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Dong X, Han B, Chen J, Luo D, Zhou Q, Liu Z. Multiomics Analyses Reveal MsC3H29 Positively Regulates Flavonoid Biosynthesis to Improve Drought Resistance of Autotetraploid Cultivated Alfalfa ( Medicago sativa L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14448-14465. [PMID: 38864675 DOI: 10.1021/acs.jafc.4c02472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Alfalfa (Medicago sativa subsp. sativa), the "queen of forage," is the most important perennial legume, with high productivity and an excellent nutritional profile. Medicago sativa subsp. falcata is a subspecies of the alfalfa complex and exhibits better drought tolerance. However, drought stress significantly hampers their development and yield. The molecular mechanisms underlying the aboveground and underground tissues of sativa and falcata responding to drought stress remain obscure. Here, we performed a comprehensive comparative analysis of the physiological and transcriptomic responses of sativa and falcata under drought stress. The results showed that photosynthesis was inhibited, and antioxidant enzymes were activated under drought stress. MsC3H29, a CCCH-type zinc finger protein, was identified as a hub gene through weighted gene coexpression network analysis (WGCNA) and was significantly induced by drought in underground tissue. The MsC3H29 protein was localized in the nucleus. Overexpression (OE) of MsC3H29 can increase the primary root length and fresh weight of transgenic alfalfa hairy roots, while RNA interference (RNAi) decreases them under drought stress. The 2',7'-dichlorodihydrofluorescein diacetate (H2DCFDA) staining revealed that MsC3H29 promoted drought tolerance of alfalfa hairy roots through decreasing ROS accumulation. The targeted metabolome analysis showed that the overexpression of MsC3H29 resulted in higher levels of accumulation for flavonoid monomers, including vicenin, daidzein, apigenin, isorhamnetin, quercetin, and tricin, in transgenic alfalfa hairy roots before and after drought stress, while RNAi led to a reduction. Our study provided a key candidate gene for molecular breeding to improve drought resistance in alfalfa.
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Affiliation(s)
- Xueming Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Bingcheng Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jiwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Dong Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Qiang Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
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Chai G, Liu H, Zhang Y, Wang C, Xu H, He G, Meng J, Tang X, Wang D, Zhou G. Integration of C3H15-mediated transcriptional and post-transcriptional regulation confers plant thermotolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38865085 DOI: 10.1111/tpj.16877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 04/23/2024] [Accepted: 05/25/2024] [Indexed: 06/13/2024]
Abstract
Heat stress is an environmental factor that significantly threatens crop production worldwide. Nevertheless, the molecular mechanisms governing plant responses to heat stress are not fully understood. Plant zinc finger CCCH proteins have roles in stress responses as well as growth and development through protein-RNA, protein-DNA, and protein-protein interactions. Here, we reveal an integrated multi-level regulation of plant thermotolerance that is mediated by the CCCH protein C3H15 in Arabidopsis. Heat stress rapidly suppressed C3H15 transcription, which attenuated C3H15-inhibited expression of its target gene HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2), a central regulator of heat stress response (HSR), thereby activating HEAT SHOCK COGNATE 70 (HSC70.3) expression. The RING-type E3 ligase MED25-BINDING RING-H2 PROTEIN 2 (MBR2) was identified as an interacting partner of C3H15. The mbr2 mutant was susceptible to heat stress compared to wild-type plants, whereas plants overexpressing MBR2 showed increased heat tolerance. MBR2-dependent ubiquitination mediated the degradation of phosphorylated C3H15 protein in the cytoplasm, which was enhanced by heat stress. Consistently, heat sensitivities of C3H15 overexpression lines increased in MBR2 loss-of-function and decreased in MBR2 overexpression backgrounds. Heat stress-induced accumulation of HSC70.3 promoted MBR2-mediated degradation of C3H15 protein, implying that an auto-regulatory loop involving C3H15, HSFA2, and HSC70.3 regulates HSR. Heat stress also led to the accumulation of C3H15 in stress granules (SGs), a kind of cytoplasmic RNA granule. This study advances our understanding of the mechanisms plants use to respond to heat stress, which will facilitate technologies to improve thermotolerance in crops.
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Affiliation(s)
- Guohua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
| | - Huanhuan Liu
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Yang Zhang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Tianjin Normal University, Tianjin, 300387, China
| | - Congpeng Wang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hua Xu
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Guo He
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jie Meng
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xianfeng Tang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
| | - Dian Wang
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Gongke Zhou
- Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
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He SL, Li B, Zahurancik WJ, Arthur HC, Sidharthan V, Gopalan V, Wang L, Jang JC. Overexpression of stress granule protein TZF1 enhances salt stress tolerance by targeting ACA11 mRNA for degradation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1375478. [PMID: 38799098 PMCID: PMC11122021 DOI: 10.3389/fpls.2024.1375478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/03/2024] [Indexed: 05/29/2024]
Abstract
Tandem CCCH zinc finger (TZF) proteins play diverse roles in plant growth and stress response. Although as many as 11 TZF proteins have been identified in Arabidopsis, little is known about the mechanism by which TZF proteins select and regulate the target mRNAs. Here, we report that Arabidopsis TZF1 is a bona-fide stress granule protein. Ectopic expression of TZF1 (TZF1 OE), but not an mRNA binding-defective mutant (TZF1H186Y OE), enhances salt stress tolerance in Arabidopsis. RNA-seq analyses of NaCl-treated plants revealed that the down-regulated genes in TZF1 OE plants are enriched for functions in salt and oxidative stress responses. Because many of these down-regulated mRNAs contain AU- and/or U-rich elements (AREs and/or UREs) in their 3'-UTRs, we hypothesized that TZF1-ARE/URE interaction might contribute to the observed gene expression changes. Results from RNA immunoprecipitation-quantitative PCR analysis, gel-shift, and mRNA half-life assays indicate that TZF1 binds and triggers degradation of the autoinhibited Ca2+-ATPase 11 (ACA11) mRNA, which encodes a tonoplast-localized calcium pump that extrudes calcium and dampens signal transduction pathways necessary for salt stress tolerance. Furthermore, this salt stress-tolerance phenotype was recapitulated in aca11 null mutants. Collectively, our findings demonstrate that TZF1 binds and initiates degradation of specific mRNAs to enhance salt stress tolerance.
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Affiliation(s)
- Siou-Luan He
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Bin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
- Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Shandong, China
| | - Walter J. Zahurancik
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Henry C. Arthur
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Vaishnavi Sidharthan
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Venkat Gopalan
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, and University of Chinese Academy of Sciences, Beijing, China
- Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Shandong, China
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
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Ren Y, Fu W, Gao Y, Chen Y, Kong D, Cao M, Pang X, Bo W. Identification of Key Genes of Fruit Shape Variation in Jujube with Integrating Elliptic Fourier Descriptors and Transcriptome. PLANTS (BASEL, SWITZERLAND) 2024; 13:1273. [PMID: 38732489 PMCID: PMC11085141 DOI: 10.3390/plants13091273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
Jujube (Ziziphus jujuba) exhibits a rich diversity in fruit shape, with natural occurrences of gourd-like, flattened, and other special shapes. Despite the ongoing research into fruit shape, studies integrating elliptical Fourier descriptors (EFDs) with both Short Time-series Expression Miner (STEM) and weighted gene co-expression network analysis (WGCNA) for gene discovery remain scarce. In this study, six cultivars of jujube fruits with distinct shapes were selected, and samples were collected from the fruit set period to the white mature stage across five time points for shape analysis and transcriptome studies. By combining EFDs with WGCNA and STEM, the study aimed to identify the critical periods and key genes involved in the formation of jujube fruit shape. The findings indicated that the D25 (25 days after flowering) is crucial for the development of jujube fruit shape. Moreover, ZjAGL80, ZjABI3, and eight other genes have been implicated to regulate the shape development of jujubes at different periods of fruit development, through seed development and fruit development pathway. In this research, EFDs were employed to precisely delineate the shape of jujube fruits. This approach, in conjunction with transcriptome, enhanced the precision of gene identification, and offered an innovative methodology for fruit shape analysis. This integration facilitates the advancement of research into the morphological characteristics of plant fruits, underpinning the development of a refined framework for the genetic underpinnings of fruit shape variation.
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Affiliation(s)
- Yue Ren
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.R.); (W.F.); (Y.G.); (Y.C.); (X.P.)
| | - Wenqing Fu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.R.); (W.F.); (Y.G.); (Y.C.); (X.P.)
| | - Yi Gao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.R.); (W.F.); (Y.G.); (Y.C.); (X.P.)
| | - Yuhan Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.R.); (W.F.); (Y.G.); (Y.C.); (X.P.)
| | - Decang Kong
- National Foundation for Improved Cultivar of Chinese Jujube, Cangzhou 061000, China; (D.K.); (M.C.)
| | - Ming Cao
- National Foundation for Improved Cultivar of Chinese Jujube, Cangzhou 061000, China; (D.K.); (M.C.)
| | - Xiaoming Pang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.R.); (W.F.); (Y.G.); (Y.C.); (X.P.)
| | - Wenhao Bo
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (Y.R.); (W.F.); (Y.G.); (Y.C.); (X.P.)
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Kearly A, Nelson ADL, Skirycz A, Chodasiewicz M. Composition and function of stress granules and P-bodies in plants. Semin Cell Dev Biol 2024; 156:167-175. [PMID: 36464613 DOI: 10.1016/j.semcdb.2022.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Stress Granules (SGs) and Processing-bodies (P-bodies) are biomolecular condensates formed in the cell with the highly conserved purpose of maintaining balance between storage, translation, and degradation of mRNA. This balance is particularly important when cells are exposed to different environmental conditions and adjustments have to be made in order for plants to respond to and tolerate stressful conditions. While P-bodies are constitutively present in the cell, SG formation is a stress-induced event. Typically thought of as protein-RNA aggregates, SGs and P-bodies are formed by a process called liquid-liquid phase separation (LLPS), and both their function and composition are very dynamic. Both foci are known to contain proteins involved in translation, protein folding, and ATPase activity, alluding to their roles in regulating mRNA and protein expression levels. From an RNA perspective, SGs and P-bodies primarily consist of mRNAs, though long non-coding RNAs (lncRNAs) have also been observed, and more focus is now being placed on the specific RNAs associated with these aggregates. Recently, metabolites such as nucleotides and amino acids have been reported in purified plant SGs with implications for the energetic dynamics of these condensates. Thus, even though the field of plant SGs and P-bodies is relatively nascent, significant progress has been made in understanding their composition and biological role in stress responses. In this review, we discuss the most recent discoveries centered around SG and P-body function and composition in plants.
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Affiliation(s)
- Alyssa Kearly
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | | | | | - Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Ma X, Li K, Cai J, Ow DW. Expression of maize OXS2a in Arabidopsis stunts plant growth but enhances heat tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111877. [PMID: 37769875 DOI: 10.1016/j.plantsci.2023.111877] [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: 06/09/2023] [Revised: 08/31/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
As plants encounter various environmental stresses, judicial allocation of resources to stress response is crucial for plant fitness. The plant OXS2 (OXIDATIVE STRESS 2) family has been reported to play important roles in growth regulation and stress response. Here, we report that the maize OXS2 family member ZmOXS2a when expressed in Arabidopsis retards growth including delayed flowering, but improves heat tolerance. ZmOXS2a can be found in the cytoplasm, nucleus and PBs/P bodies (mRNA processing bodies), but heat treatment induces higher accumulation in the PBs. Deletion of ARR (arginine rich region) and TZF (tandem zinc finger) domains for high-affinity RNA-binding reduced PBs accumulation of ZmOXS2a; and unlike ZmOXS2a, expression of this deletion mutant gene affected neither Arabidopsis growth nor heat tolerance. This suggests that ZmOXS2a might be involved in RNA degradation, which would also account for the larger amount of down-regulated genes found in ZmOXS2a expressing lines. Furthermore, 240 of 890 down-regulated genes contain ARE (AU-rich elements) in the mRNA 3'UTR that might be potential targets of ZmOXS2a. Expression of ZmOXS2a also disturbs the response to ABA (abscisic acid) and cytokinin, as GO (gene ontology) analysis shows that 50 and 15 DEGs (differentially expressed genes) are enriched in the GO term for ABA and cytokinin responses, respectively. ZmOXS2a expression lines are more sensitive to ABA, but less sensitive to cytokinin. It is likely that ZmOXS2a promotes the degradation of the mRNA of down-regulated genes containing ARE, which consequently perturbs the hormone pathways that affect stress response-related plant growth.
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Affiliation(s)
- Xiaoling Ma
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Kangjia Li
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jiajia Cai
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - David W Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China.
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Xu L, Xiong X, Liu T, Cao J, Yu Y. Heterologous Expression of Two Brassica campestris CCCH Zinc-Finger Proteins in Arabidopsis Induces Cytoplasmic Foci and Causes Pollen Abortion. Int J Mol Sci 2023; 24:16862. [PMID: 38069184 PMCID: PMC10706035 DOI: 10.3390/ijms242316862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
The membrane-less organelles in cytoplasm that are presented as cytoplasmic foci were successively identified. Although multiple CCCH zinc-finger proteins have been found to be localized in cytoplasmic foci, the relationship between their specific localization and functions still needs further clarification. Here, we report that the heterologous expression of two Brassica campestris CCCH zinc-finger protein genes (BcMF30a and BcMF30c) in Arabidopsis thaliana can affect microgametogenesis by involving the formation of cytoplasmic foci. By monitoring the distribution of proteins and observing pollen phenotypes, we found that, when these two proteins were moderately expressed in pollen, they were mainly dispersed in the cytoplasm, and the pollen developed normally. However, high expression induced the assembly of cytoplasmic foci, leading to pollen abortion. These findings suggested that the continuous formation of BcMF30a/BcMF30c-associated cytoplasmic foci due to high expression was the inducement of male sterility. A co-localization analysis further showed that these two proteins can be recruited into two well-studied cytoplasmic foci, processing bodies (PBs), and stress granules (SGs), which were confirmed to function in mRNA metabolism. Together, our data suggested that BcMF30a and BcMF30c play component roles in the assembly of pollen cytoplasmic foci. Combined with our previous study on the homologous gene of BcMF30a/c in Arabidopsis, we concluded that the function of these homologous genes is conserved and that cytoplasmic foci containing BcMF30a/c may participate in the regulation of gene expression in pollen by regulating mRNA metabolism.
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Affiliation(s)
- Liai Xu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China;
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (X.X.); (T.L.)
| | - Xingpeng Xiong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (X.X.); (T.L.)
| | - Tingting Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (X.X.); (T.L.)
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (X.X.); (T.L.)
| | - Youjian Yu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China;
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Deng Z, Yang Z, Liu X, Dai X, Zhang J, Deng K. Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato ( Solanum tuberosum L.). Int J Mol Sci 2023; 24:12888. [PMID: 37629069 PMCID: PMC10454627 DOI: 10.3390/ijms241612888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Transcription factors containing a CCCH structure (C3H) play important roles in plant growth and development, and their stress response, but research on the C3H gene family in potato has not been reported yet. In this study, we used bioinformatics to identify 50 C3H genes in potato and named them StC3H-1 to StC3H-50 according to their location on chromosomes, and we analyzed their physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, collinearity relationship, and cis-regulatory element. The gene expression pattern analysis showed that many StC3H genes are involved in potato growth and development, and their response to diverse environmental stresses. Furthermore, RT-qPCR data showed that the expression of many StC3H genes was induced by high temperatures, indicating that StC3H genes may play important roles in potato response to heat stress. In addition, Some StC3H genes were predominantly expressed in the stolon and developing tubers, suggesting that these StC3H genes may be involved in the regulation of tuber development. Together, these results provide new information on StC3H genes and will be helpful for further revealing the function of StC3H genes in the heat stress response and tuber development in potato.
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Affiliation(s)
- Zeyi Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Zhijiang Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xinyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xiumei Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kexuan Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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9
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Wu Z, Liang J, Li T, Zhang D, Teng N. A LlMYB305-LlC3H18-LlWRKY33 module regulates thermotolerance in lily. MOLECULAR HORTICULTURE 2023; 3:15. [PMID: 37789438 PMCID: PMC10514960 DOI: 10.1186/s43897-023-00064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/31/2023] [Indexed: 10/05/2023]
Abstract
The CCCH proteins play important roles in plant growth and development, hormone response, pathogen defense and abiotic stress tolerance. However, the knowledge of their roles in thermotolerance are scarce. Here, we identified a heat-inducible CCCH gene LlC3H18 from lily. LlC3H18 was localized in the cytoplasm and nucleus under normal conditions, while it translocated in the cytoplasmic foci and co-located with the markers of two messenger ribonucleoprotein (mRNP) granules, processing bodies (PBs) and stress granules (SGs) under heat stress conditions, and it also exhibited RNA-binding ability. In addition, LlC3H18 exhibited transactivation activity in both yeast and plant cells. In lily and Arabidopsis, overexpression of LlC3H18 damaged their thermotolerances, and silencing of LlC3H18 in lily also impaired its thermotolerance. Similarly, Arabidopsis atc3h18 mutant also showed decreased thermotolerance. These results indicated that the appropriate expression of C3H18 was crucial for establishing thermotolerance. Further analysis found that LlC3H18 directly bound to the promoter of LlWRKY33 and activated its expression. Besides, it was found that LlMYB305 acted as an upstream factor of LlC3H18 and activated its expression. In conclusion, we demonstrated that there may be a LlMYB305-LlC3H18-LlWRKY33 regulatory module in lily that is involved in the establishment of thermotolerance and finely regulates heat stress response.
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Affiliation(s)
- Ze Wu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing, 210043, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahui Liang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ting Li
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing, 210043, China
| | - Dehua Zhang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing, 210043, China
| | - Nianjun Teng
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing, 210043, China.
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10
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Moulick D, Bhutia KL, Sarkar S, Roy A, Mishra UN, Pramanick B, Maitra S, Shankar T, Hazra S, Skalicky M, Brestic M, Barek V, Hossain A. The intertwining of Zn-finger motifs and abiotic stress tolerance in plants: Current status and future prospects. FRONTIERS IN PLANT SCIENCE 2023; 13:1083960. [PMID: 36684752 PMCID: PMC9846276 DOI: 10.3389/fpls.2022.1083960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Environmental stresses such as drought, high salinity, and low temperature can adversely modulate the field crop's ability by altering the morphological, physiological, and biochemical processes of the plants. It is estimated that about 50% + of the productivity of several crops is limited due to various types of abiotic stresses either presence alone or in combination (s). However, there are two ways plants can survive against these abiotic stresses; a) through management practices and b) through adaptive mechanisms to tolerate plants. These adaptive mechanisms of tolerant plants are mostly linked to their signalling transduction pathway, triggering the action of plant transcription factors and controlling the expression of various stress-regulated genes. In recent times, several studies found that Zn-finger motifs have a significant function during abiotic stress response in plants. In the first report, a wide range of Zn-binding motifs has been recognized and termed Zn-fingers. Since the zinc finger motifs regulate the function of stress-responsive genes. The Zn-finger was first reported as a repeated Zn-binding motif, comprising conserved cysteine (Cys) and histidine (His) ligands, in Xenopus laevis oocytes as a transcription factor (TF) IIIA (or TFIIIA). In the proteins where Zn2+ is mainly attached to amino acid residues and thus espousing a tetrahedral coordination geometry. The physical nature of Zn-proteins, defining the attraction of Zn-proteins for Zn2+, is crucial for having an in-depth knowledge of how a Zn2+ facilitates their characteristic function and how proteins control its mobility (intra and intercellular) as well as cellular availability. The current review summarized the concept, importance and mechanisms of Zn-finger motifs during abiotic stress response in plants.
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Affiliation(s)
- Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal, India
| | - Karma Landup Bhutia
- Department of Agricultural Biotechnology & Molecular Breeding, College of Basic Science and Humanities, Dr. Rajendra Prasad Central Agricultural University, Samastipur, India
| | - Sukamal Sarkar
- School of Agriculture and Rural Development, Faculty Centre for Integrated Rural Development and Management (IRDM), Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India
| | - Anirban Roy
- School of Agriculture and Rural Development, Faculty Centre for Integrated Rural Development and Management (IRDM), Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India
| | - Udit Nandan Mishra
- Department of Crop Physiology and Biochemistry, Sri University, Cuttack, Odisha, India
| | - Biswajit Pramanick
- Department of Agronomy, Dr. Rajendra Prasad Central Agricultural University, PUSA, Samastipur, Bihar, India
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, Scottsbluff, NE, United States
| | - Sagar Maitra
- Department of Agronomy and Agroforestry, Centurion University of Technology and Management, Paralakhemundi, Odisha, India
| | - Tanmoy Shankar
- Department of Agronomy and Agroforestry, Centurion University of Technology and Management, Paralakhemundi, Odisha, India
| | - Swati Hazra
- School of Agricultural Sciences, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Institute of Plant and Environmental Sciences, Slovak University of Agriculture, Nitra, Slovakia
| | - Viliam Barek
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Nitra, Slovakia
| | - Akbar Hossain
- Division of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, Bangladesh
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11
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Comparative Transcriptome Analysis of CCCH Family in Roles of Flower Opening and Abiotic Stress in Osmanthus fragrans. Int J Mol Sci 2022; 23:ijms232315363. [PMID: 36499688 PMCID: PMC9735588 DOI: 10.3390/ijms232315363] [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: 10/30/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
CCCH is a zinc finger family with a typical CCCH-type motif which performs a variety of roles in plant growth and development and responses to environmental stressors. However, the information about this family has not been reported for Osmanthus fragrans. In this study, a total of 66 CCCH predicted genes were identified from the O. fragrans genome, the majority of which had multiple CCCH motifs. The 66 OfCCCHs were found to be unevenly distributed on 21 chromosomes and were clustered into nine groups based on their phylogenetic analysis. In each group, the gene structure and domain makeup were comparatively conserved. The expression profiles of the OfCCCH genes were examined in various tissues, the flower-opening processes, and under various abiotic stresses using transcriptome sequencing and qRT-PCR (quantitative real-time PCR). The results demonstrated the widespread expression of OfCCCHs in various tissues, the differential expression of 22 OfCCCHs during flower-opening stages, and the identification of 4, 5, and 13 OfCCCHs after ABA, salt, and drought stress treatment, respectively. Furthermore, characterization of the representative OfCCCHs (OfCCCH8, 23, 27, and 36) revealed that they were all localized in the nucleus and that the majority of them had transcriptional activation in the yeast system. Our research offers the first thorough examination of the OfCCCH family and lays the groundwork for future investigations regarding the functions of CCCH genes in O. fragrans.
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12
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Hormone Regulation of CCCH Zinc Finger Proteins in Plants. Int J Mol Sci 2022; 23:ijms232214288. [PMID: 36430765 PMCID: PMC9698766 DOI: 10.3390/ijms232214288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
CCCH zinc finger proteins contain one to six tandem CCCH motifs composed of three cysteine and one histidine residues and have been widely found in eukaryotes. Plant CCCH proteins control a wide range of developmental and adaptive processes through DNA-protein, RNA-protein and/or protein-protein interactions. The complex networks underlying these processes regulated by plant CCCH proteins are often involved in phytohormones as signal molecules. In this review, we described the evolution of CCCH proteins from green algae to vascular plants and summarized the functions of plant CCCH proteins that are influenced by six major hormones, including abscisic acid, gibberellic acid, brassinosteroid, jasmonate, ethylene and auxin. We further compared the regulatory mechanisms of plant and animal CCCH proteins via hormone signaling. Among them, Arabidopsis AtC3H14, 15 and human hTTP, three typical CCCH proteins, are able to integrate multiple hormones to participate in various biological processes.
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13
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Liu H, Xiao S, Sui S, Huang R, Wang X, Wu H, Liu X. A tandem CCCH type zinc finger protein gene CpC3H3 from Chimonanthus praecox promotes flowering and enhances drought tolerance in Arabidopsis. BMC PLANT BIOLOGY 2022; 22:506. [PMID: 36309643 PMCID: PMC9617390 DOI: 10.1186/s12870-022-03877-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND CCCH-type zinc finger proteins play important roles in plant development and biotic/abiotic stress responses. Wintersweet (Chimonanthus praecox) is a popular ornamental plant with strong resistance to various stresses, which is a good material for exploring gene resource for stress response. In this study, we isolated a CCCH type zinc finger protein gene CpC3H3 (MZ964860) from flower of wintersweet and performed functional analysis with a purpose of identifying gene resource for floral transition and stress tolerance. RESULTS CpC3H3 was predicted a CCCH type zinc finger protein gene encoding a protein containing 446 amino acids with five conserved C-X8-C-X5-C-X3-H motifs. CpC3H3 was localized in the cell membrane but with a nuclear export signal at the N-terminal. Transcripts of CpC3H3 were significantly accumulated in flower buds at floral meristem formation stage, and were induced by polyethylene glycol. Overexpression of CpC3H3 promoted flowering, and enhanced drought tolerance in transgenic A. thaliana. CpC3H3 overexpression affects the expression level of genes involved in flower inducement and stress responses. Further comparative studies on physiological indices showed the contents of proline and soluble sugar, activity of peroxidase and the rates of electrolyte leakage were significantly increased and the content of malondialdehyde and osmotic potential was significantly reduced in transgenic A. thaliana under PEG stress. CONCLUSION Overall, CpC3H3 plays a role in flowering inducement and drought tolerance in transgenic A. thaliana. The CpC3H3 gene has the potential to be used to promote flowering and enhance drought tolerance in plants.
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Affiliation(s)
- Huamin Liu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160, China
| | - Shiqi Xiao
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Shunzhao Sui
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Renwei Huang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, 611130, China
| | - Xia Wang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Huafeng Wu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Xia Liu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160, China.
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14
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Yang Y, Kong Q, Lim ARQ, Lu S, Zhao H, Guo L, Yuan L, Ma W. Transcriptional regulation of oil biosynthesis in seed plants: Current understanding, applications, and perspectives. PLANT COMMUNICATIONS 2022; 3:100328. [PMID: 35605194 PMCID: PMC9482985 DOI: 10.1016/j.xplc.2022.100328] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/28/2022] [Accepted: 04/14/2022] [Indexed: 05/11/2023]
Abstract
Plants produce and accumulate triacylglycerol (TAG) in their seeds as an energy reservoir to support the processes of seed germination and seedling development. Plant seed oils are vital not only for the human diet but also as renewable feedstocks for industrial use. TAG biosynthesis consists of two major steps: de novo fatty acid biosynthesis in the plastids and TAG assembly in the endoplasmic reticulum. The latest advances in unraveling transcriptional regulation have shed light on the molecular mechanisms of plant oil biosynthesis. We summarize recent progress in understanding the regulatory mechanisms of well-characterized and newly discovered transcription factors and other types of regulators that control plant fatty acid biosynthesis. The emerging picture shows that plant oil biosynthesis responds to developmental and environmental cues that stimulate a network of interacting transcriptional activators and repressors, which in turn fine-tune the spatiotemporal regulation of the pathway genes.
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Affiliation(s)
- Yuzhou Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Audrey R Q Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
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15
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Chen X, Guo HY, Zhang QY, Wang L, Guo R, Zhan YX, Lv P, Xu YP, Guo MB, Zhang Y, Zhang K, Liu YH, Yang M. Whole-genome resequencing of wild and cultivated cannabis reveals the genetic structure and adaptive selection of important traits. BMC PLANT BIOLOGY 2022; 22:371. [PMID: 35883045 PMCID: PMC9327241 DOI: 10.1186/s12870-022-03744-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cannabis is an important industrial crop species whose fibre, seeds, flowers and leaves are widely used by humans. The study of cannabinoids extracted from plants has been popular research topic in recent years. China is one of the origins of cannabis and one of the few countries with wild cannabis plants. However, the genetic structure of Chinese cannabis and the degree of adaptive selection remain unclear. RESULTS The main morphological characteristics of wild cannabis in China were assessed. Based on whole-genome resequencing SNPs, Chinese cannabis could be divided into five groups in terms of geographical source and ecotype: wild accessions growing in the northwestern region; wild accessions growing in the northeastern region; cultivated accessions grown for fibre in the northeastern region; cultivated accessions grown for seed in northwestern region, and cultivated accessions in southwestern region. We further identified genes related to flowering time, seed germination, seed size, embryogenesis, growth, and stress responses selected during the process of cannabis domestication. The expression of flowering-related genes under long-day (LD) and short-day (SD) conditions showed that Chinese cultivated cannabis is adapted to different photoperiods through the regulation of Flowering locus T-like (FT-like) expression. CONCLUSION This study clarifies the genetic structure of Chinese cannabis and offers valuable genomic resources for cannabis breeding.
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Affiliation(s)
- Xuan Chen
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Hong-Yan Guo
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Qing-Ying Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Lu Wang
- State Key Laboratory for Conservation, School of Life Sciences, Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500 China
| | - Rong Guo
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Yi-Xun Zhan
- State Key Laboratory for Conservation, School of Life Sciences, Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500 China
| | - Pin Lv
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Yan-Ping Xu
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Meng-Bi Guo
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Yuan Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Kun Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China
| | - Ming Yang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
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16
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Xu L, Liu T, Xiong X, Shen X, Huang L, Yu Y, Cao J. Highly Overexpressed AtC3H18 Impairs Microgametogenesis via Promoting the Continuous Assembly of mRNP Granules. FRONTIERS IN PLANT SCIENCE 2022; 13:932793. [PMID: 35909782 PMCID: PMC9335048 DOI: 10.3389/fpls.2022.932793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Plant CCCH zinc-finger proteins form a large family of regulatory proteins function in many aspects of plant growth, development and environmental responses. Despite increasing reports indicate that many CCCH zinc-finger proteins exhibit similar subcellular localization of being localized in cytoplasmic foci, the underlying molecular mechanism and the connection between this specific localization pattern and protein functions remain largely elusive. Here, we identified another cytoplasmic foci-localized CCCH zinc-finger protein, AtC3H18, in Arabidopsis thaliana. AtC3H18 is predominantly expressed in developing pollen during microgametogenesis. Although atc3h18 mutants did not show any abnormal phenotype, possibly due to redundant gene(s), aberrant AtC3H18 expression levels caused by overexpression resulted in the assembly of AtC3H18-positive granules in a dose-dependent manner, which in turn led to male sterility phenotype, highlighting the importance of fine-tuned AtC3H18 expression. Further analyzes demonstrated that AtC3H18-positive granules are messenger ribonucleoprotein (mRNP) granules, since they can exhibit liquid-like physical properties, and are associated with another two mRNP granules known as processing bodies (PBs) and stress granules (SGs), reservoirs of translationally inhibited mRNAs. Moreover, the assembly of AtC3H18-positive granules depends on mRNA availability. Combined with our previous findings on the AtC3H18 homologous genes in Brassica campestris, we concluded that appropriate expression level of AtC3H18 during microgametogenesis is essential for normal pollen development, and we also speculated that AtC3H18 may act as a key component of mRNP granules to modulate pollen mRNAs by regulating the assembly/disassembly of mRNP granules, thereby affecting pollen development.
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Affiliation(s)
- Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Tingting Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Xingpeng Xiong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Xiuping Shen
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Youjian Yu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
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17
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Ji X, Li J, Niu J, Mao R, Cao F, Li M. DiZF-C3H1, a zinc finger transcription factor from the dove tree (Davidia involucrata Baill.), plays a negative role in seed development and plant growth in Arabidopsis and tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111248. [PMID: 35487657 DOI: 10.1016/j.plantsci.2022.111248] [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: 08/12/2020] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 05/15/2023]
Abstract
Low seed fertility seriously limits the survival and adaption of rare plant species. Here, we identified a seed-specific gene, DiZF-C3H1, from the dove tree and verified its function. Overexpression of DiZF-C3H1 caused retarded root development, delayed anthesis, abnormal floral organs, and deformed siliques in transgenic Arabidopsis lines. No offspring were obtained in transgenic Arabidopsis lines due to serious seed abortion. Therefore, we performed further verification in tobacco. Similarly, overexpression of DiZF-C3H1 retarded root development and reduced berry size and seed yield in transgenic tobacco lines. Moreover, although transgenic tobacco offspring were obtained, the viability of transgenic seeds was reduced and their germination was delayed. In addition, faded flowers were observed in transgenic tobacco lines. Taken together, DiZF-C3H1 was verified to play a negative role in root growth, floral organ development, and especially seed development in Arabidopsis and tobacco. This appears to be a deleterious gene for these model plants with high seed fertility. However, this function might be of special significance for Davidia, whose seed dormancy period is extremely long; DiZF-C3H1 might play a critical role in the distinctive reproduction strategy adopted by this rare and endangered species.
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Affiliation(s)
- Xiaomin Ji
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jian Li
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jie Niu
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Rongjie Mao
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Fuxiang Cao
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410004, China
| | - Meng Li
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China.
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18
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Kim K, Choi BY, Kang J, Shim D, Martinoia E, Lee Y. Arabidopsis ABCG27 plays an essential role in flower and leaf development by modulating abscisic acid content. PHYSIOLOGIA PLANTARUM 2022; 174:e13734. [PMID: 35699652 DOI: 10.1111/ppl.13734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Abscisic acid (ABA) is a phytohormone that mediates stress responses and regulates plant development. Several ATP-binding cassette (ABC) transporters in the G subfamily of ABC (ABCG) proteins have been reported to transport ABA. We investigated whether there are any other ABCG proteins that mediate plant developmental processes regulated by ABA in Arabidopsis (Arabidopsis thaliana). The ABCG27 gene was upregulated in response to exogenous ABA treatment. The abcg27 knockout mutant exhibited two developmental defects: epinastic leaves and abnormally long pistils, which reduced fertility and silique length. ABCG27 expression was induced threefold when flower buds were exposed to exogenous ABA, and the promoter of ABCG27 had two ABA-responsive elements. ABA content in the pistil and true leaves were increased in the abcg27 knockout mutant. Detached abcg27 pistils exposed to exogenous ABA grew longer than those of the wild-type control. ABCG27 fused to GFP localized to the plasma membrane when expressed in Arabidopsis mesophyll protoplasts. A transcriptome analysis of the pistils and true leaves of the wild type and abcg27 knockout mutant revealed that the expression of organ development-related genes changed in the knockout mutant. In particular, the expression of trans-acting small interference (ta-si) RNA processing enzyme genes, which regulate flower and leaf development, was low in the knockout mutant. Together, these results suggest that ABCG27 most likely function as an ABA transporter at the plasma membrane, modulating ABA levels and thereby regulating the development of the pistils and leaves under normal, non-stressed conditions.
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Affiliation(s)
- Kyungyoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Bae Young Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Joohyun Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Youngsook Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
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19
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Wang W, Gu Y. The emerging role of biomolecular condensates in plant immunity. THE PLANT CELL 2022; 34:1568-1572. [PMID: 34599333 PMCID: PMC9048959 DOI: 10.1093/plcell/koab240] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/22/2021] [Indexed: 05/29/2023]
Abstract
Biomolecular condensates are dynamic nonmembranous structures that seclude and concentrate molecules involved in related biochemical and molecular processes. Recent studies have revealed that a surprisingly large number of fundamentally important cellular processes are driven and regulated by this potentially ancient biophysical principle. Here, we summarize critical findings and new insights from condensate studies that are related to plant immunity. We discuss the role of stress granules and newly identified biomolecular condensates in coordinating plant immune responses and plant-microbe interactions.
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Affiliation(s)
- Wei Wang
- Author for correspondence: (W.W.), (Y.G.)
| | - Yangnan Gu
- Author for correspondence: (W.W.), (Y.G.)
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20
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Ai Q, Pan W, Zeng Y, Li Y, Cui L. CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis. BMC PLANT BIOLOGY 2022; 22:117. [PMID: 35291942 PMCID: PMC8922935 DOI: 10.1186/s12870-022-03500-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/01/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. RESULTS In this study, a total of 53 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into eleven subfamilies according to their distinct features, and this classification was supported by intron-exon structure and conserved motif analysis. Both segmental and tandem duplication contributed to the expansion of CCCH gene family in barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The HvC3H1, HvC3H2 and HvC3H13 of arginine-rich tandem CCCH zinc finger (RR-TZF) genes were significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make them as excellent targets for the molecular breeding of barley. CONCLUSIONS Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.
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Affiliation(s)
- Qi Ai
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, 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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21
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Zhu S, Gu J, Yao J, Li Y, Zhang Z, Xia W, Wang Z, Gui X, Li L, Li D, Zhang H, Liu C. Liquid-liquid phase separation of RBGD2/4 is required for heat stress resistance in Arabidopsis. Dev Cell 2022; 57:583-597.e6. [DOI: 10.1016/j.devcel.2022.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 08/24/2021] [Accepted: 02/02/2022] [Indexed: 12/28/2022]
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22
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Guo C, Chen L, Cui Y, Tang M, Guo Y, Yi Y, Li Y, Liu L, Chen L. RNA Binding Protein OsTZF7 Traffics Between the Nucleus and Processing Bodies/Stress Granules and Positively Regulates Drought Stress in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:802337. [PMID: 35265093 PMCID: PMC8899535 DOI: 10.3389/fpls.2022.802337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/05/2022] [Indexed: 05/16/2023]
Abstract
Tandem CCCH zinc finger (TZF) proteins are the essential components of processing bodies (PBs) and stress granules (SGs), which play critical roles in growth development and stress response in both animals and plants through posttranscriptional regulation of target mRNA. In this study, we characterized the biological and molecular functions of a novel tandem zinc finger protein, OsTZF7. The expression of OsTZF7 was upregulated by abiotic stresses, including polyethylene glycol (PEG) 4000, NaCl, and abscisic acid (ABA) in rice. Accordingly, the overexpression of OsTZF7 increased drought tolerance and enhanced sensitivity to exogenous ABA in rice, whereas the knockdown of OsTZF7 resulted in the opposite phenotype. RNA-seq analysis revealed that genes related to "response to stress," "abscisic acid signaling," "methylated histone binding," and "cytoplasmic mRNA processing body" are regulated by OsTZF7. We demonstrated that OsTZF7 can traffic between the nucleus and PBs/SGs, and the leucine-rich nuclear export signal (NES) mediates the nuclear export of OsTZF7. Additionally, we revealed that OsTZF7 can bind adenine- and uridine-rich (AU-rich) element (ARE) or ARE-like motifs within the 3' untranslated region of downregulated mRNAs, and interact with PWWP family proteins in vitro. Together, these results indicate that OsTZF7 positively regulates drought response in rice via ABA signaling and may be involved in mRNA turnover.
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Affiliation(s)
- Chiming Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Lingli Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ming Tang
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwestern, School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Ying Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Yin Yi
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwestern, School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yan Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liqing Liu
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- *Correspondence: Liang Chen,
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Liu Y, Liu S, Shi H, Ma J, Jing M, Han Y. The TSN1 Binding Protein RH31 Is a Component of Stress Granules and Participates in Regulation of Salt-Stress Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:804356. [PMID: 35003193 PMCID: PMC8733394 DOI: 10.3389/fpls.2021.804356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/02/2021] [Indexed: 05/29/2023]
Abstract
Tudor staphylococcal nucleases (TSNs) are evolutionarily conserved RNA binding proteins, which include redundant TSN1 and TSN2 in Arabidopsis. It has been showed TSNs are the components of stress granules (SGs) and regulate plant growth under salt stress. In this study, we find a binding protein of TSN1, RH31, which is a DEAD-box RNA helicase (RH). Subcellular localization studies show that RH31 is mainly located in the nucleus, but under salinity, it translocates to the cytoplasm where it accumulates in cytoplasmic granules. After cycloheximide (CHX) treatment which can block the formation of SGs by interfering with mRNP homeostasis, these cytoplasmic granules disappeared. More importantly, RH31 co-localizes with SGs marker protein RBP47. RH31 deletion results in salt-hypersensitive phenotype, while RH31 overexpression causes more resistant to salt stress. In summary, we demonstrate that RH31, the TSN1 binding protein, is a component of plant SGs and participates in regulation of salt-stress tolerance in Arabidopsis.
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Affiliation(s)
- Yanan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- Wheat Research Institute, Weifang Academy of Agricultural Sciences, Weifang, China
| | - Shijie Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huiying Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | | | - Meng Jing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuzhen Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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24
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Pi B, Pan J, Xiao M, Hu X, Zhang L, Chen M, Liu B, Ruan Y, Huang Y. Systematic analysis of CCCH zinc finger family in Brassica napus showed that BnRR-TZFs are involved in stress resistance. BMC PLANT BIOLOGY 2021; 21:555. [PMID: 34814855 PMCID: PMC8609832 DOI: 10.1186/s12870-021-03340-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/10/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND CCCH zinc finger family is one of the largest transcription factor families related to multiple biotic and abiotic stresses. Brassica napus L., an allotetraploid oilseed crop formed by natural hybridization between two diploid progenitors, Brassica rapa and Brassica oleracea. A systematic identification of rapeseed CCCH family genes is missing and their functional characterization is still in infancy. RESULTS In this study, 155 CCCH genes, 81 from its parent B. rapa and 74 from B. oleracea, were identified and divided into 15 subfamilies in B. napus. Organization and syntenic analysis explained the distribution and collinearity relationship of CCCH genes, the selection pressure and evolution of duplication gene pairs in B. napus genome. 44 diploid duplication gene pairs and 4 triple duplication gene groups were found in B. napus of CCCH family and the segmental duplication is attributed to most CCCH gene duplication events in B. napus. Nine types of CCCH motifs exist in B. napus CCCH family members, and motif C-X7/8-C-X5-C-X3-H is the most common and a new conserved CCH motif (C-X5-C-X3-H) has been identified. In addition, abundant stress-related cis-elements exist in promoters of 27 subfamily IX (RR-TZF) genes and their expression profiles indicated that RR-TZF genes could be involved in responses to hormone and abiotic stress. CONCLUSIONS The results provided a foundation to understand the basic characterization and genes evolution of CCCH gene family in B. napus, and provided potential targets for genetic engineering in Brassicaceae crops in pursuit of stress-tolerant traits.
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Affiliation(s)
- Boyi Pi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Jiao Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Mu Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Xinchang Hu
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Lei Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Min Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Boyu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China.
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25
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Sharmin RA, Karikari B, Chang F, Al Amin GM, Bhuiyan MR, Hina A, Lv W, Chunting Z, Begum N, Zhao T. Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean. BMC PLANT BIOLOGY 2021; 21:497. [PMID: 34715792 PMCID: PMC8555181 DOI: 10.1186/s12870-021-03268-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/29/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Seed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage. RESULTS In the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis-elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation. CONCLUSIONS Our findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.
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Affiliation(s)
- Ripa Akter Sharmin
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jagannath University, Dhaka, 1100, Bangladesh
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Fangguo Chang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - G M Al Amin
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mashiur Rahman Bhuiyan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenhuan Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhang Chunting
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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26
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Han G, Qiao Z, Li Y, Wang C, Wang B. The Roles of CCCH Zinc-Finger Proteins in Plant Abiotic Stress Tolerance. Int J Mol Sci 2021; 22:ijms22158327. [PMID: 34361093 PMCID: PMC8347928 DOI: 10.3390/ijms22158327] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 01/07/2023] Open
Abstract
Zinc-finger proteins, a superfamily of proteins with a typical structural domain that coordinates a zinc ion and binds nucleic acids, participate in the regulation of growth, development, and stress adaptation in plants. Most zinc fingers are C2H2-type or CCCC-type, named after the configuration of cysteine (C) and histidine (H); the less-common CCCH zinc-finger proteins are important in the regulation of plant stress responses. In this review, we introduce the domain structures, classification, and subcellular localization of CCCH zinc-finger proteins in plants and discuss their functions in transcriptional and post-transcriptional regulation via interactions with DNA, RNA, and other proteins. We describe the functions of CCCH zinc-finger proteins in plant development and tolerance to abiotic stresses such as salt, drought, flooding, cold temperatures and oxidative stress. Finally, we summarize the signal transduction pathways and regulatory networks of CCCH zinc-finger proteins in their responses to abiotic stress. CCCH zinc-finger proteins regulate the adaptation of plants to abiotic stress in various ways, but the specific molecular mechanisms need to be further explored, along with other mechanisms such as cytoplasm-to-nucleus shuttling and post-transcriptional regulation. Unraveling the molecular mechanisms by which CCCH zinc-finger proteins improve stress tolerance will facilitate the breeding and genetic engineering of crops with improved traits.
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Affiliation(s)
- Guoliang Han
- Correspondence: (G.H.); (B.W.); Tel./Fax: +86-531-8618-0197 (B.W.)
| | | | | | | | - Baoshan Wang
- Correspondence: (G.H.); (B.W.); Tel./Fax: +86-531-8618-0197 (B.W.)
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27
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Hu X, Zuo J. The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis. BMC Genomics 2021; 22:511. [PMID: 34233625 PMCID: PMC8261996 DOI: 10.1186/s12864-021-07787-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. The zf_CCCH family have been reported involving in various processes of plant development and adaptation. RESULTS In this study, the zf_CCCH genes were identified via a genome-wide search and were systematically analyzed. 116 Gmzf_CCCHs were obtained and classified into seventeen subfamilies. Gene duplication and expansion analysis showed that tandem and segmental duplications contributed to the expansion of the Gmzf_CCCH gene family, and that segmental duplication play the main role. The expression patterns of Gmzf_CCCH genes were tissue-specific. Eleven domesticated genes were detected involved in the regulation of seed oil and protein synthesis as well as growth and development of soybean through GWAS and haplotype analysis for Gmzf_CCCH genes among the 164 of 302 soybeans resequencing data. Among which, 8 genes play an important role in the synthesis of seed oil or fatty acid, and the frequency of their elite haplotypes changes significantly among wild, landrace and improved cultivars, indicating that they have been strongly selected in the process of soybean domestication. CONCLUSIONS This study provides a scientific foundation for the comprehensive understanding, future cloning and functional studies of Gmzf_CCCH genes in soybean, meanwhile, it was also helpful for the improvement of soybean with high oil content.
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Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China.
| | - Jianfang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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28
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Xie Z, Yu G, Lei S, Zhang C, Bin Xu, Huang B. CCCH protein-PvCCCH69 acted as a repressor for leaf senescence through suppressing ABA-signaling pathway. HORTICULTURE RESEARCH 2021; 8:165. [PMID: 34234106 PMCID: PMC8263708 DOI: 10.1038/s41438-021-00604-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 05/19/2023]
Abstract
CCCH is a subfamily of zinc finger proteins involved in plant growth, development, and stresses response. The function of CCCH in regulating leaf senescence, especially its roles in abscisic acid (ABA)-mediated leaf senescence is largely unknown. The objective of this study was to determine functions and mechanisms of CCCH gene in regulating leaf senescence in switchgrass (Panicum virgatum). A CCCH gene, PvCCCH69 (PvC3H69), was cloned from switchgrass. Overexpressing PvC3H69 in rice suppressed both natural senescence with leaf aging and dark-induced leaf senescence. Endogenous ABA content, ABA biosynthesis genes (NCED3, NCED5, and AAO3), and ABA signaling-related genes (SnRKs, ABI5, and ABF2/3/4) exhibited significantly lower levels in senescencing leaves of PvC3H69-OE plants than those in WT plants. PvC3H69-suppression of leaf senescence was associated with transcriptional upregulation of genes mainly involved in the light-dependent process of photosynthesis, including light-harvesting complex proteins, PSI proteins, and PSII proteins and downregulation of ABA biosynthesis and signaling genes and senescence-associated genes. PvC3H69 could act as a repressor for leaf senescence via upregulating photosynthetic proteins and repressing ABA synthesis and ABA signaling pathways.
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Affiliation(s)
- Zheni Xie
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Guohui Yu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Shanshan Lei
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chenchen Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bin Xu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA.
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29
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Lu L, Wei W, Li QT, Bian XH, Lu X, Hu Y, Cheng T, Wang ZY, Jin M, Tao JJ, Yin CC, He SJ, Man WQ, Li W, Lai YC, Zhang WK, Chen SY, Zhang JS. A transcriptional regulatory module controls lipid accumulation in soybean. THE NEW PHYTOLOGIST 2021; 231:661-678. [PMID: 33864683 DOI: 10.1111/nph.17401] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/29/2021] [Indexed: 05/19/2023]
Abstract
Soybean (Glycine max) is one of the most important oilseed crops. However, the regulatory mechanism that governs the process of oil accumulation in soybean remains poorly understood. In this study, GmZF392, a tandem CCCH zinc finger (TZF) protein which was identified in our previous RNA-seq analysis of seed-preferred transcription factors, was found to function as a positive regulator of lipid production. GmZF392 promotes seed oil accumulation in both transgenic Arabidopsis and stable transgenic soybean plants by binding to a bipartite cis-element, containing TG- and TA-rich sequences, in promoter regions, activating the expression of genes in the lipid biosynthesis pathway. GmZF392 physically interacts with GmZF351, our previously identified transcriptional regulator of lipid biosynthesis, to synergistically promote downstream gene expression. Both GmZF392 and GmZF351 are further upregulated by GmNFYA, another transcription factor involved in lipid biosynthesis, directly (in the former case) and indirectly (in the latter case). Promoter sequence diversity analysis showed that the GmZF392 promoter may have been selected at the origin of the Glycine genus and further mildly selected during domestication from wild soybeans to cultivated soybeans. Our study reveals a regulatory module containing three transcription factors in the lipid biosynthesis pathway, and manipulation of the module may improve oil production in soybean and other oilseed crops.
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Affiliation(s)
- Long Lu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Wei
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing-Tian Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao-Hua Bian
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang Lu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Hu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhou-Ya Wang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Jin
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Jun Tao
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cui-Cui Yin
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Si-Jie He
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei-Qun Man
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wei Li
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yong-Cai Lai
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Kim J, Lee H, Lee HG, Seo PJ. Get closer and make hotspots: liquid-liquid phase separation in plants. EMBO Rep 2021; 22:e51656. [PMID: 33913240 DOI: 10.15252/embr.202051656] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/14/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless compartments in a cell and allows the spatiotemporal organization of biochemical reactions by concentrating macromolecules locally. In plants, LLPS defines cellular reaction hotspots, and stimulus-responsive LLPS is tightly linked to a variety of cellular and biological functions triggered by exposure to various internal and external stimuli, such as stress responses, hormone signaling, and temperature sensing. Here, we provide an overview of the current understanding of physicochemical forces and molecular factors that drive LLPS in plant cells. We illustrate how the biochemical features of cellular condensates contribute to their biological functions. Additionally, we highlight major challenges for the comprehensive understanding of biological LLPS, especially in view of the dynamic and robust organization of biochemical reactions underlying plastic responses to environmental fluctuations in plants.
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Affiliation(s)
- Jiwoo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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Tai L, Wang HJ, Xu XJ, Sun WH, Ju L, Liu WT, Li WQ, Sun J, Chen KM. Pre-harvest sprouting in cereals: genetic and biochemical mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2857-2876. [PMID: 33471899 DOI: 10.1093/jxb/erab024] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/18/2021] [Indexed: 05/22/2023]
Abstract
With the growth of the global population and the increasing frequency of natural disasters, crop yields must be steadily increased to enhance human adaptability to risks. Pre-harvest sprouting (PHS), a term mainly used to describe the phenomenon in which grains germinate on the mother plant directly before harvest, is a serious global problem for agricultural production. After domestication, the dormancy level of cultivated crops was generally lower than that of their wild ancestors. Although the shortened dormancy period likely improved the industrial performance of cereals such as wheat, barley, rice, and maize, the excessive germination rate has caused frequent PHS in areas with higher rainfall, resulting in great economic losses. Here, we systematically review the causes of PHS and its consequences, the major indicators and methods for PHS assessment, and emphasize the biological significance of PHS in crop production. Wheat quantitative trait loci functioning in the control of PHS are also comprehensively summarized in a meta-analysis. Finally, we use Arabidopsis as a model plant to develop more complete PHS regulatory networks for wheat. The integration of this information is conducive to the development of custom-made cultivated lines suitable for different demands and regions, and is of great significance for improving crop yields and economic benefits.
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Affiliation(s)
- Li Tai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hong-Jin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiao-Jing Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei-Hang Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lan Ju
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
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32
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Li CH, Fang QX, Zhang WJ, Li YH, Zhang JZ, Chen S, Yin ZG, Li WJ, Liu WD, Yi Z, Mu ZS, Du JD. Genome-wide identification of the CCCH gene family in rose (Rosa chinensis Jacq.) reveals its potential functions. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1901609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Cai-hua Li
- Economic Plant Research Laboratory, Institute of Economic Botany, Jilin Academy of Agricultural Science, Changchun, Jilin, PR China
| | - Qing-xi Fang
- Ornamental Plant Breeding Laboratory, Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Wen-Jing Zhang
- Agricultural Sector, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Yu-huan Li
- Economic Plant Research Laboratory, Institute of Economic Botany, Jilin Academy of Agricultural Science, Changchun, Jilin, PR China
| | - Jin-zhu Zhang
- Ornamental Plant Breeding Laboratory, Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Shuai Chen
- Ornamental Plant Breeding Laboratory, Agricultural College, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Zhen-Gong Yin
- Edible Bean Research Laboratory, Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences Harbin, Heilongjiang, PR China
| | - Wei-Jia Li
- Agricultural Sector, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Wen-da Liu
- Agricultural Sector, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Zheng Yi
- Economic Plant Research Laboratory, Institute of Economic Botany, Jilin Academy of Agricultural Science, Changchun, Jilin, PR China
| | - Zhong-sheng Mu
- Economic Plant Research Laboratory, Institute of Economic Botany, Jilin Academy of Agricultural Science, Changchun, Jilin, PR China
| | - Ji-dao Du
- Agricultural Sector, National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
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Shim JS, Park SH, Lee DK, Kim YS, Park SC, Redillas MCFR, Seo JS, Kim JK. The Rice GLYCINE-RICH PROTEIN 3 Confers Drought Tolerance by Regulating mRNA Stability of ROS Scavenging-Related Genes. RICE (NEW YORK, N.Y.) 2021; 14:31. [PMID: 33742286 PMCID: PMC7979854 DOI: 10.1186/s12284-021-00473-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/10/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant glycine-rich proteins are categorized into several classes based on their protein structures. The glycine-rich RNA binding proteins (GRPs) are members of class IV subfamily possessing N-terminus RNA-recognition motifs (RRMs) and proposed to be involved in post-transcriptional regulation of its target transcripts. GRPs are involved in developmental process and cellular stress responses, but the molecular mechanisms underlying these regulations are still elusive. RESULTS Here, we report the functional characterization of rice GLYCINE-RICH PROTEIN 3 (OsGRP3) and its physiological roles in drought stress response. Both drought stress and ABA induce the expression of OsGRP3. Transgenic plants overexpressing OsGRP3 (OsGRP3OE) exhibited tolerance while knock-down plants (OsGRP3KD) were susceptible to drought compared to the non-transgenic control. In vivo, subcellular localization analysis revealed that OsGRP3-GFP was transported from cytoplasm/nucleus into cytoplasmic foci following exposure to ABA and mannitol treatments. Comparative transcriptomic analysis between OsGRP3OE and OsGRP3KD plants suggests that OsGRP3 is involved in the regulation of the ROS related genes. RNA-immunoprecipitation analysis revealed the associations of OsGRP3 with PATHOGENESIS RELATED GENE 5 (PR5), METALLOTHIONEIN 1d (MT1d), 4,5-DOPA-DIOXYGENASE (DOPA), and LIPOXYGENASE (LOX) transcripts. The half-life analysis showed that PR5 transcripts decayed slower in OsGRP3OE but faster in OsGRP3KD, while MT1d and LOX transcripts decayed faster in OsGRP3OE but slower in OsGRP3KD plants. H2O2 accumulation was reduced in OsGRP3OE and increased in OsGRP3KD plants compared to non-transgenic plants (NT) under drought stress. CONCLUSION OsGRP3 plays a positive regulator in rice drought tolerance and modulates the transcript level and mRNA stability of stress-responsive genes, including ROS-related genes. Moreover, OsGRP3 contributes to the reduction of ROS accumulation during drought stress. Our results suggested that OsGRP3 alleviates ROS accumulation by regulating ROS-related genes' mRNA stability under drought stress, which confers drought tolerance.
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Affiliation(s)
- Jae Sung Shim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Hyun Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Dong-Keun Lee
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- E GREEN GLOBAL, Gunpo, 15843, South Korea
| | - Youn Shic Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, 24341, South Korea
| | - Soo-Chul Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 54874, South Korea
| | | | - Jun Sung Seo
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
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Zhang X, Ding W, Xue D, Li X, Zhou Y, Shen J, Feng J, Guo N, Qiu L, Xing H, Zhao J. Genome-wide association studies of plant architecture-related traits and 100-seed weight in soybean landraces. BMC Genom Data 2021; 22:10. [PMID: 33676409 PMCID: PMC7937308 DOI: 10.1186/s12863-021-00964-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant architecture-related traits (e.g., plant height (PH), number of nodes on main stem (NN), branch number (BN) and stem diameter (DI)) and 100-seed weight (100-SW) are important agronomic traits and are closely related to soybean yield. However, the genetic basis and breeding potential of these important agronomic traits remain largely ambiguous in soybean (Glycine max (L.) Merr.). RESULTS In this study, we collected 133 soybean landraces from China, phenotyped them in two years at two locations for the above five traits and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). As a result, we found that a total of 59 SNPs were repeatedly detected in at least two environments. There were 12, 12, 4, 4 and 27 SNPs associated with PH, NN, BN, DI and 100-SW, respectively. Among these markers, seven SNPs (AX-90380587, AX-90406013, AX-90387160, AX-90317160, AX-90449770, AX-90460927 and AX-90520043) were large-effect markers for PH, NN, BN, DI and 100-SW, and 15 potential candidate genes were predicted to be in linkage disequilibrium (LD) decay distance or LD block. In addition, real-time quantitative PCR (qRT-PCR) analysis was performed on four 100-SW potential candidate genes, three of them showed significantly different expression levels between the extreme materials at the seed development stage. Therefore, Glyma.05 g127900, Glyma.05 g128000 and Glyma.05 g129000 were considered as candidate genes with 100-SW in soybean. CONCLUSIONS These findings shed light on the genetic basis of plant architecture-related traits and 100-SW in soybean, and candidate genes could be used for further positional cloning.
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Affiliation(s)
- Xiaoli Zhang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wentao Ding
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dong Xue
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiangnan Li
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yang Zhou
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiacheng Shen
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jianying Feng
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Na Guo
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Han Xing
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jinming Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
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Cheng X, Cao J, Gao C, Gao W, Yan S, Yao H, Xu K, Liu X, Xu D, Pan X, Lu J, Chang C, Zhang H, Ma C. Identification of the wheat C3H gene family and expression analysis of candidates associated with seed dormancy and germination. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:524-537. [PMID: 33053501 DOI: 10.1016/j.plaphy.2020.09.032] [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: 07/20/2020] [Accepted: 09/28/2020] [Indexed: 05/01/2023]
Abstract
C3H zinc finger transcription factors play important roles in managing various biotic/abiotic stresses in Aarabidopsis, rice, and maize. The functions of these factors in wheat, however, remain largely unclear. We identified 88 TaC3H genes that were divided into four subfamilies in this analysis. Gene structure and conserved domain analyses indicate that most members of the same subfamily have similar structures. A total of 76 paralogous and 48 orthologous pairs were identified and Ka/Ks values were used to analyze replication relationships amongst wheat, rice, and Arabidopsis. Gene ontology (GO) annotation analysis showed that most TaC3H genes possessed molecular functions, while transcriptome results showed that the 88 TaC3H genes responded to water imbibition. Microarray data for 53 TaC3H genes were obtained and heat maps were generated; these results indicate that these genes are expressed in 13 wheat tissues. Subcellular localization prediction analysis indicates that most TaC3H genes are located in the nucleus. Promoter analysis indicates that most TaC3H genes contained cis-elements including ABRE, GARE-motif, and MBS, indicating that these can respond to various biotic/abiotic stresses. Transcriptome data and quantitative real-time PCR analysis of wheat cultivars with contrasting seed dormancy phenotypes show that five genes TaC3H4/-18/-37/-51/-72 were very likely involved in seed dormancy and germination. Exogenous ABA treatment further indicated that these five genes were responsive to ABA, suggesting that there may be a crosstalk between these genes and ABA signaling pathway in controlling seed dormancy and germination. These results provide a theoretical basis for subsequent studies on TaC3H gene function and also contribute to studies on the C3H gene in other species.
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Affiliation(s)
- Xinran Cheng
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Jiajia Cao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Chang Gao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Wei Gao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Shengnan Yan
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Hui Yao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Kangle Xu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Xue Liu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Dongmei Xu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Xu Pan
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China.
| | - Haiping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China.
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, Anhui, China
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Xu L, Liu T, Xiong X, Liu W, Yu Y, Cao J. Overexpression of Two CCCH-type Zinc-Finger Protein Genes Leads to Pollen Abortion in Brassica campestris ssp. chinensis. Genes (Basel) 2020; 11:E1287. [PMID: 33138166 PMCID: PMC7693475 DOI: 10.3390/genes11111287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022] Open
Abstract
The pollen grains produced by flowering plants are vital for sexual reproduction. Previous studies have shown that two CCCH-type zinc-finger protein genes in Brassica campestris, BcMF30a and BcMF30c, are involved in pollen development. Due to their possible functional redundancy, gain-of-function analysis is helpful to reveal their respective biological functions. Here, we found that the phenotypes of BcMF30a and BcMF30c overexpression transgenic plants driven by their native promoters were similar, suggesting their functional redundancy. The results showed that the vegetative growth was not affected in both transgenic plants, but male fertility was reduced. Further analysis found that the abortion of transgenic pollen was caused by the degradation of pollen contents from the late uninucleate microspore stage. Subcellular localization analysis demonstrated that BcMF30a and BcMF30c could localize in cytoplasmic foci. Combined with the studies of other CCCH-type genes, we speculated that the overexpression of these genes can induce the continuous assembly of abnormal cytoplasmic foci, thus resulting in defective plant growth and development, which, in this study, led to pollen abortion. Both the overexpression and knockout of BcMF30a and BcMF30c lead to abnormal pollen development, indicating that the appropriate expression levels of these two genes are critical for the maintenance of normal pollen development.
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Affiliation(s)
- Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (T.L.); (X.X.); (W.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Tingting Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (T.L.); (X.X.); (W.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Xingpeng Xiong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (T.L.); (X.X.); (W.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Weimiao Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (T.L.); (X.X.); (W.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Youjian Yu
- Department of Horticulture, College of Agriculture and Food Science, Zhejiang A & F University, Lin’an 311300, China;
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (T.L.); (X.X.); (W.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
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Seong SY, Shim JS, Bang SW, Kim JK. Overexpression of OsC3H10, a CCCH-Zinc Finger, Improves Drought Tolerance in Rice by Regulating Stress-Related Genes. PLANTS 2020; 9:plants9101298. [PMID: 33019599 PMCID: PMC7599559 DOI: 10.3390/plants9101298] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
Abstract
CCCH zinc finger proteins are members of the zinc finger protein family, and are known to participate in the regulation of development and stress responses via the posttranscriptional regulation of messenger RNA in animals and yeast. However, the molecular mechanism of CCCHZF-mediated drought tolerance is not well understood. We analyzed the functions of OsC3H10, a member of the rice CCCHZF family. OsC3H10 is predominantly expressed in seeds, and its expression levels rapidly declined during seed imbibition. The expression of OsC3H10 was induced by drought, high salinity and abscisic acid (ABA). Subcellular localization analysis revealed that OsC3H10 localized not only in the nucleus but also to the processing bodies and stress granules upon stress treatment. Root-specific overexpression of OsC3H10 was insufficient to induce drought tolerance, while the overexpression of OsC3H10 throughout the entire plant enhanced the drought tolerance of rice plants. Transcriptome analysis revealed that OsC3H10 overexpression elevated the expression levels of genes involved in stress responses, including LATE EMBRYOGENESIS ABUNDANT PROTEINs (LEAs), PATHOGENESIS RELATED GENEs (PRs) and GERMIN-LIKE PROTEINs (GLPs). Our results demonstrated that OsC3H10 is involved in the regulation of the drought tolerance pathway by modulating the expression of stress-related genes.
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Affiliation(s)
- So Yoon Seong
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (S.Y.S.); (J.S.S.); (S.W.B.)
| | - Jae Sung Shim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (S.Y.S.); (J.S.S.); (S.W.B.)
- Present address: School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Seung Woon Bang
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (S.Y.S.); (J.S.S.); (S.W.B.)
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (S.Y.S.); (J.S.S.); (S.W.B.)
- Correspondence:
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Xu L, Xiong X, Liu W, Liu T, Yu Y, Cao J. BcMF30a and BcMF30c, Two Novel Non-Tandem CCCH Zinc-Finger Proteins, Function in Pollen Development and Pollen Germination in Brassica campestris ssp. chinensis. Int J Mol Sci 2020; 21:ijms21176428. [PMID: 32899329 PMCID: PMC7504113 DOI: 10.3390/ijms21176428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/19/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
Chinese cabbage (Brassica campestris) is an economically important leaf vegetable crop worldwide. Mounting studies have shown that cysteine-cysteine-cysteine-histidine (CCCH) zinc-finger protein genes are involved in various plant growth and development processes. However, research on the involvement of these genes in male reproductive development is still in its infancy. Here, we identified 11 male fertility-related CCCH genes in Chinese cabbage. Among them, a pair of paralogs encoding novel non-tandem CCCH zinc-finger proteins, Brassica campestris Male Fertility 30a (BcMF30a) and BcMF30c, were further characterized. They were highly expressed in pollen during microgametogenesis and continued to express in germinated pollen. Further analyses demonstrated that both BcMF30a and BcMF30c may play a dual role as transcription factors and RNA-binding proteins in plant cells. Functional analysis showed that partial bcmf30a bcmf30c pollen grains were aborted due to the degradation of pollen inclusion at the microgametogenesis phase, and the germination rate of viable pollen was also greatly reduced, indicating that BcMF30a and BcMF30c are required for both pollen development and pollen germination. This research provided insights into the function of CCCH proteins in regulating male reproductive development and laid a theoretical basis for hybrid breeding of Chinese cabbage.
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Affiliation(s)
- Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Xingpeng Xiong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Weimiao Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Tingting Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Youjian Yu
- Department of Horticulture, College of Agriculture and Food Science, Zhejiang A & F University, Lin’an 311300, China;
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (L.X.); (X.X.); (W.L.); (T.L.)
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-131-8501-1958
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Chen F, Liu HL, Wang K, Gao YM, Wu M, Xiang Y. Identification of CCCH Zinc Finger Proteins Family in Moso Bamboo ( Phyllostachys edulis), and PeC3H74 Confers Drought Tolerance to Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:579255. [PMID: 33240298 PMCID: PMC7680867 DOI: 10.3389/fpls.2020.579255] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/12/2020] [Indexed: 05/12/2023]
Abstract
CCCH zinc finger proteins are a class of important zinc-finger transcription factors and have functions in various plant growth and stress responses, but their functions in moso bamboo (Phyllostachys edulis) are unclear. In this current study, we main investigated the structures, phylogenetic relationships, promoter elements and microsynteny of PeC3Hs. In this research, 119 CCCH zinc finger proteins (PeC3H1-119) identified genes in moso bamboo were divided into 13 subfamilies (A-M) based on phylogenetic analysis. Meanwhile, moso bamboo were treated with abscisic acid (ABA), methyl jasmonate (Me-JA) and gibberellic acid (GA) and 12 CCCH genes expression levels were assayed using qRT-PCR. In the three hormone treatments, 12 genes were up-regulated or down-regulated, respectively. In addition, PeC3H74 was localized on the cytomembrane, and it had self-activation activities. Phenotypic and physiological analysis showed that PeC3H74 (PeC3H74-OE) conferred drought tolerance of transgenic Arabidopsis, including H2O2 content, survival rate, electrolyte leakage as well as malondialdehyde content. Additionally, compared with wild-type plants, transgenic Arabidopsis thaliana seedling roots growth developed better under 10 μM ABA; Moreover, the stomatal of over-expressing PeC3H74 in Arabidopsis changed significantly under ABA treatment. The above results suggest that PeC3H74 was quickly screened by bioinformatics, and it may enhanced drought tolerance in plants through the ABA-dependent signaling pathway.
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Affiliation(s)
- Feng Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Huan-Long Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Kang Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Ya-Meng Gao
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- *Correspondence: Yan Xiang,
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Li B, Wang Y, Zhang Y, Tian W, Chong K, Jang JC, Wang L. PRR5, 7 and 9 positively modulate TOR signaling-mediated root cell proliferation by repressing TANDEM ZINC FINGER 1 in Arabidopsis. Nucleic Acids Res 2019; 47:5001-5015. [PMID: 30892623 PMCID: PMC6547441 DOI: 10.1093/nar/gkz191] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 12/22/2022] Open
Abstract
Circadian clock coordinates numerous plant growth and developmental processes including cell elongation in the hypocotyl, whether or not it modulates cell proliferation is largely unknown. Here we have found that Pseudo Response Regulators (PRRs), essential components of circadian core oscillators, affect root meristem cell proliferation mediated by Target Of Rapamycin (TOR) signaling. The null mutants of PRRs display much reduced sensitivities to sugar-activated TOR signaling. We have subsequently identified Tandem Zinc Finger 1, encoding a processing body localized RNA-binding protein, as a direct target repressed by PRRs in mediating TOR signaling. Multiple lines of biochemical and genetic evidence have demonstrated that TZF1 acts downstream of PRRs to attenuate TOR signaling. Furthermore, TZF1 could directly bind TOR mRNA via its tandem zinc finger motif to affect TOR mRNA stability. Our findings support a notion that PRR-TZF1-TOR molecular axis modulates root meristem cell proliferation by integrating both transcriptional and post-transcriptional regulatory mechanisms.
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Affiliation(s)
- Bin Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China
| | - Yan Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China.,University of Chinese Academy of Sciences
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China
| | - Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China.,University of Chinese Academy of Sciences
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China.,University of Chinese Academy of Sciences
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Zhang H, Gao X, Zhi Y, Li X, Zhang Q, Niu J, Wang J, Zhai H, Zhao N, Li J, Liu Q, He S. A non-tandem CCCH-type zinc-finger protein, IbC3H18, functions as a nuclear transcriptional activator and enhances abiotic stress tolerance in sweet potato. THE NEW PHYTOLOGIST 2019; 223:1918-1936. [PMID: 31091337 DOI: 10.1111/nph.15925] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/08/2019] [Indexed: 05/21/2023]
Abstract
CCCH-type zinc-finger proteins play essential roles in regulating plant development and stress responses. However, the molecular and functional properties of non-tandem CCCH-type zinc-finger (non-TZF) proteins have been rarely characterized in plants. Here, we report the biological and molecular characterization of a sweet potato non-TZF gene, IbC3H18. We show that IbC3H18 exhibits tissue- and abiotic stress-specific expression, and could be effectively induced by abiotic stresses, including NaCl, polyethylene glycol (PEG) 6000, H2 O2 and abscisic acid (ABA) in sweet potato. Accordingly, overexpression of IbC3H18 led to increased, whereas knock-down of IbC3H18 resulted in decreased tolerance of sweet potato to salt, drought and oxidation stresses. In addition, IbC3H18 functions as a nuclear transcriptional activator and regulates the expression of a range of abiotic stress-responsive genes involved in reactive oxygen species (ROS) scavenging, ABA signaling, photosynthesis and ion transport pathways. Moreover, our data demonstrate that IbC3H18 physically interacts with IbPR5, and that overexpression of IbPR5 enhances salt and drought tolerance in transgenic tobacco plants. Collectively, our data indicate that IbC3H18 functions in enhancing abiotic stress tolerance in sweet potato, which may serve as a candidate gene for use in improving abiotic stress resistance in crops.
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Affiliation(s)
- Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoru Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yuhai Zhi
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xu Li
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qian Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinbiao Niu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Wang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, 100193, China
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Zuo J, Lin CT, Cao H, Chen F, Liu Y, Liu J. Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.). PLANTA 2019; 250:187-198. [PMID: 30972483 DOI: 10.1007/s00425-019-03164-9] [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] [Received: 11/10/2018] [Accepted: 04/06/2019] [Indexed: 05/06/2023]
Abstract
Totally, 23 and 26 loci for the first count germination ratio and the final germination ratio were detected by quantitative trait loci (QTL) mapping and association mapping, respectively, which could be used to facilitate wheat pre-harvest sprouting breeding. Weak dormancy can cause pre-harvest sprouting in seeds of common wheat which significantly reduces grain yield. In this study, both quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) were used to identify loci controlling seed dormancy. The analyses were based on a recombinant inbred line population derived from Zhou 8425B/Chinese Spring cross and 166 common wheat accessions. Inclusive composite interval mapping detected 8 QTL, while 45 loci were identified in the 166 wheat accessions by GWAS. Among these, four loci (Qbifcgr.cas-3AS/Qfcgr.cas-3AS, Qbifcgr.cas-6AL.1/Qfcgr.cas-6AL.1, Qbifcgr.cas-7BL.2/Qfcgr.cas-7BL.2, and Qbigr.cas-3DL/Qgr.cas-3DL) were detected in both QTL mapping and GWAS. In addition, 41 loci co-located with QTL reported previously, whereas 8 loci (Qfcgr.cas-5AL, Qfcgr.cas-6DS, Qfcgr.cas-7AS, Qgr.cas-3DS.1, Qgr.cas-3DS.2, Qbigr.cas-3DL/Qgr.cas-3DL, Qgr.cas-4B, and Qgr.cas-5A) were likely to be new. Linear regression showed the first count germination ratio or the final germination ratio reduced while multiple favorable alleles increased. It is suggested that QTL pyramiding was effective to reduce pre-harvest sprouting risk. This study could enrich the research on pre-harvest sprouting and provide valuable information of marker exploration for wheat breeding programs.
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Affiliation(s)
- Jinghong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Science, Beijing, China
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- College of Life Science, University of Chinese Academy of Science, Beijing, China.
| | - Jindong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
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Li X, Liu S, Yuan G, Zhao P, Yang W, Jia J, Cheng L, Qi D, Chen S, Liu G. Comparative transcriptome analysis provides insights into the distinct germination in sheepgrass (Leymus chinensis) during seed development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:446-458. [PMID: 30999132 DOI: 10.1016/j.plaphy.2019.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/05/2019] [Accepted: 04/07/2019] [Indexed: 05/12/2023]
Abstract
Sheepgrass (Leymus chinensis ((Trin.) Tzvel)) is an important perennial forage grass that is widely distributed in the Eurasia steppe. The seed germination percentage show significant variation among the different germplasm in sheepgrass. However, the underlying molecular mechanisms of distinct germination during seed development are still mostly unknown. Here, we performed comparative transcriptomic analyses of high seed germination percentage (H) and low seed germination percentage (L) at 14, 28, and 42 days after pollination. After comparing 3 consecutive development stages, 9255, 5366, and 4306 genes were found to be significantly differently expressed between H and L. Pathway analysis indicated that transcripts related to starch and sucrose metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, amino sugar and nucleotide sugar metabolism, and photosynthesis were significantly changed between the two germplasm at three stages. ABA and GA metabolism- and signaling transduction-related genes were differentially expressed between two germplasm at development stages, suggesting that the reduced signaling of GA and ABA is likely to be related to seed germination and dormancy in sheepgrass. We also identified 81 transcription factor (TF) families, and some TFs genes such as NAC48, NAC78, WRKY80, ZnFP, C3H14 and ILR3 were significantly differential expressed in two germplasm. Our results provide insights into seed development, germination and dormancy in sheepgrass at the transcriptional level.
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Affiliation(s)
- Xiaoxia Li
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Shu Liu
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Guangxiao Yuan
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Pincang Zhao
- College of Management Science and Engineering, Hebei University of Economics and Business, Shijiazhuang, China
| | - Weiguang Yang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; Institute of Animal Science of Heilongjiang Province, Heilongjiang, Qiqihar, China
| | - Junting Jia
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Liqin Cheng
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Dongmei Qi
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Shuangyan Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.
| | - Gongshe Liu
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.
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Sun H, Meng M, Yan Z, Lin Z, Nie X, Yang X. Genome-wide association mapping of stress-tolerance traits in cotton. THE CROP JOURNAL 2019; 7:77-88. [PMID: 0 DOI: 10.1016/j.cj.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Pi B, He X, Ruan Y, Jang JC, Huang Y. Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa. BMC PLANT BIOLOGY 2018; 18:373. [PMID: 30587139 PMCID: PMC6307296 DOI: 10.1186/s12870-018-1608-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/17/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ubiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms. CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear. RESULTS In this study, 103 CCCH genes in B. rapa were identified. A comparative analysis of the chromosomal position, gene structure, domain organization and duplication event between B. rapa and Arabidopsis thaliana were performed. Results showed that CCCH genes could be divided into 18 subfamilies, and segmental duplication might mainly contribute to this family expansion. C-X7/8-C-X5-C3-H was the most commonly found motif, but some novel CCCH motifs were also found, along with some loses of typical CCCH motifs widespread in other plant species. The multifarious gene structures and domain organizations implicated functional diversity of CCCH genes in B. rapa. Evidence also suggested functional redundancy in at least one subfamily due to high conservation between members. Finally, the expression profiles of subfamily-IX genes indicated that they are likely involved in various stress responses. CONCLUSION This study provides the first genome-wide characterization of the CCCH genes in B. rapa. The results suggest that B. rapa CCCH genes are likely functionally divergent, but mostly involved in plant development and stress response. These results are expected to facilitate future functional characterization of this potential RNA-binding protein family in Brassica crops.
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Affiliation(s)
- Boyi Pi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Xinghui He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, Molecular Genetics, and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
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Chen K, Luan M, Xiong H, Chen P, Chen J, Gao G, Huang K, Zhu A, Yu C. Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.). BMC PLANT BIOLOGY 2018; 18:345. [PMID: 30541445 PMCID: PMC6292125 DOI: 10.1186/s12870-018-1573-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 11/26/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ramie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known. RESULTS A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170-64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170-64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie. CONCLUSIONS The identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.
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Affiliation(s)
- Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Heping Xiong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Kunyong Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
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Qiu A, Lei Y, Yang S, Wu J, Li J, Bao B, Cai Y, Wang S, Lin J, Wang Y, Shen L, Cai J, Guan D, He S. CaC3H14 encoding a tandem CCCH zinc finger protein is directly targeted by CaWRKY40 and positively regulates the response of pepper to inoculation by Ralstonia solanacearum. MOLECULAR PLANT PATHOLOGY 2018; 19:2221-2235. [PMID: 29683552 PMCID: PMC6638151 DOI: 10.1111/mpp.12694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/27/2018] [Accepted: 04/20/2018] [Indexed: 05/10/2023]
Abstract
Tandem CCCH zinc finger (TZnF) proteins have been implicated in plant defence, but their role in pepper (Capsicum annuum) is unclear. In the present study, the role of CaC3H14, a pepper TZnF protein, in the immune response of pepper plants to Ralstonia solanacearum infection was characterized. When fused to the green fluorescent protein, CaC3H14 was localized exclusively to the nuclei in leaf cells of Nicotiana benthamiana plants transiently overexpressing CaC3H14. Transcript abundance of CaC3H14 was up-regulated by inoculation with R. solanacearum. Virus-induced silencing of CaC3H14 increased the susceptibility of the plants to R. solanacearum and down-regulated the genes associated with the hypersensitive response (HR), specifically HIR1 and salicylic acid (SA)-dependent PR1a. By contrast, silencing resulted in the up-regulation of jasmonic acid (JA)-dependent DEF1 and ethylene (ET) biosynthesis-associated ACO1. Transient overexpression of CaC3H14 in pepper triggered an intensive HR, indicated by cell death and hydrogen peroxide (H2 O2 ) accumulation, up-regulated PR1a and down-regulated DEF1 and ACO1. Ectopic overexpression of CaC3H14 in tobacco plants significantly decreased the susceptibility of tobacco plants to R. solanacearum. It also up-regulated HR-associated HSR515, immunity-associated GST1 and the SA-dependent marker genes NPR1 and PR2, but down-regulated JA-dependent PR1b and ET-dependent EFE26. The CaC3H14 promoter and was bound and its transcription was up-regulated by CaWRKY40. Collectively, these results indicate that CaC3H14 is transcriptionally targeted by CaWRKY40, is a modulator of the antagonistic interaction between SA and JA/ET signalling, and enhances the defence response of pepper plants to infection by R. solanacearum.
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Affiliation(s)
- Ailian Qiu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yufen Lei
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Sheng Yang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Ji Wu
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jiazhi Li
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Bingjin Bao
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yiting Cai
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Song Wang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jinhui Lin
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Yuzhu Wang
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Lei Shen
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Jinsen Cai
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Deyi Guan
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
| | - Shuilin He
- National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China
- College of Crop ScienceFujian Agriculture and Forestry UniversityFuzhouFujian 350002China
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Alberto D, Couée I, Pateyron S, Sulmon C, Gouesbet G. Low doses of triazine xenobiotics mobilize ABA and cytokinin regulations in a stress- and low-energy-dependent manner. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:8-22. [PMID: 30080643 DOI: 10.1016/j.plantsci.2018.04.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/25/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
The extent of residual contaminations of pesticides through drift, run-off and leaching is a potential threat to non-target plant communities. Arabidopsis thaliana responds to low doses of the herbicide atrazine, and of its degradation products, desethylatrazine and hydroxyatrazine, not only in the long term, but also under conditions of short-term exposure. In order to investigate underlying molecular mechanisms of low-dose responses and to decipher commonalities and specificities between different chemical treatments, parallel transcriptomic studies of the early effects of the atrazine-desethylatrazine-hydroxyatrazine chemical series were undertaken using whole-genome microarrays. All of the triazines under study produced coordinated and specific changes in gene expression. Hydroxyatrazine-responsive genes were mainly linked to root development, whereas atrazine and desethylatrazine mostly affected molecular signaling networks implicated in stress and hormone responses. Analysis of signaling-related genes, promoter sites and shared-function interaction networks highlighted the involvement of energy-, stress-, abscisic acid- and cytokinin-regulated processes, and emphasized the importance of cold-, heat- and drought-related signaling in the perception of low doses of triazines. These links between low-dose xenobiotic impacts and stress-hormone crosstalk pathways give novel insights into plant-pesticide interactions and plant-pollution interactions that are essential for toxicity evaluation in the context of environmental risk assessment.
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Affiliation(s)
- Diana Alberto
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Ivan Couée
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Cécile Sulmon
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France
| | - Gwenola Gouesbet
- Université de Rennes 1 / Centre National de la Recherche Scientifique, UMR 6553 ECOBIO, Rennes, F-35000, France.
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49
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Jarret DA, Morris J, Cullen DW, Gordon SL, Verrall SR, Milne L, Hedley PE, Allwood JW, Brennan RM, Hancock RD. A Transcript and Metabolite Atlas of Blackcurrant Fruit Development Highlights Hormonal Regulation and Reveals the Role of Key Transcription Factors. FRONTIERS IN PLANT SCIENCE 2018; 9:1235. [PMID: 30210515 PMCID: PMC6119775 DOI: 10.3389/fpls.2018.01235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/06/2018] [Indexed: 05/14/2023]
Abstract
Blackcurrant fruit collected at six stages of development were assessed for changes in gene expression using custom whole transcriptome microarrays and for variation in metabolite content using a combination of liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. Principal components analysis demonstrated that fruit development could be clearly defined according to their transcript or metabolite profiles. During early developmental stages, metabolite profiles were dominated by amino acids and tannins, whilst transcript profiles were enriched in functions associated with cell division, anatomical structure morphogenesis and cell wall metabolism. During mid fruit development, fatty acids accumulated and transcript profiles were consistent with seed and embryo development. At the later stages, sugars and anthocyanins accumulated consistent with transcript profiles that were associated with secondary metabolism. Transcript data also indicated active signaling during later stages of fruit development. A targeted analysis of signaling networks revealed a dynamic activation and repression of almost 60 different transcripts encoding transcription factors across the course of fruit development, many of which have been demonstrated as pivotal to controlling such processes in other species. Transcripts associated with cytokinin and gibberellin were highly abundant at early fruit development, whilst those associated with ABA and ethylene tended to be more abundant at later stages. The data presented here provides an insight into fruit development in blackcurrant and provides a foundation for further work in the elucidation of the genetic basis of fruit quality.
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Affiliation(s)
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Danny W. Cullen
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sandra L. Gordon
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Susan R. Verrall
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Linda Milne
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - J. William Allwood
- Environmental and Biochemical Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Rex M. Brennan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robert D. Hancock
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
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50
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Deng Y, Zheng H, Yan Z, Liao D, Li C, Zhou J, Liao H. Full-Length Transcriptome Survey and Expression Analysis of Cassia obtusifolia to Discover Putative Genes Related to Aurantio-Obtusin Biosynthesis, Seed Formation and Development, and Stress Response. Int J Mol Sci 2018; 19:ijms19092476. [PMID: 30134624 PMCID: PMC6163539 DOI: 10.3390/ijms19092476] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/23/2022] Open
Abstract
The seed is the pharmaceutical and breeding organ of Cassia obtusifolia, a well-known medical herb containing aurantio-obtusin (a kind of anthraquinone), food, and landscape. In order to understand the molecular mechanism of the biosynthesis of aurantio-obtusin, seed formation and development, and stress response of C. obtusifolia, it is necessary to understand the genomics information. Although previous seed transcriptome of C. obtusifolia has been carried out by short-read next-generation sequencing (NGS) technology, the vast majority of the resulting unigenes did not represent full-length cDNA sequences and supply enough gene expression profile information of the various organs or tissues. In this study, fifteen cDNA libraries, which were constructed from the seed, root, stem, leaf, and flower (three repetitions with each organ) of C. obtusifolia, were sequenced using hybrid approach combining single-molecule real-time (SMRT) and NGS platform. More than 4,315,774 long reads with 9.66 Gb sequencing data and 361,427,021 short reads with 108.13 Gb sequencing data were generated by SMRT and NGS platform, respectively. 67,222 consensus isoforms were clustered from the reads and 81.73% (61,016) of which were longer than 1000 bp. Furthermore, the 67,222 consensus isoforms represented 58,106 nonredundant transcripts, 98.25% (57,092) of which were annotated and 25,573 of which were assigned to specific metabolic pathways by KEGG. CoDXS and CoDXR genes were directly used for functional characterization to validate the accuracy of sequences obtained from transcriptome. A total of 658 seed-specific transcripts indicated their special roles in physiological processes in seed. Analysis of transcripts which were involved in the early stage of anthraquinone biosynthesis suggested that the aurantio-obtusin in C. obtusifolia was mainly generated from isochorismate and Mevalonate/methylerythritol phosphate (MVA/MEP) pathway, and three reactions catalyzed by Menaquinone-specific isochorismate synthase (ICS), 1-deoxy-d-xylulose-5-phosphate synthase (DXS) and isopentenyl diphosphate (IPPS) might be the limited steps. Several seed-specific CYPs, SAM-dependent methyltransferase, and UDP-glycosyltransferase (UDPG) supplied promising candidate genes in the late stage of anthraquinone biosynthesis. In addition, four seed-specific transcriptional factors including three MYB Transcription Factor (MYB) and one MADS-box Transcription Factor (MADS) transcriptional factors) and alternative splicing might be involved with seed formation and development. Meanwhile, most members of Hsp20 genes showed high expression level in seed and flower; seven of which might have chaperon activities under various abiotic stresses. Finally, the expressional patterns of genes with particular interests showed similar trends in both transcriptome assay and qRT-PCR. In conclusion, this is the first full-length transcriptome sequencing reported in Caesalpiniaceae family, and thus providing a more complete insight into aurantio-obtusin biosynthesis, seed formation and development, and stress response as well in C. obtusifolia.
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Affiliation(s)
- Yin Deng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Hui Zheng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Zicheng Yan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Dongying Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Chaolin Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
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