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Mondal P, Krishnamurthy VV, Sharum SR, Haack N, Zhou H, Cheng J, Yang J, Zhang K. Repurposing Protein Degradation for Optogenetic Modulation of Protein Activities. ACS Synth Biol 2019; 8:2585-2592. [PMID: 31600062 DOI: 10.1021/acssynbio.9b00285] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Non-neuronal optogenetic approaches empower precise regulation of protein dynamics in live cells but often require target-specific protein engineering. To address this challenge, we developed a generalizable light-modulated protein stabilization system (GLIMPSe) to control the intracellular protein level independent of its functionality. We applied GLIMPSe to control two distinct classes of proteins: mitogen-activated protein kinase phosphatase 3 (MKP3), a negative regulator of the extracellular signal-regulated kinase (ERK) pathway, and a constitutively active form of MEK (CA MEK), a positive regulator of the same pathway. Kinetics study showed that light-induced protein stabilization could be achieved within 30 min of blue light stimulation. GLIMPSe enables target-independent optogenetic control of protein activities and therefore minimizes the systematic variation embedded within different photoactivatable proteins. Overall, GLIMPSe promises to achieve light-mediated post-translational stabilization of a wide array of target proteins in live cells.
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Affiliation(s)
| | | | | | | | | | | | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana−Champaign, 2001 S Lincoln Avenue, Urbana, Illinois 61802, United States
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Chadchankar J, Korboukh V, Conway LC, Wobst HJ, Walker CA, Doig P, Jacobsen SJ, Brandon NJ, Moss SJ, Wang Q. Inactive USP14 and inactive UCHL5 cause accumulation of distinct ubiquitinated proteins in mammalian cells. PLoS One 2019; 14:e0225145. [PMID: 31703099 PMCID: PMC6839854 DOI: 10.1371/journal.pone.0225145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/29/2019] [Indexed: 12/12/2022] Open
Abstract
USP14 is a cysteine protease deubiquitinase associated with the proteasome and plays important catalytic and allosteric roles in proteasomal degradation. USP14 inhibition has been considered a therapeutic strategy for accelerating degradation of aggregation-prone proteins in neurodegenerative diseases and for inhibiting proteasome function to induce apoptotic cell death in cancers. Here we studied the effects of USP14 inhibition in mammalian cells using small molecule inhibitors and an inactive USP14 mutant C114A. Neither the inhibitors nor USP14 C114A showed consistent or significant effects on the level of TDP-43, tau or α-synuclein in HEK293T cells. However, USP14 C114A led to a robust accumulation of ubiquitinated proteins, which were isolated by ubiquitin immunoprecipitation and identified by mass spectrometry. Among these proteins we confirmed that ubiquitinated β-catenin accumulated in the cells expressing USP14 C114A with immunoblotting and immunoprecipitation experiments. The proteasome binding domain of USP14 C114A is required for its effect on ubiquitinated proteins. UCHL5 is the other cysteine protease deubiquitinase associated with the proteasome. Interestingly, the inactive mutant of UCHL5 C88A also caused an accumulation of ubiquitinated proteins in HEK293T cells but did not affect β-catenin, demonstrating USP14 but not UCHL5 has a specific effect on β-catenin. We used ubiquitin immunoprecipitation and mass spectrometry to identify the accumulated ubiquitinated proteins in UCHL5 C88A expressing cells which are mostly distinct from those identified in USP14 C114A expressing cells. Among the identified proteins are well established proteasome substrates and proteasome subunits. Besides β-catenin, we also verified with immunoblotting that UCHL5 C88A inhibits its own deubiquitination and USP14 C114A inhibits deubiquitination of two proteasomal subunits PSMC1 and PSMD4. Together our data suggest that USP14 and UCHL5 can deubiquitinate distinct substrates at the proteasome and regulate the ubiquitination of the proteasome itself which is tightly linked to its function.
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Affiliation(s)
- Jayashree Chadchankar
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Tufts University, Boston, MA, United States of America
| | - Victoria Korboukh
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, United States of America
| | - Leslie C. Conway
- AstraZeneca Tufts Laboratory for Basic and Translational Neuroscience, Tufts University, Boston, MA, United States of America
| | - Heike J. Wobst
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, United States of America
| | - Chandler A. Walker
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, United States of America
| | - Peter Doig
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, United States of America
| | - Steve J. Jacobsen
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, United States of America
| | - Nicholas J. Brandon
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, United States of America
| | - Stephen J. Moss
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, United States of America
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States of America
- Department of Neuroscience, Physiology and Pharmacology, University College, London, United Kingdom
| | - Qi Wang
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, United States of America
- * E-mail:
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Proteasome Activation to Combat Proteotoxicity. Molecules 2019; 24:molecules24152841. [PMID: 31387243 PMCID: PMC6696185 DOI: 10.3390/molecules24152841] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Loss of proteome fidelity leads to the accumulation of non-native protein aggregates and oxidatively damaged species: hallmarks of an aged cell. These misfolded and aggregated species are often found, and suggested to be the culpable party, in numerous neurodegenerative diseases including Huntington's, Parkinson's, Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Diseases (AD). Many strategies for therapeutic intervention in proteotoxic pathologies have been put forth; one of the most promising is bolstering the efficacy of the proteasome to restore normal proteostasis. This strategy is ideal as monomeric precursors and oxidatively damaged proteins, so called "intrinsically disordered proteins" (IDPs), are targeted by the proteasome. This review will provide an overview of disorders in proteins, both intrinsic and acquired, with a focus on susceptibility to proteasomal degradation. We will then examine the proteasome with emphasis on newly published structural data and summarize current known small molecule proteasome activators.
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Abstract
Skeletal muscle atrophy is a common side effect of most human diseases. Muscle loss is not only detrimental for the quality of life but it also dramatically impairs physiological processes of the organism and decreases the efficiency of medical treatments. While hypothesized for years, the existence of an atrophying programme common to all pathologies is still incompletely solved despite the discovery of several actors and key regulators of muscle atrophy. More than a decade ago, the discovery of a set of genes, whose expression at the mRNA levels were similarly altered in different catabolic situations, opened the way of a new concept: the presence of atrogenes, i.e. atrophy-related genes. Importantly, the atrogenes are referred as such on the basis of their mRNA content in atrophying muscles, the regulation at the protein level being sometimes more complicate to elucidate. It should be noticed that the atrogenes are markers of atrophy and that their implication as active inducers of atrophy is still an open question for most of them. While the atrogene family has grown over the years, it has mostly been incremented based on data coming from rodent models. Whether the rodent atrogenes are valid for humans still remain to be established. An "atrogene" was originally defined as a gene systematically up- or down-regulated in several catabolic situations. Even if recent works often restrict this notion to the up-regulation of a limited number of proteolytic enzymes, it is important to keep in mind the big picture view. In this review, we provide an update of the validated and potential rodent atrogenes and the metabolic pathways they belong, and based on recent work, their relevance in human physio-pathological situations. We also propose a more precise definition of the atrogenes that integrates rapid recovery when catabolic stimuli are stopped or replaced by anabolic ones.
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Affiliation(s)
- Daniel Taillandier
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, F-63000, Clermont-Ferrand, France.
| | - Cécile Polge
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, F-63000, Clermont-Ferrand, France
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Cellular Responses to Proteasome Inhibition: Molecular Mechanisms and Beyond. Int J Mol Sci 2019; 20:ijms20143379. [PMID: 31295808 PMCID: PMC6678303 DOI: 10.3390/ijms20143379] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023] Open
Abstract
Proteasome inhibitors have been actively tested as potential anticancer drugs and in the treatment of inflammatory and autoimmune diseases. Unfortunately, cells adapt to survive in the presence of proteasome inhibitors activating a variety of cell responses that explain why these therapies have not fulfilled their expected results. In addition, all proteasome inhibitors tested and approved by the FDA have caused a variety of side effects in humans. Here, we describe the different types of proteasome complexes found within cells and the variety of regulators proteins that can modulate their activities, including those that are upregulated in the context of inflammatory processes. We also summarize the adaptive cellular responses activated during proteasome inhibition with special emphasis on the activation of the Autophagic-Lysosomal Pathway (ALP), proteaphagy, p62/SQSTM1 enriched-inclusion bodies, and proteasome biogenesis dependent on Nrf1 and Nrf2 transcription factors. Moreover, we discuss the role of IRE1 and PERK sensors in ALP activation during ER stress and the involvement of two deubiquitinases, Rpn11 and USP14, in these processes. Finally, we discuss the aspects that should be currently considered in the development of novel strategies that use proteasome activity as a therapeutic target for the treatment of human diseases.
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Electrochemical assay for 20S proteasome activity and inhibition with anti-cancer drugs. Talanta 2019; 199:32-39. [DOI: 10.1016/j.talanta.2019.02.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 01/09/2023]
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Aristizábal D, Rivas V, Cassab GI, Lledías F. Heat stress reveals high molecular mass proteasomes in Arabidopsis thaliana suspension cells cultures. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 140:78-87. [PMID: 31085449 DOI: 10.1016/j.plaphy.2019.04.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/01/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Because of their sessile nature, plants have evolved complex and robust mechanisms to respond to adverse environments. Stress conditions trigger an increase in protein turnover and degradation. Proteasomes are essential to the cell for removing, in a highly regulated manner, partially denatured or oxidized proteins thus minimizing their cytotoxicity. We observed that suspension cells of Arabidopsis thaliana treated with high temperature (37 °C) directed the assembly of high molecular mass proteasomes. The removal of a 75% of the original ubiquitin conjugates and the maintenance of protein carbonyls at basal levels correlated with a specific proteasome profiles. The profiles obtained by the separation of different proteasomes populations by Blue-Native Polyacrylamide Gel Electrophoresis and western blot analysis suggest that synthesis, assembly, and heavy ubiquitination of 20S (CP) subunits are promoted by heat stress.
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Affiliation(s)
- Daniel Aristizábal
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor, 62250, Mexico
| | - Viridiana Rivas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor, 62250, Mexico
| | - Gladys I Cassab
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor, 62250, Mexico
| | - Fernando Lledías
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor, 62250, Mexico.
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Sequiera GL, Sareen N, Sharma V, Surendran A, Abu-El-Rub E, Ravandi A, Dhingra S. High throughput screening reveals no significant changes in protein synthesis, processing, and degradation machinery during passaging of mesenchymal stem cells. Can J Physiol Pharmacol 2019; 97:536-543. [DOI: 10.1139/cjpp-2018-0553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Increasing reports of successful and safe application of bone marrow derived mesenchymal stem cells (BM-MSCs) for cell therapy are pouring in from numerous studies. However poor survival of transplanted cells in the recipient has impaired the benefits of BM-MSCs based therapies. Therefore cell product preparation procedures pertaining to MSC therapy need to be optimized to improve the survival of transplanted cells. One of the important ex vivo procedures in the preparation of cells for therapy is passaging of BM-MSCs to ensure a suitable number of cells for transplantation, which may affect the turnover of proteins involved in regulation of cell survival and (or) death pathways. In the current study, we investigated the effect of an increase in passage number of BM-MSCs in cell culture on the intracellular protein turnover (protein synthesis, processing, and degradation machinery). We performed proteomic analysis of BM-MSCs at different passages. There was no significant difference observed in the ribosomal, protein processing, and proteasomal pathways related proteins in BM-MSCs with an increase in passage number from P3 to P7. Therefore, expansion of MSCs in the cell culture in clinically relevant passages (Passage 3–7) does not affect the quality of MSCs in terms of intracellular protein synthesis and turnover.
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Affiliation(s)
- Glen Lester Sequiera
- Institute of Cardiovascular Sciences, St. Boniface Hospital Research Centre, Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
| | - Niketa Sareen
- Institute of Cardiovascular Sciences, St. Boniface Hospital Research Centre, Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
| | - Vikram Sharma
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, England
| | - Arun Surendran
- Institute of Cardiovascular Sciences, St. Boniface Hospital Research Centre, Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
| | - Ejlal Abu-El-Rub
- Institute of Cardiovascular Sciences, St. Boniface Hospital Research Centre, Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
| | - Amir Ravandi
- Institute of Cardiovascular Sciences, St. Boniface Hospital Research Centre, Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
| | - Sanjiv Dhingra
- Institute of Cardiovascular Sciences, St. Boniface Hospital Research Centre, Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
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Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx. Structure 2019; 27:923-936.e6. [DOI: 10.1016/j.str.2019.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/31/2019] [Accepted: 03/14/2019] [Indexed: 11/18/2022]
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Buneeva OA, Medvedev AE. [Ubiquitin-independent protein degradation in proteasomes]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2019; 64:134-148. [PMID: 29723144 DOI: 10.18097/pbmc20186402134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proteasomes are large supramolecular protein complexes present in all prokaryotic and eukaryotic cells, where they perform targeted degradation of intracellular proteins. Until recently, it was generally accepted that prior proteolytic degradation in proteasomes the proteins had to be targeted by ubiquitination: the ATP-dependent addition of (typically four sequential) residues of the low-molecular ubiquitin protein, involving the ubiquitin-activating enzyme, ubiquitin-conjugating enzyme and ubiquitin ligase. The cytoplasm and nucleoplasm proteins labeled in this way are then digested in 26S proteasomes. However, in recent years it has become increasingly clear that using this route the cell eliminates only a part of unwanted proteins. Many proteins can be cleaved by the 20S proteasome in an ATP-independent manner and without previous ubiquitination. Ubiquitin-independent protein degradation in proteasomes is a relatively new area of studies of the role of the ubiquitin-proteasome system. However, recent data obtained in this direction already correct existing concepts about proteasomal degradation of proteins and its regulation. Ubiquitin-independent proteasome degradation needs the main structural precondition in proteins: the presence of unstructured regions in the amino acid sequences that provide interaction with the proteasome. Taking into consideration that in humans almost half of all genes encode proteins that contain a certain proportion of intrinsically disordered regions, it appears that the list of proteins undergoing ubiquitin-independent degradation will demonstrate further increase. Since 26S of proteasomes account for only 30% of the total proteasome content in mammalian cells, most of the proteasomes exist in the form of 20S complexes. The latter suggests that ubiquitin-independent proteolysis performed by the 20S proteasome is a natural process of removing damaged proteins from the cell and maintaining a constant level of intrinsically disordered proteins. In this case, the functional overload of proteasomes in aging and/or other types of pathological processes, if it is not accompanied by triggering more radical mechanisms for the elimination of damaged proteins, organelles and whole cells, has the most serious consequences for the whole organism.
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Affiliation(s)
- O A Buneeva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
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Mutational and Combinatorial Control of Self-Assembling and Disassembling of Human Proteasome α Subunits. Int J Mol Sci 2019; 20:ijms20092308. [PMID: 31075988 PMCID: PMC6539845 DOI: 10.3390/ijms20092308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic proteasomes harbor heteroheptameric α-rings, each composed of seven different but homologous subunits α1–α7, which are correctly assembled via interactions with assembly chaperones. The human proteasome α7 subunit is reportedly spontaneously assembled into a homotetradecameric double ring, which can be disassembled into single rings via interaction with monomeric α6. We comprehensively characterized the oligomeric state of human proteasome α subunits and demonstrated that only the α7 subunit exhibits this unique, self-assembling property and that not only α6 but also α4 can disrupt the α7 double ring. We also demonstrated that mutationally monomerized α7 subunits can interact with the intrinsically monomeric α4 and α6 subunits, thereby forming heterotetradecameric complexes with a double-ring structure. The results of this study provide additional insights into the mechanisms underlying the assembly and disassembly of proteasomal subunits, thereby offering clues for the design and creation of circularly assembled hetero-oligomers based on homo-oligomeric structural frameworks.
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Satoh T, Yagi-Utsumi M, Okamoto K, Kurimoto E, Tanaka K, Kato K. Molecular and Structural Basis of the Proteasome α Subunit Assembly Mechanism Mediated by the Proteasome-Assembling Chaperone PAC3-PAC4 Heterodimer. Int J Mol Sci 2019; 20:ijms20092231. [PMID: 31067643 PMCID: PMC6539346 DOI: 10.3390/ijms20092231] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 01/07/2023] Open
Abstract
The 26S proteasome is critical for the selective degradation of proteins in eukaryotic cells. This enzyme complex is composed of approximately 70 subunits, including the structurally homologous proteins α1–α7, which combine to form heptameric rings. The correct arrangement of these α subunits is essential for the function of the proteasome, but their assembly does not occur autonomously. Assembly of the α subunit is assisted by several chaperones, including the PAC3-PAC4 heterodimer. In this study we showed that the PAC3-PAC4 heterodimer functions as a molecular matchmaker, stabilizing the α4-α5-α6 subcomplex during the assembly of the α-ring. We solved a 0.96-Å atomic resolution crystal structure for a PAC3 homodimer which, in conjunction with nuclear magnetic resonance (NMR) data, highlighted the mobility of the loop comprised of residues 51 to 61. Based on these structural and dynamic data, we created a three-dimensional model of the PAC3-4/α4/α5/α6 quintet complex, and used this model to investigate the molecular and structural basis of the mechanism of proteasome α subunit assembly, as mediated by the PAC3-PAC4 heterodimeric chaperone. Our results provide a potential basis for the development of selective inhibitors against proteasome biogenesis.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.
| | - Kenta Okamoto
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya 468-8503, Japan.
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.
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Hwang H, Jin Z, Krishnamurthy VV, Saha A, Klein PS, Garcia B, Mei W, King ML, Zhang K, Yang J. Novel functions of the ubiquitin-independent proteasome system in regulating Xenopus germline development. Development 2019; 146:dev172700. [PMID: 30910828 PMCID: PMC6503979 DOI: 10.1242/dev.172700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/20/2019] [Indexed: 01/22/2023]
Abstract
In most species, early germline development occurs in the absence of transcription with germline determinants subject to complex translational and post-translational regulations. Here, we report for the first time that early germline development is influenced by dynamic regulation of the proteasome system, previously thought to be ubiquitously expressed and to serve 'housekeeping' roles in controlling protein homeostasis. We show that proteasomes are present in a gradient with the highest levels in the animal hemisphere and extending into the vegetal hemisphere of Xenopus oocytes. This distribution changes dramatically during the oocyte-to-embryo transition, with proteasomes becoming enriched in and restricted to the animal hemisphere and therefore separated from vegetally localized germline determinants. We identify Dead-end1 (Dnd1), a master regulator of vertebrate germline development, as a novel substrate of the ubiquitin-independent proteasomes. In the oocyte, ubiquitin-independent proteasomal degradation acts together with translational repression to prevent premature accumulation of Dnd1 protein. In the embryo, artificially increasing ubiquitin-independent proteasomal degradation in the vegetal pole interferes with germline development. Our work thus reveals novel inhibitory functions and spatial regulation of the ubiquitin-independent proteasome during vertebrate germline development.
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Affiliation(s)
- Hyojeong Hwang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, 3411 Veterinary Medicine Basic Sciences Building, Urbana, IL 61802, USA
| | - Zhigang Jin
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, 3411 Veterinary Medicine Basic Sciences Building, Urbana, IL 61802, USA
- College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang 321004, China
| | - Vishnu Vardhan Krishnamurthy
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S Mathews, 314B Roger Adams Laboratory, Urbana, IL 61801, USA
| | - Anumita Saha
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Peter S Klein
- Department of Medicine (Hematology-Oncology), Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Wenyan Mei
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, 3411 Veterinary Medicine Basic Sciences Building, Urbana, IL 61802, USA
| | - Mary Lou King
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S Mathews, 314B Roger Adams Laboratory, Urbana, IL 61801, USA
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, 3411 Veterinary Medicine Basic Sciences Building, Urbana, IL 61802, USA
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Xue C, Liu S, Chen C, Zhu J, Yang X, Zhou Y, Guo R, Liu X, Gong Z. Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in Oryza Sativa. Proteomics 2019; 18. [PMID: 29106068 DOI: 10.1002/pmic.201700036] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 10/11/2017] [Indexed: 01/26/2023]
Abstract
Lysine acetylation (Kac) is an important protein post-translational modification in both eukaryotes and prokaryotes. Herein, we report the results of a global proteome analysis of Kac and its diverse functions in rice (Oryza sativa). We identified 1353 Kac sites in 866 proteins in rice seedlings. A total of 11 Kac motifs are conserved, and 45% of the identified proteins are localized to the chloroplast. Among all acetylated proteins, 38 Kac sites are combined in core histones. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Protein-protein interaction networks of the identified proteins provided further evidence that Kac contributes to a wide range of regulatory functions. Furthermore, we demonstrated that the acetylation level of histone H3 (lysine 27 and 36) is increased in response to cold stress. In summary, our approach comprehensively profiles the regulatory roles of Kac in the growth and development of rice.
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Affiliation(s)
- Chao Xue
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Shuai Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Jun Zhu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, P. R. China
| | - Xibin Yang
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, P. R. China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Rui Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Xiaoyu Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
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66
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Ubiquitin-dependent switch during assembly of the proteasomal ATPases mediated by Not4 ubiquitin ligase. Proc Natl Acad Sci U S A 2018; 115:13246-13251. [PMID: 30530678 DOI: 10.1073/pnas.1805353115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the proteasome holoenzyme, the hexameric ATPases (Rpt1-Rpt6) enable degradation of ubiquitinated proteins by unfolding and translocating them into the proteolytic core particle. During early-stage proteasome assembly, individual Rpt proteins assemble into the hexameric "Rpt ring" through binding to their cognate chaperones: Nas2, Hsm3, Nas6, and Rpn14. Here, we show that Rpt ring assembly employs a specific ubiquitination-mediated control. An E3 ligase, Not4, selectively ubiquitinates Rpt5 during Rpt ring assembly. To access Rpt5, Not4 competes with Nas2 until the penultimate step and then with Hsm3 at the final step of Rpt ring completion. Using the known Rpt-chaperone cocrystal structures, we show that Not4-mediated ubiquitination sites in Rpt5 are obstructed by Nas2 and Hsm3. Thus, Not4 can distinguish a Rpt ring that matures without these chaperones, based on its accessibility to Rpt5. Rpt5 ubiquitination does not destabilize the ring but hinders incorporation of incoming subunits-Rpn1 ubiquitin receptor and Ubp6 deubiquitinase-thereby blocking progression of proteasome assembly and ubiquitin regeneration from proteasome substrates. Our findings reveal an assembly checkpoint where Not4 monitors chaperone actions during hexameric ATPase ring assembly, thereby ensuring the accuracy of proteasome holoenzyme maturation.
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67
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Kühnle S, Martínez-Noël G, Leclere F, Hayes SD, Harper JW, Howley PM. Angelman syndrome-associated point mutations in the Zn 2+-binding N-terminal (AZUL) domain of UBE3A ubiquitin ligase inhibit binding to the proteasome. J Biol Chem 2018; 293:18387-18399. [PMID: 30257870 PMCID: PMC6254356 DOI: 10.1074/jbc.ra118.004653] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/16/2018] [Indexed: 12/26/2022] Open
Abstract
Deregulation of the HECT ubiquitin ligase UBE3A/E6AP has been implicated in Angelman syndrome as well as autism spectrum disorders. We and others have previously identified the 26S proteasome as one of the major UBE3A-interacting protein complexes. Here, we characterize the interaction of UBE3A and the proteasomal subunit PSMD4 (Rpn10/S5a). We map the interaction to the highly conserved Zn2+-binding N-terminal (AZUL) domain of UBE3A, the integrity of which is crucial for binding to PSMD4. Interestingly, two Angelman syndrome point mutations that affect the AZUL domain show an impaired ability to bind PSMD4. Although not affecting the ubiquitin ligase or the estrogen receptor α-mediated transcriptional regulation activities, these AZUL domain mutations prevent UBE3A from stimulating the Wnt/β-catenin signaling pathway. Taken together, our data indicate that impaired binding to the 26S proteasome and consequential deregulation of Wnt/β-catenin signaling might contribute to the functional defect of these mutants in Angelman syndrome.
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Affiliation(s)
- Simone Kühnle
- From the Departments of Microbiology and Immunobiology and
| | | | | | | | - J Wade Harper
- Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Peter M Howley
- From the Departments of Microbiology and Immunobiology and.
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68
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Pishesha N, Ingram JR, Ploegh HL. Sortase A: A Model for Transpeptidation and Its Biological Applications. Annu Rev Cell Dev Biol 2018; 34:163-188. [PMID: 30110557 DOI: 10.1146/annurev-cellbio-100617-062527] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular biologists and chemists alike have long sought to modify proteins with substituents that cannot be installed by standard or even advanced genetic approaches. We here describe the use of transpeptidases to achieve these goals. Living systems encode a variety of transpeptidases and peptide ligases that allow for the enzyme-catalyzed formation of peptide bonds, and protein engineers have used directed evolution to enhance these enzymes for biological applications. We focus primarily on the transpeptidase sortase A, which has become popular over the past few years for its ability to perform a remarkably wide variety of protein modifications, both in vitro and in living cells.
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Affiliation(s)
- Novalia Pishesha
- Program in Molecular and Cellular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jessica R Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Hidde L Ploegh
- Program in Molecular and Cellular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
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69
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Jalovecka M, Hartmann D, Miyamoto Y, Eckmann L, Hajdusek O, O'Donoghue AJ, Sojka D. Validation of Babesia proteasome as a drug target. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:394-402. [PMID: 30103207 PMCID: PMC6092455 DOI: 10.1016/j.ijpddr.2018.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 11/06/2022]
Abstract
Babesiosis is a tick-transmitted zoonosis caused by apicomplexan parasites of the genus Babesia. Treatment of this emerging malaria-related disease has relied on antimalarial drugs and antibiotics. The proteasome of Plasmodium, the causative agent of malaria, has recently been validated as a target for anti-malarial drug development and therefore, in this study, we investigated the effect of epoxyketone (carfilzomib, ONX-0914 and epoxomicin) and boronic acid (bortezomib and ixazomib) proteasome inhibitors on the growth and survival of Babesia. Testing the compounds against Babesia divergens ex vivo revealed suppressive effects on parasite growth with activity that was higher than the cytotoxic effects on a non-transformed mouse macrophage cell line. Furthermore, we showed that the most-effective compound, carfilzomib, significantly reduces parasite multiplication in a Babesia microti infected mouse model without noticeable adverse effects. In addition, treatment with carfilzomib lead to an ex vivo and in vivo decrease in proteasome activity and accumulation of polyubiquitinated proteins compared to untreated control. Overall, our results demonstrate that the Babesia proteasome is a valid target for drug development and warrants the design of potent and selective B. divergens proteasome inhibitors for the treatment of babesiosis.
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Affiliation(s)
- Marie Jalovecka
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, CZ-370 05, Ceske Budejovice, Czech Republic
| | - David Hartmann
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, CZ-370 05, Ceske Budejovice, Czech Republic
| | - Yukiko Miyamoto
- Department of Medicine, University of California, San Diego, La Jolla, USA
| | - Lars Eckmann
- Department of Medicine, University of California, San Diego, La Jolla, USA
| | - Ondrej Hajdusek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05, Ceske Budejovice, Czech Republic
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA.
| | - Daniel Sojka
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05, Ceske Budejovice, Czech Republic.
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70
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Aim for the core: suitability of the ubiquitin-independent 20S proteasome as a drug target in neurodegeneration. Transl Res 2018; 198:48-57. [PMID: 30244692 PMCID: PMC6154511 DOI: 10.1016/j.trsl.2018.05.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023]
Abstract
Neurodegenerative diseases are a class of age-associated proteopathies characterized by the accumulation of misfolded and/or aggregation-prone proteins. This imbalance has been attributed, in part, to an age-dependent decay in the capacity of protein turnover. Most proteins are degraded by the ubiquitin-proteasome system (UPS), which is composed of ubiquitin ligases and regulatory particles, such as the 19S, that deliver cargo to the proteolytically active 20S proteasome (20S) core. However, a subset of clients, especially intrinsically disordered proteins (IDPs), are also removed by the action of the ubiquitin-independent proteasome system (UIPS). What are the specific contributions of the UPS and UIPS in the context of neurodegeneration? Here, we explore how age-associated changes in the relative contribution of the UPS and UIPS, combined with the IDP-like structure of many neurodegenerative disease-associated proteins, might contribute. Strikingly, the 20S has been shown to predominate in older neurons and to preferentially act on relevant substrates, such as synuclein and tau. Moreover, pharmacological activation of the 20S has been shown to accelerate removal of aggregation-prone proteins in some models. Together, these recent studies are turning attention to the 20S and the UIPS as potential therapeutic targets in neurodegeneration.
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71
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Monda JK, Cheeseman IM. Nde1 promotes diverse dynein functions through differential interactions and exhibits an isoform-specific proteasome association. Mol Biol Cell 2018; 29:2336-2345. [PMID: 30024347 PMCID: PMC6249811 DOI: 10.1091/mbc.e18-07-0418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Nde1 is a key regulator of cytoplasmic dynein, binding directly to both dynein itself and the dynein adaptor, Lis1. Nde1 and Lis1 are thought to function together to promote dynein function, yet mutations in each result in distinct neurodevelopment phenotypes. To reconcile these phenotypic differences, we sought to dissect the contribution of Nde1 to dynein regulation and explore the cellular functions of Nde1. Here we show that an Nde1–Lis1 interaction is required for spindle pole focusing and Golgi organization but is largely dispensable for centrosome placement, despite Lis1 itself being required. Thus, diverse functions of dynein rely on distinct Nde1- and Lis1-mediated regulatory mechanisms. Additionally, we discovered a robust, isoform-specific interaction between human Nde1 and the 26S proteasome and identify precise mutations in Nde1 that disrupt the proteasome interaction. Together, our work suggests that Nde1 makes unique contributions to human neurodevelopment through its regulation of both dynein and proteasome function.
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Affiliation(s)
- Julie K Monda
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
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72
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Nabavi SF, Atanasov AG, Khan H, Barreca D, Trombetta D, Testai L, Sureda A, Tejada S, Vacca RA, Pittalà V, Gulei D, Berindan-Neagoe I, Shirooie S, Nabavi SM. Targeting ubiquitin-proteasome pathway by natural, in particular polyphenols, anticancer agents: Lessons learned from clinical trials. Cancer Lett 2018; 434:101-113. [PMID: 30030139 DOI: 10.1016/j.canlet.2018.07.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/21/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022]
Abstract
The ubiquitin-proteasome pathway (UPP) is the main non-lysosomal proteolytic system responsible for degradation of most intracellular proteins, specifically damaged and regulatory proteins. The UPP is implicated in all aspects of the cellular metabolic networks including physiological or pathological conditions. Alterations in the components of the UPP can lead to stabilization of oncoproteins or augmented degradation of tumour suppressor favouring cancer appearance and progression. Polyphenols are natural compounds that can modulate proteasome activity or the expression of proteasome subunits. All together and due to the pleiotropic functions of UPP, there is a great interest in this proteasome system as a promising therapeutic target for the development of novel anti-cancer drugs. In the present review, the main features of the UPP and its implication in cancer development and progression are described, highlighting the importance of bioactive polyphenols that target the UPP as potential anti-cancer agents.
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Affiliation(s)
- Seyed Fazel Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Atanas G Atanasov
- The Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Postępu 36A, Jastrzębiec, 05-552, Magdalenka, Poland; Department of Pharmacognosy, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakistan
| | - Davide Barreca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168, Messina, Italy.
| | - Domenico Trombetta
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168, Messina, Italy
| | - Lara Testai
- Department of Pharmacy, University of Pisa, Pisa, Italy; Interdepartmental Center of Nutrafood, University of Pisa, Pisa, Italy
| | - Antoni Sureda
- Research Group on Community Nutrition and Oxidative Stress (NUCOX) and CIBEROBN (Physiopathology of Obesity and Nutrition CB12/03/30038), University of Balearic Islands, Palma de Mallorca, E-07122, Balearic Islands, Spain
| | - Silvia Tejada
- Laboratory of Neurophysiology, Department of Biology, University of Balearic Islands, Ctra. Valldemossa, Km 7,5, Ed, Guillem Colom, 07122, Balearic Islands, Spain
| | - Rosa Anna Vacca
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Italian National Council of Research, Bari, Italy
| | - Valeria Pittalà
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Diana Gulei
- MEDFUTURE-Research Center for Advanced Medicine, "Iuliu-Hatieganu" University of Medicine and Pharmacy, Marinescu 23 Street, 400337, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- MEDFUTURE-Research Center for Advanced Medicine, "Iuliu-Hatieganu" University of Medicine and Pharmacy, Marinescu 23 Street, 400337, Cluj-Napoca, Romania; Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 400337, Cluj-Napoca, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34 Street, 400015, Cluj-Napoca, Romania
| | - Samira Shirooie
- Department of Pharmacology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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73
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Buneeva OA, Medvedev AE. Ubiquitin-Independent Degradation of Proteins in Proteasomes. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2018. [DOI: 10.1134/s1990750818030022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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74
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Bustamante HA, González AE, Cerda-Troncoso C, Shaughnessy R, Otth C, Soza A, Burgos PV. Interplay Between the Autophagy-Lysosomal Pathway and the Ubiquitin-Proteasome System: A Target for Therapeutic Development in Alzheimer's Disease. Front Cell Neurosci 2018; 12:126. [PMID: 29867359 PMCID: PMC5954036 DOI: 10.3389/fncel.2018.00126] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of age-related dementia leading to severe irreversible cognitive decline and massive neurodegeneration. While therapeutic approaches for managing symptoms are available, AD currently has no cure. AD associates with a progressive decline of the two major catabolic pathways of eukaryotic cells—the autophagy-lysosomal pathway (ALP) and the ubiquitin-proteasome system (UPS)—that contributes to the accumulation of harmful molecules implicated in synaptic plasticity and long-term memory impairment. One protein recently highlighted as the earliest initiator of these disturbances is the amyloid precursor protein (APP) intracellular C-terminal membrane fragment β (CTFβ), a key toxic agent with deleterious effects on neuronal function that has become an important pathogenic factor for AD and a potential biomarker for AD patients. This review focuses on the involvement of regulatory molecules and specific post-translational modifications (PTMs) that operate in the UPS and ALP to control a single proteostasis network to achieve protein balance. We discuss how these aspects can contribute to the development of novel strategies to strengthen the balance of key pathogenic proteins associated with AD.
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Affiliation(s)
- Hianara A Bustamante
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Alexis E González
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Fundación Ciencia y Vida, Santiago, Chile
| | - Cristobal Cerda-Troncoso
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ronan Shaughnessy
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carola Otth
- Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia, Chile.,Institute of Clinical Microbiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Andrea Soza
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia V Burgos
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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75
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Cotranslocational processing of the protein substrate calmodulin by an AAA+ unfoldase occurs via unfolding and refolding intermediates. Proc Natl Acad Sci U S A 2018; 115:E4786-E4795. [PMID: 29735657 DOI: 10.1073/pnas.1721811115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Protein remodeling by AAA+ enzymes is central for maintaining proteostasis in a living cell. However, a detailed structural description of how this is accomplished at the level of the substrate molecules that are acted upon is lacking. Here, we combine chemical cross-linking and methyl transverse relaxation-optimized NMR spectroscopy to study, at atomic resolution, the stepwise unfolding and subsequent refolding of the two-domain substrate calmodulin by the VAT AAA+ unfoldase from Thermoplasma acidophilum By engineering intermolecular disulphide bridges between the substrate and VAT we trap the substrate at different stages of translocation, allowing structural studies throughout the translocation process. Our results show that VAT initiates substrate translocation by pulling on intrinsically unstructured N or C termini of substrate molecules without showing specificity for a particular amino acid sequence. Although the B1 domain of protein G is shown to unfold cooperatively, translocation of calmodulin leads to the formation of intermediates, and these differ on an individual domain level in a manner that depends on whether pulling is from the N or C terminus. The approach presented generates an atomic resolution picture of substrate unfolding and subsequent refolding by unfoldases that can be quite different from results obtained via in vitro denaturation experiments.
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76
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Increased proteasomal activity supports photoreceptor survival in inherited retinal degeneration. Nat Commun 2018; 9:1738. [PMID: 29712894 PMCID: PMC5928105 DOI: 10.1038/s41467-018-04117-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/04/2018] [Indexed: 12/14/2022] Open
Abstract
Inherited retinal degenerations, affecting more than 2 million people worldwide, are caused by mutations in over 200 genes. This suggests that the most efficient therapeutic strategies would be mutation independent, i.e., targeting common pathological conditions arising from many disease-causing mutations. Previous studies revealed that one such condition is an insufficiency of the ubiquitin–proteasome system to process misfolded or mistargeted proteins in affected photoreceptor cells. We now report that retinal degeneration in mice can be significantly delayed by increasing photoreceptor proteasomal activity. The largest effect is observed upon overexpression of the 11S proteasome cap subunit, PA28α, which enhanced ubiquitin-independent protein degradation in photoreceptors. Applying this strategy to mice bearing one copy of the P23H rhodopsin mutant, a mutation frequently encountered in human patients, quadruples the number of surviving photoreceptors in the inferior retina of 6-month-old mice. This striking therapeutic effect demonstrates that proteasomes are an attractive target for fighting inherited blindness. Proteasomal overload can be found in a broad spectrum of mouse models of retinal degeneration. Here the authors find that overexpressing the PA28α subunit of the 11S proteasome cap increased the number of surviving functional photoreceptor cells in a mouse model of retinal degeneration bearing the P23H mutation in rhodopsin.
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77
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Zhu Y, Wang WL, Yu D, Ouyang Q, Lu Y, Mao Y. Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome. Nat Commun 2018; 9:1360. [PMID: 29636472 PMCID: PMC5893597 DOI: 10.1038/s41467-018-03785-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 03/12/2018] [Indexed: 01/08/2023] Open
Abstract
The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of the substrate–translocation channel leading to the proteolytic chamber of the core particle (CP). Here we report three alternative states of the ATP-γ-S-bound human proteasome, in which the CP gates are asymmetrically open, visualized by cryo-EM at near-atomic resolutions. At least four nucleotides are bound to the AAA-ATPase ring in these open-gate states. Variation in nucleotide binding gives rise to an axial movement of the pore loops narrowing the substrate-translation channel, which exhibit remarkable structural transitions between the spiral-staircase and saddle-shaped-circle topologies. Gate opening in the CP is thus regulated by nucleotide-driven conformational changes of the AAA-ATPase unfoldase. These findings demonstrate an elegant mechanism of allosteric coordination among sub-machines within the human proteasome holoenzyme. The 26S proteasome consists of a core particle that is capped at each side by a regulatory particle. Here the authors present cryo-EM structures of the activated human 26S proteasome holoenzyme in three alternative open-gate states, which provides mechanistic insights into gate opening and dynamic remodeling of the substrate–translocation pathway.
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Affiliation(s)
- Yanan Zhu
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Wei Li Wang
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Daqi Yu
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Qi Ouyang
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Youdong Mao
- Center for Quantitative Biology, Peking University, Beijing, 100871, China. .,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing, 100871, China. .,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
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78
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A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms. Sci Rep 2018; 8:5742. [PMID: 29636505 PMCID: PMC5893539 DOI: 10.1038/s41598-018-24039-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/21/2018] [Indexed: 01/06/2023] Open
Abstract
To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured transcription rate (TR), mRNA abundance (RA) and translation activity (TA). This revealed multiple insights. First, the three parameters displayed systematic statistical differences. Sequentially more genes exhibited extreme (low or high) expression values from TR to RA, and then to TA; that is, cellular coordination of multiple transcriptome regulatory mechanisms leads to sequentially enhanced gene expression selectivity as the genetic information flow from the genome to the proteome. Second, contribution of the stabilization-by-translation regulatory mechanism to the cellular coordination process was assessed. The data enabled an estimation of mRNA stability, revealing a moderate but significant positive correlation between mRNA stability and translation activity. Third, the proportion of mRNA occupied by un-translated regions (UTR) exhibited a negative relationship with the level of this correlation, and was thus a major determinant of the mode of regulation of the mRNA. High-UTR-proportion mRNAs tend to defy the stabilization-by-translation regulatory mechanism, staying out of the polysome but remaining stable; mRNAs with little UTRs largely followed this regulation. In summary, we quantitatively delineated the relationship among multiple transcriptome regulation parameters, i.e., cellular coordination of corresponding regulatory mechanisms.
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79
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Li Y, Huang J, Sun J, Xiang S, Yang D, Ying X, Lu M, Li H, Ren G. The transcription levels and prognostic values of seven proteasome alpha subunits in human cancers. Oncotarget 2018; 8:4501-4519. [PMID: 27966459 PMCID: PMC5354849 DOI: 10.18632/oncotarget.13885] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 12/01/2016] [Indexed: 11/25/2022] Open
Abstract
Proteasome alpha subunits (PSMAs) have been shown to participate in the malignant progression of human cancers. However, the expression patterns and prognostic values of individual PSMAs remain elusive in most cancers. In the present study, we investigated the mRNA expression levels of seven PSMAs in different kinds of cancers using Oncomine and The Cancer Genome Atlas (TCGA) databases. The prognostic significance of PSMAs was also determined by Kaplan-Meier Plotter and PrognScan databases. Combined with Oncomine and TCGA, the mRNA expression levels of PSMA1-7 were significantly upregulated in breast, lung, gastric, bladder and head and neck cancer compared with normal tissues. Moreover, only PSMA6 and PSMA5 were not overexpressed in colorectal and kidney cancer, respectively. In survival analyses based on Kaplan-Meier Plotter, PSMA1-7 showed significant prognostic values in breast, lung and gastric cancer. Furthermore, potential correlations between PSMAs and survival outcomes were also observed in ovarian cancer, colorectal cancer and melanoma by Kaplan-Meier Plotter and PrognScan. These data indicated that PSMAs might serve as novel biomarkers and potential therapeutic targets for multiple human cancers. However, further studies are needed to explore the detailed biological functions and molecular mechanisms involved in tumor progression.
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Affiliation(s)
- Yunhai Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Huang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiazheng Sun
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shili Xiang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dejuan Yang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuedong Ying
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mengqi Lu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongzhong Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guosheng Ren
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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80
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Hu K, Jastrab JB, Zhang S, Kovach A, Zhao G, Darwin KH, Li H. Proteasome substrate capture and gate opening by the accessory factor PafE from Mycobacterium tuberculosis. J Biol Chem 2018; 293:4713-4723. [PMID: 29414791 DOI: 10.1074/jbc.ra117.001471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/31/2018] [Indexed: 11/06/2022] Open
Abstract
In all domains of life, proteasomes are gated, chambered proteases that require opening by activators to facilitate protein degradation. Twelve proteasome accessory factor E (PafE) monomers assemble into a single dodecameric ring that promotes proteolysis required for the full virulence of the human bacterial pathogen Mycobacterium tuberculosis Whereas the best characterized proteasome activators use ATP to deliver proteins into a proteasome, PafE does not require ATP. Here, to unravel the mechanism of PafE-mediated protein targeting and proteasome activation, we studied the interactions of PafE with native substrates, including a newly identified proteasome substrate, the ParA-like protein, Rv3213c, and with proteasome core particles. We characterized the function of a highly conserved feature in bacterial proteasome activator proteins: a glycine-glutamine-tyrosine-leucine (GQYL) motif at their C termini that is essential for stimulating proteolysis. Using cryo-electron microscopy (cryo-EM), we found that the GQYL motif of PafE interacts with specific residues in the α subunits of the proteasome core particle to trigger gate opening and degradation. Finally, we also found that PafE rings have 40-Å openings lined with hydrophobic residues that form a chamber for capturing substrates before they are degraded, suggesting PafE has a previously unrecognized chaperone activity. In summary, we have identified the interactions between PafE and the proteasome core particle that cause conformational changes leading to the opening of the proteasome gate and have uncovered a mechanism of PafE-mediated substrate degradation. Collectively, our results provide detailed insights into the mechanism of ATP-independent proteasome degradation in bacteria.
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Affiliation(s)
- Kuan Hu
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Jordan B Jastrab
- Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Susan Zhang
- Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Amanda Kovach
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Gongpu Zhao
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, New York, New York 10016.
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503.
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81
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Berner N, Reutter KR, Wolf DH. Protein Quality Control of the Endoplasmic Reticulum and Ubiquitin-Proteasome-Triggered Degradation of Aberrant Proteins: Yeast Pioneers the Path. Annu Rev Biochem 2018; 87:751-782. [PMID: 29394096 DOI: 10.1146/annurev-biochem-062917-012749] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells must constantly monitor the integrity of their macromolecular constituents. Proteins are the most versatile class of macromolecules but are sensitive to structural alterations. Misfolded or otherwise aberrant protein structures lead to dysfunction and finally aggregation. Their presence is linked to aging and a plethora of severe human diseases. Thus, misfolded proteins have to be rapidly eliminated. Secretory proteins constitute more than one-third of the eukaryotic proteome. They are imported into the endoplasmic reticulum (ER), where they are folded and modified. A highly elaborated machinery controls their folding, recognizes aberrant folding states, and retrotranslocates permanently misfolded proteins from the ER back to the cytosol. In the cytosol, they are degraded by the highly selective ubiquitin-proteasome system. This process of protein quality control followed by proteasomal elimination of the misfolded protein is termed ER-associated degradation (ERAD), and it depends on an intricate interplay between the ER and the cytosol.
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Affiliation(s)
- Nicole Berner
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
| | - Karl-Richard Reutter
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
| | - Dieter H Wolf
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
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82
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Structural insights on the dynamics of proteasome formation. Biophys Rev 2017; 10:597-604. [PMID: 29243089 DOI: 10.1007/s12551-017-0381-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/27/2017] [Indexed: 12/28/2022] Open
Abstract
Molecular organization in biological systems comprises elaborately programmed processes involving metastable complex formation of biomolecules. This is exemplified by the formation of the proteasome, which is one of the largest and most complicated biological supramolecular complexes. This biomolecular machinery comprises approximately 70 subunits, including structurally homologous, but functionally distinct, ones, thereby exerting versatile proteolytic functions. In eukaryotes, proteasome formation is non-autonomous and is assisted by assembly chaperones, which transiently associate with assembly intermediates, operating as molecular matchmakers and checkpoints for the correct assembly of proteasome subunits. Accumulated data also suggest that eukaryotic proteasome formation involves scrap-and-build mechanisms. However, unlike the eukaryotic proteasome subunits, the archaeal subunits show little structural divergence and spontaneously assemble into functional machinery. Nevertheless, the archaeal genomes encode homologs of eukaryotic proteasome assembly chaperones. Recent structural and functional studies of these proteins have advanced our understanding of the evolution of molecular mechanisms involved in proteasome biogenesis. This knowledge, in turn, provides a guiding principle in designing molecular machineries using protein engineering approaches and de novo synthesis of artificial molecular systems.
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83
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Fuchs ACD, Maldoner L, Hipp K, Hartmann MD, Martin J. Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties. J Biol Chem 2017; 293:920-930. [PMID: 29183996 PMCID: PMC5777263 DOI: 10.1074/jbc.m117.815258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/10/2017] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family Betaproteobacteria proteasome homolog (BPH). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the Thiobacillus denitrificans and Cupriavidus metallidurans BPHs disclosed a homo-oligomeric double-ring architecture in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. Although the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases.
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Affiliation(s)
| | | | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany
| | | | - Jörg Martin
- From the Department of Protein Evolution and
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84
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Probing the cooperativity of Thermoplasma acidophilum proteasome core particle gating by NMR spectroscopy. Proc Natl Acad Sci U S A 2017; 114:E9846-E9854. [PMID: 29087330 DOI: 10.1073/pnas.1712297114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The 20S proteasome core particle (20S CP) plays an integral role in cellular homeostasis by degrading proteins no longer required for function. The process is, in part, controlled via gating residues localized to the ends of the heptameric barrel-like CP structure that occlude substrate entry pores, preventing unregulated degradation of substrates that might otherwise enter the proteasome. Previously, we showed that the N-terminal residues of the α-subunits of the CP from the archaeon Thermoplasma acidophilum are arranged such that, on average, two of the seven termini are localized inside the lumen of the proteasome, thereby plugging the entry pore and functioning as a gate. However, the mechanism of gating remains unclear. Using solution NMR and a labeling procedure in which a series of mixed proteasome rings are prepared such that the percentage of gate-containing subunits is varied, we address the energetics of gating and establish whether gating is a cooperative process involving the concerted action of residues from more than a single protomer. Our results establish that the intrinsic probability of a gate entering the lumen favors the in state by close to 20-fold, that entry of each gate is noncooperative, with the number of gates that can be accommodated inside the lumen a function of the substrate entry pore size and the bulkiness of the gating residues. Insight into the origin of the high affinity for the in state is obtained from spin-relaxation experiments. More generally, our approach provides an avenue for dissecting interactions of individual protomers in homo-oligomeric complexes.
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85
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Cullen PK, Ferrara NC, Pullins SE, Helmstetter FJ. Context memory formation requires activity-dependent protein degradation in the hippocampus. ACTA ACUST UNITED AC 2017; 24:589-596. [PMID: 29038220 PMCID: PMC5647928 DOI: 10.1101/lm.045443.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/09/2017] [Indexed: 01/10/2023]
Abstract
Numerous studies have indicated that the consolidation of contextual fear memories supported by an aversive outcome like footshock requires de novo protein synthesis as well as protein degradation mediated by the ubiquitin-proteasome system (UPS). Context memory formed in the absence of an aversive stimulus by simple exposure to a novel environment requires de novo protein synthesis in both the dorsal (dHPC) and ventral (vHPC) hippocampus. However, the role of UPS-mediated protein degradation in the consolidation of context memory in the absence of a strong aversive stimulus has not been investigated. In the present study, we used the context preexposure facilitation effect (CPFE) procedure, which allows for the dissociation of context learning from context-shock learning, to investigate the role of activity-dependent protein degradation in the dHPC and vHPC during the formation of a context memory. We report that blocking protein degradation with the proteasome inhibitor clasto-lactacystin β-lactone (βLac) or blocking protein synthesis with anisomycin (ANI) immediately after context preexposure significantly impaired context memory formation. Additionally, we examined 20S proteasome activity at different time points following context exposure and saw that the activity of proteasomes in the dHPC increases immediately after stimulus exposure while the vHPC exhibits a biphasic pattern of proteolytic activity. Taken together, these data suggest that the requirement of increased proteolysis during memory consolidation is not driven by processes triggered by the strong aversive outcome (i.e., shock) normally used to support fear conditioning.
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Affiliation(s)
- Patrick K Cullen
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, USA
| | - Nicole C Ferrara
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, USA
| | - Shane E Pullins
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, USA
| | - Fred J Helmstetter
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, USA
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86
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Aryal RP, Kwak PB, Tamayo AG, Gebert M, Chiu PL, Walz T, Weitz CJ. Macromolecular Assemblies of the Mammalian Circadian Clock. Mol Cell 2017; 67:770-782.e6. [PMID: 28886335 PMCID: PMC5679067 DOI: 10.1016/j.molcel.2017.07.017] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/14/2017] [Accepted: 07/13/2017] [Indexed: 10/18/2022]
Abstract
The mammalian circadian clock is built on a feedback loop in which PER and CRY proteins repress their own transcription. We found that in mouse liver nuclei all three PERs, both CRYs, and Casein Kinase-1δ (CK1δ) are present together in an ∼1.9-MDa repressor assembly that quantitatively incorporates its CLOCK-BMAL1 transcription factor target. Prior to incorporation, CLOCK-BMAL1 exists in an ∼750-kDa complex. Single-particle electron microscopy (EM) revealed nuclear PER complexes purified from mouse liver to be quasi-spherical ∼40-nm structures. In the cytoplasm, PERs, CRYs, and CK1δ were distributed into several complexes of ∼0.9-1.1 MDa that appear to constitute an assembly pathway regulated by GAPVD1, a cytoplasmic trafficking factor. Single-particle EM of two purified cytoplasmic PER complexes revealed ∼20-nm and ∼25-nm structures, respectively, characterized by flexibly tethered globular domains. Our results define the macromolecular assemblies comprising the circadian feedback loop and provide an initial structural view of endogenous eukaryotic clock machinery.
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Affiliation(s)
- Rajindra P Aryal
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pieter Bas Kwak
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alfred G Tamayo
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Gebert
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Po-Lin Chiu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY 10065, USA
| | - Charles J Weitz
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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87
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Cromm PM, Crews CM. The Proteasome in Modern Drug Discovery: Second Life of a Highly Valuable Drug Target. ACS CENTRAL SCIENCE 2017; 3:830-838. [PMID: 28852696 PMCID: PMC5571462 DOI: 10.1021/acscentsci.7b00252] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 06/07/2023]
Abstract
As the central figure of the cellular protein degradation machinery, the proteasome is critical for cell survival. Having been extensively targeted for inhibition, the constitutive proteasome has proven its role as a highly valuable drug target. However, recent advances in the protein homeostasis field suggest that additional chapters can be added to this successful story. For example, selective immunoproteasome inhibition promises high clinical efficacy for autoimmune disorders and inflammation, and proteasome inhibitors might serve as novel therapeutics for malaria or other microorganisms. Furthermore, utilizing the destructive force of the proteasome for selective degradation of essential drivers of human disorders has opened up a new and exciting area of drug discovery. Thus, the field of proteasome drug discovery still holds exciting questions to be answered and does not simply end with inhibiting the constitutive proteasome.
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Affiliation(s)
- Philipp M. Cromm
- Department
of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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88
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Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC. Capturing protein communities by structural proteomics in a thermophilic eukaryote. Mol Syst Biol 2017; 13:936. [PMID: 28743795 PMCID: PMC5527848 DOI: 10.15252/msb.20167412] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, we simultaneously characterized the abundance, interactions, and structure of a third of the C. thermophilum proteome within these extracts. We identified 27 distinct protein communities that include 108 interconnected complexes, which dynamically associate with each other and functionally benefit from being in close proximity in the cell. Furthermore, we investigated the structure of fatty acid synthase within these extracts by cryoEM and this revealed multiple, flexible states of the enzyme in adaptation to its association with other complexes, thus exemplifying the need for in situ studies. As the components of the captured protein communities are known—at both the protein and complex levels—this study constitutes another step forward toward a molecular understanding of subcellular organization.
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Affiliation(s)
- Panagiotis L Kastritis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Francis J O'Reilly
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Thomas Bock
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Yuanyue Li
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Matt Z Rogon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Katarzyna Buczak
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Natalie Romanov
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Matthew J Betts
- Cell Networks, Bioquant & Biochemie Zentrum Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Khanh Huy Bui
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Wim J Hagen
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Marco L Hennrich
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Marie-Therese Mackmull
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Robert B Russell
- Cell Networks, Bioquant & Biochemie Zentrum Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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89
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Proteostasis of Huntingtin in Health and Disease. Int J Mol Sci 2017; 18:ijms18071568. [PMID: 28753941 PMCID: PMC5536056 DOI: 10.3390/ijms18071568] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/15/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder characterized by motor dysfunction, cognitive deficits and psychosis. HD is caused by mutations in the Huntingtin (HTT) gene, resulting in the expansion of polyglutamine (polyQ) repeats in the HTT protein. Mutant HTT is prone to aggregation, and the accumulation of polyQ-expanded fibrils as well as intermediate oligomers formed during the aggregation process contribute to neurodegeneration. Distinct protein homeostasis (proteostasis) nodes such as chaperone-mediated folding and proteolytic systems regulate the aggregation and degradation of HTT. Moreover, polyQ-expanded HTT fibrils and oligomers can lead to a global collapse in neuronal proteostasis, a process that contributes to neurodegeneration. The ability to maintain proteostasis of HTT declines during the aging process. Conversely, mechanisms that preserve proteostasis delay the onset of HD. Here we will review the link between proteostasis, aging and HD-related changes.
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90
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Esaki M, Islam MT, Tani N, Ogura T. Deviation of the typical AAA substrate-threading pore prevents fatal protein degradation in yeast Cdc48. Sci Rep 2017; 7:5475. [PMID: 28710470 PMCID: PMC5511170 DOI: 10.1038/s41598-017-05806-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Yeast Cdc48 is a well-conserved, essential chaperone of ATPases associated with diverse cellular activity (AAA) proteins, which recognizes substrate proteins and modulates their conformations to carry out many cellular processes. However, the fundamental mechanisms underlying the diverse pivotal roles of Cdc48 remain unknown. Almost all AAA proteins form a ring-shaped structure with a conserved aromatic amino acid residue that is essential for proper function. The threading mechanism hypothesis suggests that this residue guides the intrusion of substrate proteins into a narrow pore of the AAA ring, thereby becoming unfolded. By contrast, the aromatic residue in one of the two AAA rings of Cdc48 has been eliminated through evolution. Here, we show that artificial retrieval of this aromatic residue in Cdc48 is lethal, and essential features to support the threading mechanism are required to exhibit the lethal phenotype. In particular, genetic and biochemical analyses of the Cdc48 lethal mutant strongly suggested that when in complex with the 20S proteasome, essential proteins are abnormally forced to thread through the Cdc48 pore to become degraded, which was not detected in wild-type Cdc48. Thus, the widely applicable threading model is less effective for wild-type Cdc48; rather, Cdc48 might function predominantly through an as-yet-undetermined mechanism.
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Affiliation(s)
- Masatoshi Esaki
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan. .,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, 332-0012, Japan.
| | - Md Tanvir Islam
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan.,Program for Leading Graduate Schools "HIGO Program", Kumamoto University, Kumamoto, 860-8556, Japan.,Department of Microbiology, Jessore University of Science and Technology, Jessore, 7408, Bangladesh
| | - Naoki Tani
- Liaison Laboratory Research Promotion Center, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Teru Ogura
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, 332-0012, Japan.,Program for Leading Graduate Schools "HIGO Program", Kumamoto University, Kumamoto, 860-8556, Japan
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91
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Korovila I, Hugo M, Castro JP, Weber D, Höhn A, Grune T, Jung T. Proteostasis, oxidative stress and aging. Redox Biol 2017; 13:550-567. [PMID: 28763764 PMCID: PMC5536880 DOI: 10.1016/j.redox.2017.07.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 12/21/2022] Open
Abstract
The production of reactive species is an inevitable by-product of metabolism and thus, life itself. Since reactive species are able to damage cellular structures, especially proteins, as the most abundant macromolecule of mammalian cells, systems are necessary which regulate and preserve a functional cellular protein pool, in a process termed “proteostasis”. Not only the mammalian protein pool is subject of a constant turnover, organelles are also degraded and rebuild. The most important systems for these removal processes are the “ubiquitin-proteasomal system” (UPS), the central proteolytic machinery of mammalian cells, mainly responsible for proteostasis, as well as the “autophagy-lysosomal system”, which mediates the turnover of organelles and large aggregates. Many age-related pathologies and the aging process itself are accompanied by a dysregulation of UPS, autophagy and the cross-talk between both systems. This review will describe the sources and effects of oxidative stress, preservation of cellular protein- and organelle-homeostasis and the effects of aging on proteostasis in mammalian cells.
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Affiliation(s)
- Ioanna Korovila
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - Martín Hugo
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - José Pedro Castro
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany; Faculty of Medicine, Department of Biomedicine, University of Porto, 4200-319, Portugal; Institute for Innovation and Health Research (I3S), Aging and Stress Group, R. Alfredo Allen, 4200-135 Porto, Portugal
| | - Daniela Weber
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; NutriAct - Competence Cluster Nutrition Research Berlin-Potsdam, 14558 Nuthetal, Germany
| | - Annika Höhn
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany; German Center for Cardiovascular Research (DZHK), 10117 Berlin, Germany; NutriAct - Competence Cluster Nutrition Research Berlin-Potsdam, 14558 Nuthetal, Germany
| | - Tobias Jung
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Cardiovascular Research (DZHK), 10117 Berlin, Germany.
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92
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Bodnar NO, Rapoport TA. Molecular Mechanism of Substrate Processing by the Cdc48 ATPase Complex. Cell 2017; 169:722-735.e9. [PMID: 28475898 DOI: 10.1016/j.cell.2017.04.020] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/18/2017] [Accepted: 04/14/2017] [Indexed: 10/19/2022]
Abstract
The Cdc48 ATPase and its cofactors Ufd1/Npl4 (UN) extract polyubiquitinated proteins from membranes or macromolecular complexes, but how they perform these functions is unclear. Cdc48 consists of an N-terminal domain that binds UN and two stacked hexameric ATPase rings (D1 and D2) surrounding a central pore. Here, we use purified components to elucidate how the Cdc48 complex processes substrates. After interaction of the polyubiquitin chain with UN, ATP hydrolysis by the D2 ring moves the polypeptide completely through the double ring, generating a pulling force on the substrate and causing its unfolding. ATP hydrolysis by the D1 ring is important for subsequent substrate release from the Cdc48 complex. This release requires cooperation of Cdc48 with a deubiquitinase, which trims polyubiquitin to an oligoubiquitin chain that is then also translocated through the pore. Together, these results lead to a new paradigm for the function of Cdc48 and its mammalian ortholog p97/VCP.
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Affiliation(s)
- Nicholas O Bodnar
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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93
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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: 74] [Impact Index Per Article: 10.6] [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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94
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Haselbach D, Schrader J, Lambrecht F, Henneberg F, Chari A, Stark H. Long-range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs. Nat Commun 2017; 8:15578. [PMID: 28541292 PMCID: PMC5458511 DOI: 10.1038/ncomms15578] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/07/2017] [Indexed: 01/03/2023] Open
Abstract
The proteasome holoenzyme is the major non-lysosomal protease; its proteolytic activity is essential for cellular homeostasis. Thus, it is an attractive target for the development of chemotherapeutics. While the structural basis of core particle (CP) inhibitors is largely understood, their structural impact on the proteasome holoenzyme remains entirely elusive. Here, we determined the structure of the 26S proteasome with and without the inhibitor Oprozomib. Drug binding modifies the energy landscape of conformational motion in the proteasome regulatory particle (RP). Structurally, the energy barrier created by Oprozomib triggers a long-range allosteric regulation, resulting in the stabilization of a non-productive state. Thereby, the chemical drug-binding signal is converted, propagated and amplified into structural changes over a distance of more than 150 Å from the proteolytic site to the ubiquitin receptor Rpn10. The direct visualization of changes in conformational dynamics upon drug binding allows new ways to screen and develop future allosteric proteasome inhibitors.
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Affiliation(s)
- David Haselbach
- Department for Structural Dynamics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jil Schrader
- Department for Structural Dynamics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Felix Lambrecht
- Department for Structural Dynamics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Fabian Henneberg
- Department for Structural Dynamics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ashwin Chari
- Department for Structural Dynamics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Holger Stark
- Department for Structural Dynamics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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95
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The Architecture of the Anbu Complex Reflects an Evolutionary Intermediate at the Origin of the Proteasome System. Structure 2017; 25:834-845.e5. [PMID: 28479063 PMCID: PMC5666114 DOI: 10.1016/j.str.2017.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/23/2016] [Accepted: 04/14/2017] [Indexed: 11/22/2022]
Abstract
Proteasomes are self-compartmentalizing proteases that function at the core of the cellular protein degradation machinery in eukaryotes, archaea, and some bacteria. Although their evolutionary history is under debate, it is thought to be linked to that of the bacterial protease HslV and the hypothetical bacterial protease Anbu (ancestral beta subunit). Here, together with an extensive bioinformatic analysis, we present the first biophysical characterization of Anbu. Anbu forms a dodecameric complex with a unique architecture that was only accessible through the combination of X-ray crystallography and small-angle X-ray scattering. While forming continuous helices in crystals and electron microscopy preparations, refinement of sections from the crystal structure against the scattering data revealed a helical open-ring structure in solution, contrasting the ring-shaped structures of proteasome and HslV. Based on this primordial architecture and exhaustive sequence comparisons, we propose that Anbu represents an ancestral precursor at the origin of self-compartmentalization. The crystal structure of the bacterial proteasome homolog Anbu has been solved The dodecameric architecture reveals unique features compared with classical proteasomes Bioinformatic analysis places Anbu at the root of the proteasome family
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96
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Structural Analysis of Mycobacterium tuberculosis Homologues of the Eukaryotic Proteasome Assembly Chaperone 2 (PAC2). J Bacteriol 2017; 199:JB.00846-16. [PMID: 28193903 DOI: 10.1128/jb.00846-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022] Open
Abstract
A previous bioinformatics analysis identified the Mycobacterium tuberculosis proteins Rv2125 and Rv2714 as orthologs of the eukaryotic proteasome assembly chaperone 2 (PAC2). We set out to investigate whether Rv2125 or Rv2714 can function in proteasome assembly. We solved the crystal structure of Rv2125 at a resolution of 3.0 Å, which showed an overall fold similar to that of the PAC2 family proteins that include the archaeal PbaB and the yeast Pba1. However, Rv2125 and Rv2714 formed trimers, whereas PbaB forms tetramers and Pba1 dimerizes with Pba2. We also found that purified Rv2125 and Rv2714 could not bind to M. tuberculosis 20S core particles. Finally, proteomic analysis showed that the levels of known proteasome components and substrate proteins were not affected by disruption of Rv2125 in M. tuberculosis Our work suggests that Rv2125 does not participate in bacterial proteasome assembly or function.IMPORTANCE Although many bacteria do not encode proteasomes, M. tuberculosis not only uses proteasomes but also has evolved a posttranslational modification system called pupylation to deliver proteins to the proteasome. Proteasomes are essential for M. tuberculosis to cause lethal infections in animals; thus, determining how proteasomes are assembled may help identify new ways to combat tuberculosis. We solved the structure of a predicted proteasome assembly factor, Rv2125, and isolated a genetic Rv2125 mutant of M. tuberculosis Our structural, biochemical, and genetic studies indicate that Rv2125 and Rv2714 do not function as proteasome assembly chaperones and are unlikely to have roles in proteasome biology in mycobacteria.
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97
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Kurimoto E, Satoh T, Ito Y, Ishihara E, Okamoto K, Yagi-Utsumi M, Tanaka K, Kato K. Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation. Protein Sci 2017; 26:1080-1085. [PMID: 28263418 DOI: 10.1002/pro.3153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/28/2017] [Accepted: 02/28/2017] [Indexed: 01/12/2023]
Abstract
The 26S proteasome is a large protein complex, responsible for degradation of ubiquinated proteins in eukaryotic cells. Eukaryotic proteasome formation is a highly ordered process that is assisted by several assembly chaperones. The assembly of its catalytic 20S core particle depends on at least five proteasome-specific chaperones, i.e., proteasome-assembling chaperons 1-4 (PAC1-4) and proteasome maturation protein (POMP). The orthologues of yeast assembly chaperones have been structurally characterized, whereas most mammalian assembly chaperones are not. In the present study, we determined a crystal structure of human PAC4 at 1.90-Å resolution. Our crystallographic data identify a hydrophobic surface that is surrounded by charged residues. The hydrophobic surface is complementary to that of its binding partner, PAC3. The surface also exhibits charge complementarity with the proteasomal α4-5 subunits. This will provide insights into human proteasome-assembling chaperones as potential anticancer drug targets.
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Affiliation(s)
- Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan.,JST, PRESTO, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Yuri Ito
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan
| | - Eri Ishihara
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan
| | - Kenta Okamoto
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan.,Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan.,Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, 444-8787, Japan
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98
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Loss-of-Function Mutations in HspR Rescue the Growth Defect of a Mycobacterium tuberculosis Proteasome Accessory Factor E ( pafE) Mutant. J Bacteriol 2017; 199:JB.00850-16. [PMID: 28096448 DOI: 10.1128/jb.00850-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/12/2017] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis uses a proteasome to degrade proteins by both ATP-dependent and -independent pathways. While much has been learned about ATP-dependent degradation, relatively little is understood about the ATP-independent pathway, which is controlled by Mycobacterium tuberculosisproteasome accessory factor E (PafE). Recently, we found that a Mycobacterium tuberculosispafE mutant has slowed growth in vitro and is sensitive to killing by heat stress. However, we did not know if these phenotypes were caused by an inability to degrade the PafE-proteasome substrate HspR (heat shock protein repressor), an inability to degrade any damaged or misfolded proteins, or a defect in another protein quality control pathway. To address this question, we characterized pafE suppressor mutants that grew similarly to pafE+ bacteria under normal culture conditions. All but one suppressor mutant analyzed contained mutations that inactivated HspR function, demonstrating that the slowed growth and heat shock sensitivity of a pafE mutant were caused primarily by the inability of the proteasome to degrade HspR.IMPORTANCEMycobacterium tuberculosis encodes a proteasome that is highly similar to eukaryotic proteasomes and is required for virulence. We recently discovered a proteasome cofactor, PafE, which is required for the normal growth, heat shock resistance, and full virulence of M. tuberculosis In this study, we demonstrate that PafE influences this phenotype primarily by promoting the expression of protein chaperone genes that are necessary for surviving proteotoxic stress.
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99
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Sasaki E, Böhringer D, van de Waterbeemd M, Leibundgut M, Zschoche R, Heck AJR, Ban N, Hilvert D. Structure and assembly of scalable porous protein cages. Nat Commun 2017; 8:14663. [PMID: 28281548 PMCID: PMC5354205 DOI: 10.1038/ncomms14663] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/20/2017] [Indexed: 12/18/2022] Open
Abstract
Proteins that self-assemble into regular shell-like polyhedra are useful, both in nature and in the laboratory, as molecular containers. Here we describe cryo-electron microscopy (EM) structures of two versatile encapsulation systems that exploit engineered electrostatic interactions for cargo loading. We show that increasing the number of negative charges on the lumenal surface of lumazine synthase, a protein that naturally assembles into a ∼1-MDa dodecahedron composed of 12 pentamers, induces stepwise expansion of the native protein shell, giving rise to thermostable ∼3-MDa and ∼6-MDa assemblies containing 180 and 360 subunits, respectively. Remarkably, these expanded particles assume unprecedented tetrahedrally and icosahedrally symmetric structures constructed entirely from pentameric units. Large keyhole-shaped pores in the shell, not present in the wild-type capsid, enable diffusion-limited encapsulation of complementarily charged guests. The structures of these supercharged assemblies demonstrate how programmed electrostatic effects can be effectively harnessed to tailor the architecture and properties of protein cages.
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Affiliation(s)
- Eita Sasaki
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Daniel Böhringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, CH Utrecht 3584, The Netherlands
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
| | - Reinhard Zschoche
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, CH Utrecht 3584, The Netherlands
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
| | - Donald Hilvert
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Zürich 8093, Switzerland
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100
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Vriend J, Marzban H. The ubiquitin-proteasome system and chromosome 17 in cerebellar granule cells and medulloblastoma subgroups. Cell Mol Life Sci 2017; 74:449-467. [PMID: 27592301 PMCID: PMC11107675 DOI: 10.1007/s00018-016-2354-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/17/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022]
Abstract
Chromosome 17 abnormalities are often observed in medulloblastomas (MBs), particularly those classified in the consensus Groups 3 and 4. Herein we review MB signature genes associated with chromosome 17 and the relationship of these signature genes to the ubiquitin-proteasome system. While clinical investigators have not focused on the ubiquitin-proteasome system in relation to MB, a substantial amount of data on the topic has been hidden in the form of supplemental datasets of gene expression. A supplemental dataset associated with the Thompson classification of MBs shows that a subgroup of MB with 17p deletions is characterized by reduced expression of genes for several core particle subunits of the beta ring of the proteasome (β1, β4, β5, β7). One of these genes (PSMB6, the gene for the β1 subunit) is located on chromosome 17, near the telomeric end of 17p. By comparison, in the WNT group of MBs only one core proteasome subunit, β6, associated with loss of a gene (PSMB1) on chromosome 6, was down-regulated in this dataset. The MB subgroups with the worst prognosis have a significant association with chromosome 17 abnormalities and irregularities of APC/C cyclosome genes. We conclude that the expression of proteasome subunit genes and genes for ubiquitin ligases can contribute to prognostic classification of MBs. The therapeutic value of targeting proteasome subunits and ubiquitin ligases in the various subgroups of MB remains to be determined separately for each classification of MB.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Rm134, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
| | - Hassan Marzban
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Rm134, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
- Children's Hospital Research Institute of Manitoba (CHRIM), Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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