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Pick E. The necessity of NEDD8/Rub1 for vitality and its association with mitochondria-derived oxidative stress. Redox Biol 2020; 37:101765. [PMID: 33099217 PMCID: PMC7582104 DOI: 10.1016/j.redox.2020.101765] [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: 08/27/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Access of molecular oxygen to the respiratory electron transport chain at the mitochondria costs in the generation of reactive oxygen-derived species (ROS). ROS induces progressive damage to macromolecules in all living cells, hence, rapid defense mechanisms to maintain cellular redox homeostasis are vital. NEDD8/Rub1 is a highly conserved ubiquitin-like modifier that has recently been identified as a key regulator of cellular redox homeostasis. In this review, I will present NEDD8/Rub1, its modification cascade of enzymes, substrates and hydrolases. After introduction, I will show that the NEDD8/Rub1 pathway is linked with mitochondria physiology, namely, oxidative stress. In the rest of the review, I will approach the Ascomycota phylum of the kingdom fungi instrumentally, to present existing links between NEDD8/Rub1 vitality and the aerobic lifestyle of model species belonging to three subphyla: Saccharomycotina (S. cerevisiae and C. albicans), Pezizomycotina (A. nidulans and N. crassa), and Taphrinomycotina (S. pombe). NEDD8/Rub1 is a key regulator of cellular redox homeostasis. Ascomycota species that produce mitochondria-derived ROS during glycolysis require NEDD8/Rub1for viability. NEDD8/Rub1 essentiality correlates with the existence of NEDP1 in the organism genome.
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Affiliation(s)
- Elah Pick
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Tivon, 3600600, Israel.
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2
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Qin N, Xu D, Li J, Deng XW. COP9 signalosome: Discovery, conservation, activity, and function. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:90-103. [PMID: 31894894 DOI: 10.1111/jipb.12903] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/26/2019] [Indexed: 05/22/2023]
Abstract
The COP9 signalosome (CSN) is a conserved protein complex, typically composed of eight subunits (designated as CSN1 to CSN8) in higher eukaryotes such as plants and animals, but of fewer subunits in some lower eukaryotes such as yeasts. The CSN complex is originally identified in plants from a genetic screen for mutants that mimic light-induced photomorphogenic development when grown in the dark. The CSN complex regulates the activity of cullin-RING ligase (CRL) families of E3 ubiquitin ligase complexes, and play critical roles in regulating gene expression, cell proliferation, and cell cycle. This review aims to summarize the discovery, composition, structure, and function of CSN in the regulation of plant development in response to external (light and temperature) and internal cues (phytohormones).
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Affiliation(s)
- Nanxun Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
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The Proteasome Lid Triggers COP9 Signalosome Activity during the Transition of Saccharomyces cerevisiae Cells into Quiescence. Biomolecules 2019; 9:biom9090449. [PMID: 31487956 PMCID: PMC6770237 DOI: 10.3390/biom9090449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
The class of Cullin-RING E3 ligases (CRLs) selectively ubiquitinate a large portion of proteins targeted for proteolysis by the 26S proteasome. Before degradation, ubiquitin molecules are removed from their conjugated proteins by deubiquitinating enzymes, a handful of which are associated with the proteasome. The CRL activity is triggered by modification of the Cullin subunit with the ubiquitin-like protein, NEDD8 (also known as Rub1 in Saccharomyces cerevisiae). Cullin modification is then reversed by hydrolytic action of the COP9 signalosome (CSN). As the NEDD8-Rub1 catalytic cycle is not essential for the viability of S. cerevisiae, this organism is a useful model system to study the alteration of Rub1-CRL conjugation patterns. In this study, we describe two distinct mutants of Rpn11, a proteasome-associated deubiquitinating enzyme, both of which exhibit a biochemical phenotype characterized by high accumulation of Rub1-modified Cdc53-Cullin1 (yCul1) upon entry into quiescence in S. cerevisiae. Further characterization revealed proteasome 19S-lid-associated deubiquitination activity that authorizes the hydrolysis of Rub1 from yCul1 by the CSN complex. Thus, our results suggest a negative feedback mechanism via proteasome capacity on upstream ubiquitinating enzymes.
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Bramasole L, Sinha A, Gurevich S, Radzinski M, Klein Y, Panat N, Gefen E, Rinaldi T, Jimenez-Morales D, Johnson J, Krogan NJ, Reis N, Reichmann D, Glickman MH, Pick E. Proteasome lid bridges mitochondrial stress with Cdc53/Cullin1 NEDDylation status. Redox Biol 2019; 20:533-543. [PMID: 30508698 PMCID: PMC6279957 DOI: 10.1016/j.redox.2018.11.010] [Citation(s) in RCA: 20] [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: 08/24/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
Cycles of Cdc53/Cullin1 rubylation (a.k.a NEDDylation) protect ubiquitin-E3 SCF (Skp1-Cullin1-F-box protein) complexes from self-destruction and play an important role in mediating the ubiquitination of key protein substrates involved in cell cycle progression, development, and survival. Cul1 rubylation is balanced by the COP9 signalosome (CSN), a multi-subunit derubylase that shows 1:1 paralogy to the 26S proteasome lid. The turnover of SCF substrates and their relevance to various diseases is well studied, yet, the extent by which environmental perturbations influence Cul1 rubylation/derubylation cycles per se is still unclear. In this study, we show that the level of cellular oxidation serves as a molecular switch, determining Cullin1 rubylation/derubylation ratio. We describe a mutant of the proteasome lid subunit, Rpn11 that exhibits accumulated levels of Cullin1-Rub1 conjugates, a characteristic phenotype of csn mutants. By dissecting between distinct phenotypes of rpn11 mutants, proteasome and mitochondria dysfunction, we were able to recognize the high reactive oxygen species (ROS) production during the transition of cells into mitochondrial respiration, as a checkpoint of Cullin1 rubylation in a reversible manner. Thus, the study adds the rubylation cascade to the list of cellular pathways regulated by redox homeostasis.
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Affiliation(s)
- L Bramasole
- Department of Human Biology, The Faculty of Natural Sciences, University of Haifa, Haifa 3190500, Israel; Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - A Sinha
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - S Gurevich
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - M Radzinski
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - Y Klein
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - N Panat
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - E Gefen
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - T Rinaldi
- Department of Biology and Biotechnology, University of Rome ''La Sapienza'', Rome 00185, Italy
| | - D Jimenez-Morales
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - J Johnson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - N J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - N Reis
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - D Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - M H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - E Pick
- Department of Human Biology, The Faculty of Natural Sciences, University of Haifa, Haifa 3190500, Israel; Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel.
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Abstract
The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCF(TIR1) [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinase-associated protein 2 (SKP2) localize to the nucleus, whereas auxin-binding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.
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Affiliation(s)
- Peter Grones
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9052 Gent, Belgium
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9052 Gent, Belgium Mendel Centre for Plant Genomics and Proteomics, Masaryk University, CEITEC MU, CZ-625 00 Brno, Czech Republic
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Moonlighting and pleiotropy within two regulators of the degradation machinery: the proteasome lid and the CSN. Biochem Soc Trans 2015; 42:1786-91. [PMID: 25399607 DOI: 10.1042/bst20140227] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The distinction between pleiotrotic and moonlighting roles of proteins is challenging; however, this distinction may be clearer when it comes to multiprotein complexes. Two examples are the proteasome lid and the COP9 signalosome (CSN), which are twin enzymes with 1:1 paralogy between subunits. In each complex, one out of eight subunits harbours a JAMM/MPN⁺ metalloprotease motif. This motif contributes the canonical activity of each complex: hydrolysis of covalently attached ubiquitin by Rpn11 in the proteasome lid and hydrolysis of ubiquitin-related 1 (Rub1/Nedd8) from Cullins by Csn5 in the CSN. In both complexes, executing this activity suggests pleiotropic effects and requires an assembled full complex. However, beyond canonical functions, both Rpn11 and Csn5 are involved in additional unique, complex-independent functions, herein referred to as moonlighting activities.
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Hu Y, Wu Y, Li Q, Zhang W, Jin C. Solution structure of yeast Rpn9: insights into proteasome lid assembly. J Biol Chem 2015; 290:6878-89. [PMID: 25631053 DOI: 10.1074/jbc.m114.626762] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The regulatory particle (RP) of the 26 S proteasome functions in preparing polyubiquitinated substrates for degradation. The lid complex of the RP contains an Rpn8-Rpn11 heterodimer surrounded by a horseshoe-shaped scaffold formed by six proteasome-COP9/CSN-initiation factor (PCI)-containing subunits. The PCI domains are essential for lid assembly, whereas the detailed molecular mechanisms remain elusive. Recent cryo-EM studies at near-atomic resolution provided invaluable information on the RP architecture in different functional states. Nevertheless, atomic resolution structural information on the RP is still limited, and deeper understanding of RP assembly mechanism requires further studies on the structures and interactions of individual subunits or subcomplexes. Herein we report the high-resolution NMR structures of the PCI-containing subunit Rpn9 from Saccharomyces cerevisiae. The 45-kDa protein contains an all-helical N-terminal domain and a C-terminal PCI domain linked via a semiflexible hinge. The N-terminal domain mediates interaction with the ubiquitin receptor Rpn10, whereas the PCI domain mediates interaction with the neighboring PCI subunit Rpn5. The Rpn9-Rpn5 interface highlights two structural motifs on the winged helix module forming a hydrophobic center surrounded by ionic pairs, which is a common pattern for all PCI-PCI interactions in the lid. The results suggest that divergence in surface composition among different PCI pairs may contribute to the modulation of lid assembly.
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Affiliation(s)
- Yunfei Hu
- From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering
| | - Yujie Wu
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Qianwen Li
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Wenbo Zhang
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Changwen Jin
- From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, College of Life Sciences, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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Jin D, Li B, Deng XW, Wei N. Plant COP9 signalosome subunit 5, CSN5. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:54-61. [PMID: 24908506 DOI: 10.1016/j.plantsci.2014.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/31/2014] [Accepted: 04/01/2014] [Indexed: 05/22/2023]
Abstract
CSN5 is a subunit of the COP9 signalosome (CSN) and carries the metallo-protease catalytic center for the complex. This highly conserved gene has been a subject of intense research in part because human Csn5 (Jab1) has been tightly linked to cancer. We briefly summarize recent research advances on the structure and mechanisms of the CSN in general, and then focus on the Arabidopsis CSN5 genes and their products, AtCSN5A and AtCSN5B. We also briefly discuss CSN6 genes, which are closely related share many similarities to CSN5. CSN5 and CSN6 genes are duplicated in mustard family of plants as well as in several plant species that have no phylogenetic correlation. Sequence homology comparison further suggests that at least some of the duplication events occurred independently. We review and analyze the phenotypic and expression differences of the two CSN5 genes in Arabidopsis, and suggest that they play overlapping as well as specialized roles in plant development. Arabidopsis CSN5 protein sequences are more similar to those of complex organisms such as humans than to yeasts and unicellular alga, suggesting that the structure and mechanism of Arabidopsis CSN5 likely resembles more to those of human than to yeast. We argue that possession of two different isoforms of CSN5s gives Arabidopsis a unique advantage as a genetic model of CSN5 to dissect the multifaceted functions and mechanistic versatilities of this important cellular regulator.
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Affiliation(s)
- Dan Jin
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing 400716, China; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Bosheng Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Xing-Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Ning Wei
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
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Ito J, Parsons HT, Heazlewood JL. The Arabidopsis cytosolic proteome: the metabolic heart of the cell. FRONTIERS IN PLANT SCIENCE 2014; 5:21. [PMID: 24550929 PMCID: PMC3914213 DOI: 10.3389/fpls.2014.00021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 01/19/2014] [Indexed: 05/09/2023]
Abstract
The plant cytosol is the major intracellular fluid that acts as the medium for inter-organellar crosstalk and where a plethora of important biological reactions take place. These include its involvement in protein synthesis and degradation, stress response signaling, carbon metabolism, biosynthesis of secondary metabolites, and accumulation of enzymes for defense and detoxification. This central role is highlighted by estimates indicating that the majority of eukaryotic proteins are cytosolic. Arabidopsis thaliana has been the subject of numerous proteomic studies on its different subcellular compartments. However, a detailed study of enriched cytosolic fractions from Arabidopsis cell culture has been performed only recently, with over 1,000 proteins reproducibly identified by mass spectrometry. The number of proteins allocated to the cytosol nearly doubles to 1,802 if a series of targeted proteomic characterizations of complexes is included. Despite this, few groups are currently applying advanced proteomic approaches to this important metabolic space. This review will highlight the current state of the Arabidopsis cytosolic proteome since its initial characterization a few years ago.
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Affiliation(s)
- Jun Ito
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
| | - Harriet T. Parsons
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
- Department of Plant and Environmental Sciences, University of Copenhagen, CopenhagenDenmark
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
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Signaling: COP9 Signalosome. Mol Biol 2014. [DOI: 10.1007/978-1-4939-0263-7_13-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Estrin E, Lopez-Blanco J, Chacón P, Martin A. Formation of an Intricate Helical Bundle Dictates the Assembly of the 26S Proteasome Lid. Structure 2013; 21:1624-35. [DOI: 10.1016/j.str.2013.06.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/15/2013] [Accepted: 06/17/2013] [Indexed: 12/18/2022]
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