steps at the proteasome and modulate substrate degradation.
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41
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Lee JH, Shin SK, Jiang Y, Choi WH, Hong C, Kim DE, Lee MJ. Facilitated Tau Degradation by USP14 Aptamers via Enhanced Proteasome Activity. Sci Rep 2015; 5:10757. [PMID: 26041011 PMCID: PMC4455164 DOI: 10.1038/srep10757] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 04/28/2015] [Indexed: 12/26/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is the primary mechanism by which intracellular proteins, transcription factors, and many proteotoxic proteins with aggregation-prone structures are degraded. The UPS is reportedly downregulated in various neurodegenerative disorders, with increased proteasome activity shown to be beneficial in many related disease models. Proteasomes function under tonic inhibitory conditions, possibly via the ubiquitin chain-trimming function of USP14, a proteasome-associated deubiquitinating enzyme (DUB). We identified three specific RNA aptamers of USP14 (USP14-1, USP14-2, and USP14-3) that inhibited its deubiquitinating activity. The nucleotide sequences of these non-cytotoxic USP14 aptamers contained conserved GGAGG motifs, with G-rich regions upstream, and similar secondary structures. They efficiently elevated proteasomal activity, as determined by the increased degradation of small fluorogenic peptide substrates and physiological polyubiquitinated Sic1 proteins. Additionally, proteasomal degradation of tau proteins was facilitated in the presence of the UPS14 aptamers in vitro. Our results indicate that these novel inhibitory UPS14 aptamers can be used to enhance proteasome activity, and to facilitate the degradation of proteotoxic proteins, thereby protecting cells from various neurodegenerative stressors.
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Affiliation(s)
- Jung Hoon Lee
- Department of Biochemistry and Molecular Biology, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Seung Kyun Shin
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Yanxialei Jiang
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Won Hoon Choi
- Department of Biochemistry and Molecular Biology, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Chaesun Hong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
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42
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Abstract
In eukaryotes, damaged or unneeded proteins are typically degraded by the ubiquitin-proteasome system. In this system, the protein substrate is often first covalently modified with a chain of ubiquitin polypeptides. This chain serves as a signal for delivery to the 26S proteasome, a 2.5-MDa, ATP-dependent multisubunit protease complex. The proteasome consists of a barrel-shaped 20S core particle (CP) that is capped on one or both of its ends by a 19S regulatory particle (RP). The RP is responsible for recognizing the substrate, unfolding it, and translocating it into the CP for destruction. Here we describe simple, one-step purifications scheme for isolating the 26S proteasome and its 19S RP and 20S CP subcomplexes from the yeast Saccharomyces cerevisiae, as well as assays for measuring ubiquitin-dependent and ubiquitin-independent proteolytic activity in vitro.
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Affiliation(s)
- Yanjie Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Robert J Tomko
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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43
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Cannon JR, Martinez-Fonts K, Robotham SA, Matouschek A, Brodbelt JS. Top-down 193-nm ultraviolet photodissociation mass spectrometry for simultaneous determination of polyubiquitin chain length and topology. Anal Chem 2015; 87:1812-20. [PMID: 25559986 PMCID: PMC4318624 DOI: 10.1021/ac5038363] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/01/2015] [Indexed: 11/29/2022]
Abstract
Protein ubiquitin modifications present a vexing analytical challenge, because of the dynamic changes in the site of modification on the substrate, the number of ubiquitin moieties attached, and the diversity of linkage patterns in which they are attached. Presented here is a method to confidently assign size and linkage type of polyubiquitin modifications. The method combines intact mass measurement to determine the number of ubiquitin moieties in the chain with backbone fragmentation by 193-nm ultraviolet photodissociation (UVPD) to determine the linkage pattern. UVPD fragmentation of proteins leads to reproducible backbone cleavage at almost every inter-residue position, and in polyubiquitin chains, the N-terminally derived fragments from each constituent monomer are identical, up to the site of conjugation. The N-terminal ubiquitin fragment ions are superimposed to create a diagnostic pattern that allows easy recognition of the dominant chain linkages. The method is demonstrated by achieving almost-complete fragmentation of monoubiquitin and then, subsequently, fragmentation of dimeric, tetrameric, and longer Lys48- and Lys63-linked ubiquitin chains. The utility of the method for the analysis of mixed linkage chains is confirmed for mixtures of Lys48 and Lys63 tetramers with known relative concentrations and for an in vitro-formulated ubiquitin chain attached to a substrate protein.
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Affiliation(s)
- Joe R. Cannon
- Department
of Chemistry, University of Texas, 105 E. 24th St., Austin, Texas 78712, United States
| | - Kirby Martinez-Fonts
- Department
of Molecular Biosciences, University of
Texas, Austin, Texas 78712, United
States
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Scott A. Robotham
- Department
of Chemistry, University of Texas, 105 E. 24th St., Austin, Texas 78712, United States
| | - Andreas Matouschek
- Department
of Molecular Biosciences, University of
Texas, Austin, Texas 78712, United
States
| | - Jennifer S. Brodbelt
- Department
of Chemistry, University of Texas, 105 E. 24th St., Austin, Texas 78712, United States
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44
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Fishbain S, Inobe T, Israeli E, Chavali S, Yu H, Kago G, Babu MM, Matouschek A. Sequence composition of disordered regions fine-tunes protein half-life. Nat Struct Mol Biol 2015; 22:214-21. [PMID: 25643324 PMCID: PMC4351145 DOI: 10.1038/nsmb.2958] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 12/19/2014] [Indexed: 02/02/2023]
Abstract
The proteasome controls the concentrations of most proteins in eukaryotic cells. It recognizes its protein substrates through ubiquitin tags and initiates degradation at disordered regions within the substrate. Here we find that the proteasome has pronounced preferences for the amino acid sequence composition of the regions at which it initiates degradation. Specifically, proteins where the initiation regions have biased amino acid compositions show longer half-lives in yeast. The relationship is also observed on a genomic scale in mouse cells. These preferences affect the degradation rates of proteins in vitro, can explain the unexpected stability of natural proteins in yeast, and may affect the accumulation of toxic proteins in disease. We propose that the proteasome’s sequence preferences provide a second component to the degradation code and may fine-tune protein half-life in cells.
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Affiliation(s)
- Susan Fishbain
- 1] Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA. [2] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Tomonao Inobe
- 1] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA. [2] Frontier Research Core for Life Sciences, University of Toyama, Toyama, Japan
| | - Eitan Israeli
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Sreenivas Chavali
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Houqing Yu
- 1] Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA. [2] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Grace Kago
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andreas Matouschek
- 1] Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA. [2] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA. [3]
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45
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Han DH, Na HK, Choi WH, Lee JH, Kim YK, Won C, Lee SH, Kim KP, Kuret J, Min DH, Lee MJ. Direct cellular delivery of human proteasomes to delay tau aggregation. Nat Commun 2014; 5:5633. [PMID: 25476420 DOI: 10.1038/ncomms6633] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 10/21/2014] [Indexed: 12/12/2022] Open
Abstract
The 26S proteasome is the primary machinery that degrades ubiquitin (Ub)-conjugated proteins, including many proteotoxic proteins implicated in neurodegeneraton. It has been suggested that the elevation of proteasomal activity is tolerable to cells and may be beneficial to prevent the accumulation of protein aggregates. Here we show that purified proteasomes can be directly transported into cells through mesoporous silica nanoparticle-mediated endocytosis. Proteasomes that are loaded onto nanoparticles through non-covalent interactions between polyhistidine tags and nickel ions fully retain their proteolytic activity. Cells treated with exogenous proteasomes are more efficient in degrading overexpressed human tau than endogenous proteasomal substrates, resulting in decreased levels of tau aggregates. Moreover, exogenous proteasome delivery significantly promotes cell survival against proteotoxic stress caused by tau and reactive oxygen species. These data demonstrate that increasing cellular proteasome activity through the direct delivery of purified proteasomes may be an effective strategy for reducing cellular levels of proteotoxic proteins.
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Affiliation(s)
- Dong Hoon Han
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Hee-Kyung Na
- Center for RNA Research, Department of Chemistry, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea
| | - Won Hoon Choi
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Jung Hoon Lee
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Yun Kyung Kim
- Center for Neuro-Medicine, Korea Institute of Science &Technology (KIST), Seoul 136-791, Republic of Korea
| | - Cheolhee Won
- Center for RNA Research, Department of Chemistry, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea
| | - Seung-Han Lee
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Jeff Kuret
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
| | - Dal-Hee Min
- Center for RNA Research, Department of Chemistry, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea
| | - Min Jae Lee
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
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46
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Park S, Krist DT, Statsyuk AV. Protein ubiquitination and formation of polyubiquitin chains without ATP, E1 and E2 enzymes. Chem Sci 2014; 6:1770-1779. [PMID: 28706640 PMCID: PMC5485889 DOI: 10.1039/c4sc02340d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 11/26/2014] [Indexed: 01/08/2023] Open
Abstract
Protein ubiquitination without ATP. This paper reports a chemical strategy to ubiquitinate proteins without ATP, E1, and E2 enzymes, offering new insights on the biochemical mechanism of E3s.
Studying protein ubiquitination is difficult due to the complexity of the E1–E2–E3 ubiquitination cascade. Here we report the discovery that C-terminal ubiquitin thioesters can undergo direct transthiolation with the catalytic cysteine of the model HECT E3 ubiquitin ligase Rsp5 to form a catalytically active Rsp5∼ubiquitin thioester (Rsp5∼Ub). The resulting Rsp5∼Ub undergoes efficient autoubiquitination, ubiquitinates protein substrates, and synthesizes polyubiquitin chains with native Ub isopeptide linkage specificity. Since the developed chemical system bypasses the need for ATP, E1 and E2 enzymes while maintaining the native HECT E3 mechanism, we named it “Bypassing System” (ByS). Importantly, ByS provides direct evidence that E2 enzymes are dispensable for K63 specific isopeptide bond formation between ubiquitin molecules by Rsp5 in vitro. Additionally, six other E3 enzymes including Nedd4-1, Nedd4-2, Itch, and Wwp1 HECT ligases, along with Parkin and HHARI RBR ligases processed Ub thioesters under ByS reaction conditions. These findings provide general mechanistic insights on protein ubiquitination, and offer new strategies for assay development to discover pharmacological modulators of E3 enzymes.
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Affiliation(s)
- Sungjin Park
- Department of Chemistry , Center for Molecular Innovation and Drug Discovery , Chemistry of Life Processes Institute , Northwestern University , Silverman Hall, 2145 Sheridan Road , Evanston , Illinois 60208 , USA .
| | - David T Krist
- Department of Chemistry , Center for Molecular Innovation and Drug Discovery , Chemistry of Life Processes Institute , Northwestern University , Silverman Hall, 2145 Sheridan Road , Evanston , Illinois 60208 , USA .
| | - Alexander V Statsyuk
- Department of Chemistry , Center for Molecular Innovation and Drug Discovery , Chemistry of Life Processes Institute , Northwestern University , Silverman Hall, 2145 Sheridan Road , Evanston , Illinois 60208 , USA .
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47
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Fang NN, Chan GT, Zhu M, Comyn SA, Persaud A, Deshaies RJ, Rotin D, Gsponer J, Mayor T. Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress. Nat Cell Biol 2014; 16:1227-37. [PMID: 25344756 PMCID: PMC5224936 DOI: 10.1038/ncb3054] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 09/17/2014] [Indexed: 12/14/2022]
Abstract
The heat-shock response is a complex cellular program that induces major changes in protein translation, folding and degradation to alleviate toxicity caused by protein misfolding. Although heat shock has been widely used to study proteostasis, it remained unclear how misfolded proteins are targeted for proteolysis in these conditions. We found that Rsp5 and its mammalian homologue Nedd4 are important E3 ligases responsible for the increased ubiquitylation induced by heat stress. We determined that Rsp5 ubiquitylates mainly cytosolic misfolded proteins upon heat shock for proteasome degradation. We found that ubiquitylation of heat-induced substrates requires the Hsp40 co-chaperone Ydj1 that is further associated with Rsp5 upon heat shock. In addition, ubiquitylation is also promoted by PY Rsp5-binding motifs found primarily in the structured regions of stress-induced substrates, which can act as heat-induced degrons. Our results support a bipartite recognition mechanism combining direct and chaperone-dependent ubiquitylation of misfolded cytosolic proteins by Rsp5.
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Affiliation(s)
- Nancy N Fang
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall Vancouver, British Columbia V6T1Z4, Canada
| | - Gerard T Chan
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall Vancouver, British Columbia V6T1Z4, Canada
| | - Mang Zhu
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall Vancouver, British Columbia V6T1Z4, Canada
| | - Sophie A Comyn
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall Vancouver, British Columbia V6T1Z4, Canada
| | - Avinash Persaud
- Program in Cell Biology, Hospital for Sick Children, and Biochemistry Department, University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Raymond J Deshaies
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, 114-96 Caltech, 1200 E. California Boulevard Pasadena, California 91125, USA
| | - Daniela Rotin
- Program in Cell Biology, Hospital for Sick Children, and Biochemistry Department, University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Joerg Gsponer
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall Vancouver, British Columbia V6T1Z4, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall Vancouver, British Columbia V6T1Z4, Canada
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48
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N-terminal α7 deletion of the proteasome 20S core particle substitutes for yeast PI31 function. Mol Cell Biol 2014; 35:141-52. [PMID: 25332237 DOI: 10.1128/mcb.00582-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The proteasome core particle (CP) is a conserved protease complex that is formed by the stacking of two outer α-rings and two inner β-rings. The α-ring is a heteroheptameric ring of subunits α1 to α7 and acts as a gate that restricts entry of substrate proteins into the catalytic cavity formed by the two abutting β-rings. The 31-kDa proteasome inhibitor (PI31) was originally identified as a protein that binds to the CP and inhibits CP activity in vitro, but accumulating evidence indicates that PI31 is required for physiological proteasome activity. To clarify the in vivo role of PI31, we examined the Saccharomyces cerevisiae PI31 ortholog Fub1. Fub1 was essential in a situation where the CP assembly chaperone Pba4 was deleted. The lethality of Δfub1 Δpba4 was suppressed by deletion of the N terminus of α7 (α7ΔN), which led to the partial activation of the CP. However, deletion of the N terminus of α3, which activates the CP more efficiently than α7ΔN by gate opening, did not suppress Δfub1 Δpba4 lethality. These results suggest that the α7 N terminus has a role in CP activation different from that of the α3 N terminus and that the role of Fub1 antagonizes a specific function of the α7 N terminus.
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49
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Piterman R, Braunstein I, Isakov E, Ziv T, Navon A, Cohen S, Stanhill A. VWA domain of S5a restricts the ability to bind ubiquitin and Ubl to the 26S proteasome. Mol Biol Cell 2014; 25:3988-98. [PMID: 25318673 PMCID: PMC4263443 DOI: 10.1091/mbc.e13-11-0697] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The only stoichiometric proteasomal subunit found to reside outside the proteasome is the ubiquitin receptor S5a. S5a-dependent binding of substrates and shuttle factors is restricted to occur only on the proteasome, thus increasing efficiency of substrate degradation by the 26S proteasome. The 26S proteasome recognizes a vast number of ubiquitin-dependent degradation signals linked to various substrates. This recognition is mediated mainly by the stoichiometric proteasomal resident ubiquitin receptors S5a and Rpn13, which harbor ubiquitin-binding domains. Regulatory steps in substrate binding, processing, and subsequent downstream proteolytic events by these receptors are poorly understood. Here we demonstrate that mammalian S5a is present in proteasome-bound and free states. S5a is required for efficient proteasomal degradation of polyubiquitinated substrates and the recruitment of ubiquitin-like (Ubl) harboring proteins; however, S5a-mediated ubiquitin and Ubl binding occurs only on the proteasome itself. We identify the VWA domain of S5a as a domain that limits ubiquitin and Ubl binding to occur only upon proteasomal association. Multiubiquitination events within the VWA domain can further regulate S5a association. Our results provide a molecular explanation to how ubiquitin and Ubl binding to S5a is restricted to the 26S proteasome.
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Affiliation(s)
- Ravit Piterman
- Department of Biochemistry, Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Ilana Braunstein
- Department of Biochemistry, Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Elada Isakov
- Department of Biochemistry, Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ami Navon
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shenhav Cohen
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Stanhill
- Department of Biochemistry, Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, Haifa 31096, Israel
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50
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Besche HC, Sha Z, Kukushkin NV, Peth A, Hock EM, Kim W, Gygi S, Gutierrez JA, Liao H, Dick L, Goldberg AL. Autoubiquitination of the 26S proteasome on Rpn13 regulates breakdown of ubiquitin conjugates. EMBO J 2014; 33:1159-76. [PMID: 24811749 PMCID: PMC4193922 DOI: 10.1002/embj.201386906] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 03/12/2014] [Accepted: 04/01/2014] [Indexed: 11/09/2022] Open
Abstract
Degradation rates of most proteins in eukaryotic cells are determined by their rates of ubiquitination. However, possible regulation of the proteasome's capacity to degrade ubiquitinated proteins has received little attention, although proteasome inhibitors are widely used in research and cancer treatment. We show here that mammalian 26S proteasomes have five associated ubiquitin ligases and that multiple proteasome subunits are ubiquitinated in cells, especially the ubiquitin receptor subunit, Rpn13. When proteolysis is even partially inhibited in cells or purified 26S proteasomes with various inhibitors, Rpn13 becomes extensively and selectively poly-ubiquitinated by the proteasome-associated ubiquitin ligase, Ube3c/Hul5. This modification also occurs in cells during heat-shock or arsenite treatment, when poly-ubiquitinated proteins accumulate. Rpn13 ubiquitination strongly decreases the proteasome's ability to bind and degrade ubiquitin-conjugated proteins, but not its activity against peptide substrates. This autoinhibitory mechanism presumably evolved to prevent binding of ubiquitin conjugates to defective or stalled proteasomes, but this modification may also be useful as a biomarker indicating the presence of proteotoxic stress and reduced proteasomal capacity in cells or patients.
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Affiliation(s)
| | - Zhe Sha
- Harvard Medical School, Boston, MA, USA
| | | | | | | | - Woong Kim
- Harvard Medical School, Boston, MA, USA
| | | | | | - Hua Liao
- Millennium Pharmaceuticals Inc., Cambridge, MA, USA
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