1
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Borgert L, Becker T, den Brave F. Conserved quality control mechanisms of mitochondrial protein import. J Inherit Metab Dis 2024. [PMID: 38790152 DOI: 10.1002/jimd.12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
Mitochondria carry out essential functions for the cell, including energy production, various biosynthesis pathways, formation of co-factors and cellular signalling in apoptosis and inflammation. The functionality of mitochondria requires the import of about 900-1300 proteins from the cytosol in baker's yeast Saccharomyces cerevisiae and human cells, respectively. The vast majority of these proteins pass the outer membrane in a largely unfolded state through the translocase of the outer mitochondrial membrane (TOM) complex. Subsequently, specific protein translocases sort the precursor proteins into the outer and inner membranes, the intermembrane space and matrix. Premature folding of mitochondrial precursor proteins, defects in the mitochondrial protein translocases or a reduction of the membrane potential across the inner mitochondrial membrane can cause stalling of precursors at the protein import apparatus. Consequently, the translocon is clogged and non-imported precursor proteins accumulate in the cell, which in turn leads to proteotoxic stress and eventually cell death. To prevent such stress situations, quality control mechanisms remove non-imported precursor proteins from the TOM channel. The highly conserved ubiquitin-proteasome system of the cytosol plays a critical role in this process. Thus, the surveillance of protein import via the TOM complex involves the coordinated activity of mitochondria-localized and cytosolic proteins to prevent proteotoxic stress in the cell.
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Affiliation(s)
- Lion Borgert
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Fabian den Brave
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
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2
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Park CR, Min JH, Gong Y, Sang H, Lee KH, Kim CS. Arabidopsis thaliana ubiquitin-associated protein 2 (AtUAP2) functions as an E4 ubiquitin factor and negatively modulates dehydration stress response. PLANT MOLECULAR BIOLOGY 2024; 114:13. [PMID: 38324104 DOI: 10.1007/s11103-024-01419-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024]
Abstract
E4, a ubiquitin (Ub) chain assembly factor and post-translational modification protein, plays a key role in the regulation of multiple cellular functions in plants during biotic or abiotic stress. We have more recently reported that E4 factor AtUAP1 is a negative regulator of the osmotic stress response and enhances the multi-Ub chain assembly of E3 ligase Arabidopsis thaliana RING Zinc Finger 1 (AtRZF1). To further investigate the function of other E4 Ub factors in osmotic stress, we isolated AtUAP2, an AtUAP1 homolog, which interacted with AtRZF1, using pull-down assay and bimolecular fluorescence complementation analysis. AtUAP2, a Ub-associated motif-containing protein, interacts with oligo-Ub5, -Ub6, and -Ub7 chains. The yeast functional complementation experiment revealed that AtUAP2 functions as an E4 Ub factor. In addition, AtUAP2 is localized in the cytoplasm, different from AtUAP1. The activity of AtUAP2 was relatively strongly induced in the leaf tissue of AtUAP2 promoter-β-glucuronidase transgenic plants by abscisic acid, dehydration, and oxidative stress. atuap2 RNAi lines were more insensitive to osmotic stress condition than wild-type during the early growth of seedlings, whereas the AtUAP2-overexpressing line exhibited relatively more sensitive responses. Analyses of molecular and physiological experiments showed that AtUAP2 could negatively mediate the osmotic stress-induced signaling. Genetic studies showed that AtRZF1 mutation could suppress the dehydration-induced sensitive phenotype of the AtUAP2-overexpressing line, suggesting that AtRZF1 acts genetically downstream of AtUAP2 during osmotic stress. Taken together, our findings show that the AtRZF1-AtUAP2 complex may play important roles in the ubiquitination pathway, which controls the osmotic stress response in Arabidopsis.
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Affiliation(s)
- Cho-Rong Park
- Department of Applied Biology, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Ji-Hee Min
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, 77843-2128, College Station, TX, USA
| | - Ying Gong
- Department of Applied Biology, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Kyeong-Hwan Lee
- Department of Convergence Biosystems Engineering, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Cheol Soo Kim
- Department of Applied Biology, Chonnam National University, 61186, Gwangju, Republic of Korea.
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3
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Yang EJN, Liao PC, Pon L. Mitochondrial protein and organelle quality control-Lessons from budding yeast. IUBMB Life 2024; 76:72-87. [PMID: 37731280 PMCID: PMC10842221 DOI: 10.1002/iub.2783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/11/2023] [Indexed: 09/22/2023]
Abstract
Mitochondria are essential for normal cellular function and have emerged as key aging determinants. Indeed, defects in mitochondrial function have been linked to cardiovascular, skeletal muscle and neurodegenerative diseases, premature aging, and age-linked diseases. Here, we describe mechanisms for mitochondrial protein and organelle quality control. These surveillance mechanisms mediate repair or degradation of damaged or mistargeted mitochondrial proteins, segregate mitochondria based on their functional state during asymmetric cell division, and modulate cellular fitness, the response to stress, and lifespan control in yeast and other eukaryotes.
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Affiliation(s)
- Emily Jie-Ning Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Pin-Chao Liao
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013
| | - Liza Pon
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
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4
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Rödl S, Herrmann JM. The role of the proteasome in mitochondrial protein quality control. IUBMB Life 2023; 75:868-879. [PMID: 37178401 DOI: 10.1002/iub.2734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/15/2023] [Indexed: 05/15/2023]
Abstract
The abundance of each cellular protein is dynamically adjusted to the prevailing metabolic and stress conditions by modulation of their synthesis and degradation rates. The proteasome represents the major machinery for the degradation of proteins in eukaryotic cells. How the ubiquitin-proteasome system (UPS) controls protein levels and removes superfluous and damaged proteins from the cytosol and the nucleus is well characterized. However, recent studies showed that the proteasome also plays a crucial role in mitochondrial protein quality control. This mitochondria-associated degradation (MAD) thereby acts on two layers: first, the proteasome removes mature, functionally compromised or mis-localized proteins from the mitochondrial surface; and second, the proteasome cleanses the mitochondrial import pore of import intermediates of nascent proteins that are stalled during translocation. In this review, we provide an overview about the components and their specific functions that facilitate proteasomal degradation of mitochondrial proteins in the yeast Saccharomyces cerevisiae. Thereby we explain how the proteasome, in conjunction with a set of intramitochondrial proteases, maintains mitochondrial protein homeostasis and dynamically adapts the levels of mitochondrial proteins to specific conditions.
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Affiliation(s)
- Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
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5
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Wilde ML, Ruparel U, Klemm T, Lee VV, Calleja DJ, Komander D, Tonkin CJ. Characterisation of the OTU domain deubiquitinase complement of Toxoplasma gondii. Life Sci Alliance 2023; 6:e202201710. [PMID: 36958824 PMCID: PMC10038098 DOI: 10.26508/lsa.202201710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023] Open
Abstract
The phylum Apicomplexa contains several parasitic species of medical and agricultural importance. The ubiquitination machinery remains, for the most part, uncharacterised in apicomplexan parasites, despite the important roles that it plays in eukaryotic biology. Bioinformatic analysis of the ubiquitination machinery in apicomplexan parasites revealed an expanded ovarian tumour domain-containing (OTU) deubiquitinase (DUB) family in Toxoplasma, potentially reflecting functional importance in apicomplexan parasites. This study presents comprehensive characterisation of Toxoplasma OTU DUBs. AlphaFold-guided structural analysis not only confirmed functional orthologues found across eukaryotes, but also identified apicomplexan-specific enzymes, subsequently enabling discovery of a cryptic OTU DUB in Plasmodium species. Comprehensive biochemical characterisation of 11 Toxoplasma OTU DUBs revealed activity against ubiquitin- and NEDD8-based substrates and revealed ubiquitin linkage preferences for Lys6-, Lys11-, Lys48-, and Lys63-linked chain types. We show that accessory domains in Toxoplasma OTU DUBs impose linkage preferences, and in case of apicomplexan-specific TgOTU9, we discover a cryptic ubiquitin-binding domain that is essential for TgOTU9 activity. Using the auxin-inducible degron (AID) to generate knockdown parasite lines, TgOTUD6B was found to be important for Toxoplasma growth.
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Affiliation(s)
- Mary-Louise Wilde
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Ushma Ruparel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Theresa Klemm
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - V Vern Lee
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, Parkville, Australia; and Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, Australia
| | - Dale J Calleja
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - David Komander
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Christopher J Tonkin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; and Department of Medical Biology, University of Melbourne, Melbourne, Australia
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6
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Badawi S, Mohamed FE, Varghese DS, Ali BR. Genetic disruption of mammalian endoplasmic reticulum-associated protein degradation: Human phenotypes and animal and cellular disease models. Traffic 2023. [PMID: 37188482 DOI: 10.1111/tra.12902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Endoplasmic reticulum-associated protein degradation (ERAD) is a stringent quality control mechanism through which misfolded, unassembled and some native proteins are targeted for degradation to maintain appropriate cellular and organelle homeostasis. Several in vitro and in vivo ERAD-related studies have provided mechanistic insights into ERAD pathway activation and its consequent events; however, a majority of these have investigated the effect of ERAD substrates and their consequent diseases affecting the degradation process. In this review, we present all reported human single-gene disorders caused by genetic variation in genes that encode ERAD components rather than their substrates. Additionally, after extensive literature survey, we present various genetically manipulated higher cellular and mammalian animal models that lack specific components involved in various stages of the ERAD pathway.
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Affiliation(s)
- Sally Badawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Divya Saro Varghese
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
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7
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Zhang XL, Gong XQ, Su XJ, Yu HX, Cheng SY, Huang JW, Li DY, Lei ZL, Li MJ, Ma FW. The ubiquitin-binding protein MdRAD23D1 mediates drought response by regulating degradation of the proline-rich protein MdPRP6 in apple (Malus domestica). PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37140026 PMCID: PMC10363924 DOI: 10.1111/pbi.14057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/13/2023] [Accepted: 04/01/2023] [Indexed: 05/05/2023]
Abstract
RAD23 (RADIATION SENSITIVE23) proteins are a group of UBL-UBA (ubiquitin-like-ubiquitin-associated) proteins that shuttle ubiquitylated proteins to the 26S proteasome for breakdown. Drought stress is a major environmental constraint that limits plant growth and production, but whether RAD23 proteins are involved in this process is unclear. Here, we demonstrated that a shuttle protein, MdRAD23D1, mediated drought response in apple plants (Malus domestica). MdRAD23D1 levels increased under drought stress, and its suppression resulted in decreased stress tolerance in apple plants. Through in vitro and in vivo assays, we demonstrated that MdRAD23D1 interacted with a proline-rich protein MdPRP6, resulting in the degradation of MdPRP6 by the 26S proteasome. And MdRAD23D1 accelerated the degradation of MdPRP6 under drought stress. Suppression of MdPRP6 resulted in enhanced drought tolerance in apple plants, mainly because the free proline accumulation is changed. And the free proline is also involved in MdRAD23D1-mediated drought response. Taken together, these findings demonstrated that MdRAD23D1 and MdPRP6 oppositely regulated drought response. MdRAD23D1 levels increased under drought, accelerating the degradation of MdPRP6. MdPRP6 negatively regulated drought response, probably by regulating proline accumulation. Thus, "MdRAD23D1-MdPRP6" conferred drought stress tolerance in apple plants.
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Affiliation(s)
- Xiao-Li Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Xiao-Qing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Xin-Jian Su
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Hai-Xia Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Si-Yuan Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Jing-Wen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Dan-Yang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Zhao-Long Lei
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Ming-Jun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
| | - Feng-Wang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China
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8
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Buel GR, Chen X, Myint W, Kayode O, Folimonova V, Cruz A, Skorupka KA, Matsuo H, Walters KJ. E6AP AZUL interaction with UBQLN1/2 in cells, condensates, and an AlphaFold-NMR integrated structure. Structure 2023; 31:395-410.e6. [PMID: 36827983 PMCID: PMC10081965 DOI: 10.1016/j.str.2023.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/13/2023] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
The E3 ligase E6AP/UBE3A has a dedicated binding site in the 26S proteasome provided by the RAZUL domain of substrate receptor hRpn10/S5a/PSMD4. Guided by RAZUL sequence similarity, we test and demonstrate here that the E6AP AZUL binds transiently to the UBA of proteasomal shuttle factor UBQLN1/2. Despite a weak binding affinity, E6AP AZUL is recruited to UBQLN2 biomolecular condensates in vitro and E6AP interacts with UBQLN1/2 in cellulo. Steady-state and transfer nuclear Overhauser effect (NOE) experiments indicate direct interaction of AZUL with UBQLN1 UBA. Intermolecular contacts identified by NOE spectroscopy (NOESY) data were combined with AlphaFold2-Multimer predictions to yield an AZUL:UBA model structure. We additionally identify an oligomerization domain directly adjacent to UBQLN1/2 UBA (UBA adjacent [UBAA]) that is α-helical and allosterically reconfigured by AZUL binding to UBA. These data lead to a model of E6AP recruitment to UBQLN1/2 by AZUL:UBA interaction and provide fundamental information on binding requirements for interactions in condensates and cells.
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Affiliation(s)
- Gwen R Buel
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Wazo Myint
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Olumide Kayode
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Varvara Folimonova
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Anthony Cruz
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Katarzyna A Skorupka
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Hiroshi Matsuo
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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9
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Grønbæk-Thygesen M, Kampmeyer C, Hofmann K, Hartmann-Petersen R. The moonlighting of RAD23 in DNA repair and protein degradation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194925. [PMID: 36863450 DOI: 10.1016/j.bbagrm.2023.194925] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
A moonlighting protein is one, which carries out multiple, often wholly unrelated, functions. The RAD23 protein is a fascinating example of this, where the same polypeptide and the embedded domains function independently in both nucleotide excision repair (NER) and protein degradation via the ubiquitin-proteasome system (UPS). Hence, through direct binding to the central NER component XPC, RAD23 stabilizes XPC and contributes to DNA damage recognition. Conversely, RAD23 also interacts directly with the 26S proteasome and ubiquitylated substrates to mediate proteasomal substrate recognition. In this function, RAD23 activates the proteolytic activity of the proteasome and engages specifically in well-characterized degradation pathways through direct interactions with E3 ubiquitin-protein ligases and other UPS components. Here, we summarize the past 40 years of research into the roles of RAD23 in NER and the UPS.
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Affiliation(s)
- Martin Grønbæk-Thygesen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark.
| | - Caroline Kampmeyer
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Germany
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark.
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10
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Schulte U, den Brave F, Haupt A, Gupta A, Song J, Müller CS, Engelke J, Mishra S, Mårtensson C, Ellenrieder L, Priesnitz C, Straub SP, Doan KN, Kulawiak B, Bildl W, Rampelt H, Wiedemann N, Pfanner N, Fakler B, Becker T. Mitochondrial complexome reveals quality-control pathways of protein import. Nature 2023; 614:153-159. [PMID: 36697829 PMCID: PMC9892010 DOI: 10.1038/s41586-022-05641-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/09/2022] [Indexed: 01/26/2023]
Abstract
Mitochondria have crucial roles in cellular energetics, metabolism, signalling and quality control1-4. They contain around 1,000 different proteins that often assemble into complexes and supercomplexes such as respiratory complexes and preprotein translocases1,3-7. The composition of the mitochondrial proteome has been characterized1,3,5,6; however, the organization of mitochondrial proteins into stable and dynamic assemblies is poorly understood for major parts of the proteome1,4,7. Here we report quantitative mapping of mitochondrial protein assemblies using high-resolution complexome profiling of more than 90% of the yeast mitochondrial proteome, termed MitCOM. An analysis of the MitCOM dataset resolves >5,200 protein peaks with an average of six peaks per protein and demonstrates a notable complexity of mitochondrial protein assemblies with distinct appearance for respiration, metabolism, biogenesis, dynamics, regulation and redox processes. We detect interactors of the mitochondrial receptor for cytosolic ribosomes, of prohibitin scaffolds and of respiratory complexes. The identification of quality-control factors operating at the mitochondrial protein entry gate reveals pathways for preprotein ubiquitylation, deubiquitylation and degradation. Interactions between the peptidyl-tRNA hydrolase Pth2 and the entry gate led to the elucidation of a constitutive pathway for the removal of preproteins. The MitCOM dataset-which is accessible through an interactive profile viewer-is a comprehensive resource for the identification, organization and interaction of mitochondrial machineries and pathways.
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Affiliation(s)
- Uwe Schulte
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Fabian den Brave
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Alexander Haupt
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Arushi Gupta
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiyao Song
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Catrin S. Müller
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jeannine Engelke
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Swadha Mishra
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Christoph Mårtensson
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,Present Address: MTIP, Basel, Switzerland
| | - Lars Ellenrieder
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.419481.10000 0001 1515 9979Present Address: Novartis, Basel, Switzerland
| | - Chantal Priesnitz
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian P. Straub
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany ,grid.482402.8Present Address: Sanofi-Aventis (Suisse), Vernier, Switzerland
| | - Kim Nguyen Doan
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bogusz Kulawiak
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.413454.30000 0001 1958 0162Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Wolfgang Bildl
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heike Rampelt
- grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Nikolaus Pfanner
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,Center for Basics in NeuroModulation, Freiburg, Germany.
| | - Thomas Becker
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
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11
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Zhang M, Berk JM, Mehrtash AB, Kanyo J, Hochstrasser M. A versatile new tool derived from a bacterial deubiquitylase to detect and purify ubiquitylated substrates and their interacting proteins. PLoS Biol 2022; 20:e3001501. [PMID: 35771886 PMCID: PMC9278747 DOI: 10.1371/journal.pbio.3001501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/13/2022] [Accepted: 05/30/2022] [Indexed: 01/07/2023] Open
Abstract
Protein ubiquitylation is an important posttranslational modification affecting a wide range of cellular processes. Due to the low abundance of ubiquitylated species in biological samples, considerable effort has been spent on methods to purify and detect ubiquitylated proteins. We have developed and characterized a novel tool for ubiquitin detection and purification based on OtUBD, a high-affinity ubiquitin-binding domain (UBD) derived from an Orientia tsutsugamushi deubiquitylase (DUB). We demonstrate that OtUBD can be used to purify both monoubiquitylated and polyubiquitylated substrates from yeast and human tissue culture samples and compare their performance with existing methods. Importantly, we found conditions for either selective purification of covalently ubiquitylated proteins or co-isolation of both ubiquitylated proteins and their interacting proteins. As proof of principle for these newly developed methods, we profiled the ubiquitylome and ubiquitin-associated proteome of the budding yeast Saccharomyces cerevisiae. Combining OtUBD affinity purification with quantitative proteomics, we identified potential substrates for the E3 ligases Bre1 and Pib1. OtUBD provides a versatile, efficient, and economical tool for ubiquitin research with specific advantages over certain other methods, such as in efficiently detecting monoubiquitylation or ubiquitin linkages to noncanonical sites. This study presents OtUBD, a new tool derived from a bacterial deubiquitylase, for the purification and analysis of a broad range of endogenous ubiquitylated proteins, including monoubiquitylation, polyubiquitylation, non-lysine ubiquitylation and potentially other macromolecules.
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Affiliation(s)
- Mengwen Zhang
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jason M. Berk
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Adrian B. Mehrtash
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jean Kanyo
- W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut, United States of America
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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12
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HECT ubiquitin ligases as accessory proteins of the plant proteasome. Essays Biochem 2022; 66:135-145. [PMID: 35635104 PMCID: PMC9400063 DOI: 10.1042/ebc20210064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/21/2022] [Accepted: 04/29/2022] [Indexed: 12/31/2022]
Abstract
The proteasome plays vital roles in eukaryotic cells by orchestrating the regulated degradation of large repertoires of substrates involved in numerous biological processes. Proteasome dysfunction is associated with a wide variety of human pathologies and in plants severely affects growth, development and responses to stress. The activity of E3 ubiquitin ligases marks proteins fated for degradation with chains of the post-translational modifier, ubiquitin. Proteasomal processing of ubiquitinated substrates involves ubiquitin chain recognition, deubiquitination, ATP-mediated unfolding and translocation, and proteolytic digestion. This complex series of steps is made possible not only by the many specialised subunits of the 1.5 MDa proteasome complex but also by a range of accessory proteins that are recruited to the proteasome. A surprising class of accessory proteins are members of the HECT-type family of ubiquitin ligases that utilise a unique mechanism for post-translational attachment of ubiquitin to their substrates. So why do proteasomes that already contain all the necessary machinery to recognise ubiquitinated substrates, harbour HECT ligase activity? It is now clear that some ubiquitin ligases physically relay their substrates to proteasome-associated HECT ligases, which prevent substrate stalling at the proteasome. Moreover, HECT ligases ubiquitinate proteasome subunits, thereby modifying the proteasome's ability to recognise substrates. They may therefore enable proteasomes to be both non-specific and extraordinarily selective in a complex substrate environment. Understanding the relationship between the proteasome and accessory HECT ligases will reveal how the proteasome controls so many diverse plant developmental and stress responses.
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13
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Zhang C, Inamdar SM, Swaminathan S, Marenda DR, Saunders AJ. Association of the Protein-Quality-Control Protein Ubiquilin-1 With Alzheimer’s Disease Both in vitro and in vivo. Front Neurosci 2022; 16:821059. [PMID: 35401099 PMCID: PMC8992708 DOI: 10.3389/fnins.2022.821059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s disease (AD) belongs to a class of diseases characterized by progressive accumulation and aggregation of pathogenic proteins, particularly Aβ proteins. Genetic analysis has identified UBQLN1 as an AD candidate gene. Ubiquilin-1 levels reduce with AD progression, suggesting a potential loss-of-function mechanism. The ubiquilin-1 protein is involved in protein quality control (PQC), which plays essential roles in cellular growth and normal cell function. Ubiquilin-1 regulates γ-secretase by increasing endoproteolysis of PS1, a key γ-secretase component. Presently, the effects of ubiquilin-1 on cellular physiology as well as Aβ-related events require further investigation. Here, we investigated the effects of ubiquilin-1 on cellular growth and viability in association with APP (amyloid-β protein precursor), APP processing-related β-secretase (BACE1, BACE) and γ-secretase using cell and animal-based models. We showed that loss-of-function in Drosophila ubqn suppresses human APP and human BACE phenotypes in wing veins and altered cell number and tissue compartment size in the wing. Additionally, we performed cell-based studies and showed that silencing UBQLN1 reduced cell viability and increased caspase-3 activity. Overexpression of UBQLN1 significantly reduced Aβ levels. Furthermore, pharmacological inhibition of γ-secretase increased ubiquilin-1 protein levels, suggesting a mechanism that regulates ubiquilin-1 levels which may associate with reduced Aβ reduction by inhibiting γ-secretase. Collectively, our results support not only a loss-of-function mechanism of ubiquilin-1 in association with AD, but also support the significance of targeting ubiquilin-1-mediated PQC as a potential therapeutic strategy for AD.
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Affiliation(s)
- Can Zhang
- Department of Biology, Drexel University, Philadelphia, PA, United States
| | | | - Swathi Swaminathan
- Department of Biology, Drexel University, Philadelphia, PA, United States
| | - Daniel R. Marenda
- Department of Biology, Drexel University, Philadelphia, PA, United States
- Division of Biological Infrastructure, National Science Foundation, Alexandria, VA, United States
| | - Aleister J. Saunders
- Department of Biology, Drexel University, Philadelphia, PA, United States
- *Correspondence: Aleister J. Saunders,
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14
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Mammalian Ddi2 is a shuttling factor containing a retroviral protease domain that influences binding of ubiquitylated proteins and proteasomal degradation. J Biol Chem 2022; 298:101875. [PMID: 35358511 PMCID: PMC9062259 DOI: 10.1016/j.jbc.2022.101875] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 11/24/2022] Open
Abstract
Although several proteasome subunits have been shown to bind ubiquitin (Ub) chains, many ubiquitylated substrates also associate with 26S proteasomes via “shuttling factors.” Unlike the well-studied yeast shuttling factors Rad23 and Dsk2, vertebrate homologs Ddi2 and Ddi1 lack a Ub-associated domain; therefore, it is unclear how they bind Ub. Here, we show that deletion of Ddi2 leads to the accumulation of Ub conjugates with K11/K48 branched chains. We found using affinity copurifications that Ddi2 binds Ub conjugates through its Ub-like domain, which is also required for Ddi2 binding to proteasomes. Furthermore, in cell extracts, adding Ub conjugates increased the amount of Ddi2 associated with proteasomes, and adding Ddi2 increased the binding of Ub conjugates to purified proteasomes. In addition, Ddi2 also contains a retroviral protease domain with undefined cellular roles. We show that blocking the endoprotease activity of Ddi2 either genetically or with the HIV protease inhibitor nelfinavir increased its binding to Ub conjugates but decreased its binding to proteasomes and reduced subsequent protein degradation by proteasomes leading to further accumulation of Ub conjugates. Finally, nelfinavir treatment required Ddi2 to induce the unfolded protein response. Thus, Ddi2 appears to function as a shuttling factor in endoplasmic reticulum–associated protein degradation and delivers K11/K48-ubiquitylated proteins to the proteasome. We conclude that the protease activity of Ddi2 influences this shuttling factor activity, promotes protein turnover, and helps prevent endoplasmic reticulum stress, which may explain nelfinavir’s ability to enhance cell killing by proteasome inhibitors.
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15
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Functional Differences between Proteasome Subtypes. Cells 2022; 11:cells11030421. [PMID: 35159231 PMCID: PMC8834425 DOI: 10.3390/cells11030421] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/30/2022] Open
Abstract
Four proteasome subtypes are commonly present in mammalian tissues: standard proteasomes, which contain the standard catalytic subunits β1, β2 and β5; immunoproteasomes containing the immuno-subunits β1i, β2i and β5i; and two intermediate proteasomes, containing a mix of standard and immuno-subunits. Recent studies revealed the expression of two tissue-specific proteasome subtypes in cortical thymic epithelial cells and in testes: thymoproteasomes and spermatoproteasomes. In this review, we describe the mechanisms that enable the ATP- and ubiquitin-dependent as well as the ATP- and ubiquitin-independent degradation of proteins by the proteasome. We focus on understanding the role of the different proteasome subtypes in maintaining protein homeostasis in normal physiological conditions through the ATP- and ubiquitin-dependent degradation of proteins. Additionally, we discuss the role of each proteasome subtype in the ATP- and ubiquitin-independent degradation of disordered proteins. We also discuss the role of the proteasome in the generation of peptides presented by MHC class I molecules and the implication of having different proteasome subtypes for the peptide repertoire presented at the cell surface. Finally, we discuss the role of the immunoproteasome in immune cells and its modulation as a potential therapy for autoimmune diseases.
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16
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den Brave F, Gupta A, Becker T. Protein Quality Control at the Mitochondrial Surface. Front Cell Dev Biol 2021; 9:795685. [PMID: 34926473 PMCID: PMC8678412 DOI: 10.3389/fcell.2021.795685] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria contain two membranes, the outer and inner membrane. The outer membrane fulfills crucial functions for the communication of mitochondria with the cellular environment like exchange of lipids via organelle contact sites, the transport of metabolites and the formation of a signaling platform in apoptosis and innate immunity. The translocase of the outer membrane (TOM complex) forms the entry gate for the vast majority of precursor proteins that are produced on cytosolic ribosomes. Surveillance of the functionality of outer membrane proteins is critical for mitochondrial functions and biogenesis. Quality control mechanisms remove defective and mistargeted proteins from the outer membrane as well as precursor proteins that clog the TOM complex. Selective degradation of single proteins is also an important mode to regulate mitochondrial dynamics and initiation of mitophagy pathways. Whereas inner mitochondrial compartments are equipped with specific proteases, the ubiquitin-proteasome system is a central player in protein surveillance on the mitochondrial surface. In this review, we summarize our current knowledge about the molecular mechanisms that govern quality control of proteins at the outer mitochondrial membrane.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Arushi Gupta
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
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17
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Min JH, Park CR, Chung JS, Kim CS. Arabidopsis thaliana Ubiquitin-Associated Protein 1 (AtUAP1) Interacts with redundant RING Zinc Finger 1 (AtRZF1) to Negatively Regulate Dehydration Response. PLANT & CELL PHYSIOLOGY 2021; 62:1044-1057. [PMID: 34086919 DOI: 10.1093/pcp/pcab082] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 05/16/2023]
Abstract
Ubiquitination, one of the most frequently occurring post-translational modifications, is essential for regulating diverse cellular processes in plants during abiotic stress. The E3 ubiquitin (Ub) ligase Arabidopsis thaliana really interesting new gene (RING) zinc finger 1 (AtRZF1) mutation is known to enhance drought tolerance in A. thaliana seedlings. To further investigate the function of AtRZF1 in osmotic stress, we isolated Ub-associated protein 1 (AtUAP1) which interacts with AtRZF1 using a yeast two-hybrid system. AtUAP1, a Ub-associated motif containing protein, increased the amount of Ub-conjugated AtRZF1. Moreover, AtUAP1 RNA interference lines were more tolerant to osmotic stress than wild type, whereas AtUAP1-overexpressing (OX) transgenic lines showed sensitive responses, including cotyledon greening, water loss, proline accumulation and changes in stress-related genes expression, indicating that AtUAP1 could negatively regulate dehydration-mediated signaling. In addition, AtUAP1-green fluorescent protein fusion protein was observed in the nuclei of root cells of transgenic seedlings. Genetic studies showed that the AtRZF1 mutation could rescue the sensitive phenotype of AtUAP1-OX lines in response to osmotic stress, suggesting that AtRZF1 was epistatic to AtUAP1 in dehydration signaling. Taken together, our findings describe a new component in the AtRZF1 ubiquitination pathway which controls the dehydration response in A. thaliana.
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Affiliation(s)
- Ji-Hee Min
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, TX 77843-2128, USA
| | - Cho-Rong Park
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jung-Sung Chung
- Department of Agricultural Plant Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Cheol Soo Kim
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
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18
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Wang D, Lv C, Guan Y, Ni X, Wu F. Dsk2 involves in conidiation, multi-stress tolerance and thermal adaptation in Beauveria bassiana. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:384-393. [PMID: 33870613 DOI: 10.1111/1758-2229.12946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
Dsk2 is a nuclear-enriched ubiquitin-like polyubiquitin-binding protein that regulates protein degradation in yeast but has not been explored yet in filamentous fungi, such as Beauveria bassiana. Here, we report Beauveria bassiana Dsk2 located both in the nucleus and in cytoplasm of hyphal cells. Deletion of Dsk2 resulted in mild growth defect on scant media with various carbon/nitrogen sources and dramatic attenuation in conidiation capability at optimal condition. Compared to the wild-type, ΔDsk2 strains are much more sensitive to high osmotic and oxidative pressure during vegetative growth. Meanwhile, the mutant strains showed an increased chemical tolerance to Congo red and calcofluor white, two cell wall perturbing agents. The transcriptional changes of genes involved in central development, superoxide dismutase and chitin synthesis pathway indicate that Dsk2 acts as a multi-functional regulator in adapting to environmental changes. Importantly, Dsk2 negatively regulated the ability of thermal resistance in B. bassiana, which makes it a potential target gene for constructing engineering anti-thermal strains in the circumstance of global warming. Altogether, our finding highlights novel roles of Dsk2 involved in the asexual cycle, multi-stress tolerance and pest control potential of B. bassiana.
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Affiliation(s)
- Dingyi Wang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Chao Lv
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yi Guan
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Xiangyin Ni
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Fuzhong Wu
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
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19
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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20
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Gene commander in the trash heap: Transcriptional regulation and ubiquitination modification mediated by RNF6 in carcinogenesis. Exp Cell Res 2021; 401:112396. [PMID: 33485842 DOI: 10.1016/j.yexcr.2020.112396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/13/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Abstract
RING finger protein 6 (RNF6), a RING finger protein, has been identified as a potential tumor promoter in several cancers. However, the exact mechanism of RNF6 in cancer remains elusive. As in various diseases, RNF6 may be involved in regulating cell growth, cell proliferation, invasion, cell cycle progression, apoptosis and cell adhesion through E3 ligase-mediated ubiquitination. Thus, the research on RNF6 is mainly focused on the ubiquitination of RNF6 in recent years. This article summarizes the role of RNF6 ubiquitination in various physiological and pathological mechanisms, such as Akt/mTOR signaling pathway, Wnt/β-catenin pathway, RNF6/ERα/Bcl-xL axis, and provides knowledge and understanding for the treatment of diseases.
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21
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Qi H, Xia FN, Xiao S. Autophagy in plants: Physiological roles and post-translational regulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:161-179. [PMID: 32324339 DOI: 10.1111/jipb.12941] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
In eukaryotes, autophagy helps maintain cellular homeostasis by degrading and recycling cytoplasmic materials via a tightly regulated pathway. Over the past few decades, significant progress has been made towards understanding the physiological functions and molecular regulation of autophagy in plant cells. Increasing evidence indicates that autophagy is essential for plant responses to several developmental and environmental cues, functioning in diverse processes such as senescence, male fertility, root meristem maintenance, responses to nutrient starvation, and biotic and abiotic stress. Recent studies have demonstrated that, similar to nonplant systems, the modulation of core proteins in the plant autophagy machinery by posttranslational modifications such as phosphorylation, ubiquitination, lipidation, S-sulfhydration, S-nitrosylation, and acetylation is widely involved in the initiation and progression of autophagy. Here, we provide an overview of the physiological roles and posttranslational regulation of autophagy in plants.
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Affiliation(s)
- Hua Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fan-Nv Xia
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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22
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Whiteley AM, Prado MA, de Poot SAH, Paulo JA, Ashton M, Dominguez S, Weber M, Ngu H, Szpyt J, Jedrychowski MP, Easton A, Gygi SP, Kurz T, Monteiro MJ, Brown EJ, Finley D. Global proteomics of Ubqln2-based murine models of ALS. J Biol Chem 2020; 296:100153. [PMID: 33277362 PMCID: PMC7873701 DOI: 10.1074/jbc.ra120.015960] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/21/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
Familial neurodegenerative diseases commonly involve mutations that result in either aberrant proteins or dysfunctional components of the proteolytic machinery that act on aberrant proteins. UBQLN2 is a ubiquitin receptor of the UBL/UBA family that binds the proteasome through its ubiquitin-like domain and is thought to deliver ubiquitinated proteins to proteasomes for degradation. UBQLN2 mutations result in familial amyotrophic lateral sclerosis (ALS)/frontotemporal dementia in humans through an unknown mechanism. Quantitative multiplexed proteomics was used to provide for the first time an unbiased and global analysis of the role of Ubqln2 in controlling the composition of the proteome. We studied several murine models of Ubqln2-linked ALS and also generated Ubqln2 null mutant mice. We identified impacts of Ubqln2 on diverse physiological pathways, most notably serotonergic signaling. Interestingly, we observed an upregulation of proteasome subunits, suggesting a compensatory response to diminished proteasome output. Among the specific proteins whose abundance is linked to UBQLN2 function, the strongest hits were the ubiquitin ligase TRIM32 and two retroelement-derived proteins, PEG10 and CXX1B. Cycloheximide chase studies using induced human neurons and HEK293 cells suggested that PEG10 and TRIM32 are direct clients. Although UBQLN2 directs the degradation of multiple proteins via the proteasome, it surprisingly conferred strong protection from degradation on the Gag-like protein CXX1B, which is expressed from the same family of retroelement genes as PEG10. In summary, this study charts the proteomic landscape of ALS-related Ubqln2 mutants and identifies candidate client proteins that are altered in vivo in disease models and whose degradation is promoted by UBQLN2.
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Affiliation(s)
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marissa Ashton
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara Dominguez
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Martin Weber
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Hai Ngu
- Department of Pathology, Genentech Inc, South San Francisco, California, USA
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark P Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy Easton
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Thimo Kurz
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Mervyn J Monteiro
- Center for Biomedical Engineering and Technology, Department of Anatomy and Neurobiology, University of Maryland Medical School, Baltimore, Maryland, USA
| | - Eric J Brown
- Department of Immunology and Infectious Diseases, Genentech Inc, South San Francisco, California, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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23
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Zhang H, Liu J, Ying Z, Li S, Wu Y, Liu Q. Toxoplasma gondii UBL-UBA shuttle proteins contribute to the degradation of ubiquitinylated proteins and are important for synchronous cell division and virulence. FASEB J 2020; 34:13711-13725. [PMID: 32808330 DOI: 10.1096/fj.202000759rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 11/11/2022]
Abstract
Toxoplasma gondii is an obligate intracellular apicomplexan parasite that causes lethal diseases in immunocompromised patients. Ubiquitin-proteasome system (UPS) regulates many cellular processes by degrading ubiquitinylated proteins. The UBL-UBA shuttle protein family, which escorts the ubiquitinylated proteins to the proteasome for degradation, are crucial components of UPS. Here, we identified three UBL-UBA shuttle proteins (TGGT1_304680, DNA damage inducible protein 1, DDI1; TGGT1_295340, UV excision repair protein rad23 protein, RAD23; and TGGT1_223680, ubiquitin family protein, DSK2) localized in the cytoplasm and nucleus of T gondii. Deletion of shuttle proteins inhibited parasites growth and resulted in accumulation of ubiquitinylated proteins. Cell division of triple-gene knockout strain was asynchronous. In addition, we found that the retroviral aspartic protease activity of the nonclassical shuttle protein DDI1 was important for the virulence of Toxoplasma in mice. These results showed the critical roles of UBL-UBA shuttle proteins in regulating the degradation of ubiquitinylated proteins and cell division of T gondii.
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Affiliation(s)
- Heng Zhang
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jing Liu
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhu Ying
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shuang Li
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yihan Wu
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qun Liu
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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24
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Releasing the Lockdown: An Emerging Role for the Ubiquitin-Proteasome System in the Breakdown of Transient Protein Inclusions. Biomolecules 2020; 10:biom10081168. [PMID: 32784966 PMCID: PMC7463783 DOI: 10.3390/biom10081168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 12/20/2022] Open
Abstract
Intracellular protein inclusions are diverse cellular entities with distinct biological properties. They vary in their protein content, sequestration sites, physiological function, conditions for their generation, and turnover rates. Major distinctions have been recognized between stationary amyloids and dynamic, misfolded protein deposits. The former being a dead end for irreversibly misfolded proteins, hence, cleared predominantly by autophagy, while the latter consists of a protein-quality control mechanism, important for cell endurance, where proteins are sequestered during proteotoxic stress and resolved upon its relief. Accordingly, the disaggregation of transient inclusions is a regulated process consisting of protein solubilization, followed by a triage step to either refolding or to ubiquitin-mediated degradation. Recent studies have demonstrated an indispensable role in disaggregation for components of the chaperone and the ubiquitin-proteasome systems. These include heat-shock chaperones of the 40/70/100 kDa families, the proteasome, proteasome substrate shuttling factors, and deubiquitylating enzymes. Thus, a functional link has been established between the chaperone machinery that extracts proteins from transient deposits and 26S proteasome-dependent disaggregation, indicative of a coordinated process. In this review, we discuss data emanating from these important studies and subsequently consolidate the information in the form of a working model for the disaggregation mechanism.
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25
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Abildgaard AB, Gersing SK, Larsen-Ledet S, Nielsen SV, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome. Biomolecules 2020; 10:biom10081141. [PMID: 32759676 PMCID: PMC7463752 DOI: 10.3390/biom10081141] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis (proteostasis) is essential for the cell and is maintained by a highly conserved protein quality control (PQC) system, which triages newly synthesized, mislocalized and misfolded proteins. The ubiquitin-proteasome system (UPS), molecular chaperones, and co-chaperones are vital PQC elements that work together to facilitate degradation of misfolded and toxic protein species through the 26S proteasome. However, the underlying mechanisms are complex and remain partly unclear. Here, we provide an overview of the current knowledge on the co-chaperones that directly take part in targeting and delivery of PQC substrates for degradation. While J-domain proteins (JDPs) target substrates for the heat shock protein 70 (HSP70) chaperones, nucleotide-exchange factors (NEFs) deliver HSP70-bound substrates to the proteasome. So far, three NEFs have been established in proteasomal delivery: HSP110 and the ubiquitin-like (UBL) domain proteins BAG-1 and BAG-6, the latter acting as a chaperone itself and carrying its substrates directly to the proteasome. A better understanding of the individual delivery pathways will improve our ability to regulate the triage, and thus regulate the fate of aberrant proteins involved in cell stress and disease, examples of which are given throughout the review.
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Affiliation(s)
- Amanda B. Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sarah K. Gersing
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sven Larsen-Ledet
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Sofie V. Nielsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (S.V.N.); (A.S.)
| | - Amelie Stein
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (S.V.N.); (A.S.)
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (A.B.A.); (S.K.G.); (S.L.-L.); (K.L.-L.)
- Correspondence:
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26
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Aichem A, Groettrup M. The ubiquitin-like modifier FAT10 - much more than a proteasome-targeting signal. J Cell Sci 2020; 133:133/14/jcs246041. [PMID: 32719056 DOI: 10.1242/jcs.246041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10) also called ubiquitin D (UBD) is a member of the ubiquitin-like modifier (ULM) family. The FAT10 gene is localized in the MHC class I locus and FAT10 protein expression is mainly restricted to cells and organs of the immune system. In all other cell types and tissues, FAT10 expression is highly inducible by the pro-inflammatory cytokines interferon (IFN)-γ and tumor necrosis factor (TNF). Besides ubiquitin, FAT10 is the only ULM which directly targets its substrates for degradation by the 26S proteasome. This poses the question as to why two ULMs sharing the proteasome-targeting function have evolved and how they differ from each other. This Review summarizes the current knowledge of the special structure of FAT10 and highlights its differences from ubiquitin. We discuss how these differences might result in differential outcomes concerning proteasomal degradation mechanisms and non-covalent target interactions. Moreover, recent insights about the structural and functional impact of FAT10 interacting with specific non-covalent interaction partners are reviewed.
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Affiliation(s)
- Annette Aichem
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280 Kreuzlingen, Switzerland.,Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marcus Groettrup
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280 Kreuzlingen, Switzerland .,Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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27
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Gemperline DC, Marshall RS, Lee KH, Zhao Q, Hu W, McLoughlin F, Scalf M, Smith LM, Vierstra RD. Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis. J Biol Chem 2019; 294:17570-17592. [PMID: 31562246 PMCID: PMC6873196 DOI: 10.1074/jbc.ra119.010219] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/17/2019] [Indexed: 01/01/2023] Open
Abstract
The 26S proteasome is an essential protease that selectively eliminates dysfunctional and short-lived regulatory proteins in eukaryotes. To define the composition of this proteolytic machine in plants, we tagged either the core protease (CP) or the regulatory particle (RP) sub-complexes in Arabidopsis to enable rapid affinity purification followed by mass spectrometric analysis. Studies on proteasomes enriched from whole seedlings, with or without ATP needed to maintain the holo-proteasome complex, identified all known proteasome subunits but failed to detect isoform preferences, suggesting that Arabidopsis does not construct distinct proteasome sub-types. We also detected a suite of proteasome-interacting proteins, including likely orthologs of the yeast and mammalian chaperones Pba1, Pba2, Pba3, and Pba4 that assist in CP assembly; Ump1 that helps connect CP half-barrels; Nas2, Nas6, and Hsm3 that assist in RP assembly; and Ecm29 that promotes CP-RP association. Proteasomes from seedlings exposed to the proteasome inhibitor MG132 accumulated assembly intermediates, reflecting partially built proteasome sub-complexes associated with assembly chaperones, and the CP capped with the PA200/Blm10 regulator. Genetic analyses of Arabidopsis UMP1 revealed that, unlike in yeast, this chaperone is essential, with mutants lacking the major UMP1a and UMP1b isoforms displaying a strong gametophytic defect. Single ump1 mutants were hypersensitive to conditions that induce proteotoxic, salt and osmotic stress, and also accumulated several proteasome assembly intermediates, consistent with its importance for CP construction. Insights into the chaperones reported here should enable study of the assembly events that generate the 26S holo-proteasome in Arabidopsis from the collection of 64 or more subunits.
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Affiliation(s)
- David C Gemperline
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard S Marshall
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Kwang-Hee Lee
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Qingzhen Zhao
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
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28
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Tufegdzic Vidakovic A, Harreman M, Dirac-Svejstrup AB, Boeing S, Roy A, Encheva V, Neumann M, Wilson M, Snijders AP, Svejstrup JQ. Analysis of RNA polymerase II ubiquitylation and proteasomal degradation. Methods 2019; 159-160:146-156. [PMID: 30769100 PMCID: PMC6617506 DOI: 10.1016/j.ymeth.2019.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 12/19/2022] Open
Abstract
Transcribing RNA polymerase II (RNAPII) is decorated by a plethora of post-translational modifications that mark different stages of transcription. One important modification is RNAPII ubiquitylation, which occurs in response to numerous different stimuli that cause RNAPII stalling, such as DNA damaging agents, RNAPII inhibitors, or depletion of the nucleotide pool. Stalled RNAPII triggers a so-called "last resort pathway", which involves RNAPII poly-ubiquitylation and proteasome-mediated degradation. Different approaches have been described to study RNAPII poly-ubiquitylation and degradation, each method with its own advantages and caveats. Here, we describe optimised strategies for detecting ubiquitylated RNAPII and studying its degradation, but these protocols are suitable for studying other ubiquitylated proteins as well.
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Affiliation(s)
- Ana Tufegdzic Vidakovic
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michelle Harreman
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - A Barbara Dirac-Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Anindya Roy
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Vesela Encheva
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michelle Neumann
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Marcus Wilson
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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29
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Kitab B, Satoh M, Ohmori Y, Munakata T, Sudoh M, Kohara M, Tsukiyama-Kohara K. Ribonucleotide reductase M2 promotes RNA replication of hepatitis C virus by protecting NS5B protein from hPLIC1-dependent proteasomal degradation. J Biol Chem 2019; 294:5759-5773. [PMID: 30755480 DOI: 10.1074/jbc.ra118.004397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 02/02/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) establishes a chronic infection that can lead to cirrhosis and hepatocellular carcinoma. The HCV life cycle is closely associated with host factors that promote or restrict viral replication, the characterization of which could help to identify potential therapeutic targets. To this end, here we performed a genome-wide microarray analysis and identified ribonucleotide reductase M2 (RRM2) as a cellular factor essential for HCV replication. We found that RRM2 is up-regulated in response to HCV infection in quiescent hepatocytes from humanized chimeric mouse livers. To elucidate the molecular basis of RRM2 expression in HCV-infected cells, we used HCV-infected hepatocytes from chimeric mice and hepatoma cells infected with the HCV strain JFH1. Both models exhibited increased RRM2 mRNA and protein expression levels. Moreover, siRNA-mediated silencing of RRM2 suppressed HCV replication and infection. Of note, RRM2 and RNA polymerase nonstructural protein 5B (NS5B) partially co-localized in cells and co-immunoprecipitated, suggesting that they might interact. RRM2 knockdown reduced NS5B expression, which depended on the protein degradation pathway, as NS5B RNA levels did not decrease and NS5B protein stability correlated with RRM2 protein levels. We also found that RRM2 silencing decreased levels of hPLIC1 (human homolog 1 of protein linking integrin-associated protein and cytoskeleton), a ubiquitin-like protein that interacts with NS5B and promotes its degradation. This finding suggests that there is a dynamic interplay between RRM2 and the NS5B-hPLIC1 complex that has an important function in HCV replication. Together, these results identify a role of host RRM2 in viral RNA replication.
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Affiliation(s)
- Bouchra Kitab
- From the Transboundary Animal Diseases Centre, Kagoshima University, Kagoshima-City 890-8580, Japan; Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima-City 890-8580, Japan
| | - Masaaki Satoh
- Virology I, National Institute of Infectious Diseases, Shinjuku-Ku, Tokyo 162-8640, Japan
| | - Yusuke Ohmori
- Research Division, Chugai Pharmaceutical Co., Ltd., Kajiwara, Kamakura-City, Kanagawa 247-8530, Japan
| | - Tsubasa Munakata
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Setagaya-Ku, Tokyo 156-8506, Japan
| | - Masayuki Sudoh
- Research Division, Chugai Pharmaceutical Co., Ltd., Kajiwara, Kamakura-City, Kanagawa 247-8530, Japan
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Setagaya-Ku, Tokyo 156-8506, Japan.
| | - Kyoko Tsukiyama-Kohara
- From the Transboundary Animal Diseases Centre, Kagoshima University, Kagoshima-City 890-8580, Japan; Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima-City 890-8580, Japan.
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30
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The Roles of Ubiquitin-Binding Protein Shuttles in the Degradative Fate of Ubiquitinated Proteins in the Ubiquitin-Proteasome System and Autophagy. Cells 2019; 8:cells8010040. [PMID: 30634694 PMCID: PMC6357184 DOI: 10.3390/cells8010040] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/24/2018] [Accepted: 01/03/2019] [Indexed: 12/15/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) and autophagy are the two major intracellular protein quality control (PQC) pathways that are responsible for cellular proteostasis (homeostasis of the proteome) by ensuring the timely degradation of misfolded, damaged, and unwanted proteins. Ubiquitination serves as the degradation signal in both these systems, but substrates are precisely targeted to one or the other pathway. Determining how and when cells target specific proteins to these two alternative PQC pathways and control the crosstalk between them are topics of considerable interest. The ubiquitin (Ub) recognition code based on the type of Ub-linked chains on substrate proteins was believed to play a pivotal role in this process, but an increasing body of evidence indicates that the PQC pathway choice is also made based on other criteria. These include the oligomeric state of the Ub-binding protein shuttles, their conformation, protein modifications, and the presence of motifs that interact with ATG8/LC3/GABARAP (autophagy-related protein 8/microtubule-associated protein 1A/1B-light chain 3/GABA type A receptor-associated protein) protein family members. In this review, we summarize the current knowledge regarding the Ub recognition code that is bound by Ub-binding proteasomal and autophagic receptors. We also discuss how cells can modify substrate fate by modulating the structure, conformation, and physical properties of these receptors to affect their shuttling between both degradation pathways.
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31
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Picher-Martel V, Renaud L, Bareil C, Julien JP. Neuronal Expression of UBQLN2 P497H Exacerbates TDP-43 Pathology in TDP-43 G348C Mice through Interaction with Ubiquitin. Mol Neurobiol 2018; 56:4680-4696. [PMID: 30377984 PMCID: PMC6647471 DOI: 10.1007/s12035-018-1411-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 12/11/2022]
Abstract
Mutations in the gene encoding ubiquilin-2 (UBQLN2) are linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). UBQLN2 plays a central role in ubiquitin proteasome system (UPS) and UBQLN2 up-regulation exacerbates TDP-43 cytoplasmic aggregates. To analyze interaction between UBQLN2 and TDP-43 and to produce a relevant ALS animal model, we have generated a new transgenic mouse expressing UBQLN2P497H under the neurofilament heavy (NFH) gene promoter. The UBQLN2P497H mice were then bred with our previously described TDP-43G348C mice to generate double-transgenic UBQLN2P497H; TDP-43G348C mice. With low-expression levels of UBQLN2, the double-transgenic mice developed TDP-43 cytosolic accumulations in motor neurons starting at 5 months of age. These double-transgenic mice exhibited motor neuron loss, muscle atrophy, as well as motor and cognitive deficits during aging. The microglia from double-transgenic mice were hyperresponsive to intraperitoneal injection of lipopolysaccharide (LPS). In vivo and in vitro analyses suggested that extra UBQLN2 proteins can exacerbate cytoplasmic TDP-43 accumulations by competing with the UPS for binding to ubiquitin. Thus, increasing the pool of ubiquitin promoted the UPS function with ensuing reduction of TDP-43 cytosolic accumulations. In conclusion, the double-transgenic UBQLN2P497H; TDP-43G348C mice provides a unique mouse model of ALS/FTD with enhanced TDP-43 pathology that can be exploited for drug testing.
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Affiliation(s)
- Vincent Picher-Martel
- Department of Psychiatry and Neuroscience, Laval University, Quebec, Canada.,CERVO Brain Research Centre, 2601 Chemin de la Canardière, Québec, QC, G1J 2G3, Canada
| | - Laurence Renaud
- Department of Psychiatry and Neuroscience, Laval University, Quebec, Canada.,CERVO Brain Research Centre, 2601 Chemin de la Canardière, Québec, QC, G1J 2G3, Canada
| | - Christine Bareil
- CERVO Brain Research Centre, 2601 Chemin de la Canardière, Québec, QC, G1J 2G3, Canada
| | - Jean-Pierre Julien
- Department of Psychiatry and Neuroscience, Laval University, Quebec, Canada. .,CERVO Brain Research Centre, 2601 Chemin de la Canardière, Québec, QC, G1J 2G3, Canada.
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32
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Wang J, Wang J, Lu Y, Fang Y, Gao X, Wang Z, Zheng W, Xu S. The heat responsive wheat TaRAD23 rescues developmental and thermotolerant defects of the rad23b mutant in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:23-31. [PMID: 30080608 DOI: 10.1016/j.plantsci.2018.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/30/2018] [Accepted: 04/30/2018] [Indexed: 05/24/2023]
Abstract
High temperature severely damage the growth and development of crops with climate change. To effectively screen heat responsive proteins in wheat (Triticum aestivum L.), the isobaric tandem mass tag (TMT)-labeled quantitative proteomic analysis and quantitative real-time PCR (qRT-PCR) were performed. Here, we found that a wheat RADIATION SENSITIVE 23 protein, TaRAD23, was up-regulated at both protein and RNA levels by exposing to heat stress. Sequence homology analysis indicated that the TaRAD23 is a conserved protein, which is closely related to the Arabidopsis thaliana proteins AtRAD23B and AtRAD23A. Genetic knockout of AtRAD23B, but not AtRAD23A, shows multiple developmental defects, as well as sensitivity to heat stress. Meanwhile, we observed that constitutive overexpression of TaRAD23 in rad23b fully rescued developmental and thermotolerant defects of the mutant. Furthermore, qRT-PCR analysis of heat responsive genes in rad23b and its complementary lines suggested that suppression of the heat shock transcription factor AtHSFA2 and heat responsive genes (HSP70, HSP90, HSP17.6 and HSA32) may be the cause of the weaker thermotolerance in rad23b. Taken together, the data suggest that the heat responsive TaRAD23 is a functionally highly conserved protein that plays an important role in development, as well as the regulation in heat stress response network.
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Affiliation(s)
- Jun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Junzhe Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Yunze Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Yan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China.
| | - Xin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Weijun Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
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33
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Bard JAM, Goodall EA, Greene ER, Jonsson E, Dong KC, Martin A. Structure and Function of the 26S Proteasome. Annu Rev Biochem 2018; 87:697-724. [PMID: 29652515 DOI: 10.1146/annurev-biochem-062917-011931] [Citation(s) in RCA: 441] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As the endpoint for the ubiquitin-proteasome system, the 26S proteasome is the principal proteolytic machine responsible for regulated protein degradation in eukaryotic cells. The proteasome's cellular functions range from general protein homeostasis and stress response to the control of vital processes such as cell division and signal transduction. To reliably process all the proteins presented to it in the complex cellular environment, the proteasome must combine high promiscuity with exceptional substrate selectivity. Recent structural and biochemical studies have shed new light on the many steps involved in proteasomal substrate processing, including recognition, deubiquitination, and ATP-driven translocation and unfolding. In addition, these studies revealed a complex conformational landscape that ensures proper substrate selection before the proteasome commits to processive degradation. These advances in our understanding of the proteasome's intricate machinery set the stage for future studies on how the proteasome functions as a major regulator of the eukaryotic proteome.
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Affiliation(s)
- Jared A M Bard
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Ellen A Goodall
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Eric R Greene
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Erik Jonsson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
| | - Ken C Dong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA; .,California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
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34
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Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ. Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins. eLife 2017; 6. [PMID: 28933694 PMCID: PMC5608509 DOI: 10.7554/elife.26435] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/22/2017] [Indexed: 12/14/2022] Open
Abstract
Ubiquilins (Ubqlns) are a family of ubiquitin receptors that promote the delivery of hydrophobic and aggregated ubiquitinated proteins to the proteasome for degradation. We carried out a proteomic analysis of a B cell lymphoma-derived cell line, BJAB, that requires UBQLN1 for survival to identify UBQLN1 client proteins. When UBQLN1 expression was acutely inhibited, 120 mitochondrial proteins were enriched in the cytoplasm, suggesting that the accumulation of mitochondrial client proteins in the absence of UBQLN1 is cytostatic. Using a Ubqln1−/− mouse strain, we found that B cell receptor (BCR) ligation of Ubqln1−/− B cells led to a defect in cell cycle entry. As in BJAB cells, mitochondrial proteins accumulated in BCR-stimulated cells, leading to protein synthesis inhibition and cell cycle block. Thus, UBQLN1 plays an important role in clearing mislocalized mitochondrial proteins upon cell stimulation, and its absence leads to suppression of protein synthesis and cell cycle arrest.
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Affiliation(s)
- Alexandra M Whiteley
- Department of Infectious Disease, Genentech, South San Francisco, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Ivan Peng
- Department of Translational Immunology, Genentech, South San Francisco, United States
| | - Alexander R Abbas
- Department of Bioinformatics, Genentech, South San Francisco, United States
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Mike Reichelt
- Department of Pathology, Genentech, South San Francisco, United States
| | - Anand Katakam
- Department of Pathology, Genentech, South San Francisco, United States
| | - Meredith Sagolla
- Department of Pathology, Genentech, South San Francisco, United States
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, United States
| | - Dong Yun Lee
- Department of Infectious Disease, Genentech, South San Francisco, United States
| | - Merone Roose-Girma
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, United States
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, United States
| | - Brent S McKenzie
- Department of Translational Immunology, Genentech, South San Francisco, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Eric J Brown
- Department of Infectious Disease, Genentech, South San Francisco, United States
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Selective Autophagy of BES1 Mediated by DSK2 Balances Plant Growth and Survival. Dev Cell 2017; 41:33-46.e7. [PMID: 28399398 DOI: 10.1016/j.devcel.2017.03.013] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 01/17/2017] [Accepted: 03/14/2017] [Indexed: 12/20/2022]
Abstract
Plants encounter a variety of stresses and must fine-tune their growth and stress-response programs to best suit their environment. BES1 functions as a master regulator in the brassinosteroid (BR) pathway that promotes plant growth. Here, we show that BES1 interacts with the ubiquitin receptor protein DSK2 and is targeted to the autophagy pathway during stress via the interaction of DSK2 with ATG8, a ubiquitin-like protein directing autophagosome formation and cargo recruitment. Additionally, DSK2 is phosphorylated by the GSK3-like kinase BIN2, a negative regulator in the BR pathway. BIN2 phosphorylation of DSK2 flanking its ATG8 interacting motifs (AIMs) promotes DSK2-ATG8 interaction, thereby targeting BES1 for degradation. Accordingly, loss-of-function dsk2 mutants accumulate BES1, have altered global gene expression profiles, and have compromised stress responses. Our results thus reveal that plants coordinate growth and stress responses by integrating BR and autophagy pathways and identify the molecular basis of this crosstalk.
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Lu K, den Brave F, Jentsch S. Receptor oligomerization guides pathway choice between proteasomal and autophagic degradation. Nat Cell Biol 2017; 19:732-739. [PMID: 28504708 DOI: 10.1038/ncb3531] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/11/2017] [Indexed: 12/17/2022]
Abstract
Abnormal or aggregated proteins have a strong cytotoxic potential and are causative for human disorders such as Alzheimer's, Parkinson's, Huntington's disease and amyotrophic lateral sclerosis. If not restored by molecular chaperones, abnormal proteins are typically degraded by proteasomes or eliminated by selective autophagy. The discovery that both pathways are initiated by substrate ubiquitylation but utilize different ubiquitin receptors incited a debate over how pathway choice is achieved. Here, we demonstrate in yeast that pathway choice is made after substrate ubiquitylation by competing ubiquitin receptors harbouring either proteasome- or autophagy-related protein 8 (Atg8/LC3)-binding modules. Proteasome pathway receptors bind ubiquitin moieties more efficiently, but autophagy receptors gain the upper hand following substrate aggregation and receptor bundling. Indeed, by using sets of modular artificial receptors harbouring identical ubiquitin-binding modules we found that proteasome/autophagy pathway choice is independent of the ubiquitin-binding properties of the receptors but largely determined by their oligomerization potentials. Our work thus suggests that proteasomal degradation and selective autophagy are two branches of an adaptive protein quality control pathway, which uses substrate ubiquitylation as a shared degradation signal.
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Affiliation(s)
- Kefeng Lu
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Fabian den Brave
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Stefan Jentsch
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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In Vivo Ubiquitin Linkage-type Analysis Reveals that the Cdc48-Rad23/Dsk2 Axis Contributes to K48-Linked Chain Specificity of the Proteasome. Mol Cell 2017; 66:488-502.e7. [DOI: 10.1016/j.molcel.2017.04.024] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 12/28/2022]
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38
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Poulsen EG, Kampmeyer C, Kriegenburg F, Johansen JV, Hofmann K, Holmberg C, Hartmann-Petersen R. UBL/BAG-domain co-chaperones cause cellular stress upon overexpression through constitutive activation of Hsf1. Cell Stress Chaperones 2017; 22:143-154. [PMID: 27966061 PMCID: PMC5225068 DOI: 10.1007/s12192-016-0751-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022] Open
Abstract
As a result of exposure to stress conditions, mutations, or defects during synthesis, cellular proteins are prone to misfold. To cope with such partially denatured proteins, cells mount a regulated transcriptional response involving the Hsf1 transcription factor, which drives the synthesis of molecular chaperones and other stress-relieving proteins. Here, we show that the fission yeast Schizosaccharomyces pombe orthologues of human BAG-1, Bag101, and Bag102, are Hsp70 co-chaperones that associate with 26S proteasomes. Only a subgroup of Hsp70-type chaperones, including Ssa1, Ssa2, and Sks2, binds Bag101 and Bag102 and key residues in the Hsp70 ATPase domains, required for interaction with Bag101 and Bag102, were identified. In humans, BAG-1 overexpression is typically observed in cancers. Overexpression of bag101 and bag102 in fission yeast leads to a strong growth defect caused by triggering Hsp70 to release and activate the Hsf1 transcription factor. Accordingly, the bag101-linked growth defect is alleviated in strains containing a reduced amount of Hsf1 but aggravated in hsp70 deletion strains. In conclusion, we propose that the fission yeast UBL/BAG proteins release Hsf1 from Hsp70, leading to constitutive Hsf1 activation and growth defects.
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Affiliation(s)
- Esben G Poulsen
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Caroline Kampmeyer
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Franziska Kriegenburg
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Jens V Johansen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Christian Holmberg
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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Cohen-Kaplan V, Livneh I, Avni N, Cohen-Rosenzweig C, Ciechanover A. The ubiquitin-proteasome system and autophagy: Coordinated and independent activities. Int J Biochem Cell Biol 2016; 79:403-418. [DOI: 10.1016/j.biocel.2016.07.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/13/2016] [Accepted: 07/18/2016] [Indexed: 01/10/2023]
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40
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Hjerpe R, Bett JS, Keuss MJ, Solovyova A, McWilliams TG, Johnson C, Sahu I, Varghese J, Wood N, Wightman M, Osborne G, Bates GP, Glickman MH, Trost M, Knebel A, Marchesi F, Kurz T. UBQLN2 Mediates Autophagy-Independent Protein Aggregate Clearance by the Proteasome. Cell 2016; 166:935-949. [PMID: 27477512 PMCID: PMC5003816 DOI: 10.1016/j.cell.2016.07.001] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/18/2016] [Accepted: 07/02/2016] [Indexed: 12/14/2022]
Abstract
Clearance of misfolded and aggregated proteins is central to cell survival. Here, we describe a new pathway for maintaining protein homeostasis mediated by the proteasome shuttle factor UBQLN2. The 26S proteasome degrades polyubiquitylated substrates by recognizing them through stoichiometrically bound ubiquitin receptors, but substrates are also delivered by reversibly bound shuttles. We aimed to determine why these parallel delivery mechanisms exist and found that UBQLN2 acts with the HSP70-HSP110 disaggregase machinery to clear protein aggregates via the 26S proteasome. UBQLN2 recognizes client-bound HSP70 and links it to the proteasome to allow for the degradation of aggregated and misfolded proteins. We further show that this process is active in the cell nucleus, where another system for aggregate clearance, autophagy, does not act. Finally, we found that mutations in UBQLN2, which lead to neurodegeneration in humans, are defective in chaperone binding, impair aggregate clearance, and cause cognitive deficits in mice. UBQLN2 clears aggregates independent of autophagy via HSP70 and the proteasome A disease mutation in UBQLN2 prevents its binding to HSP70 Mutant UBQLN2 is defective in clearance of aggregates in vivo UBQLN2 knockin mice develop cognitive impairment and brain pathology
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Affiliation(s)
- Roland Hjerpe
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Davidson Building, Henry Wellcome Lab of Cell Biology, University of Glasgow, G12 8QQ Glasgow, UK; The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - John S Bett
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Davidson Building, Henry Wellcome Lab of Cell Biology, University of Glasgow, G12 8QQ Glasgow, UK; The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland.
| | - Matthew J Keuss
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Alexandra Solovyova
- Newcastle University Protein and Proteome Analysis, Devonshire Building, Devonshire Terrace, Newcastle upon Tyne NE1 7RU, UK
| | - Thomas G McWilliams
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Clare Johnson
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Indrajit Sahu
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Joby Varghese
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Nicola Wood
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Melanie Wightman
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Georgina Osborne
- Department of Medical and Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Gillian P Bates
- Department of Medical and Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Matthias Trost
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Axel Knebel
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Francesco Marchesi
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Thimo Kurz
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Davidson Building, Henry Wellcome Lab of Cell Biology, University of Glasgow, G12 8QQ Glasgow, UK; The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland.
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41
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The life cycle of the 26S proteasome: from birth, through regulation and function, and onto its death. Cell Res 2016; 26:869-85. [PMID: 27444871 PMCID: PMC4973335 DOI: 10.1038/cr.2016.86] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The 26S proteasome is a large, ∼2.5 MDa, multi-catalytic ATP-dependent protease complex that serves as the degrading arm of the ubiquitin system, which is the major pathway for regulated degradation of cytosolic, nuclear and membrane proteins in all eukaryotic organisms.
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42
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Yu H, Kago G, Yellman CM, Matouschek A. Ubiquitin-like domains can target to the proteasome but proteolysis requires a disordered region. EMBO J 2016; 35:1522-36. [PMID: 27234297 DOI: 10.15252/embj.201593147] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 04/27/2016] [Indexed: 11/09/2022] Open
Abstract
Ubiquitin and some of its homologues target proteins to the proteasome for degradation. Other ubiquitin-like domains are involved in cellular processes unrelated to the proteasome, and proteins containing these domains remain stable in the cell. We find that the 10 yeast ubiquitin-like domains tested bind to the proteasome, and that all 11 identified domains can target proteins for degradation. Their apparent proteasome affinities are not directly related to their stabilities or functions. That is, ubiquitin-like domains in proteins not part of the ubiquitin proteasome system may bind the proteasome more tightly than domains in proteins that are bona fide components. We propose that proteins with ubiquitin-like domains have properties other than proteasome binding that confer stability. We show that one of these properties is the absence of accessible disordered regions that allow the proteasome to initiate degradation. In support of this model, we find that Mdy2 is degraded in yeast when a disordered region in the protein becomes exposed and that the attachment of a disordered region to Ubp6 leads to its degradation.
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Affiliation(s)
- Houqing Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Grace Kago
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christopher M Yellman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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43
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Shi Y, Chen X, Elsasser S, Stocks BB, Tian G, Lee BH, Shi Y, Zhang N, de Poot SAH, Tuebing F, Sun S, Vannoy J, Tarasov SG, Engen JR, Finley D, Walters KJ. Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Science 2016; 351:351/6275/aad9421. [PMID: 26912900 DOI: 10.1126/science.aad9421] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hundreds of pathways for degradation converge at ubiquitin recognition by a proteasome. Here, we found that the five known proteasomal ubiquitin receptors in yeast are collectively nonessential for ubiquitin recognition and identified a sixth receptor, Rpn1. A site ( T1: ) in the Rpn1 toroid recognized ubiquitin and ubiquitin-like ( UBL: ) domains of substrate shuttling factors. T1 structures with monoubiquitin or lysine 48 diubiquitin show three neighboring outer helices engaging two ubiquitins. T1 contributes a distinct substrate-binding pathway with preference for lysine 48-linked chains. Proximal to T1 within the Rpn1 toroid is a second UBL-binding site ( T2: ) that assists in ubiquitin chain disassembly, by binding the UBL of deubiquitinating enzyme Ubp6. Thus, a two-site recognition domain intrinsic to the proteasome uses distinct ubiquitin-fold ligands to assemble substrates, shuttling factors, and a deubiquitinating enzyme.
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Affiliation(s)
- Yuan Shi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Suzanne Elsasser
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Bradley B Stocks
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Byung-Hoon Lee
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Yanhong Shi
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Naixia Zhang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Stefanie A H de Poot
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Fabian Tuebing
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Shuangwu Sun
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jacob Vannoy
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Linganore High School, Frederick, MD 21701, USA
| | - Sergey G Tarasov
- Biophysics Resource, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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44
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Xu C, Ng DTW. Glycosylation-directed quality control of protein folding. Nat Rev Mol Cell Biol 2015; 16:742-52. [PMID: 26465718 DOI: 10.1038/nrm4073] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane-bound and soluble proteins of the secretory pathway are commonly glycosylated in the endoplasmic reticulum. These adducts have many biological functions, including, notably, their contribution to the maturation of glycoproteins. N-linked glycans are of oligomeric structure, forming configurations that provide blueprints to precisely instruct the folding of protein substrates and the quality control systems that scrutinize it. O-linked mannoses are simpler in structure and were recently found to have distinct functions in protein quality control that do not require the complex structure of N-linked glycans. Together, recent studies reveal the breadth and sophistication of the roles of these glycan-directed modifications in protein biogenesis.
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Affiliation(s)
- Chengchao Xu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Davis T W Ng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Duke University-National University of Singapore Graduate Medical School, 8 College Road, Singapore 169857
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45
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Ferreira RT, Menezes RA, Rodrigues-Pousada C. E4-Ubiquitin ligase Ufd2 stabilizes Yap8 and modulates arsenic stress responses independent of the U-box motif. Biol Open 2015; 4:1122-31. [PMID: 26276098 PMCID: PMC4582114 DOI: 10.1242/bio.010405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Adaptation of Saccharomyces cerevisiae cells to arsenic stress is mediated through the activation of arsenic detoxification machinery by the Yap8 transcription factor. Yap8 is targeted by the ubiquitin proteasome system for degradation under physiological conditions, yet it escapes proteolysis in arsenic-injured cells by a mechanism that remains to be elucidated. Here, we show that Ufd2, an E4-Ubiquitin (Ub) ligase, is upregulated by arsenic compounds both at mRNA and protein levels. Under these conditions, Ufd2 interacts with Yap8 mediating its stabilization, thereby controlling expression of ACR3 and capacity of cells to adapt to arsenic injury. We also show that Ufd2 U-box domain, which is associated to the ubiquitination activity of specific ubiquitin ligases, is dispensable for Yap8 stability and has no role in cell tolerance to arsenic stress. Thus, our data disclose a novel Ufd2 role beyond degradation. This finding is further supported by genetic analyses showing that proteins belonging to Ufd2 proteolytic pathways, namely Ubc4, Rad23 and Dsk2, mediate Yap8 degradation.
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Affiliation(s)
- Rita T Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2781-901, Portugal
| | - Regina A Menezes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2781-901, Portugal
| | - Claudina Rodrigues-Pousada
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2781-901, Portugal
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46
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An intrinsically disordered region of RPN10 plays a key role in restricting ubiquitin chain elongation in RPN10 monoubiquitination. Biochem J 2015. [DOI: 10.1042/bj20141571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The proteasomal ubiquitin receptor Rpn10 (regulatory particle non-ATPase 10) is monoubiquitinated by Rsp5 (reverses SPT-phenotype protein 5). We show that a disordered region flanking the ubiquitin-interacting motif of Rpn10 is required for restricting polyubiquitination in the process of Rpn10 monoubiquitination. A novel role of an unstructured protein domain in controlling ubiquitin chain elongation is proposed.
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47
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Li X, Zhang SS, Ma JX, Guo GY, Zhang XY, Liu X, Bi CL. TaUBA, a UBA domain-containing protein in wheat (Triticum aestivum L.), is a negative regulator of salt and drought stress response in transgenic Arabidopsis. PLANT CELL REPORTS 2015; 34:755-766. [PMID: 25604990 DOI: 10.1007/s00299-015-1739-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 11/30/2014] [Accepted: 01/06/2015] [Indexed: 06/04/2023]
Abstract
TaUBA functions as a negative regulator of salt and drought stress response in transgenic Arabidopsis, either the UBA domain or the zinc finger domain is crucial for TaUBA's function. TaUBA (DQ211935), which is a UBA domain-containing protein in wheat, was cloned and functionally characterized. Southern blot suggested that TaUBA is a low copy gene in common wheat. qRT-PCR assay showed that the expression of TaUBA was strongly induced by salt and drought stress. When suffering from drought and salt stresses, lower proline content and much higher MDA content in the TaUBA overexpressors were observed than those of the wild-type control, suggesting TaUBA may function as a negative regulator of salt and drought stress response in plants. To study whether the UBA domain or the zinc finger domain affects the function of TaUBA, TaUBAΔUBA (deletion of UBA domain) and TaUBA-M (Cys464Gly and Cys467Gly) overexpression vectors were constructed and transformed into Arabidopsis. Upon drought and salt stresses, the TaUBAΔUBA-and TaUBA-M-overexpressed plants accumulated much more proline and lower MDA than the wild-type control, the TaUBA-overexpressors lost water more quickly than TaUBAΔUBA-and TaUBA-M-overexpressed plants as well as the wild-type control, suggesting that overexpression of TaUBAΔUBA or TaUBA-M improved the drought and salt tolerance of transgenic Arabidopsis plants and the possibility of ubiquitination role in the regulation of osmolyte synthesis and oxidative stress responses in mediating stress tolerance. qRT-PCR assay of stress-related genes in transgenic plants upon drought and salt stresses suggested that TaUBA may function through down-regulating some stress related-transcription factors and by regulating P5CSs to cope with osmotic stress.
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Affiliation(s)
- Xiao Li
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
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48
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Wu Q, Liu M, Huang C, Liu X, Huang B, Li N, Zhou H, Xia XG. Pathogenic Ubqln2 gains toxic properties to induce neuron death. Acta Neuropathol 2015; 129:417-28. [PMID: 25388785 DOI: 10.1007/s00401-014-1367-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/14/2022]
Abstract
Mutations in ubiquilin 2 (Ubqln2) is linked to amyotrophic lateral sclerosis and frontotemporal lobar degeneration. A foremost question regarding Ubqln2 pathogenesis is whether pathogenically mutated Ubqln2 causes neuron death via a gain or loss of functions. To better understand Ubqln2 pathobiology, we created Ubqln2 transgenic and knockout rats and compared phenotypic expression in these novel rat models. Overexpression of Ubqln2 with a pathogenic mutation (P497H substitution) caused cognitive deficits and neuronal loss in transgenic rats at the age of 130 days. In the transgenic rats, neuronal loss was preceded by the progressive formation of Ubqln2 aggregates and was accompanied by the progressive accumulation of the autophagy substrates p62 and LC3-II and the impairment of endosome pathways. In contrast, none of these pathologies observed in mutant Ubqln2 transgenic rats was detected in Ubqln2 knockout rats at the age of 300 days. Together, our findings in Ubqln2 transgenic and knockout rats collectively suggest that pathogenic Ubqln2 causes neuron death mainly through a gain of unrevealed functions rather than a loss of physiological functions.
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Affiliation(s)
- Qinxue Wu
- Department of Pathology, Thomas Jefferson University, JAH506, 1020 Locust Street, Philadelphia, PA, 19107, USA
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Sinha A, Datta SP, Ray A, Sarkar S. A reduced VWA domain-containing proteasomal ubiquitin receptor of Giardia lamblia localizes to the flagellar pore regions in microtubule-dependent manner. Parasit Vectors 2015; 8:120. [PMID: 25888841 PMCID: PMC4352536 DOI: 10.1186/s13071-015-0737-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/13/2015] [Indexed: 11/22/2022] Open
Abstract
Background Giardia lamblia switches its lifecycle between trophozoite and cyst forms and the proteasome plays a pivotal role in this switching event. Compared to most model eukaryotes, the proteasome of this parasite has already been documented to have certain variations. This study was undertaken to characterize the ubiquitin receptor, GlRpn10, of the 19S regulatory particle of the Giardia proteasome and determine its cellular localization in trophozoites, encysting trophozoites and cysts. Method Sequence alignment and domain architecture analyses were performed to characterize GlRpn10. In vitro ubiquitin binding assay, functional complementation and biochemical studies verified the protein’s ability to function as ubiquitin receptor in the context of the yeast proteasome. Immunofluorescence localization was performed with antibody against GlRpn10 to determine its distribution in trophozoites, encysting trophozoites and cysts. Real-time PCR and Western blotting were performed to monitor the expression pattern of GlRpn10 during encystation. Result GlRpn10 contained a functional ubiquitin interacting motif, which was capable of binding to ubiquitin. Although it contained a truncated VWA domain, it was still capable of partially complementing the function of the yeast Rpn10 orthologue. Apart from localizing to the nucleus and cytosol, GlRpn10 was also present at flagellar pores of trophozoites and this localization was microtubule-dependent. Although there was no change in the cellular levels of GlRpn10 during encystation, its selective distribution at the flagellar pores was absent. Conclusion GlRpn10 contains a noncanonical VWA domain that is partially functional in yeast. Besides the expected nuclear and cytosolic distribution, the protein displays microtubule-dependent flagellar pore localization in trophozoites. While the protein remained in the nucleus and cytosol in encysting trophozoites, it could no longer be detected at the flagellar pores. This absence at the flagellar pore regions in encysting trophozoites is likely to involve redistribution of the protein, rather than decreased gene expression or selective protein degradation. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0737-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abhishek Sinha
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Shankari Prasad Datta
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Atrayee Ray
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Srimonti Sarkar
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
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Nowicka U, Zhang D, Walker O, Krutauz D, Castañeda CA, Chaturvedi A, Chen TY, Reis N, Glickman MH, Fushman D. DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Structure 2015; 23:542-557. [PMID: 25703377 DOI: 10.1016/j.str.2015.01.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/19/2014] [Accepted: 01/12/2015] [Indexed: 11/28/2022]
Abstract
Ddi1 belongs to a family of shuttle proteins targeting polyubiquitinated substrates for proteasomal degradation. Unlike the other proteasomal shuttles, Rad23 and Dsk2, Ddi1 remains an enigma: its function is not fully understood and structural properties are poorly characterized. We determined the structure and binding properties of the ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains of Ddi1 from Saccharomyces cerevisiae. We found that while Ddi1UBA forms a characteristic UBA:ubiquitin complex, Ddi1UBL has entirely uncharacteristic binding preferences. Despite having a ubiquitin-like fold, Ddi1UBL does not interact with typical UBL receptors but unexpectedly binds ubiquitin, forming a unique interface mediated by hydrophobic contacts and by salt bridges between oppositely charged residues of Ddi1UBL and ubiquitin. In stark contrast to ubiquitin and other UBLs, the β-sheet surface of Ddi1UBL is negatively charged and therefore is recognized in a completely different way. The dual functionality of Ddi1UBL, capable of binding both ubiquitin and proteasome, suggests an intriguing mechanism for Ddi1 as a proteasomal shuttle.
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Affiliation(s)
- Urszula Nowicka
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Daoning Zhang
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Olivier Walker
- Institut des Sciences Analytiques, UMR5280-Université de Lyon, 69100 Villeurbanne, France
| | - Daria Krutauz
- Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Carlos A Castañeda
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Apurva Chaturvedi
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Tony Y Chen
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Noa Reis
- Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Michael H Glickman
- Department of Biology, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
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