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Gou H, Lu S, Guo L, Che L, Li M, Zeng B, Yang J, Chen B, Mao J. Evolution of PIN gene family between monocotyledons and dicotyledons and VvPIN1 negatively regulates freezing tolerance in transgenic Arabidopsis. PHYSIOLOGIA PLANTARUM 2024; 176:e14464. [PMID: 39157882 DOI: 10.1111/ppl.14464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/07/2024] [Accepted: 07/18/2024] [Indexed: 08/20/2024]
Abstract
The PIN-FORMED (PIN) proteins mediate the auxin flow throughout the plant and have been identified in many species. However, evolution differences in the PIN gene families have not been systematically analyzed, and their functions under abiotic stresses in grape are largely unexplored. In this study, 373 PIN genes were identified from 25 species and divided into 3 subgroups. Physicochemical properties analysis indicated that most of the PIN proteins were unstable alkaline hydrophobic proteins in nature. The synteny analysis showed that the PINs contained strong gene duplication. Motif composition revealed that PIN gene sequence differences between monocotyledons and dicotyledons were due to evolutionary-induced base loss, and the loss was more common in dicotyledonous. Meanwhile, the codon usage bias showed that the PINs showed stronger codon preference in monocotyledons, monocotyledons biased towards C3s and G3s, and dicotyledons biased towards A3s and T3s. In addition, the VvPIN1 can interact with VvCSN5. Significantly, under freezing treatment, the ion leakage,O 2 · - $$ \left({O}_2^{\cdotp -}\right) $$ , H2O2, and malondialdehyde (MDA) were obviously increased, while the proline (Pro) content, peroxidase (POD) activity, and glutathione (GSH) content were decreased in VvPIN1-overexpressing Arabidopsis compared to the wild type (WT). And quantitative real-time PCR (qRT-PCR) showed that AtICE1, AtICE2, AtCBF1, AtCBF2, and AtCBF3 were down-regulated in overexpression lines. These results demonstrated that VvPIN1 negatively regulated the freezing tolerance in transgenic Arabidopsis. Collectively, this study provides a novel insight into the evolution and a basis for further studies on the biological functions of PIN genes in monocotyledons and dicotyledons.
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Affiliation(s)
- Huimin Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
| | - Lili Guo
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
| | - Lili Che
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
| | - Min Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
| | - Baozhen Zeng
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
| | - Juanbo Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu Province, People's Republic of China
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Dong J, Li Y, Cheng S, Li X, Wei N. COP9 signalosome-mediated deneddylation of CULLIN1 is necessary for SCF EBF1 assembly in Arabidopsis thaliana. Cell Rep 2024; 43:113638. [PMID: 38184853 DOI: 10.1016/j.celrep.2023.113638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/06/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
Functions of the SKP1-CUL1-F box (SCF) ubiquitin E3 ligases are essential in plants. The F box proteins (FBPs) are substrate receptors that recruit substrates and assemble an active SCF complex, but the regulatory mechanism underlying the FBPs binding to CUL1 to activate the SCF cycle is not fully understood. We show that Arabidopsis csn1-10 is defective in SCFEBF1-mediated PIF3 degradation during de-etiolation, due to impaired association of EBF1 with CUL1 in csn1-10. EBF1 preferentially associates with un-neddylated CUL1 that is deficient in csn1-10 and the EBF1-CUL1 binding is rescued by the neddylation inhibitor MLN4924. Furthermore, we identify a subset of FBPs with impaired binding to CUL1 in csn1-10, indicating their assembly to form SCF complexes may depend on COP9 signalosome (CSN)-mediated deneddylation of CUL1. This study reports that a key role of CSN-mediated CULLIN deneddylation is to gate the binding of the FBP-substrate module to CUL1, thus initiating the SCF cycle of substrate ubiquitination.
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Affiliation(s)
- Jie Dong
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Li
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuyang Cheng
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xuehui Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang 261325, China
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing 400715, China.
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Zhang K, Feng X, Liu Y, Yang Y, Hao X, Li D, Wang X, Wang L. Integrative transcriptome and whole-genome bisulfite sequencing analyses of a temperature-sensitive albino tea plant cultivar. PHYSIOLOGIA PLANTARUM 2023; 175:e14064. [PMID: 38148243 DOI: 10.1111/ppl.14064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/28/2023]
Abstract
Green tea made from albino buds and leaves has a strong umami taste and aroma. The cultivar 'Zhonghuang 2' (ZH2, Camellia sinensis) is a natural mutant with young shoots that are yellow in spring and green or yellow-green in summer. However, the mechanism of leaf color change remains unclear. Here, we found that young shoots of ZH2 were yellow at low temperature (LT) and green at high temperature (HT), indicating that ZH2 is a temperature-sensitive cultivar. Transmission electron microscopy analysis showed that the grana in the chloroplasts of young shoots grown at LT were poorly stacked, which caused a lack of photoreactions and chlorophyll. RNA-seq results showed 1279 genes differentially expressed in the young shoots grown at LT compared with those at HT, including genes related to cytochrome synthesis, chloroplast development, photosynthesis, and DNA methylation. A whole-genome bisulfite sequencing assay revealed that the dynamics of DNA methylation levels in the CG, CHG, and CHH contexts decreased under LT, and the change was most obvious in the CHH context. Furthermore, 72 genes showed significant changes in both expression and DNA methylation levels, and most of them were related to cytochrome synthesis, chloroplast development, photosynthesis, transcription factors, and signaling pathways. These results demonstrate that DNA methylation is involved in the LT-regulated albino processes of ZH2. Changes in DNA methylation levels were associated with changes in gene expression levels, affecting the structure and function of chloroplasts, which may have a phenotypic impact on shoot and leaf color.
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Affiliation(s)
- Kexin Zhang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xia Feng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Liu
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yajun Yang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyuan Hao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Dongliang Li
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Xinchao Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Lu Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs of the People's Republic of China/National Center for Tea Improvement/Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, Hainan, China
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Jin L, Zhang G, Yang G, Dong J. Identification of the Karyopherin Superfamily in Maize and Its Functional Cues in Plant Development. Int J Mol Sci 2022; 23:ijms232214103. [PMID: 36430578 PMCID: PMC9699179 DOI: 10.3390/ijms232214103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/06/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Appropriate nucleo-cytoplasmic partitioning of proteins is a vital regulatory mechanism in phytohormone signaling and plant development. However, how this is achieved remains incompletely understood. The Karyopherin (KAP) superfamily is critical for separating the biological processes in the nucleus from those in the cytoplasm. The KAP superfamily is divided into Importin α (IMPα) and Importin β (IMPβ) families and includes the core components in mediating nucleocytoplasmic transport. Recent reports suggest the KAPs play crucial regulatory roles in Arabidopsis development and stress response by regulating the nucleo-cytoplasmic transport of members in hormone signaling. However, the KAP members and their associated molecular mechanisms are still poorly understood in maize. Therefore, we first identified seven IMPα and twenty-seven IMPβ genes in the maize genome and described their evolution traits and the recognition rules for substrates with nuclear localization signals (NLSs) or nuclear export signals (NESs) in plants. Next, we searched for the protein interaction partners of the ZmKAPs and selected the ones with Arabidopsis orthologs functioning in auxin biosynthesis, transport, and signaling to predict their potential function. Finally, we found that several ZmKAPs share similar expression patterns with their interacting proteins, implying their function in root development. Overall, this article focuses on the Karyopherin superfamily in maize and starts with this entry point by systematically comprehending the KAP-mediated nucleo-cytoplasmic transport process in plants, and then predicts the function of the ZmKAPs during maize development, with a perspective on a closely associated regulatory mechanism between the nucleo-cytoplasmic transport and the phytohormone network.
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Affiliation(s)
- Lu Jin
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Guobin Zhang
- College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Guixiao Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiaqiang Dong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
- Correspondence:
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Sia J, Zhang W, Jonckheere E, Cook D, Bogdan P. Inferring functional communities from partially observed biological networks exploiting geometric topology and side information. Sci Rep 2022; 12:10883. [PMID: 35760826 PMCID: PMC9237089 DOI: 10.1038/s41598-022-14631-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
Cellular biological networks represent the molecular interactions that shape function of living cells. Uncovering the organization of a biological network requires efficient and accurate algorithms to determine the components, termed communities, underlying specific processes. Detecting functional communities is challenging because reconstructed biological networks are always incomplete due to technical bias and biological complexity, and the evaluation of putative communities is further complicated by a lack of known ground truth. To address these challenges, we developed a geometric-based detection framework based on Ollivier-Ricci curvature to exploit information about network topology to perform community detection from partially observed biological networks. We further improved this approach by integrating knowledge of gene function, termed side information, into the Ollivier-Ricci curvature algorithm to aid in community detection. This approach identified essential conserved and varied biological communities from partially observed Arabidopsis protein interaction datasets better than the previously used methods. We show that Ollivier-Ricci curvature with side information identified an expanded auxin community to include an important protein stability complex, the Cop9 signalosome, consistent with previous reported links to auxin response and root development. The results show that community detection based on Ollivier-Ricci curvature with side information can uncover novel components and novel communities in biological networks, providing novel insight into the organization and function of complex networks.
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Affiliation(s)
- Jayson Sia
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Wei Zhang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Edmond Jonckheere
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Paul Bogdan
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
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Zeng Y, Schotte S, Trinh HK, Verstraeten I, Li J, Van de Velde E, Vanneste S, Geelen D. Genetic Dissection of Light-Regulated Adventitious Root Induction in Arabidopsis thaliana Hypocotyls. Int J Mol Sci 2022; 23:5301. [PMID: 35628112 PMCID: PMC9140560 DOI: 10.3390/ijms23105301] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
Photomorphogenic responses of etiolated seedlings include the inhibition of hypocotyl elongation and opening of the apical hook. In addition, dark-grown seedlings respond to light by the formation of adventitious roots (AR) on the hypocotyl. How light signaling controls adventitious rooting is less well understood. Hereto, we analyzed adventitious rooting under different light conditions in wild type and photomorphogenesis mutants in Arabidopsis thaliana. Etiolation was not essential for AR formation but raised the competence to form AR under white and blue light. The blue light receptors CRY1 and PHOT1/PHOT2 are key elements contributing to the induction of AR formation in response to light. Furthermore, etiolation-controlled competence for AR formation depended on the COP9 signalosome, E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC (COP1), the COP1 interacting SUPPRESSOR OF PHYA-105 (SPA) kinase family members (SPA1,2 and 3) and Phytochrome-Interacting Factors (PIF). In contrast, ELONGATED HYPOCOTYL5 (HY5), suppressed AR formation. These findings provide a genetic framework that explains the high and low AR competence of Arabidopsis thaliana hypocotyls that were treated with dark, and light, respectively. We propose that light-induced auxin signal dissipation generates a transient auxin maximum that explains AR induction by a dark to light switch.
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Affiliation(s)
- Yinwei Zeng
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (Y.Z.); (S.S.); (H.K.T.); (I.V.); (J.L.); (E.V.d.V.)
| | - Sebastien Schotte
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (Y.Z.); (S.S.); (H.K.T.); (I.V.); (J.L.); (E.V.d.V.)
| | - Hoang Khai Trinh
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (Y.Z.); (S.S.); (H.K.T.); (I.V.); (J.L.); (E.V.d.V.)
- Biotechnology Research and Development Institute, Can Tho University, Can Tho City 900000, Vietnam
| | - Inge Verstraeten
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (Y.Z.); (S.S.); (H.K.T.); (I.V.); (J.L.); (E.V.d.V.)
| | - Jing Li
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (Y.Z.); (S.S.); (H.K.T.); (I.V.); (J.L.); (E.V.d.V.)
| | - Ellen Van de Velde
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (Y.Z.); (S.S.); (H.K.T.); (I.V.); (J.L.); (E.V.d.V.)
| | - Steffen Vanneste
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (Y.Z.); (S.S.); (H.K.T.); (I.V.); (J.L.); (E.V.d.V.)
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant SystemsBiology, VIB, Technologiepark 71, 9052 Ghent, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon 21985, Korea
| | - Danny Geelen
- Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (Y.Z.); (S.S.); (H.K.T.); (I.V.); (J.L.); (E.V.d.V.)
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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: 2] [Impact Index Per Article: 1.0] [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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Al-Saharin R, Hellmann H, Mooney S. Plant E3 Ligases and Their Role in Abiotic Stress Response. Cells 2022; 11:cells11050890. [PMID: 35269512 PMCID: PMC8909703 DOI: 10.3390/cells11050890] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
Plants, as sessile organisms, have limited means to cope with environmental changes. Consequently, they have developed complex regulatory systems to ameliorate abiotic stresses im-posed by environmental changes. One such system is the ubiquitin proteasome pathway, which utilizes E3 ligases to target proteins for proteolytic degradation via the 26S proteasome. Plants ex-press a plethora of E3 ligases that are categorized into four major groups depending on their structure. They are involved in many biological and developmental processes in plants, such as DNA repair, photomorphogenesis, phytohormones signaling, and biotic stress. Moreover, many E3 ligase targets are proteins involved in abiotic stress responses, such as salt, drought, heat, and cold. In this review, we will provide a comprehensive overview of E3 ligases and their substrates that have been connected with abiotic stress in order to illustrate the diversity and complexity of how this pathway enables plant survival under stress conditions.
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Affiliation(s)
- Raed Al-Saharin
- Department of Applied Biology, Tafila Technical University, At-Tafilah 66110, Jordan
- Correspondence:
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA; (H.H.); (S.M.)
| | - Sutton Mooney
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA; (H.H.); (S.M.)
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Gulabani H, Goswami K, Walia Y, Roy A, Noor JJ, Ingole KD, Kasera M, Laha D, Giehl RFH, Schaaf G, Bhattacharjee S. Arabidopsis inositol polyphosphate kinases IPK1 and ITPK1 modulate crosstalk between SA-dependent immunity and phosphate-starvation responses. PLANT CELL REPORTS 2022; 41:347-363. [PMID: 34797387 DOI: 10.1007/s00299-021-02812-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE Selective Arabidopsis thaliana inositol phosphate kinase functions modulate response amplitudes in innate immunity by balancing signalling adjustments with phosphate homeostasis networks. Pyrophosphorylation of InsP6 generates InsP7 and/or InsP8 containing high-energy phosphoanhydride bonds that are harnessed during energy requirements of a cell. As bona fide co-factors for several phytohormone networks, InsP7/InsP8 modulate key developmental processes. With requirements in transducing jasmonic acid (JA) and phosphate-starvation responses (PSR), InsP8 exemplifies a versatile metabolite for crosstalks between different cellular pathways during diverse stress exposures. Here we show that Arabidopsis thaliana INOSITOL PENTAKISPHOSPHATE 2-KINASE 1 (IPK1), INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE 1 (ITPK1), and DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2 (VIH2) implicated in InsP8 biosynthesis, suppress salicylic acid (SA)-dependent immunity. In ipk1, itpk1 or vih2 mutants, constitutive activation of defenses lead to enhanced resistance against the Pseudomonas syringae pv tomato DC3000 (PstDC3000) strain. Our data reveal that upregulated SA-signaling sectors potentiate increased expression of several phosphate-starvation inducible (PSI)-genes, previously known in these mutants. In reciprocation, upregulated PSI-genes moderate expression amplitudes of defense-associated markers. We demonstrate that SA is induced in phosphate-deprived plants, however its defense-promoting functions are likely diverted to PSR-supportive roles. Overall, our investigations reveal selective InsPs as crosstalk mediators in defense-phosphate homeostasis and in reprogramming stress-appropriate response intensities.
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Affiliation(s)
- Hitika Gulabani
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Manipal Academy of Higher Education (MAHE), Manipal University, Manipal, Karnataka, 576104, India
| | - Krishnendu Goswami
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Yashika Walia
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Abhisha Roy
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Jewel Jameeta Noor
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Kishor D Ingole
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha, 751024, India
| | - Mritunjay Kasera
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560 012, India
| | - Ricardo F H Giehl
- Department of Physiology and Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Gabriel Schaaf
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Saikat Bhattacharjee
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
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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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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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12
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Kale L, Nakurte I, Jalakas P, Kunga-Jegere L, Brosché M, Rostoks N. Arabidopsis mutant dnd2 exhibits increased auxin and abscisic acid content and reduced stomatal conductance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 140:18-26. [PMID: 31078052 DOI: 10.1016/j.plaphy.2019.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/23/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Arabidopsis thaliana cyclic nucleotide-gated ion channel gene 4 (AtCNGC4) loss-of-function mutant dnd2 exhibits elevated accumulation of salicylic acid (SA), dwarfed morphology, reduced hypersensitive response (HR), altered disease resistance and spontaneous lesions on plant leaves. An orthologous barley mutant, nec1, has been reported to over-accumulate indole-3-acetic acid (IAA) and to exhibit changes in stomatal regulation in response to exogenous auxin. Here we show that the Arabidopsis dnd2 over-accumulates both IAA and abscisic acid (ABA) and displays related phenotypic and physiological changes, such as, reduced stomatal size, higher stomatal density and stomatal index. dnd2 showed increased salt tolerance in root growth assay and significantly reduced stomatal conductance, while maintaining near wt reaction in stomatal conductance upon external application of ABA, and probably consequently increased drought stress tolerance. Introduction of both sid2-1 and fmo1 into dnd2 background resulting in removal of SA did not alter stomatal conductance. Hence, the closed stomata of dnd2 is probably a result of increased ABA levels and not increased SA levels. The triple dnd2sid2abi1-1 mutant exhibited intermediate stomatal conductance compared to dnd2 and abi1-1 (ABA insensitive, open stomata), while the response to external ABA was as in abi1-1 suggesting that reduced stomatal conductance in dnd2 is not due to impaired ABA signaling. In conclusion, Arabidopsis dnd2 mutant exhibited ABA overaccumulation and stomatal phenotypes, which may contribute to the observed improvement in drought stress resistance. Thus, Arabidopsis dnd2 mutant may serve as a model for studying crosstalk between biotic and abiotic stress and hormonal response in plants.
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Affiliation(s)
- Liga Kale
- Faculty of Biology, University of Latvia, 1 Jelgavas Street, Riga, LV-1004, Latvia
| | - Ilva Nakurte
- Faculty of Chemistry, University of Latvia, 1 Jelgavas Street, Riga, LV-1004, Latvia
| | - Pirko Jalakas
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Laura Kunga-Jegere
- Faculty of Biology, University of Latvia, 1 Jelgavas Street, Riga, LV-1004, Latvia
| | - Mikael Brosché
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Nils Rostoks
- Faculty of Biology, University of Latvia, 1 Jelgavas Street, Riga, LV-1004, Latvia.
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13
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Xu D, Marino G, Klingl A, Enderle B, Monte E, Kurth J, Hiltbrunner A, Leister D, Kleine T. Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance. PLANT PHYSIOLOGY 2019; 180:323-341. [PMID: 30760637 PMCID: PMC6501107 DOI: 10.1104/pp.19.00070] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/05/2019] [Indexed: 05/18/2023]
Abstract
Chloroplast biogenesis is indispensable for proper plant development and environmental acclimation. In a screen for mutants affected in photosynthesis, we identified the protein phosphatase7-like (pp7l) mutant, which displayed delayed chloroplast development in cotyledons and young leaves. PP7L, PP7, and PP7-long constitute a subfamily of phosphoprotein phosphatases. PP7 is thought to transduce a blue-light signal perceived by crys and phy a that induces expression of SIGMA FACTOR5 (SIG5). We observed that, like PP7, PP7L was predominantly localized to the nucleus in Arabidopsis (Arabidopsis thaliana), and the pp7l phenotype was similar to that of the sig6 mutant. However, SIG6 expression was unaltered in pp7l mutants. Instead, loss of PP7L compromised translation and ribosomal RNA (rRNA) maturation in chloroplasts, pointing to a distinct mechanism influencing chloroplast development. Promoters of genes deregulated in pp7l-1 were enriched in PHYTOCHROME-INTERACTING FACTOR (PIF)-binding motifs and the transcriptome of pp7l-1 resembled those of pif and CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) signalosome complex (csn) mutants. However, pif and csn mutants, as well as cop1, cryptochromes (cry)1 cry2, and phytochromes (phy)A phyB mutants, do not share the pp7l photosynthesis phenotype. PhyB protein levels were elevated in pp7l mutants, but phyB overexpression plants did not resemble pp7l These results indicate that PP7L operates through a different pathway and that the control of greening and photosystem biogenesis can be separated. The lack of PP7L increased susceptibility to salt and high-light stress, whereas PP7L overexpression conferred resistance to high-light stress. Strikingly, PP7L was specifically recruited to Brassicales for the regulation of chloroplast development. This study adds another player involved in chloroplast biogenesis.
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Affiliation(s)
- Duorong Xu
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Giada Marino
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Andreas Klingl
- Plant Development, Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Beatrix Enderle
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Elena Monte
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics Consejo Superior de Investigaciones Científicas-Institute of Agrifood Research and Technology-Universidad Autonoma de Barcelona-Universidad de Barcelona, 08193 Barcelona, Spain
| | - Joachim Kurth
- Plant Development, Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
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Betsch L, Boltz V, Brioudes F, Pontier G, Girard V, Savarin J, Wipperman B, Chambrier P, Tissot N, Benhamed M, Mollereau B, Raynaud C, Bendahmane M, Szécsi J. TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals. PLoS Genet 2019; 15:e1007899. [PMID: 30695029 PMCID: PMC6368322 DOI: 10.1371/journal.pgen.1007899] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 02/08/2019] [Accepted: 12/15/2018] [Indexed: 11/30/2022] Open
Abstract
Translationally Controlled Tumor Protein (TCTP) controls growth by regulating the G1/S transition during cell cycle progression. Our genetic interaction studies show that TCTP fulfills this role by interacting with CSN4, a subunit of the COP9 Signalosome complex, known to influence CULLIN-RING ubiquitin ligases activity by controlling CULLIN (CUL) neddylation status. In agreement with these data, downregulation of CSN4 in Arabidopsis and in tobacco cells leads to delayed G1/S transition comparable to that observed when TCTP is downregulated. Loss-of-function of AtTCTP leads to increased fraction of deneddylated CUL1, suggesting that AtTCTP interferes negatively with COP9 function. Similar defects in cell proliferation and CUL1 neddylation status were observed in Drosophila knockdown for dCSN4 or dTCTP, respectively, demonstrating a conserved mechanism between plants and animals. Together, our data show that CSN4 is the missing factor linking TCTP to the control of cell cycle progression and cell proliferation during organ development and open perspectives towards understanding TCTP's role in organ development and disorders associated with TCTP miss-expression.
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Affiliation(s)
- Léo Betsch
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Véronique Boltz
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Florian Brioudes
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Garance Pontier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Victor Girard
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Univ Lyon, Lyon, France
| | - Julie Savarin
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Barbara Wipperman
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Pierre Chambrier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Nicolas Tissot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Orsay, France
| | - Bertrand Mollereau
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Univ Lyon, Lyon, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Orsay, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Judit Szécsi
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
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15
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Schwechheimer C. NEDD8-its role in the regulation of Cullin-RING ligases. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:112-119. [PMID: 29909289 DOI: 10.1016/j.pbi.2018.05.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 05/26/2018] [Accepted: 05/31/2018] [Indexed: 05/10/2023]
Abstract
The ubiquitin-related protein NEDD8 is conjugated and deconjugated to and from proteins in processes related to ubiquitin conjugation and deconjugation. Neddylation is a well-studied posttranslational modification of Cullin-RING E3 ligases (CRLs). Biochemical and structural studies aiming at understanding the role of NEDD8 in CRL function have now resulted in a convincing model of how neddylation and deneddylation antagonistically regulate CRL stability, conformation, activity as well as degradation substrate receptor exchange. Studies of the Arabidopsis thaliana deneddylation-deficient den1 mutant led to the identification of many low abundant, non-Cullin NEDD8 conjugates. Examination of neddylated AUXIN RESISTANT1 (AXR1), a prominent neddylated protein in den1, suggests, however, that AXR1 neddylation may be an auto-catalytic side-reaction of Cullin-targeted neddylation and that DEN1 may serve to antagonize non-productive, auto-neddylation from substrates to provide free NEDD8 for CRL regulation.
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Affiliation(s)
- Claus Schwechheimer
- Plant Systems Biology, Emil-Ramann-Strasse 8, Technical University of Munich, 85354 Freising, Germany.
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16
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Eroglu S, Aksoy E. Genome-wide analysis of gene expression profiling revealed that COP9 signalosome is essential for correct expression of Fe homeostasis genes in Arabidopsis. Biometals 2017; 30:685-698. [PMID: 28744713 DOI: 10.1007/s10534-017-0036-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/15/2017] [Indexed: 10/19/2022]
Abstract
In plant cells, either excess or insufficient iron (Fe) concentration triggers stress responses, therefore it is strictly controlled. Proteasome-mediated degradation through ubiquitination of Fe homeostasis proteins has just become the focus of research in recent years. Deactivating ubiquitin ligases, COP9 signalosome has a central importance in the translational control of various stress responses. The aim of the study was to investigate COP9 signalosome in Fe deficiency response of Strategy I plants. In silico analysis of a set of Fe-deficiency-responsive genes was conducted against the transcriptome of Arabidopsis csn mutant lines using Genevestigator software. Induced and suppressed genes were clustered in a hierarchical way and gene ontology enrichment categories were identified. In wild-type Arabidopsis, CSN genes did not respond to iron deficiency. In csn mutant lines, under Fe-sufficient conditions, hundreds of Fe-deficiency-responsive genes were misregulated. Among the ones previously characterized for their physiological roles under Fe deficiency IRT1, NAS4, BTS, NRAMP1 were down-regulated while AHA2, MTP8, FRD3 were up-regulated. Unexpectedly, from those which were regulated in opposite ways, some had been repeatedly shown to be tightly co-regulated by the same transcription factor, FIT. Two proteins from DELLA family, which were reported to interact with FIT to repress its downstream, were found to be strikingly repressed in csn mutants. Overall, the study underlined that the absence of a functional CSN greatly impacted the regulation of Fe homeostasis-related genes, in a manner which cannot be explained simply by the induction of the master transcription factor, FIT. Correct expression of Fe deficiency-responsive genes requires an intact COP9 signalosome in Arabidopsis.
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Affiliation(s)
- Seckin Eroglu
- Department of Genetics and Bioengineering, Faculty of Engineering, İzmir University of Economics, Sakarya Cad., No: 156, Balcova, 35330, İzmir, Turkey
| | - Emre Aksoy
- Department of Agricultural Genetic Engineering, Ayhan Sahenk Faculty of Agricultural Sciences and Technologies, Ömer Halisdemir University, Merkez, 51240, Nigde, Turkey.
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17
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Pacurar DI, Pacurar ML, Lakehal A, Pacurar AM, Ranjan A, Bellini C. The Arabidopsis Cop9 signalosome subunit 4 (CNS4) is involved in adventitious root formation. Sci Rep 2017; 7:628. [PMID: 28377589 PMCID: PMC5429640 DOI: 10.1038/s41598-017-00744-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 03/14/2017] [Indexed: 11/09/2022] Open
Abstract
The COP9 signalosome (CSN) is an evolutionary conserved multiprotein complex that regulates many aspects of plant development by controlling the activity of CULLIN-RING E3 ubiquitin ligases (CRLs). CRLs ubiquitinate and target for proteasomal degradation a vast number of specific substrate proteins involved in many developmental and physiological processes, including light and hormone signaling and cell division. As a consequence of CSN pleiotropic function, complete loss of CSN activity results in seedling lethality. Therefore, a detailed analysis of CSN physiological functions in adult Arabidopsis plants has been hampered by the early seedling lethality of csn null mutants. Here we report the identification and characterization of a viable allele of the Arabidopsis COP9 signalosome subunit 4 (CSN4). The allele, designated csn4-2035, suppresses the adventitious root (AR) phenotype of the Arabidopsis superroot2-1 mutant, potentially by altering its auxin signaling. Furthermore, we show that although the csn4-2035 mutation affects primary and lateral root (LR) formation in the 2035 suppressor mutant, CSN4 and other subunits of the COP9 complex seem to differentially control AR and LR development.
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Affiliation(s)
- Daniel Ioan Pacurar
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden. .,SweTree Technologies AB, P.O. Box 4095, SE-904 03, Umeå, Sweden.
| | - Monica Lacramioara Pacurar
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden.,University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj Napoca, Romania.,SweTree Technologies AB, P.O. Box 4095, SE-904 03, Umeå, Sweden
| | - Abdellah Lakehal
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden
| | - Andrea Mariana Pacurar
- University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj Napoca, Romania
| | - Alok Ranjan
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden
| | - Catherine Bellini
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden. .,Institut National de la Research Agronomic, UMR1318 INRA-AgroParisTech, Institut Jean-Pierre Bourgin, Univ. Paris-Sud, F-78000, Versailles, France.
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18
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Franciosini A, Moubayidin L, Du K, Matari NH, Boccaccini A, Butera S, Vittorioso P, Sabatini S, Jenik PD, Costantino P, Serino G. The COP9 SIGNALOSOME Is Required for Postembryonic Meristem Maintenance in Arabidopsis thaliana. MOLECULAR PLANT 2015; 8:1623-34. [PMID: 26277260 DOI: 10.1016/j.molp.2015.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/29/2015] [Accepted: 08/02/2015] [Indexed: 05/24/2023]
Abstract
Cullin-RING E3 ligases (CRLs) regulate different aspects of plant development and are activated by modification of their cullin subunit with the ubiquitin-like protein NEDD8 (NEural precursor cell expressed Developmentally Down-regulated 8) (neddylation) and deactivated by NEDD8 removal (deneddylation). The constitutively photomorphogenic9 (COP9) signalosome (CSN) acts as a molecular switch of CRLs activity by reverting their neddylation status, but its contribution to embryonic and early seedling development remains poorly characterized. Here, we analyzed the phenotypic defects of csn mutants and monitored the cullin deneddylation/neddylation ratio during embryonic and early seedling development. We show that while csn mutants can complete embryogenesis (albeit at a slower pace than wild-type) and are able to germinate (albeit at a reduced rate), they progressively lose meristem activity upon germination until they become unable to sustain growth. We also show that the majority of cullin proteins are progressively neddylated during the late stages of seed maturation and become deneddylated upon seed germination. This developmentally regulated shift in the cullin neddylation status is absent in csn mutants. We conclude that the CSN and its cullin deneddylation activity are required to sustain postembryonic meristem function in Arabidopsis.
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Affiliation(s)
- Anna Franciosini
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Laila Moubayidin
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Kaiqi Du
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17604-3003, USA
| | - Nahill H Matari
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17604-3003, USA
| | - Alessandra Boccaccini
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Simone Butera
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Paola Vittorioso
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Sabrina Sabatini
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Pablo D Jenik
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17604-3003, USA.
| | - Paolo Costantino
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Serino
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; Institute of Agricultural Biology and Biotechnology, National Research Council of Italy (CNR), via Salaria km 29,300, 00015 Monterotondo Scalo, Rome, Italy.
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19
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Höwing T, Huesmann C, Hoefle C, Nagel MK, Isono E, Hückelhoven R, Gietl C. Endoplasmic reticulum KDEL-tailed cysteine endopeptidase 1 of Arabidopsis (AtCEP1) is involved in pathogen defense. FRONTIERS IN PLANT SCIENCE 2014; 5:58. [PMID: 24605116 PMCID: PMC3932416 DOI: 10.3389/fpls.2014.00058] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/05/2014] [Indexed: 05/20/2023]
Abstract
Programmed cell death (PCD) is a genetically determined process in all multicellular organisms. Plant PCD is effected by a unique group of papain-type cysteine endopeptidases (CysEP) with a C-terminal KDEL endoplasmic reticulum (ER) retention signal (KDEL CysEP). KDEL CysEPs can be stored as pro-enzymes in ER-derived endomembrane compartments and are released as mature CysEPs in the final stages of organelle disintegration. KDEL CysEPs accept a wide variety of amino acids at the active site, including the glycosylated hydroxyprolines of the extensins that form the basic scaffold of the cell wall. In Arabidopsis, three KDEL CysEPs (AtCEP1, AtCEP2, and AtCEP3) are expressed. Cell- and tissue-specific activities of these three genes suggest that KDEL CysEPs participate in the abscission of flower organs and in the collapse of tissues in the final stage of PCD as well as in developmental tissue remodeling. We observed that AtCEP1 is expressed in response to biotic stress stimuli in the leaf. atcep1 knockout mutants showed enhanced susceptibility to powdery mildew caused by the biotrophic ascomycete Erysiphe cruciferarum. A translational fusion protein of AtCEP1 with a three-fold hemaglutinin-tag and the green fluorescent protein under control of the endogenous AtCEP1 promoter (PCEP1::pre-pro-3xHA-EGFP-AtCEP1-KDEL) rescued the pathogenesis phenotype demonstrating the function of AtCEP1 in restriction of powdery mildew. The spatiotemporal AtCEP1-reporter expression during fungal infection together with microscopic inspection of the interaction phenotype suggested a function of AtCEP1 in controlling late stages of compatible interaction including late epidermal cell death. Additionally, expression of stress response genes appeared to be deregulated in the interaction of atcep1 mutants and E. cruciferarum. Possible functions of AtCEP1 in restricting parasitic success of the obligate biotrophic powdery mildew fungus are discussed.
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Affiliation(s)
- Timo Höwing
- Lehrstuhl für Botanik, Center of Life and Food Sciences Weihenstephan, Technische Universität MünchenFreising, Germany
| | - Christina Huesmann
- Lehrstuhl für Phytopathologie, Center of Life and Food Sciences Weihenstephan, Technische Universität MünchenFreising, Germany
| | - Caroline Hoefle
- Lehrstuhl für Phytopathologie, Center of Life and Food Sciences Weihenstephan, Technische Universität MünchenFreising, Germany
| | - Marie-Kristin Nagel
- Department of Plant Systems Biology, Center of Life and Food Sciences Weihenstephan, Technische Universität MünchenFreising, Germany
| | - Erika Isono
- Department of Plant Systems Biology, Center of Life and Food Sciences Weihenstephan, Technische Universität MünchenFreising, Germany
| | - Ralph Hückelhoven
- Lehrstuhl für Phytopathologie, Center of Life and Food Sciences Weihenstephan, Technische Universität MünchenFreising, Germany
| | - Christine Gietl
- Lehrstuhl für Botanik, Center of Life and Food Sciences Weihenstephan, Technische Universität MünchenFreising, Germany
- *Correspondence: Christine Gietl, Lehrstuhl für Botanik, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Emil-Ramann-Str. 4, D-85350 Freising, Germany e-mail:
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Mergner J, Schwechheimer C. The NEDD8 modification pathway in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:103. [PMID: 24711811 PMCID: PMC3968751 DOI: 10.3389/fpls.2014.00103] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 03/03/2014] [Indexed: 05/19/2023]
Abstract
NEDD8, in plants and yeasts also known as RELATED TO UBIQUITIN (RUB), is an evolutionarily conserved 76 amino acid protein highly related to ubiquitin. Like ubiquitin, NEDD8 can be conjugated to and deconjugated from target proteins, but unlike ubiquitin, NEDD8 has not been reported to form chains similar to the different polymeric ubiquitin chains that have a role in a diverse set of cellular processes. NEDD8-modification is best known as a post-translational modification of the cullin subunits of cullin-RING E3 ubiquitin ligases. In this context, structural analyses have revealed that neddylation induces a conformation change of the cullin that brings the ubiquitylation substrates into proximity of the interacting E2 conjugating enzyme. In turn, NEDD8 deconjugation destabilizes the cullin RING ligase complex allowing for the exchange of substrate recognition subunits via the exchange factor CAND1. In plants, components of the neddylation and deneddylation pathway were identified based on mutants with defects in auxin and light responses and the characterization of these mutants has been instrumental for the elucidation of the neddylation pathway. More recently, there has been evidence from animal and plant systems that NEDD8 conjugation may also regulate the behavior or fate of non-cullin substrates in a number of ways. Here, the current knowledge on NEDD8 processing, conjugation and deconjugation is presented, where applicable, in the context of specific signaling pathways from plants.
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Affiliation(s)
| | - Claus Schwechheimer
- *Correspondence: Claus Schwechheimer, Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 4, 85354 Freising, Germany e-mail:
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Choi CM, Gray WM, Mooney S, Hellmann H. Composition, roles, and regulation of cullin-based ubiquitin e3 ligases. THE ARABIDOPSIS BOOK 2014; 12:e0175. [PMID: 25505853 PMCID: PMC4262284 DOI: 10.1199/tab.0175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Due to their sessile nature, plants depend on flexible regulatory systems that allow them to adequately regulate developmental and physiological processes in context with environmental cues. The ubiquitin proteasome pathway, which targets a great number of proteins for degradation, is cellular tool that provides the necessary flexibility to accomplish this task. Ubiquitin E3 ligases provide the needed specificity to the pathway by selectively binding to particular substrates and facilitating their ubiquitylation. The largest group of E3 ligases known in plants is represented by CULLIN-REALLY INTERESTING NEW GENE (RING) E3 ligases (CRLs). In recent years, a great amount of knowledge has been generated to reveal the critical roles of these enzymes across all aspects of plant life. This review provides an overview of the different classes of CRLs in plants, their specific complex compositions, the variety of biological processes they control, and the regulatory steps that can affect their activities.
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Affiliation(s)
| | | | | | - Hanjo Hellmann
- Washington State University, Pullman, Washington
- Address correspondence to
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22
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Licursi V, Salvi C, De Cesare V, Rinaldi T, Mattei B, Fabbri C, Serino G, Bramasole L, Zimbler JZ, Pick E, Barnes BM, Bard M, Negri R. The COP9 signalosome is involved in the regulation of lipid metabolism and of transition metals uptake inSaccharomyces cerevisiae. FEBS J 2013; 281:175-90. [DOI: 10.1111/febs.12584] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/12/2013] [Accepted: 10/08/2013] [Indexed: 01/16/2023]
Affiliation(s)
- Valerio Licursi
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Chiara Salvi
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Virginia De Cesare
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Teresa Rinaldi
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Benedetta Mattei
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Claudia Fabbri
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Giovanna Serino
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
| | - Laylan Bramasole
- Department of Biology; University of Haifa at Oranim; Tivon Israel
| | - Jacob Z. Zimbler
- Department of Biology; University of Haifa at Oranim; Tivon Israel
- Department of Evolutionary and Environmental Biology; University of Haifa; Israel
| | - Elah Pick
- Department of Biology; University of Haifa at Oranim; Tivon Israel
- Department of Evolutionary and Environmental Biology; University of Haifa; Israel
| | - Brett M. Barnes
- Department of Biology; Indiana University - Purdue University; Indianapolis IN USA
| | - Martin Bard
- Department of Biology; Indiana University - Purdue University; Indianapolis IN USA
| | - Rodolfo Negri
- Istituto Pasteur - Fondazione Cenci Bolognetti; Department of Biology and Biotechnology ‘C. Darwin’; Sapienza University of Rome; Italy
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23
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Oxley D, Ktistakis N, Farmaki T. Differential isolation and identification of PI(3)P and PI(3,5)P2 binding proteins from Arabidopsis thaliana using an agarose-phosphatidylinositol-phosphate affinity chromatography. J Proteomics 2013; 91:580-94. [PMID: 24007659 DOI: 10.1016/j.jprot.2013.08.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/25/2013] [Accepted: 08/20/2013] [Indexed: 12/13/2022]
Abstract
UNLABELLED A phosphatidylinositol-phosphate affinity chromatographic approach combined with mass spectrometry was used in order to identify novel PI(3)P and PI(3,5)P2 binding proteins from Arabidopsis thaliana suspension cell extracts. Most of the phosphatidylinositol-phosphate interacting candidates identified from this differential screening are characterized by lysine/arginine rich patches. Direct phosphoinositide binding was identified for important membrane trafficking regulators as well as protein quality control proteins such as the ATG18p orthologue involved in autophagosome formation and the lipid Sec14p like transfer protein. A pentatricopeptide repeat (PPR) containing protein was shown to directly bind to PI(3,5)P2 but not to PI(3)P. PIP chromatography performed using extracts obtained from high salt (0.4M and 1M NaCl) pretreated suspensions showed that the association of an S5-1 40S ribosomal protein with both PI(3)P and PI(3,5)P2 was abolished under salt stress whereas salinity stress induced an increase in the phosphoinositide association of the DUF538 domain containing protein SVB, associated with trichome size. Additional interacting candidates were co-purified with the phosphoinositide bound proteins. Binding of the COP9 signalosome, the heat shock proteins, and the identified 26S proteasomal subunits, is suggested as an indirect effect of their interaction with other proteins directly bound to the PI(3)P and the PI(3,5)P2 phosphoinositides. BIOLOGICAL SIGNIFICANCE PI(3,5)P2 is of special interest because of its low abundance. Furthermore, no endogenous levels have yet been detected in A. thaliana (although there is evidence for its existence in plants). Therefore the isolation of novel interacting candidates in vitro would be of a particular importance since the future study and localization of the respective endogenous proteins may indicate possible targeted compartments or tissues where PI(3,5)P2 could be enriched and thereafter identified. In addition, PI(3,5)P2 is a phosphoinositide extensively studied in mammalian and yeast systems. However, our knowledge of its role in plants as well as a list of its effectors from plants is very limited.
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Affiliation(s)
- David Oxley
- The Mass Spectrometry Group, Babraham Institute, Cambridge, CB2 4AT, UK
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24
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Franciosini A, Lombardi B, Iafrate S, Pecce V, Mele G, Lupacchini L, Rinaldi G, Kondou Y, Gusmaroli G, Aki S, Tsuge T, Deng XW, Matsui M, Vittorioso P, Costantino P, Serino G. The Arabidopsis COP9 SIGNALOSOME INTERACTING F-BOX KELCH 1 protein forms an SCF ubiquitin ligase and regulates hypocotyl elongation. MOLECULAR PLANT 2013; 6:1616-29. [PMID: 23475998 DOI: 10.1093/mp/sst045] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The regulation of protein turnover by the ubiquitin proteasome system (UPS) is a major posttranslational mechanism in eukaryotes. One of the key components of the UPS, the COP9 signalosome (CSN), regulates 'cullin-ring' E3 ubiquitin ligases. In plants, CSN participates in diverse cellular and developmental processes, ranging from light signaling to cell cycle control. In this work, we isolated a new plant-specific CSN-interacting F-box protein, which we denominated CFK1 (COP9 INTERACTING F-BOX KELCH 1). We show that, in Arabidopsis thaliana, CFK1 is a component of a functional ubiquitin ligase complex. We also show that CFK1 stability is regulated by CSN and by proteasome-dependent proteolysis, and that light induces accumulation of the CFK1 transcript in the hypocotyl. Analysis of CFK1 knockdown, mutant, and overexpressing seedlings indicates that CFK1 promotes hypocotyl elongation by increasing cell size. Reduction of CSN levels enhances the short hypocotyl phenotype of CFK1-depleted seedlings, while complete loss of CSN activity suppresses the long-hypocotyl phenotype of CFK1-overexpressing seedlings. We propose that CFK1 (and its regulation by CSN) is a novel component of the cellular mechanisms controlling hypocotyl elongation.
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Affiliation(s)
- Anna Franciosini
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Italy
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25
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Huang H, Quint M, Gray WM. The eta7/csn3-3 auxin response mutant of Arabidopsis defines a novel function for the CSN3 subunit of the COP9 signalosome. PLoS One 2013; 8:e66578. [PMID: 23762492 PMCID: PMC3676356 DOI: 10.1371/journal.pone.0066578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 05/07/2013] [Indexed: 12/02/2022] Open
Abstract
The COP9 signalosome (CSN) is an eight subunit protein complex conserved in all higher eukaryotes. In Arabidopsis thaliana, the CSN regulates auxin response by removing the ubiquitin-like protein NEDD8/RUB1 from the CUL1 subunit of the SCF(TIR1/AFB) ubiquitin-ligase (deneddylation). Previously described null mutations in any CSN subunit result in the pleiotropic cop/det/fus phenotype and cause seedling lethality, hampering the study of CSN functions in plant development. In a genetic screen to identify enhancers of the auxin response defects conferred by the tir1-1 mutation, we identified a viable csn mutant of subunit 3 (CSN3), designated eta7/csn3-3. In addition to enhancing tir1-1 mutant phenotypes, the csn3-3 mutation alone confers several phenotypes indicative of impaired auxin signaling including auxin resistant root growth and diminished auxin responsive gene expression. Unexpectedly however, csn3-3 plants are not defective in either the CSN-mediated deneddylation of CUL1 or in SCF(TIR1)-mediated degradation of Aux/IAA proteins. These findings suggest that csn3-3 is an atypical csn mutant that defines a novel CSN or CSN3-specific function. Consistent with this possibility, we observe dramatic differences in double mutant interactions between csn3-3 and other auxin signaling mutants compared to another weak csn mutant, csn1-10. Lastly, unlike other csn mutants, assembly of the CSN holocomplex is unaffected in csn3-3 plants. However, we detected a small CSN3-containing protein complex that is altered in csn3-3 plants. We hypothesize that in addition to its role in the CSN as a cullin deneddylase, CSN3 functions in a distinct protein complex that is required for proper auxin signaling.
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Affiliation(s)
- He Huang
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Marcel Quint
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - William M. Gray
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
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26
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Nakasone A, Fujiwara M, Fukao Y, Biswas KK, Rahman A, Kawai-Yamada M, Narumi I, Uchimiya H, Oono Y. SMALL ACIDIC PROTEIN1 acts with RUB modification components, the COP9 signalosome, and AXR1 to regulate growth and development of Arabidopsis. PLANT PHYSIOLOGY 2012; 160:93-105. [PMID: 22576848 PMCID: PMC3440233 DOI: 10.1104/pp.111.188409] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 05/09/2012] [Indexed: 05/25/2023]
Abstract
Previously, a dysfunction of the SMALL ACIDIC PROTEIN1 (SMAP1) gene was identified as the cause of the anti-auxin resistant1 (aar1) mutant of Arabidopsis (Arabidopsis thaliana). SMAP1 is involved in the response pathway of synthetic auxin, 2,4-dichlorophenoxyacetic acid, and functions upstream of the auxin/indole-3-acetic acid protein degradation step in auxin signaling. However, the exact mechanism by which SMAP1 functions in auxin signaling remains unknown. Here, we demonstrate that SMAP1 is required for normal plant growth and development and the root response to indole-3-acetic acid or methyl jasmonate in the auxin resistant1 (axr1) mutation background. Deletion analysis and green fluorescent protein/glutathione S-transferase pull-down assays showed that SMAP1 physically interacts with the CONSTITUTIVE PHOTOMORPHOGENIC9 SIGNALOSOME (CSN) via the SMAP1 F/D region. The extremely dwarf phenotype of the aar1-1 csn5a-1 double mutant confirms the functional role of SMAP1 in plant growth and development under limiting CSN functionality. Our findings suggest that SMAP1 is involved in the auxin response and possibly in other cullin-RING ubiquitin ligase-regulated signaling processes via its interaction with components associated with RELATED TO UBIQUITIN modification.
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27
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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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28
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Topp SH, Rasmussen SK. Evaluating the potential of SHI expression as a compacting tool for ornamental plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 187:19-30. [PMID: 22404829 DOI: 10.1016/j.plantsci.2012.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 01/17/2012] [Accepted: 01/18/2012] [Indexed: 05/31/2023]
Abstract
Control of plant growth, especially elongation of stems, is important in modern plant production, and many plant species, including cereals, grasses, fruit trees and ornamentals, are regularly treated chemically to control their stature and flowering time. Chemical treatments ensure short, homogenous plants, which are more robust and easy to harvest, transport and sell. Although growth retardants are an expensive and undesirable step in plant production, it is unfortunately necessary at present. Compact growth is desirable in most ornamentals and this trait can be difficult to obtain by traditional breeding. As an alternative, biotechnology could provide plant varieties with optimized growth habits. This review is an introduction to the family of SHI transcription factors, which has recently been used to produce compact plants of very diverse species. The possible functions and regulations of the SHI proteins are discussed, and the potential of using overexpression as means to dwarf plants is assessed. In conclusion the breeding of some species, especially flowering ornamentals, could benefit from this strategy. Furthermore, detailed knowledge about the role of SHI proteins in plant growth and development could help shed more light on the interactions between plant hormone signaling pathways.
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Affiliation(s)
- Sine H Topp
- Department of Agriculture and Ecology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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29
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Stratmann JW, Gusmaroli G. Many jobs for one good cop - the COP9 signalosome guards development and defense. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:50-64. [PMID: 22325866 DOI: 10.1016/j.plantsci.2011.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 10/10/2011] [Accepted: 10/11/2011] [Indexed: 05/08/2023]
Abstract
The COP9 signalosome (CSN) is a multiprotein complex that regulates the activity of CULLIN-RING E3 ubiquitin ligases (CRLs). CRLs ubiquitinate substrate proteins and thus target them for proteasomal degradation. This post-translational modification of proteins is arguably as important as reversible protein phosphorylation. The number of putative CRLs that recognize specific substrate proteins is vast, and known CRL substrates are involved in many cellular plant processes such as hormone signaling, the cell cycle, and regulation of growth, development, and defenses. By controlling the activity of CRLs, the CSN may integrate and fine-tune all of these processes. Recent research has unraveled in great mechanistic detail how the two multiprotein complexes CSN and CRL interact. As a consequence of CSN pleiotropy, complete loss of CSN function results in seedling lethality. However, recent work on plants that exhibit a partial loss of CSN function, has uncovered a role of the CSN during later life stages in processes such as development and defenses against pathogens and herbivorous insects. Not all aspects of development and defense are affected equally by CSN silencing, probably due to the differential participation and importance of CSN-regulated CRLs in these processes. This review will provide an overview of the highly complex regulation of CRL activity by CSN, and the many roles of the CSN in plant development and defense.
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Affiliation(s)
- Johannes W Stratmann
- University of South Carolina, Department of Biological Sciences, Columbia, SC 29208, USA.
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Chigri F, Flosdorff S, Pilz S, Kölle E, Dolze E, Gietl C, Vothknecht UC. The Arabidopsis calmodulin-like proteins AtCML30 and AtCML3 are targeted to mitochondria and peroxisomes, respectively. PLANT MOLECULAR BIOLOGY 2012; 78:211-22. [PMID: 22116655 DOI: 10.1007/s11103-011-9856-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 11/08/2011] [Indexed: 05/24/2023]
Abstract
Calmodulin (CaM) is a ubiquitous sensor/transducer of calcium signals in eukaryotic organisms. While CaM mediated calcium regulation of cytosolic processes is well established, there is growing evidence for the inclusion of organelles such as chloroplasts, mitochondria and peroxisomes into the calcium/calmodulin regulation network. A number of CaM-binding proteins have been identified in these organelles and processes such as protein import into chloroplasts and mitochondria have been shown to be governed by CaM regulation. What have been missing to date are the mediators of this regulation since no CaM or calmodulin-like protein (CML) has been identified in any of these organelles. Here we show that two Arabidopsis CMLs, AtCML3 and AtCML30, are localized in peroxisomes and mitochondria, respectively. AtCML3 is targeted via an unusual C-terminal PTS1-like tripeptide while AtCML30 utilizes an N-terminal, non-cleavable transit peptide. Both proteins possess the typical structure of CaMs, with two pairs of EF-hand motifs separated by a short linker domain. They furthermore display common characteristics, such as calcium-dependent alteration of gel mobility and calcium-dependent exposure of a hydrophobic surface. This indicates that they can function in a similar manner as canonical CaMs. The presence of close homologues to AtCML3 and AtCML30 in other plants further indicates that organellar targeting of these CMLs is not a specific feature of Arabidopsis. The identification of peroxisomal and mitochondrial CMLs is an important step in the understanding how these organelles are integrated into the cellular calcium/calmodulin signaling pathways.
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Affiliation(s)
- Fatima Chigri
- Department of Biology of the LMU Munich, Center for Integrated Protein Science (Munich), 82152 Martinsried, Germany
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Halimi Y, Dessau M, Pollak S, Ast T, Erez T, Livnat-Levanon N, Karniol B, Hirsch JA, Chamovitz DA. COP9 signalosome subunit 7 from Arabidopsis interacts with and regulates the small subunit of ribonucleotide reductase (RNR2). PLANT MOLECULAR BIOLOGY 2011; 77:77-89. [PMID: 21614643 DOI: 10.1007/s11103-011-9795-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 05/13/2011] [Indexed: 05/30/2023]
Abstract
The COP9 Signalosome protein complex (CSN) is a pleiotropic regulator of plant development and contains eight-subunits. Six of these subunits contain the PCI motif which mediates specific protein interactions necessary for the integrity of the complex. COP9 complex subunit 7 (CSN7) contains an N-terminal PCI motif followed by a C-terminal extension which is also necessary for CSN function. A yeast-interaction trap assay identified the small subunit of ribonucelotide reductase (RNR2) from Arabidopsis as interacting with the C-terminal section of CSN7. This interaction was confirmed in planta by both bimolecular fluorescence complementation and immuoprecipitation assays with endogenous proteins. The subcellular localization of RNR2 was primarily nuclear in meristematic regions, and cytoplasmic in adult cells. RNR2 was constitutively nuclear in csn7 mutant seedlings, and was also primarily nuclear in wild type seedlings following exposure to UV-C. These two results correlate with constitutive expression of several DNA-damage response genes in csn7 mutants, and to increased tolerance of csn7 seedlings to UV-C treatment. We propose that the CSN is a negative regulator of RNR activity in Arabidopsis.
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Affiliation(s)
- Yair Halimi
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, 69978 Ramat Aviv, Israel
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32
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Hind SR, Pulliam SE, Veronese P, Shantharaj D, Nazir A, Jacobs NS, Stratmann JW. The COP9 signalosome controls jasmonic acid synthesis and plant responses to herbivory and pathogens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:480-91. [PMID: 21265900 DOI: 10.1111/j.1365-313x.2010.04437.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The COP9 signalosome (CSN) is a multi-protein complex that regulates the activities of cullin-RING E3 ubiquitin ligases (CRLs). CRLs ubiquitinate proteins in order to target them for proteasomal degradation. The CSN is required for proper plant development. Here we show that the CSN also has a profound effect on plant defense responses. Silencing of genes for CSN subunits in tomato plants resulted in a mild morphological phenotype and reduced expression of wound-responsive genes in response to mechanical wounding, attack by Manduca sexta larvae, and Prosystemin over-expression. In contrast, expression of pathogenesis-related genes was increased in a stimulus-independent manner in these plants. The reduced wound response in CSN-silenced plants corresponded with reduced synthesis of jasmonic acid (JA), but levels of salicylic acid (SA) were unaltered. As a consequence, these plants exhibited reduced resistance against herbivorous M. sexta larvae and the necrotrophic fungal pathogen Botrytis cinerea. In contrast, susceptibility to tobacco mosaic virus (TMV) was not altered in CSN-silenced plants. These data demonstrate that the CSN orchestrates not only plant development but also JA-dependent plant defense responses.
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Affiliation(s)
- Sarah R Hind
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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New suppressors of THO mutations identify Thp3 (Ypr045c)-Csn12 as a protein complex involved in transcription elongation. Mol Cell Biol 2010; 31:674-85. [PMID: 21149575 DOI: 10.1128/mcb.01188-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Formation of a ribonucleoprotein particle (mRNP) competent for export requires the coupling of transcription with mRNA processing and RNA export. A key link between these processes is provided by the THO complex. To progress in our understanding of this coupling, we have performed a search for suppressors of the transcription defect caused by the hpr1Δ mutation. This has permitted us to identify mutations in the genes for the RNA polymerase II mediator component Med10, the Sch9 protein kinase, and the Ypr045c protein. We report a role in transcription elongation for Ypr045c (Thp3) and the Csn12 component of the COP9 signalosome. Thp3 and Csn12 form a complex that is recruited to transcribed genes. Their mutations suppress the gene expression defects of THO complex mutants involved in mRNP biogenesis and export and show defects in mRNA accumulation. Transcription elongation impairment of thp3Δ mutants is shown by in vivo transcript run-on analysis performed in G-less systems. Thp3-Csn12 establishes a novel link between transcription and mRNA processing that opens new perspectives on our understanding of gene expression and reveals novel functions for a component of the COP9 signalosome. Thp3-Csn12 also copurifies with ribosomal proteins, which opens the possibility that it has other functions in addition to transcription.
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Wang J, Hu Q, Chen H, Zhou Z, Li W, Wang Y, Li S, He Q. Role of individual subunits of the Neurospora crassa CSN complex in regulation of deneddylation and stability of cullin proteins. PLoS Genet 2010; 6:e1001232. [PMID: 21151958 PMCID: PMC2996332 DOI: 10.1371/journal.pgen.1001232] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 11/01/2010] [Indexed: 11/18/2022] Open
Abstract
The Cop9 signalosome (CSN) is an evolutionarily conserved multifunctional complex that controls ubiquitin-dependent protein degradation in eukaryotes. We found seven CSN subunits in Neurospora crassa in a previous study, but only one subunit, CSN-2, was functionally characterized. In this study, we created knockout mutants for the remaining individual CSN subunits in N. crassa. By phenotypic observation, we found that loss of CSN-1, CSN-2, CSN-4, CSN-5, CSN-6, or CSN-7 resulted in severe defects in growth, conidiation, and circadian rhythm; the defect severity was gene-dependent. Unexpectedly, CSN-3 knockout mutants displayed the same phenotype as wild-type N. crassa. Consistent with these phenotypic observations, deneddylation of cullin proteins in csn-1, csn-2, csn-4, csn-5, csn-6, or csn-7 mutants was dramatically impaired, while deletion of csn-3 did not cause any alteration in the neddylation/deneddylation state of cullins. We further demonstrated that CSN-1, CSN-2, CSN-4, CSN-5, CSN-6, and CSN-7, but not CSN-3, were essential for maintaining the stability of Cul1 in SCF complexes and Cul3 and BTB proteins in Cul3-BTB E3s, while five of the CSN subunits, but not CSN-3 and CSN-5, were also required for maintaining the stability of SKP-1 in SCF complexes. All seven CSN subunits were necessary for maintaining the stability of Cul4-DDB1 complexes. In addition, CSN-3 was also required for maintaining the stability of the CSN-2 subunit and FWD-1 in the SCFFWD-1 complex. Together, these results not only provide functional insights into the different roles of individual subunits in the CSN complex, but also establish a functional framework for understanding the multiple functions of the CSN complex in biological processes. Protein degradation is precisely controlled in cells. The ubiquitin-mediated protein degradation pathway is highly conserved in eukaryotes, and the activity of ubiquitin ligases is regulated by the Cop9 signalosome (CSN), a multisubunit complex that is evolutionarily conserved from yeast to humans. Determining how the CSN complex functions biologically is crucial for understanding regulation of the ubiquitin-mediated protein degradation pathway. The filamentous fungus N. crassa is commonly used to study protein degradation. Its CSN complex contains seven subunits (CSN-1 to CSN-7). In this study, we generated knockout mutants of individual CSN subunits and observed the phenotypes of each mutant. We demonstrated that six of the seven CSN subunits were essential for cleaving the ubiquitin-like protein Nedd8 from cullin proteins (which act as scaffolds for ubiquitin ligases). In contrast, loss of the CSN-3 subunit had no effect on cullin neddylation. We also found that each CSN subunit had distinct roles in maintaining the stability of key components of cullin-based ubiquitin ligases. In summary, we systematically investigated the unequal contributions of CSN subunits to deneddylation and the maintenance of cullin-based ubiquitin ligases in N. crassa. Our work establishes a framework for understanding the function of CSN subunits in other eukaryotes.
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Affiliation(s)
- Jiyong Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiwen Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huijie Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhipeng Zhou
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Weihua Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Ying Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shaojie Li
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (Q. He); (S. Li)
| | - Qun He
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- * E-mail: (Q. He); (S. Li)
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Braus GH, Irniger S, Bayram O. Fungal development and the COP9 signalosome. Curr Opin Microbiol 2010; 13:672-6. [PMID: 20934903 DOI: 10.1016/j.mib.2010.09.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Revised: 09/13/2010] [Accepted: 09/15/2010] [Indexed: 12/26/2022]
Abstract
The conserved COP9 signalosome (CSN) multiprotein complex is located at the interface between cellular signaling, protein modification, life span and the development of multicellular organisms. CSN is required for light-controlled responses in filamentous fungi. This includes the circadian rhythm of Neurospora crassa or the repression of sexual development by light in Aspergillus nidulans. In contrast to plants and animals, CSN is not essential for fungal viability. Therefore fungi are suitable models to study CSN composition, activity and cellular functions and its role in light controlled development.
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Affiliation(s)
- Gerhard H Braus
- Institut für Mikrobiologie und Genetik, Abteilung Molekulare Mikrobiologie und Genetik, Georg-August-Universität, Grisebachstr. 8, D-37077 Göttingen, Germany.
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Isono E, Katsiarimpa A, Müller IK, Anzenberger F, Stierhof YD, Geldner N, Chory J, Schwechheimer C. The deubiquitinating enzyme AMSH3 is required for intracellular trafficking and vacuole biogenesis in Arabidopsis thaliana. THE PLANT CELL 2010; 22:1826-37. [PMID: 20543027 PMCID: PMC2910964 DOI: 10.1105/tpc.110.075952] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 05/21/2010] [Accepted: 05/26/2010] [Indexed: 05/18/2023]
Abstract
Ubiquitination, deubiquitination, and the formation of specific ubiquitin chain topologies have been implicated in various cellular processes. Little is known, however, about the role of ubiquitin in the development of cellular organelles. Here, we identify and characterize the deubiquitinating enzyme AMSH3 from Arabidopsis thaliana. AMSH3 hydrolyzes K48- and K63-linked ubiquitin chains in vitro and accumulates both ubiquitin chain types in vivo. amsh3 mutants fail to form a central lytic vacuole, accumulate autophagosomes, and mis-sort vacuolar protein cargo to the intercellular space. Furthermore, AMSH3 is required for efficient endocytosis of the styryl dye FM4-64 and the auxin efflux facilitator PIN2. We thus present evidence for a role of deubiquitination in intracellular trafficking and vacuole biogenesis.
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Affiliation(s)
- Erika Isono
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
| | - Anthi Katsiarimpa
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
| | - Isabel Karin Müller
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
| | - Franziska Anzenberger
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
| | - York-Dieter Stierhof
- Microscopy Unit, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
| | - Niko Geldner
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute, La Jolla, California 92037
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute, La Jolla, California 92037
| | - Claus Schwechheimer
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
- Address correspondence to
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Chen KM, Holmström M, Raksajit W, Suorsa M, Piippo M, Aro EM. Small chloroplast-targeted DnaJ proteins are involved in optimization of photosynthetic reactions in Arabidopsis thaliana. BMC PLANT BIOLOGY 2010; 10:43. [PMID: 20205940 PMCID: PMC2844072 DOI: 10.1186/1471-2229-10-43] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 03/07/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND DnaJ proteins participate in many metabolic pathways through dynamic interactions with various components of these processes. The role of three small chloroplast-targeted DnaJ proteins, AtJ8 (At1 g80920), AtJ11 (At4 g36040) and AtJ20 (At4 g13830), was investigated here using knock-out mutants of Arabidopsis thaliana. Photochemical efficiency, capacity of CO2 assimilation, stabilization of Photosystem (PS) II dimers and supercomplexes under high light illumination, energy distribution between PSI and PSII and phosphorylation of PSII-LHCII proteins, global gene expression profiles and oxidative stress responses of these DnaJ mutants were analyzed. RESULTS Knockout of one of these proteins caused a series of events including a decrease in photosynthetic efficiency, destabilization of PSII complexes and loss of control for balancing the redox reactions in chloroplasts. Data obtained with DNA microarray analysis demonstrated that the lack of one of these DnaJ proteins triggers a global stress response and therefore confers the plants greater tolerance to oxidative stress induced by high light or methyl viologen treatments. Expression of a set of genes encoding enzymes that detoxify reactive oxygen species (ROS) as well as a number of stress-related transcription factors behaved in the mutants at growth light similarly to that when wild-type (WT) plants were transferred to high light. Also a set of genes related to redox regulation were upregulated in the mutants. On the other hand, although the three DnaJ proteins reside in chloroplasts, the expression of most genes encoding thylakoid membrane proteins was not changed in the mutants. CONCLUSION It is proposed that the tolerance of the DnaJ protein knockout plants to oxidative stress occurs at the expense of the flexibility of photosynthetic reactions. Despite the fact that the effects of the individual protein knockout on the response of plants to high light treatment are quite similar, it is conceivable that both specific- and cross-talk functions exist between the three small chloroplast-targeted DnaJ proteins, AtJ8, AtJ11 and AtJ20.
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Affiliation(s)
- Kun-Ming Chen
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, 310029 Hangzhou, China
| | - Maija Holmström
- Department of Biochemistry and Food Chemistry, Plant Physiology and Molecular Biology, University of Turku, FI-20014 Turku, Finland
| | - Wuttinun Raksajit
- Department of Biochemistry and Food Chemistry, Plant Physiology and Molecular Biology, University of Turku, FI-20014 Turku, Finland
| | - Marjaana Suorsa
- Department of Biochemistry and Food Chemistry, Plant Physiology and Molecular Biology, University of Turku, FI-20014 Turku, Finland
| | - Mirva Piippo
- Department of Biochemistry and Food Chemistry, Plant Physiology and Molecular Biology, University of Turku, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Department of Biochemistry and Food Chemistry, Plant Physiology and Molecular Biology, University of Turku, FI-20014 Turku, Finland
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Sumoylation and other ubiquitin-like post-translational modifications in plants. Trends Cell Biol 2010; 20:223-32. [PMID: 20189809 DOI: 10.1016/j.tcb.2010.01.007] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 01/08/2010] [Accepted: 01/18/2010] [Indexed: 11/22/2022]
Abstract
Post-translational modifications diversify proteome activity to mediate complex hierarchical regulatory processes that are crucial to eukaryotic cell function. Protein modification by Ub (ubiquitin) and Ubls (ubiquitin-like proteins) in plants, as in yeast and metazoans, is necessary for numerous cellular and developmental processes and for the genetic reprogramming that occurs in response to hormonal stimuli, host-pathogen interaction-related stimuli and environmental stimuli. Ub and Ubl modifications, such as sumoylation, facilitate molecular interaction with specific substrates. Recent evidence has permitted inference of the mechanisms by which Ubl modifications regulate physiological processes such as cell-cycle progression, abscisic acid signaling, development, and biotic and abiotic stress responses. This review presents our current understanding of sumoylation and other Ubl conjugation processes in plant biology.
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Dohmann EMN, Nill C, Schwechheimer C. DELLA proteins restrain germination and elongation growth in Arabidopsis thaliana COP9 signalosome mutants. Eur J Cell Biol 2010; 89:163-8. [PMID: 20083325 DOI: 10.1016/j.ejcb.2009.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The COP9 signalosome (CSN) is an evolutionarily conserved multiprotein complex with an essential role in the development of higher eukaryotes. CSN deconjugates the ubiquitin-related modifier NEDD8 from the cullin subunit of cullin-RING type E3 ubiquitin ligases (CRLs), and CSN-mediated cullin deneddylation is required for full CRL activity. Although several plant E3 CRL functions have been shown to be compromised in Arabidopsis csn mutants, none of these functions have so far been shown to limit growth in these mutants. Here, we examine the role of CSN in the context of the E3 ubiquitin ligase SCF(SLEEPY1 (SLY1)), which promotes gibberellic acid (GA)-dependent responses in Arabidopsis thaliana. We show that csn mutants are impaired in GA- and SCF(SLY1)-dependent germination and elongation growth, and we show that these defects correlate with an accumulation and reduced turnover of an SCF(SLY1)-degradation target, the DELLA protein REPRESSOR-OF-ga1-3 (RGA). Genetic interaction studies between csn mutants and loss-of-function alleles of RGA and its functional homologue GIBBERELLIC ACID INSENSITIVE (GAI) further reveal that RGA and GAI repress defects of germination in strong csn mutants. In addition, we find that these two DELLA proteins are largely responsible for the elongation defects of a weak csn5 mutant allele. We thus conclude that an impairment of SCF(SLY1) is at least in part causative for the germination and elongation defects of csn mutants, and suggest that DELLA proteins are major growth repressors in these mutants.
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Affiliation(s)
- Esther Mirjam Natascha Dohmann
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, Auf der Morgenstelle 5, 72076 Tübingen, Germany
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Schwechheimer C, Isono E. The COP9 signalosome and its role in plant development. Eur J Cell Biol 2009; 89:157-62. [PMID: 20036030 DOI: 10.1016/j.ejcb.2009.11.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The COP9 signalosome (CSN) is an evolutionarily conserved multiprotein complex with a role in the regulation of cullin-RING type E3 ubiquitin ligases (CRLs). CSN exerts its function on E3 ligases by deconjugating the ubiquitin-related protein NEDD8 from the CRL cullin subunit. Thereby, CSN has an impact on multiple CRL-dependent processes. In recent years, advances have been made in understanding the structural organisation and biochemical function of CSN: Crystal structure analysis and mass spectrometry-assisted studies have come up with first models of the pair-wise and complex interactions of the 8 CSN subunits. Based on the analysis of mutant phenotypes, it can now be taken as an accepted fact that--at least in plants--the major biochemical function of CSN resides in its deneddylation activity, which is mediated by CSN subunit 5 (CSN5). Furthermore, it could be demonstrated that CSN function and deneddylation are required but not essential for CRL-mediated processes, and models for the role of neddylation and deneddylation in controlling CRL activity are emerging. Significant advances have also been made in identifying pathways that are growth restricting in the Arabidopsis csn mutants. Recently it has been shown that a G2 phase arrest, possibly due to genomic instability, restricts growth in Arabidopsis csn mutants. This review provides an update on recent advances in understanding CSN structure and function and summarises the current knowledge on its role in plant development and cell cycle progression.
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Affiliation(s)
- Claus Schwechheimer
- Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany.
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Nishimura N, Okamoto M, Narusaka M, Yasuda M, Nakashita H, Shinozaki K, Narusaka Y, Hirayama T. ABA Hypersensitive Germination2-1 Causes the Activation of Both Abscisic Acid and Salicylic Acid Responses in Arabidopsis. ACTA ACUST UNITED AC 2009; 50:2112-22. [DOI: 10.1093/pcp/pcp146] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Stuttmann J, Parker JE, Noël LD. Novel aspects of COP9 signalosome functions revealed through analysis of hypomorphic csn mutants. PLANT SIGNALING & BEHAVIOR 2009; 4:896-8. [PMID: 19847120 PMCID: PMC2802793 DOI: 10.4161/psb.4.9.9526] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The COP9 signalosome (CSN) is a conserved eukaryotic protein complex implicated in the regulation of cullin-RING type E3 ubiquitin ligases by cleaving the small peptide RUB/Nedd8 from cullins. However, detailed analysis of CSN physiological functions in Arabidopsis has been hampered by the early seedling-lethality of csn null mutants. We and others have now identified a number of viable hypomorphic csn mutants which start to reveal novel CSN-dependent activities in adult Arabidopsis plants. Here, we present a detailed comparative analysis of the csn5a-1 and csn2-5 mutants as a mean to improve understanding of CSN functions in plant cells. Our observations point to CSN-independent activities of CSN5 and suggest a role of the CSN in cytoskeleton assembly/organization.
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Affiliation(s)
- Johannes Stuttmann
- Institut de Biologie Environnementale et Biotechnologie, UMR 6191 CNRS-CEA-Université de la méditerranée Aix-Marseille II, CEN Cadarache, Saint Paul-lez-Durance, France.
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Chamovitz DA. Revisiting the COP9 signalosome as a transcriptional regulator. EMBO Rep 2009; 10:352-8. [PMID: 19305390 DOI: 10.1038/embor.2009.33] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2009] [Accepted: 02/16/2009] [Indexed: 11/09/2022] Open
Abstract
The COP9 signalosome (CSN) is a highly conserved protein complex that was originally described as a repressor of light-dependent growth and transcription in Arabidopsis. The most studied CSN function is the regulation of protein degradation, which occurs primarily through the removal of the ubiquitin-like modifier Nedd8 from cullin-based E3 ubiquitin ligases. This activity can regulate transcription-factor stability and, therefore, transcriptional activity. Recent data suggest that the CSN also regulates transcription on the chromatin by mechanisms that are not yet clearly understood. Furthermore, the CSN subunits CSN5 and CSN2 seem to act as transcriptional coactivators and corepressors, respectively. Here, I re-evaluate the mechanisms by which the CSN acts as a transcriptional regulator, and suggest that they could extend beyond the regulation of protein stability.
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Affiliation(s)
- Daniel A Chamovitz
- Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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