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Wang D, Musazade E, Wang H, Liu J, Zhang C, Liu W, Liu Y, Guo L. Regulatory Mechanism of the Constitutive Photomorphogenesis 9 Signalosome Complex in Response to Abiotic Stress in Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2777-2788. [PMID: 35199516 DOI: 10.1021/acs.jafc.1c07224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a highly conserved protein complex that regulates signaling pathways in plants under abiotic stress. We discuss the potential molecular mechanisms of CSN under abiotic stress, including oxidative stress with reactive oxygen species signaling, salt stress with jasmonic acid, gibberellic acid, and abscisic acid signaling, high-temperature stress with auxin signaling, and optical radiation with DNA damage and repair response. We conclude that CSN likely participates in affecting antioxidant biosynthesis and hormone signaling by targeting receptors, kinases, and transcription factors in response to abiotic stress, which potentially provides valuable information for engineering stress-tolerant crops.
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Affiliation(s)
- Dan Wang
- College of Life Science, Key Laboratory of Straw Biology and Higher Value Application, Ministry of Education, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
- School of Public Health, Jilin Medical University, Jilin, Jilin 132013, People's Republic of China
| | - Elshan Musazade
- College of Life Science, Key Laboratory of Straw Biology and Higher Value Application, Ministry of Education, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Huan Wang
- Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Junmei Liu
- Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Chunyu Zhang
- College of Food and Biotechnology, Changchun Polytechnic, Changchun, Jilin 130033, People's Republic of China
| | - Wencong Liu
- College of Resources and Environment, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Yanxi Liu
- College of Life Science, Key Laboratory of Straw Biology and Higher Value Application, Ministry of Education, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Liquan Guo
- College of Life Science, Key Laboratory of Straw Biology and Higher Value Application, Ministry of Education, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
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Tuller T, Diament A, Yahalom A, Zemach A, Atar S, Chamovitz DA. The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana. Bioinformatics 2020; 35:2718-2723. [PMID: 30596896 DOI: 10.1093/bioinformatics/bty1053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/20/2018] [Accepted: 12/21/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. RESULTS We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function Arabidopsis mutants of the COP9 signalosome. Our results support the hypothesis that the COP9 signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. Our analyses suggest that COP9 signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 signalosome conservation among eukaryotes may also suggest that COP9 signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tamir Tuller
- Department of Biomedical Engineering.,Sagol School of Neuroscience
| | | | - Avital Yahalom
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Assaf Zemach
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Daniel A Chamovitz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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Role of Cop9 Signalosome Subunits in the Environmental and Hormonal Balance of Plant. Biomolecules 2019; 9:biom9060224. [PMID: 31181827 PMCID: PMC6628103 DOI: 10.3390/biom9060224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/06/2019] [Accepted: 06/08/2019] [Indexed: 11/17/2022] Open
Abstract
The COP9 (Constitutive photomorphogenesis 9) signalosome (CSN) is a highly conserved protein complex that influences several signaling and developmental processes. The COP9 signalosome consists of eight subunits, among which two subunits, CSN5 and CSN6, contain an Mpr1/Pad1 N-terminal (MPN) domain and the remaining six subunits contain a proteasome, COP9 signalosome, and initiation factor 3 (PCI) domain. In plants, each MPN subunit is encoded by two genes, which is not the case in other organisms. This review aims to provide in-depth knowledge of each COP9 signalosome subunit, concentrating on genetic analysis of both partial and complete loss-of-function mutants. At the beginning of this review, the role of COP9 signalosome in the hormonal signaling and defense is discussed, whereas later sections deal in detail with the available partial loss-of-function, hypomorphic mutants of each subunit. All available hypomorphic mutants are compared based on their growth response and deneddylation activity.
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Nikitaki Z, Holá M, Donà M, Pavlopoulou A, Michalopoulos I, Angelis KJ, Georgakilas AG, Macovei A, Balestrazzi A. Integrating plant and animal biology for the search of novel DNA damage biomarkers. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 775:21-38. [DOI: 10.1016/j.mrrev.2018.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
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Puts GS, Spadafora N. Detection of Protein-Protein Interactions in Tobacco BY-2 Cells Using Bimolecular Fluorescence Complementation. Methods Mol Biol 2016; 1342:269-77. [PMID: 26254930 DOI: 10.1007/978-1-4939-2957-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knowledge of protein-protein interactions in the plant cell is invaluable for furthering our understanding of the functions of these proteins. Many of the methods available for the study of these interactions, such as yeast two-hybrid and co-immunoprecipitation assays, rely on in vitro techniques. Here we describe the use of bimolecular fluorescence complementation for the study of protein-protein interactions in vivo, using simple techniques and accessible materials.
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Affiliation(s)
- Gemma S Puts
- Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD, 21201, USA,
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Lu Y, Tian Y, Wang R, Wu Q, Zhang Y, Li X. Dual fluorescent protein-based bioassay system for the detection of genotoxic chemical substances in Saccharomyces cerevisiae. Toxicol Mech Methods 2015; 25:698-707. [DOI: 10.3109/15376516.2015.1070305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yixin Lu
- Department of Preventive Medicine, Yangzhou Medical College, Yangzhou University, Yangzhou, Jiangsu, PR China and
| | - Yongjie Tian
- Department of Preventive Medicine, Yangzhou Medical College, Yangzhou University, Yangzhou, Jiangsu, PR China and
| | - Ruikun Wang
- Department of Preventive Medicine, Yangzhou Medical College, Yangzhou University, Yangzhou, Jiangsu, PR China and
| | - Qianqian Wu
- Department of Preventive Medicine, Yangzhou Medical College, Yangzhou University, Yangzhou, Jiangsu, PR China and
| | - Yu Zhang
- Department of Preventive Medicine, Yangzhou Medical College, Yangzhou University, Yangzhou, Jiangsu, PR China and
| | - Xiangming Li
- Department of Preventive Medicine, Yangzhou Medical College, Yangzhou University, Yangzhou, Jiangsu, PR China and
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, PR China
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Singer R, Atar S, Atias O, Oron E, Segal D, Hirsch JA, Tuller T, Orian A, Chamovitz DA. Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development. Nucleic Acids Res 2014; 42:9761-70. [PMID: 25106867 PMCID: PMC4150811 DOI: 10.1093/nar/gku723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The COP9 signalosome protein complex has a central role in the regulation of development of multicellular organisms. While the function of this complex in ubiquitin-mediated protein degradation is well established, results over the past few years have hinted that the COP9 signalosome may function more broadly in the regulation of gene expression. Here, using DamID technology, we show that COP9 signalosome subunit 7 functionally associates with a large number of genomic loci in the Drosophila genome, and show that the expression of many genes within these loci is COP9 signalosome-dependent. This association is likely direct as we show CSN7 binds DNA in vitro. The genes targeted by CSN7 are preferentially enriched for transcriptionally active regions of the genome, and are involved in the regulation of distinct gene ontology groupings including imaginal disc development and cell-cycle control. In accord, loss of CSN7 function leads to cell-cycle delay and altered wing development. These results indicate that CSN7, and by extension the entire COP9 signalosome, functions directly in transcriptional control. While the COP9 signalosome protein complex has long been known to regulate protein degradation, here we expand the role of this complex by showing that subunit 7 binds DNA in vitro and functions directly in vivo in transcriptional control of developmentally important pathways that are relevant for human health.
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Affiliation(s)
- Ruth Singer
- Department of Molecular Biology and Ecology of Plants
| | | | - Osnat Atias
- Department of Molecular Biology and Ecology of Plants
| | - Efrat Oron
- Department of Molecular Biology and Ecology of Plants
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology
| | - Joel A Hirsch
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | | | - Amir Orian
- Cancer and Vascular Biology Research Center, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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ZHANG C, LIU G, HUANG M. Ribonucleotide reductase metallocofactor: assembly, maintenance and inhibition. FRONTIERS IN BIOLOGY 2014; 9:104-113. [PMID: 24899886 PMCID: PMC4041730 DOI: 10.1007/s11515-014-1302-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Ribonucleotide reductase (RNR) supplies cellular deoxyribonucleotide triphosphates (dNTP) pools by converting ribonucleotides to the corresponding deoxy forms using radical-based chemistry. Eukaryotic RNR comprises α and β subunits: α contains the catalytic and allosteric sites; β houses a diferric-tyrosyl radical cofactor (FeIII2-Y•) that is required to initiates nucleotide reduction in α. Cells have evolved multi-layered mechanisms to regulate RNR level and activity in order to maintain the adequate sizes and ratios of their dNTP pools to ensure high-fidelity DNA replication and repair. The central role of RNR in nucleotide metabolism also makes it a proven target of chemotherapeutics. In this review, we discuss recent progress in understanding the function and regulation of eukaryotic RNRs, with a focus on studies revealing the cellular machineries involved in RNR metallocofactor biosynthesis and its implication in RNR-targeting therapeutics.
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Affiliation(s)
- Caiguo ZHANG
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Guoqi LIU
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mingxia HUANG
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Serino G, Pick E. Duplication and familial promiscuity within the proteasome lid and COP9 signalosome kin complexes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 203-204:89-97. [PMID: 23415332 DOI: 10.1016/j.plantsci.2012.12.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 12/28/2012] [Accepted: 12/29/2012] [Indexed: 05/13/2023]
Abstract
Two paralogous complexes, the proteasome lid and the COP9 signalosome (CSN), have diverged from a common ancestor; yet fulfill distinctive roles within the ubiquitin-proteasome sphere. The CSN regulates the largest family of E3 ubiquitin ligases, called CRLs (Cullin-RING ubiquitin Ligases), while the lid is a subcomplex of the 26S proteasome, a proteolytic machinery responsible for the degradation of ubiquitinated proteins. Remarkably, in many organisms, several subunits of both complexes are duplicated, a circumstance that can hypothetically increase the number of different complexes that can be formed. Duplication, however, is not the only complexity trait within the lid and the CSN, because many of their subunits are not fully committed only to one of the two complexes, but they are able to associate with both. Indeed, their corresponding mutants have features that can be due to the absence of more than one complex. This could be simply explained by the subunits being able to carry an identical function within more than one paralogous complex or by the subunits having a certain level of promiscuity, i.e. being able to carry more than one function, depending on the complex they are associating with. Recent data show that both options are possible and, although their functional relevance still needs to be fully uncovered, evidence is accumulating, which indicates a promiscuous trading of paralogous subunits, and suggests that this may occur transiently, and/or in response to particular environmental conditions.
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Affiliation(s)
- Giovanna Serino
- Istituto Pasteur- Fondazione Cenci-Bolognetti, Department of Biology and Biotechnology, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Rome, Italy.
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Kotiguda GG, Weinberg D, Dessau M, Salvi C, Serino G, Chamovitz DA, Hirsch JA. The organization of a CSN5-containing subcomplex of the COP9 signalosome. J Biol Chem 2012; 287:42031-41. [PMID: 23086934 PMCID: PMC3516749 DOI: 10.1074/jbc.m112.387977] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 09/19/2012] [Indexed: 11/06/2022] Open
Abstract
The COP9 signalosome (CSN) is an evolutionarily conserved multi-protein complex that interfaces with the ubiquitin-proteasome pathway and plays critical developmental roles in both animals and plants. Although some subunits are present only in an ∼320-kDa complex-dependent form, other subunits are also detected in configurations distinct from the 8-subunit holocomplex. To date, the only known biochemical activity intrinsic to the complex, deneddylation of the Cullin subunits from Cullin-RING ubiquitin ligases, is assigned to CSN5. As an essential step to understanding the structure and assembly of a CSN5-containing subcomplex of the CSN, we reconstituted a CSN4-5-6-7 subcomplex. The core of the subcomplex is based on a stable heterotrimeric association of CSN7, CSN4, and CSN6, requiring coexpression in a bacterial reconstitution system. To this heterotrimer, we could then add CSN5 in vitro to reconstitute a quaternary complex. Using biochemical and biophysical methods, we identified pairwise and combinatorial interactions necessary for the formation of the CSN4-5-6-7 subcomplex. The subcomplex is stabilized by three types of interactions: MPN-MPN between CSN5 and CSN6, PCI-PCI between CSN4 and CSN7, and interactions mediated through the CSN6 C terminus with CSN4 and CSN7. CSN8 was also found to interact with the CSN4-6-7 core. These data provide a strong framework for further investigation of the organization and assembly of this pivotal regulatory complex.
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Affiliation(s)
- Giri Gowda Kotiguda
- From the Departments of Molecular Biology and Ecology of Plants and
- Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Dahlia Weinberg
- From the Departments of Molecular Biology and Ecology of Plants and
| | - Moshe Dessau
- Biochemistry and Molecular Biology
- Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Chiara Salvi
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy, and
| | - Giovanna Serino
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy, and
- The New York Botanical Garden, Bronx, New York 10458
| | | | - Joel A. Hirsch
- Biochemistry and Molecular Biology
- Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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Nezames CD, Deng XW. The COP9 signalosome: its regulation of cullin-based E3 ubiquitin ligases and role in photomorphogenesis. PLANT PHYSIOLOGY 2012; 160:38-46. [PMID: 22715109 PMCID: PMC3440213 DOI: 10.1104/pp.112.198879] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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