1
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Gubat J, Sjöstrand L, Selvaraju K, Telli K, D'Arcy P. Loss of the proteasomal deubiquitinase USP14 induces growth defects and a senescence phenotype in colorectal cancer cells. Sci Rep 2024; 14:13037. [PMID: 38844605 PMCID: PMC11156967 DOI: 10.1038/s41598-024-63791-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
The proteasome-associated deubiquitinase USP14 is a potential drug target. Using an inducible USP14 knockout system in colon cancer cells, we found that USP14 depletion impedes cellular proliferation, induces cell cycle arrest, and leads to a senescence-like phenotype. Transcriptomic analysis revealed altered gene expression related to cell division and cellular differentiation. USP14 knockout cells also exhibited changes in morphology, actin distribution, and expression of actin cytoskeletal components. Increased ubiquitin turnover was observed, offset by upregulation of polyubiquitin genes UBB and UBC. Pharmacological inhibition of USP14 with IU1 increased ubiquitin turnover but did not affect cellular growth or morphology. BioGRID data identified USP14 interactors linked to actin cytoskeleton remodeling, DNA damage repair, mRNA splicing, and translation. In conclusion, USP14 loss in colon cancer cells induces a transient quiescent cancer phenotype not replicated by pharmacologic inhibition of its deubiquitinating activity.
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Affiliation(s)
- Johannes Gubat
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Linda Sjöstrand
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Karthik Selvaraju
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Kübra Telli
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Pádraig D'Arcy
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden.
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2
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Manzoor Y, Aouida M, Ramadoss R, Moovarkumudalvan B, Ahmed N, Sulaiman AA, Mohanty A, Ali R, Mifsud B, Ramotar D. Loss of the yeast transporter Agp2 upregulates the pleiotropic drug-resistant pump Pdr5 and confers resistance to the protein synthesis inhibitor cycloheximide. PLoS One 2024; 19:e0303747. [PMID: 38776347 PMCID: PMC11111045 DOI: 10.1371/journal.pone.0303747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/30/2024] [Indexed: 05/24/2024] Open
Abstract
The transmembrane protein Agp2, initially shown as a transporter of L-carnitine, mediates the high-affinity transport of polyamines and the anticancer drug bleomycin-A5. Cells lacking Agp2 are hyper-resistant to polyamine and bleomycin-A5. In these earlier studies, we showed that the protein synthesis inhibitor cycloheximide blocked the uptake of bleomycin-A5 into the cells suggesting that the drug uptake system may require de novo synthesis. However, our recent findings demonstrated that cycloheximide, instead, induced rapid degradation of Agp2, and in the absence of Agp2 cells are resistant to cycloheximide. These observations raised the possibility that the degradation of Agp2 may allow the cell to alter its drug resistance network to combat the toxic effects of cycloheximide. In this study, we show that membrane extracts from agp2Δ mutants accentuated several proteins that were differentially expressed in comparison to the parent. Mass spectrometry analysis of the membrane extracts uncovered the pleiotropic drug efflux pump, Pdr5, involved in the efflux of cycloheximide, as a key protein upregulated in the agp2Δ mutant. Moreover, a global gene expression analysis revealed that 322 genes were differentially affected in the agp2Δ mutant versus the parent, including the prominent PDR5 gene and genes required for mitochondrial function. We further show that Agp2 is associated with the upstream region of the PDR5 gene, leading to the hypothesis that cycloheximide resistance displayed by the agp2Δ mutant is due to the derepression of the PDR5 gene.
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Affiliation(s)
- Yusra Manzoor
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Ramya Ramadoss
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, India
| | - Balasubramanian Moovarkumudalvan
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, India
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Nisar Ahmed
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Abdallah Alhaj Sulaiman
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Ashima Mohanty
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Reem Ali
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Borbala Mifsud
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
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3
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Cao H, Zhou X, Xu B, Hu H, Guo J, Ma Y, Wang M, Li N, Jun Z. Advances in the study of protein folding and endoplasmic reticulum-associated degradation in mammal cells. J Zhejiang Univ Sci B 2024; 25:212-232. [PMID: 38453636 PMCID: PMC10918413 DOI: 10.1631/jzus.b2300403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/03/2023] [Indexed: 03/09/2024]
Abstract
The endoplasmic reticulum is a key site for protein production and quality control. More than one-third of proteins are synthesized and folded into the correct three-dimensional conformation in the endoplasmic reticulum. However, during protein folding, unfolded and/or misfolded proteins are prone to occur, which may lead to endoplasmic reticulum stress. Organisms can monitor the quality of the proteins produced by endoplasmic reticulum quality control (ERQC) and endoplasmic reticulum-associated degradation (ERAD), which maintain endoplasmic reticulum protein homeostasis by degrading abnormally folded proteins. The underlying mechanisms of protein folding and ERAD in mammals have not yet been fully explored. Therefore, this paper reviews the process and function of protein folding and ERAD in mammalian cells, in order to help clinicians better understand the mechanism of ERAD and to provide a scientific reference for the treatment of diseases caused by abnormal ERAD.
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Affiliation(s)
- Hong Cao
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
- National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai 200433, China
| | - Xuchang Zhou
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
| | - Bowen Xu
- National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai 200433, China
| | - Han Hu
- National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai 200433, China
| | - Jianming Guo
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
| | - Yuwei Ma
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
| | - Miao Wang
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China
| | - Nan Li
- National Key Laboratory of Immunity and Inflammation, Naval Medical University, Shanghai 200433, China.
| | - Zou Jun
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai 200438, China.
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4
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Nogami R, Nagata M, Imada R, Kai K, Kawaguchi T, Tani S. Cycloheximide in the nanomolar range inhibits seed germination of Orobanche minor. JOURNAL OF PESTICIDE SCIENCE 2024; 49:22-30. [PMID: 38450089 PMCID: PMC10912901 DOI: 10.1584/jpestics.d23-038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/29/2023] [Indexed: 03/08/2024]
Abstract
From the 992 samples of culture extracts of microorganisms isolated from soil in Japan, we found that the extract of Streptomyces sp. no. 226 inhibited Orobanche minor seed germination without significantly affecting the seed germination of Trifolium pratense and the growth of Aspergillus oryzae and Escherichia coli. Using ESI-MS, 1H-NMR, and 13C-NMR, we identified the active compound as cycloheximide. Cycloheximide had half-maximum inhibitory concentrations of 2.6 ng/mL for the inhibition of seed germination of O. minor and 2.5 µg/mL for that of the conidial germination of A. oryzae. Since cycloheximide is known to inhibit translation by interacting with ribosomal protein L28 (RPL28) in yeast, we investigated whether RPL protein of O. minor plays a critical role in the inhibition of O. minor seed germination. Our data suggested that O. minor RPL27A was not sensitive to cycloheximide by comparing it to the strain expressing S. cerevisiae RPL28. These findings suggest the presence of an unidentified mechanism by which cycloheximide hinders O. minor seed germination.
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Affiliation(s)
- Ryosuke Nogami
- Graduate School of Agriculture, Osaka Metropolitan University
| | - Mari Nagata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Risa Imada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Kenji Kai
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Takashi Kawaguchi
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Shuji Tani
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
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5
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Heigl T, Netzer MA, Zanetti L, Ganglberger M, Fernández-Quintero ML, Koschak A. Characterization of two pathological gating-charge substitutions in Cav1.4 L-type calcium channels. Channels (Austin) 2023; 17:2192360. [PMID: 36943941 PMCID: PMC10038055 DOI: 10.1080/19336950.2023.2192360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/14/2023] [Indexed: 03/23/2023] Open
Abstract
Cav1.4 L-type calcium channels are predominantly expressed at the photoreceptor terminals and in bipolar cells, mediating neurotransmitter release. Mutations in its gene, CACNA1F, can cause congenital stationary night-blindness type 2 (CSNB2). Due to phenotypic variability in CSNB2, characterization of pathological variants is necessary to better determine pathological mechanism at the site of action. A set of known mutations affects conserved gating charges in the S4 voltage sensor, two of which have been found in male CSNB2 patients. Here, we describe two disease-causing Cav1.4 mutations with gating charge neutralization, exchanging an arginine 964 with glycine (RG) or arginine 1288 with leucine (RL). In both, charge neutralization was associated with a reduction channel expression also reflected in smaller ON gating currents. In RL channels, the strong decrease in whole-cell current densities might additionally be explained by a reduction of single-channel currents. We further identified alterations in their biophysical properties, such as a hyperpolarizing shift of the activation threshold and an increase in slope factor of activation and inactivation. Molecular dynamic simulations in RL substituted channels indicated water wires in both, resting and active, channel states, suggesting the development of omega (ω)currents as a new pathological mechanism in CSNB2. This sum of the respective channel property alterations might add to the differential symptoms in patients beside other factors, such as genomic and environmental deviations.
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Affiliation(s)
- Thomas Heigl
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Michael A. Netzer
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Lucia Zanetti
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Matthias Ganglberger
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
| | - Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Alexandra Koschak
- University of Innsbruck, Institute of Pharmacy, Pharmacology and Toxicology, Innsbruck, Austria
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6
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Farrawell NE, Bax M, McAlary L, McKenna J, Maksour S, Do-Ha D, Rayner SL, Blair IP, Chung RS, Yerbury JJ, Ooi L, Saunders DN. ALS-linked CCNF variant disrupts motor neuron ubiquitin homeostasis. Hum Mol Genet 2023; 32:2386-2398. [PMID: 37220877 PMCID: PMC10652331 DOI: 10.1093/hmg/ddad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders that share pathological features, including the aberrant accumulation of ubiquitinated protein inclusions within motor neurons. Previously, we have shown that the sequestration of ubiquitin (Ub) into inclusions disrupts Ub homeostasis in cells expressing ALS-associated variants superoxide dismutase 1 (SOD1), fused in sarcoma (FUS) and TAR DNA-binding protein 43 (TDP-43). Here, we investigated whether an ALS/FTD-linked pathogenic variant in the CCNF gene, encoding the E3 Ub ligase Cyclin F (CCNF), also perturbs Ub homeostasis. The presence of a pathogenic CCNF variant was shown to cause ubiquitin-proteasome system (UPS) dysfunction in induced pluripotent stem cell-derived motor neurons harboring the CCNF S621G mutation. The expression of the CCNFS621G variant was associated with an increased abundance of ubiquitinated proteins and significant changes in the ubiquitination of key UPS components. To further investigate the mechanisms responsible for this UPS dysfunction, we overexpressed CCNF in NSC-34 cells and found that the overexpression of both wild-type (WT) and the pathogenic variant of CCNF (CCNFS621G) altered free Ub levels. Furthermore, double mutants designed to decrease the ability of CCNF to form an active E3 Ub ligase complex significantly improved UPS function in cells expressing both CCNFWT and the CCNFS621G variant and were associated with increased levels of free monomeric Ub. Collectively, these results suggest that alterations to the ligase activity of the CCNF complex and the subsequent disruption to Ub homeostasis play an important role in the pathogenesis of CCNF-associated ALS/FTD.
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Affiliation(s)
- Natalie E Farrawell
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Monique Bax
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Jessie McKenna
- School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Simon Maksour
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Dzung Do-Ha
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney 2109, New South Wales, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney 2109, New South Wales, Australia
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney 2109, New South Wales, Australia
| | - Justin J Yerbury
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Lezanne Ooi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Darren N Saunders
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- School of Medical Sciences, University of Sydney, Sydney 2006, Australia
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7
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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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8
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Schneider KL, Ahmadpour D, Keuenhof KS, Eisele-Bürger AM, Berglund LL, Eisele F, Babazadeh R, Höög JL, Nyström T, Widlund PO. Using reporters of different misfolded proteins reveals differential strategies in processing protein aggregates. J Biol Chem 2022; 298:102476. [PMID: 36096201 PMCID: PMC9636550 DOI: 10.1016/j.jbc.2022.102476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
The accumulation of misfolded proteins is a hallmark of aging and many neurodegenerative diseases, making it important to understand how the cellular machinery recognizes and processes such proteins. A key question in this respect is whether misfolded proteins are handled in a similar way regardless of their genetic origin. To approach this question, we compared how three different misfolded proteins, guk1-7, gus1-3, and pro3-1, are handled by the cell. We show that all three are nontoxic, even though highly overexpressed, highlighting their usefulness in analyzing the cellular response to misfolding in the absence of severe stress. We found significant differences between the aggregation and disaggregation behavior of the misfolded proteins. Specifically, gus1-3 formed some aggregates that did not efficiently recruit the protein disaggregase Hsp104 and did not colocalize with the other misfolded reporter proteins. Strikingly, while all three misfolded proteins generally coaggregated and colocalized to specific sites in the cell, disaggregation was notably different; the rate of aggregate clearance of pro3-1 was faster than that of the other misfolded proteins, and its clearance rate was not hindered when pro3-1 colocalized with a slowly resolved misfolded protein. Finally, we observed using super-resolution light microscopy as well as immunogold labeling EM in which both showed an even distribution of the different misfolded proteins within an inclusion, suggesting that misfolding characteristics and remodeling, rather than spatial compartmentalization, allows for differential clearance of these misfolding reporters residing in the same inclusion. Taken together, our results highlight how properties of misfolded proteins can significantly affect processing.
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Affiliation(s)
- Kara L Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Doryaneh Ahmadpour
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Katharina S Keuenhof
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anna Maria Eisele-Bürger
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden; Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Lisa Larsson Berglund
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Frederik Eisele
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Roja Babazadeh
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Johanna L Höög
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Per O Widlund
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden.
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9
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Simões V, Cizubu BK, Harley L, Zhou Y, Pajak J, Snyder NA, Bouvette J, Borgnia MJ, Arya G, Bartesaghi A, Silva GM. Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes. Cell Rep 2022; 39:110860. [PMID: 35613580 PMCID: PMC9215706 DOI: 10.1016/j.celrep.2022.110860] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 01/11/2023] Open
Abstract
Protein ubiquitination is an essential process that rapidly regulates protein synthesis, function, and fate in dynamic environments. Within its non-proteolytic functions, we showed that K63-linked polyubiquitinated conjugates heavily accumulate in yeast cells exposed to oxidative stress, stalling ribosomes at elongation. K63-ubiquitinated conjugates accumulate mostly because of redox inhibition of the deubiquitinating enzyme Ubp2; however, the role and regulation of ubiquitin-conjugating enzymes (E2) in this pathway remained unclear. Here, we show that the E2 Rad6 associates and modifies ribosomes during stress. We further demonstrate that Rad6 and its human homolog UBE2A are redox regulated by forming a reversible disulfide with the E1 ubiquitin-activating enzyme (Uba1). This redox regulation is part of a negative feedback regulation, which controls the levels of K63 ubiquitination under stress. Finally, we show that Rad6 activity is necessary to regulate translation, antioxidant defense, and adaptation to stress, thus providing an additional physiological role for this multifunctional enzyme.
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Affiliation(s)
- Vanessa Simões
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Lana Harley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Ye Zhou
- Department of Computer Science, Department of Biochemistry, and Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Nathan A Snyder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jonathan Bouvette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC 27709, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Department of Biochemistry, and Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA.
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10
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Morey TM, Esmaeili MA, Duennwald ML, Rylett RJ. SPAAC Pulse-Chase: A Novel Click Chemistry-Based Method to Determine the Half-Life of Cellular Proteins. Front Cell Dev Biol 2021; 9:722560. [PMID: 34557490 PMCID: PMC8452969 DOI: 10.3389/fcell.2021.722560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Assessing the stability and degradation of proteins is central to the study of cellular biological processes. Here, we describe a novel pulse-chase method to determine the half-life of cellular proteins that overcomes the limitations of other commonly used approaches. This method takes advantage of pulse-labeling of nascent proteins in living cells with the bioorthogonal amino acid L-azidohomoalanine (AHA) that is compatible with click chemistry-based modifications. We validate this method in both mammalian and yeast cells by assessing both over-expressed and endogenous proteins using various fluorescent and chemiluminescent click chemistry-compatible probes. Importantly, while cellular stress responses are induced to a limited extent following live-cell AHA pulse-labeling, we also show that this response does not result in changes in cell viability and growth. Moreover, this method is not compromised by the cytotoxicity evident in other commonly used protein half-life measurement methods and it does not require the use of radioactive amino acids. This new method thus presents a versatile, customizable, and valuable addition to the toolbox available to cell biologists to determine the stability of cellular proteins.
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Affiliation(s)
- Trevor M Morey
- Molecular Medicine Research Group, Robarts Research Institute, Western University, London, ON, Canada.,Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Mohammad Ali Esmaeili
- Department of Anatomy and Cell Biology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Martin L Duennwald
- Department of Anatomy and Cell Biology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - R Jane Rylett
- Molecular Medicine Research Group, Robarts Research Institute, Western University, London, ON, Canada.,Department of Physiology and Pharmacology, Western University, London, ON, Canada
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11
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Popova B, Galka D, Häffner N, Wang D, Schmitt K, Valerius O, Knop M, Braus GH. α-Synuclein Decreases the Abundance of Proteasome Subunits and Alters Ubiquitin Conjugates in Yeast. Cells 2021; 10:cells10092229. [PMID: 34571878 PMCID: PMC8468666 DOI: 10.3390/cells10092229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 01/18/2023] Open
Abstract
Parkinson’s disease (PD) is the most prevalent movement disorder characterized with loss of dopaminergic neurons in the brain. One of the pathological hallmarks of the disease is accumulation of aggregated α-synuclein (αSyn) in cytoplasmic Lewy body inclusions that indicates significant dysfunction of protein homeostasis in PD. Accumulation is accompanied with highly elevated S129 phosphorylation, suggesting that this posttranslational modification is linked to pathogenicity and altered αSyn inclusion dynamics. To address the role of S129 phosphorylation on protein dynamics further we investigated the wild type and S129A variants using yeast and a tandem fluorescent timer protein reporter approach to monitor protein turnover and stability. Overexpression of both variants leads to inhibited yeast growth. Soluble S129A is more stable and additional Y133F substitution permits αSyn degradation in a phosphorylation-independent manner. Quantitative cellular proteomics revealed significant αSyn-dependent disturbances of the cellular protein homeostasis, which are increased upon S129 phosphorylation. Disturbances are characterized by decreased abundance of the ubiquitin-dependent protein degradation machinery. Biotin proximity labelling revealed that αSyn interacts with the Rpt2 base subunit. Proteasome subunit depletion by reducing the expression of the corresponding genes enhances αSyn toxicity. Our studies demonstrate that turnover of αSyn and depletion of the proteasome pool correlate in a complex relationship between altered proteasome composition and increased αSyn toxicity.
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Affiliation(s)
- Blagovesta Popova
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
- Correspondence: (B.P.); (G.H.B.)
| | - Dajana Galka
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Nicola Häffner
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Dan Wang
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany;
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
- Correspondence: (B.P.); (G.H.B.)
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Koyuncu S, Loureiro R, Lee HJ, Wagle P, Krueger M, Vilchez D. Rewiring of the ubiquitinated proteome determines ageing in C. elegans. Nature 2021; 596:285-290. [PMID: 34321666 PMCID: PMC8357631 DOI: 10.1038/s41586-021-03781-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/29/2021] [Indexed: 12/20/2022]
Abstract
Ageing is driven by a loss of cellular integrity1. Given the major role of ubiquitin modifications in cell function2, here we assess the link between ubiquitination and ageing by quantifying whole-proteome ubiquitin signatures in Caenorhabditis elegans. We find a remodelling of the ubiquitinated proteome during ageing, which is ameliorated by longevity paradigms such as dietary restriction and reduced insulin signalling. Notably, ageing causes a global loss of ubiquitination that is triggered by increased deubiquitinase activity. Because ubiquitination can tag proteins for recognition by the proteasome3, a fundamental question is whether deficits in targeted degradation influence longevity. By integrating data from worms with a defective proteasome, we identify proteasomal targets that accumulate with age owing to decreased ubiquitination and subsequent degradation. Lowering the levels of age-dysregulated proteasome targets prolongs longevity, whereas preventing their degradation shortens lifespan. Among the proteasomal targets, we find the IFB-2 intermediate filament4 and the EPS-8 modulator of RAC signalling5. While increased levels of IFB-2 promote the loss of intestinal integrity and bacterial colonization, upregulation of EPS-8 hyperactivates RAC in muscle and neurons, and leads to alterations in the actin cytoskeleton and protein kinase JNK. In summary, age-related changes in targeted degradation of structural and regulatory proteins across tissues determine longevity.
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Affiliation(s)
- Seda Koyuncu
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Rute Loureiro
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Hyun Ju Lee
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Prerana Wagle
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Marcus Krueger
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Faculty of Medicine, University Hospital Cologne, Cologne, Germany.
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Small-Molecule Inhibitors Targeting Proteasome-Associated Deubiquitinases. Int J Mol Sci 2021; 22:ijms22126213. [PMID: 34207520 PMCID: PMC8226605 DOI: 10.3390/ijms22126213] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 02/06/2023] Open
Abstract
The 26S proteasome is the principal protease for regulated intracellular proteolysis. This multi-subunit complex is also pivotal for clearance of harmful proteins that are produced throughout the lifetime of eukaryotes. Recent structural and kinetic studies have revealed a multitude of conformational states of the proteasome in substrate-free and substrate-engaged forms. These conformational transitions demonstrate that proteasome is a highly dynamic machinery during substrate processing that can be also controlled by a number of proteasome-associated factors. Essentially, three distinct family of deubiquitinases–USP14, RPN11, and UCH37–are associated with the 19S regulatory particle of human proteasome. USP14 and UCH37 are capable of editing ubiquitin conjugates during the process of their dynamic engagement into the proteasome prior to the catalytic commitment. In contrast, RPN11-mediated deubiquitination is directly coupled to substrate degradation by sensing the proteasome’s conformational switch into the commitment steps. Therefore, proteasome-bound deubiquitinases are likely to tailor the degradation events in accordance with substrate processing steps and for dynamic proteolysis outcomes. Recent chemical screening efforts have yielded highly selective small-molecule inhibitors for targeting proteasomal deubiquitinases, such as USP14 and RPN11. USP14 inhibitors, IU1 and its progeny, were found to promote the degradation of a subset of substrates probably by overriding USP14-imposed checkpoint on the proteasome. On the other hand, capzimin, a RPN11 inhibitor, stabilized the proteasome substrates and showed the anti-proliferative effects on cancer cells. It is highly conceivable that these specific inhibitors will aid to dissect the role of each deubiquitinase on the proteasome. Moreover, customized targeting of proteasome-associated deubiquitinases may also provide versatile therapeutic strategies for induced or repressed protein degradation depending on proteolytic demand and cellular context.
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14
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Sharma M, Yadav P, Doshi A, Brahmbhatt HD, Prabha CR. Probing the effects of double mutations on the versatile protein ubiquitin in Saccharomyces cerevisiae. Int J Biol Macromol 2021; 179:299-308. [PMID: 33662424 DOI: 10.1016/j.ijbiomac.2021.02.208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/21/2021] [Accepted: 02/27/2021] [Indexed: 11/17/2022]
Abstract
Ubiquitin is an indispensable protein of eukaryotic origin with an extraordinarily high degree of sequence conservation. It is used to tag proteins post-translationally and the process of ubiquitination regulates the activity of the modified proteins or drives them for degradation. Double mutations produce varied effects in proteins, depending on the structural relationship of the mutated residues, their role in the overall structure and functions of a protein. Six double mutants derived from the ubiquitin mutant UbEP42, namely S20F-A46S, S20F-L50P, S20F-I61T, A46S-L50P, A46S-I61T, and L50P-I61T, have been studied here to understand how they influence the ubiquitination related functions, by analysing their growth and viability, Cdc28 levels, K-48 linked polyubiquitination, UFD pathway, lysosomal degradation, endosomal sorting, survival under heat, and antibiotic stresses. The double mutation L50P-I61T is the most detrimental, followed by S20F-I61T and A46S-I61T. The double mutations studied here, in general, make cells more sensitive than the wild type to one or the other stress. However, the excessive negative effects of L50P and I61T are compensated under certain conditions by S20F and A46S mutations. The competitive inhibition produced by these substitutions could be used to manage certain ubiquitination associated diseases.
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Affiliation(s)
- Mrinal Sharma
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, India
| | - Prranshu Yadav
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, India
| | - Ankita Doshi
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, India
| | - Hemang D Brahmbhatt
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, India
| | - C Ratna Prabha
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, India.
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15
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Regulation of Treg Functions by the Ubiquitin Pathway. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1278:47-62. [PMID: 33523442 DOI: 10.1007/978-981-15-6407-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Regulatory T (Tregs) cells, required to maintain immune homeostasis, have significant power in disease outcomes. Treg dysfunction, predominantly characterized by the loss of the master transcription factor FoxP3 and the acquisition of Teff-like phenotypes, can promote autoimmunity as well as enhance anti-tumor immunity. As FoxP3 expression and stability are pinnacle for Treg suppressive functions, understanding the pathways that regulate FoxP3 is crucial to ascertain Treg-mediated therapies for autoimmune diseases and cancer. Mechanisms controlling FoxP3 expression and stability range from transcriptional to posttranslational, revealing multiple therapeutic opportunities. While many of the transcriptional pathways have been explored in detail, a recent surge in interest on the posttranslational mechanisms regulating FoxP3 has arisen. Particularly, the role of ubiquitination on Tregs both directly and indirectly involving FoxP3 has gained interest. Here, we summarize the current knowledge on ubiquitin-dependent, FoxP3-mediated control of Treg function as it pertains to human diseases.
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16
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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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17
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Park SH, Moon Y. Enterocyte-Based Bioassay via Quantitative Combination of Proinflammatory Sentinels Specific to 8-keto-trichothecenes. Front Immunol 2020; 11:1530. [PMID: 32765531 PMCID: PMC7378738 DOI: 10.3389/fimmu.2020.01530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/10/2020] [Indexed: 12/12/2022] Open
Abstract
Type B 8-keto-trichothecenes are muco-active mycotoxins that exist as inevitable contaminants in cereal-based foodstuffs. Gut-associated inflammation is an early frontline response during human and animal exposure to these mycotoxins. Despite various tools for chemical identification, optimized biomonitoring of sentinel response-associated biomarkers is required to assess the specific proinflammatory actions of 8-keto-trichothecenes in the gut epithelial barrier. In the present study, intoxication with 8-keto-trichothecenes in human intestinal epithelial cells was found to trigger early response gene 1 product (EGR-1) that plays crucial roles in proinflammatory chemokine induction. In contrast, epithelial exposure to 8-keto-trichothecenes resulted in downregulated expression of nuclear factor NF-kappa-B p65 protein, a key transcription factor, during general inflammatory responses in the gut. Based on the early molecular patterns of expression, the inflammation-inducing activity of 8-keto-trichothecenes was quantified using intestinal epithelial cells with dual reporters for EGR-1 and p65 proteins. EGR-1-responsive elements were linked to luciferase reporter while p65 promoter was bound to secretory alkaline phosphatase (SEAP) reporter. In response to conventional inflammagens such as endotoxins and cytokines such as TNF-α, both luciferase and SEAP activity were elevated in a dose-dependent manner. However, as expected from the mechanistic evaluation, 8-keto-trichothecene-exposed dual reporters of luciferase and SEAP displayed contrasting expression patterns. Furthermore, 8-keto-trichothecene-elevated EGR-1-responsive luciferase activity was improved by deficiency of PSMA3, an α-type subunit of the 20S proteasome core complex for ubiquitin-dependent EGR-1 degradation. This molecular event-based dual biomonitoring in epithelial cells is a promising supplementary tool for detecting typical molecular inflammatory pathways in response to 8-keto-trichothecenes in the food matrix.
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Affiliation(s)
- Seong-Hwan Park
- Laboratory of Mucosal Exposome and Biomodulation, Department of Biomedical Sciences, Pusan National University, Yangsan, South Korea
| | - Yuseok Moon
- Laboratory of Mucosal Exposome and Biomodulation, Department of Biomedical Sciences, Pusan National University, Yangsan, South Korea.,Biomedical Research Institute, Pusan National University, Yangsan, South Korea
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18
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Su Z, Lin M, Su Y, Li J, Lin R, Wu M, Wang X, Huang L, Chen Y, Shu X, Liang S, Zhang H, Huang T, Nie R, Wang J, Xie S. Oxidized low-density lipoprotein inhibits the degradation of cyclophilin A via the lysosome in vascular smooth muscle cells. Am J Transl Res 2020; 12:3964-3973. [PMID: 32774749 PMCID: PMC7407676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Cyclophilin A (CyPA) plays an important role in the progression of atherosclerosis. Additionally, it has been reported that lysosomal function is markedly impaired in atherosclerosis induced by oxidized low-density lipoprotein (ox-LDL). As the CyPA degradation pathway remains to be elucidated, we aimed to uncover the role of lysosomes and ox-LDL in the degradation of CyPA. METHODS We exploited RNA interference (RNAi) in combination with either the lysosomal inhibitor chloroquine (CQ) or the proteasomal inhibitor MG-132 to examine CyPA turnover. We also investigated the role of ox-LDL in lysosomal function and the CyPA degradation pathway and determined whether CyPA interacts with the selective autophagy adaptor p62. RESULTS CQ markedly reversed the CyPA downregulation induced by RNAi and increased intracellular levels of LC3 and p62. MG-132 significantly suppressed polyubiquitinated protein degradation but did not inhibit RNAi-induced CyPA downregulation. Additionally, neither CQ nor MG-132 influenced the gene-silencing efficiency of CyPA siRNA. Moreover, ox-LDL induced cytosolic accumulation of p62 was inconsistent with increased expression of LC3-II. Meanwhile, ox-LDL inhibited RNAi-induced downregulation of CyPA. Immunofluorescence indicated colocalization of endogenous CyPA with ubiquitin and with p62 in response to CQ treatment, and co-immunoprecipitation analysis confirmed interaction between CyPA and p62. CONCLUSION CyPA is degraded by a lysosome-dependent pathway that may involve p62-mediated selective autophagy. Furthermore, ox-LDL modulates the degradation of CyPA via its inhibitory role in lysosomes, contributing to increased expression of CyPA in atherosclerotic plaques.
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Affiliation(s)
- Zizhuo Su
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Maohuan Lin
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Yinqing Su
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Jiajie Li
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Rongjie Lin
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Maoxiong Wu
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Xiaoyu Wang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Lili Huang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Yuyang Chen
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Xiaorong Shu
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Shumin Liang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Haifeng Zhang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Tucheng Huang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Ruqiong Nie
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Jingfeng Wang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
| | - Shuanglun Xie
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, Guangdong, China
- Guangdong Province Key Laboratory of Arrhythmia and ElectrophysiologyGuangzhou 510120, Guangdong, China
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Hu X, Wang L, Wang Y, Ji J, Li J, Wang Z, Li C, Zhang Y, Zhang ZR. RNF126-Mediated Reubiquitination Is Required for Proteasomal Degradation of p97-Extracted Membrane Proteins. Mol Cell 2020; 79:320-331.e9. [DOI: 10.1016/j.molcel.2020.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 12/13/2022]
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Park CW, Jung BK, Ryu KY. Reduced free ubiquitin levels and proteasome activity in cultured neurons and brain tissues treated with amyloid beta aggregates. Mol Brain 2020; 13:89. [PMID: 32513213 PMCID: PMC7281939 DOI: 10.1186/s13041-020-00632-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/03/2020] [Indexed: 11/20/2022] Open
Abstract
Neurodegenerative diseases are characterized by progressive cognitive decline and the loss of neurons in the central nervous system; many are also characterized by abnormal aggregation of misfolded proteins. Ubiquitin (Ub) is a eukaryotic protein that plays pivotal roles in protein degradation and cellular signaling. Ubiquitinated aggregates are observed in neurodegenerative diseases; this ultimately results in reduced levels of available or free Ub. However, it remains unclear whether neurotoxicity arises from the aggregates or a deficiency of free Ub. To investigate this, we treated primary neurons of mouse embryonic brains with amyloid beta (Aβ) 42 and found that free Ub levels were decreased and cell viability was reduced in Aβ42-treated neurons. As reduced levels of free Ub are closely related to impaired function of the proteasome, we evaluated proteasome activity and found that proteasome activity was reduced upon treatment of primary neurons and mouse brain slices with Aβ42. Therefore, we conclude that proteotoxic stress from Aβ42 treatment reduced the levels of available Ub and decreased proteasome activity, resulting in inflammatory stress and apoptosis of neurons.
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Affiliation(s)
- Chul-Woo Park
- Department of Life Science, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Byung-Kwon Jung
- Department of Life Science, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
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The degradation-promoting roles of deubiquitinases Ubp6 and Ubp3 in cytosolic and ER protein quality control. PLoS One 2020; 15:e0232755. [PMID: 32401766 PMCID: PMC7219781 DOI: 10.1371/journal.pone.0232755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/21/2020] [Indexed: 11/19/2022] Open
Abstract
The quality control of intracellular proteins is achieved by degrading misfolded proteins which cannot be refolded by molecular chaperones. In eukaryotes, such degradation is handled primarily by the ubiquitin-proteasome system. However, it remained unclear whether and how protein quality control deploys various deubiquitinases. To address this question, we screened deletions or mutation of the 20 deubiquitinase genes in Saccharomyces cerevisiae and discovered that almost half of the mutations slowed the removal of misfolded proteins whereas none of the remaining mutations accelerated this process significantly. Further characterization revealed that Ubp6 maintains the level of free ubiquitin to promote the elimination of misfolded cytosolic proteins, while Ubp3 supports the degradation of misfolded cytosolic and ER luminal proteins by different mechanisms.
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22
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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: 12] [Impact Index Per Article: 3.0] [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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23
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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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Wang DY, Ren K, Tong SM, Ying SH, Feng MG. Pleiotropic effects of Ubi4, a polyubiquitin precursor required for ubiquitin accumulation, conidiation and pathogenicity of a fungal insect pathogen. Environ Microbiol 2020; 22:2564-2580. [PMID: 32056334 DOI: 10.1111/1462-2920.14940] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 12/15/2019] [Accepted: 02/11/2020] [Indexed: 11/30/2022]
Abstract
Ubi4 is a polyubiquitin precursor well characterized in yeasts but unexplored in insect mycopathogens. Here, we report that orthologous Ubi4 plays a core role in ubiquitin- and asexual lifestyle-required cellular events in Beauveria bassiana. Deletion of ubi4 led to abolished ubiquitin accumulation, blocked autophagic process, severe defects in conidiation and conidial quality, reduced cell tolerance to oxidative, osmotic, cell wall perturbing and heat-shock stresses, decreased transcript levels of development-activating and antioxidant genes, but light effect on radial growth under normal conditions. The deletion mutant lost insect pathogenicity via normal cuticle infection and was severely compromised in virulence via cuticle-bypassing infection due to a block of dimorphic transition critical for acceleration of host mummification. Proteomic and ubiquitylomic analyses revealed 1081 proteins differentially expressed and 639 lysine residues significantly hyper- or hypo-ubiquitylated in the deletion mutant, including dozens of ubiquitin-activating, conjugating and ligating enzymes, core histones, and many more involved in proteasomes, autophagy-lysosome process and protein degradation. Singular deletions of seven ubiquitin-conjugating enzyme genes exerted differential Ubi4-like effects on conidiation level and conidial traits. These findings uncover an essential role of Ubi4 in ubiquitin transfer cascade and its pleiotropic effects on the in vitro and in vivo asexual cycle of B. bassiana.
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Affiliation(s)
- Ding-Yi Wang
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kang Ren
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sen-Miao Tong
- College of Agricultural and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, China
| | - Sheng-Hua Ying
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ming-Guang Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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Kovács L, Nagy Á, Pál M, Deák P. Usp14 is required for spermatogenesis and ubiquitin stress responses in Drosophila melanogaster. J Cell Sci 2020; 133:133/2/jcs237511. [DOI: 10.1242/jcs.237511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Deubiquitylating (DUB) enzymes free covalently linked ubiquitin moieties from ubiquitin–ubiquitin and ubiquitin–protein conjugates, and thereby maintain the equilibrium between free and conjugated ubiquitin moieties and regulate ubiquitin-mediated cellular processes. Here, we performed genetic analyses of mutant phenotypes in Drosophila melanogaster and demonstrate that loss of Usp14 function results in male sterility, with defects in spermatid individualization and reduced testicular free monoubiquitin levels. These phenotypes were rescued by germline-specific overexpression of wild-type Usp14. Synergistic genetic interactions with Ubi-p63E and cycloheximide sensitivity suggest that ubiquitin shortage is a primary cause of male sterility. In addition, Usp14 is predominantly expressed in testes in Drosophila, indicating a higher demand for this DUB in testes that is also reflected by testis-specific loss-of-function Usp14 phenotypes. Collectively, these results suggest a major role of Usp14 in maintaining normal steady state free monoubiquitin levels during the later stages of Drosophila spermatogenesis.
This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Levente Kovács
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - Ágota Nagy
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - Margit Pál
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - Peter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
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Finley D, Prado MA. The Proteasome and Its Network: Engineering for Adaptability. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033985. [PMID: 30833452 DOI: 10.1101/cshperspect.a033985] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteasome, the most complex protease known, degrades proteins that have been conjugated to ubiquitin. It faces the unique challenge of acting enzymatically on hundreds and perhaps thousands of structurally diverse substrates, mechanically unfolding them from their native state and translocating them vectorially from one specialized compartment of the enzyme to another. Moreover, substrates are modified by ubiquitin in myriad configurations of chains. The many unusual design features of the proteasome may have evolved in part to endow this enzyme with a robust ability to process substrates regardless of their identity. The proteasome plays a major role in preserving protein homeostasis in the cell, which requires adaptation to a wide variety of stress conditions. Modulation of proteasome function is achieved through a large network of proteins that interact with it dynamically, modify it enzymatically, or fine-tune its levels. The resulting adaptability of the proteasome, which is unique among proteases, enables cells to control the output of the ubiquitin-proteasome pathway on a global scale.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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27
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A negative feedback mechanism links UBC gene expression to ubiquitin levels by affecting RNA splicing rather than transcription. Sci Rep 2019; 9:18556. [PMID: 31811203 PMCID: PMC6898720 DOI: 10.1038/s41598-019-54973-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/20/2019] [Indexed: 12/16/2022] Open
Abstract
UBC gene plays a critical role in maintaining ubiquitin (Ub) homeostasis. It is upregulated under stress conditions, and herein we report that it is downregulated upon Ub overexpression. Downregulation occurs in a dose-dependent manner, suggesting the existence of a fine-tuned Ub sensing mechanism. This “sensor” requires a conjugation competent ubiquitin to detect Ub levels. Searching the sensor among the transcription factors involved in basal and stress-induced UBC gene expression was unsuccessful. Neither HSF1 and HSF2, nor Sp1 and YY1 are affected by the increased Ub levels. Moreover, mutagenesis of their binding sites in the UBC promoter-driven reporter constructs does not impair the downmodulation effect. Epigenetic studies show that H2A and H2B ubiquitination within the UBC promoter region is unchanged upon ubiquitin overexpression. Noteworthy, quantification of nascent RNA molecules excludes that the downmodulation arises in the transcription initiation step, rather pointing towards a post-transcriptional mechanism. Indeed, a significantly higher fraction of unspliced UBC mRNA is detected in ubiquitin overexpressing cells, compared to empty vector transfected cells. Our findings suggest how increasing cellular ubiquitin levels may control the expression of UBC gene by negatively affecting the splicing of its pre-mRNA, providing a straightforward feedback strategy for the homeostatic control of ubiquitin pools.
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Manohar S, Jacob S, Wang J, Wiechecki KA, Koh HW, Simões V, Choi H, Vogel C, Silva GM. Polyubiquitin Chains Linked by Lysine Residue 48 (K48) Selectively Target Oxidized Proteins In Vivo. Antioxid Redox Signal 2019; 31:1133-1149. [PMID: 31482721 PMCID: PMC6798811 DOI: 10.1089/ars.2019.7826] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Aims: Ubiquitin is a highly conserved protein modifier that heavily accumulates during the oxidative stress response. Here, we investigated the role of the ubiquitination system, particularly at the linkage level, in the degradation of oxidized proteins. The function of ubiquitin in the removal of oxidized proteins remains elusive because of the wide range of potential targets and different roles that polyubiquitin chains play. Therefore, we describe in detail the dynamics of the K48 ubiquitin response as the canonical signal for protein degradation. We identified ubiquitin targets and defined the relationship between protein ubiquitination and oxidation during the stress response. Results: Combining oxidized protein isolation, linkage-specific ubiquitination screens, and quantitative proteomics, we found that K48 ubiquitin accumulated at both the early and late phases of the stress response. We further showed that a fraction of oxidized proteins are conjugated with K48 ubiquitin. We identified ∼750 ubiquitinated proteins and ∼400 oxidized proteins that were modified during oxidative stress, and around half of which contain both modifications. These proteins were highly abundant and function in translation and energy metabolism. Innovation and Conclusion: Our work showed for the first time that K48 ubiquitin modifies a large fraction of oxidized proteins, demonstrating that oxidized proteins can be targeted by the ubiquitin/proteasome system. We suggest that oxidized proteins that rapidly accumulate during stress are subsequently ubiquitinated and degraded during the late phase of the response. This delay between oxidation and ubiquitination may be necessary for reprogramming protein dynamics, restoring proteostasis, and resuming cell growth.
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Affiliation(s)
- Sandhya Manohar
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Samson Jacob
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Jade Wang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Keira A. Wiechecki
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Hiromi W.L. Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vanessa Simões
- Department of Biology, Duke University, Durham, North Carolina
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christine Vogel
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, North Carolina
- Address correspondence to: Dr. Gustavo M. Silva, Department of Biology, Duke University, 130 Science Drive, Durham, NC 27708
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29
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Twomey EC, Ji Z, Wales TE, Bodnar NO, Ficarro SB, Marto JA, Engen JR, Rapoport TA. Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Science 2019; 365:science.aax1033. [PMID: 31249135 DOI: 10.1126/science.aax1033] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/13/2019] [Indexed: 12/13/2022]
Abstract
The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear. Here, we report cryo-electron microscopy structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and polyubiquitinated substrate. The structures show that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule. The unfolded ubiquitin molecule binds to Npl4 and projects its N-terminal segment through both hexameric ATPase rings. Pore loops of the second ring form a staircase that acts as a conveyer belt to move the polypeptide through the central pore. Inducing the unfolding of ubiquitin allows the Cdc48 ATPase complex to process a broad range of substrates.
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Affiliation(s)
- Edward C Twomey
- Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Zhejian Ji
- Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Nicholas O Bodnar
- Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Tom A Rapoport
- Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA.
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Nahar A, Fu X, Polovin G, Orth JD, Park S. Two alternative mechanisms regulate the onset of chaperone-mediated assembly of the proteasomal ATPases. J Biol Chem 2019; 294:6562-6577. [PMID: 30814255 DOI: 10.1074/jbc.ra118.006298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/23/2019] [Indexed: 01/03/2023] Open
Abstract
The proteasome holoenzyme is a molecular machine that degrades most proteins in eukaryotes. In the holoenzyme, its heterohexameric ATPase injects protein substrates into the proteolytic core particle, where degradation occurs. The heterohexameric ATPase, referred to as 'Rpt ring', assembles through six ATPase subunits (Rpt1-Rpt6) individually binding to specific chaperones (Rpn14, Nas6, Nas2, and Hsm3). Here, our findings suggest that the onset of Rpt ring assembly can be regulated by two alternative mechanisms. Excess Rpt subunits relative to their chaperones are sequestered into multiple puncta specifically during early-stage Rpt ring assembly. Sequestration occurs during stressed conditions, for example heat, which transcriptionally induce Rpt subunits. When the free Rpt pool is limited experimentally, Rpt subunits are competent for proteasome assembly even without their cognate chaperones. These data suggest that sequestration may regulate amounts of individual Rpt subunits relative to their chaperones, allowing for proper onset of Rpt ring assembly. Indeed, Rpt subunits in the puncta can later resume their assembly into the proteasome. Intriguingly, when proteasome assembly resumes in stressed cells or is ongoing in unstressed cells, excess Rpt subunits are recognized by an alternative mechanism-degradation by the proteasome holoenzyme itself. Rpt subunits undergo proteasome assembly until the holoenzyme complex is generated at a sufficient level. The fully-formed holoenzyme can then degrade any remaining excess Rpt subunits, thereby regulating its own Rpt ring assembly. These two alternative mechanisms, degradation and sequestration of Rpt subunits, may help control the onset of chaperone-mediated Rpt ring assembly, thereby promoting proper proteasome holoenzyme formation.
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Affiliation(s)
- Asrafun Nahar
- From the Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309
| | - Xinyi Fu
- From the Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309
| | - George Polovin
- From the Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309
| | - James D Orth
- From the Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309
| | - Soyeon Park
- From the Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309
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31
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Aprile-Garcia F, Tomar P, Hummel B, Khavaran A, Sawarkar R. Nascent-protein ubiquitination is required for heat shock–induced gene downregulation in human cells. Nat Struct Mol Biol 2019; 26:137-146. [DOI: 10.1038/s41594-018-0182-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022]
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32
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Meza-Gutierrez F, Simsek D, Toczyski DP. A genetic approach to study polyubiquitination in Saccharomyces cerevisiae. Methods Enzymol 2019; 618:49-72. [DOI: 10.1016/bs.mie.2018.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP. Genetic analysis reveals functions of atypical polyubiquitin chains. eLife 2018; 7:42955. [PMID: 30547882 PMCID: PMC6305200 DOI: 10.7554/elife.42955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022] Open
Abstract
Although polyubiquitin chains linked through all lysines of ubiquitin exist, specific functions are well-established only for lysine-48 and lysine-63 linkages in Saccharomyces cerevisiae. To uncover pathways regulated by distinct linkages, genetic interactions between a gene deletion library and a panel of lysine-to-arginine ubiquitin mutants were systematically identified. The K11R mutant had strong genetic interactions with threonine biosynthetic genes. Consistently, we found that K11R mutants import threonine poorly. The K11R mutant also exhibited a strong genetic interaction with a subunit of the anaphase-promoting complex (APC), suggesting a role in cell cycle regulation. K11-linkages are important for vertebrate APC function, but this was not previously described in yeast. We show that the yeast APC also modifies substrates with K11-linkages in vitro, and that those chains contribute to normal APC-substrate turnover in vivo. This study reveals comprehensive genetic interactomes of polyubiquitin chains and characterizes the role of K11-chains in two biological pathways.
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Affiliation(s)
- Fernando Meza Gutierrez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Arda Mizrak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Raquel Tamse-Kuehn
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Curt Palm
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - David P Toczyski
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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34
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Ubiquitin-dependent switch during assembly of the proteasomal ATPases mediated by Not4 ubiquitin ligase. Proc Natl Acad Sci U S A 2018; 115:13246-13251. [PMID: 30530678 DOI: 10.1073/pnas.1805353115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the proteasome holoenzyme, the hexameric ATPases (Rpt1-Rpt6) enable degradation of ubiquitinated proteins by unfolding and translocating them into the proteolytic core particle. During early-stage proteasome assembly, individual Rpt proteins assemble into the hexameric "Rpt ring" through binding to their cognate chaperones: Nas2, Hsm3, Nas6, and Rpn14. Here, we show that Rpt ring assembly employs a specific ubiquitination-mediated control. An E3 ligase, Not4, selectively ubiquitinates Rpt5 during Rpt ring assembly. To access Rpt5, Not4 competes with Nas2 until the penultimate step and then with Hsm3 at the final step of Rpt ring completion. Using the known Rpt-chaperone cocrystal structures, we show that Not4-mediated ubiquitination sites in Rpt5 are obstructed by Nas2 and Hsm3. Thus, Not4 can distinguish a Rpt ring that matures without these chaperones, based on its accessibility to Rpt5. Rpt5 ubiquitination does not destabilize the ring but hinders incorporation of incoming subunits-Rpn1 ubiquitin receptor and Ubp6 deubiquitinase-thereby blocking progression of proteasome assembly and ubiquitin regeneration from proteasome substrates. Our findings reveal an assembly checkpoint where Not4 monitors chaperone actions during hexameric ATPase ring assembly, thereby ensuring the accuracy of proteasome holoenzyme maturation.
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35
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Protein Degradation and the Pathologic Basis of Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 189:94-103. [PMID: 30312581 DOI: 10.1016/j.ajpath.2018.09.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/05/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022]
Abstract
The abundance of any protein is determined by the balance of protein synthesis and protein degradation. Regulated protein degradation has emerged as a powerful means of precisely controlling individual protein abundance within cells and is largely mediated by the ubiquitin-proteasome system (UPS). By controlling the levels of key regulatory proteins, the UPS contributes to nearly every aspect of cellular function. The UPS also functions in protein quality control, rapidly identifying and destroying misfolded or otherwise aberrant proteins that may be toxic to cells. Increasingly, we understand that dysregulation of protein degradation pathways is critical for many human diseases. Conversely, the versatility and scope of the UPS provides opportunities for therapeutic intervention. In this review, we will discuss the basic mechanisms of protein degradation by the UPS. We will then consider some paradigms of human disease related to protein degradation using selected examples. Finally, we will highlight several established and emerging therapeutic strategies based on altering pathways of protein degradation.
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36
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Mapa CE, Arsenault HE, Conti MM, Poti KE, Benanti JA. A balance of deubiquitinating enzymes controls cell cycle entry. Mol Biol Cell 2018; 29:2821-2834. [PMID: 30207830 PMCID: PMC6249862 DOI: 10.1091/mbc.e18-07-0425] [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] [Indexed: 12/11/2022] Open
Abstract
Protein degradation during the cell cycle is controlled by the opposing activities of ubiquitin ligases and deubiquitinating enzymes (DUBs). Although the functions of ubiquitin ligases in the cell cycle have been studied extensively, the roles of DUBs in this process are less well understood. Here, we used an overexpression screen to examine the specificities of each of the 21 DUBs in budding yeast for 37 cell cycle-regulated proteins. We find that DUBs up-regulate specific subsets of proteins, with five DUBs regulating the greatest number of targets. Overexpression of Ubp10 had the largest effect, stabilizing 15 targets and delaying cells in mitosis. Importantly, UBP10 deletion decreased the stability of the cell cycle regulator Dbf4, delayed the G1/S transition, and slowed proliferation. Remarkably, deletion of UBP10 together with deletion of four additional DUBs restored proliferation to near-wild-type levels. Among this group, deletion of the proteasome-associated DUB Ubp6 alone reversed the G1/S delay and restored the stability of Ubp10 targets in ubp10Δ cells. Similarly, deletion of UBP14, another DUB that promotes proteasomal activity, rescued the proliferation defect in ubp10Δ cells. Our results suggest that DUBs function through a complex genetic network in which their activities are coordinated to facilitate accurate cell cycle progression.
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Affiliation(s)
- Claudine E Mapa
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Heather E Arsenault
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Michelle M Conti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Kristin E Poti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Jennifer A Benanti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605
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37
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Farrawell NE, Lambert-Smith I, Mitchell K, McKenna J, McAlary L, Ciryam P, Vine KL, Saunders DN, Yerbury JJ. SOD1 A4V aggregation alters ubiquitin homeostasis in a cell model of ALS. J Cell Sci 2018; 131:jcs.209122. [PMID: 29748379 DOI: 10.1242/jcs.209122] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 05/01/2018] [Indexed: 12/11/2022] Open
Abstract
A hallmark of amyotrophic lateral sclerosis (ALS) pathology is the accumulation of ubiquitylated protein inclusions within motor neurons. Recent studies suggest the sequestration of ubiquitin (Ub) into inclusions reduces the availability of free Ub, which is essential for cellular function and survival. However, the dynamics of the Ub landscape in ALS have not yet been described. Here, we show that Ub homeostasis is altered in a cell model of ALS induced by expressing mutant SOD1 (SOD1A4V). By monitoring the distribution of Ub in cells expressing SOD1A4V, we show that Ub is present at the earliest stages of SOD1A4V aggregation, and that cells containing SOD1A4V aggregates have greater ubiquitin-proteasome system (UPS) dysfunction. Furthermore, SOD1A4V aggregation is associated with the redistribution of Ub and depletion of the free Ub pool. Ubiquitomics analysis indicates that expression of SOD1A4V is associated with a shift of Ub to a pool of supersaturated proteins, including those associated with oxidative phosphorylation and metabolism, corresponding with altered mitochondrial morphology and function. Taken together, these results suggest that misfolded SOD1 contributes to UPS dysfunction and that Ub homeostasis is an important target for monitoring pathological changes in ALS.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Natalie E Farrawell
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
| | - Isabella Lambert-Smith
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
| | - Kristen Mitchell
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
| | - Jessie McKenna
- School of Medical Sciences, Faculty of Medicine, UNSW Australia 2052
| | - Luke McAlary
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522.,Department of Physics & Astronomy, University of British Columbia, Vancouver, British Columbia, Canada V6T 2B5
| | - Prajwal Ciryam
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.,Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208-3500, USA.,Department of Neurology, Columbia University College of Physicians & Surgeons, New York, NY 10032-3784, USA
| | - Kara L Vine
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
| | - Darren N Saunders
- School of Medical Sciences, Faculty of Medicine, UNSW Australia 2052
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522 .,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
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Chen H, Sirupangi T, Wu ZH, Johnson DL, Laribee RN. The conserved RNA recognition motif and C3H1 domain of the Not4 ubiquitin ligase regulate in vivo ligase function. Sci Rep 2018; 8:8163. [PMID: 29802328 PMCID: PMC5970261 DOI: 10.1038/s41598-018-26576-1] [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: 11/17/2017] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
The Ccr4-Not complex controls RNA polymerase II (Pol II) dependent gene expression and proteasome function. The Not4 ubiquitin ligase is a Ccr4-Not subunit that has both a RING domain and a conserved RNA recognition motif and C3H1 domain (referred to as the RRM-C domain) with unknown function. We demonstrate that while individual Not4 RING or RRM-C mutants fail to replicate the proteasomal defects found in Not4 deficient cells, mutation of both exhibits a Not4 loss of function phenotype. Transcriptome analysis revealed that the Not4 RRM-C affects a specific subset of Pol II-regulated genes, including those involved in transcription elongation, cyclin-dependent kinase regulated nutrient responses, and ribosomal biogenesis. The Not4 RING, RRM-C, or RING/RRM-C mutations cause a generalized increase in Pol II binding at a subset of these genes, yet their impact on gene expression does not always correlate with Pol II recruitment which suggests Not4 regulates their expression through additional mechanisms. Intriguingly, we find that while the Not4 RRM-C is dispensable for Ccr4-Not association with RNA Pol II, the Not4 RING domain is required for these interactions. Collectively, these data elucidate previously unknown roles for the conserved Not4 RRM-C and RING domains in regulating Ccr4-Not dependent functions in vivo.
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Affiliation(s)
- Hongfeng Chen
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, 38163, United States of America
| | - Tirupataiah Sirupangi
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, 38163, United States of America
| | - Zhao-Hui Wu
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, 38163, United States of America
| | - Daniel L Johnson
- Molecular Bioinformatics Core and the University of Tennessee Health Science Center Office of Research, University of Tennessee Health Science Center, Memphis, TN, 38163, United States of America
| | - R Nicholas Laribee
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, 38163, United States of America.
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Steinbuck MP, Arakcheeva K, Winandy S. Novel TCR-Mediated Mechanisms of Notch Activation and Signaling. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 200:997-1007. [PMID: 29288204 PMCID: PMC5854196 DOI: 10.4049/jimmunol.1700070] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 11/22/2017] [Indexed: 01/04/2023]
Abstract
The Notch receptor is an evolutionarily highly conserved transmembrane protein that is essential to a wide spectrum of cellular systems. Notch signaling is especially important to T cell development, and its deregulation leads to leukemia. Although not well characterized, it continues to play an integral role in peripheral T cells, in which a unique mode of Notch activation can occur. In contrast to canonical Notch activation initiated by adjacent ligand-expressing cells, TCR stimulation is sufficient to induce Notch signaling. However, the interactions between these two pathways have not been defined. In this article, we show that Notch activation occurs in peripheral T cells within a few hours post-TCR stimulation and is required for optimal T cell activation. Using a panel of inhibitors against components of the TCR signaling cascade, we demonstrate that Notch activation is facilitated through initiation of protein kinase C-induced ADAM activity. Moreover, our data suggest that internalization of Notch via endocytosis plays a role in this process. Although ligand-mediated Notch stimulation relies on mechanical pulling forces that disrupt the autoinhibitory domain of Notch, we hypothesized that, in T cells in the absence of ligands, these conformational changes are induced through chemical adjustments in the endosome, causing alleviation of autoinhibition and receptor activation. Thus, T cells may have evolved a unique method of Notch receptor activation, which is described for the first time, to our knowledge, in this article.
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Affiliation(s)
- Martin Peter Steinbuck
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Ksenia Arakcheeva
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Susan Winandy
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
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40
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Simões T, Schuster R, den Brave F, Escobar-Henriques M. Cdc48 regulates a deubiquitylase cascade critical for mitochondrial fusion. eLife 2018; 7:30015. [PMID: 29309037 PMCID: PMC5798933 DOI: 10.7554/elife.30015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/04/2018] [Indexed: 12/27/2022] Open
Abstract
Cdc48/p97, a ubiquitin-selective chaperone, orchestrates the function of E3 ligases and deubiquitylases (DUBs). Here, we identify a new function of Cdc48 in ubiquitin-dependent regulation of mitochondrial dynamics. The DUBs Ubp12 and Ubp2 exert opposing effects on mitochondrial fusion and cleave different ubiquitin chains on the mitofusin Fzo1. We demonstrate that Cdc48 integrates the activities of these two DUBs, which are themselves ubiquitylated. First, Cdc48 promotes proteolysis of Ubp12, stabilizing pro-fusion ubiquitylation on Fzo1. Second, loss of Ubp12 stabilizes Ubp2 and thereby facilitates removal of ubiquitin chains on Fzo1 inhibiting fusion. Thus, Cdc48 synergistically regulates the ubiquitylation status of Fzo1, allowing to control the balance between activation or repression of mitochondrial fusion. In conclusion, we unravel a new cascade of ubiquitylation events, comprising Cdc48 and two DUBs, fine-tuning the fusogenic activity of Fzo1. Mitochondria are little compartments within a cell that produce the energy needed for most biological processes. Each cell possesses several mitochondria, which can fuse together and then break again into smaller units. This fusion process is essential for cellular health. Two proteins in the cell have a major role in controlling mitochondrial fusion: Ubp12 and Ubp2. Ubp12 prevents fusion, while Ubp2 activates it. These molecules carry out their roles by acting on a third protein called mitofusin, which is a key gatekeeper of the fusion mechanism. Cells often ‘tag’ proteins with small molecules called ubiquitin to change the protein’s role and how it interacts with other cellular structures. Depending on how they are ‘tagged’, mitofusins can exist in two forms. One type of tagging means that the protein then promotes fusion of the mitochondria; the other leads to the mitofusin being destroyed by the cell. It is still unclear how Ubp12, Ubp2 and the different forms of mitofusins interact with each other to finely control mitochondrial fusion. Here, Simões, Schuster et al. clarify these interactions in yeast and show how these proteins are themselves regulated. Ubp2 promotes fusion by attaching to the mitofusin that is labeled to be destroyed, and removing this tag: the mitofusin will then not be degraded, and can promote fusion. Ubp12 prevents fusion through two mechanisms. First, it can remove the ‘pro-fusion’ tag on the mitofusin that prompts mitochondrial fusion. Second, Simões, Schuster et al. now show that Ubp12 also inhibits Ubp2 and its fusion-promoting activity. In turn, the experiments reveal that a master protein called Cdc48 can control the entire Ubp12-Ubp2-mitofusin pathway. Cdc48 directly represses Ubp12 and therefore its anti-fusion activity. This inhibition also leaves Ubp2 free to stimulate fusion through its action on mitofusin. The molecules involved in controlling mitochondrial fusion in yeast are very similar to the ones in people. In humans, improper regulation of mitofusins causes an incurable disease of the nerves and the brain called Charcot-Marie-Tooth 2A. Understanding how the fusion of mitochondria is controlled can lead to new drug discoveries.
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Affiliation(s)
- Tânia Simões
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Ramona Schuster
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Fabian den Brave
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Mafalda Escobar-Henriques
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
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41
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Huseinovic A, van Dijk M, Vermeulen NPE, van Leeuwen F, Kooter JM, Vos JC. Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine. Toxicol In Vitro 2017; 47:259-268. [PMID: 29258884 DOI: 10.1016/j.tiv.2017.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/05/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
Abstract
Post-translational protein modification by addition or removal of the small polypeptide ubiquitin is involved in a range of critical cellular processes, like proteasomal protein degradation, DNA repair, gene expression, internalization of membrane proteins, and drug sensitivity. We recently identified genes important for acetaminophen (APAP) toxicity in a comprehensive screen and our findings suggested that a small set of yeast strains carrying deletions of ubiquitin-related genes can be informative for drug toxicity profiling. In yeast, approximately 20 different deubiquitinating enzymes (DUBs) have been identified, of which only one is essential for viability. We investigated whether the toxicity profile of DUB deletion yeast strains would be informative about the toxicological mode of action of APAP. A set of DUB deletion strains was tested for sensitivity and resistance to a diverse series of compounds, including APAP, quinine, ibuprofen, rapamycin, cycloheximide, cadmium, peroxide and amino acids and a cluster analysis was performed. Most DUB deletion strains showed an altered growth pattern when exposed to these compounds by being either more sensitive or more resistant than WT. Toxicity profiling of the DUB strains revealed a remarkable overlap between the amino acid tyrosine and acetaminophen (APAP), but not its stereoisomer AMAP. Furthermore, co-exposure of cells to both APAP and tyrosine showed an enhancement of the cellular growth inhibition, suggesting that APAP and tyrosine have a similar mode of action.
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Affiliation(s)
- Angelina Huseinovic
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Marc van Dijk
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Nico P E Vermeulen
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Jan M Kooter
- AIMMS, Department of Molecular Cell Biology, Section Genetics, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - J Chris Vos
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands.
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42
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de Poot SAH, Tian G, Finley D. Meddling with Fate: The Proteasomal Deubiquitinating Enzymes. J Mol Biol 2017; 429:3525-3545. [PMID: 28988953 DOI: 10.1016/j.jmb.2017.09.015] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 01/06/2023]
Abstract
Three deubiquitinating enzymes-Rpn11, Usp14, and Uch37-are associated with the proteasome regulatory particle. These enzymes allow proteasomes to remove ubiquitin from substrates before they are translocated into the core particle to be degraded. Although the translocation channel is too narrow for folded proteins, the force of translocation unfolds them mechanically. As translocation proceeds, ubiquitin chains bound to substrate are drawn to the channel's entry port, where they can impede further translocation. Rpn11, situated over the port, can remove these chains without compromising degradation because substrates must be irreversibly committed to degradation before Rpn11 acts. This coupling between deubiquitination and substrate degradation is ensured by the Ins-1 loop of Rpn11, which controls ubiquitin access to its catalytic site. In contrast to Rpn11, Usp14 and Uch37 can rescue substrates from degradation by promoting substrate dissociation from the proteasome prior to the commitment step. Uch37 is unique in being a component of both the proteasome and a second multisubunit assembly, the INO80 complex. However, only recruitment into the proteasome activates Uch37. Recruitment to the proteasome likewise activates Usp14. However, the influence of Usp14 on the proteasome depends on the substrate, due to its marked preference for proteins that carry multiple ubiquitin chains. Usp14 exerts complex control over the proteasome, suppressing proteasome activity even when inactive in deubiquitination. A major challenge for the field will be to elucidate the specificities of Rpn11, Usp14, and Uch37 in greater depth, employing not only model in vitro substrates but also their endogenous targets.
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Affiliation(s)
- Stefanie A H de Poot
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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43
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Gemayel R, Yang Y, Dzialo MC, Kominek J, Vowinckel J, Saels V, Van Huffel L, van der Zande E, Ralser M, Steensels J, Voordeckers K, Verstrepen KJ. Variable repeats in the eukaryotic polyubiquitin gene ubi4 modulate proteostasis and stress survival. Nat Commun 2017; 8:397. [PMID: 28855501 PMCID: PMC5577197 DOI: 10.1038/s41467-017-00533-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/05/2017] [Indexed: 01/23/2023] Open
Abstract
Ubiquitin conjugation signals for selective protein degradation by the proteasome. In eukaryotes, ubiquitin is encoded both as a monomeric ubiquitin unit fused to a ribosomal gene and as multiple ubiquitin units in tandem. The polyubiquitin gene is a unique, highly conserved open reading frame composed solely of tandem repeats, yet it is still unclear why cells utilize this unusual gene structure. Using the Saccharomyces cerevisiae UBI4 gene, we show that this multi-unit structure allows cells to rapidly produce large amounts of ubiquitin needed to respond to sudden stress. The number of ubiquitin units encoded by UBI4 influences cellular survival and the rate of ubiquitin-proteasome system (UPS)-mediated proteolysis following heat stress. Interestingly, the optimal number of repeats varies under different types of stress indicating that natural variation in repeat numbers may optimize the chance for survival. Our results demonstrate how a variable polycistronic transcript provides an evolutionary alternative for gene copy number variation. Eukaryotic cells rely on the ubiquitin-proteasome system for selective degradation of proteins, a process vital to organismal fitness. Here the authors show that the number of repeats in the polyubiquitin gene is evolutionarily unstable within and between yeast species, and that this variability may tune the cell’s capacity to respond to sudden environmental perturbations.
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Affiliation(s)
- Rita Gemayel
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Yudi Yang
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Maria C Dzialo
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Jacek Kominek
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Veerle Saels
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Leen Van Huffel
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Elisa van der Zande
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis Court Road, Cambridge, CB2 1GA, UK.,The Francis Crick Institute, 1 Midland Rd, London, NW11AT, UK
| | - Jan Steensels
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Karin Voordeckers
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Kevin J Verstrepen
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium. .,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium.
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44
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Goto GH, Ogi H, Biswas H, Ghosh A, Tanaka S, Sugimoto K. Two separate pathways regulate protein stability of ATM/ATR-related protein kinases Mec1 and Tel1 in budding yeast. PLoS Genet 2017; 13:e1006873. [PMID: 28827813 PMCID: PMC5578694 DOI: 10.1371/journal.pgen.1006873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 08/31/2017] [Accepted: 06/15/2017] [Indexed: 11/18/2022] Open
Abstract
Checkpoint signaling requires two conserved phosphatidylinositol 3-kinase-related protein kinases (PIKKs): ATM and ATR. In budding yeast, Tel1 and Mec1 correspond to ATM and ATR, respectively. The Tel2-Tti1-Tti2 (TTT) complex connects to the Rvb1-Rvb2-Tah1-Pih1 (R2TP) complex for the protein stability of PIKKs; however, TTT-R2TP interaction only partially mediates ATM and ATR protein stabilization. How TTT controls protein stability of ATM and ATR remains to be precisely determined. Here we show that Asa1, like Tel2, plays a major role in stabilization of newly synthesized Mec1 and Tel1 proteins whereas Pih1 contributes to Mec1 and Tel1 stability at high temperatures. Although Asa1 and Pih1 both interact with Tel2, no Asa1-Pih1 interaction is detected. Pih1 is distributed in both the cytoplasm and nucleus wheres Asa1 localizes largely in the cytoplasm. Asa1 and Pih1 are required for proper DNA damage checkpoint signaling. Our findings provide a model in which two different Tel2 pathways promote protein stabilization of Mec1 and Tel1 in budding yeast.
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Affiliation(s)
- Greicy H. Goto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Hiroo Ogi
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Himadri Biswas
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Avik Ghosh
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
| | - Seiji Tanaka
- Division of Microbial Genetics, National Institute of Genetics, and Department of Genetics, School of Life Science, Graduate School for Advanced Studies, (SOKENDAI), Mishima, Shizuoka, Japan
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States of America
- * E-mail:
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45
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The Logic of the 26S Proteasome. Cell 2017; 169:792-806. [PMID: 28525752 DOI: 10.1016/j.cell.2017.04.023] [Citation(s) in RCA: 557] [Impact Index Per Article: 79.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 12/14/2022]
Abstract
The ubiquitin proteasome pathway is responsible for most of the protein degradation in mammalian cells. Rates of degradation by this pathway have generally been assumed to be determined by rates of ubiquitylation. However, recent studies indicate that proteasome function is also tightly regulated and determines whether a ubiquitylated protein is destroyed or deubiquitylated and survives longer. This article reviews recent advances in our understanding of the proteasome's multistep ATP-dependent mechanism, its biochemical and structural features that ensure efficient proteolysis and ubiquitin recycling while preventing nonselective proteolysis, and the regulation of proteasome activity by interacting proteins and subunit modifications, especially phosphorylation.
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46
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Abstract
Autophagy and the ubiquitin-proteasome system are the two major quality control pathways responsible for cellular homeostasis. As such, they provide protection against age-associated changes and a plethora of human diseases. Ubiquitination is utilized as a degradation signal by both systems, albeit in different ways, to mark cargoes for proteasomal and lysosomal degradation. Both systems intersect and communicate at multiple points to coordinate their actions in proteostasis and organelle homeostasis. This review summarizes molecular details of how proteasome and autophagy pathways are functionally interconnected in cells and indicates common principles and nodes of communication that can be therapeutically exploited.
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Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University, 60598 Frankfurt am Main, Germany; .,Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
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47
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Doshi A, Sharma M, Prabha CR. Structural changes induced by L50P and I61T single mutations of ubiquitin affect cell cycle progression while impairing its regulatory and degradative functions in Saccharomyces cerevisiae. Int J Biol Macromol 2017; 99:128-140. [DOI: 10.1016/j.ijbiomac.2017.02.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/07/2017] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
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48
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Liu J, Zhang C. The equilibrium of ubiquitination and deubiquitination at PLK1 regulates sister chromatid separation. Cell Mol Life Sci 2017; 74:2127-2134. [PMID: 28188342 PMCID: PMC11107562 DOI: 10.1007/s00018-017-2457-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 12/15/2022]
Abstract
PLK1 regulates almost every aspect of mitotic events, including mitotic entry, spindle assembly, chromosome alignment, sister chromatid segregation, metaphase-anaphase transition, cytokinesis, etc. In regulating the chromosome alignment and sister chromatid segregation, PLK1 has to be localized to and removed from kinetochores at the right times, and the underlying mechanism that regulates PLK1 both spatially and temporally only became clearer recently. It has been found that deubiquitination and ubiquitination of PLK1 are responsible for its localization to and dissociation from the kinetochores, respectively. The equilibrium of this ubiquitination and deubiquitination plays an important role in regulating proper chromosome alignment and timely sister chromatid segregation. Here, we summarize and discuss the recent findings in investigating the spatial and temporal regulation of PLK1 during chromosome alignment and sister chromatid segregation.
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Affiliation(s)
- Junjun Liu
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, 91768, USA.
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100871, China.
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49
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Ubiquitylation of p62/sequestosome1 activates its autophagy receptor function and controls selective autophagy upon ubiquitin stress. Cell Res 2017; 27:657-674. [PMID: 28322253 DOI: 10.1038/cr.2017.40] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/06/2016] [Accepted: 01/22/2017] [Indexed: 12/16/2022] Open
Abstract
Alterations in cellular ubiquitin (Ub) homeostasis, known as Ub stress, feature and affect cellular responses in multiple conditions, yet the underlying mechanisms are incompletely understood. Here we report that autophagy receptor p62/sequestosome-1 interacts with E2 Ub conjugating enzymes, UBE2D2 and UBE2D3. Endogenous p62 undergoes E2-dependent ubiquitylation during upregulation of Ub homeostasis, a condition termed as Ub+ stress, that is intrinsic to Ub overexpression, heat shock or prolonged proteasomal inhibition by bortezomib, a chemotherapeutic drug. Ubiquitylation of p62 disrupts dimerization of the UBA domain of p62, liberating its ability to recognize polyubiquitylated cargoes for selective autophagy. We further demonstrate that this mechanism might be critical for autophagy activation upon Ub+ stress conditions. Delineation of the mechanism and regulatory roles of p62 in sensing Ub stress and controlling selective autophagy could help to understand and modulate cellular responses to a variety of endogenous and environmental challenges, potentially opening a new avenue for the development of therapeutic strategies against autophagy-related maladies.
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50
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Huseinovic A, van Leeuwen JS, van Welsem T, Stulemeijer I, van Leeuwen F, Vermeulen NPE, Kooter JM, Vos JC. The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae. PLoS One 2017; 12:e0173573. [PMID: 28291796 PMCID: PMC5349473 DOI: 10.1371/journal.pone.0173573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/23/2017] [Indexed: 02/05/2023] Open
Abstract
Acetaminophen (APAP), although considered a safe drug, is one of the major causes of acute liver failure by overdose, and therapeutic chronic use can cause serious health problems. Although the reactive APAP metabolite N-acetyl-p-benzoquinoneimine (NAPQI) is clearly linked to liver toxicity, toxicity of APAP is also found without drug metabolism of APAP to NAPQI. To get more insight into mechanisms of APAP toxicity, a genome-wide screen in Saccharomyces cerevisiae for APAP-resistant deletion strains was performed. In this screen we identified genes related to the DNA damage response. Next, we investigated the link between genotype and APAP-induced toxicity or resistance by performing a more detailed screen with a library containing mutants of 1522 genes related to nuclear processes, like DNA repair and chromatin remodelling. We identified 233 strains that had an altered growth rate relative to wild type, of which 107 showed increased resistance to APAP and 126 showed increased sensitivity. Gene Ontology analysis identified ubiquitin homeostasis, regulation of transcription of RNA polymerase II genes, and the mitochondria-to-nucleus signalling pathway to be associated with APAP resistance, while histone exchange and modification, and vesicular transport were connected to APAP sensitivity. Indeed, we observed a link between ubiquitin levels and APAP resistance, whereby ubiquitin deficiency conferred resistance to APAP toxicity while ubiquitin overexpression resulted in sensitivity. The toxicity profile of various chemicals, APAP, and its positional isomer AMAP on a series of deletion strains with ubiquitin deficiency showed a unique resistance pattern for APAP. Furthermore, exposure to APAP increased the level of free ubiquitin and influenced the ubiquitination of proteins. Together, these results uncover a role for ubiquitin homeostasis in APAP-induced toxicity.
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Affiliation(s)
- Angelina Huseinovic
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jolanda S. van Leeuwen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris Stulemeijer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jan M. Kooter
- AIMMS-Department of Molecular Cell Biology, Section Genetics, VU University Amsterdam, Amsterdam, The Netherlands
| | - J. Chris Vos
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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