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Rudolf J, Tomovicova L, Panzarova K, Fajkus J, Hejatko J, Skalak J. Epigenetics and plant hormone dynamics: a functional and methodological perspective. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5267-5294. [PMID: 38373206 PMCID: PMC11389840 DOI: 10.1093/jxb/erae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.
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Affiliation(s)
- Jiri Rudolf
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Lucia Tomovicova
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Klara Panzarova
- Photon Systems Instruments, Prumyslova 470, CZ-664 24 Drasov, Czech Republic
| | - Jiri Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Jan Hejatko
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Jan Skalak
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
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Vogel K, Isono E. Erasing marks: Functions of plant deubiquitylating enzymes in modulating the ubiquitin code. THE PLANT CELL 2024; 36:3057-3073. [PMID: 38656977 PMCID: PMC11371157 DOI: 10.1093/plcell/koae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Plant cells need to respond to environmental stimuli and developmental signals accurately and promptly. Ubiquitylation is a reversible posttranslational modification that enables the adaptation of cellular proteostasis to internal or external factors. The different topologies of ubiquitin linkages serve as the structural basis for the ubiquitin code, which can be interpreted by ubiquitin-binding proteins or readers in specific processes. The ubiquitylation status of target proteins is regulated by ubiquitylating enzymes or writers, as well as deubiquitylating enzymes (DUBs) or erasers. DUBs can remove ubiquitin molecules from target proteins. Arabidopsis (A. thaliana) DUBs belong to 7 protein families and exhibit a wide range of functions and play an important role in regulating selective protein degradation processes, including proteasomal, endocytic, and autophagic protein degradation. DUBs also shape the epigenetic landscape and modulate DNA damage repair processes. In this review, we summarize the current knowledge on DUBs in plants, their cellular functions, and the molecular mechanisms involved in the regulation of plant DUBs.
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Affiliation(s)
- Karin Vogel
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
- Division of Molecular Cell Biology, National Institute for Basic Biology, Okazaki 444-8585 Aichi, Japan
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Liang S, Duan Z, He X, Yang X, Yuan Y, Liang Q, Pan Y, Zhou G, Zhang M, Liu S, Tian Z. Natural variation in GmSW17 controls seed size in soybean. Nat Commun 2024; 15:7417. [PMID: 39198482 PMCID: PMC11358545 DOI: 10.1038/s41467-024-51798-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 08/17/2024] [Indexed: 09/01/2024] Open
Abstract
Seed size/weight plays an important role in determining crop yield, yet only few genes controlling seed size have been characterized in soybean. Here, we perform a genome-wide association study and identify a major quantitative trait locus (QTL), named GmSW17 (Seed Width 17), on chromosome 17 that determine soybean seed width/weight in natural population. GmSW17 encodes a ubiquitin-specific protease, an ortholog to UBP22, belonging to the ubiquitin-specific protease (USPs/UBPs) family. Further functional investigations reveal that GmSW17 interacts with GmSGF11 and GmENY2 to form a deubiquitinase (DUB) module, which influences H2Bub levels and negatively regulates the expression of GmDP-E2F-1, thereby inhibiting the G1-to-S transition. Population analysis demonstrates that GmSW17 undergo artificial selection during soybean domestication but has not been fixed in modern breeding. In summary, our study identifies a predominant gene related to soybean seed weight, providing potential advantages for high-yield breeding in soybean.
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Affiliation(s)
- Shan Liang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xuemei He
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xia Yang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yaqin Yuan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qianjin Liang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yi Pan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Guoan Zhou
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Zhixi Tian
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Baile F, Calonje M. Dynamics of polycomb group marks in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102553. [PMID: 38776572 DOI: 10.1016/j.pbi.2024.102553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/08/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Polycomb Group (PcG) histone-modifying system is key in maintaining gene repression, providing a mitotically heritable cellular memory. Nevertheless, to allow plants to transition through distinct transcriptional programs during development or to respond to external cues, PcG-mediated repression requires reversibility. Several data suggest that the dynamics of PcG marks may vary considerably in different cell contexts; however, how PcG marks are established, maintained, or removed in each case is far from clear. In this review, we survey the knowns and unknowns of the molecular mechanisms underlying the maintenance or turnover of PcG marks in different cell stages.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain.
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Chen R, Gu G, Zhang B, Du C, Lin X, Cai W, Zheng Y, Li T, Wang R, Xie X. Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to bacterial wilt resistance in tobacco ( Nicotiana tabacum L.) and eggplant ( Solanum melongena L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1425651. [PMID: 39139726 PMCID: PMC11319268 DOI: 10.3389/fpls.2024.1425651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
The E3 enzyme in the UPS pathway is a crucial factor for inhibiting substrate specificity. In Solanaceae, the U-box E3 ubiquitin ligase has a complex relationship with plant growth and development, and plays a pivotal role in responding to various biotic and abiotic stresses. The analysis of the U-box gene family in Solanaceae and its expression profile under different stresses holds significant implications. A total of 116 tobacco NtU-boxs and 56 eggplant SmU-boxs were identified based on their respective genome sequences. Phylogenetic analysis of U-box genes in tobacco, eggplant, tomato, Arabidopsis, pepper, and potato revealed five distinct subgroups (I-V). Gene structure and protein motifs analysis found a high degree of conservation in both exon/intron organization and protein motifs among tobacco and eggplant U-box genes especially the members within the same subfamily. A total of 15 pairs of segmental duplication and 1 gene pair of tandem duplication were identified in tobacco based on the analysis of gene duplication events, while 10 pairs of segmental duplication in eggplant. It is speculated that segmental duplication events are the primary driver for the expansion of the U-box gene family in both tobacco and eggplant. The promoters of NtU-box and SmU-box genes contained cis-regulatory elements associated with cellular development, phytohormones, environment stress, and photoresponsive elements. Transcriptomic data analysis shows that the expression levels of the tobacco and eggplant U-box genes in different tissues and various abiotic stress conditions. Using cultivar Hongda of tobacco and cultivar Yanzhi of eggplant as materials, qRT-PCR analysis has revealed that 15 selected NtU-box genes and 8 SmU-box may play important roles in response to pathogen Ras invasion both in tobacco and eggplant.
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Affiliation(s)
- Rui Chen
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Gang Gu
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | - Binghui Zhang
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | | | | | | | - Yan Zheng
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Tong Li
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Ruiqi Wang
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou, China
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Wang W, Sung S. Chromatin sensing: integration of environmental signals to reprogram plant development through chromatin regulators. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4332-4345. [PMID: 38436409 PMCID: PMC11263488 DOI: 10.1093/jxb/erae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Chromatin regulation in eukaryotes plays pivotal roles in controlling the developmental regulatory gene network. This review explores the intricate interplay between chromatin regulators and environmental signals, elucidating their roles in shaping plant development. As sessile organisms, plants have evolved sophisticated mechanisms to perceive and respond to environmental cues, orchestrating developmental programs that ensure adaptability and survival. A central aspect of this dynamic response lies in the modulation of versatile gene regulatory networks, mediated in part by various chromatin regulators. Here, we summarized current understanding of the molecular mechanisms through which chromatin regulators integrate environmental signals, influencing key aspects of plant development.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
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Wang Y, Sun X, Peng J, Li F, Ali F, Wang Z. Regulation of seed germination: ROS, epigenetic, and hormonal aspects. J Adv Res 2024:S2090-1232(24)00225-X. [PMID: 38838783 DOI: 10.1016/j.jare.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus. AIM of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement. KEY SCIENTIFIC CONCEPTS OF REVIEW We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.
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Affiliation(s)
- Yakong Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiangyang Sun
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jun Peng
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Fu W, Fan D, Liu S, Bu Y. Genome-wide identification and expression analysis of Ubiquitin-specific protease gene family in maize (Zea mays L.). BMC PLANT BIOLOGY 2024; 24:404. [PMID: 38750451 PMCID: PMC11097515 DOI: 10.1186/s12870-024-04953-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Ubiquitin-specific proteases (UBPs) are a large family of deubiquitinating enzymes (DUBs). They are widespread in plants and are critical for plant growth, development, and response to external stresses. However, there are few studies on the functional characteristics of the UBP gene family in the important staple crop, maize (Zea mays L.). RESULTS In this study, we performed a bioinformatic analysis of the entire maize genome and identified 45 UBP genes. Phylogenetic analysis indicated that 45 ZmUBP genes can be divided into 15 subfamilies. Analysis of evolutionary patterns and divergence levels indicated that ZmUBP genes were present before the isolation of dicotyledons, were highly conserved and subjected to purifying selection during evolution. Most ZmUBP genes exhibited different expression levels in different tissues and developmental stages. Based on transcriptome data and promoter element analysis, we selected eight ZmUBP genes whose promoters contained a large number of plant hormones and stress response elements and were up-regulated under different abiotic stresses for RT-qPCR analysis, results showed that these genes responded to abiotic stresses and phytohormones to varying degrees, indicating that they play important roles in plant growth and stress response. CONCLUSIONS In this study, the structure, location and evolutionary relationship of maize UBP gene family members were analyzed for the first time, and the ZmUBP genes that may be involved in stress response and plant growth were identified by combining promoter element analysis, transcriptome data and RT-qPCR analysis. This study informs research on the involvement of maize deubiquitination in stress response.
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Affiliation(s)
- Weichao Fu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Delong Fan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, Hangzhou, 311300, China
| | - Yuanyuan Bu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China.
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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Chen Y, Vermeersch M, Van Leene J, De Jaeger G, Li Y, Vanhaeren H. A dynamic ubiquitination balance of cell proliferation and endoreduplication regulators determines plant organ size. SCIENCE ADVANCES 2024; 10:eadj2570. [PMID: 38478622 PMCID: PMC10936951 DOI: 10.1126/sciadv.adj2570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Ubiquitination plays a crucial role throughout plant growth and development. The E3 ligase DA2 has been reported to activate the peptidase DA1 by ubiquitination, hereby limiting cell proliferation. However, the molecular mechanisms that regulate DA2 remain elusive. Here, we demonstrate that DA2 has a very high turnover and auto-ubiquitinates with K48-linkage polyubiquitin chains, which is counteracted by two deubiquitinating enzymes, UBIQUITIN-SPECIFIC PROTEASE 12 (UBP12) and UBP13. Unexpectedly, we found that auto-ubiquitination of DA2 does not influence its stability but determines its E3 ligase activity. We also demonstrate that impairing the protease activity of DA1 abolishes the growth-reducing effect of DA2. Last, we show that synthetic, constitutively activated DA1-ubiquitin fusion proteins overrule this complex balance of ubiquitination and deubiquitination and strongly restrict growth and promote endoreduplication. Our findings highlight a nonproteolytic function of K48-linked polyubiquitination and reveal a mechanism by which DA2 auto-ubiquitination levels, in concert with UBP12 and UBP13, precisely monitor the activity of DA1 and fine-tune plant organ size.
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Affiliation(s)
- Ying Chen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Mattias Vermeersch
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hannes Vanhaeren
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Proeftuinstraat 86, 9000 Ghent, Belgium
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Vogel K, Isono E. Deubiquitylating enzymes in Arabidopsis thaliana endocytic protein degradation. Biochem Soc Trans 2024; 52:291-299. [PMID: 38174770 DOI: 10.1042/bst20230561] [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: 11/08/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
The regulation of ubiquitylation is key for plant growth and development, in which the activities of ubiquitylating enzymes as well as deubiquitylating enzymes (DUBs) determine the stability or function of the modified proteins. In contrast with ubiquitylating enzymes, there are less numbers of DUBs. DUBs can be classified into seven protein families according to the amino acid sequence of their catalytic domains. The catalytic domains of animal and plant DUB families show high homology, whereas the regions outside of the catalytic site can vary a lot. By hydrolyzing the ubiquitin molecules from ubiquitylated proteins, DUBs control ubiquitin-dependent selective protein degradation pathways such as the proteasomal-, autophagic-, and endocytic degradation pathways. In the endocytic degradation pathway, DUBs can modulate the endocytic trafficking and thus the stability of plasma membrane proteins including receptors and transporters. To date, three DUB families were shown to control the endocytic degradation pathway namely associated molecule with the SH3 domain of STAM (AMSH) 3, ubiquitin-specific protease (UBP) 12 and UBP13, and ovarian tumor protease (OTU) 11 and OTU12. In this review we will summarize the activity, molecular functions, and target protein of these DUBs and how they contribute to the environmental response of plants.
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Affiliation(s)
- Karin Vogel
- Department of Biology, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
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11
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Zhou X, Li Y, Wang J, Zhao Y, Wang H, Han Y, Lin X. Genome-wide identification of U-box gene family and expression analysis in response to saline-alkali stress in foxtail millet ( Setaria italica L. Beauv). Front Genet 2024; 15:1356807. [PMID: 38435060 PMCID: PMC10904469 DOI: 10.3389/fgene.2024.1356807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
E3 ubiquitin ligases are central modifiers of plant signaling pathways that regulate protein function, localization, degradation, and other biological processes by linking ubiquitin to target proteins. E3 ubiquitin ligases include proteins with the U-box domain. However, there has been no report about the foxtail millet (Setaria italica L. Beauv) U-box gene family (SiPUB) to date. To explore the function of SiPUBs, this study performed genome-wide identification of SiPUBs and expression analysis of them in response to saline-alkali stress. A total of 70 SiPUBs were identified, which were unevenly distributed on eight chromosomes. Phylogenetic and conserved motif analysis demonstrated that SiPUBs could be clustered into six subfamilies (I-VI), and most SiPUBs were closely related to the homologues in rice. Twenty-eight types of cis-acting elements were identified in SiPUBs, most of which contained many light-responsive elements and plant hormone-responsive elements. Foxtail millet had 19, 78, 85, 18, and 89 collinear U-box gene pairs with Arabidopsis, rice, sorghum, tomato, and maize, respectively. Tissue specific expression analysis revealed great variations in SiPUB expression among different tissues, and most SiPUBs were relatively highly expressed in roots, indicating that SiPUBs may play important roles in root development or other growth and development processes of foxtail millet. Furthermore, the responses of 15 SiPUBs to saline-alkali stress were detected by qRT-PCR. The results showed that saline-alkali stress led to significantly differential expression of these 15 SiPUBs, and SiPUB20/48/70 may play important roles in the response mechanism against saline-alkali stress. Overall, this study provides important information for further exploration of the biological function of U-box genes.
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Affiliation(s)
- Xiaoke Zhou
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yun Li
- Research Center of Rural Vitalization, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jian Wang
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuxue Zhao
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Huimin Wang
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yucui Han
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xiaohu Lin
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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12
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Godwin J, Govindasamy M, Nedounsejian K, March E, Halton R, Bourbousse C, Wolff L, Fort A, Krzyszton M, López Corrales J, Swiezewski S, Barneche F, Schubert D, Farrona S. The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development. Nat Commun 2024; 15:667. [PMID: 38253560 PMCID: PMC10803359 DOI: 10.1038/s41467-023-44546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs' interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs' epigenetic hallmarks in Arabidopsis thaliana. We demonstrated that UBP5 is a plant developmental regulator based on functional analyses of ubp5-CRISPR Cas9 mutant plants. UBP5 promotes H2A monoubiquitination erasure, leading to transcriptional de-repression. Furthermore, preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, acting as an antagonist of the pivotal epigenetic repressive marks H2Aub and H3K27me3, UBP5 provides novel insights to disentangle the complex regulation of PRCs' activities.
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Affiliation(s)
- James Godwin
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Mohan Govindasamy
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Kiruba Nedounsejian
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Eduardo March
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Ronan Halton
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Antoine Fort
- Dept. of Veterinary and Microbial Sciences, Technological University of The Shannon: Midlands, Athlone, Co., Roscommon, Ireland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Jesús López Corrales
- Molecular Parasitology Laboratory (MPL), Centre for One Health and Ryan Institute, School of Natural Sciences, University of Galway, Galway, H91 DK59, Ireland
| | - Szymon Swiezewski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland.
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13
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Hua Z. Deciphering the protein ubiquitylation system in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6487-6504. [PMID: 37688404 DOI: 10.1093/jxb/erad354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023]
Abstract
Protein ubiquitylation is a post-translational modification (PTM) process that covalently modifies a protein substrate with either mono-ubiquitin moieties or poly-ubiquitin chains often at the lysine residues. In Arabidopsis, bioinformatic predictions have suggested that over 5% of its proteome constitutes the protein ubiquitylation system. Despite advancements in functional genomic studies in plants, only a small fraction of this bioinformatically predicted system has been functionally characterized. To expand our understanding about the regulatory function of protein ubiquitylation to that rivalling several other major systems, such as transcription regulation and epigenetics, I describe the status, issues, and new approaches of protein ubiquitylation studies in plant biology. I summarize the methods utilized in defining the ubiquitylation machinery by bioinformatics, identifying ubiquitylation substrates by proteomics, and characterizing the ubiquitin E3 ligase-substrate pathways by functional genomics. Based on the functional and evolutionary analyses of the F-box gene superfamily, I propose a deleterious duplication model for the large expansion of this family in plant genomes. Given this model, I present new perspectives of future functional genomic studies on the plant ubiquitylation system to focus on core and active groups of ubiquitin E3 ligase genes.
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Affiliation(s)
- Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
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14
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Zheng SY, Guan BB, Yuan DY, Zhao QQ, Ge W, Tan LM, Chen SS, Li L, Chen S, Xu RM, He XJ. Dual roles of the Arabidopsis PEAT complex in histone H2A deubiquitination and H4K5 acetylation. MOLECULAR PLANT 2023; 16:1847-1865. [PMID: 37822080 DOI: 10.1016/j.molp.2023.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/06/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023]
Abstract
Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. In this study, we found that the previously identified PWWP-EPCR-ARID-TRB (PEAT) complex components interact with both the ubiquitin-specific protease UBP5 and the redundant histone acetyltransferases HAM1 and HAM2 (HAM1/2) to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. HAM1/2 are shared subunits of the PEAT complex and the conserved NuA4 histone acetyltransferase complex, and are responsible for histone H4K5 acetylation. Within the PEAT complex, the PWWP components (PWWP1, PWWP2, and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. Collectively, our study not only identifies dual roles of the PEAT complex in H2A deubiquitination and H4K5 acetylation but also illustrates how these processes collaborate at the whole-genome level to regulate the transcription and development in plants.
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Affiliation(s)
- Si-Yao Zheng
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | - Bin-Bin Guan
- National Institute of Biological Sciences, Beijing, China
| | - Dan-Yang Yuan
- National Institute of Biological Sciences, Beijing, China
| | | | - Weiran Ge
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Mei Tan
- National Institute of Biological Sciences, Beijing, China
| | - Shan-Shan Chen
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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15
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Li S, Yao X, Zhang B, Tang H, Lu L. Genome-wide characterization of the U-box gene in Camellia sinensis and functional analysis in transgenic tobacco under abiotic stresses. Gene 2023; 865:147301. [PMID: 36813060 DOI: 10.1016/j.gene.2023.147301] [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: 05/11/2022] [Revised: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 02/22/2023]
Abstract
Plants U-box genes are crucial for plant survival, and they extensively regulate plant growth, reproduction and development as well as coping with stress and other processes. In this study, we identified 92 CsU-box genes through genome-wide analysis in the tea plant (Camellia sinensis), all of them contained the conserved U-box domain and were divided into 5 groups, which supported by the further genes structure analysis. The expression profiles in eight tea plant tissues and under abiotic and hormone stresses were analyzed using the TPIA database. 7 CsU-box genes (CsU-box27/28/39/46/63/70/91) were selected to verify and analyze expression patterns under PEG-induced drought and heat stress in tea plant respectively, the qRT-PCR results showed consistent with transcriptome datasets; and the CsU-box39 were further heterologous expressed in tobacco to perform gene function analysis. Phenotypic analyses of overexpression transgenic tobacco seedlings and physiological experiments revealed that CsU-box39 positively regulated the plant response to drought stress. These results lay a solid foundation for studying the biological function of CsU-box, and will provide breeding strategy basis for tea plant breeders.
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Affiliation(s)
- Shiyu Li
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Xinzhuan Yao
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Baohui Zhang
- Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China
| | - Hu Tang
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China.
| | - Litang Lu
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China.
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16
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Dai Y, Ma S, Guo Y, Zhang X, Liu D, Gao Y, Zhai C, Chen Q, Xiao S, Zhang Z, Yu L. Evolution and Expression of the Meprin and TRAF Homology Domain-Containing Gene Family in Solanaceae. Int J Mol Sci 2023; 24:ijms24108782. [PMID: 37240124 DOI: 10.3390/ijms24108782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Meprin and TRAF homology (MATH)-domain-containing proteins are pivotal in modulating plant development and environmental stress responses. To date, members of the MATH gene family have been identified only in a few plant species, including Arabidopsis thaliana, Brassica rapa, maize, and rice, and the functions of this gene family in other economically important crops, especially the Solanaceae family, remain unclear. The present study identified and analyzed 58 MATH genes from three Solanaceae species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum), and pepper (Capsicum annuum). Phylogenetic analysis and domain organization classified these MATH genes into four groups, consistent with those based on motif organization and gene structure. Synteny analysis found that segmental and tandem duplication might have contributed to MATH gene expansion in the tomato and the potato, respectively. Collinearity analysis revealed high conservation among Solanaceae MATH genes. Further cis-regulatory element prediction and gene expression analysis showed that Solanaceae MATH genes play essential roles during development and stress response. These findings provide a theoretical basis for other functional studies on Solanaceae MATH genes.
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Affiliation(s)
- Yangshuo Dai
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Sirui Ma
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yixian Guo
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xue Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Di Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yan Gao
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chendong Zhai
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qinfang Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenfei Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Lujun Yu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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17
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Zou T, Li G, Liu M, Liu R, Yang S, Wang K, Lu L, Ye Q, Liu J, Liang J, Deng Q, Wang S, Zhu J, Liang Y, Liu H, Yu X, Sun C, Li P, Li S. A ubiquitin-specific protease functions in regulating cell death and immune responses in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1312-1326. [PMID: 36624579 DOI: 10.1111/pce.14540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/29/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Ubiquitin-specific proteases (UBPs) process deubiquitination in eukaryotic organisms and are widely involved in plant development and responses to environmental stress. However, their role in cell death and plant immunity remains largely unknown. Here, we identified a rice lesion mimic mutant (LMM) and cloned its causative gene, LMM22. Both dysfunction and overexpression of LMM22 gave rise to the hypersensitive response-like cell death, reactive oxygen species bursts, and activated defence responses. LMM22 encodes an active UBP that is localised to the endoplasmic reticulum (ER) and displays a constitutive expression pattern in rice. LMM22 interacts with SPOTTED LEAF 35 (SPL35), a coupling of ubiquitin conjugation to ER degradation domain-containing protein that is known to participate in ubiquitination and the regulation of cell death and disease response in rice. Additional analyses suggest that LMM22 can positively regulate and stabilise the abundance of SPL35 protein likely through its deubiquitination activity. These data therefore improve our understanding of the function of UBP in rice innate immune responses by demonstrating that LMM22 functions as a critical regulator of SPL35 in cell death and disease resistance.
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Affiliation(s)
- Ting Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Gongwen Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Miaomiao Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Rui Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shangyu Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Kang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Liuhui Lu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiuyu Ye
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiaxu Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yueyang Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huainian Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Changhui Sun
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Rice Research Institute, State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
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18
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Luo R, Yang K, Xiao W. Plant deubiquitinases: from structure and activity to biological functions. PLANT CELL REPORTS 2023; 42:469-486. [PMID: 36567335 DOI: 10.1007/s00299-022-02962-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.
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Affiliation(s)
- Runbang Luo
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Kun Yang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China.
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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19
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Arabidopsis LSH10 transcription factor and OTLD1 histone deubiquitinase interact and transcriptionally regulate the same target genes. Commun Biol 2023; 6:58. [PMID: 36650214 PMCID: PMC9845307 DOI: 10.1038/s42003-023-04424-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Histone ubiquitylation/deubiquitylation plays a major role in the epigenetic regulation of gene expression. In plants, OTLD1, a member of the ovarian tumor (OTU) deubiquitinase family, deubiquitylates histone 2B and represses the expression of genes involved in growth, cell expansion, and hormone signaling. OTLD1 lacks the intrinsic ability to bind DNA. How OTLD1, as well as most other known plant histone deubiquitinases, recognizes its target genes remains unknown. Here, we show that Arabidopsis transcription factor LSH10, a member of the ALOG protein family, interacts with OTLD1 in living plant cells. Loss-of-function LSH10 mutations relieve the OTLD1-promoted transcriptional repression of the target genes, resulting in their elevated expression, whereas recovery of the LSH10 function results in down-regulated transcription of the same genes. We show that LSH10 associates with the target gene chromatin as well as with DNA sequences in the promoter regions of the target genes. Furthermore, without LSH10, the degree of H2B monoubiquitylation in the target promoter chromatin increases. Hence, our data suggest that OTLD1-LSH10 acts as a co-repressor complex potentially representing a general mechanism for the specific function of plant histone deubiquitinases at their target chromatin.
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20
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Vogel K, Bläske T, Nagel MK, Globisch C, Maguire S, Mattes L, Gude C, Kovermann M, Hauser K, Peter C, Isono E. Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking. Nat Commun 2022; 13:6897. [PMID: 36371501 PMCID: PMC9653390 DOI: 10.1038/s41467-022-34637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
The abundance of plasma membrane-resident receptors and transporters has to be tightly regulated by ubiquitin-mediated endosomal degradation for the proper coordination of environmental stimuli and intracellular signaling. Arabidopsis OVARIAN TUMOR PROTEASE (OTU) 11 and OTU12 are plasma membrane-localized deubiquitylating enzymes (DUBs) that bind to phospholipids through a polybasic motif in the OTU domain. Here we show that the DUB activity of OTU11 and OTU12 towards K63-linked ubiquitin is stimulated by binding to lipid membranes containing anionic lipids. In addition, we show that the DUB activity of OTU11 against K6- and K11-linkages is also stimulated by anionic lipids, and that OTU11 and OTU12 can modulate the endosomal degradation of a model cargo and the auxin efflux transporter PIN2-GFP in vivo. Our results suggest that the catalytic activity of OTU11 and OTU12 is tightly connected to their ability to bind membranes and that OTU11 and OTU12 are involved in the fine-tuning of plasma membrane proteins in Arabidopsis.
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Affiliation(s)
- Karin Vogel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Tobias Bläske
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Marie-Kristin Nagel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Christoph Globisch
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Shane Maguire
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Lorenz Mattes
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christian Gude
- grid.6936.a0000000123222966School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Kovermann
- grid.9811.10000 0001 0658 7699NMR, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Karin Hauser
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christine Peter
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Erika Isono
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
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21
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Vo Phan MS, Tran PT, Citovsky V. Investigating Interactions Between Histone Modifying Enzymes and Transcription Factors in vivo by Fluorescence Resonance Energy Transfer. JOURNAL OF VISUALIZED EXPERIMENTS : JOVE 2022:10.3791/64656. [PMID: 36314833 PMCID: PMC9629860 DOI: 10.3791/64656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Epigenetic regulation of gene expression is commonly affected by histone modifying enzymes (HMEs) that generate heterochromatic or euchromatic histone marks for transcriptional repression or activation, respectively. HMEs are recruited to their target chromatin by transcription factors (TFs). Thus, detecting and characterizing direct interactions between HMEs and TFs are critical for understanding their function and specificity better. These studies would be more biologically relevant if performed in vivo within living tissues. Here, a protocol is described for visualizing interactions in plant leaves between a plant histone deubiquitinase and a plant transcription factor using fluorescence resonance energy transfer (FRET), which allows the detection of complexes between protein molecules that are within <10 nm from each other. Two variations of the FRET technique are presented: SE-FRET (sensitized emission) and AB-FRET (acceptor bleaching), in which the energy is transferred non-radiatively from the donor to the acceptor or emitted radiatively by the donor upon photobleaching of the acceptor. Both SE-FRET and AB-FRET approaches can be adapted easily to discover other interactions between other proteins in planta.
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Affiliation(s)
- Mi Sa Vo Phan
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, USA,corresponding author: Mi Sa Vo Phan ()
| | - Phu Tri Tran
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, USA
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, USA
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22
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Deubiquitinating enzymes UBP12 and UBP13 regulate carbon/nitrogen-nutrient stress responses by interacting with the membrane-localized ubiquitin ligase ATL31 in Arabidopsis. Biochem Biophys Res Commun 2022; 636:55-61. [DOI: 10.1016/j.bbrc.2022.10.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022]
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23
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Park SH, Jeong JS, Zhou Y, Binte Mustafa NF, Chua NH. Deubiquitination of BES1 by UBP12/UBP13 promotes brassinosteroid signaling and plant growth. PLANT COMMUNICATIONS 2022; 3:100348. [PMID: 35706355 PMCID: PMC9483116 DOI: 10.1016/j.xplc.2022.100348] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 05/26/2023]
Abstract
As a key transcription factor in the brassinosteroid (BR) signaling pathway, the activity and expression of BES1 (BRI1-EMS-SUPPRESSOR 1) are stringently regulated. BES1 degradation is mediated by ubiquitin-related 26S proteasomal and autophagy pathways, which attenuate and terminate BR signaling; however, the opposing deubiquitinases (DUBs) are still unknown. Here, we showed that the ubp12-2w/13-3 double mutant phenocopies the BR-deficient dwarf mutant, suggesting that the two DUBs UBP12/UBP13 antagonize ubiquitin-mediated degradation to stabilize BES1. These two DUBs can trim tetraubiquitin with K46 and K63 linkages in vitro. UBP12/BES1 and UBP13/BES1 complexes are localized in both cytosol and nuclei. UBP12/13 can deubiquitinate polyubiquitinated BES1 in vitro and in planta, and UBP12 interacts with and deubiquitinates both inactive, phosphorylated BES1 and active, dephosphorylated BES1 in vivo. UBP12 overexpression in BES1OE plants significantly enhances cell elongation in hypocotyls and petioles and increases the ratio of leaf length to width compared with BES1OE or UBP12OE plants. Hypocotyl elongation and etiolation result from elevated BES1 levels because BES1 degradation is retarded by UBP12 in darkness or in light with BR. Protein degradation inhibitor experiments show that the majority of BES1 can be degraded by either the proteasomal or the autophagy pathway, but a minor BES1 fraction remains pathway specific. In conclusion, UBP12/UBP13 deubiquitinate BES1 to stabilize the latter as a positive regulator for BR responses.
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Affiliation(s)
- Su-Hyun Park
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Jin Seo Jeong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Yu Zhou
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nur Fatimah Binte Mustafa
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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24
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Genome-Wide Identification and Characterization of G2-Like Transcription Factor Genes in Moso Bamboo (Phyllostachys edulis). Molecules 2022; 27:molecules27175491. [PMID: 36080259 PMCID: PMC9457811 DOI: 10.3390/molecules27175491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
G2-like (GLK) transcription factors contribute significantly and extensively in regulating chloroplast growth and development in plants. This study investigated the genome-wide identification, phylogenetic relationships, conserved motifs, promoter cis-elements, MCScanX, divergence times, and expression profile analysis of PeGLK genes in moso bamboo (Phyllostachys edulis). Overall, 78 putative PeGLKs (PeGLK1–PeGLK78) were identified and divided into 13 distinct subfamilies. Each subfamily contains members displaying similar gene structure and motif composition. By synteny analysis, 42 orthologous pairs and highly conserved microsynteny between regions of GLK genes across moso bamboo and maize were found. Furthermore, an analysis of the divergence times indicated that PeGLK genes had a duplication event around 15 million years ago (MYA) and a divergence happened around 38 MYA between PeGLK and ZmGLK. Tissue-specific expression analysis showed that PeGLK genes presented distinct expression profiles in various tissues, and many members were highly expressed in leaves. Additionally, several PeGLKs were significantly up-regulated under cold stress, osmotic stress, and MeJA and GA treatment, implying that they have a likelihood of affecting abiotic stress and phytohormone responses in plants. The results of this study provide a comprehensive understanding of the moso bamboo GLK gene family, as well as elucidating the potential functional characterization of PeGLK genes.
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25
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Lindbäck LN, Hu Y, Ackermann A, Artz O, Pedmale UV. UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue light receptor to regulate Arabidopsis growth. Curr Biol 2022; 32:3221-3231.e6. [PMID: 35700731 PMCID: PMC9378456 DOI: 10.1016/j.cub.2022.05.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/22/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
Light is a crucial exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. However, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. Furthermore, CRY2 protein levels and activity are tightly regulated in light to fine-tune hypocotyl growth; however, details of the mechanisms that explain precise control of CRY2 levels are not fully understood. We show that in Arabidopsis, UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulates CRY2 by promoting its ubiquitination and turnover to modulate hypocotyl growth. Growth and development were explicitly affected in blue light when UBP12/13 were disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted with and stabilized COP1, which is partially required for CRY2 turnover. Our combined genetic and molecular data support a mechanistic model in which UBP12/13 interact with CRY2 and COP1, leading to the stabilization of COP1. Stabilized COP1 then promotes the ubiquitination and degradation of CRY2 under blue light. Despite decades of studies on deubiquitinases, the knowledge of how their activity is regulated is limited. Our study provides insight into how exogenous signals and ligands, along with their receptors, regulate deubiquitinase activity by protein-protein interaction. Collectively, our results provide a framework of cryptochromes and deubiquitinases to detect and interpret light signals to control plant growth at the most appropriate time.
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Affiliation(s)
- Louise N Lindbäck
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Yuzhao Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Amanda Ackermann
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Oliver Artz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Ullas V Pedmale
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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26
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Skelly MJ. The emerging roles of deubiquitinases in plant proteostasis. Essays Biochem 2022; 66:147-154. [PMID: 35678302 PMCID: PMC9400064 DOI: 10.1042/ebc20210060] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 01/22/2023]
Abstract
Proper regulation of protein homeostasis (proteostasis) is essential for all organisms to survive. A diverse range of post-translational modifications (PTMs) allow precise control of protein abundance, function and cellular localisation. In eukaryotic cells, ubiquitination is a widespread, essential PTM that regulates most, if not all cellular processes. Ubiquitin is added to target proteins via a well-defined enzymatic cascade involving a range of conjugating enzymes and ligases, while its removal is catalysed by a class of enzymes known as deubiquitinases (DUBs). Many human diseases have now been linked to DUB dysfunction, demonstrating the importance of these enzymes in maintaining cellular function. These findings have led to a recent explosion in studying the structure, molecular mechanisms and physiology of DUBs in mammalian systems. Plant DUBs have however remained relatively understudied, with many DUBs identified but their substrates, binding partners and the cellular pathways they regulate only now beginning to emerge. This review focuses on the most recent findings in plant DUB biology, particularly on newly identified DUB substrates and how these offer clues to the wide-ranging roles that DUBs play in the cell. Furthermore, the future outlook on how new technologies in mammalian systems can accelerate the plant DUB field forward is discussed.
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Affiliation(s)
- Michael J Skelly
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, U.K
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27
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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28
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Godwin J, Farrona S. The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors. EPIGENOMES 2022; 6:epigenomes6010008. [PMID: 35323212 PMCID: PMC8948837 DOI: 10.3390/epigenomes6010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.
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29
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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30
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Baile F, Gómez-Zambrano Á, Calonje M. Roles of Polycomb complexes in regulating gene expression and chromatin structure in plants. PLANT COMMUNICATIONS 2022; 3:100267. [PMID: 35059633 PMCID: PMC8760139 DOI: 10.1016/j.xplc.2021.100267] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 05/16/2023]
Abstract
The evolutionary conserved Polycomb Group (PcG) repressive system comprises two central protein complexes, PcG repressive complex 1 (PRC1) and PRC2. These complexes, through the incorporation of histone modifications on chromatin, have an essential role in the normal development of eukaryotes. In recent years, a significant effort has been made to characterize these complexes in the different kingdoms, and despite there being remarkable functional and mechanistic conservation, some key molecular principles have diverged. In this review, we discuss current views on the function of plant PcG complexes. We compare the composition of PcG complexes between animals and plants, highlight the role of recently identified plant PcG accessory proteins, and discuss newly revealed roles of known PcG partners. We also examine the mechanisms by which the repression is achieved and how these complexes are recruited to target genes. Finally, we consider the possible role of some plant PcG proteins in mediating local and long-range chromatin interactions and, thus, shaping chromatin 3D architecture.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Ángeles Gómez-Zambrano
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
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31
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Tang X, Ghimire S, Liu W, Fu X, Zhang H, Sun F, Zhang N, Si H. Genome-wide identification of U-box genes and protein ubiquitination under PEG-induced drought stress in potato. PHYSIOLOGIA PLANTARUM 2022; 174:e13475. [PMID: 34114235 DOI: 10.1111/ppl.13475] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/30/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Protein ubiquitination is one of the most important posttranslational modifications in eukaryotic cells, and it is involved in a variety of biological processes, including abiotic stress response. The ubiquitination modification is highly specific, which depends on the accurate recognition of substrate proteins by ubiquitin ligase. Plant U-box (PUB) proteins are a class of ubiquitin ligases, multiple members of which have shown to participate in water-deficit stress in Arabidopsis and rice. U-box gene family and large-scale profiling of the ubiquitome in potato has not been reported to date, although it is one of the most important food crops. The identified 66 U-box genes from the potato genome database were unevenly distributed on 10 chromosomes. These StPUBs have a large number of tandem repeat sequences. Analysis of gene expression characteristics revealed that many StPUBs responded to abiotic stress. Three hundred and fourteen lys modification sites were identified under PEG-induced drought stress, which were distributed on 200 proteins, with 25 differential ubiquitination modification sites, most of which were up-regulated. The ubiquitination modification in potato protein was enhanced under PEG-induced drought stress, and U-box ubiquitin ligase was involved. This study provides an overall strategy and rich data set to clarify the effects of ubiquitination on potatoes under PEG-induced drought stress and the ubiquitination modification involved in potato U-box genes in response to PEG-induced drought stress.
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Affiliation(s)
- Xun Tang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shantwana Ghimire
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Weigang Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xue Fu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huanhuan Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Fujun Sun
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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32
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Wang T, Ye W, Wang Y, Zhang M, Aihara Y, Kinoshita T. Protease Inhibitor-Dependent Inhibition of Light-Induced Stomatal Opening. FRONTIERS IN PLANT SCIENCE 2021; 12:735328. [PMID: 34567048 PMCID: PMC8462734 DOI: 10.3389/fpls.2021.735328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Stomata in the epidermis of plants play essential roles in the regulation of photosynthesis and transpiration. Stomata open in response to blue light (BL) by phosphorylation-dependent activation of the plasma membrane (PM) H+-ATPase in guard cells. Under water stress, the plant hormone abscisic acid (ABA) promotes stomatal closure via the ABA-signaling pathway to reduce water loss. We established a chemical screening method to identify compounds that affect stomatal movements in Commelina benghalensis. We performed chemical screening using a protease inhibitor (PI) library of 130 inhibitors to identify inhibitors of stomatal movement. We discovered 17 PIs that inhibited light-induced stomatal opening by more than 50%. Further analysis of the top three inhibitors (PI1, PI2, and PI3; inhibitors of ubiquitin-specific protease 1, membrane type-1 matrix metalloproteinase, and matrix metalloproteinase-2, respectively) revealed that these inhibitors suppressed BL-induced phosphorylation of the PM H+-ATPase but had no effect on the activity of phototropins or ABA-dependent responses. The results suggest that these PIs suppress BL-induced stomatal opening at least in part by inhibiting PM H+-ATPase activity but not the ABA-signaling pathway. The targets of PI1, PI2, and PI3 were predicted by bioinformatics analyses, which provided insight into factors involved in BL-induced stomatal opening.
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Affiliation(s)
- Tenghua Wang
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Wenxiu Ye
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yin Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Institute of Ecology, Peking University, Beijing, China
| | - Maoxing Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Department of Horticulture, International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Yusuke Aihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Toshinori Kinoshita
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
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33
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Zheng W, Du L. The DUB family in Populus: identification, characterization, evolution and expression patterns. BMC Genomics 2021; 22:541. [PMID: 34266381 PMCID: PMC8281628 DOI: 10.1186/s12864-021-07844-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/24/2021] [Indexed: 11/20/2022] Open
Abstract
Background The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants. Results In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus. Conclusions The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07844-3.
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Affiliation(s)
- Wenqing Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083, China. .,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Orr JN, Waugh R, Colas I. Ubiquitination in Plant Meiosis: Recent Advances and High Throughput Methods. FRONTIERS IN PLANT SCIENCE 2021; 12:667314. [PMID: 33897750 PMCID: PMC8058418 DOI: 10.3389/fpls.2021.667314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/15/2021] [Indexed: 06/06/2023]
Abstract
Meiosis is a specialized cell division which is essential to sexual reproduction. The success of this highly ordered process involves the timely activation, interaction, movement, and removal of many proteins. Ubiquitination is an extraordinarily diverse post-translational modification with a regulatory role in almost all cellular processes. During meiosis, ubiquitin localizes to chromatin and the expression of genes related to ubiquitination appears to be enhanced. This may be due to extensive protein turnover mediated by proteasomal degradation. However, degradation is not the only substrate fate conferred by ubiquitination which may also mediate, for example, the activation of key transcription factors. In plant meiosis, the specific roles of several components of the ubiquitination cascade-particularly SCF complex proteins, the APC/C, and HEI10-have been partially characterized indicating diverse roles in chromosome segregation, recombination, and synapsis. Nonetheless, these components remain comparatively poorly understood to their counterparts in other processes and in other eukaryotes. In this review, we present an overview of our understanding of the role of ubiquitination in plant meiosis, highlighting recent advances, remaining challenges, and high throughput methods which may be used to overcome them.
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Affiliation(s)
- Jamie N. Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
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Melo FV, Oliveira MM, Saibo NJM, Lourenço TF. Modulation of Abiotic Stress Responses in Rice by E3-Ubiquitin Ligases: A Promising Way to Develop Stress-Tolerant Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:640193. [PMID: 33833769 PMCID: PMC8021960 DOI: 10.3389/fpls.2021.640193] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/17/2021] [Indexed: 05/25/2023]
Abstract
Plants are unable to physically escape environmental constraints and have, therefore, evolved a range of molecular and physiological mechanisms to maximize survival in an ever-changing environment. Among these, the post-translational modification of ubiquitination has emerged as an important mechanism to understand and improve the stress response. The ubiquitination of a given protein can change its abundance (through degradation), alter its localization, or even modulate its activity. Hence, ubiquitination increases the plasticity of the plant proteome in response to different environmental cues and can contribute to improve stress tolerance. Although ubiquitination is mediated by different enzymes, in this review, we focus on the importance of E3-ubiquitin ligases, which interact with the target proteins and are, therefore, highly associated with the mechanism specificity. We discuss their involvement in abiotic stress response and place them as putative candidates for ubiquitination-based development of stress-tolerant crops. This review covers recent developments in this field using rice as a reference for crops, highlighting the questions still unanswered.
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Grasser KD, Rubio V, Barneche F. Multifaceted activities of the plant SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194613. [PMID: 32745625 DOI: 10.1016/j.bbagrm.2020.194613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
From yeast to human, the Spt-Ada-GCN5-acetyltransferase (SAGA) gigantic complex modifies chromatin during RNA polymerase II initiation and elongation steps to facilitate transcription. Its enzymatic activity involves a histone acetyltransferase module (HATm) that acetylates multiple lysine residues on the N-terminal tails of histones H2B and H3 and a deubiquitination module (DUBm) that triggers co-transcriptional deubiquitination of histone H2B. With a few notable exceptions described in this review, most SAGA subunits identified in yeast and metazoa are present in plants. Studies from the last 20 years have unveiled that different SAGA subunits are involved in gene expression regulation during the plant life cycle and in response to various types of stress or environmental cues. Their functional analysis in the Arabidopsis thaliana model species is increasingly shedding light on their intrinsic properties and how they can themselves be regulated during plant adaptive responses. Recent biochemical studies have also uncovered multiple associations between plant SAGA and chromatin machineries linked to RNA Pol II transcription. Still, considerably less is known about the molecular links between SAGA or SAGA-like complexes and chromatin dynamics during transcription in Arabidopsis and other plant species. We summarize the emerging knowledge on plant SAGA complex composition and activity, with a particular focus on the best-characterized subunits from its HAT (such as GCN5) and DUB (such as UBP22) modules, and implication of these ensembles in plant development and adaptive responses.
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Affiliation(s)
- Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
| | - Vicente Rubio
- Plant Molecular Genetics Dept., Centro Nacional de Biotecnología (CNB-CSIC), Darwin, 3, 28049 Madrid, Spain.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
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Majumdar P, Nath U. De-ubiquitinases on the move: an emerging field in plant biology. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:563-572. [PMID: 32233097 DOI: 10.1111/plb.13118] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
A balance between the synthesis and degradation of active proteins governs diverse cellular processes in plants, spanning from cell-cycle progression and circadian rhythm to the outcome of several hormone signalling pathways. Ubiquitin-mediated post-translational modification determines the degradative fate of the target proteins, thereby altering the output of cellular processes. An equally important, and perhaps under-appreciated, aspect of this pathway is the antagonistic process of de-ubiquitination. De-ubiquitinases (DUBs), a group of processing enzymes, play an important role in maintaining cellular ubiquitin homeostasis by hydrolyzing ubiquitin poly-proteins and free poly-ubiquitin chains into mono-ubiquitin. Further, DUBs rescue the cellular proteins from 26S proteasome-mediated degradation to their active form by cleaving the poly-ubiquitin chain from the target protein. Any perturbation in DUB activity is likely to affect proteostasis and downstream cellular processes. This review illustrates recent findings on the biological significance and mechanisms of action of the DUBs in Arabidopsis thaliana, with an emphasis on ubiquitin-specific proteases (UBPs), the largest family among the DUBs. We focus on the putative roles of various protein-protein interaction interfaces in DUBs and their generalized function in ubiquitin recycling, along with their pre-eminent role in plant development.
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Affiliation(s)
- P Majumdar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - U Nath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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38
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Keren I, Lacroix B, Kohrman A, Citovsky V. Histone Deubiquitinase OTU1 Epigenetically Regulates DA1 and DA2, Which Control Arabidopsis Seed and Organ Size. iScience 2020; 23:100948. [PMID: 32169818 PMCID: PMC7068640 DOI: 10.1016/j.isci.2020.100948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 01/05/2020] [Accepted: 02/24/2020] [Indexed: 12/31/2022] Open
Abstract
Seeds are central to plant life cycle and to human nutrition, functioning as the major supplier of human population energy intake. To understand better the roles of enzymic writers and erasers of the epigenetic marks, in particular, histone ubiquitylation and the corresponding histone modifiers, involved in control of seed development, we identified the otubain-like cysteine protease OTU1 as a histone deubiquitinase involved in transcriptional repression of the DA1 and DA2 genes known to regulate seed and organ size in Arabidopsis. Loss-of-function mutants of OTU1 accumulate H2B monoubiquitylation and such euchromatic marks as H3 trimethylation and hyperacetylation in the DA1 and DA2 chromatin. These data advance our knowledge about epigenetic regulation of the DA1 and DA2 genes by recognizing OTU1 as a member of a putative repressor complex that negatively regulates their transcription. Histone ubiquitylation regulates transcription of DA1/DA2 that control seed/organ size OTU1 deubiquitinase is involved in deubiquitylation of the DA1/DA2 chromatin OTU1 acts as an epigenetic transcriptional repressor of the DA1/DA2 genes OTU1 is nucleocytoplasmic, indicating involvement in nuclear and cytoplasmic processes
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Affiliation(s)
- Ido Keren
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA.
| | - Benoît Lacroix
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
| | - Abraham Kohrman
- Graduate Program in Genetics, State University of New York, Stony Brook, NY 11794-5222, USA
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
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39
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Ozkuru E, Ates D, Nemli S, Erdogmus S, Karaca N, Yilmaz H, Yagmur B, Kartal C, Tosun M, Ozdestan O, Otles S, Kahriman A, Tanyolac B. Association mapping of loci linked to copper, phosphorus, and potassium concentrations in the seeds of C. arietinum and C. reticulatum. Genomics 2019; 111:1873-1881. [DOI: 10.1016/j.ygeno.2018.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/26/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022]
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40
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Wu R, Zheng W, Tan J, Sammer R, Du L, Lu C. Protein partners of plant ubiquitin-specific proteases (UBPs). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:227-236. [PMID: 31630936 DOI: 10.1016/j.plaphy.2019.08.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/16/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
As one type of deubiquitinases (DUBs), ubiquitin-specific proteases (UBPs) play an extensive and significant role in plant life involving the regulation of plant development and stress responses. However, comprehensive studies are still needed to determine the functional mechanisms, which are largely unclear. Here, we summarized recent progress of plant UBPs' functional partners, particularly the molecular mechanisms by which UBPs work with their partners. We believe that functional analyses of UBPs and their partners will provide new insights into protein deubiquitination and lead to a better understanding of the physiological roles of UBPs in plants.
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Affiliation(s)
- Ruihua Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenqing Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jinyi Tan
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rana Sammer
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Cunfu Lu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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41
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Skelly MJ, Furniss JJ, Grey H, Wong KW, Spoel SH. Dynamic ubiquitination determines transcriptional activity of the plant immune coactivator NPR1. eLife 2019; 8:47005. [PMID: 31589140 PMCID: PMC6850887 DOI: 10.7554/elife.47005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/05/2019] [Indexed: 01/27/2023] Open
Abstract
Activation of systemic acquired resistance in plants is associated with transcriptome reprogramming induced by the unstable coactivator NPR1. Immune-induced ubiquitination and proteasomal degradation of NPR1 are thought to facilitate continuous delivery of active NPR1 to target promoters, thereby maximising gene expression. Because of this potentially costly sacrificial process, we investigated if ubiquitination of NPR1 plays transcriptional roles prior to its proteasomal turnover. Here we show ubiquitination of NPR1 is a progressive event in which initial modification by a Cullin-RING E3 ligase promotes its chromatin association and expression of target genes. Only when polyubiquitination of NPR1 is enhanced by the E4 ligase, UBE4, it is targeted for proteasomal degradation. Conversely, ubiquitin ligase activities are opposed by UBP6/7, two proteasome-associated deubiquitinases that enhance NPR1 longevity. Thus, immune-induced transcriptome reprogramming requires sequential actions of E3 and E4 ligases balanced by opposing deubiquitinases that fine-tune activity of NPR1 without strict requirement for its sacrificial turnover.
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Affiliation(s)
- Michael J Skelly
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - James J Furniss
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Heather Grey
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ka-Wing Wong
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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42
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Wu R, Shi Y, Zhang Q, Zheng W, Chen S, Du L, Lu C. Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2019; 20:E4309. [PMID: 31484390 PMCID: PMC6747111 DOI: 10.3390/ijms20174309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 02/02/2023] Open
Abstract
The largest group of deubiquitinases-ubiquitin-specific proteases (UBPs)-perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants.
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Affiliation(s)
- Ruihua Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yanrong Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qian Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wenqing Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shaoliang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Cunfu Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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Nassrallah A, Rougée M, Bourbousse C, Drevensek S, Fonseca S, Iniesto E, Ait-Mohamed O, Deton-Cabanillas AF, Zabulon G, Ahmed I, Stroebel D, Masson V, Lombard B, Eeckhout D, Gevaert K, Loew D, Genovesio A, Breyton C, De Jaeger G, Bowler C, Rubio V, Barneche F. DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis. eLife 2018; 7:37892. [PMID: 30192741 PMCID: PMC6128693 DOI: 10.7554/elife.37892] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.
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Affiliation(s)
- Amr Nassrallah
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Martin Rougée
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Sud, Orsay, France
| | - Clara Bourbousse
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Sud, Orsay, France
| | - Stephanie Drevensek
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sandra Fonseca
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Elisa Iniesto
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Ouardia Ait-Mohamed
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Gerald Zabulon
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ikhlak Ahmed
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - David Stroebel
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vanessa Masson
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Berangere Lombard
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Dominique Eeckhout
- Department of Plant Systems Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium.,VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Auguste Genovesio
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cecile Breyton
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
| | - Geert De Jaeger
- Department of Plant Systems Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vicente Rubio
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Fredy Barneche
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
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Miricescu A, Goslin K, Graciet E. Ubiquitylation in plants: signaling hub for the integration of environmental signals. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4511-4527. [PMID: 29726957 DOI: 10.1093/jxb/ery165] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/27/2018] [Indexed: 05/20/2023]
Abstract
A fundamental question in biology is how organisms integrate the plethora of environmental cues that they perceive to trigger a co-ordinated response. The regulation of protein stability, which is largely mediated by the ubiquitin-proteasome system in eukaryotes, plays a pivotal role in these processes. Due to their sessile lifestyle and the need to respond rapidly to a multitude of environmental factors, plants are thought to be especially dependent on proteolysis to regulate cellular processes. In this review, we present the complexity of the ubiquitin system in plants, and discuss the relevance of the proteolytic and non-proteolytic roles of this system in the regulation and co-ordination of plant responses to environmental signals. We also discuss the role of the ubiquitin system as a key regulator of plant signaling pathways. We focus more specifically on the functions of E3 ligases as regulators of the jasmonic acid (JA), salicylic acid (SA), and ethylene hormone signaling pathways that play important roles to mount a co-ordinated response to multiple environmental stresses. We also provide examples of new players in this field that appear to integrate different cues and signaling pathways.
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Affiliation(s)
- Alexandra Miricescu
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Kevin Goslin
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
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