1
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Mangini V, Grasso G, Belviso BD, Sciacca MFM, Lanza V, Caliandro R, Milardi D. Stretching the chains: the destabilizing impact of Cu 2+ and Zn 2+ ions on K48-linked diubiquitin. Dalton Trans 2023; 52:11835-11849. [PMID: 37581921 DOI: 10.1039/d3dt01815f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Ubiquitin signalling and metal homeostasis play key roles in controlling several physiological cellular activities, including protein trafficking and degradation. While some relationships between these two biochemical pathways have started to surface, our knowledge of their interplay remains limited. Here, we employ a variety of techniques, such as circular dichroism, differential scanning calorimetry, pressure perturbation calorimetry, fluorescence emission, SDS-PAGE, and small-angle X-ray scattering (SAXS) to evaluate the impact of Cu2+ and Zn2+ ions on the structure and stability of K48 linked diubiquitin (K48-Ub2), a simple model for polyubiquitin chains. The SAXS analysis results show that the structure of the metal-free protein is similar to that observed when the protein is bound to the E2 conjugating enzyme, lending support to the idea that the structure of unanchored K48-linked ubiquitin chains is sufficient for identification by conjugating enzymes without the need for an induced fit mechanism. Our results indicate that K48-Ub2 can coordinate up to four metal ions with both copper and zinc ions inducing slight changes to the secondary structure of the protein. However, we noted significant distinctions in their impacts on protein stability and overall architecture. Specifically, Cu2+ ions resulted in a destabilization of the protein structure, which facilitated the formation of dimer aggregates. Next, we observed a shift in the conformational dynamics of K48-Ub2 toward less compact and more flexible states upon metal ion binding, with Zn2+ inducing a more significant effect than Cu2+ ions. Our structural modelling study demonstrates that both metal ions induced perturbations in the K48-Ub2 structure, leading to the separation of the two monomers thus inhibiting interactions with E2 enzymes. In conclusion, the findings from this study enhance our comprehension of the mechanisms underlying Ub chains recognition. Moreover, they strengthen the notion that drug discovery initiatives aimed at targeting metal-mediated disruptions in Ub signaling hold great potential for treating a wide range of diseases that stem from abnormal protein accumulation.
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Affiliation(s)
- Vincenzo Mangini
- Istituto di Cristallografia - CNR sede di Bari, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Giulia Grasso
- Istituto di Cristallografia - CNR sede secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy.
| | - Benny Danilo Belviso
- Istituto di Cristallografia - CNR sede di Bari, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Michele F M Sciacca
- Istituto di Cristallografia - CNR sede secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy.
| | - Valeria Lanza
- Istituto di Cristallografia - CNR sede secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy.
| | - Rocco Caliandro
- Istituto di Cristallografia - CNR sede di Bari, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Danilo Milardi
- Istituto di Cristallografia - CNR sede secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy.
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2
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Suresh HG, Bonneil E, Albert B, Dominique C, Costanzo M, Pons C, David Masinas MP, Shuteriqi E, Shore D, Henras AK, Thibault P, Boone C, Andrews BJ. K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539259. [PMID: 37205480 PMCID: PMC10187189 DOI: 10.1101/2023.05.03.539259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs), Ubp2 and Ubp14, and E3 ligases, Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the Ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the Intranuclear Quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with Ribosomopathies.
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3
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Wang J, Zhou Q, Ding J, Yin T, Ye P, Zhang Y. The Conceivable Functions of Protein Ubiquitination and Deubiquitination in Reproduction. Front Physiol 2022; 13:886261. [PMID: 35910557 PMCID: PMC9326170 DOI: 10.3389/fphys.2022.886261] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
Protein ubiquitination with general existence in virtually all eukaryotic cells serves as a significant post-translational modification of cellular proteins, which leads to the degradation of proteins via the ubiquitin-proteasome system. Deubiquitinating enzymes (DUBs) can reverse the ubiquitination effect by removing the ubiquitin chain from the target protein. Together, these two processes participate in regulating protein stability, function, and localization, thus modulating cell cycle, DNA repair, autophagy, and transcription regulation. Accumulating evidence indicates that the ubiquitination/deubiquitination system regulates reproductive processes, including the cell cycle, oocyte maturation, oocyte-sperm binding, and early embryonic development, primarily by regulating protein stability. This review summarizes the extensive research concerning the role of ubiquitin and DUBs in gametogenesis and early embryonic development, which helps us to understand human pregnancy further.
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Affiliation(s)
- Jiayu Wang
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Qi Zhou
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Jinli Ding
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Tailang Yin
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Peng Ye
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yan Zhang
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
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4
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Tseng CC, Piper RC, Katzmann DJ. Bro1 family proteins harmonize cargo sorting with vesicle formation. Bioessays 2022; 44:e2100276. [PMID: 35770783 PMCID: PMC9575758 DOI: 10.1002/bies.202100276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022]
Abstract
The Endosomal Sorting Complexes Required for Transport (ESCRTs) drive membrane remodeling in a variety of cellular processes that include the formation of endosomal intralumenal vesicles (ILVs) during multivesicular body (MVB) biogenesis. During MVB sorting, ESCRTs recognize ubiquitin (Ub) attached to membrane protein cargo and execute ILV formation by controlling the activities of ESCRT-III polymers regulated by the AAA-ATPase Vps4. Exactly how these events are coordinated to ensure proper cargo loading into ILVs remains unclear. Here we discuss recent work documenting the ability of Bro1, an ESCRT-associated Ub-binding protein, to coordinate ESCRT-III and Vps4-dependent ILV biogenesis with upstream events such as cargo recognition.
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Affiliation(s)
- Chun-Che Tseng
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.,Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.,Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
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5
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Lu Z, Wu Y, Chen Y, Chen X, Wu R, Lu Q, Chen D, Huang R. Role of spt23 in Saccharomyces cerevisiae thermal tolerance. Appl Microbiol Biotechnol 2022; 106:3691-3705. [PMID: 35476152 PMCID: PMC9151549 DOI: 10.1007/s00253-022-11920-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/02/2022]
Abstract
spt23 plays multiple roles in the thermal tolerance of budding yeast. spt23 regulates unsaturated lipid acid (ULA) content in the cell, which can then significantly affect cellular thermal tolerance. Being a Ty suppressor, spt23 can also interact with transposons (Tys) that are contributors to yeast's adaptive evolution. Nevertheless, few studies have investigated whether and how much spt23 can exert its regulatory functions through transposons. In this study, expression quantitative trait loci (eQTL) analysis was conducted with thermal-tolerant Saccharomyces cerevisiae strains, and spt23 was identified as one of the most important genes in mutants. spt23-overexpression (OE), deletion (Del), and integrative-expressed (IE) strains were constructed. Their heat tolerance, ethanol production, the expression level of key genes, and lipid acid contents in the cell membranes were measured. Furthermore, LTR (long terminal repeat)-amplicon sequencing was used to profile yeast transposon activities in the treatments. The results showed the Del type had a higher survival rate, biomass, and ethanol production, revealing negative correlations between spt23 expression levels and thermal tolerance. Total unsaturated lipid acid (TULA) contents in cell membranes were lower in the Del type, indicating its negative association with spt23 expression levels. The Del type resulted in the lower richness and higher evenness in LTR distributions, as well as higher transposon activities. The intersection of 3 gene sets and regression analysis revealed the relative weight of spt23's direct and TY-induced influence is about 4:3. These results suggested a heat tolerance model in which spt23 increases cell thermal tolerance through transcriptional regulation in addition to spt23-transposon triggered unknown responses. KEY POINTS: • spt23 is a key gene for heat tolerance, important for LA contents but not vital. • Deletion of spt23 decreases in yeast's LTR richness but not in evenness. • The relative weight of spt23's direct and TY-induced influence is about 4:3.
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Affiliation(s)
- Zhilong Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China.,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China.,National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, People's Republic of China
| | - Yanling Wu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, People's Republic of China
| | - Ying Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, People's Republic of China
| | - Xiaoling Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, People's Republic of China
| | - Renzhi Wu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, People's Republic of China
| | - Qi Lu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, People's Republic of China
| | - Dong Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, People's Republic of China
| | - Ribo Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China. .,College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, People's Republic of China. .,National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, People's Republic of China.
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6
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Mulas F, Wang X, Song S, Nishanth G, Yi W, Brunn A, Larsen PK, Isermann B, Kalinke U, Barragan A, Naumann M, Deckert M, Schlüter D. The deubiquitinase OTUB1 augments NF-κB-dependent immune responses in dendritic cells in infection and inflammation by stabilizing UBC13. Cell Mol Immunol 2021; 18:1512-1527. [PMID: 32024978 PMCID: PMC8167118 DOI: 10.1038/s41423-020-0362-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/01/2020] [Indexed: 01/09/2023] Open
Abstract
Dendritic cells (DCs) are indispensable for defense against pathogens but may also contribute to immunopathology. Activation of DCs upon the sensing of pathogens by Toll-like receptors (TLRs) is largely mediated by pattern recognition receptor/nuclear factor-κB (NF-κB) signaling and depends on the appropriate ubiquitination of the respective signaling molecules. However, the ubiquitinating and deubiquitinating enzymes involved and their interactions are only incompletely understood. Here, we reveal that the deubiquitinase OTU domain, ubiquitin aldehyde binding 1 (OTUB1) is upregulated in DCs upon murine Toxoplasma gondii infection and lipopolysaccharide challenge. Stimulation of DCs with the TLR11/12 ligand T. gondii profilin and the TLR4 ligand lipopolysaccharide induced an increase in NF-κB activation in OTUB1-competent cells, resulting in elevated interleukin-6 (IL-6), IL-12, and tumor necrosis factor (TNF) production, which was also observed upon the specific stimulation of TLR2, TLR3, TLR7, and TLR9. Mechanistically, OTUB1 promoted NF-κB activity in DCs by K48-linked deubiquitination and stabilization of the E2-conjugating enzyme UBC13, resulting in increased K63-linked ubiquitination of IRAK1 (IL-1 receptor-associated kinase 1) and TRAF6 (TNF receptor-associated factor 6). Consequently, DC-specific deletion of OTUB1 impaired the production of cytokines, in particular IL-12, by DCs over the first 2 days of T. gondii infection, resulting in the diminished production of protective interferon-γ (IFN-γ) by natural killer cells, impaired control of parasite replication, and, finally, death from chronic T. encephalitis, all of which could be prevented by low-dose IL-12 treatment in the first 3 days of infection. In contrast, impaired OTUB1-deficient DC activation and cytokine production by OTUB1-deficient DCs protected mice from lipopolysaccharide-induced immunopathology. Collectively, these findings identify OTUB1 as a potent novel regulator of DCs during infectious and inflammatory diseases.
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Affiliation(s)
- Floriana Mulas
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany
| | - Xu Wang
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany.
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany.
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, 325035, Wenzhou, China.
| | - Shanshan Song
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany
| | - Gopala Nishanth
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany
| | - Wenjing Yi
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany
| | - Anna Brunn
- Department of Neuropathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Pia-Katharina Larsen
- Institute for Experimental Infection Research, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, 30625, Hannover, Germany
| | - Berend Isermann
- Institute for Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, 30625, Hannover, Germany
- Cluster of Excellence-Resolving Infection Susceptibility (RESIST), Hannover Medical School, 30625, Hannover, Germany
| | - Antonio Barragan
- Department of Molecular Biosciences, Stockholm University, 10691, Stockholm, Sweden
| | - Michael Naumann
- Institute for Experimental Internal Medicine, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany
| | - Martina Deckert
- Department of Neuropathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Dirk Schlüter
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany.
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany.
- Cluster of Excellence-Resolving Infection Susceptibility (RESIST), Hannover Medical School, 30625, Hannover, Germany.
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7
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Higgins R, Kabbaj MH, Sherwin D, Howell LA, Hatcher A, Tomko RJ, Wang Y. The Cdc48 Complex Alleviates the Cytotoxicity of Misfolded Proteins by Regulating Ubiquitin Homeostasis. Cell Rep 2021; 32:107898. [PMID: 32668237 DOI: 10.1016/j.celrep.2020.107898] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 05/04/2020] [Accepted: 06/22/2020] [Indexed: 10/23/2022] Open
Abstract
The accumulation of misfolded proteins is associated with multiple neurodegenerative disorders, but it remains poorly defined how this accumulation causes cytotoxicity. Here, we demonstrate that the Cdc48/p97 segregase machinery drives the clearance of ubiquitinated model misfolded protein Huntingtin (Htt103QP) and limits its aggregation. Nuclear ubiquitin ligase San1 acts upstream of Cdc48 to ubiquitinate Htt103QP. Unexpectedly, deletion of SAN1 and/or its cytosolic counterpart UBR1 rescues the toxicity associated with Cdc48 deficiency, suggesting that ubiquitin depletion, rather than compromised proteolysis of misfolded proteins, causes the growth defect in cells with Cdc48 deficiency. Indeed, Cdc48 deficiency leads to elevated protein ubiquitination levels and decreased free ubiquitin, which depends on San1/Ubr1. Furthermore, enhancing free ubiquitin levels rescues the toxicity in various Cdc48 pathway mutants and restores normal turnover of a known Cdc48-independent substrate. Our work highlights a previously unappreciated function for Cdc48 in ensuring the regeneration of monoubiquitin that is critical for normal cellular function.
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Affiliation(s)
- Ryan Higgins
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Marie-Helene Kabbaj
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Delaney Sherwin
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Lauren A Howell
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Alexa Hatcher
- College of Nursing, Florida State University, 600 West College Avenue, Tallahassee, FL 32306, USA
| | - Robert J Tomko
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306, USA.
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8
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Pinto MJ, Tomé D, Almeida RD. The Ubiquitinated Axon: Local Control of Axon Development and Function by Ubiquitin. J Neurosci 2021; 41:2796-2813. [PMID: 33789876 PMCID: PMC8018891 DOI: 10.1523/jneurosci.2251-20.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 02/01/2023] Open
Abstract
Ubiquitin tagging sets protein fate. With a wide range of possible patterns and reversibility, ubiquitination can assume many shapes to meet specific demands of a particular cell across time and space. In neurons, unique cells with functionally distinct axons and dendrites harboring dynamic synapses, the ubiquitin code is exploited at the height of its power. Indeed, wide expression of ubiquitination and proteasome machinery at synapses, a diverse brain ubiquitome, and the existence of ubiquitin-related neurodevelopmental diseases support a fundamental role of ubiquitin signaling in the developing and mature brain. While special attention has been given to dendritic ubiquitin-dependent control, how axonal biology is governed by this small but versatile molecule has been considerably less discussed. Herein, we set out to explore the ubiquitin-mediated spatiotemporal control of an axon's lifetime: from its differentiation and growth through presynaptic formation, function, and pruning.
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Affiliation(s)
- Maria J Pinto
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, 3004-504, Portugal
| | - Diogo Tomé
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, 3004-504, Portugal
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Ramiro D Almeida
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, 3004-504, Portugal
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, 3810-193, Portugal
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9
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Suresh HG, Pascoe N, Andrews B. The structure and function of deubiquitinases: lessons from budding yeast. Open Biol 2020; 10:200279. [PMID: 33081638 PMCID: PMC7653365 DOI: 10.1098/rsob.200279] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination is a key post-translational modification that regulates diverse cellular processes in eukaryotic cells. The specificity of ubiquitin (Ub) signalling for different bioprocesses and pathways is dictated by the large variety of mono-ubiquitination and polyubiquitination events, including many possible chain architectures. Deubiquitinases (DUBs) reverse or edit Ub signals with high sophistication and specificity, forming an integral arm of the Ub signalling machinery, thus impinging on fundamental cellular processes including DNA damage repair, gene expression, protein quality control and organellar integrity. In this review, we discuss the many layers of DUB function and regulation, with a focus on insights gained from budding yeast. Our review provides a framework to understand key aspects of DUB biology.
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Affiliation(s)
- Harsha Garadi Suresh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Natasha Pascoe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Brenda Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
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10
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Sakai H, Ikeno Y, Tsukimura Y, Inomata M, Suzuki Y, Kon R, Ikarashi N, Chiba Y, Yamada T, Kamei J. Upregulation of ubiquitinated proteins and their degradation pathway in muscle atrophy induced by cisplatin in mice. Toxicol Appl Pharmacol 2020; 403:115165. [PMID: 32738330 DOI: 10.1016/j.taap.2020.115165] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/13/2020] [Accepted: 07/26/2020] [Indexed: 12/26/2022]
Abstract
We previously demonstrated that cisplatin administration in mice induces muscle atrophy and an increase in the expression of two muscle-specific ubiquitin E3 ligase genes, muscle ring finger protein 1 (MuRF1), and atrophy gene-1 (atrogin-1), in skeletal muscle. Ubiquitination serves as a degradation signal in both the ubiquitin-proteasome and selective autophagy pathways. In the present study, we investigated changes in the expression of ubiquitin and ubiquitinated proteins and their degradation pathways. Ubiquitin and ubiquitinated protein levels were increased by cisplatin compared with those in the vehicle and dietary restriction (DR) groups. To quantify the levels of ubiquitin and ubiquitinated proteins, we conducted a dot blot assay using an anti-ubiquitin antibody. The expression of ubiquitin was also significantly increased by cisplatin compared with that in the vehicle and DR groups. Since the ubiquitin proteins were upregulated by cisplatin, we measured the mRNA levels of the ubiquitin genes: Ubb, Ubc, Rps27a, and Uba52. All these four genes were increased by cisplatin administration compared with those in both the vehicle-treated and DR groups in quadriceps muscle tissue. The anti-ubiquitin antibody-sensitive bands increased when C2C12 myotubes were treated with cisplatin. Furthermore, MG-132 (26 s proteasome inhibitor), but not bafilomycin A1 (autophagy inhibitor), caused a further increase in expression. In conclusion, ubiquitin and ubiquitinated proteins are upregulated in cisplatin-induced muscle atrophy. Cisplatin-induced ubiquitinated proteins are degraded by the 26 s proteasome pathway.
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Affiliation(s)
- Hiroyasu Sakai
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan.
| | - Yohei Ikeno
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan
| | - Yuka Tsukimura
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan
| | - Maya Inomata
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan
| | - Yuta Suzuki
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan
| | - Risako Kon
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan
| | - Nobutomo Ikarashi
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan
| | - Yoshihiko Chiba
- Department of Physiology and Molecular Sciences, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 1138602, Japan
| | - Junzo Kamei
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 1428501, Japan
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11
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Mat Nanyan NSB, Takagi H. Proline Homeostasis in Saccharomyces cerevisiae: How Does the Stress-Responsive Transcription Factor Msn2 Play a Role? Front Genet 2020; 11:438. [PMID: 32411186 PMCID: PMC7198862 DOI: 10.3389/fgene.2020.00438] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Overexpression of MSN2, which is the transcription factor gene in response to stress, is well-known to increase the tolerance of the yeast Saccharomyces cerevisiae cells to a wide variety of environmental stresses. Recent studies have found that the Msn2 is a feasible potential mediator of proline homeostasis in yeast. This result is based on the finding that overexpression of the MSN2 gene exacerbates the cytotoxicity of yeast to various amino acid analogs whose uptake is increased by the active amino acid permeases localized on the plasma membrane as a result of a dysfunctional deubiquitination process. Increased understanding of the cellular responses induced by the Msn2-mediated proline incorporation will provide better comprehension of how cells respond to and counteract to different kinds of stimuli and will also contribute to the breeding of industrial yeast strains with increased productivity.
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Affiliation(s)
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
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12
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Mat Nanyan NSB, Watanabe D, Sugimoto Y, Takagi H. Effect of the deubiquitination enzyme gene UBP6 on the stress-responsive transcription factor Msn2-mediated control of the amino acid permease Gnp1 in yeast. J Biosci Bioeng 2020; 129:423-427. [DOI: 10.1016/j.jbiosc.2019.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/08/2019] [Accepted: 10/01/2019] [Indexed: 11/16/2022]
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13
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NAKATOGAWA H. Autophagic degradation of the endoplasmic reticulum. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:1-9. [PMID: 31932525 PMCID: PMC6974406 DOI: 10.2183/pjab.96.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Autophagy is an intracellular degradation system that is present in most eukaryotes. In the process of autophagy, double membrane vesicles called autophagosomes sequester a wide variety of cellular constituents and deliver them to lytic organelles: lysosomes in mammals and vacuoles in yeast and plants. Although autophagy used to be considered a non-selective process in its target sequestration into autophagosomes, recent studies have revealed that autophagosomes can also selectively sequester certain proteins and organelles that have become unnecessary or harmful for the cell. We recently discovered that the endoplasmic reticulum (ER) is degraded by autophagy in a selective manner in the budding yeast Saccharomyces cerevisiae, and identified "receptor proteins" that play pivotal roles in this "ER-phagy" pathway. Moreover, several ER-phagy receptors in mammalian cells have also been reported. This report provides an overview of our current knowledge on ER-phagy and discuss their mechanisms, physiological roles, and possible links to human diseases.
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Affiliation(s)
- Hitoshi NAKATOGAWA
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
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14
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Que Y, Xu Z, Wang C, Lv W, Yue X, Xu L, Tang S, Dai H, Wang Z. The putative deubiquitinating enzyme MoUbp4 is required for infection-related morphogenesis and pathogenicity in the rice blast fungus Magnaporthe oryzae. Curr Genet 2019; 66:561-576. [PMID: 31872271 DOI: 10.1007/s00294-019-01049-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/28/2022]
Abstract
Ubiquitination is a key regulatory mechanism that affects numerous important biological processes, including cellular differentiation and pathogenesis in eukaryotic cells. Attachment of proteins to ubiquitin is reversed by specialized proteases, deubiquitinating enzymes (DUBs), which are essential for precursor processing, maintaining ubiquitin homeostasis and promoting protein degradation by recycling ubiquitins. Here, we report the identification of a novel non-pathogenic T-DNA-tagged mutant T612 of Magnaporthe oryzae with a single insertion in the second exon of MoUBP4, which encodes a putative ubiquitin carboxyl-terminal hydrolase. Targeted gene deletion mutants of MoUBP4 are significantly reduced in mycelial growth, conidiation, and increased in tolerance to SDS and CR (Congo red) cell-wall damage. The ΔMoubp4 mutants are blocked in penetration and invasive growth, which results in the loss of pathogenicity. Many conidia produced by the ΔMoubp4 mutants are unable to form appressoria and mobilization and degradation of glycogen and lipid droplets are significantly delayed. Moreover, immunohybridization analysis revealed that total protein ubiquitination levels of the null mutants were significantly increased, indicating that MoUbp4 functions as a deubiquitination enzyme. Taken together, we conclude that MoUbp4 is required for deubiquitination, infection-related morphogenesis and pathogenicity in M. oryzae.
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Affiliation(s)
- Yawei Que
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhe Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Chunyan Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wuyun Lv
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaofeng Yue
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Lin Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Shuai Tang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Han Dai
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhengyi Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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15
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High-affinity free ubiquitin sensors for quantifying ubiquitin homeostasis and deubiquitination. Nat Methods 2019; 16:771-777. [PMID: 31308549 PMCID: PMC6669086 DOI: 10.1038/s41592-019-0469-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023]
Abstract
Ubiquitin (Ub) conjugation is an essential post-translational modification that affects nearly all proteins in eukaryotes. The functions and mechanisms of ubiquitination are areas of extensive study, and yet the dynamics and regulation of even free (i.e., unconjugated) Ub are poorly understood. A major impediment has been the lack of simple and robust techniques to quantify Ub levels in cells and to monitor Ub release from conjugates. Here we describe avidity-based fluorescent sensors that address this need. The sensors bind specifically to free Ub, have Kd values down to 60 pM, and, in concert with a newly developed workflow, allow us to distinguish and quantify the pools of free, protein-conjugated, and thioesterified forms of Ub from cell lysates. Alternatively, free Ub in fixed cells can be visualized microscopically by staining with a sensor. Real-time assays using the sensors afford unprecedented flexibility and precision to measure deubiquitination of virtually any (poly)Ub conjugate.
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16
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Nagy Á, Kovács L, Lipinszki Z, Pál M, Deák P. Developmental and tissue specific changes of ubiquitin forms in Drosophila melanogaster. PLoS One 2018; 13:e0209080. [PMID: 30543682 PMCID: PMC6292614 DOI: 10.1371/journal.pone.0209080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/29/2018] [Indexed: 11/19/2022] Open
Abstract
In most Eukaryotes, ubiquitin either exists as free monoubiquitin or as a molecule that is covalently linked to other proteins. These two forms cycle between each other and due to the concerted antagonistic activity of ubiquitylating and deubiquitylating enzymes, an intracellular ubiquitin equilibrium is maintained that is essential for normal biological function. However, measuring the level and ratio of these forms of ubiquitin has been difficult and time consuming. In this paper, we have adapted a simple immunoblotting technique to monitor ubiquitin content and equilibrium dynamics in different developmental stages and tissues of Drosophila. Our data show that the level of total ubiquitin is distinct in different developmental stages, lowest at the larval-pupal transition and in three days old adult males, and highest in first instar larvae. Interestingly, the ratio of free mono-ubiquitin remains within 30–50% range of the total throughout larval development, but peaks to 70–80% at the larval-pupal and the pupal-adult transitions. It stays within the 70–80% range in adults. In developmentally and physiologically active tissues, the ratio of free ubiquitin is similarly high, most likely reflecting a high demand for ubiquitin availability. We also used this method to demonstrate the disruption of the finely tuned ubiquitin equilibrium by the abolition of proteasome function or the housekeeping deubiquitylase, Usp5. Our data support the notion that the ubiquitin equilibrium is regulated by tissue- and developmental stage-specific mechanisms.
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Affiliation(s)
- Ágota Nagy
- Department of Genetics, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Levente Kovács
- Department of Genetics, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Zoltán Lipinszki
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Biological Research Centre, Szeged, Hungary
| | - Margit Pál
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Péter Deák
- Department of Genetics, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- * E-mail:
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17
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Lacave JM, Vicario-Parés U, Bilbao E, Gilliland D, Mura F, Dini L, Cajaraville MP, Orbea A. Waterborne exposure of adult zebrafish to silver nanoparticles and to ionic silver results in differential silver accumulation and effects at cellular and molecular levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1209-1220. [PMID: 30045502 DOI: 10.1016/j.scitotenv.2018.06.128] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/06/2018] [Accepted: 06/10/2018] [Indexed: 06/08/2023]
Abstract
Effects of silver nanoparticles (Ag NPs) on freshwater species have been reported in several studies, but there is not information on the potential long-term consequences of a previous exposure. In this work, we investigated the long-term effects of maltose-coated Ag NPs (20 nm) and of ionic silver (10 μg/L) after 21 days of exposure and at 6 months post-exposure (mpe) in adult zebrafish. Exposure resulted in significant silver accumulation in the whole body of fish exposed to ionic silver, but not in those exposed to Ag NPs. However, autometallography revealed metal accumulation in the liver and intestine of fish treated with the two silver forms and especially in the intestine of fish exposed to Ag NPs. X-ray microanalysis showed the presence of silver in gills, liver and intestine and of Ag NPs in gill and liver cells. Inflammation and hyperplasia were evident in the gills after both treatments and these histopathological conditions remained at 6 mpe. According to the hepatic transcriptome analysis, at 3 days ionic silver regulated a larger number of transcripts (410) than Ag NPs (129), while at 21 days Ag NPs provoked a stronger effect (799 vs 165 regulated sequences). Gene ontology terms such as "metabolic processes" and "response to stimulus" appeared enriched after all treatments, while "immune system" or "reproductive processes" were specifically enriched after the exposure to Ag NPs. This suggests that the toxicity of Ag NPs may not be solely related to the release of Ag ions, but also to the NP form. No evident effects were found on protein oxidation or on hepatocyte lysosomal membrane stability during exposure, but effects recorded on liver lysosomes and persistent damage on gill tissue at 6 mpe could indicate potential for long-term effects in exposed fish.
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Affiliation(s)
- José María Lacave
- CBET Research group, Dept. of Zoology and Animal Cell Biology, Research Centre for Experimental Marine Biology and Biotechnology PiE and Science and Technology Faculty, University of the Basque Country (UPV/EHU), Sarriena z/g, E-48940 Leioa, Basque Country, Spain
| | - Unai Vicario-Parés
- CBET Research group, Dept. of Zoology and Animal Cell Biology, Research Centre for Experimental Marine Biology and Biotechnology PiE and Science and Technology Faculty, University of the Basque Country (UPV/EHU), Sarriena z/g, E-48940 Leioa, Basque Country, Spain
| | - Eider Bilbao
- CBET Research group, Dept. of Zoology and Animal Cell Biology, Research Centre for Experimental Marine Biology and Biotechnology PiE and Science and Technology Faculty, University of the Basque Country (UPV/EHU), Sarriena z/g, E-48940 Leioa, Basque Country, Spain
| | - Douglas Gilliland
- European Commission, JRC Directorate F - Health, Consumers and Reference Materials, Via E. Fermi, 2749, I-21027 Ispra, VA, Italy
| | - Francesco Mura
- Dept. of Basic and Applied Sciences for Engineering and Center for Nanotechnologies Applied to Engineering, Sapienza University of Rome, Via A. Scarpa 16, Rome 00161, Italy
| | - Luciana Dini
- Dept. of Biological and Environmental Science and Technology, University of Salento, Prov.le Lecce-Monteroni, 73100 Lecce, Italy; CNR, Nanotec, 73100 Lecce, Italy
| | - Miren P Cajaraville
- CBET Research group, Dept. of Zoology and Animal Cell Biology, Research Centre for Experimental Marine Biology and Biotechnology PiE and Science and Technology Faculty, University of the Basque Country (UPV/EHU), Sarriena z/g, E-48940 Leioa, Basque Country, Spain
| | - Amaia Orbea
- CBET Research group, Dept. of Zoology and Animal Cell Biology, Research Centre for Experimental Marine Biology and Biotechnology PiE and Science and Technology Faculty, University of the Basque Country (UPV/EHU), Sarriena z/g, E-48940 Leioa, Basque Country, Spain.
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18
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Natural Genetic Variation in Yeast Reveals That NEDD4 Is a Conserved Modifier of Mutant Polyglutamine Aggregation. G3-GENES GENOMES GENETICS 2018; 8:3421-3431. [PMID: 30194090 PMCID: PMC6222566 DOI: 10.1534/g3.118.200289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A feature common to late onset proteinopathic disorders is an accumulation of toxic protein conformers and aggregates in affected tissues. In the search for potential drug targets, many studies used high-throughput screens to find genes that modify the cytotoxicity of misfolded proteins. A complement to this approach is to focus on strategies that use protein aggregation as a phenotypic readout to identify pathways that control aggregate formation and maintenance. Here we use natural variation between strains of budding yeast to genetically map loci that influence the aggregation of a polyglutamine-containing protein derived from a mutant form of huntingtin, the causative agent in Huntington disease. Linkage analysis of progeny derived from a cross between wild and laboratory yeast strains revealed two polymorphic loci that modify polyglutamine aggregation. One locus contains the gene RFU1 which modifies ubiquitination states of misfolded proteins targeted by the E3-ubiquitin ligase complex Rsp5 Activity of the Rsp5 complex, and the mammalian homolog NEDD4, are critical in maintaining protein homeostasis in response to proteomic stress. Our analysis also showed linkage of the aggregation phenotype to a distinct locus containing a gene encoding the Rsp5-interacting Bul2 protein. Allele-swap experiments validated the impact of both RFU1 and BUL2 on huntingtin aggregation. Furthermore, we found that the nematode Caenorhabditis elegans' ortholog of Rsp5, wwp-1, also negatively regulates polyglutamine aggregation. Knockdown of the NEDD4 in human cells likewise altered polyglutamine aggregation. Taken together, these results implicate conserved processes involving the ubiquitin regulation network that modify protein aggregation and provide novel therapeutic targets for polyglutamine and other protein folding diseases.
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19
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Sem1 links proteasome stability and specificity to multicellular development. PLoS Genet 2018; 14:e1007141. [PMID: 29401458 PMCID: PMC5821377 DOI: 10.1371/journal.pgen.1007141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 02/21/2018] [Accepted: 12/01/2017] [Indexed: 12/18/2022] Open
Abstract
The transition from vegetative growth to multicellular development represents an evolutionary hallmark linked to an oxidative stress signal and controlled protein degradation. We identified the Sem1 proteasome subunit, which connects stress response and cellular differentiation. The sem1 gene encodes the fungal counterpart of the human Sem1 proteasome lid subunit and is essential for fungal cell differentiation and development. A sem1 deletion strain of the filamentous fungus Aspergillus nidulans is able to grow vegetatively and expresses an elevated degree of 20S proteasomes with multiplied ATP-independent catalytic activity compared to wildtype. Oxidative stress induces increased transcription of the genes sem1 and rpn11 for the proteasomal deubiquitinating enzyme. Sem1 is required for stabilization of the Rpn11 deubiquitinating enzyme, incorporation of the ubiquitin receptor Rpn10 into the 19S regulatory particle and efficient 26S proteasome assembly. Sem1 maintains high cellular NADH levels, controls mitochondria integrity during stress and developmental transition. The cellular ubiquitin-proteasome pathway is essential to control cell cycle, gene expression or the response to oxidative stress. Sem1 is conserved in eukaryotes from single cell yeasts to humans as intrinsically disordered and multifunctional protein. Sem1 supports the assembly of several multiprotein complexes but becomes eventually exclusively a subunit of the lid of the 26S proteasome, a cellular machine with a molecular mass of about two megadalton. Defects in the function of the proteasome, which degrades a large fraction of intracellular proteins, result in cancer or neurodegenerative diseases. We showed that Sem1 from a multicellular fungus is required for accurate 26S proteasome assembly and specific activity as prerequisites for mitochondria integrity, oxidative stress response and cell differentiation. Our findings of the complex and dynamic interplay between multiple cellular processes mediated by a small conserved intrinsically unordered protein sheds light and supports current efforts to understand and explore in more details potential therapies to eventually treat age-related human diseases.
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20
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Zaffagnini G, Savova A, Danieli A, Romanov J, Tremel S, Ebner M, Peterbauer T, Sztacho M, Trapannone R, Tarafder AK, Sachse C, Martens S. p62 filaments capture and present ubiquitinated cargos for autophagy. EMBO J 2018; 37:embj.201798308. [PMID: 29343546 PMCID: PMC5830917 DOI: 10.15252/embj.201798308] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/03/2018] [Accepted: 01/03/2018] [Indexed: 12/14/2022] Open
Abstract
The removal of misfolded, ubiquitinated proteins is an essential part of the protein quality control. The ubiquitin-proteasome system (UPS) and autophagy are two interconnected pathways that mediate the degradation of such proteins. During autophagy, ubiquitinated proteins are clustered in a p62-dependent manner and are subsequently engulfed by autophagosomes. However, the nature of the protein substrates targeted for autophagy is unclear. Here, we developed a reconstituted system using purified components and show that p62 and ubiquitinated proteins spontaneously coalesce into larger clusters. Efficient cluster formation requires substrates modified with at least two ubiquitin chains longer than three moieties and is based on p62 filaments cross-linked by the substrates. The reaction is inhibited by free ubiquitin, K48-, and K63-linked ubiquitin chains, as well as by the autophagosomal marker LC3B, suggesting a tight cross talk with general proteostasis and autophagosome formation. Our study provides mechanistic insights on how substrates are channeled into autophagy.
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Affiliation(s)
- Gabriele Zaffagnini
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Adriana Savova
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Alberto Danieli
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Julia Romanov
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Shirley Tremel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Ebner
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Thomas Peterbauer
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Martin Sztacho
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Riccardo Trapannone
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Abul K Tarafder
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
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21
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Lee S, Tumolo JM, Ehlinger AC, Jernigan KK, Qualls-Histed SJ, Hsu PC, McDonald WH, Chazin WJ, MacGurn JA. Ubiquitin turnover and endocytic trafficking in yeast are regulated by Ser57 phosphorylation of ubiquitin. eLife 2017; 6:29176. [PMID: 29130884 PMCID: PMC5706963 DOI: 10.7554/elife.29176] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/10/2017] [Indexed: 11/30/2022] Open
Abstract
Despite its central role in protein degradation little is known about the molecular mechanisms that sense, maintain, and regulate steady state concentration of ubiquitin in the cell. Here, we describe a novel mechanism for regulation of ubiquitin homeostasis that is mediated by phosphorylation of ubiquitin at the Ser57 position. We find that loss of Ppz phosphatase activity leads to defects in ubiquitin homeostasis that are at least partially attributable to elevated levels of Ser57 phosphorylated ubiquitin. Phosphomimetic mutation at the Ser57 position of ubiquitin conferred increased rates of endocytic trafficking and ubiquitin turnover. These phenotypes are associated with bypass of recognition by endosome-localized deubiquitylases - including Doa4 which is critical for regulation of ubiquitin recycling. Thus, ubiquitin homeostasis is significantly impacted by the rate of ubiquitin flux through the endocytic pathway and by signaling pathways that converge on ubiquitin itself to determine whether it is recycled or degraded in the vacuole.
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Affiliation(s)
- Sora Lee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Jessica M Tumolo
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Aaron C Ehlinger
- Department of Biochemistry, Vanderbilt University, Nashville, United States
| | - Kristin K Jernigan
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Susan J Qualls-Histed
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Pi-Chiang Hsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States
| | - W Hayes McDonald
- Department of Biochemistry, Vanderbilt University, Nashville, United States.,Mass Spectrometry Research Center, Vanderbilt University, Nashville, United States
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, United States
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
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22
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Wang CH, Huang YC, Chen PY, Cheng YJ, Kao HH, Pi H, Chien CT. USP5/Leon deubiquitinase confines postsynaptic growth by maintaining ubiquitin homeostasis through Ubiquilin. eLife 2017; 6. [PMID: 28489002 PMCID: PMC5438252 DOI: 10.7554/elife.26886] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/09/2017] [Indexed: 12/14/2022] Open
Abstract
Synapse formation and growth are tightly controlled processes. How synaptic growth is terminated after reaching proper size remains unclear. Here, we show that Leon, the Drosophila USP5 deubiquitinase, controls postsynaptic growth. In leon mutants, postsynaptic specializations of neuromuscular junctions are dramatically expanded, including the subsynaptic reticulum, the postsynaptic density, and the glutamate receptor cluster. Expansion of these postsynaptic features is caused by a disruption of ubiquitin homeostasis with accumulation of free ubiquitin chains and ubiquitinated substrates in the leon mutant. Accumulation of Ubiquilin (Ubqn), the ubiquitin receptor whose human homolog ubiquilin 2 is associated with familial amyotrophic lateral sclerosis, also contributes to defects in postsynaptic growth and ubiquitin homeostasis. Importantly, accumulations of postsynaptic proteins cause different aspects of postsynaptic overgrowth in leon mutants. Thus, the deubiquitinase Leon maintains ubiquitin homeostasis and proper Ubqn levels, preventing postsynaptic proteins from accumulation to confine postsynaptic growth. DOI:http://dx.doi.org/10.7554/eLife.26886.001
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Affiliation(s)
- Chien-Hsiang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Institute of Neuroscience, National Yang Ming University, Taipei, Taiwan
| | - Yi-Chun Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Pei-Yi Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Institute of Neuroscience, National Yang Ming University, Taipei, Taiwan
| | - Ying-Ju Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Hua Kao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Haiwei Pi
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Ting Chien
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Institute of Neuroscience, National Yang Ming University, Taipei, Taiwan
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23
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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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24
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Takayama K, Matsuura A, Itakura E. Dissection of ubiquitinated protein degradation by basal autophagy. FEBS Lett 2017; 591:1199-1211. [PMID: 28369861 PMCID: PMC5435929 DOI: 10.1002/1873-3468.12641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/16/2017] [Accepted: 03/25/2017] [Indexed: 11/23/2022]
Abstract
Basal autophagy plays an essential role as a protein quality control system. Although it has been demonstrated that the loss of autophagy results in the accumulation of ubiquitin‐positive aggregates and the development of neurodegenerative diseases, the precise autophagy substrate(s) remain unclear. Here, we determined whether ubiquitinated proteins are direct substrates for basal autophagy using a fluorescent ratiometric probe for ubiquitin. We show that the degradation of polyubiquitinated proteins is not dependent on basal autophagy. Although ubiquitin‐positive aggregates are observed in autophagy knockout cultured cells, the aggregates consist of soluble and mobile polyubiquitinated proteins, which are trapped by p62 without an increase in the total amount of ubiquitinated proteins. These results suggest that ubiquitinated proteins are not major targets for basal autophagy.
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Affiliation(s)
- Kaori Takayama
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Japan
| | - Akira Matsuura
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Japan
| | - Eisuke Itakura
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Inage-ku, Japan
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25
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Zhang Y, Huang X, Zhao XY, Hu YJ, Sun HY, Kong WJ. Role of the Ubiquitin C-Terminal Hydrolase L1-Modulated Ubiquitin Proteasome System in Auditory Cortex Senescence. ORL J Otorhinolaryngol Relat Spec 2017; 79:153-163. [PMID: 28407635 DOI: 10.1159/000468944] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/06/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND/AIMS According to recent studies, central auditory impairments are closely related to neurodegenerative diseases. However, the mechanism of central presbycusis remains unclear. Ubiquitin C-terminal hydrolase L1 (UCHL1) is important in maintaining proteasomal activity; however, the detailed mechanism has not yet been fully elucidated. This study aims to investigate the molecular alterations involved in UCHL1 regulation during auditory cortex aging. METHODS D-Galactose (D-gal) induces oxidative stress and senescence in the auditory cortex, as reported in our previous studies. Primary auditory cortex cells were treated with D-gal for 72 h or 5 days. The proteins related to the ubiquitin proteasome system (UPS) and proteasomal activities were evaluated. UCHL1 was overexpressed, and the effects of UCHL1 on the UPS and proteasomal activity were analyzed. RESULTS Proteasomal activity was elevated at 72 h and decreased at 5 days in D-gal-treated primary auditory cortex cells. We also found that overexpression of UCHL1 increased the UPS-related proteins UBE1, PSMA7, ubiquitinated proteins, and monoubiquitin, and proteasomal activity. CONCLUSION The results suggest that UCHL1 may modify the aging process in the auditory cortex by regulating UPS- related proteins.
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Affiliation(s)
- Ya Zhang
- Department of Otolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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26
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Kobayashi M, Oshima S, Maeyashiki C, Nibe Y, Otsubo K, Matsuzawa Y, Nemoto Y, Nagaishi T, Okamoto R, Tsuchiya K, Nakamura T, Watanabe M. The ubiquitin hybrid gene UBA52 regulates ubiquitination of ribosome and sustains embryonic development. Sci Rep 2016; 6:36780. [PMID: 27829658 PMCID: PMC5103194 DOI: 10.1038/srep36780] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/20/2016] [Indexed: 01/23/2023] Open
Abstract
Ubiquitination is a crucial post-translational modification; however, the functions of ubiquitin-coding genes remain unclear. UBA52 encodes a fusion protein comprising ubiquitin at the N-terminus and ribosomal protein L40 (RPL40) at the C-terminus. Here we showed that Uba52-deficient mice die during embryogenesis. UBA52-deficient cells exhibited normal levels of total ubiquitin. However, UBA52-deficient cells displayed decreased protein synthesis and cell-cycle arrest. The overexpression of UBA52 ameliorated the cell-cycle arrest caused by UBA52 deficiency. Surprisingly, RPL40 expression itself is insufficient to regulate cyclin D expression. The cleavage of RPL40 from UBA52 was required for maintaining protein synthesis. Furthermore, we found that RPL40 formed a ribosomal complex with ubiquitin cleaved from UBA52. UBA52 supplies RPL40 and ubiquitin simultaneously to the ribosome. Our study demonstrated that the ubiquitin-coding gene UBA52 is not just an ubiquitin supplier to the ubiquitin pool but is also a regulator of the ribosomal protein complex. These findings provide novel insights into the regulation of ubiquitin-dependent translation and embryonic development.
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Affiliation(s)
- Masanori Kobayashi
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Shigeru Oshima
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Chiaki Maeyashiki
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Yoichi Nibe
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Kana Otsubo
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Yu Matsuzawa
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Yasuhiro Nemoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Takashi Nagaishi
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan.,Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Kiichiro Tsuchiya
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Tetsuya Nakamura
- Department of Advanced Therapeutics for GI Diseases, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Mamoru Watanabe
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
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27
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Morimoto D, Shirakawa M. The evolving world of ubiquitin: transformed polyubiquitin chains. Biomol Concepts 2016; 7:157-67. [PMID: 27226101 DOI: 10.1515/bmc-2016-0009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/15/2016] [Indexed: 12/22/2022] Open
Abstract
The regulation of diverse cellular events by proteins that have undergone post-translational modification with ubiquitin is well documented. Ubiquitin can be polymerized and eight types of polyubiquitin chain contribute to the complexity and specificity of the ubiquitin signal. Unexpectedly, recent studies have shown that ubiquitin itself undergoes post-translational modification by acetylation and phosphorylation; moreover, amyloid-like fibrils comprised of polyubiquitin chains have been discovered. Thus, ubiquitin is not only conjugated to substrate proteins, but also modified and transformed itself. Here, we review these novel forms of ubiquitin signal, with a focus on fibril formation of polyubiquitin chains and its underlying biological relevance.
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28
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Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. eLife 2016; 5. [PMID: 27111525 PMCID: PMC4862753 DOI: 10.7554/elife.15802] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 04/06/2016] [Indexed: 12/31/2022] Open
Abstract
Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover 'shared sensitized positions' localized to areas around the hydrophobic patch and the C-terminus. In addition, we identified perturbation specific effects such as a sensitization of His68 in HU and a tolerance to mutation at Lys63 in DTT. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum. DOI:http://dx.doi.org/10.7554/eLife.15802.001 The ability of an organism to grow and reproduce, that is, it’s “fitness”, is determined by how its genes interact with the environment. Yeast is a model organism in which researchers can control the exact mutations present in the yeast’s genes (its genotype) and the conditions in which the yeast cells live (their environment). This allows researchers to measure how a yeast cell’s genotype and environment affect its fitness. Ubiquitin is a protein that many organisms depend on to manage cell stress by acting as a tag that targets other proteins for degradation. Essential proteins such as ubiquitin often remain unchanged by mutation over long periods of time. As a result, these proteins evolve very slowly. Like all proteins, ubiquitin is built from a chain of amino acid molecules linked together, and the ubiquitin proteins of yeast and humans are made of almost identical sequences of amino acids. Although ubiquitin has barely changed its sequence over evolution, previous studies have shown that – under normal growth conditions in the laboratory – most amino acids in ubiquitin can be mutated without any loss of cell fitness. This led Mavor et al. to hypothesize that treating the yeast cells with chemicals that cause cell stress might lead to amino acids in ubiquitin becoming more sensitive to mutation. To test this idea, a class of graduate students at the University of California, San Francisco grew yeast cells with different ubiquitin mutations together, and with different chemicals that induce cell stress, and measured their growth rates. Sequencing the ubiquitin gene in the thousands of tested yeast cells revealed that three of the chemicals cause a shared set of amino acids in ubiquitin to become more sensitive to mutation. This result suggests that these amino acids are important for the stress response, possibly by altering the ability of yeast cells to target certain proteins for degradation. Conversely, another chemical causes yeast to become more tolerant to changes in the ubiquitin sequence. The experiments also link changes in particular amino acids in ubiquitin to specific stress responses. Mavor et al. show that many of ubquitin’s amino acids are sensitive to mutation under different stress conditions, while others can be mutated to form different amino acids without effecting fitness. By testing the effects of other chemicals, future experiments could further characterize how the yeast’s genotype and environment interact. DOI:http://dx.doi.org/10.7554/eLife.15802.002
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Affiliation(s)
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Kyle Barlow
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Samuel Thompson
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Benjamin A Barad
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Alain R Bonny
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Clinton L Cario
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Garrett Gaskins
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Zairan Liu
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Laura Deming
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Seth D Axen
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Elena Caceres
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Adolfo Cuesta
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Rachel E Gate
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Evan M Green
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Kaitlin R Hulce
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Weiyue Ji
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Lillian R Kenner
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Leanna S Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Steven M Moss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Marco Mravic
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Ryan K Muir
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Stefan Niekamp
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Chimno I Nnadi
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Eugene Palovcak
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Erin M Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Tyler D Ross
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Eugenia C Salcedo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Stephanie K See
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Meena Subramaniam
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Allison W Wong
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Jennifer Li
- UCSF Science and Health Education Partnership, University of California, San Francisco, San Francisco, United States
| | - Kurt S Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Shane Ó Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
| | - Benjamin P Roscoe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Center for Advanced Technology, University of California, San Francisco, San Francisco, United States
| | - Joseph L DeRisi
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
| | - Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
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29
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Yerbury JJ, Ooi L, Dillin A, Saunders DN, Hatters DM, Beart PM, Cashman NR, Wilson MR, Ecroyd H. Walking the tightrope: proteostasis and neurodegenerative disease. J Neurochem 2016; 137:489-505. [DOI: 10.1111/jnc.13575] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Justin J. Yerbury
- Proteostasis and Disease Research Centre; School of Biological Sciences; Faculty of Science, Medicine and Health; University of Wollongong; Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute; Wollongong; New South Wales Australia
| | - Lezanne Ooi
- Proteostasis and Disease Research Centre; School of Biological Sciences; Faculty of Science, Medicine and Health; University of Wollongong; Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute; Wollongong; New South Wales Australia
| | - Andrew Dillin
- Department of Molecular and Cell Biology; Li Ka Shing Center for Biomedical and Health Sciences; The University of California; California USA
- Howard Hughes Medical Institute; The University of California; Berkeley California USA
| | - Darren N. Saunders
- School of Medical Sciences; Faculty of Medicine; University of New South Wales; Randwick New South Wales Australia
- The Kinghorn Cancer Centre; Garvan Institute of Medical Research; Darlinghurst New South Wales Australia
| | - Danny M. Hatters
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
| | - Philip M. Beart
- Florey Institute of Neuroscience and Mental Health; University of Melbourne; Parkville Victoria Australia
| | - Neil R. Cashman
- Department of Medicine (Neurology); University of British Columbia and Vancouver Coastal Health Research Institute; Brain Research Centre; University of British Columbia; Vancouver British Columbia Canada
| | - Mark R. Wilson
- Proteostasis and Disease Research Centre; School of Biological Sciences; Faculty of Science, Medicine and Health; University of Wollongong; Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute; Wollongong; New South Wales Australia
| | - Heath Ecroyd
- Proteostasis and Disease Research Centre; School of Biological Sciences; Faculty of Science, Medicine and Health; University of Wollongong; Wollongong New South Wales Australia
- Illawarra Health and Medical Research Institute; Wollongong; New South Wales Australia
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30
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Ryu HW, Ryu KY. Ubiquitin homeostasis: from neural stem cell differentiation to neuronal development. Neural Regen Res 2015; 10:1209-10. [PMID: 26487838 PMCID: PMC4590223 DOI: 10.4103/1673-5374.162693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Han-Wook Ryu
- Department of Life Science, University of Seoul, Seoul 130-743, Republic of Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul 130-743, Republic of Korea
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31
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The N-terminal domains determine cellular localization and functions of the Doa4 and Ubp5 deubiquitinating enzymes. Biochem Biophys Res Commun 2015; 467:570-6. [PMID: 26427873 DOI: 10.1016/j.bbrc.2015.09.136] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/24/2015] [Indexed: 11/24/2022]
Abstract
Ubiquitination is involved in numerous cellular regulatory mechanisms including the cell cycle, signal transduction and quality control. Ubiquitin modifies proteins by consecutive actions of ubiquitin-activating/conjugating enzymes. Attachment of ubiquitin is reversible. Deubiquitinating enzymes are responsible for removal of ubiquitin from ubiquitin-protein conjugates. Genome of the yeast Saccharomyces cerevisiae encodes structurally related but functionally distinct enzymes - Doa4 and Ubp5. Doa4 is involved in general ubiquitin-dependent proteolysis and is responsible for deubiquitination of ubiquitin-protein conjugates at the cytoplasmic face of the late endosome. The N-terminal domain targets the enzyme to the endosome membrane after ESCRT-III complex has formed there. By contrast, corresponding region of homologous Ubp5 is critical for its bud neck localization in dividing cells. Conceivably, Ubp5 plays an essential role in cytokinesis. Here we show that Doa4 physically interacts with the ESCRT-III component Snf7 and preferentially cleaves Lys63-linked ubiquitin oligomers involved in membrane protein trafficking. We also demonstrate that the unstable regulator of cytokinesis Hof1 accumulates in proteasomal mutants and is required for cellular localization of Ubp5.
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32
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Huang G, Li L, Zhou W. USP14 activation promotes tumor progression in hepatocellular carcinoma. Oncol Rep 2015; 34:2917-24. [PMID: 26397990 DOI: 10.3892/or.2015.4296] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 07/06/2015] [Indexed: 11/06/2022] Open
Abstract
To elucidate the molecular mechanisms underlying the pathogenesis and treatment of human primary hepatocellular carcinoma (HCC), it is important to explore novel HCC-associated genes. In the present study, we examined the expression of ubiquitin-specific peptidase 14 (USP14) in patients with HCC using quantitative PCR and immunohistochemical techniques. The expression of USP14 in tumor tissues of patients with HCC was significantly higher than that in adjacent non-cancerous and normal liver tissues. It was also determined whether the expression profile of USP14 was associated with the clinical characteristics of HCC. Increased USP14 expression was associated with some clinicopatho-logical variables, such as advancing tumor stage. A Kaplan-Meier curve analysis demonstrated that patients with HCC having a high USP14 expression had a significantly poorer prognosis after surgery than patients with lower USP14 expression levels. Knockdown of USP14 with the lentiviral vector delivery of shRNA in human hepatocarcinoma SMMC7721 cells suppressed cell proliferation, altered the cell cycle and induced cell apoptosis. Additionally, the Wnt/β-catenin pathway was activated in HCC patients with USP14 overexpression. These findings strongly suggested that USP14 activation plays an oncogenic role in promoting tumor progression in HCC. Thus, our findings suggested that USP14 is involved in the progression of HCC and may be a useful therapeutic target in HCC. These findings likely reflect the key role that USP14 plays in the pathogenesis of HCC. Therefore, the identification of USP14 and USP14-driven genes may promote the investigation of its functional role to develop more effective therapies for HCC, especially advanced HCC.
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Affiliation(s)
- Gang Huang
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Limei Li
- Clinical and Translational Research Center Shanghai East Hospital, Key Laboratory of Arrhythmias of Ministry of Education, Shanghai, P.R. China
| | - Weiping Zhou
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, P.R. China
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33
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Conserved Mode of Interaction between Yeast Bro1 Family V Domains and YP(X)nL Motif-Containing Target Proteins. EUKARYOTIC CELL 2015; 14:976-82. [PMID: 26150415 DOI: 10.1128/ec.00091-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/02/2015] [Indexed: 11/20/2022]
Abstract
Yeast Bro1 and Rim20 belong to a family of proteins which possess a common architecture of Bro1 and V domains. Alix and His domain protein tyrosine phosphatase (HD-PTP), mammalian Bro1 family proteins, bind YP(X)nL (n = 1 to 3) motifs in their target proteins through their V domains. In Alix, the Phe residue, which is located in the hydrophobic groove of the V domain, is critical for binding to the YP(X)nL motif. Although the overall sequences are not highly conserved between mammalian and yeast V domains, we show that the conserved Phe residue in the yeast Bro1 V domain is important for binding to its YP(X)nL-containing target protein, Rfu1. Furthermore, we show that Rim20 binds to its target protein Rim101 through the interaction between the V domain of Rim20 and the YPIKL motif of Rim101. The mutation of either the critical Phe residue in the Rim20 V domain or the YPIKL motif of Rim101 affected the Rim20-mediated processing of Rim101. These results suggest that the interactions between V domains and YP(X)nL motif-containing proteins are conserved from yeast to mammalian cells. Moreover, the specificities of each V domain to their target protein suggest that unidentified elements determine the binding specificity.
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34
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Sahtoe DD, Sixma TK. Layers of DUB regulation. Trends Biochem Sci 2015; 40:456-67. [PMID: 26073511 DOI: 10.1016/j.tibs.2015.05.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/06/2015] [Accepted: 05/11/2015] [Indexed: 11/15/2022]
Abstract
Proteolytic enzymes, such as (iso-)peptidases, are potentially hazardous for cells. To neutralize their potential danger, tight control of their activities has evolved. Deubiquitylating enzymes (DUBs) are isopeptidases involved in eukaryotic ubiquitylation. They reverse ubiquitin signals by hydrolyzing ubiquitin adducts, giving them control over all aspects of ubiquitin biology. The importance of DUB function is underscored by their frequent deregulation in human disease, making these enzymes potential drug targets. Here, we review the different layers of DUB enzyme regulation. We discuss how post-translational modification (PTM), regulatory domains within DUBs, and incorporation of DUBs into macromolecular complexes contribute to their activity. We conclude that most DUBs are likely to use a combination of these basic regulatory mechanisms.
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Affiliation(s)
- Danny D Sahtoe
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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35
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Abstract
Ubiquitin (Ub) is a versatile signaling molecule that plays important roles in a variety of cellular processes. Cellular Ub pools, which are composed of free Ub and Ub conjugates, are in dynamic equilibrium inside cells. In particular, increasing evidence suggests that Ub homeostasis, or the maintenance of free Ub above certain threshold levels, is important for cellular function and survival under normal or stress conditions. Accurate determination of various Ub species, including levels of free Ub and specific Ub chain linkages, have become possible in biological specimens as a result of the introduction of the proteomic approach using mass spectrometry. This technology has facilitated research on dynamic properties of cellular Ub pools and has provided tools for in-depth investigation of Ub homeostasis. In this review, we have also discussed the consequences of the disruption of Ub pool dynamics and homeostasis via deletion of polyubiquitin genes or mutations of deubiquitinating enzymes. The common consequence was a reduced availability of free Ub and a significant impact on the function and viability of cells. These observations further indicate that the levels of free Ub are important determinants for cellular protection. [BMB Reports 2014; 47(9): 475-482]
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Affiliation(s)
- Chul-Woo Park
- Department of Life Science, University of Seoul, Seoul 130-743, Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul 130-743, Korea
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36
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Wang CH, Chen GC, Chien CT. The deubiquitinase Leon/USP5 regulates ubiquitin homeostasis during Drosophila development. Biochem Biophys Res Commun 2014; 452:369-75. [PMID: 25152394 DOI: 10.1016/j.bbrc.2014.08.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 08/14/2014] [Indexed: 01/09/2023]
Abstract
Ubiquitination and the reverse process deubiquitination regulate protein stability and function during animal development. The Drosophila USP5 homolog Leon functions as other family members of unconventional deubiquitinases, disassembling free, substrate-unconjugated polyubiquitin chains to replenish the pool of mono-ubiquitin, and maintaining cellular ubiquitin homeostasis. However, the significance of Leon/USP5 in animal development is still unexplored. In this study, we generated leon mutants to show that Leon is essential for animal viability and tissue integrity during development. Both free and substrate-conjugated polyubiquitin chains accumulate in leon mutants, suggesting that abnormal ubiquitin homeostasis caused tissue disorder and lethality in leon mutants. Further analysis of protein expression profiles in leon mutants shows that the levels of all proteasomal subunits were elevated. Also, proteasomal enzymatic activities were elevated in leon mutants. However, proteasomal degradation of ubiquitinated substrates was impaired. Thus, aberrant ubiquitin homeostasis in leon mutants disrupts normal proteasomal degradation, which is compensated by elevating the levels of proteasomal subunits and activities. Ultimately, the failure to fully compensate the dysfunctional proteasome in leon mutants leads to animal lethality and tissue disorder.
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Affiliation(s)
- Chien-Hsiang Wang
- Institute of Neuroscience, National Yang-Ming University, Taipei 112, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Cheng-Ting Chien
- Institute of Neuroscience, National Yang-Ming University, Taipei 112, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.
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37
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Kimura Y, Kawawaki J, Kakiyama Y, Shimoda A, Tanaka K. The ESCRT-III adaptor protein Bro1 controls functions of regulator for free ubiquitin chains 1 (Rfu1) in ubiquitin homeostasis. J Biol Chem 2014; 289:21760-9. [PMID: 24962567 DOI: 10.1074/jbc.m114.550871] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast Rfu1 (regulator for free ubiquitin chain 1) localizes to endosomes and plays a role in ubiquitin homeostasis by inhibiting the activity of Doa4. We show that Bro1, a member of the class E vacuolar protein sorting proteins that recruits Doa4 to endosomes and stimulates Doa4 deubiquitinating activity, also recruits Rfu1 to endosomes for involvement in ubiquitin homeostasis. This recruitment was mediated by the direct interaction between a region containing the YPEL motif in Rfu1 and the V domain in Bro1, which could be analogous to the interaction between the mammalian Alix V domain and YPXnL motifs of viral and cellular proteins. Furthermore, overexpression of Bro1, particularly the V domain, prevented Rfu1 degradation in response to heat shock. Thus, Bro1, a Doa4 positive regulator, regulated Rfu1, a negative regulator of Doa4. Rfu1 degradation partly involved the proteasome and a ubiquitin ligase Rsp5, suggesting that Rfu1 stability was regulated by ubiquitin-proteasome pathways.
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Affiliation(s)
- Yoko Kimura
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and the Department of Applied Biological Chemistry, Graduate School of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
| | - Junko Kawawaki
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and
| | - Yukie Kakiyama
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and
| | - Ayumi Shimoda
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and
| | - Keiji Tanaka
- From the Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 113-8613 and
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Tang YY, Tang ZH, Zhang Y, Zhuo M, Zang GQ, Chen XH, Yu YS. The Fusion Protein of CTP-HBcAg18-27-Tapasin Mediates the Apoptosis of CD8(+)T Cells and CD8(+) T Cell Response in HLA-A2 Transgenic Mice. HEPATITIS MONTHLY 2014; 14:e16161. [PMID: 24693311 PMCID: PMC3950630 DOI: 10.5812/hepatmon.16161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/20/2014] [Accepted: 02/02/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND HBV-specific cytotoxic T lymphocyte (CTL) activity is believed to play a critical role in controlling HBV infection. The phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway manipulates cell fate decisions in many different cell types by regulating the activity of downstream effectors. We have previously testified that the fusion protein of CTP-HBcAg18-27--Tapasin could enter the cytoplasm of dendritic cells and efficiently induce robust specific CTL response in vitro. OBJECTIVES In the present study, we evaluated specific CTL response and the level of apoptosis of CD8+ T cells induced by CTP-HBcAg18-27-Tapasin in HLA-A2 transgenic mice (H-2Kb). Meanwhile, we preliminary investigated PI3K, phosphorylation level of Akt, and mammalian target of rapamycin (mTOR) as positive regulator of the magnitude and effector function of the hepatitis B virus-specific cytotoxic T lymphocytes in HLA-A2 transgenic mice. MATERIALS AND METHODS HLA-A2 transgenic mice were immunized by intramuscular injection in the hind legs three times at one-week intervals with PBS, CTP-HBcAg18-27-Tapasin (50 μg), CTP-HBcAg18-27 (50 μg), HBcAg18-27-Tapasin (50 μg), and HBcAg18-27 (50 μg). One week after the last immunization, mice were sacrificed and splenocytes were harvested in strile condition. The specific CTL response was analyzed by flow cytometry and enzyme linked immunosorbent assay (ELISA); the expression of (PI3K)/Akt signaling was detected by RT-PCR and western blot. RESULTS The results showed that CTP-HBcAg18-27-Tapasin significantly increased the percentages of IFN-γ(+) CD8α(+) T cells, the numbers of these polyfunctional triple-cytokine-producing (IFN-γ, TNF-α, and IL-2) CD8(+)T cells, the secretion of cytokine IFN-γ, IL-2, and TNF-α, while in comparison to control group, it significantly decreased the percentage of apoptotic CD8(+) T cells in HLA-A2 transgenic mice. Moreover, the expression of PI3K, P-Akt, and P-mTOR was significantly upregulated in CTP-HBcAg18-27-Tapasin group compared with control groups. CONCLUSIONS In conclusion, CTP-HBcAg18-27-Tapasin could reduce apoptosis of CD8(+) T cells, increase the percentages of IFN-γ(+) CD8α(+) T cells, and elicit cell-mediated immunity in HLA-A2 transgenic mice; these processes were associated with activation of the PI3K/Akt signaling pathway.
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Affiliation(s)
- Yu-Yan Tang
- Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Zheng-Hao Tang
- Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Yi Zhang
- Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Meng Zhuo
- Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Guo-Qing Zang
- Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiao-Hua Chen
- Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- Corresponding Authors: Xiao-Hua Chen, Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, 200233 Shanghai, China. Tel/Fax: +86-2164369181, E-mail: ; Yong-Sheng Yu, Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, 200233 Shanghai, China. Tel/Fax: +86-2164369181, E-mail:
| | - Yong-Sheng Yu
- Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- Corresponding Authors: Xiao-Hua Chen, Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, 200233 Shanghai, China. Tel/Fax: +86-2164369181, E-mail: ; Yong-Sheng Yu, Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, 200233 Shanghai, China. Tel/Fax: +86-2164369181, E-mail:
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39
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Piper RC, Dikic I, Lukacs GL. Ubiquitin-dependent sorting in endocytosis. Cold Spring Harb Perspect Biol 2014; 6:6/1/a016808. [PMID: 24384571 DOI: 10.1101/cshperspect.a016808] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
When ubiquitin (Ub) is attached to membrane proteins on the plasma membrane, it directs them through a series of sorting steps that culminate in their delivery to the lumen of the lysosome where they undergo complete proteolysis. Ubiquitin is recognized by a series of complexes that operate at a number of vesicle transport steps. Ubiquitin serves as a sorting signal for internalization at the plasma membrane and is the major signal for incorporation into intraluminal vesicles of multivesicular late endosomes. The sorting machineries that catalyze these steps can bind Ub via a variety of Ub-binding domains. At the same time, many of these complexes are themselves ubiquitinated, thus providing a plethora of potential mechanisms to regulate their activity. Here we provide an overview of how membrane proteins are selected for ubiquitination and deubiquitination within the endocytic pathway and how that ubiquitin signal is interpreted by endocytic sorting machineries.
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Affiliation(s)
- Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242
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Wiener R, DiBello AT, Lombardi P, Guzzo CM, Zhang X, Matunis MJ, Wolberger C. E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1. Nat Struct Mol Biol 2013; 20:1033-9. [PMID: 23955022 PMCID: PMC3941643 DOI: 10.1038/nsmb.2655] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 07/18/2013] [Indexed: 12/17/2022]
Abstract
OTUB1 is a Lys48-specific deubiquitinating enzyme that forms a complex in vivo with E2 ubiquitin (Ub)-conjugating enzymes including UBC13 and UBCH5. OTUB1 binds E2~Ub thioester intermediates and prevents ubiquitin transfer, thereby noncatalytically inhibiting accumulation of polyubiquitin. We report here that a second role of OTUB1-E2 interactions is to stimulate OTUB1 cleavage of Lys48 polyubiquitin. This stimulation is regulated by the ratio of charged to uncharged E2 and by the concentration of Lys48-linked polyubiquitin and free ubiquitin. Structural and biochemical studies of human and worm OTUB1 and UBCH5B show that the E2 enzyme stimulates binding of the Lys48 polyubiquitin substrate by stabilizing folding of the OTUB1 N-terminal ubiquitin-binding helix. Our results suggest that OTUB1-E2 complexes in the cell are poised to regulate polyubiquitin chain elongation or degradation in response to changing levels of E2 charging and available free ubiquitin.
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Affiliation(s)
- Reuven Wiener
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Anthony T. DiBello
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Patrick Lombardi
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Catherine M. Guzzo
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Xiangbin Zhang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Michael J. Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
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41
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Disruption of polyubiquitin gene Ubc leads to defective proliferation of hepatocytes and bipotent fetal liver epithelial progenitor cells. Biochem Biophys Res Commun 2013; 435:434-40. [DOI: 10.1016/j.bbrc.2013.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/02/2013] [Indexed: 12/29/2022]
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42
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Tanaka K, Matsuda N. Proteostasis and neurodegeneration: the roles of proteasomal degradation and autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:197-204. [PMID: 23523933 DOI: 10.1016/j.bbamcr.2013.03.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/01/2013] [Accepted: 03/10/2013] [Indexed: 11/30/2022]
Abstract
All proteins in a cell continuously turn over, each at its own rate, contributing to a cell's development, differentiation, or aging. Of course, unnecessary protein(s), or those synthesized in excess, that hamper cellular homeostasis should be discarded rapidly. Furthermore, cells that have been subjected to various environmental stresses, e.g., reactive oxygen species (ROS) and UV irradiation, may incur various types of protein damage, which vitiate normal and homeostatic functions in the cell. Thereby, the prompt elimination of impaired proteins is essential for cell viability. This housekeeping is accomplished by two major catabolic routes-proteasomal digestion and autophagy. Strict maintenance of proteostasis is particularly important in non-proliferative cells, especially neurons, and it is plausible that its failure leads to a number of the neurodegenerative diseases becoming prominent in the growing elderly population. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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Affiliation(s)
- Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa 2-1-6, Setagaya-ku, Tokyo 156-8506, Japan.
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43
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Wiegant F. Hormesis and Cellular Quality Control: A Possible Explanation for the Molecular Mechanisms that Underlie the Benefits of Mild Stress. Dose Response 2012; 11:413-30. [PMID: 23983668 PMCID: PMC3748852 DOI: 10.2203/dose-response.12-030.wiegant] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In contrast to the detrimental action of severe stress conditions, the beneficial effects of mild stress, known as hormesis, is increasingly discussed and studied. A variety of applications for hormesis in risk assessment processes, anti-ageing strategies and clinical therapies have been proposed. The molecular mechanisms underlying the phenomenon of hormesis, however, are not yet fully understood. A possible mechanism that has been proposed for hormesis, the homoeostasis overshoot hypothesis, assumes that an overshoot of repair- and self-recovery mechanisms in response to mild damage can be held responsible for the beneficial effects of hormesis. The present paper proposes 'cellular quality control' as a further explanation of the molecular mechanisms underlying the benefits observed after exposure to mild stress. The most important quality control mechanisms are outlined and their known and hypothesised actions in hormesis are discussed. As an example, different aspects of protein quality control will be described in more detail, which includes the reaction of the cell upon stress-induced protein damage and -aggregation. The regulation of Heat Shock Proteins and components from the ubiquitin proteasome system as part of cellular quality control is described in relation to its beneficial role in hormesis.
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Affiliation(s)
- F.A.C. Wiegant
- University College Utrecht, Science Department, Utrecht University, and Faculty of Science; Department of Biology, Institute of Education, Utrecht University
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44
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Dong G, Callegari E, Gloeckner CJ, Ueffing M, Wang H. Mass spectrometric identification of novel posttranslational modification sites in Huntingtin. Proteomics 2012; 12:2060-4. [PMID: 22623107 DOI: 10.1002/pmic.201100380] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Huntington's disease (HD) is caused by a CAG triplet repeat expansion in exon 1 of the Huntingtin (Htt) gene, encoding an abnormal expanded polyglutamine (polyQ) tract that confers toxicity to the mutant Htt (mHtt) protein. Recent data suggest that posttranslational modifications of mHtt modulate its cytotoxicity. To further understand the cytotoxic mechanisms of mHtt, we have generated HEK293 cell models stably expressing Strep- and FLAG-tagged Htt containing either 19Q (wild-type Htt), 55Q (mHtt), or 94Q (mHtt) repeats. Following tandem affinity purification, the tagged Htt and associated proteins were subjected to tandem mass spectrometry or 2D nano-LC tandem mass spectrometry and several novel modification sites of mHtt containing 55Q or 94Q were identified. These were phosphorylation sites located at Ser431 and Ser432, and ubiquitination site located at Lys444. The two phosphorylation sites were confirmed by Western blot analysis using phosphorylation site-specific antibodies. In addition, prevention of phosphorylation at the two serine sites altered mHtt toxicity and accumulation. These modifications of mHtt may provide novel therapeutic targets for effective treatment of the disorder.
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Affiliation(s)
- Gaofeng Dong
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069, USA
| | - Eduardo Callegari
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069, USA
| | - Christian J Gloeckner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit for Protein Science, Neuherberg, Germany.,Institute for Ophthalmic Research, Medical Proteome Center, University of Tubingen, Tubingen, Germany
| | - Marius Ueffing
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit for Protein Science, Neuherberg, Germany.,Institute for Ophthalmic Research, Medical Proteome Center, University of Tubingen, Tubingen, Germany
| | - Hongmin Wang
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069, USA
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45
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Finley D, Ulrich HD, Sommer T, Kaiser P. The ubiquitin-proteasome system of Saccharomyces cerevisiae. Genetics 2012; 192:319-60. [PMID: 23028185 PMCID: PMC3454868 DOI: 10.1534/genetics.112.140467] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/28/2012] [Indexed: 12/14/2022] Open
Abstract
Protein modifications provide cells with exquisite temporal and spatial control of protein function. Ubiquitin is among the most important modifiers, serving both to target hundreds of proteins for rapid degradation by the proteasome, and as a dynamic signaling agent that regulates the function of covalently bound proteins. The diverse effects of ubiquitylation reflect the assembly of structurally distinct ubiquitin chains on target proteins. The resulting ubiquitin code is interpreted by an extensive family of ubiquitin receptors. Here we review the components of this regulatory network and its effects throughout the cell.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Helle D. Ulrich
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, United Kingdom
| | - Thomas Sommer
- Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, California 92697
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46
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Clague M, Liu H, Urbé S. Governance of Endocytic Trafficking and Signaling by Reversible Ubiquitylation. Dev Cell 2012; 23:457-67. [DOI: 10.1016/j.devcel.2012.08.011] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/27/2012] [Accepted: 08/21/2012] [Indexed: 12/17/2022]
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47
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Rescue of growth defects of yeast cdc48 mutants by pathogenic IBMPFD-VCPs. J Struct Biol 2012; 179:93-103. [DOI: 10.1016/j.jsb.2012.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 06/05/2012] [Accepted: 06/10/2012] [Indexed: 12/22/2022]
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48
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Generation of free ubiquitin chains is up-regulated in stress and facilitated by the HECT domain ubiquitin ligases UFD4 and HUL5. Biochem J 2012; 444:611-7. [DOI: 10.1042/bj20111840] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polyubiquitin chains serve a variety of physiological roles. Typically the chains are bound covalently to a protein substrate and in many cases target it for degradation by the 26S proteasome. However, several studies have demonstrated the existence of free polyubiquitin chains which are not linked to a specific substrate. Several physiological functions have been attributed to these chains, among them playing a role in signal transduction and serving as storage of ubiquitin for utilization under stress. In the present study, we have established a system for the detection of free ubiquitin chains and monitoring their level under changing conditions. Using this system, we show that UFD4 (ubiquitin fusion degradation 4), a HECT (homologous with E6-AP C-terminus) domain ubiquitin ligase, is involved in free chain generation. We also show that generation of these chains is stimulated in response to a variety of stresses, particularly those caused by DNA damage. However, it appears that the stress-induced synthesis of free chains is catalysed by a different ligase, HUL5 (HECT ubiquitin ligase 5), which is also a HECT domain E3.
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49
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Protein degradation and the stress response. Semin Cell Dev Biol 2012; 23:515-22. [PMID: 22414377 DOI: 10.1016/j.semcdb.2012.01.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/24/2012] [Accepted: 01/26/2012] [Indexed: 11/23/2022]
Abstract
Environmental stresses are manifold and so are the responses they elicit. This is particularly true for higher eukaryotes where various tissues and cell types are differentially affected by the insult. Type and scope of the stress response can therefore differ greatly among cell types. Given the importance of the ubiquitin proteasome system (UPS) for most cellular processes, it comes as no surprise that the UPR plays a pivotal role in counteracting the effects of stressors. Here we outline contributions of the UPS to stress sensing, signaling, and response pathways. We make no claim to comprehensiveness but choose selected examples to illustrate concepts and mechanisms by which protein modification with ubiquitin and proteasomal degradation of key regulators ensures cellular integrity during stress situations.
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50
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Ryu KY, Park H, Rossi DJ, Weissman IL, Kopito RR. Perturbation of the hematopoietic system during embryonic liver development due to disruption of polyubiquitin gene Ubc in mice. PLoS One 2012; 7:e32956. [PMID: 22393459 PMCID: PMC3290595 DOI: 10.1371/journal.pone.0032956] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 02/02/2012] [Indexed: 11/29/2022] Open
Abstract
Disruption of the polyubiquitin gene Ubc leads to a defect in fetal liver development, which can be partially rescued by increasing the amount of ubiquitin. However, it is still not known why Ubc is required for fetal liver development and the nature of the defective cell types responsible for embryonic lethality have not been characterized. In this study, we assessed the cause of embryonic lethality with respect to the fetal liver hematopoietic system. We found that Ubc was highly expressed in the embryonic liver, and the proliferation capacity of fetal liver cells was reduced in Ubc−/− embryos. Specifically, Ubc was most highly expressed in hematopoietic cells, and the proliferation capacity of hematopoietic cells was significantly impaired in Ubc−/− embryos. While hematopoietic cell and hematopoietic stem cell (HSC) frequency was maintained in Ubc−/− embryos, the absolute number of these cells was diminished because of reduced total liver cell number in Ubc−/− embryos. Transplantations of fetal liver cells into lethally irradiated recipient mice by non-competitive and competitive reconstitution methods indicated that disruption of Ubc does not significantly impair the intrinsic function of fetal liver HSCs. These findings suggest that disruption of Ubc reduces the absolute number of HSCs in embryonic livers, but has no significant effect on the autonomous function of HSCs. Thus, the lethality of Ubc−/− embryos is not the result of intrinsic HSC failure.
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Affiliation(s)
- Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul, Republic of Korea.
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