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Akizuki Y, Kaypee S, Ohtake F, Ikeda F. The emerging roles of non-canonical ubiquitination in proteostasis and beyond. J Cell Biol 2024; 223:e202311171. [PMID: 38517379 PMCID: PMC10959754 DOI: 10.1083/jcb.202311171] [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: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Ubiquitin regulates various cellular functions by posttranslationally modifying substrates with diverse ubiquitin codes. Recent discoveries of new ubiquitin chain topologies, types of bonds, and non-protein substrates have substantially expanded the complexity of the ubiquitin code. Here, we describe the ubiquitin system covering the basic principles and recent discoveries related to mechanisms, technologies, and biological importance.
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Affiliation(s)
- Yoshino Akizuki
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Stephanie Kaypee
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Fumiyo Ikeda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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2
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Gomez-Diaz C, Jonsson G, Schodl K, Deszcz L, Bestehorn A, Eislmayr K, Almagro J, Kavirayani A, Seida M, Fennell LM, Hagelkruys A, Kovarik P, Penninger JM, Ikeda F. The ubiquitin ligase HOIL-1L regulates immune responses by interacting with linear ubiquitin chains. iScience 2021; 24:103241. [PMID: 34755089 PMCID: PMC8561004 DOI: 10.1016/j.isci.2021.103241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/30/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022] Open
Abstract
The Linear Ubiquitin Chain Assembly Complex (LUBAC), composed of HOIP, HOIL-1L, and SHARPIN, promotes tumor necrosis factor (TNF)-dependent NF-κB signaling in diverse cell types. HOIL-1L contains an Npl4 Zinc Finger (NZF) domain that specifically recognizes linear ubiquitin chains, but its physiological role in vivo has remained unclear. Here, we demonstrate that the HOIL-1L NZF domain has important regulatory functions in inflammation and immune responses in mice. We generated knockin mice (Hoil-1lT201A;R208A/T201A;R208A) expressing a HOIL-1L NZF mutant and observed attenuated responses to TNF- and LPS-induced shock, including prolonged survival, stabilized body temperature, reduced cytokine production, and liver damage markers. Cells derived from Hoil-1lT201A;R208A/T201A;R208A mice show reduced TNF-dependent NF-κB activation and incomplete recruitment of HOIL-1L into TNF Receptor (TNFR) Complex I. We further show that HOIL-1L NZF cooperates with SHARPIN to prevent TNFR-dependent skin inflammation. Collectively, our data suggest that linear ubiquitin-chain binding by HOIL-1L regulates immune responses and inflammation in vivo. An RBR-type E3 ligase HOIL-1L decodes linear ubiquitin chains via the NZF domain HOIL-1L NZF is essential for proper responses to LPS and TNF-induced shock in mice Intact HOIL-1L NZF is required for activating the TNF-induced NF-kB pathway HOIL-1L NZF cooperates with SHARPIN to control inflammation in mice
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Affiliation(s)
- Carlos Gomez-Diaz
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Gustav Jonsson
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Katrin Schodl
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Luiza Deszcz
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Annika Bestehorn
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Kevin Eislmayr
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Jorge Almagro
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Anoop Kavirayani
- Vienna Biocenter Core Facilities (VBCF), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Mayu Seida
- Medical Institute of Bioregulation (MIB), Kyushu University, Fukuoka 812-8582, Japan
| | - Lilian M Fennell
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Astrid Hagelkruys
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Pavel Kovarik
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Josef M Penninger
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.,Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Fumiyo Ikeda
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.,Medical Institute of Bioregulation (MIB), Kyushu University, Fukuoka 812-8582, Japan
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3
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Fennell LM, Gomez Diaz C, Deszcz L, Kavirayani A, Hoffmann D, Yanagitani K, Schleiffer A, Mechtler K, Hagelkruys A, Penninger J, Ikeda F. Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling. EMBO J 2020; 39:e103303. [PMID: 33215740 DOI: 10.15252/embj.2019103303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/29/2020] [Accepted: 10/12/2020] [Indexed: 01/01/2023] Open
Abstract
HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), is a critical regulator of inflammation. However, how HOIP itself is regulated to control inflammatory responses is unclear. Here, we discover that site-specific ubiquitination of K784 within human HOIP promotes tumor necrosis factor (TNF)-induced inflammatory signaling. A HOIP K784R mutant is catalytically active but shows reduced induction of an NF-κB reporter relative to wild-type HOIP. HOIP K784 is evolutionarily conserved, equivalent to HOIP K778 in mice. We generated HoipK778R/K778R knock-in mice, which show no overt developmental phenotypes; however, in response to TNF, HoipK778R/K778R mouse embryonic fibroblasts display mildly suppressed NF-κB activation and increased apoptotic markers. On the other hand, HOIP K778R enhances the TNF-induced formation of TNFR complex II and an interaction between TNFR complex II and LUBAC. Loss of the LUBAC component SHARPIN leads to embryonic lethality in HoipK778R/K778R mice, which is rescued by knockout of TNFR1. We propose that site-specific ubiquitination of HOIP regulates a LUBAC-dependent switch between survival and apoptosis in TNF signaling.
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Affiliation(s)
- Lilian M Fennell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Carlos Gomez Diaz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Luiza Deszcz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Anoop Kavirayani
- Vienna Biocenter Core Facilities (VBCF), Vienna Biocenter (VBC), Vienna, Austria
| | - David Hoffmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Kota Yanagitani
- Medical Institute of Bioregulation (MIB), Kyushu University, Fukuoka, Japan
| | - Alexander Schleiffer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Josef Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,Medical Institute of Bioregulation (MIB), Kyushu University, Fukuoka, Japan
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4
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Verma S, Shukla S, Pandey M, MacLennan GT, Gupta S. Differentially Expressed Genes and Molecular Pathways in an Autochthonous Mouse Prostate Cancer Model. Front Genet 2019; 10:235. [PMID: 30972102 PMCID: PMC6445055 DOI: 10.3389/fgene.2019.00235] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/04/2019] [Indexed: 12/17/2022] Open
Abstract
Prostate cancer remains a major public health problem and the second leading cause of cancer-related deaths in men in the United States. The present study aims to understand the molecular pathway(s) of prostate cancer which is essential for early detection and treatment. Dorsolateral prostate from 20 week transgenic adenocarcinoma of the mouse prostate (TRAMP) mice, which spontaneously develops prostate cancer and recapitulates human disease and age-matched non-transgenic littermates were utilized for microarray analysis. Mouse genome network and pathway analyses were mapped to the human genome using the Ingenuity Pathway Analysis (IPA) database for annotation, visualization, and integrated discovery. In total, 136 differentially expressed genes, including 32 downregulated genes and 104 upregulated genes were identified in the dorsolateral prostate of TRAMP, compared to non-transgenic mice. A subset of differentially expressed genes were validated by qRT-PCR. Alignment with human genome database identified 18 different classes of proteins, among these, 36% were connected to the nucleic acid binding, including ribosomal proteins, which play important role in protein synthesis—the most enriched pathway in the development of prostate cancer. Furthermore, the results suggest deregulation of signaling molecules (9%) and enzyme modulators (8%) affect various pathways. An imbalance in other protein classes, including transporter proteins (7%), hydrolases (6%), oxidoreductases, and cytoskeleton proteins (5%), contribute to cancer progression. Our study evaluated the underlying pathways and its connection to human prostate cancer, which may further help assess the risk of disease development and progression and identify potential targets for therapeutic intervention.
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Affiliation(s)
- Shiv Verma
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Sanjeev Shukla
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Mitali Pandey
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Vancouver Prostate Center, Vancouver, BC, Canada
| | - Gregory T MacLennan
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Sanjay Gupta
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Department of Nutrition, Case Western Reserve University, Cleveland, OH, United States.,Department of Urology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, United States.,Division of General Medical Sciences, Case Comprehensive Cancer Center, Cleveland, OH, United States
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5
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Seo J, Kim MW, Bae KH, Lee SC, Song J, Lee EW. The roles of ubiquitination in extrinsic cell death pathways and its implications for therapeutics. Biochem Pharmacol 2018; 162:21-40. [PMID: 30452908 DOI: 10.1016/j.bcp.2018.11.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/14/2018] [Indexed: 01/24/2023]
Abstract
Regulation of cell survival and death, including apoptosis and necroptosis, is important for normal development and tissue homeostasis, and disruption of these processes can cause cancer, inflammatory diseases, and degenerative diseases. Ubiquitination is a cellular process that induces proteasomal degradation by covalently attaching ubiquitin to the substrate protein. In addition to proteolytic ubiquitination, nonproteolytic ubiquitination, such as M1-linked and K63-linked ubiquitination, has been shown to be important in recent studies, which have demonstrated its function in cell signaling pathways that regulate inflammation and cell death pathways. In this review, we summarize the TRAIL- and TNF-induced death receptor signaling pathways along with recent advances in this field and illustrate how different types of ubiquitination control cell death and survival. In particular, we provide an overview of the different types of ubiquitination, target residues, and modifying enzymes, including E3 ligases and deubiquitinating enzymes. Given the relevance of these regulatory pathways in human disease, we hope that a better understanding of the regulatory mechanisms of cell death pathways will provide insights into and therapeutic strategies for related diseases.
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Affiliation(s)
- Jinho Seo
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Min Wook Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Kwang-Hee Bae
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Sang Chul Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Jaewhan Song
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
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6
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Roles of ubiquitin in autophagy and cell death. Semin Cell Dev Biol 2018; 93:125-135. [PMID: 30195063 PMCID: PMC6854449 DOI: 10.1016/j.semcdb.2018.09.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/28/2018] [Accepted: 09/03/2018] [Indexed: 01/12/2023]
Abstract
The balance between cell survival and cell death is often lost in human pathologies such as inflammation and cancer. Autophagy plays a critical role in cell survival: essential nutrients are generated by autophagy-dependent degradation and recycling of cellular garbage. On the other hand, cell death is induced by different programs, such as apoptosis, pyroptosis, and necroptosis. Emerging evidence is revealing how cell survival and cell death pathways are coordinated to determine cell fate. For instance, posttranslational modification of proteins with ubiquitin regulates many steps of autophagy and cell death pathways. In this review article, we will discuss how the ubiquitin system influences cell death and autophagy.
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7
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Fennell LM, Rahighi S, Ikeda F. Linear ubiquitin chain-binding domains. FEBS J 2018; 285:2746-2761. [PMID: 29679476 DOI: 10.1111/febs.14478] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/08/2018] [Accepted: 04/13/2018] [Indexed: 12/25/2022]
Abstract
Ubiquitin modification (ubiquitination) of target proteins can vary with respect to chain lengths, linkage type, and chain forms, such as homologous, mixed, and branched ubiquitin chains. Thus, ubiquitination can generate multiple unique surfaces on a target protein substrate. Ubiquitin-binding domains (UBDs) recognize ubiquitinated substrates, by specifically binding to these unique surfaces, modulate the formation of cellular signaling complexes and regulate downstream signaling cascades. Among the eight different homotypic chain types, Met1-linked (also termed linear) chains are the only chains in which linkage occurs on a non-Lys residue of ubiquitin. Linear ubiquitin chains have been implicated in immune responses, cell death and autophagy, and several UBDs - specific for linear ubiquitin chains - have been identified. In this review, we describe the main principles of ubiquitin recognition by UBDs, focusing on linear ubiquitin chains and their roles in biology.
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Affiliation(s)
- Lilian M Fennell
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Austria
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Health Science Campus, Chapman University, Irvine, CA, USA
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Austria
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8
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Zhang C, Shi S. Physiological and Proteomic Responses of Contrasting Alfalfa ( Medicago sativa L.) Varieties to PEG-Induced Osmotic Stress. FRONTIERS IN PLANT SCIENCE 2018; 9:242. [PMID: 29541085 PMCID: PMC5835757 DOI: 10.3389/fpls.2018.00242] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/12/2018] [Indexed: 05/23/2023]
Abstract
Drought severely limits global plant distribution and agricultural production. Elucidating the physiological and molecular mechanisms governing alfalfa stress responses will contribute to the improvement of drought tolerance in leguminous crops. In this study, the physiological and proteomic responses of two alfalfa (Medicago sativa L.) varieties contrasting in drought tolerance, Longzhong (drought-tolerant) and Gannong No. 3 (drought-sensitive), were comparatively assayed when seedlings were exposed to -1.2 MPa polyethylene glycol (PEG-6000) treatments for 15 days. The results showed that the levels of proline, malondialdehyde (MDA), hydrogen peroxide (H2O2), hydroxyl free radical (OH•) and superoxide anion free radical (O2•-) in both varieties were significantly increased, while the root activity, the superoxide dismutase (SOD) and glutathione reductase (GR) activities, and the ratios of reduced/oxidized ascorbate (AsA/DHA) and reduced/oxidized glutathione (GSH/GSSG) were significantly decreased. The soluble protein and soluble sugar contents, the total antioxidant capability (T-AOC) and the activities of peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) first increased and then decreased with the increase in treatment days. Under osmotic stress, Longzhong exhibited lower levels of MDA, H2O2, OH• and O2•- but higher levels of SOD, CAT, APX, T-AOC and ratios of AsA/DHA and GSH/GSSG compared with Gannong No.3. Using isobaric tags for relative and absolute quantification (iTRAQ), 142 differentially accumulated proteins (DAPs) were identified from two alfalfa varieties, including 52 proteins (34 up-regulated and 18 down-regulated) in Longzhong, 71 proteins (28 up-regulated and 43 down-regulated) in Gannong No. 3, and 19 proteins (13 up-regulated and 6 down-regulated) shared by both varieties. Most of these DAPs were involved in stress and defense, protein metabolism, transmembrane transport, signal transduction, as well as cell wall and cytoskeleton metabolism. In conclusion, the stronger drought-tolerance of Longzhong was attributed to its higher osmotic adjustment capacity, greater ability to orchestrate its enzymatic and non-enzymatic antioxidant systems and thus avoid great oxidative damage in comparison to Gannong No. 3. Moreover, the involvement of other pathways, including carbohydrate metabolism, ROS detoxification, secondary metabolism, protein processing, ion and water transport, signal transduction, and cell wall adjustment, are important mechanisms for conferring drought tolerance in alfalfa.
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Affiliation(s)
- Cuimei Zhang
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Centers for Grazing Land Ecosystem Sustainability, Gansu Agricultural University, Lanzhou, China
| | - Shangli Shi
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Centers for Grazing Land Ecosystem Sustainability, Gansu Agricultural University, Lanzhou, China
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9
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Mothersill C, Smith R, Wang J, Rusin A, Fernandez-Palomo C, Fazzari J, Seymour C. Biological Entanglement-Like Effect After Communication of Fish Prior to X-Ray Exposure. Dose Response 2018; 16:1559325817750067. [PMID: 29479295 PMCID: PMC5818098 DOI: 10.1177/1559325817750067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 08/31/2017] [Accepted: 09/26/2017] [Indexed: 12/24/2022] Open
Abstract
The phenomenon by which irradiated organisms including cells in vitro communicate with unirradiated neighbors is well established in biology as the radiation-induced bystander effect (RIBE). Generally, the purpose of this communication is thought to be protective and adaptive, reflecting a highly conserved evolutionary mechanism enabling rapid adjustment to stressors in the environment. Stressors known to induce the effect were recently shown to include chemicals and even pathological agents. The mechanism is unknown but our group has evidence that physical signals such as biophotons acting on cellular photoreceptors may be implicated. This raises the question of whether quantum biological processes may occur as have been demonstrated in plant photosynthesis. To test this hypothesis, we decided to see whether any form of entanglement was operational in the system. Fish from 2 completely separate locations were allowed to meet for 2 hours either before or after which fish from 1 location only (group A fish) were irradiated. The results confirm RIBE signal production in both skin and gill of fish, meeting both before and after irradiation of group A fish. The proteomic analysis revealed that direct irradiation resulted in pro-tumorigenic proteomic responses in rainbow trout. However, communication from these irradiated fish, both before and after they had been exposed to a 0.5 Gy X-ray dose, resulted in largely beneficial proteomic responses in completely nonirradiated trout. The results suggest that some form of anticipation of a stressor may occur leading to a preconditioning effect or temporally displaced awareness after the fish become entangled.
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Affiliation(s)
| | | | - Jiaxi Wang
- Department of Chemistry, Mass Spectrometry Facility, Queen’s University, Kingston, Ontario, Canada
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10
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Proapoptotic function of deubiquitinase DUSP31 in Drosophila. Oncotarget 2017; 8:70452-70462. [PMID: 29050293 PMCID: PMC5642568 DOI: 10.18632/oncotarget.19715] [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: 05/27/2017] [Accepted: 06/26/2017] [Indexed: 11/25/2022] Open
Abstract
Drosophila have been used to identify new components in apoptosis regulation. The Drosophila protein Dark forms an octameric apoptosome complex that induces the initiator caspase Dronc to trigger the caspase cell death pathway and, therefore, plays an important role in controlling apoptosis. Caspases and Dark are constantly expressed in cells, but their activity is blocked by DIAP1 E3 ligase-mediated ubiquitination and subsequent inactivation or proteasomal degradation. One of the regulatory mechanisms that stabilize proapoptotic factors is the removal of ubiquitin chains by deubiquitinases. In this study performed a modified genetic screen for deubiquitinases (dsRNA lines) to identify those involved in stabilizing proapoptotic components. Loss-of-function alleles of deubiquitinase DUSP31 were identified as suppressors of the Dronc overexpression phenotype. DUSP31 deficiency also suppresses apoptosis induced by the RHG protein, Grim. Genetic analysis revealed for the first time that DUSP31 deficiency sufficiently suppresses the Dark phenotype, indicating its involvement in the control of Dark/Dronc apoptosome function in invertebrate apoptosis.
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11
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Ebner P, Versteeg GA, Ikeda F. Ubiquitin enzymes in the regulation of immune responses. Crit Rev Biochem Mol Biol 2017; 52:425-460. [PMID: 28524749 PMCID: PMC5490640 DOI: 10.1080/10409238.2017.1325829] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/06/2017] [Accepted: 04/28/2017] [Indexed: 12/25/2022]
Abstract
Ubiquitination plays a central role in the regulation of various biological functions including immune responses. Ubiquitination is induced by a cascade of enzymatic reactions by E1 ubiquitin activating enzyme, E2 ubiquitin conjugating enzyme, and E3 ubiquitin ligase, and reversed by deubiquitinases. Depending on the enzymes, specific linkage types of ubiquitin chains are generated or hydrolyzed. Because different linkage types of ubiquitin chains control the fate of the substrate, understanding the regulatory mechanisms of ubiquitin enzymes is central. In this review, we highlight the most recent knowledge of ubiquitination in the immune signaling cascades including the T cell and B cell signaling cascades as well as the TNF signaling cascade regulated by various ubiquitin enzymes. Furthermore, we highlight the TRIM ubiquitin ligase family as one of the examples of critical E3 ubiquitin ligases in the regulation of immune responses.
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12
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Rittinger K, Ikeda F. Linear ubiquitin chains: enzymes, mechanisms and biology. Open Biol 2017; 7:170026. [PMID: 28446710 PMCID: PMC5413910 DOI: 10.1098/rsob.170026] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination is a versatile post-translational modification that regulates a multitude of cellular processes. Its versatility is based on the ability of ubiquitin to form multiple types of polyubiquitin chains, which are recognized by specific ubiquitin receptors to induce the required cellular response. Linear ubiquitin chains are linked through Met 1 and have been established as important players of inflammatory signalling and apoptotic cell death. These chains are generated by a ubiquitin E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) that is thus far the only E3 ligase capable of forming linear ubiquitin chains. The complex consists of three subunits, HOIP, HOIL-1L and SHARPIN, each of which have specific roles in the observed biological functions of LUBAC. Furthermore, LUBAC has been found to be associated with OTULIN and CYLD, deubiquitinases that disassemble linear chains and counterbalance the E3 ligase activity of LUBAC. Gene mutations in HOIP, HOIL-1L and OTULIN are found in human patients who suffer from autoimmune diseases, and HOIL-1L mutations are also found in myopathy patients. In this paper, we discuss the mechanisms of linear ubiquitin chain generation and disassembly by their respective enzymes and review our current understanding of their biological functions and association with human diseases.
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Affiliation(s)
- Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), Dr Bohr-gasse 3, 1030 Vienna, Austria
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