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Yang J, Guo C, Chen F, Lv B, Song J, Ning G, He Y, Lin J, He H, Yang Y, Xiang F. Heat-induced modulation of flavonoid biosynthesis via a LhMYBC2-Mediated regulatory network in oriental hybrid lily. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108966. [PMID: 39059274 DOI: 10.1016/j.plaphy.2024.108966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/22/2024] [Accepted: 07/22/2024] [Indexed: 07/28/2024]
Abstract
Global warming significantly threatens crop production, and adversely affects plant physiology due to rising temperatures. Oriental hybrid lily, an ornamental plant of economic importance, experiences flower color changes in response to elevated temperatures. Anthocyanins belong to a subgroup of flavonoids and are the primary pigments responsible for the coloration of oriental hybrid lily petals. However, the regulatory mechanisms governing flavonoid biosynthesis under high temperature conditions in lilies remain poorly understood. In this study, we revealed the altered metabolite profiles in flavonoid biosynthesis using quasi-targeted metabolomic and transcriptomic analyses. Isoflavonoids accumulate substantially under high temperature conditions, whereas the accumulation of anthocyanin decreases. The expression of the isoflavone reductase gene (LhIFR) and the transcription factor LhMYBC2 were upregulated in response to high temperatures. The LhMYBC2 protein, which belongs to Subgroup 4-AtMYB4, competes with the anthocyanin positive regulator LhMYBA1 for the LhTT8 partner, thereby repressing the formation of a positively regulated transcription complex. Heterologous overexpression of LhMYBC2 in tobacco led to reduced anthocyanin accumulation and increased isoflavonoid accumulation, corroborating its role in inhibiting anthocyanin biosynthesis. This study proposes a regulatory model wherein LhMYBC2 acts as a mediator of flavonoid biosynthesis, influencing the coloration of lily flowers under high-temperature stress. These findings deepen our understanding of the metabolic and transcriptional responses of lily to heat stress and underscore the potential role of LhMYBC2 in mitigating anthocyanin accumulation.
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Affiliation(s)
- Jie Yang
- Hubei Research Center of Flower, Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China; Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068, China.
| | - Cong Guo
- Hubei Research Center of Flower, Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Feng Chen
- Hubei Research Center of Flower, Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Bo Lv
- Hubei Research Center of Flower, Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Jurong Song
- Hubei Research Center of Flower, Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Guogui Ning
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanhong He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Lin
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068, China
| | - Hengbing He
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yuanyuan Yang
- Hubei Research Center of Flower, Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Fayun Xiang
- Hubei Research Center of Flower, Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
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Traverse KKF, Breselge S, Trautman JG, Dee A, Wang J, Childs KL, Lee-Parsons CWT. Characterization of the ZCTs, a subgroup of Cys2-His2 zinc finger transcription factors regulating alkaloid biosynthesis in Catharanthus roseus. PLANT CELL REPORTS 2024; 43:209. [PMID: 39115578 PMCID: PMC11310244 DOI: 10.1007/s00299-024-03295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 07/26/2024] [Indexed: 08/11/2024]
Abstract
KEY MESSAGE The C. roseus ZCTs are jasmonate-responsive, can be induced by CrMYC2a, and can act as significant regulators of the terpenoid indole alkaloid pathway when highly expressed. Catharanthus roseus is the sole known producer of the anti-cancer terpenoid indole alkaloids (TIAs), vinblastine and vincristine. While the enzymatic steps of the pathway have been elucidated, an understanding of its regulation is still emerging. The present study characterizes an important subgroup of Cys2-His2 zinc finger transcription factors known as Zinc finger Catharanthus Transcription factors (ZCTs). We identified three new ZCT members (named ZCT4, ZCT5, and ZCT6) that clustered with the putative repressors of the TIA pathway, ZCT1, ZCT2, and ZCT3. We characterized the role of these six ZCTs as potential redundant regulators of the TIA pathway, and their tissue-specific and jasmonate-responsive expression. These ZCTs share high sequence conservation in their two Cys2-His2 zinc finger domains but differ in the spacer length and sequence between these zinc fingers. The transient overexpression of ZCTs in seedlings significantly repressed the promoters of the terpenoid (pLAMT) and condensation branch (pSTR1) of the TIA pathway, consistent with that previously reported for ZCT1, ZCT2, and ZCT3. In addition, ZCTs significantly repressed and indirectly activated several promoters of the vindoline pathway (not previously studied). The ZCTs differed in their tissue-specific expression but similarly increased with jasmonate in a dosage-dependent manner (except for ZCT5). We showed significant activation of the pZCT1 and pZCT3 promoters by the de-repressed CrMYC2a, suggesting that the jasmonate-responsive expression of the ZCTs can be mediated by CrMYC2a. In summary, the C. roseus ZCTs are jasmonate-responsive, can be induced by CrMYC2a, and can act as significant regulators of the TIA pathway when highly expressed.
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Affiliation(s)
| | - Samuel Breselge
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Juliet G Trautman
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Amanda Dee
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Carolyn W T Lee-Parsons
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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3
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Carrera-Castaño G, Mira S, Fañanás-Pueyo I, Sánchez-Montesino R, Contreras Á, Weiste C, Dröge-Laser W, Gómez L, Oñate-Sánchez L. Complex control of seed germination timing by ERF50 involves RGL2 antagonism and negative feedback regulation of DOG1. THE NEW PHYTOLOGIST 2024; 242:2026-2042. [PMID: 38494681 DOI: 10.1111/nph.19681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
Seed dormancy governs germination timing, with both evolutionary and applied consequences. Despite extensive studies on the hormonal and genetic control of these processes, molecular mechanisms directly linking dormancy and germination remain poorly understood. By screening a collection of lines overexpressing Arabidopsis transcription factors, we identified ERF50 as a key gene to control dormancy and germination. To study its regulation, we measured seed-related physiological parameters in loss-of-function mutants and carried out transactivation, protein interaction and ChIP-PCR analyses. We found direct ERF50-mediated repression of DOG1 and activation of EXPA2 transcription, which results in enhanced seed germination. Although ERF50 expression is increased by DOG1 in dormant seeds, ERF50 germination-promoting activity is blocked by RGL2. The physiological, genetic and molecular evidence gathered here supports that ERF50 controls germination timing by regulating DOG1 levels to leverage its role as enhancer of seed germination, via RGL2 antagonism on EXPA2 expression. Our results highlight the central role of ERF50 as a feedback regulator to couple and fine-tune seed dormancy and germination.
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Affiliation(s)
- Gerardo Carrera-Castaño
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Sara Mira
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Iris Fañanás-Pueyo
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Rocío Sánchez-Montesino
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Ángela Contreras
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Christoph Weiste
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg, 97082, Germany
| | - Wolfgang Dröge-Laser
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg, 97082, Germany
| | - Luis Gómez
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, 28040, Madrid, Spain
- Centro para la Conservación de la Biodiversidad y el Desarrollo Sostenible, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
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Manser B, Zbinden H, Herren G, Steger J, Isaksson J, Bräunlich S, Wicker T, Keller B. Wheat zinc finger protein TaZF interacts with both the powdery mildew AvrPm2 protein and the corresponding wheat Pm2a immune receptor. PLANT COMMUNICATIONS 2024; 5:100769. [PMID: 37978798 PMCID: PMC11121201 DOI: 10.1016/j.xplc.2023.100769] [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: 08/01/2023] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
Plant defense responses to pathogens are induced after direct or indirect perception of effector proteins or their activity on host proteins. In fungal-plant interactions, relatively little is known about whether, in addition to avirulence effectors and immune receptors, other proteins contribute to specific recognition. The nucleotide-binding leucine-rich repeat (NLR) immune receptor Pm2a in wheat recognizes the fungal powdery mildew effector AvrPm2. We found that the predicted wheat zinc finger TaZF interacts with both the fungal avirulence protein AvrPm2 and the wheat NLR Pm2a. We further demonstrated that the virulent AvrPm2-H2 variant does not interact with TaZF. TaZF silencing in wheat resulted in a reduction but not a loss of Pm2a-mediated powdery mildew resistance. Interaction studies showed that the leucine-rich repeat domain of Pm2a is the mediator of the interaction with TaZF. TaZF recruits both Pm2a and AvrPm2 from the cytosol to the nucleus, resulting in nuclear localization of Pm2a, TaZF, and AvrPm2 in wheat. We propose that TaZF acts as a facilitator of Pm2a-dependent AvrPm2 effector recognition. Our findings highlight the importance of identifying effector host targets for characterization of NLR-mediated effector recognition.
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Affiliation(s)
- Beatrice Manser
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Helen Zbinden
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Joel Steger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Jonatan Isaksson
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Stephanie Bräunlich
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
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Adhikari PB, Liu X, Huang C, Mitsuda N, Notaguchi M, Kasahara RD. Transcription Factors behind MYB98 Regulation: What Does the Discovery of SaeM Suggest? PLANTS (BASEL, SWITZERLAND) 2024; 13:1007. [PMID: 38611536 PMCID: PMC11013860 DOI: 10.3390/plants13071007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
MYB98 is master regulator of the molecular network involved in pollen tube attraction. Until recently, it was unclear how this gene exhibits exclusively synergid cell-specific expression in ovule. Our recent study has established that a 16-bp-long SaeM element is crucial for its synergid cell-specific expression in ovule, and an 84-bp-long fragment harboring SaeM is sufficient to drive the process. In this study, we have developed a workflow to predict functional roles of potential transcription factors (TFs) putatively binding to the promoter region, taking MYB98 promoter as a test subject. After sequential assessment of co-expression pattern, network analysis, and potential master regulator identification, we have proposed a multi-TF model for MYB98 regulation. Our study suggests that ANL2, GT-1, and their respective homologs could be direct regulators of MYB98 and indicates that TCP15, TCP16, FRS9, and HB34 are likely master regulators of the majority of the TFs involved in its regulation. Comprehensive studies in the future are expected to offer more insights into such propositions. Developed workflow can be used while designing similar regulome-related studies for any other species and genes.
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Affiliation(s)
- Prakash B. Adhikari
- Biotechnology and Bioscience Research Center, Nagoya University, Nagoya 464-8601, Japan;
| | - Xiaoyan Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (C.H.)
| | - Chen Huang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (C.H.)
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8560, Japan;
| | - Michitaka Notaguchi
- Biotechnology and Bioscience Research Center, Nagoya University, Nagoya 464-8601, Japan;
| | - Ryushiro Dora Kasahara
- Biotechnology and Bioscience Research Center, Nagoya University, Nagoya 464-8601, Japan;
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Bajpai SK, Nisha, Pandita S, Bahadur A, Verma PC. Recent advancements in the role of histone acetylation dynamics to improve stress responses in plants. Mol Biol Rep 2024; 51:413. [PMID: 38472555 DOI: 10.1007/s11033-024-09300-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
In eukaryotes, transcriptional regulation is determined by the DNA sequence and is facilitated through sophisticated and complex chromatin alterations and histone remodelling. Recent research has shown that the histone acetylation dynamic, an intermittent and reversible substitution, constitutes a prerequisite for chromatin modification. These changes in chromatin structure modulate genome-wide and specific changes in response to external and internal cues like cell differentiation, development, growth, light temperature, and biotic stresses. Histone acetylation dynamics also control the cell cycle. HATs and HDACs play a critical role in gene expression modulation during plant growth and response to environmental circumstances. It has been well established that HATs and HDACs interact with various distinct transcription factors and chromatin-remodelling proteins (CRPs) involved in the transcriptional regulation of several developmental processes. This review explores recent research on histone acyltransferases and histone deacetylases, mainly focusing on their involvement in plant biotic stress responses. Moreover, we also emphasized the research gaps that must be filled to fully understand the complete function of histone acetylation dynamics during biotic stress responses in plants. A thorough understanding of histone acetylation will make it possible to enhance tolerance against various kinds of stress and decrease yield losses in many crops.
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Affiliation(s)
- Sanjay Kumar Bajpai
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Nisha
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Shivali Pandita
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - Anand Bahadur
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - Praveen C Verma
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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7
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Wu S, Da L, Xiao Q, Pan Q, Zhang J, Yang J. ASAP: a platform for gene functional analysis in Angelica sinensis. BMC Genomics 2024; 25:96. [PMID: 38262929 PMCID: PMC10804808 DOI: 10.1186/s12864-024-09971-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Angelica sinensis (Danggui), a renowned medicinal orchid, has gained significant recognition for its therapeutic effects in treating a wide range of ailments. Genome information serves as a valuable resource, enabling researchers to gain a deeper understanding of gene function. In recent times, the availability of chromosome-level genomes for A. sinensis has opened up vast opportunities for exploring gene functionality. Integrating multiomics data can allow researchers to unravel the intricate mechanisms underlying gene function in A. sinensis and further enhance our knowledge of its medicinal properties. RESULTS In this study, we utilized genomic and transcriptomic data to construct a coexpression network for A. sinensis. To annotate genes, we aligned them with sequences from various databases, such as the NR, TAIR, trEMBL, UniProt, and SwissProt databases. For GO and KEGG annotations, we employed InterProScan and GhostKOALA software. Additionally, gene families were predicted using iTAK, HMMER, OrholoFinder, and KEGG annotation. To facilitate gene functional analysis in A. sinensis, we developed a comprehensive platform that integrates genomic and transcriptomic data with processed functional annotations. The platform includes several tools, such as BLAST, GSEA, Heatmap, JBrowse, and Sequence Extraction. This integrated resource and approach will enable researchers to explore the functional aspects of genes in A. sinensis more effectively. CONCLUSION We developed a platform, named ASAP, to facilitate gene functional analysis in A. sinensis. ASAP ( www.gzybioinformatics.cn/ASAP ) offers a comprehensive collection of genome data, transcriptome resources, and analysis tools. This platform serves as a valuable resource for researchers conducting gene functional research in their projects, providing them with the necessary data and tools to enhance their studies.
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Affiliation(s)
- Silan Wu
- Resource Institute for Chinese and Ethnic Materia MedicaGuizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Lingling Da
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Qiaoqiao Xiao
- Resource Institute for Chinese and Ethnic Materia MedicaGuizhou University of Traditional Chinese Medicine, Guizhou, 550025, China.
| | - Qi Pan
- Resource Institute for Chinese and Ethnic Materia MedicaGuizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Jinqiang Zhang
- Resource Institute for Chinese and Ethnic Materia MedicaGuizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia MedicaGuizhou University of Traditional Chinese Medicine, Guizhou, 550025, China.
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Yan H, Liu F, Zhang G, Liu S, Ma W, Yang T, Li Y, Yang J, Cui H. PlantCHRs: A comprehensive database of plant chromatin remodeling factors. Comput Struct Biotechnol J 2023; 21:4974-4987. [PMID: 37867975 PMCID: PMC10589754 DOI: 10.1016/j.csbj.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
The Snf2 protein family is a group of ATP-dependent chromatin remodeling factors (CHRs) that play an essential role in gene expression regulation. In plants, Snf2 is involved in growth, development, as well as stress resistance. However, only a very limited number of experimentally validated Snf2 have been identified and reported, while the majority remaining undiscovered in most species . In this study, we predicted 3135 Snf2 proteins and 8398 chromatin remodeling complex (CRC) subunits in diverse plant species, and constructed the Plant Chromatin Remodeling Factors Database (PlantCHRs, http://www.functionalgenomics.cn/PlantCHRs/), which provide a comprehensive resource for researchers to access information about plant CHRs. We also developed an online tool capable of predicting CHRs and CRC subunits. Moreover, we investigated the distribution of Snf2 proteins in different species and observed a significant increase in the number of Snf2 proteins and the diversity of the Snf2 subfamily during the evolution, highlighting their evolutionary importance. By analyzing the expression patterns of the Snf2 genes in different tissues of maize and Arabidopsis, we found that the Snf2 proteins may show some conservation across different species in regulating plant growth and development. Over the all, we established a comprehensive database for plant CHRs, which will facilitate the researches on plant chromatin remodeling.
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Affiliation(s)
- Hengyu Yan
- College of Agronomy, Qingdao Agricultural University, China
| | - Fangyuan Liu
- College of Agronomy, Qingdao Agricultural University, China
| | - Guowei Zhang
- College of Agronomy, Qingdao Agricultural University, China
| | - Shuai Liu
- College of Agronomy, Qingdao Agricultural University, China
| | - Weiwei Ma
- College of Agronomy, Qingdao Agricultural University, China
| | - Ting Yang
- College of Agronomy, Qingdao Agricultural University, China
| | - Yubin Li
- College of Agronomy, Qingdao Agricultural University, China
| | - Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hailong Cui
- College of Economics and Management (Cooperative College), Qingdao Agricultural University, China
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9
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Zhang Q, Wang S, Xie Q, Xia Y, Lu L, Wang M, Wang G, Long S, Cai Y, Xu L, Wang E, Jiang Y. Control of arbuscule development by a transcriptional negative feedback loop in Medicago. Nat Commun 2023; 14:5743. [PMID: 37717076 PMCID: PMC10505183 DOI: 10.1038/s41467-023-41493-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/06/2023] [Indexed: 09/18/2023] Open
Abstract
Most terrestrial plants establish a symbiosis with arbuscular mycorrhizal fungi (AMF), which provide them with lipids and sugars in exchange for phosphorus and nitrogen. Nutrient exchange must be dynamically controlled to maintain a mutually beneficial relationship between the two symbiotic partners. The WRI5a and its homologues play a conserved role in lipid supply to AMF. Here, we demonstrate that the AP2/ERF transcription factor MtERM1 binds directly to AW-box and AW-box-like cis-elements in the promoters of MtSTR2 and MtSTR, which are required for host lipid efflux and arbuscule development. The EAR domain-containing transcription factor MtERF12 is also directly activated by MtERM1/MtWRI5a to negatively regulate arbuscule development, and the TOPLESS co-repressor is further recruited by MtERF12 through EAR motif to oppose MtERM1/MtWRI5a function, thereby suppressing arbuscule development. We therefore reveal an ERM1/WRI5a-ERF12-TOPLESS negative feedback loop that enables plants to flexibly control nutrient exchange and ensure a mutually beneficial symbiosis.
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Affiliation(s)
- Qiang Zhang
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Shuangshuang Wang
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Qiujin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yuanjun Xia
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Lei Lu
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Mingxing Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Gang Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Siyu Long
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Yunfei Cai
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Ling Xu
- School of Life Sciences, East China Normal University, 200241, Shanghai, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
| | - Yina Jiang
- School of Life Sciences, East China Normal University, 200241, Shanghai, China.
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10
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Yang Y, Kong Q, Tee WT, Li Y, Low PM, Patra B, Guo L, Yuan L, Ma W. Transcription factor bZIP52 modulates Arabidopsis seed oil biosynthesis through interaction with WRINKLED1. PLANT PHYSIOLOGY 2023; 192:2628-2639. [PMID: 37148285 DOI: 10.1093/plphys/kiad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/08/2023]
Abstract
Transcriptional regulation mediated by combinatorial interaction of transcription factors (TFs) is a key molecular mechanism modulating plant development and metabolism. Basic leucine zipper (bZIP) TFs play important roles in various plant developmental and physiological processes. However, their involvement in fatty acid biosynthesis is largely unknown. Arabidopsis (Arabidopsis thaliana) WRINKLED1 (WRI1) is a pivotal TF in regulation of plant oil biosynthesis and interacts with other positive and negative regulators. In this study, we identified two bZIP TFs, bZIP21 and bZIP52, as interacting partners of AtWRI1 by yeast-two-hybrid (Y2H)-based screening of an Arabidopsis TF library. We found that coexpression of bZIP52, but not bZIP21, with AtWRI1 reduced AtWRI1-mediated oil biosynthesis in Nicotiana benthamiana leaves. The AtWRI1-bZIP52 interaction was further verified by Y2H, in vitro pull-down, and bimolecular fluorescence complementation assays. Transgenic Arabidopsis plants overexpressing bZIP52 showed reduced seed oil accumulation, while the CRISPR/Cas9-edited bzip52 knockout mutant exhibited increased seed oil accumulation. Further analysis revealed that bZIP52 represses the transcriptional activity of AtWRI1 on the fatty acid biosynthetic gene promoters. Together, our findings suggest that bZIP52 represses fatty acid biosynthesis genes through interaction with AtWRI1, resulting in a reduction of oil production. Our work reports a previously uncharacterized regulatory mechanism that enables fine-tuning of seed oil biosynthesis.
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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
| | - Wan Ting Tee
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yuqing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Pui Man Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Barunava Patra
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - 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
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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11
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Seo PJ, Lee HG, Choi HY, Lee S, Park CM. Complexity of SMAX1 signaling during seedling establishment. TRENDS IN PLANT SCIENCE 2023; 28:902-912. [PMID: 37069002 DOI: 10.1016/j.tplants.2023.03.014] [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: 08/19/2022] [Revised: 03/12/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Karrikins (KARs) are small butenolide compounds identified in the smoke of burning vegetation. Along with the stimulating effects on seed germination, KARs also regulate seedling vigor and adaptive behaviors, such as seedling morphogenesis, root hair development, and stress acclimation. The pivotal KAR signaling repressor, SUPPRESSOR OF MAX2 1 (SMAX1), plays central roles in these developmental and morphogenic processes through an extensive signaling network that governs seedling responses to endogenous and environmental cues. Here, we summarize the versatile roles of SMAX1 reported in recent years and discuss how SMAX1 integrates multiple growth hormone signals into optimizing seedling establishment. We also discuss the evolutionary relevance of the SMAX1-mediated signaling pathways during the colonization of aqueous plants to terrestrial environments.
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Affiliation(s)
- Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Hye-Young Choi
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sangmin Lee
- Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
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12
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Sun H, Hu K, Wei S, Yao G, Zhang H. ETHYLENE RESPONSE FACTORS 4.1/4.2 with an EAR motif repress anthocyanin biosynthesis in red-skinned pears. PLANT PHYSIOLOGY 2023; 192:1892-1912. [PMID: 36732887 PMCID: PMC10315276 DOI: 10.1093/plphys/kiad068] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/06/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Red-skinned pears (Pyrus L.) are preferred to consumers for their attractive color and abundant anthocyanins. Pyrus ETHYLENE RESPONSE FACTOR 3 (PyERF3) positively regulates anthocyanin biosynthesis through interacting with Pyrus myeloblastosis family 114 (PyMYB114) and Pyrus basic helix-loop-helix 3 (PybHLH3) in red-skinned pears. However, the role of APETALA2/ethylene response factors (AP2/ERFs), which negatively regulate anthocyanin biosynthesis, remains unclear in red-skinned pears. Here, we validated that 2 AP2/ERFs, PyERF4.1 and PyERF4.2, screened from the transcriptome data of 'Starkrimson' pear (Pyrus communis L.) and its green mutant, inhibit anthocyanin biosynthesis in transgenic pear calli, as well as in overexpression and gene-edited tomato (Solanum lycopersicum) fruits. Meanwhile, the co-transformation of PyERF4.1/PyERF4.2 with PyERF3-PyMYB114-PybHLH3 inhibited anthocyanin biosynthesis in pear fruits and strawberry (Fragaria vesca) receptacles. Further assays showed that PyMYB114 activated the transcription of PyERF4.1/PyERF4.2; PyERF4.1/PyERF4.2 then interacted with PyERF3 to affect the stability of the PyERF3-PyMYB114-PybHLH3 complex, thereby inhibiting the transcription of the anthocyanin biosynthesis gene Pyrus anthocyanidin synthase (PyANS). Furthermore, deletion of the ERF-associated-amphiphilic repression (EAR) motif eliminated the inhibitory effect of PyERF4.1/PyERF4.2 on anthocyanin biosynthesis, and a mutation of the PyERF4.2-EAR motif (LxLxM to LxLxL) strengthened the inhibitory effect, demonstrating that the EAR motif is indispensable for the inhibitory effect of PyERF4.1/PyERF4.2 on anthocyanin biosynthesis in pears. Our study has shed light on a feedback regulatory loop mechanism that balances the excessive accumulation of anthocyanins in red-skinned pears, providing insights into the regulatory mechanism of anthocyanin biosynthesis and the regulatory network of coloration in red-skinned pears.
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Affiliation(s)
- Hongye Sun
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Kangdi Hu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shuwei Wei
- Shandong Institute of Pomology, Tai’an 271000, China
| | - Gaifang Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Hua Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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13
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Yang J, Li P, Li Y, Xiao Q. GelFAP v2.0: an improved platform for Gene functional analysis in Gastrodia elata. BMC Genomics 2023; 24:164. [PMID: 37016293 PMCID: PMC10074892 DOI: 10.1186/s12864-023-09260-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Gastrodia elata (tianma), a well-known medicinal orchid, is widely used to treat various kinds of diseases with its dried tuber. In recent years, new chromosome-level genomes of G.elata have been released in succession, which offer an enormous resource pool for understanding gene function. Previously we have constructed GelFAP for gene functional analysis of G.elata. As genomes are updated and transcriptome data is accumulated, collection data in GelFAP cannot meet the need of researchers. RESULTS Based on new chromosome-level genome and transcriptome data, we constructed co-expression network of G. elata, and then we annotated genes by aligning with sequences from NR, TAIR, Uniprot and Swissprot database. GO (Gene Ontology) and KEGG (Kyoto Encylopaedia of Genes and Genomes) annotations were predicted by InterProScan and GhostKOALA software. Gene families were further predicted by iTAK (Plant Transcription factor and Protein kinase Identifier and Classifier), HMMER (hidden Markov models), InParanoid. Finally, we developed an improved platform for gene functional analysis in G. elata (GelFAP v2.0) by integrating new genome, transcriptome data and processed functional annotation. Several tools were also introduced to platform including BLAST (Basic Local Alignment Search Tool), GSEA (Gene Set Enrichment Analysis), Heatmap, JBrowse, Motif analysis and Sequence extraction. Based on this platform, we found that the flavonoid biosynthesis might be regulated by transcription factors (TFs) such as MYB, HB and NAC. We also took C4H and GAFP4 as examples to show the usage of our platform. CONCLUSION An improved platform for gene functional analysis in G. elata (GelFAP v2.0, www.gzybioinformatics.cn/Gelv2 ) was constructed, which provides better genome data, more transcriptome resources and more analysis tools. The updated platform might be preferably benefit researchers to carry out gene functional research for their project.
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Affiliation(s)
- Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Pengfei Li
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Yuping Li
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Qiaoqiao Xiao
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China.
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Lend Me Your EARs: A Systematic Review of the Broad Functions of EAR Motif-Containing Transcriptional Repressors in Plants. Genes (Basel) 2023; 14:genes14020270. [PMID: 36833197 PMCID: PMC9956375 DOI: 10.3390/genes14020270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/22/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, defined by the consensus sequence patterns LxLxL or DLNx(x)P, is found in a diverse range of plant species. It is the most predominant form of active transcriptional repression motif identified so far in plants. Despite its small size (5 to 6 amino acids), the EAR motif is primarily involved in the negative regulation of developmental, physiological and metabolic functions in response to abiotic and biotic stresses. Through an extensive literature review, we identified 119 genes belonging to 23 different plant species that contain an EAR motif and function as negative regulators of gene expression in various biological processes, including plant growth and morphology, metabolism and homeostasis, abiotic stress response, biotic stress response, hormonal pathways and signalling, fertility, and ripening. Positive gene regulation and transcriptional activation are studied extensively, but there remains much more to be discovered about negative gene regulation and the role it plays in plant development, health, and reproduction. This review aims to fill the knowledge gap and provide insights into the role that the EAR motif plays in negative gene regulation, and provoke further research on other protein motifs specific to repressors.
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15
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Che X, Splitt BL, Eckholm MT, Miller ND, Spalding EP. BRXL4-LAZY1 interaction at the plasma membrane controls Arabidopsis branch angle and gravitropism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:211-224. [PMID: 36478485 PMCID: PMC10107345 DOI: 10.1111/tpj.16055] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Gravitropism guides growth to shape plant architecture above and below ground. Mutations in LAZY1 impair stem gravitropism and cause less upright inflorescence branches (wider angles). The LAZY1 protein resides at the plasma membrane and in the nucleus. The plasma membrane pool is necessary and sufficient for setting branch angles. To investigate the molecular mechanism of LAZY1 function, we screened for LAZY1-interacting proteins in yeast. We identified BRXL4, a shoot-specific protein related to BREVIS RADIX. The BRXL4-LAZY1 interaction occurred at the plasma membrane in plant cells, and not detectably in the nucleus. Mutations in the C-terminus of LAZY1, but not other conserved regions, prevented the interaction. Opposite to lazy1, brxl4 mutants displayed faster gravitropism and more upright branches. Overexpressing BRXL4 produced strong lazy1 phenotypes. The apparent negative regulation of LAZY1 function is consistent with BRXL4 reducing LAZY1 expression or the amount of LAZY1 at the plasma membrane. Measurements indicated that both are true. LAZY1 mRNA was three-fold more abundant in brxl4 mutants and almost undetectable in BRXL4 overexpressors. Plasma membrane LAZY1 was higher and nuclear LAZY1 lower in brxl4 mutants compared with the wild type. To explain these results, we suggest that BRXL4 reduces the amount of LAZY1 at the plasma membrane where it functions in gravity signaling and promotes LAZY1 accumulation in the nucleus where it reduces LAZY1 expression, possibly by suppressing its own transcription. This explanation of how BRXL4 negatively regulates LAZY1 suggests ways to modify shoot system architecture for practical purposes.
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Affiliation(s)
- Ximing Che
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Bessie L. Splitt
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Magnus T. Eckholm
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Nathan D. Miller
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Edgar P. Spalding
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
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Jia H, Zuo Q, Sadeghnezhad E, Zheng T, Chen X, Dong T, Fang J. HDAC19 recruits ERF4 to the MYB5a promoter and diminishes anthocyanin accumulation during grape ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:127-144. [PMID: 36423230 DOI: 10.1111/tpj.16040] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
DNA acetylation alters the expression of responsive genes during plant development. In grapes (Vitis vinifera), however, little is known about this regulatory mechanism. In the present study, 'Kyoho' grapes treated with trichostatin A (TSA, a deacetylase inhibitor) were used for transcriptome sequencing and quantitative proteomics analysis. We observed that acetylation was associated with anthocyanin accumulation and gene expression. Acetylation positively regulated phenylalanine metabolism and flavonoid biosynthesis pathways. Using omics analysis, we detected an increase in the levels of the AP2/EREBP transcription factor family after TSA treatment, indicating its association with acetylation-deacetylation dynamics in grapes. Furthermore, ethylene response factor 4 (ERF4) physically interacted with VvHDAC19, a histone deacetylase, which synergistically reduced the expression of target genes involved in anthocyanin biosynthesis owing to the binding of VvERF4 to the GCC-box cis-regulatory element in the VvMYB5a promoter. VvHDAC19 and VvERF4 also controlled anthocyanin biosynthesis and accumulation by regulating acetylation levels of histones H3 and H4. Therefore, alterations in histone modification can significantly regulate the expression of genes involved in anthocyanin biosynthesis and affect grape ripening.
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Affiliation(s)
- Haifeng Jia
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
- NJAU (Suqian) Academy of Protected Horticultures, Suqian, China
| | - Qianqian Zuo
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ehsan Sadeghnezhad
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ting Zheng
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Xueqin Chen
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - JinggGui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
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AtEAU1 and AtEAU2, Two EAR Motif-Containing ABA Up-Regulated Novel Transcription Repressors Regulate ABA Response in Arabidopsis. Int J Mol Sci 2022; 23:ijms23169053. [PMID: 36012319 PMCID: PMC9409118 DOI: 10.3390/ijms23169053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
EAR (Ethylene-responsive element binding factor-associated Amphiphilic Repression) motif-containing transcription repressors have been shown to regulate plant growth and development, and plant responses to plant hormones and environmental stresses including biotic and abiotic stresses. However, the functions of most EAR-motif-containing proteins remain largely uncharacterized. The plant hormone abscisic acid (ABA) also plays important roles in regulating plant responses to abiotic stresses via activation/repression of ABA-responsive genes. We report here the identification and functional characterization of two ABA-responsive EAR motif-containing protein genes, AtEAU1 (Arabidopsis thaliana EAR motif-containing ABAUp-regulated 1) and AtEAU2. Quantitative RT-PCR results show that the expressions of AtEAU1 and AtEAU2 were increased by ABA treatment, and were decreased in the ABA biosynthesis mutant aba1-5. Assays in transfected Arabidopsis protoplasts show that both AtEAU1 and AtEAU2 were specifically localized in the nucleus, and when recruited to the promoter region of the reporter gene by a fused DNA binding domain, repressed reporter gene expression. By using T-DNA insertion mutants and a gene-edited transgene-free mutant generated by CRISPR/Cas9 gene editing, we performed ABA sensitivity assays, and found that ABA sensitivity in the both ateau1 and ateau2 single mutants was increased in seedling greening assays. ABA sensitivity in the ateau1 ateau2 double mutants was also increased, but was largely similar to the ateau1 single mutants. On the other hand, all the mutants showed a wild type response to ABA in root elongation assays. Quantitative RT-PCR results show that the expression level of PYL4, an ABA receptor gene was increased, whereas that of ABI2, a PP2C gene was decreased in the ateau1 and ateau1 single, and the ateau1 ateau2 double mutants. In summary, our results suggest that AtEAU1 and AtEAU2 are ABA-response genes, and AtEAU1 and AtEAU2 are novel EAR motif-containing transcription repressors that negatively regulate ABA responses in Arabidopsis, likely by regulating the expression of some ABA signaling key regulator genes.
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18
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Genetic and Genomic Resources for Soybean Breeding Research. PLANTS 2022; 11:plants11091181. [PMID: 35567182 PMCID: PMC9101001 DOI: 10.3390/plants11091181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022]
Abstract
Soybean (Glycine max) is a legume species of significant economic and nutritional value. The yield of soybean continues to increase with the breeding of improved varieties, and this is likely to continue with the application of advanced genetic and genomic approaches for breeding. Genome technologies continue to advance rapidly, with an increasing number of high-quality genome assemblies becoming available. With accumulating data from marker arrays and whole-genome resequencing, studying variations between individuals and populations is becoming increasingly accessible. Furthermore, the recent development of soybean pangenomes has highlighted the significant structural variation between individuals, together with knowledge of what has been selected for or lost during domestication and breeding, information that can be applied for the breeding of improved cultivars. Because of this, resources such as genome assemblies, SNP datasets, pangenomes and associated databases are becoming increasingly important for research underlying soybean crop improvement.
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19
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Yang J, Yan H, Liu Y, Da L, Xiao Q, Xu W, Su Z. GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis. Front Genet 2022; 13:823966. [PMID: 35495163 PMCID: PMC9039005 DOI: 10.3389/fgene.2022.823966] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
Glycyrrhiza uralensis (Licorice), which belongs to Leguminosae, is famous for the function of pharmacologic action and natural sweetener with its dried roots and rhizomes. In recent years, the whole-genome sequence of G. uralensis has been completed, which will help to lay the foundation for the study of gene function. Here, we integrated the available genomic and transcriptomic data of G. uralensis and constructed the G. uralensis gene co-expression network. We then annotated gene functions of G. uralensis via aligning with public databases. Furthermore, gene families of G. uralensis were predicted by tools including iTAK (Plant Transcription factor and Protein kinase Identifier and Classifier), HMMER (hidden Markov models), InParanoid, and PfamScan. Finally, we constructed a platform for gene function analysis in G. uralensis (GURFAP, www.gzybioinfoormatics.cn/GURFAP). For analyzed and predicted gene function, we introduced various tools including BLAST (Basic local alignment search tool), GSEA (Gene set enrichment analysis), Motif, Heatmap, and JBrowse. Our analysis based on this platform indicated that the biosynthesis of glycyrrhizin might be regulated by MYB and bHLH. We also took CYP88D6, CYP72A154, and bAS gene in the synthesis pathway of glycyrrhizin as examples to demonstrate the reliability and availability of our platform. Our platform GURFAP will provide convenience for researchers to mine the gene function of G. uralensis and thus discover more key genes involved in the biosynthetic pathway of active ingredients.
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Affiliation(s)
- Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hengyu Yan
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Lingling Da
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Qiaoqiao Xiao
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- *Correspondence: Qiaoqiao Xiao, ; Wenying Xu, ; Zhen Su,
| | - Wenying Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
- *Correspondence: Qiaoqiao Xiao, ; Wenying Xu, ; Zhen Su,
| | - Zhen Su
- College of Biological Sciences, China Agricultural University, Beijing, China
- *Correspondence: Qiaoqiao Xiao, ; Wenying Xu, ; Zhen Su,
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20
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Isolation and Molecular Characterisation of TtDro1A and TtDro1B Genes from Triticum turgidum Subspecies durum and turgidum, Study of Their Influences on Seedling Root Angles. PLANTS 2022; 11:plants11060821. [PMID: 35336704 PMCID: PMC8954752 DOI: 10.3390/plants11060821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022]
Abstract
Durum wheat (Triticum turgidum, 2n = 4x = AABB) includes several subspecies with differential characteristics in their root system architecture (RSA). Subspecies durum has longer and more vertical roots, while subspecies turgidum has smaller and shallower roots. The homeologous genes TtDro1A and TtDro1B of both subspecies have been identified and found to differ in their sizes, sequences and the proteins they encode. To determine whether there is a relationship between the level of expression of these two genes and the angle adopted by the roots of durum wheat seedlings, their expressions has been studied by RT-qPCR, both in the primary seminal root and in the other seminal roots. The results of the analyses showed that the TtDro1A gene is expressed 1.4 times more in the primary seminal root than in the other seminal roots. Furthermore, this gene is expressed 2.49 to 8.76 times more than TtDro1B depending on root type (primary or seminal) and subspecies. There are positive correlations between the expression ratio of both genes (TtDro1A/TtDro1B) and the mean of all root angles, the most vertical root angle and the most horizontal root angle of the seedlings. The higher the expression of TtDro1B gene, the lower the root growth angles.
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21
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Zhang L, Chen L, Pang S, Zheng Q, Quan S, Liu Y, Xu T, Liu Y, Qi M. Function Analysis of the ERF and DREB Subfamilies in Tomato Fruit Development and Ripening. FRONTIERS IN PLANT SCIENCE 2022; 13:849048. [PMID: 35310671 PMCID: PMC8931701 DOI: 10.3389/fpls.2022.849048] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/02/2022] [Indexed: 05/26/2023]
Abstract
APETALA2/ethylene responsive factors (AP2/ERF) are unique regulators in the plant kingdom and are involved in the whole life activity processes such as development, ripening, and biotic and abiotic stresses. In tomato (Solanum lycopersicum), there are 140 AP2/ERF genes; however, their functionality remains poorly understood. In this work, the 14th and 19th amino acid differences in the AP2 domain were used to distinguish DREB and ERF subfamily members. Even when the AP2 domain of 68 ERF proteins from 20 plant species and motifs in tomato DREB and ERF proteins were compared, the binding ability of DREB and ERF proteins with DRE/CRT and/or GCC boxes remained unknown. During fruit development and ripening, the expressions of 13 DREB and 19 ERF subfamily genes showed some regular changes, and the promoters of most genes had ARF, DRE/CRT, and/or GCC boxes. This suggests that these genes directly or indirectly respond to IAA and/or ethylene (ET) signals during fruit development and ripening. Moreover, some of these may feedback regulate IAA or ET biosynthesis. In addition, 16 EAR motif-containing ERF genes in tomato were expressed in many organs and their total transcripts per million (TPM) values exceeded those of other ERF genes in most organs. To determine whether the EAR motif in EAR motif-containing ERF proteins has repression function, their EAR motifs were retained or deleted in a yeast one-hybrid (YIH) assay. The results indicate that most of EAR motif-containing ERF proteins lost repression activity after deleting the EAR motif. Moreover, some of these were expressed during ripening. Thus, these EAR motif-containing ERF proteins play vital roles in balancing the regulatory functions of other ERF proteins by completing the DRE/CRT and/or GCC box sites of target genes to ensure normal growth and development in tomato.
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Affiliation(s)
- Li Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - LiJing Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - ShengQun Pang
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - Qun Zheng
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - ShaoWen Quan
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - YuFeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - YuDong Liu
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - MingFang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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22
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Nowak K, Morończyk J, Grzyb M, Szczygieł-Sommer A, Gaj MD. miR172 Regulates WUS during Somatic Embryogenesis in Arabidopsis via AP2. Cells 2022; 11:718. [PMID: 35203367 PMCID: PMC8869827 DOI: 10.3390/cells11040718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
In plants, the embryogenic transition of somatic cells requires the reprogramming of the cell transcriptome, which is under the control of genetic and epigenetic factors. Correspondingly, the extensive modulation of genes encoding transcription factors and miRNAs has been indicated as controlling the induction of somatic embryogenesis in Arabidopsis and other plants. Among the MIRNAs that have a differential expression during somatic embryogenesis, members of the MIRNA172 gene family have been identified, which implies a role of miR172 in controlling the embryogenic transition in Arabidopsis. In the present study, we found a disturbed expression of both MIRNA172 and candidate miR172-target genes, including AP2, TOE1, TOE2, TOE3, SMZ and SNZ, that negatively affected the embryogenic response of transgenic explants. Next, we examined the role of AP2 in the miR172-mediated mechanism that controls the embryogenic response. We found some evidence that by controlling AP2, miR172 might repress the WUS that has an important function in embryogenic induction. We showed that the mechanism of the miR172-AP2-controlled repression of WUS involves histone acetylation. We observed the upregulation of the WUS transcripts in an embryogenic culture that was overexpressing AP2 and treated with trichostatin A (TSA), which is an inhibitor of HDAC histone deacetylases. The increased expression of the WUS gene in the embryogenic culture of the hdac mutants further confirmed the role of histone acetylation in WUS control during somatic embryogenesis. A chromatin-immunoprecipitation analysis provided evidence about the contribution of HDA6/19-mediated histone deacetylation to AP2-controlled WUS repression during embryogenic induction. The upstream regulatory elements of the miR172-AP2-WUS pathway might involve the miR156-controlled SPL9/SPL10, which control the level of mature miR172 in an embryogenic culture.
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Affiliation(s)
- Katarzyna Nowak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland; (J.M.); (A.S.-S.); (M.D.G.)
| | - Joanna Morończyk
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland; (J.M.); (A.S.-S.); (M.D.G.)
| | - Małgorzata Grzyb
- Polish Academy of Sciences Botanical Garden—Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-973 Warsaw, Poland;
| | - Aleksandra Szczygieł-Sommer
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland; (J.M.); (A.S.-S.); (M.D.G.)
| | - Małgorzata D. Gaj
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland; (J.M.); (A.S.-S.); (M.D.G.)
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23
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Meng JX, Wei J, Chi RF, Qiao YH, Zhou J, Wang YL, Wang H, Li HH. MrMYB44-Like Negatively Regulates Anthocyanin Biosynthesis and Causes Spring Leaf Color of Malus 'Radiant' to Fade From Red to Green. FRONTIERS IN PLANT SCIENCE 2022; 13:822340. [PMID: 35178062 PMCID: PMC8843855 DOI: 10.3389/fpls.2022.822340] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/05/2022] [Indexed: 05/29/2023]
Abstract
The "Spring-red-leaf" crabapple cultivar has young red leaves and mature green leaves. However, the mechanism of anthocyanin biosynthesis in crabapple leaves in spring remains unknown. In this study, Illumina RNA sequencing (RNA-Seq) was performed on Malus 'Radiant' leaf tissues in different stages of development. Twenty-two genes in the anthocyanin biosynthesis pathway and 44 MYB transcription factors (TFs) were significantly enriched among differentially expressed genes (DEGs). Three R2R3-MYB TFs in subgroup 22 of the MYB TF family, MrMYB44-like1, MrMYB44-like2, and MrMYB44-like3, were highly expressed in green leaves according to RNA-Seq and quantitative real-time quantitative PCR results. Their expression levels were negatively correlated with anthocyanin content. In transient assays, overexpression of MrMYB44-like1, MrMYB44-like2, or MrMYB44-like3 inhibited anthocyanin accumulation and reduced pigment in leaf disks of M. 'Radiant' and fruit peels of M. domestica 'Fuji.' When the conserved region of the three MrMYB44-likes was silenced, the anthocyanin biosynthesis pathway was activated and pigments increased in both tissues. Moreover, bimolecular fluorescence complementation assays showed MrMYB44-likes interacted with MrWRKY6 to form protein complexes that regulated anthocyanin biosynthesis.
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24
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Lemaire-Chamley M, Koutouan C, Jorly J, Assali J, Yoshida T, Nogueira M, Tohge T, Ferrand C, Peres LEP, Asamizu E, Ezura H, Fraser PD, Hajirezaei MR, Fernie AR, Rothan C. A Chimeric TGA Repressor Slows Down Fruit Maturation and Ripening in Tomato. PLANT & CELL PHYSIOLOGY 2022; 63:120-134. [PMID: 34665867 DOI: 10.1093/pcp/pcab150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/29/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The bZIP transcription factor (TF) SlTGA2.2 was previously highlighted as a possible hub in a network regulating fruit growth and transition to ripening (maturation phase). It belongs to a clade of TFs well known for their involvement in the regulation of the salicylic acid-dependent systemic acquired resistance. To investigate if this TGA TF plays a role in tomato fruit growth and maturation, we took advantage of the fruit-specific SlPPC2 promoter (PPC2pro) to target the expression of a SlTGA2.2-SRDX chimeric repressor in a developmental window restricted to early fruit growth and maturation. Here, we show that this SlTGA2.2-SRDX repressor alters early fruit development and metabolism, including chloroplast number and structure, considerably extends the time necessary to reach the mature green stage and slows down fruit ripening. RNA sequencing and plant hormone analyses reveal that PPC2pro:SlTGA2.2-SRDX fruits are maintained in an immature stage as long as PPC2pro is active, through early modifications of plant hormonal signaling and down-regulation of MADS-RIN and NAC-NOR ripening regulators. Once PPC2pro becomes inactive and therefore SlTGA2.2-SRDX expression is reduced, ripening can proceed, albeit at a slower pace than normal. Altogether, this work emphasizes the developmental continuum between fruit growth, maturation and ripening and provides a useful tool to alter and study the molecular bases of tomato fruit transition to ripening.
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Affiliation(s)
- Martine Lemaire-Chamley
- INRAE, University of Bordeaux, UMR1332 BFP, 71 Av E Bourlaux, Villenave d'Ornon 33882, France
| | - Claude Koutouan
- INRAE, University of Bordeaux, UMR1332 BFP, 71 Av E Bourlaux, Villenave d'Ornon 33882, France
| | - Joana Jorly
- INRAE, University of Bordeaux, UMR1332 BFP, 71 Av E Bourlaux, Villenave d'Ornon 33882, France
| | - Julien Assali
- INRAE, University of Bordeaux, UMR1332 BFP, 71 Av E Bourlaux, Villenave d'Ornon 33882, France
| | - Takuya Yoshida
- Max-Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Marilise Nogueira
- Department of Biological Sciences, Holloway University of London, Egham Hill, Egham, UK
| | - Takayuki Tohge
- Max-Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Carine Ferrand
- INRAE, University of Bordeaux, UMR1332 BFP, 71 Av E Bourlaux, Villenave d'Ornon 33882, France
| | - Lázaro E P Peres
- Department of Biological Science, São Paulo University, Avenida Pádua Dias, Piracicaba 13418-900, Brazil
| | - Erika Asamizu
- Tsukuba Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Shiga 520-2194, Japan
| | - Hiroshi Ezura
- Tsukuba Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Paul D Fraser
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Shiga 520-2194, Japan
| | - Mohammad-Reza Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Corrensstraße 3, Seeland 06466, Germany
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Christophe Rothan
- INRAE, University of Bordeaux, UMR1332 BFP, 71 Av E Bourlaux, Villenave d'Ornon 33882, France
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25
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Underwood CJ, Vijverberg K, Rigola D, Okamoto S, Oplaat C, Camp RHMOD, Radoeva T, Schauer SE, Fierens J, Jansen K, Mansveld S, Busscher M, Xiong W, Datema E, Nijbroek K, Blom EJ, Bicknell R, Catanach A, Erasmuson S, Winefield C, van Tunen AJ, Prins M, Schranz ME, van Dijk PJ. A PARTHENOGENESIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce. Nat Genet 2022; 54:84-93. [PMID: 34992267 DOI: 10.1038/s41588-021-00984-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/03/2021] [Indexed: 01/21/2023]
Abstract
Apomixis, the clonal formation of seeds, is a rare yet widely distributed trait in flowering plants. We have isolated the PARTHENOGENESIS (PAR) gene from apomictic dandelion that triggers embryo development in unfertilized egg cells. PAR encodes a K2-2 zinc finger, EAR-domain protein. Unlike the recessive sexual alleles, the dominant PAR allele is expressed in egg cells and has a miniature inverted-repeat transposable element (MITE) transposon insertion in the promoter. The MITE-containing promoter can invoke a homologous gene from sexual lettuce to complement dandelion LOSS OF PARTHENOGENESIS mutants. A similar MITE is also present in the promoter of the PAR gene in apomictic forms of hawkweed, suggesting a case of parallel evolution. Heterologous expression of dandelion PAR in lettuce egg cells induced haploid embryo-like structures in the absence of fertilization. Sexual PAR alleles are expressed in pollen, suggesting that the gene product releases a block on embryogenesis after fertilization in sexual species while in apomictic species PAR expression triggers embryogenesis in the absence of fertilization.
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Affiliation(s)
- Charles J Underwood
- Keygene N.V., Wageningen, the Netherlands
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kitty Vijverberg
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands
- Naturalis Biodiversity Center, Radboud University, Nijmegen, the Netherlands
| | | | - Shunsuke Okamoto
- Keygene N.V., Wageningen, the Netherlands
- Takii & Co. Ltd, Plant Breeding and Experiment Station, Konan Shiga, Japan
| | - Carla Oplaat
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands
- National Reference Centre of Plant Health, National Plant Protection Organization, Wageningen, the Netherlands
| | | | | | | | | | - Kim Jansen
- Keygene N.V., Wageningen, the Netherlands
| | | | - Marco Busscher
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands
| | - Wei Xiong
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands
| | | | | | | | - Ross Bicknell
- New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
| | - Andrew Catanach
- New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
| | - Sylvia Erasmuson
- New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
| | | | | | | | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands.
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26
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Kim MH, Cho JS, Bae EK, Choi YI, Eom SH, Lim YJ, Lee H, Park EJ, Ko JH. PtrMYB120 functions as a positive regulator of both anthocyanin and lignin biosynthetic pathway in a hybrid poplar. TREE PHYSIOLOGY 2021; 41:2409-2423. [PMID: 34100089 DOI: 10.1093/treephys/tpab082] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
Both anthocyanins and lignins are essential secondary metabolites in plant growth and development. Their biosynthesis is metabolically interconnected and diverges in the central metabolite 4-coumaroyl CoA of the phenylpropanoid pathway. Considerable progress has been made in understanding transcriptional regulation of genes involved in lignin and anthocyanin synthesis pathways, but the concerted regulation of these pathways is not yet fully understood. Here, we functionally characterized PtrMYB120, a R2R3-MYB transcription factor from Populus trichocarpa. Overexpression of PtrMYB120 in a hybrid poplar (i.e., 35S::PtrMYB120) was associated with increased anthocyanin (i.e., cyanidin 3-O-glucoside) accumulation and upregulation of anthocyanin biosynthetic genes. However, transgenic poplars with dominant suppression of PtrMYB120 function achieved by fusing the ERF-associated amphiphilic repression motif to PtrMYB120 (i.e., 35S::PtrMYB120-SRDX) had a dramatic decrease in not only anthocyanin but also Klason lignin content with downregulation of both anthocyanin and lignin biosynthetic genes. Indeed, 35S::PtrMYB120-SRDX poplars had irregularly shaped xylem vessels with reduced S-lignin content in stems, which was proportionally related to the level of the introduced PtrMYB120-SRDX gene. Furthermore, protoplast-based transcriptional activation assay using the PtrMYB120-GR system suggested that PtrMYB120 directly regulates genes involved in both anthocyanin and lignin biosynthesis, including chalcone synthase and ferulate-5 hydroxylase. Interestingly, the saccharification efficiency of line #6 of 35S::PtrMYB120-SRDX poplars, which had slightly reduced lignin content with a normal growth phenotype, was dramatically enhanced (>45%) by NaOH treatment. Taken together, our results suggest that PtrMYB120 functions as a positive regulator of both anthocyanin and lignin biosynthetic pathways and can be targeted to enhance saccharification efficiency in woody perennials.
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Affiliation(s)
- Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
- Abio materials Co., Ltd., 7-44 Jamsil-gil, Cheonan 31005, Republic of Korea
| | - Eun-Kyung Bae
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Young-Im Choi
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - You Jin Lim
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Hyoshin Lee
- Department of Horticultural Biotechnology, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Eung-Jun Park
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
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27
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Chun JI, Kim SM, Kim H, Cho JY, Kwon HW, Kim JI, Seo JK, Jung C, Kang JH. SlHair2 Regulates the Initiation and Elongation of Type I Trichomes on Tomato Leaves and Stems. PLANT & CELL PHYSIOLOGY 2021; 62:1446-1459. [PMID: 34155514 DOI: 10.1093/pcp/pcab090] [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: 04/12/2021] [Revised: 05/18/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Trichomes are hair-like structures that are essential for abiotic and biotic stress responses. Tomato Hair (H), encoding a C2H2 zinc finger protein, was found to regulate the multicellular trichomes on stems. Here, we characterized Solyc10g078990 (hereafter Hair2, H2), its closest homolog, to examine whether it was involved in trichome development. The H2 gene was highly expressed in the leaves, and its protein contained a single C2H2 domain and was localized to the nucleus. The number and length of type I trichomes on the leaves and stems of knock-out h2 plants were reduced when compared to the wild-type, while overexpression increased their number and length. An auto-activation test with various truncated forms of H2 using yeast two-hybrid (Y2H) suggested that H2 acts as a transcriptional regulator or co-activator and that its N-terminal region is important for auto-activation. Y2H and pull-down analyses showed that H2 interacts with Woolly (Wo), which regulates the development of type I trichomes in tomato. Luciferase complementation imaging assays confirmed that they had direct interactions, implying that H2 and Wo function together to regulate the development of trichomes. These results suggest that H2 has a role in the initiation and elongation of type I trichomes in tomato.
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Affiliation(s)
- Jae-In Chun
- Department of Agriculture, Forestry and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institutes of Green-bio Science & Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Seong-Min Kim
- Department of Agriculture, Forestry and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institutes of Green-bio Science & Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Heejin Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Gyeongbuk, Republic of Korea
| | - Jae-Yong Cho
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyun-Woo Kwon
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jang-Kyun Seo
- Institutes of Green-bio Science & Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Choonkyun Jung
- Department of Agriculture, Forestry and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institutes of Green-bio Science & Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Jin-Ho Kang
- Department of Agriculture, Forestry and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institutes of Green-bio Science & Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
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28
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Ma X, Yan H, Yang J, Liu Y, Li Z, Sheng M, Cao Y, Yu X, Yi X, Xu W, Su Z. PlantGSAD: a comprehensive gene set annotation database for plant species. Nucleic Acids Res 2021; 50:D1456-D1467. [PMID: 34534340 PMCID: PMC8728169 DOI: 10.1093/nar/gkab794] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
With the accumulation of massive data sets from high-throughput experiments and the rapid emergence of new types of omics data, gene sets have become more diverse and essential for the refinement of gene annotation at multidimensional levels. Accordingly, we collected and defined 236 007 gene sets across different categories for 44 plant species in the Plant Gene Set Annotation Database (PlantGSAD). These gene sets were divided into nine main categories covering many functional subcategories, such as trait ontology, co-expression modules, chromatin states, and liquid-liquid phase separation. The annotations from the collected gene sets covered all of the genes in the Brassicaceae species Arabidopsis and Poaceae species Oryza sativa. Several GSEA tools are implemented in PlantGSAD to improve the efficiency of the analysis, including custom SEA for a flexible strategy based on customized annotations, SEACOMPARE for the cross-comparison of SEA results, and integrated visualization features for ontological analysis that intuitively reflects their parent-child relationships. In summary, PlantGSAD provides numerous gene sets for multiple plant species and highly efficient analysis tools. We believe that PlantGSAD will become a multifunctional analysis platform that can be used to predict and elucidate the functions and mechanisms of genes of interest. PlantGSAD is publicly available at http://systemsbiology.cau.edu.cn/PlantGSEAv2/.
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Affiliation(s)
- Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiaotong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhongqiu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Minghao Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xinyue Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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29
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Luo C, Wang S, Ning K, Chen Z, Wang Y, Yang J, Wang Q. LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2 in lettuce. HORTICULTURE RESEARCH 2021; 8:184. [PMID: 34465756 PMCID: PMC8408249 DOI: 10.1038/s41438-021-00622-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 04/21/2021] [Accepted: 05/20/2021] [Indexed: 05/24/2023]
Abstract
Leaf size and flatness directly affect photosynthesis and are closely related to agricultural yield. The final leaf size and shape are coordinately determined by cell proliferation, differentiation, and expansion during leaf development. Lettuce (Lactuca sativa L.) is one of the most important leafy vegetables worldwide, and lettuce leaves vary in shape and size. However, the molecular mechanisms of leaf development in lettuce are largely unknown. In this study, we showed that the lettuce APETALA2 (LsAP2) gene regulates leaf morphology. LsAP2 encodes a transcriptional repressor that contains the conserved EAR motif, which mediates interactions with the TOPLESS/TOPLESS-RELATED (TPL/TPR) corepressors. Overexpression of LsAP2 led to small and crinkly leaves, and many bulges were seen on the surface of the leaf blade. LsAP2 physically interacted with the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors and inhibited their transcriptional activation activity. RNA sequencing analysis showed that LsAP2 affected the expression of auxin- and polarity-related genes. In addition, LsAP2 directly repressed the abaxial identity gene KANADI2 (LsKAN2). Together, these results indicate that LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2, and our work provides insights into the regulatory mechanisms of leaf development in lettuce.
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Affiliation(s)
- Chen Luo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shenglin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Kang Ning
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zijing Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yixin Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jingjing Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Qian Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Xiao Q, Li Z, Qu M, Xu W, Su Z, Yang J. LjaFGD: Lonicera japonica functional genomics database. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1422-1436. [PMID: 33982879 DOI: 10.1111/jipb.13112] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
Lonicera japonica Thunb., a traditional Chinese herb, has been used for treating human diseases for thousands of years. Recently, the genome of L. japonica has been decoded, providing valuable information for research into gene function. However, no comprehensive database for gene functional analysis and mining is available for L. japonica. We therefore constructed LjaFGD (www.gzybioinformatics.cn/LjaFGD and bioinformatics.cau.edu.cn/LjaFGD), a database for analyzing and comparing gene function in L. japonica. We constructed a gene co-expression network based on 77 RNA-seq samples, and then annotated genes of L. japonica by alignment against protein sequences from public databases. We also introduced several tools for gene functional analysis, including Blast, motif analysis, gene set enrichment analysis, heatmap analysis, and JBrowse. Our co-expression network revealed that MYB and WRKY transcription factor family genes were co-expressed with genes encoding key enzymes in the biosynthesis of chlorogenic acid and luteolin in L. japonica. We used flavonol synthase 1 (LjFLS1) as an example to show the reliability and applicability of our database. LjaFGD and its various associated tools will provide researchers with an accessible platform for retrieving functional information on L. japonica genes to further biological discovery.
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Affiliation(s)
- Qiaoqiao Xiao
- Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Zhongqiu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Mengmeng Qu
- Research Center for Clinical & Translational Medicine, Fifth Medical Center for General Hospital of PLA, Beijing, 100039, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiaotong Yang
- Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
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31
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Liu P, Nie WF, Xiong X, Wang Y, Jiang Y, Huang P, Lin X, Qin G, Huang H, Niu Q, Du J, Lang Z, Lozano-Duran R, Zhu JK. A novel protein complex that regulates active DNA demethylation in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:772-786. [PMID: 33615694 DOI: 10.1111/jipb.13045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression. The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at 1 000s of genomic regions in Arabidopsis. How ROS1 is regulated and targeted to specific genomic regions is not well understood. Here, we report the discovery of an Arabidopsis protein complex that contains ROS1, regulates ROS1 gene expression, and likely targets the ROS1 protein to specific genomic regions. ROS1 physically interacts with a WD40 domain protein (RWD40), which in turn interacts with a methyl-DNA binding protein (RMB1) as well as with a zinc finger and homeobox domain protein (RHD1). RMB1 binds to DNA that is methylated in any sequence context, and this binding is necessary for its function in vivo. Loss-of-function mutations in RWD40, RMB1, or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1. Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter, plants mutated in RWD40, RMB1, or RHD1 show increased ROS1 expression. Importantly, ROS1 binding to the ROS1 promoter requires RWD40, RMB1, and RHD1, suggesting that this complex dictates ROS1 targeting to this locus. Our results demonstrate that ROS1 forms a protein complex with RWD40, RMB1, and RHD1, and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.
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Affiliation(s)
- Pan Liu
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Feng Nie
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Xiansong Xiong
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhua Wang
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuwei Jiang
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pei Huang
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueqiang Lin
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Guochen Qin
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Qingfeng Niu
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jiamu Du
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, Indiana, 47906, USA
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Su D, Xiang W, Wen L, Lu W, Shi Y, Liu Y, Li Z. Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato. BMC PLANT BIOLOGY 2021; 21:161. [PMID: 33784975 PMCID: PMC8010994 DOI: 10.1186/s12870-021-02933-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/17/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family. RESULTS Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses. CONCLUSIONS In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.
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Affiliation(s)
- Deding Su
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Wei Xiang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Ling Wen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Wang Lu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yuan Shi
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yudong Liu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
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Sun P, Shi Y, Valerio AGO, Borrego EJ, Luo Q, Qin J, Liu K, Yan Y. An updated census of the maize TIFY family. PLoS One 2021; 16:e0247271. [PMID: 33621269 PMCID: PMC7901733 DOI: 10.1371/journal.pone.0247271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/03/2021] [Indexed: 11/21/2022] Open
Abstract
The TIFY gene family is a plant-specific gene family encoding a group of proteins characterized by its namesake, the conservative TIFY domain and members can be organized into four subfamilies: ZML, TIFY, PPD and JAZ (Jasmonate ZIM-domain protein) by presence of additional conserved domains. The TIFY gene family is intensively explored in several model and agriculturally important crop species and here, yet the composition of the TIFY family of maize has remained unresolved. This study increases the number of maize TIFY family members known by 40%, bringing the total to 47 including 38 JAZ, 5 TIFY, and 4 ZML genes. The majority of the newly identified genes were belonging to the JAZ subfamily, six of which had aberrant TIFY domains, suggesting loss JAZ-JAZ or JAZ-NINJA interactions. Six JAZ genes were found to have truncated Jas domain or an altered degron motif, suggesting resistance to classical JAZ degradation. In addition, seven membranes were found to have an LxLxL-type EAR motif which allows them to recruit TPL/TPP co-repressors directly without association to NINJA. Expression analysis revealed that ZmJAZ14 was specifically expressed in the seeds and ZmJAZ19 and 22 in the anthers, while the majority of other ZmJAZs were generally highly expressed across diverse tissue types. Additionally, ZmJAZ genes were highly responsive to wounding and JA treatment. This study provides a comprehensive update of the maize TIFY/JAZ gene family paving the way for functional, physiological, and ecological analysis.
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Affiliation(s)
- Pingdong Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Crop Breeding & Cultivation Research Institution, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yannan Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Aga Guido Okwana Valerio
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Eli James Borrego
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Qingyun Luo
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jia Qin
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kang Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yuanxin Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Ma Y, Tian H, Lin R, Wang W, Zhang N, Hussain S, Yang W, Zhang C, Zhou G, Wang T, Wang S. AITRL, an evolutionarily conserved plant specific transcription repressor regulates ABA response in Arabidopsis. Sci Rep 2021; 11:721. [PMID: 33436924 PMCID: PMC7804847 DOI: 10.1038/s41598-020-80695-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/24/2020] [Indexed: 12/23/2022] Open
Abstract
Expression of stress response genes can be regulated by abscisic acid (ABA) dependent and ABA independent pathways. Osmotic stresses promote ABA accumulation, therefore inducing the expression of stress response genes via ABA signaling. Whereas cold and heat stresses induce the expression of stress response genes via ABA independent pathway. ABA induced transcription repressors (AITRs) are a family of novel transcription factors that play a role in ABA signaling, and Drought response gene (DRG) has previously been shown to play a role in regulating plant response to drought and freezing stresses. We report here the identification of DRG as a novel transcription factor and a regulator of ABA response in Arabidopsis. We found that the expression of DRG was induced by ABA treatment. Homologs searching identified AITR5 as the most closely related Arabidopsis protein to DRG, and homologs of DRG, including the AITR-like (AITRL) proteins in bryophytes and gymnosperms, are specifically presented in embryophytes. Therefore we renamed DRG as AITRL. Protoplast transfection assays show that AITRL functioned as a transcription repressor. In seed germination and seedling greening assays, the aitrl mutants showed an increased sensitivity to ABA. By using qRT-PCR, we show that ABA responses of some ABA signaling component genes including some PYR1-likes (PYLs), PROTEIN PHOSPHATASE 2Cs (PP2Cs) and SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASES 2s (SnRK2s) were reduced in the aitrl mutants. Taken together, our results suggest that AITRLs are a family of novel transcription repressors evolutionally conserved in embryophytes, and AITRL regulates ABA response in Arabidopsis by affecting ABA response of some ABA signaling component genes.
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Affiliation(s)
- Yanxing Ma
- Laboratory of Plant Molecular Genetics and Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China.,Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Hainan Tian
- Laboratory of Plant Molecular Genetics and Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China
| | - Rao Lin
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Wei Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Na Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Saddam Hussain
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Wenting Yang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Chen Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Ganghua Zhou
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Shucai Wang
- Laboratory of Plant Molecular Genetics and Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China. .,Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China.
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Yang J, Xiao Q, Xu J, Da L, Guo L, Huang L, Liu Y, Xu W, Su Z, Yang S, Pan Q, Jiang W, Zhou T. GelFAP: Gene Functional Analysis Platform for Gastrodia elata. FRONTIERS IN PLANT SCIENCE 2020; 11:563237. [PMID: 33193491 PMCID: PMC7642037 DOI: 10.3389/fpls.2020.563237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Gastrodia elata, also named Tianma, is a valuable traditional Chinese herbal medicine. It has numerous important pharmacological roles such as in sedation and lowering blood pressure and as anticonvulsant and anti-aging, and it also has effects on the immune and cardiovascular systems. The whole genome sequencing of G. elata has been completed in recent years, which provides a strong support for the construction of the G. elata gene functional analysis platform. Therefore, in our research, we collected and processed 39 transcriptome data of G. elata and constructed the G. elata gene co-expression networks, then we identified functional modules by the weighted correlation network analysis (WGCNA) package. Furthermore, gene families of G. elata were identified by tools including HMMER, iTAK, PfamScan, and InParanoid. Finally, we constructed a gene functional analysis platform for G. elata . In our platform, we introduced functional analysis tools such as BLAST, gene set enrichment analysis (GSEA), and cis-elements (motif) enrichment analysis tool. In addition, we analyzed the co-expression relationship of genes which might participate in the biosynthesis of gastrodin and predicted 19 mannose-binding lectin antifungal proteins of G. elata. We also introduced the usage of the G. elata gene function analysis platform (GelFAP) by analyzing CYP51G1 and GFAP4 genes. Our platform GelFAP may help researchers to explore the gene function of G. elata and make novel discoveries about key genes involved in the biological processes of gastrodin.
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Affiliation(s)
- Jiaotong Yang
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiaoqiao Xiao
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jiao Xu
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Lingling Da
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Wenying Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhen Su
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shiping Yang
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qi Pan
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Weike Jiang
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Tao Zhou
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
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Wang W, Wang X, Wang Y, Zhou G, Wang C, Hussain S, Adnan, Lin R, Wang T, Wang S. SlEAD1, an EAR motif-containing ABA down-regulated novel transcription repressor regulates ABA response in tomato. GM CROPS & FOOD 2020; 11:275-289. [PMID: 32706315 DOI: 10.1080/21645698.2020.1790287] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
EAR motif-containing proteins are able to repress gene expression, therefore play important roles in regulating plants growth and development, plant response to environmental stimuli, as well as plant hormone signal transduction. ABA is a plant hormone that regulates abiotic stress tolerance in plants via signal transduction. ABA signaling via the PYR1/PYLs/RCARs receptors, the PP2Cs phosphatases, and SnRK2s protein kinases activates the ABF/AREB/ABI5-type bZIP transcription factors, resulting in the activation/repression of ABA response genes. However, functions of many ABA response genes remained largely unknown. We report here the identification of the ABA-responsive gene SlEAD1 (Solanum lycopersicum EAR motif-containing ABA down-regulated 1) as a novel EAR motif-containing transcription repressor gene in tomato. We found that the expression of SlEAD1 was down-regulated by ABA treatment, and SlEAD1 repressed reporter gene expression in transfected protoplasts. By using CRISPR gene editing, we generated transgene-free slead1 mutants and found that the mutants produced short roots. By using seed germination and root elongation assays, we examined ABA response of the slead1 mutants and found that ABA sensitivity in the mutants was increased. By using qRT-PCR, we further show that the expression of some of the ABA biosynthesis and signaling component genes were increased in the slead1 mutants. Taken together, our results suggest that SlEAD1 is an ABA response gene, that SlEAD1 is a novel EAR motif-containing transcription repressor, and that SlEAD1 negatively regulates ABA responses in tomato possibly by repressing the expression of some ABA biosynthesis and signaling genes.
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Affiliation(s)
- Wei Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University , Linyi, China.,Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Yating Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Ganghua Zhou
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Chen Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Saddam Hussain
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Adnan
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Rao Lin
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
| | - Shucai Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University , Linyi, China.,Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University , Changchun, China
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37
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Jiang J, Ding AB, Liu F, Zhong X. Linking signaling pathways to histone acetylation dynamics in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5179-5190. [PMID: 32333777 PMCID: PMC7475247 DOI: 10.1093/jxb/eraa202] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/22/2020] [Indexed: 05/04/2023]
Abstract
As sessile organisms, plants face versatile environmental challenges and require proper responses at multiple levels for survival. Epigenetic modification of DNA and histones is a conserved gene-regulatory mechanism and plays critical roles in diverse aspects of biological processes, ranging from genome defense and imprinting to development and physiology. In recent years, emerging studies have revealed the interplay between signaling transduction pathways, epigenetic modifications, and chromatin cascades. Specifically, histone acetylation and deacetylation dictate plant responses to environmental cues by modulating chromatin dynamics to regulate downstream gene expression as signaling outputs. In this review, we summarize current understandings of the link between plant signaling pathways and epigenetic modifications with a focus on histone acetylation and deacetylation.
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Affiliation(s)
- Jianjun Jiang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Correspondence: or
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Correspondence: or
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Zhang Z, Li W, Gao X, Xu M, Guo Y. DEAR4, a Member of DREB/CBF Family, Positively Regulates Leaf Senescence and Response to Multiple Stressors in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:367. [PMID: 32296455 PMCID: PMC7136848 DOI: 10.3389/fpls.2020.00367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/13/2020] [Indexed: 05/25/2023]
Abstract
Leaf senescence is a programmed developmental process regulated by various endogenous and exogenous factors. Here we report the characterization of the senescence-regulating role of DEAR4 (AT4G36900) from the DREB1/CBF (dehydration-responsive element binding protein 1/C-repeat binding factor) family in Arabidopsis. The expression of DEAR4 is associated with leaf senescence and can be induced by ABA, JA, darkness, drought and salt stress. Transgenic plants over-expressing DEAR4 showed a dramatically enhanced leaf senescence phenotype under normal and dark conditions while the dear4 knock-down mutant displayed delayed senescence. DEAR4 over-expressing plants showed decreased seed germination rate under ABA and salt stress conditions as well as decreased drought tolerance, indicating that DEAR4 was involved in both senescence and stress response processes. Furthermore, we found that DEAR4 protein displayed transcriptional repressor activities in yeast cells. DEAR4 could directly repress the expression of a subset of COLD-REGULATED (COR) and RESPONSIVE TO DEHYDRATION (RD) genes which have been shown to be involved in leaf longevity and stress response. Also we found that DERA4 could induce the production of Reactive oxygen species (ROS), the common signal of senescence and stress responses, which gives us the clue that DEAR4 may play an integrative role in senescence and stress response via regulating ROS production.
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Chao J, Zhao Y, Jin J, Wu S, Deng X, Chen Y, Tian WM. Genome-Wide Identification and Characterization of the JAZ Gene Family in Rubber Tree ( Hevea brasiliensis). Front Genet 2019; 10:372. [PMID: 31118943 PMCID: PMC6504806 DOI: 10.3389/fgene.2019.00372] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/09/2019] [Indexed: 11/13/2022] Open
Abstract
Jasmonate signaling plays a vital role in the regulation of secondary laticifer differentiation and natural rubber biosynthesis in Hevea brasiliensis. Jasmonate ZIM-domain (JAZ) proteins are the master regulators of jasmonate signaling. Although several JAZs have been reported in the laticifer cells of H. brasiliensis, the genome-wide screening of HbJAZ members has not yet been explored. In the present study, 18 HbJAZs were identified based on the recent H. brasiliensis genome. Phylogenetic construction revealed that the HbJAZs were clustered into five subgroups and that members within the same subgroup shared highly conserved gene structures and protein motifs. Cis-element analysis of HbJAZ promoters suggested the presence of hormone, stress and development-related cis-elements. HbJAZ1.0, HbJAZ2.0, and HbJAZ5.0 interacted with CORONATINE INSENSITIVE1 (COI1) in the presence of coronatine (COR, a JA mimic). HbJAZ1.0, HbJAZ2.0, HbJAZ5.0, and HbJAZ12.0 could also interact with each other. Of the 18 HbJAZs, transcripts of 15 HbJAZs were present in the vascular cambium region except for that of HbJAZ7.0, HbJAZ8.0d, and HbJAZ13.0. Fourteen of the 15 HbJAZs were significantly up-regulated upon COR treatment. The transcripts of three genes that were absent from vascular cambium region were also absent from the latex. Among the 15 HbJAZs in the latex, the expression patterns of 13 HbJAZs were different between the tapping and ethrel treatments. Eight of the 14 COR-up-regulated HbJAZs in the vascular cambium region were also activated by tapping in latex. Of the eight tapping-activated HbJAZs, 5 HbJAZs were repressed by ethrel application. Based on the computational analyses and gene expression patterns described in this study, the HbJAZ5.0 and HbJAZ10.0b may be associated with laticifer differentiation while the HbJAZ8.0b is a negative regulator for natural rubber biosynthesis in H. brasiliensis.
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Affiliation(s)
- Jinquan Chao
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yue Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Jin
- Nextomics Biosciences Co., Ltd., Wuhan, China
| | - Shaohua Wu
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaomin Deng
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yueyi Chen
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei-Min Tian
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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