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Fang K, Yao X, Tian Y, He Y, Lin Y, Lei W, Peng S, Pan G, Shi H, Zhang D, Lin H. Ubiquitin-specific protease UBP14 stabilizes HY5 by deubiquitination to promote photomorphogenesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2024; 121:e2404883121. [PMID: 39102535 DOI: 10.1073/pnas.2404883121] [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: 03/08/2024] [Accepted: 06/12/2024] [Indexed: 08/07/2024] Open
Abstract
Transcription factor ELONGATED HYPOCOTYL5 (HY5) is the central hub for seedling photomorphogenesis. E3 ubiquitin (Ub) ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) inhibits HY5 protein accumulation through ubiquitination. However, the process of HY5 deubiquitination, which antagonizes E3 ligase-mediated ubiquitination to maintain HY5 homeostasis has never been studied. Here, we identified that Arabidopsis thaliana deubiquitinating enzyme, Ub-SPECIFIC PROTEASE 14 (UBP14) physically interacts with HY5 and enhances its protein stability by deubiquitination. The da3-1 mutant lacking UBP14 function exhibited a long hypocotyl phenotype, and UBP14 deficiency led to the failure of rapid accumulation of HY5 during dark to light. In addition, UBP14 preferred to stabilize nonphosphorylated form of HY5 which is more readily bound to downstream target genes. HY5 promoted the expression and protein accumulation of UBP14 for positive feedback to facilitate photomorphogenesis. Our findings thus established a mechanism by which UBP14 stabilizes HY5 protein by deubiquitination to promote photomorphogenesis in A. thaliana.
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Affiliation(s)
- Ke Fang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xiuhong Yao
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Department of Agriculture Forestry and Food Engineering, Yibin University, Yibin 644000, China
| | - Yu'ang Tian
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Yang He
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Yingru Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Wei Lei
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Sihan Peng
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Guohui Pan
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Haoyu Shi
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Dawei Zhang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
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Wu R, Song K, Jing R, Du L. The de-ubiquitinase UBQUITIN SPECIFIC PROTEASE 15 (UBP15) interacts with the SCF E3 complex adaptor ARABIDOPSIS SKP1 HOMOLOGUE 1 (ASK1) to regulate petal size and fertility in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112112. [PMID: 38750799 DOI: 10.1016/j.plantsci.2024.112112] [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: 11/28/2023] [Revised: 04/14/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Ubiquitination is a pivotal type of post-translational modification, which plays a far-reaching role in plant growth and development, as well as in the response of plants to stress. Just like the two sides of a coin, de-ubiquitination also plays an important role in plant life, which has been gradually discovered in recent years. Here, we demonstrate that the UBQUITIN SPECIFIC PROTEASE 15 (UBP15), which is a UBP-type de-ubiquitinase, interacts with the SCF E3 complex adaptor ARABIDOPSIS SKP1 HOMOLOGUE 1 (ASK1) and influences its protein stability to regulate plant fertility and petal size. The UBP15 is associated with the ASK1 physically, as verified by yeast-two-hybrid (Y2H) and protein pull-down in vitro assays. Disruption of ASK1 by a T-DNA insertion generates some abnormal phenotypes, such as low fertility and small petals. Genetic analysis shows that the UBP15 mutation enhances the low-fertility and small-petal phenotypes of ask1 mutant plants. By proteomic analysis, many types of proteins were identified as potential candidate downstream genes associated with the phenotypes of ubp15 ask1 double mutant plants. Taken together, these findings reveal a molecular relationship between ASK1 and UBP15 and their interaction in the regulation of petal size and fertility, which would benefit in-depth research about the ubiquitin-related pathway in plant physiological processes in the future.
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Affiliation(s)
- Ruihua Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Kaixuan Song
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Ruotong Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China.
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3
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Yoshida T, Mergner J, Yang Z, Liu J, Kuster B, Fernie AR, Grill E. Integrating multi-omics data reveals energy and stress signaling activated by abscisic acid in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1112-1133. [PMID: 38613775 DOI: 10.1111/tpj.16765] [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: 07/08/2023] [Revised: 03/24/2024] [Accepted: 03/31/2024] [Indexed: 04/15/2024]
Abstract
Phytohormones are essential signaling molecules regulating various processes in growth, development, and stress responses. Genetic and molecular studies, especially using Arabidopsis thaliana (Arabidopsis), have discovered many important players involved in hormone perception, signal transduction, transport, and metabolism. Phytohormone signaling pathways are extensively interconnected with other endogenous and environmental stimuli. However, our knowledge of the huge and complex molecular network governed by a hormone remains limited. Here we report a global overview of downstream events of an abscisic acid (ABA) receptor, REGULATORY COMPONENTS OF ABA RECEPTOR (RCAR) 6 (also known as PYRABACTIN RESISTANCE 1 [PYR1]-LIKE [PYL] 12), by integrating phosphoproteomic, proteomic and metabolite profiles. Our data suggest that the RCAR6 overexpression constitutively decreases the protein levels of its coreceptors, namely clade A protein phosphatases of type 2C, and activates sucrose non-fermenting-1 (SNF1)-related protein kinase 1 (SnRK1) and SnRK2, the central regulators of energy and ABA signaling pathways. Furthermore, several enzymes in sugar metabolism were differentially phosphorylated and expressed in the RCAR6 line, and the metabolite profile revealed altered accumulations of several organic acids and amino acids. These results indicate that energy- and water-saving mechanisms mediated by the SnRK1 and SnRK2 kinases, respectively, are under the control of the ABA receptor-coreceptor complexes.
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Affiliation(s)
- Takuya Yoshida
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
| | - Julia Mergner
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Zhenyu Yang
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Jinghui Liu
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
| | - Erwin Grill
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
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Wang X, Liu X, Song K, Du L. An insight into the roles of ubiquitin-specific proteases in plants: development and growth, morphogenesis, and stress response. FRONTIERS IN PLANT SCIENCE 2024; 15:1396634. [PMID: 38993940 PMCID: PMC11236618 DOI: 10.3389/fpls.2024.1396634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024]
Abstract
Ubiquitination is a highly conserved and dynamic post-translational modification in which protein substrates are modified by ubiquitin to influence their activity, localization, or stability. Deubiquitination enzymes (DUBs) counter ubiquitin signaling by removing ubiquitin from the substrates. Ubiquitin-specific proteases (UBPs), the largest subfamily of DUBs, are conserved in plants, serving diverse functions across various cellular processes, although members within the same group often exhibit functional redundancy. Here, we briefly review recent advances in understanding the biological roles of UBPs, particularly the molecular mechanism by which UBPs regulate plant development and growth, morphogenesis, and stress response, which sheds light on the mechanistic roles of deubiquitination in plants.
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Affiliation(s)
- Xiuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuan Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kaixuan Song
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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5
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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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6
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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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Feng H, Tan J, Deng Z. Decoding plant adaptation: deubiquitinating enzymes UBP12 and UBP13 in hormone signaling, light response, and developmental processes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:721-732. [PMID: 37904584 DOI: 10.1093/jxb/erad429] [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: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 11/01/2023]
Abstract
Ubiquitination, a vital post-translational modification in plants, plays a significant role in regulating protein activity, localization, and stability. This process occurs through a complex enzyme cascade that involves E1, E2, and E3 enzymes, leading to the covalent attachment of ubiquitin molecules to substrate proteins. Conversely, deubiquitinating enzymes (DUBs) work in opposition to this process by removing ubiquitin moieties. Despite extensive research on ubiquitination in plants, our understanding of the function of DUBs is still emerging. UBP12 and UBP13, two plant DUBs, have received much attention recently and are shown to play pivotal roles in hormone signaling, light perception, photoperiod responses, leaf development, senescence, and epigenetic transcriptional regulation. This review summarizes current knowledge of these two enzymes, highlighting the central role of deubiquitination in regulating the abundance and activity of critical regulators such as receptor kinases and transcription factors during phytohormone and developmental signaling.
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Affiliation(s)
- Hanqian Feng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Jinjuan Tan
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
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Guo X, Zhang X, Jiang S, Qiao X, Meng B, Wang X, Wang Y, Yang K, Zhang Y, Li N, Chen T, Kang Y, Yao M, Zhang X, Wang X, Zhang E, Li J, Yan D, Hu Z, Botella JR, Song CP, Li Y, Guo S. E3 ligases MAC3A and MAC3B ubiquitinate UBIQUITIN-SPECIFIC PROTEASE14 to regulate organ size in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:684-697. [PMID: 37850874 PMCID: PMC10828200 DOI: 10.1093/plphys/kiad559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
The molecular mechanisms controlling organ size during plant development ultimately influence crop yield. However, a deep understanding of these mechanisms is still lacking. UBIQUITIN-SPECIFIC PROTEASE14 (UBP14), encoded by DA3, is an essential factor determining organ size in Arabidopsis (Arabidopsis thaliana). Here, we identified two suppressors of the da3-1 mutant phenotype, namely SUPPRESSOR OF da3-1 1 and 2 (SUD1 and SUD2), which encode the E3 ligases MOS4-ASSOCIATED COMPLEX 3A (MAC3A) and MAC3B, respectively. The mac3a-1 and mac3b-1 mutations partially suppressed the high ploidy level and organ size phenotypes observed in the da3-1 mutant. Biochemical analysis showed that MAC3A and MAC3B physically interacted with and ubiquitinated UBP14/DA3 to modulate its stability. We previously reported that UBP14/DA3 acts upstream of the B-type cyclin-dependent kinase CDKB1;1 and maintains its stability to inhibit endoreduplication and cell growth. In this work, MAC3A and MAC3B were found to promote the degradation of CDKB1;1 by ubiquitinating UBP14/DA3. Genetic analysis suggests that MAC3A and MAC3B act in a common pathway with UBP14/DA3 to control endoreduplication and organ size. Thus, our findings define a regulatory module, MAC3A/MAC3B-UBP14-CDKB1;1, that plays a critical role in determining organ size and endoreduplication in Arabidopsis.
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Affiliation(s)
- Xiaopeng Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute, Henan University, Sanya 572025, China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute, Henan University, Sanya 572025, China
| | - Shan Jiang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Qiao
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Bolun Meng
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Xiaohang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Yanan Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Kaihuan Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Yilan Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Tianyan Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Yunnan University, Kunming 650500, China
| | - Yiyang Kang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Mengyi Yao
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Xuan Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Xinru Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Erling Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Junhua Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Dawei Yan
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute, Henan University, Sanya 572025, China
| | - José Ramón Botella
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute, Henan University, Sanya 572025, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute, Henan University, Sanya 572025, China
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9
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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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10
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Ye Y, Wang P, Zhang M, Abbas M, Zhang J, Liang C, Wang Y, Wei Y, Meng Z, Zhang R. UAV-based time-series phenotyping reveals the genetic basis of plant height in upland cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:937-951. [PMID: 37154288 DOI: 10.1111/tpj.16272] [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: 01/18/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023]
Abstract
Plant height (PH) is an important agronomic trait affecting crop architecture, biomass, resistance to lodging and mechanical harvesting. Elucidating the genetic governance of plant height is crucial because of the global demand for high crop yields. However, during the rapid growth period of plants the PH changes a lot on a daily basis, which makes it difficult to accurately phenotype the trait by hand on a large scale. In this study, an unmanned aerial vehicle (UAV)-based remote-sensing phenotyping platform was applied to obtain time-series PHs of 320 upland cotton accessions in three different field trials. The results showed that the PHs obtained from UAV images were significantly correlated with ground-based manual measurements, for three trials (R2 = 0.96, 0.95 and 0.96). Two genetic loci on chromosomes A01 and A11 associated with PH were identified by genome-wide association studies (GWAS). GhUBP15 and GhCUL1 were identified to influence PH in further analysis. We obtained a time series of PH values for three field conditions based on remote sensing with UAV. The key genes identified in this study are of great value for the breeding of ideal plant architecture in cotton.
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Affiliation(s)
- Yulu Ye
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Man Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaxin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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11
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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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12
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BSR and Full-Length Transcriptome Approaches Identified Candidate Genes for High Seed Ratio in Camellia vietnamensis. Curr Issues Mol Biol 2022; 45:311-326. [PMID: 36661508 PMCID: PMC9857833 DOI: 10.3390/cimb45010022] [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: 11/27/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
(1) Background: C. vietnamensis is very suitable for growth in the low hilly areas of southern subtropical regions. Under appropriate conditions, the oil yield of C. vietnamensis can reach 1125 kg/ha (the existing varieties can reach 750 kg/ha). Moreover, the fruit of C. vietnamensis is large and the pericarp is thick (>5 cm). Therefore, a high seed ratio has become the main target economic trait for the breeding of C. vietnamensis. (2) Methods: A half-sibling population of C. vietnamensis plants with a combination of high and low seed ratios was constructed by crossing a C. vietnamensis female parent. Bulked segregant RNA analysis and full-length transcriptome sequencing were performed to determine the molecular mechanisms underlying a high seed ratio. (3) Results: Seed ratio is a complex quantitative trait with a normal distribution, which is significantly associated with four other traits of fruit (seed weight, seed number, fruit diameter, and pericarp thickness). Two candidate regions related to high seed ratio (HSR) were predicted. One spanned 140.8−148.4 Mb of chromosome 2 and was associated with 97 seed-yield-related candidate genes ranging in length from 278 to 16,628 bp. The other spanned 35.3−37.3 Mb on chromosome 15 and was associated with 38 genes ranging in length from 221 to 16,928 bp. Using the full-length transcript as a template, a total of 115 candidate transcripts were obtained, and 78 transcripts were predicted to be functionally annotated. The DEGs from two set pairs of cDNA sequencing bulks were enriched to cytochrome p450 CYP76F14 (KOG0156; GO:0055114, HSR4, HSR7), the gibberellin phytohormone pathway (GO:0016787, HSR5), the calcium signaling pathway (GO:0005509, HSR6), the polyubiquitin-PPAR signaling pathway (GO:0005515, HSR2, HSR3), and several main transcription factors (bZIP transcription factor, HSR1) in C. vietnamensis.
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13
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Developing Genetic Engineering Techniques for Control of Seed Size and Yield. Int J Mol Sci 2022; 23:ijms232113256. [PMID: 36362043 PMCID: PMC9655546 DOI: 10.3390/ijms232113256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.
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14
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Xiong J, Yang F, Yao X, Zhao Y, Wen Y, Lin H, Guo H, Yin Y, Zhang D. The deubiquitinating enzymes UBP12 and UBP13 positively regulate recovery after carbon starvation by modulating BES1 stability in Arabidopsis thaliana. THE PLANT CELL 2022; 34:4516-4530. [PMID: 35944221 PMCID: PMC9614486 DOI: 10.1093/plcell/koac245] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
BRI1-EMS-SUPPRESSOR1 (BES1), a core transcription factor in the brassinosteroid (BR) signaling pathway, primarily regulates plant growth and development by influencing BR-regulated gene expression. Several E3 ubiquitin (Ub) ligases regulate BES1 stability, but little is known about BES1 deubiquitination, which antagonizes E3 ligase-mediated ubiquitination to maintain BES1 homeostasis. Here, we report that two Arabidopsis thaliana deubiquitinating enzymes, Ub-SPECIFIC PROTEASE (UBP) 12 and UBP13, interact with BES1. UBP12 and UBP13 removed Ub from polyubiquitinated BES1 to stabilize both phosphorylated and dephosphorylated forms of BES1. A double mutant, ubp12-2w ubp13-3, lacking UBP12 and UBP13 function showed both BR-deficient and BR-insensitive phenotypes, whereas transgenic plants overexpressing UBP12 or UBP13 exhibited an increased BR response. Expression of UBP12 and UPB13 was induced during recovery after carbon starvation, which led to BES1 accumulation and quick recovery of stressed plants. Our work thus establishes a mechanism by which UBP12 and UBP13 regulate BES1 protein abundance to enhance BR-regulated growth during recovery after carbon starvation.
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Affiliation(s)
- Jiawei Xiong
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Fabin Yang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xiuhong Yao
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Yuqing Zhao
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Yu Wen
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Hongqing Guo
- Department of Genetics, Development, and Cell Biology, Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA
| | - Yanhai Yin
- Department of Genetics, Development, and Cell Biology, Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA
| | - Dawei Zhang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
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15
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Jiang R, Zhou S, Da X, Chen T, Xu J, Yan P, Mo X. Ubiquitin-Specific Protease 2 (OsUBP2) Negatively Regulates Cell Death and Disease Resistance in Rice. PLANTS 2022; 11:plants11192568. [PMID: 36235432 PMCID: PMC9571816 DOI: 10.3390/plants11192568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022]
Abstract
Lesion mimic mutants (LMMs) are great materials for studying programmed cell death and immune mechanisms in plants. Various mechanisms are involved in the phenotypes of different LMMs, but few studies have explored the mechanisms linking deubiquitination and LMMs in rice (Oryza sativa). Here, we identified a rice LMM, rust spots rice (rsr1), resulting from the mutation of a single recessive gene. This LMM has spontaneous reddish-brown spots on its leaves, and displays enhanced resistance to both fungal leaf blast (caused by Magnaporthe oryzae) and bacterial blight (caused by Xanthomonas oryzae pv. oryzae). Map-based cloning showed that the mutated gene in rsr1 encodes a Ubiquitin-Specific Protease 2 (OsUBP2). The mutation of OsUBP2 was shown to result in reactive oxygen species (ROS) accumulation, chloroplast structural defects, and programmed cell death, while the overexpression of OsUBP2 weakened rice resistance to leaf blast. OsUBP2 is therefore a negative regulator of immune processes and ROS production. OsUBP2 has deubiquitinating enzyme activity in vitro, and the enzyme active site includes a cysteine at the 234th residue. The ubiquitinated proteomics data of rsr1 and WT provide some possible target protein candidates for OsUBP2.
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16
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Cao Y, Li Y, Wang L, Zhang L, Jiang L. Evolution and function of ubiquitin-specific proteases (UBPs): Insight into seed development roles in tung tree (Vernicia fordii). Int J Biol Macromol 2022; 221:796-805. [PMID: 36037910 DOI: 10.1016/j.ijbiomac.2022.08.163] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
The tung oil produced by the tung tree (Vernicia fordii) provides resources for the manufacture of biodiesel. Ubiquitin-specific proteases (UBPs) are the largest group of deubiquitinases and play key roles in regulating development and stress responses. Here, 21 UBPs were identified in V. fordii, roughly one-half the number found in Manihot esculenta and Hevea brasiliensis. Most UBP duplications are produced from whole-genome duplication (WGD), and significant differences in gene retention existed among Euphorbiaceae. The great majority of UBP-containing blocks in V. fordii, V. montana, Ricinus communis, and Jatropha curcas exhibited extensive conservation with the duplicated regions of M. esculenta and H. brasiliensis. These blocks formed 14 orthologous groups, indicating they shared WGD with UBPs in M. esculenta and H. brasiliensis, but most of these UBPs copies were lost. The UBP orthologs contained significant functional divergence which explained the susceptibility of V. fordii to Fusarium wilt and the resistance of V. montana to Fusarium wilt. The expression patterns and experiments suggested that Vf03G1417 could affect the seed-related traits and positively regulate the seed oil accumulation. This study provided important insights into the evolution of UBPs in Euphorbiaceae and identified important candidate VfUBPs for marker-assisted breeding in V. fordii.
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Affiliation(s)
- Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Yanli Li
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Lin Zhang
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, 430000 Wuhan, China.
| | - Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China.
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17
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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: 5] [Impact Index Per Article: 2.5] [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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18
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Gong P, Demuynck K, De Block J, Aesaert S, Coussens G, Pauwels L, Inzé D, Nelissen H. Modulation of the DA1 pathway in maize shows that translatability of information from Arabidopsis to crops is complex. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111295. [PMID: 35696903 DOI: 10.1016/j.plantsci.2022.111295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 06/15/2023]
Abstract
Modern agriculture is struggling to meet the increasing food, silage and raw material demands due to the rapid growth of population and climate change. In Arabidopsis, DA1 and DAR1 are proteases that negatively regulate cell proliferation and control organ size. DA1 and DAR1 are activated by ubiquitination catalyzed by the E3 ligase BIG BROTHER (BB). Here, we characterized the DA1, DAR1 and BB gene families in maize and analyzed whether perturbation of these genes regulates organ size similar to what was observed in Arabidopsis. We generated da1_dar1a_dar1b triple CRISPR maize mutants and bb1_bb2 double mutants. Detailed phenotypic analysis showed that the size of leaf, stem, cob, and seed was not consistently enlarged in these mutants. Also overexpression of a dominant-negative DA1R333K allele, resembling the da1-1 allele of Arabidopsis which has larger leaves and seeds, did not alter the maize phenotype. The mild negative effects on plant height of the DA1R333K_bb1_bb2 mutant indicate that the genes in the DA1 pathway may control organ size in maize, albeit less obvious than in Arabidopsis.
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Affiliation(s)
- Pan Gong
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Kirin Demuynck
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jolien De Block
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Stijn Aesaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Griet Coussens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Laurens Pauwels
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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19
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Cai X, Xiang S, He W, Tang M, Zhang S, Chen D, Zhang X, Liu C, Li G, Xing J, Li Y, Chen X, Nie Y. Deubiquitinase Ubp3 regulates ribophagy and deubiquitinates Smo1 for appressorium-mediated infection by Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2022; 23:832-844. [PMID: 35220670 PMCID: PMC9104258 DOI: 10.1111/mpp.13196] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The Ubp family of deubiquitinating enzymes has been found to play important roles in plant-pathogenic fungi, but their regulatory mechanisms are still largely unknown. In this study, we revealed the regulatory mechanism of the deubiquitinating enzyme Ubp3 during the infection process of Magnaporthe oryzae. AUBP3 deletion mutant was severely defective in appressorium turgor accumulation, leading to the impairment of appressorial penetration. During appressorium formation, the mutant was also defective in glycogen and lipid metabolism. Interestingly, we found that nitrogen starvation and rapamycin treatment induced the ribophagy process in M. oryzae, which is closely dependent on Ubp3. In the ∆ubp3 mutant, the ribosome proteins and rRNAs were not well degraded on nitrogen starvation and rapamycin treatment. We also found that Ubp3 interacted with the GTPase-activating protein Smo1 and regulated its de-ubiquitination. Ubp3-dependent de-ubiquitination of Smo1 may be required for Smo1 to coordinate Ras signalling. Taken together, our results showed at least two roles of Ubp3 in M. oryzae: it regulates the ribophagy process and it regulates de-ubiquitination of GTPase-activating protein Smo1 for appressorium-mediated infection.
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Affiliation(s)
- Xuan Cai
- Laboratory of Physiological Plant PathologySouth China Agricultural UniversityGuangzhouChina
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shikun Xiang
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wenhui He
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Mengxi Tang
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shimei Zhang
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Deng Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xinrong Zhang
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Caiyun Liu
- Laboratory of Physiological Plant PathologySouth China Agricultural UniversityGuangzhouChina
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Guotian Li
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Junjie Xing
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterChangshaChina
| | - Yunfeng Li
- Laboratory of Physiological Plant PathologySouth China Agricultural UniversityGuangzhouChina
| | - Xiao‐Lin Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yanfang Nie
- Laboratory of Physiological Plant PathologySouth China Agricultural UniversityGuangzhouChina
- College of Materials and EnergySouth China Agricultural UniversityGuangzhouChina
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20
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Lim J, Lim CW, Lee SC. Core Components of Abscisic Acid Signaling and Their Post-translational Modification. FRONTIERS IN PLANT SCIENCE 2022; 13:895698. [PMID: 35712559 PMCID: PMC9195418 DOI: 10.3389/fpls.2022.895698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/03/2022] [Indexed: 05/13/2023]
Abstract
Abscisic acid (ABA) is a major phytohormone that regulates plant growth, development, and abiotic/biotic stress responses. Under stress, ABA is synthesized in various plant organs, and it plays roles in diverse adaptive processes, including seed dormancy, growth inhibition, and leaf senescence, by modulating stomatal closure and gene expression. ABA receptor, clade A protein phosphatase 2C (PP2C), and SNF1-related protein kinase 2 (SnRK2) proteins have been identified as core components of ABA signaling, which is initiated via perception of ABA with receptor and subsequent activation or inactivation by phosphorylation/dephosphorylation. The findings of several recent studies have established that the post-translational modification of these components, including phosphorylation and ubiquitination/deubiquitination, play important roles in regulating their activity and stability. In this review, we discuss the functions of the core components of ABA signaling and the regulation of their activities via post-translational modification under normal and stress conditions.
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21
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Lim CW, Baek W, Lee SC. Tobacco ubiquitin-specific protease 12 (NbUBP12) positively modulates drought resistance. PLANT SIGNALING & BEHAVIOR 2021; 16:1974725. [PMID: 34658295 PMCID: PMC9208778 DOI: 10.1080/15592324.2021.1974725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 05/27/2023]
Abstract
Deubiquitination, a type of post-translational modification, cleaves ubiquitin from target proteins, thereby regulating their stability or activity. Deubiquitination enzymes, ubiquitin-specific proteases (UBP/USP), have been reported to be involved in numerous cellular processes in plants, including meristem development, circadian clock regulation, and immunity. In contrast to model plants, however, the functions of UBP in other higher plants remain poorly understood. Here, we isolated a deubiquitination enzyme, ubiquitin-specific protease 12 (NbUBP12), from Nicotiana benthamiana, which shows high sequence homology with the core enzyme regions of UBP12 from other plants. Quantitative reverse-transcription PCR analysis revealed that NbUBP12 gene expression was significantly induced after drought treatment, and its level was higher in seed than in other tissues. Using a virus-induced gene silencing technique, we generated NbUBP12-silenced tobacco plants to analyze NbUBP12 gene function in response to drought stress and found that compared with control plants, NbUBP12-silenced plants exhibited a lower survival rate after exposure to drought stress. In addition, they were characterized by lower leaf surface temperatures and larger stomatal pore size following abscisic acid (ABA) treatment. On the basis of these observations, we suggest that NbUBP12 is involved in modulating drought resistance in N. benthamiana, which is associated with ABA-mediated stomatal closure.
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Affiliation(s)
- Chae Woo Lim
- Department of Life Science (Bk21 Program), Chung-Ang University, SeoulSouth Korea
| | - Woonhee Baek
- Department of Life Science (Bk21 Program), Chung-Ang University, SeoulSouth Korea
| | - Sung Chul Lee
- Department of Life Science (Bk21 Program), Chung-Ang University, SeoulSouth Korea
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22
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Ubiquitin-specific proteases UBP12 and UBP13 promote shade avoidance response by enhancing PIF7 stability. Proc Natl Acad Sci U S A 2021; 118:2103633118. [PMID: 34732572 PMCID: PMC8609341 DOI: 10.1073/pnas.2103633118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 11/25/2022] Open
Abstract
For plants grown in a crowded environment, PHYTOCHROME INTERACTING FACTOR 7 (PIF7) plays a critical role by initiating a series of adaptive growth responses. Here, we demonstrate that, in addition to transcription activity and subcellular localization, the PIF7 protein level, which is stringently regulated, is also important for shade avoidance responses. We identified two ubiquitin-specific proteases, UBP12 and UBP13, which positively regulate rapid plant growth in response to shade light. These two ubiquitin proteases directly interact with PIF7 and protect the latter from destruction by 26S proteasomes. The dynamic changes of PIF7 abundance regulated by UBP12 and UBP13 provide insight into the roles of posttranslational modifications of PIF7 in integrating environmental changes with endogenous responses. Changes in light quality caused by the presence of neighbor proximity regulate many growth and development processes of plants. PHYTOCHROME INTERACTING FACTOR 7 (PIF7), whose subcellular localization, DNA-binding properties, and protein abundance are regulated in a photoreversible manner, plays a central role in linking shade light perception and growth responses. How PIF7 activity is regulated during shade avoidance responses has been well studied, and many factors involved in this process have been identified. However, the detailed molecular mechanism by which shade light regulates the PIF7 protein level is still largely unknown. Here, we show that the PIF7 protein level regulation is important for shade-induced growth. Two ubiquitin-specific proteases, UBP12 and UBP13, were identified as positive regulators in shade avoidance responses by increasing the PIF7 protein level. The ubp12-2w/13–3 double mutant displayed significantly impaired sensitivity to shade-induced cell elongation and reproduction acceleration. Our genetic and biochemical analysis showed that UBP12 and UBP13 act downstream of phyB and directly interact with PIF7 to maintain PIF7 stability and abundance through deubiquitination.
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Sharma P, Gayen D. Plant protease as regulator and signaling molecule for enhancing environmental stress-tolerance. PLANT CELL REPORTS 2021; 40:2081-2095. [PMID: 34173047 DOI: 10.1007/s00299-021-02739-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Proteases are ubiquitous in prokaryotes and eukaryotes. Plant proteases are key regulators of various physiological processes, including protein homeostasis, organelle development, senescence, seed germination, protein processing, environmental stress response, and programmed cell death. Proteases are involved in the breakdown of peptide bonds resulting in irreversible posttranslational modification of the protein. Proteases act as signaling molecules that specifically regulate cellular function by cleaving and triggering receptor molecules. Peptides derived from proteolysis regulate ROS signaling under oxidative stress in the plant. It degrades misfolded and abnormal proteins into amino acids to repair the cell damage and regulates the biological process in response to environmental stress. Proteases modulate the biogenesis of phytohormones which control plant growth, development, and environmental stresses. Protein homeostasis, the overall balance between protein synthesis and proteolysis, is required for plant growth and development. Abiotic and biotic stresses are major factors that negatively impact cellular survivability, biomass production, and reduced crop yield potentials. Therefore, the identification of various stress-responsive proteases and their molecular functions may elucidate valuable information for the development of stress-resilient crops with higher yield potentials. However, the understanding of molecular mechanisms of plant protease remains unexplored. This review provides an overview of proteases related to development, signaling, and growth regulation to acclimatize environmental stress in plants.
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Affiliation(s)
- Punam Sharma
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, Rajasthan, India
| | - Dipak Gayen
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, Rajasthan, India.
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24
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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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25
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Lim CW, Baek W, Lim J, Hong E, Lee SC. Pepper ubiquitin-specific protease, CaUBP12, positively modulates dehydration resistance by enhancing CaSnRK2.6 stability. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1148-1165. [PMID: 34145668 DOI: 10.1111/tpj.15374] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/31/2021] [Accepted: 06/14/2021] [Indexed: 05/27/2023]
Abstract
Abscisic acid (ABA) is a plant hormone that activates adaptive mechanisms to environmental stress conditions. Plant adaptive mechanisms are complex and highly modulated processes induced by stress-responsive proteins; however, the precise mechanisms by which these processes function under adverse conditions remain unclear. Here, we isolated CaUBP12 (Capsicum annuum ubiquitin-specific protease 12) from pepper (C. annuum) leaves. We show that CaUBP12 expression is significantly induced after exposure to abiotic stress treatments. We conducted loss-of-function and gain-of-function genetic studies to elucidate the biological functions of CaUBP12 in response to ABA and dehydration stress. CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants displayed dehydration-sensitive and dehydration-tolerant phenotypes, respectively; these phenotypes were characterized by regulation of transpirational water loss and stomatal aperture. Under dehydration stress conditions, CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants exhibited lower and higher expression levels of stress-related genes, respectively, than the control plants. We isolated a CaUBP12 interaction protein, CaSnRK2.6, which is a homolog of Arabidopsis OST1; degradation of this protein was partially inhibited by CaUBP12. Similar to CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants, CaSnRK2.6-silenced pepper plants and CaSnRK2.6-overexpressing Arabidopsis displayed dehydration-sensitive and dehydration-tolerant phenotypes, respectively. Our findings suggest that CaUBP12 positively modulates the dehydration stress response by suppressing CaSnRK2.6 protein degradation.
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Affiliation(s)
- Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
| | - Woonhee Baek
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
| | - Junsub Lim
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
| | - Eunji Hong
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Dongjak-Gu, Republic of Korea
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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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27
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Macnee N, Hilario E, Tahir J, Currie A, Warren B, Rebstock R, Hallett IC, Chagné D, Schaffer RJ, Bulley SM. Peridermal fruit skin formation in Actinidia sp. (kiwifruit) is associated with genetic loci controlling russeting and cuticle formation. BMC PLANT BIOLOGY 2021; 21:334. [PMID: 34261431 PMCID: PMC8278711 DOI: 10.1186/s12870-021-03025-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/10/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND The skin (exocarp) of fleshy fruit is hugely diverse across species. Most fruit types have a live epidermal skin covered by a layer of cuticle made up of cutin while a few create an outermost layer of dead cells (peridermal layer). RESULTS In this study we undertook crosses between epidermal and peridermal skinned kiwifruit, and showed that epidermal skin is a semi-dominant trait. Furthermore, backcrossing these epidermal skinned hybrids to a peridermal skinned fruit created a diverse range of phenotypes ranging from epidermal skinned fruit, through fruit with varying degrees of patches of periderm (russeting), to fruit with a complete periderm. Quantitative trait locus (QTL) analysis of this population suggested that periderm formation was associated with four loci. These QTLs were aligned either to ones associated with russet formation on chromosome 19 and 24, or cuticle integrity and coverage located on chromosomes 3, 11 and 24. CONCLUSION From the segregation of skin type and QTL analysis, it appears that skin development in kiwifruit is controlled by two competing factors, cuticle strength and propensity to russet. A strong cuticle will inhibit russeting while a strong propensity to russet can create a continuous dead skinned periderm.
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Affiliation(s)
- Nikolai Macnee
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
- School of Biological Science, The University of Auckland, Auckland, 1146, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Jibran Tahir
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | - Ben Warren
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - David Chagné
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Robert J Schaffer
- School of Biological Science, The University of Auckland, Auckland, 1146, New Zealand
- PFR, 55 Old Mill Road, RD3, Motueka, 7198, New Zealand
| | - Sean M Bulley
- PFR, 412 No 1 Road RD 2, Te Puke, 3182, New Zealand.
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28
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Xu M, Jin P, Liu T, Gao S, Zhang T, Zhang F, Han X, He L, Chen J, Yang J. Genome-wide identification and characterization of UBP gene family in wheat ( Triticum aestivum L.). PeerJ 2021; 9:e11594. [PMID: 34178465 PMCID: PMC8212830 DOI: 10.7717/peerj.11594] [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: 01/10/2021] [Accepted: 05/20/2021] [Indexed: 12/25/2022] Open
Abstract
Ubiquitination is essential for plant growth and development. Deubiquitination cooperates with ubiquitination to regulate the ubiquitination levels of target proteins. The ubiquitin-specific protease (UBP) family is the largest group of deubiquitinases (DUBs), which perform extensive and significant roles in eukaryotic organisms. However, the UBP genes in wheat (TaUBPs) are not identified, and the functions of TaUBPs are unknown. The present study identified 97 UBP genes in the whole genome of T. aestivum. These genes were divided into 15 groups and non-randomly distributed on chromosomes of T. aestivum. Analyses of evolutionary patterns revealed that TaUBPs mainly underwent purification selection. The studies of cis-acting regulatory elements indicated that they might be involved in response to hormones. Quantitative real-time PCR (qRT-PCR) results showed that TaUBPs were differentially expressed in different tissues. Besides, several TaUBPs were significantly up-regulated when plants were treated with salicylic acid (SA), implying that these DUBs may play a role in abiotic stress responses in plants and few TaUBPs displayed differential expression after viral infection. Furthermore, TaUBP1A.1 (TraesCS1A02G432600.1) silenced by virus-induced gene silencing (VIGS) facilitates Chinese wheat mosaic virus (CWMV) infection in wheat, indicating that TaUBP1A.1 may be involved in a defense mechanism against viruses. This study comprehensively analyzed the UBP gene family in wheat and provided a basis for further research of TaUBPs functions in wheat plant response to viral infection.
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Affiliation(s)
- Miaoze Xu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Peng Jin
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tingting Liu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shiqi Gao
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tianye Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Fan Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xiaolei Han
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Long He
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
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29
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Chen Y, Inzé D, Vanhaeren H. Post-translational modifications regulate the activity of the growth-restricting protease DA1. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3352-3366. [PMID: 33587751 DOI: 10.1093/jxb/erab062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Plants are a primary food source and can form the basis for renewable energy resources. The final size of their organs is by far the most important trait to consider when seeking increased plant productivity. Being multicellular organisms, plant organ size is mainly determined by the coordination between cell proliferation and cell expansion. The protease DA1 limits the duration of cell proliferation and thereby restricts final organ size. Since its initial identification as a negative regulator of organ growth, various transcriptional regulators of DA1, but also interacting proteins, have been identified. These interactors include cleavage substrates of DA1, and also proteins that modulate the activity of DA1 through post-translational modifications, such as ubiquitination, deubiquitination, and phosphorylation. In addition, many players in the DA1 pathway display conserved phenotypes in other dicot and even monocot species. In this review, we provide a timely overview of the complex, but intriguing, molecular mechanisms that fine-tune the activity of DA1 and therefore final organ size. Moreover, we lay out a roadmap to identify and characterize substrates of proteases and frame the substrate cleavage events in their biological context.
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Affiliation(s)
- Ying Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Hannes Vanhaeren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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30
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Srikanta SB, Cermakian N. To Ub or not to Ub: Regulation of circadian clocks by ubiquitination and deubiquitination. J Neurochem 2020; 157:11-30. [PMID: 32717140 DOI: 10.1111/jnc.15132] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/28/2022]
Abstract
Circadian clocks are internal timing systems that enable organisms to adjust their behavioral and physiological rhythms to the daily changes of their environment. These clocks generate self-sustained oscillations at the cellular, tissue, and behavioral level. The rhythm-generating mechanism is based on a gene expression network with a delayed negative feedback loop that causes the transcripts to oscillate with a period of approximately 24 hr. This oscillatory nature of the proteins involved in this network necessitates that they are intrinsically unstable, with a short half-life. Hence, post-translational modifications (PTMs) are important to precisely time the presence, absence, and interactions of these proteins at appropriate times of the day. Ubiquitination and deubiquitination are counter-balancing PTMs which play a key role in this regulatory process. In this review, we take a comprehensive look at the roles played by the processes of ubiquitination and deubiquitination in the clock machinery of the most commonly studied eukaryotic models of the circadian clock: plants, fungi, fruit flies, and mammals. We present the effects exerted by ubiquitinating and deubiquitinating enzymes on the stability, but also the activity, localization, and interactions of clock proteins. Overall, these PTMs have key roles in regulating not only the pace of the circadian clocks but also their response to external cues and their control of cellular functions.
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Affiliation(s)
- Shashank Bangalore Srikanta
- Integrated Program in Neuroscience, McGill University, Montréal, QC, Canada.,Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada
| | - Nicolas Cermakian
- Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada.,Department of Psychiatry, McGill University, Montréal, QC, Canada
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31
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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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32
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Hussain Q, Shi J, Scheben A, Zhan J, Wang X, Liu G, Yan G, King GJ, Edwards D, Wang H. Genetic and signalling pathways of dry fruit size: targets for genome editing-based crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1124-1140. [PMID: 31850661 PMCID: PMC7152616 DOI: 10.1111/pbi.13318] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/20/2019] [Accepted: 12/08/2019] [Indexed: 05/24/2023]
Abstract
Fruit is seed-bearing structures specific to angiosperm that form from the gynoecium after flowering. Fruit size is an important fitness character for plant evolution and an agronomical trait for crop domestication/improvement. Despite the functional and economic importance of fruit size, the underlying genes and mechanisms are poorly understood, especially for dry fruit types. Improving our understanding of the genomic basis for fruit size opens the potential to apply gene-editing technology such as CRISPR/Cas to modulate fruit size in a range of species. This review examines the genes involved in the regulation of fruit size and identifies their genetic/signalling pathways, including the phytohormones, transcription and elongation factors, ubiquitin-proteasome and microRNA pathways, G-protein and receptor kinases signalling, arabinogalactan and RNA-binding proteins. Interestingly, different plant taxa have conserved functions for various fruit size regulators, suggesting that common genome edits across species may have similar outcomes. Many fruit size regulators identified to date are pleiotropic and affect other organs such as seeds, flowers and leaves, indicating a coordinated regulation. The relationships between fruit size and fruit number/seed number per fruit/seed size, as well as future research questions, are also discussed.
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Affiliation(s)
- Quaid Hussain
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Armin Scheben
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Guijun Yan
- UWA School of Agriculture and EnvironmentThe UWA Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
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33
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Vercruysse J, Baekelandt A, Gonzalez N, Inzé D. Molecular networks regulating cell division during Arabidopsis leaf growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2365-2378. [PMID: 31748815 PMCID: PMC7178401 DOI: 10.1093/jxb/erz522] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 05/02/2023]
Abstract
Leaves are the primary organs for photosynthesis, and as such have a pivotal role for plant growth and development. Leaf development is a multifactorial and dynamic process involving many genes that regulate size, shape, and differentiation. The processes that mainly drive leaf development are cell proliferation and cell expansion, and numerous genes have been identified that, when ectopically expressed or down-regulated, increase cell number and/or cell size during leaf growth. Many of the genes regulating cell proliferation are functionally interconnected and can be grouped into regulatory modules. Here, we review our current understanding of six important gene regulatory modules affecting cell proliferation during Arabidopsis leaf growth: ubiquitin receptor DA1-ENHANCER OF DA1 (EOD1), GROWTH REGULATING FACTOR (GRF)-GRF-INTERACTING FACTOR (GIF), SWITCH/SUCROSE NON-FERMENTING (SWI/SNF), gibberellin (GA)-DELLA, KLU, and PEAPOD (PPD). Furthermore, we discuss how post-mitotic cell expansion and these six modules regulating cell proliferation make up the final leaf size.
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Affiliation(s)
- Jasmien Vercruysse
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Alexandra Baekelandt
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Nathalie Gonzalez
- INRAE, Université de Bordeaux, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, Villenave d’Ornon cedex, France
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Correspondence:
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34
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The deubiquitinating enzyme MoUbp8 is required for infection-related development, pathogenicity, and carbon catabolite repression in Magnaporthe oryzae. Appl Microbiol Biotechnol 2020; 104:5081-5094. [PMID: 32274561 DOI: 10.1007/s00253-020-10572-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/29/2020] [Accepted: 03/22/2020] [Indexed: 12/22/2022]
Abstract
Deubiquitination is an essential regulatory step in the Ub-dependent pathway. Deubiquitinating enzymes (DUBs) mediate the removal of ubiquitin moieties from substrate proteins, which are involved in many regulatory mechanisms. As a component of the DUB module (Ubp8/Sgf11/Sus1/Sgf73) in the SAGA (Spt-Ada-Gcn5-acetyltransferase) complex, Ubp8 plays a crucial role in both Saccharomyces cerevisiae and humans. In S. cerevisiae, Ubp8-mediated deubiquitination regulates transcriptional activation processes. To investigate the contributions of Ubp8 to physiological and pathological development of filamentous fungi, we generated the deletion mutant of ortholog MoUBP8 (MGG-03527) in Magnaporthe oryzae (syn. Pyricularia oryzae). The ΔMoubp8 strain showed reduced sporulation, pathogenicity, and resistance to distinct stresses. Even though the conidia of the ΔMoubp8 mutant were delayed in appressorium formation, the normal and abnormal (none-septum or one-septum) conidia could finally form appressoria. Reduced melanin in the ΔMoubp8 mutant is highly responsible for the attenuated pathogenicity since the appressoria of the ΔMoubp8 mutant was much more fragile than those of the wild type, due to the defective turgidity. The weakened ability to detoxify or scavenge host-derived reactive oxygen species (ROS) further restricted the invasion of the pathogen. We also showed that carbon derepression, on the one hand, rendered the ΔMoubp8 strain highly sensitive to allyl alcohol, on the other hand, it enhances the resistance of the MoUBP8 defective strain to deoxyglucose. Overall, we suggest that MoUbp8 is not only required for sporulation, melanin formation, appressoria development, and pathogenicity but also involved in carbon catabolite repression of M. oryzae.
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35
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Vanhaeren H, Chen Y, Vermeersch M, De Milde L, De Vleeschhauwer V, Natran A, Persiau G, Eeckhout D, De Jaeger G, Gevaert K, Inzé D. UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2. eLife 2020; 9:52276. [PMID: 32209225 PMCID: PMC7141810 DOI: 10.7554/elife.52276] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Protein ubiquitination is a very diverse post-translational modification leading to protein degradation or delocalization, or altering protein activity. In Arabidopsis thaliana, two E3 ligases, BIG BROTHER (BB) and DA2, activate the latent peptidases DA1, DAR1 and DAR2 by mono-ubiquitination at multiple sites. Subsequently, these activated peptidases destabilize various positive growth regulators. Here, we show that two ubiquitin-specific proteases, UBP12 and UBP13, deubiquitinate DA1, DAR1 and DAR2, hence reducing their peptidase activity. Overexpression of UBP12 or UBP13 strongly decreased leaf size and cell area, and resulted in lower ploidy levels. Mutants in which UBP12 and UBP13 were downregulated produced smaller leaves that contained fewer and smaller cells. Remarkably, neither UBP12 nor UBP13 were found to be cleavage substrates of the activated DA1. Our results therefore suggest that UBP12 and UBP13 work upstream of DA1, DAR1 and DAR2 to restrict their protease activity and hence fine-tune plant growth and development.
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Affiliation(s)
- Hannes Vanhaeren
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium.,VIB Center for Medical Biotechnology, Albert Baertsoenkaai, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai, Ghent, Belgium
| | - Ying Chen
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Mattias Vermeersch
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Liesbeth De Milde
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Valerie De Vleeschhauwer
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Annelore Natran
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Geert Persiau
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Dominique Eeckhout
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Geert De Jaeger
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai, Ghent, Belgium
| | - Dirk Inzé
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
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36
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Que Y, Xu Z, Wang C, Lv W, Yue X, Xu L, Tang S, Dai H, Wang Z. The putative deubiquitinating enzyme MoUbp4 is required for infection-related morphogenesis and pathogenicity in the rice blast fungus Magnaporthe oryzae. Curr Genet 2019; 66:561-576. [PMID: 31872271 DOI: 10.1007/s00294-019-01049-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/28/2022]
Abstract
Ubiquitination is a key regulatory mechanism that affects numerous important biological processes, including cellular differentiation and pathogenesis in eukaryotic cells. Attachment of proteins to ubiquitin is reversed by specialized proteases, deubiquitinating enzymes (DUBs), which are essential for precursor processing, maintaining ubiquitin homeostasis and promoting protein degradation by recycling ubiquitins. Here, we report the identification of a novel non-pathogenic T-DNA-tagged mutant T612 of Magnaporthe oryzae with a single insertion in the second exon of MoUBP4, which encodes a putative ubiquitin carboxyl-terminal hydrolase. Targeted gene deletion mutants of MoUBP4 are significantly reduced in mycelial growth, conidiation, and increased in tolerance to SDS and CR (Congo red) cell-wall damage. The ΔMoubp4 mutants are blocked in penetration and invasive growth, which results in the loss of pathogenicity. Many conidia produced by the ΔMoubp4 mutants are unable to form appressoria and mobilization and degradation of glycogen and lipid droplets are significantly delayed. Moreover, immunohybridization analysis revealed that total protein ubiquitination levels of the null mutants were significantly increased, indicating that MoUbp4 functions as a deubiquitination enzyme. Taken together, we conclude that MoUbp4 is required for deubiquitination, infection-related morphogenesis and pathogenicity in M. oryzae.
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Affiliation(s)
- Yawei Que
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhe Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Chunyan Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wuyun Lv
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaofeng Yue
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Lin Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Shuai Tang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Han Dai
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhengyi Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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37
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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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38
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Hayama R, Yang P, Valverde F, Mizoguchi T, Furutani-Hayama I, Vierstra RD, Coupland G. Ubiquitin carboxyl-terminal hydrolases are required for period maintenance of the circadian clock at high temperature in Arabidopsis. Sci Rep 2019; 9:17030. [PMID: 31745110 PMCID: PMC6863813 DOI: 10.1038/s41598-019-53229-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022] Open
Abstract
Protein ubiquitylation participates in a number of essential cellular processes including signal transduction and transcription, often by initiating the degradation of specific substrates through the 26S proteasome. Within the ubiquitin-proteasome system, deubiquitylating enzymes (DUBs) not only help generate and maintain the supply of free ubiquitin monomers, they also directly control functions and activities of specific target proteins by modulating the pool of ubiquitylated species. Ubiquitin carboxyl-terminal hydrolases (UCHs) belong to an enzymatic subclass of DUBs, and are represented by three members in Arabidopsis, UCH1, UCH2 and UCH3. UCH1 and UCH2 influence auxin-dependent developmental pathways in Arabidopsis through their deubiquitylation activities, whereas biological and enzymatic functions of UCH3 remain unclear. Here, we demonstrate that Arabidopsis UCH3 acts to maintain the period of the circadian clock at high temperatures redundantly with UCH1 and UCH2. Whereas single uch1, uch2 and uch3 mutants have weak circadian phenotypes, the triple uch mutant displays a drastic lengthening of period at high temperatures that is more extreme than the uch1 uch2 double mutant. UCH3 also possesses a broad deubiquitylation activity against a range of substrates that link ubiquitin via peptide and isopeptide linkages. While the protein target(s) of UCH1-3 are not yet known, we propose that these DUBs act on one or more factors that control period length of the circadian clock through removal of their bound ubiquitin moieties, thus ensuring that the clock oscillates with a proper period even at elevated temperatures.
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Affiliation(s)
- Ryosuke Hayama
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany. .,Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan.
| | - Peizhen Yang
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,, Bayer Crop Science, 800 N Lindbergh Blvd, St Louis, Missouri, 63146, USA
| | - Federico Valverde
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany.,Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 49th Américo Vespucio Avenue, Sevilla, 41092, Spain
| | - Tsuyoshi Mizoguchi
- Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan
| | - Ikuyo Furutani-Hayama
- Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany.
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39
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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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40
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Lv MJ, Wan W, Yu F, Meng LS. New Insights into the Molecular Mechanism Underlying Seed Size Control under Drought Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9697-9704. [PMID: 31403787 DOI: 10.1021/acs.jafc.9b02497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In higher plants, seed size is an important parameter and agricultural trait in many aspects of evolutionary fitness. The loss of water-deficiency-induced crop yield is the largest among all natural hazards. Under water-deficient stress, the most prevalent response to terminal stress is to accelerate the early arrest of floral development and, thereby, to accelerate fruit/seed production, which consequently reduces seed size. This phenomenon is well-known, but its molecular mechanism is not well-reviewed and characterized. However, increasing evidence have indicated that water-deficient stress is always coordinated with three genetic signals (i.e., seed size regulators, initial seed size, and fruit number) that decide the final seed size. Here, our review presents new insights into the mechanism underlying cross-talk water-deficient stress signaling with three genetic signals controlling final seed size. These new insights may aid in preliminary screening, identifying novel genetic factors and future design strategies, or breeding to increase crop yield.
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Affiliation(s)
- Meng-Jiao Lv
- Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
| | - Wen Wan
- Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
| | - Fei Yu
- Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
| | - Lai-Sheng Meng
- Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
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41
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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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42
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Park SH, Jeong JS, Seo JS, Park BS, Chua NH. Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency. THE NEW PHYTOLOGIST 2019; 223:1447-1460. [PMID: 31050353 DOI: 10.1111/nph.15879] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/18/2019] [Indexed: 05/09/2023]
Abstract
Nitrogen deficiency (-N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1. Little is known about post-translational regulation of ORE1 in this process. Here, we show that UBP12/UBP13 (ubiquitin-specific protease 12/13) antagonize the action of NLA (nitrogen limitation adaptation) E3 ligase to maintain ORE1 homeostasis. In vitro pull-down and in vivo co-immunoprecipitation assays demonstrated specific binding between UBP12/UBP13 and ORE1. We further analyzed in various genotypes total Chl content and expression levels of senescence-related genes under -N conditions. We found that UBP12/UBP13 can deubiquitinate polyubiquitinated ORE1 in vitro and increase the stability of ORE1 in vivo in MG132/cycloheximide-chase experiments. Plants overexpressing UBP12/UBP13 display accelerated leaf senescence which is reversed by the ore1 mutation. By contrast, the senescence phenotype of plants overexpressing ORE1 is exacerbated by UBP12/UBP13 overexpression. The expression of senescence-related genes tracks the senescence phenotype. ORE1 protein levels can be elevated by UBP12/UBP13 overexpression but decreased in ubp12-2w/13-3. In conclusion, UBP12/UBP13 deubiquitinate ORE1 to stabilize this transcription factor and promote its activity as a positive regulator for leaf senescence under -N conditions. Our study shows that UBP12/UBP13 counteracts the effect of NLA E3 ligase to accelerate leaf senescence under nitrogen starvation.
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Affiliation(s)
- Su-Hyun Park
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jin Seo Jeong
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jun Sung Seo
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
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43
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Wu L, Sadhukhan A, Kobayashi Y, Ogo N, Tokizawa M, Agrahari RK, Ito H, Iuchi S, Kobayashi M, Asai A, Koyama H. Involvement of phosphatidylinositol metabolism in aluminum-induced malate secretion in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3329-3342. [PMID: 30977815 DOI: 10.1093/jxb/erz179] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/03/2019] [Indexed: 05/27/2023]
Abstract
To identify the upstream signaling of aluminum-induced malate secretion through aluminum-activated malate transporter 1 (AtALMT1), a pharmacological assay using inhibitors of human signal transduction pathways was performed. Early aluminum-induced transcription of AtALMT1 and other aluminum-responsive genes was significantly suppressed by phosphatidylinositol 4-kinase (PI4K) and phospholipase C (PLC) inhibitors, indicating that the PI4K-PLC metabolic pathway activates early aluminum signaling. Inhibitors of phosphatidylinositol 3-kinase (PI3K) and PI4K reduced aluminum-activated malate transport by AtALMT1, suggesting that both the PI3K and PI4K metabolic pathways regulate this process. These results were validated using T-DNA insertion mutants of PI4K and PI3K-RNAi lines. A human protein kinase inhibitor, putatively inhibiting homologous calcineurin B-like protein-interacting protein kinase and/or Ca-dependent protein kinase in Arabidopsis, suppressed late-phase aluminum-induced expression of AtALMT1, which was concomitant with the induction of an AtALMT1 repressor, WRKY46, and suppression of an AtALMT1 activator, Calmodulin-binding transcription activator 2 (CAMTA2). In addition, a human deubiquitinase inhibitor suppressed aluminum-activated malate transport, suggesting that deubiquitinases can regulate this process. We also found a reduction of aluminum-induced citrate secretion in tobacco by applying inhibitors of PI3K and PI4K. Taken together, our results indicated that phosphatidylinositol metabolism regulates organic acid secretion in plants under aluminum stress.
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Affiliation(s)
- Liujie Wu
- Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Ayan Sadhukhan
- Applied Biological Sciences, Gifu University, Gifu, Japan
| | | | - Naohisa Ogo
- Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | | | | | - Hiroki Ito
- Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Satoshi Iuchi
- Experimental Plant Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Masatomo Kobayashi
- Experimental Plant Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Akira Asai
- Graduate Division of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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Li N, Song D, Peng W, Zhan J, Shi J, Wang X, Liu G, Wang H. Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:736-749. [PMID: 30191657 PMCID: PMC6419582 DOI: 10.1111/pbi.13011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 05/16/2023]
Abstract
Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA-seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up-regulated in the seeds of the large-seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.
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Affiliation(s)
- Na Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural SciencesThe Laboratory of Melon CropsZhengzhouHenan ProvinceChina
| | - Dongji Song
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Wei Peng
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
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Ma X, Zhang J, Han B, Tang J, Cui D, Han L. FLA, which encodes a homolog of UBP, is required for chlorophyll accumulation and development of lemma and palea in rice. PLANT CELL REPORTS 2019; 38:321-331. [PMID: 30603810 DOI: 10.1007/s00299-018-2368-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
FLA, the homolog of ubiquitin-specific protease does not have deubiquitination activity, but it is essential for flower and chloroplast development in rice. Ubiquitin-specific proteases (UBPs) are widely distributed and highly conserved proteins and are also members of the most important family of deubiquitination enzymes. Although the functions and phylogenies of UBPs from yeast, mammals and Arabidopsis have been widely reported, the functions and evolutionary relationships of UBPs in rice remain unclear. In this study, we characterized the rice flower and leaf color aberrant mutant (fla), which exhibited a variety of developmental defects, including abnormal floral organs and pollen development, and leaf bleaching. We isolated FLA by positional cloning and found that it encodes a homolog of ubiquitin-specific protease. FLA is a ubiquitously expressed gene with the highest expression in floral organs. Subcellular localization analysis indicated that FLA is a cell membrane protein. Through searches of the rice genome database ( http://rice.plantbiology.msu.edu ), we identified 35 UBP family members in the rice genome. These proteins were grouped into 16 subfamilies based on phylogenetic analysis, and FLA was found to belong to the G8 subfamily. In vitro activity assays revealed that FLA does not have deubiquitination activity. Our data suggest that FLA plays an important role in the development of floral organs and chloroplast in rice, but that this role probably does not involve deubiquitination activity, because FLA does not have an active site and deubiquitination activity.
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Affiliation(s)
- Xiaoding Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiani Zhang
- Chongqing Normal University, Chongqing, 401331, China
| | - Bing Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | | | - Di Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Longzhi Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Wang Z, Zhang H, Liu C, Xing J, Chen XL. A Deubiquitinating Enzyme Ubp14 Is Required for Development, Stress Response, Nutrient Utilization, and Pathogenesis of Magnaporthe oryzae. Front Microbiol 2018; 9:769. [PMID: 29720973 PMCID: PMC5915541 DOI: 10.3389/fmicb.2018.00769] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/04/2018] [Indexed: 02/02/2023] Open
Abstract
Ubiquitination is an essential protein modification in eukaryotic cells, which is reversible. Deubiquitinating enzymes (DUBs) catalyze deubiquitination process to reverse ubiquitination, maintain ubiquitin homeostasis or promote protein degradation by recycling ubiquitins. In order to investigate effects of deubiquitination process in plant pathogenic fungus Magnaporthe oryzae, we generated deletion mutants of MoUBP14. Ortholog of MoUbp14 was reported to play general roles in ubiquitin-mediated protein degradation in Saccharomyces cerevisiae. The ΔMoubp14 mutant lost its pathogenicity and was severely reduced in mycelial growth, sporulation, carbon source utilization, and increased in sensitivity to distinct stresses. The mutant was blocked in penetration, which could due to defect in turgor generation. It is also blocked in invasive growth, which could due to reduction in stress tolerance and nutrient utilization. Deletion of UBP14 also led to accumulation of free polyubiquitin chains. Pulldown assay identified some proteins related to carbohydrate metabolism and stress response may putatively interact with MoUbp14, including two key rate-limiting enzymes of gluconeogenesis, MoFbp1 and MoPck1. These two proteins were degraded when the glucose was supplied to M. oryzae grown in low glucose media for a short period of time (∼12 h), and this process required MoUbp14. In summary, pleiotropic phenotypes of the deletion mutants indicated that MoUbp14 is required for different developments and pathogenicity of M. oryzae.
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Affiliation(s)
- Zhao Wang
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong Zhang
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Caiyun Liu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Xiao-Lin Chen
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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Wang DH, Song W, Wei SW, Zheng YF, Chen ZS, Han JD, Zhang HT, Luo JC, Qin YM, Xu ZH, Bai SN. Characterization of the Ubiquitin C-Terminal Hydrolase and Ubiquitin-Specific Protease Families in Rice ( Oryza sativa). FRONTIERS IN PLANT SCIENCE 2018; 9:1636. [PMID: 30498503 PMCID: PMC6249995 DOI: 10.3389/fpls.2018.01636] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/22/2018] [Indexed: 05/11/2023]
Abstract
The ubiquitin C-terminal hydrolase (UCH) and ubiquitin-specific processing protease (UBP) protein families both function in protein deubiquitination, playing important roles in a wide range of biological processes in animals, fungi, and plants. Little is known about the functions of these proteins in rice (Oryza sativa), and the numbers of genes reported for these families have not been consistent between different rice database resources. To further explore their functions, it is necessary to first clarify the basic molecular and biochemical nature of these two gene families. Using a database similarity search, we clarified the numbers of genes in these two families in the rice genome, examined the enzyme activities of their corresponding proteins, and characterized the expression patterns of all OsUCH and representative OsUBP genes. Five OsUCH and 44 OsUBP genes were identified in the rice genome, with four OsUCH proteins and 10 of 16 tested representative OsUBP proteins showing enzymatic activities. Two OsUCHs and five OsUBPs were found to be preferentially expressed in the early development of rice stamens. This work thus lays down a reliable bioinformatic foundation for future investigations of genes in these two families, particularly for exploring their potential roles in rice stamen development.
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Affiliation(s)
- Dong-Hui Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Wei Song
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Shao-Wei Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Ya-Feng Zheng
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Zhi-Shan Chen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Jing-Dan Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Tao Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Jing-Chu Luo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Yong-Mei Qin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Zhi-Hong Xu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Shu-Nong Bai
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
- *Correspondence: Shu-Nong Bai,
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Zhou H, Zhao J, Cai J, Patil SB. UBIQUITIN-SPECIFIC PROTEASES function in plant development and stress responses. PLANT MOLECULAR BIOLOGY 2017; 94:565-576. [PMID: 28695315 DOI: 10.1007/s11103-017-0633-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/05/2017] [Indexed: 05/08/2023]
Abstract
UBIQUITIN-SPECIFIC PROTEASES play important roles in plant development and stress responses. Protein ubiquitination and deubiquitination are reversible processes, which can modulate the stability, activity as well as subcellular localization of the substrate proteins. UBIQUITIN-SPECIFIC PROTEASE (UBP) protein family participates in protein deubiquitination. Members of UBP family are involved in a variety of physiological processes in plants, as evidenced by their functional characterization in model plant Arabidopsis and other plants. UBPs are conserved in plants and distinct UBPs function in different regulatory processes, although functional redundancies exist between some members. Here we briefly reviewed recent advances in understanding the biological functions of UBP protein family in Arabidopsis, particularly the molecular mechanisms by which UBPs regulate plant development and stress responses. We believe that elucidation of UBPs function and regulation in Arabidopsis will provide new insights about protein deubiquitination and might shed light on the understanding of the mechanistic roles of UBPs in general, which will definitely contribute to crop improvement in agriculture.
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Affiliation(s)
- Huapeng Zhou
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingqing Cai
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Suyash B Patil
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Dong H, Dumenil J, Lu FH, Na L, Vanhaeren H, Naumann C, Klecker M, Prior R, Smith C, McKenzie N, Saalbach G, Chen L, Xia T, Gonzalez N, Seguela M, Inze D, Dissmeyer N, Li Y, Bevan MW. Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis. Genes Dev 2017; 31:197-208. [PMID: 28167503 PMCID: PMC5322733 DOI: 10.1101/gad.292235.116] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/11/2017] [Indexed: 12/31/2022]
Abstract
The characteristic shapes and sizes of organs are established by cell proliferation patterns and final cell sizes, but the underlying molecular mechanisms coordinating these are poorly understood. Here we characterize a ubiquitin-activated peptidase called DA1 that limits the duration of cell proliferation during organ growth in Arabidopsis thaliana The peptidase is activated by two RING E3 ligases, Big Brother (BB) and DA2, which are subsequently cleaved by the activated peptidase and destabilized. In the case of BB, cleavage leads to destabilization by the RING E3 ligase PROTEOLYSIS 1 (PRT1) of the N-end rule pathway. DA1 peptidase activity also cleaves the deubiquitylase UBP15, which promotes cell proliferation, and the transcription factors TEOSINTE BRANCED 1/CYCLOIDEA/PCF 15 (TCP15) and TCP22, which promote cell proliferation and repress endoreduplication. We propose that DA1 peptidase activity regulates the duration of cell proliferation and the transition to endoreduplication and differentiation during organ formation in plants by coordinating the destabilization of regulatory proteins.
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Affiliation(s)
- Hui Dong
- John Innes Centre, Norwich NR4 7QA, United Kingdom
| | - Jack Dumenil
- John Innes Centre, Norwich NR4 7QA, United Kingdom
| | - Fu-Hao Lu
- John Innes Centre, Norwich NR4 7QA, United Kingdom
| | - Li Na
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre of Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hannes Vanhaeren
- VIB-UGent Centre for Plant Systems Biology, Ghent University, 9052 Gent, Belgium
| | - Christin Naumann
- Leibniz Institute of Plant Biochemistry (IPB), D-06120 Halle, Germany
| | - Maria Klecker
- Leibniz Institute of Plant Biochemistry (IPB), D-06120 Halle, Germany
| | - Rachel Prior
- John Innes Centre, Norwich NR4 7QA, United Kingdom
| | | | | | | | - Liangliang Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre of Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Xia
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre of Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Nathalie Gonzalez
- VIB-UGent Centre for Plant Systems Biology, Ghent University, 9052 Gent, Belgium
| | | | - Dirk Inze
- VIB-UGent Centre for Plant Systems Biology, Ghent University, 9052 Gent, Belgium
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), D-06120 Halle, Germany
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre of Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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March E, Farrona S. Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones. FRONTIERS IN PLANT SCIENCE 2017; 8:2274. [PMID: 29387079 PMCID: PMC5776116 DOI: 10.3389/fpls.2017.02274] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/29/2017] [Indexed: 05/11/2023]
Abstract
Selective degradation of proteins in the cell occurs through ubiquitination, which consists of post-translational deposition of ubiquitin on proteins to target them for degradation by proteases. However, ubiquitination does not only impact on protein stability, but promotes changes in their functions. Whereas the deposition of ubiquitin has been amply studied and discussed, the antagonistic activity, deubiquitination, is just emerging and the full model and players involved in this mechanism are far from being completely understood. Nevertheless, it is the dynamic balance between ubiquitination and deubiquitination that is essential for the development and homeostasis of organisms. In this review, we present a detailed analysis of the members of the deubiquitinase (DUB) superfamily in plants and its division in different clades. We describe current knowledge in the molecular and functional characterisation of DUB proteins, focusing primarily on Arabidopsis thaliana. In addition, the striking function of the duality between ubiquitination and deubiquitination in the control of gene expression through the modification of chromatin is discussed and, using the available information of the activities of the DUB superfamily in yeast and animals as scaffold, we propose possible scenarios for the role of these proteins in plants.
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