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Li D, Li H, Feng H, Qi P, Wu Z. Unveiling kiwifruit TCP genes: evolution, functions, and expression insights. PLANT SIGNALING & BEHAVIOR 2024; 19:2338985. [PMID: 38597293 PMCID: PMC11008546 DOI: 10.1080/15592324.2024.2338985] [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: 02/21/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.
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Affiliation(s)
- Donglin Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Haibo Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Huimin Feng
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Ping Qi
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Zhicheng Wu
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
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Li Y, Liu X, Xu X, Zhu G, Xiang D, Liu P. Identification and characterization of the RcTCP gene family and its expression in response to abiotic stresses in castor bean. BMC Genomics 2024; 25:670. [PMID: 38965476 PMCID: PMC11223397 DOI: 10.1186/s12864-024-10347-6] [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: 11/28/2023] [Accepted: 04/25/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND The TCP (teosinte branched1/cincinnata/proliferating cell factor) family plays a prominent role in plant development and stress responses. However, TCP family genes have thus far not been identified in castor bean, and therefore an understanding of the expression and functional aspects of castor bean TCP genes is lacking. To identify the potential biological functions of castor bean (RcTCP) TCP members, the composition of RcTCP family members, their basic physicochemical properties, subcellular localizations, interacting proteins, miRNA target sites, and gene expression patterns under stress were assessed. RESULTS The presence of 20 RcTCP genes on the nine chromosomes of castor bean was identified, all of which possess TCP domains. Phylogenetic analysis indicated a close relationship between RcTCP genes and Arabidopsis AtTCP genes, suggesting potential functional similarity. Subcellular localization experiments confirmed that RcTC01/02/03/10/16/18 are all localized in the nucleus. Protein interaction analysis revealed that the interaction quantity of RcTCP03/06/11 proteins is the highest, indicating a cascade response in the functional genes. Furthermore, it was found that the promoter region of RcTCP genes contains a large number of stress-responsive elements and hormone-induced elements, indicating a potential link between RcTCP genes and stress response functions. qRT-PCR showed that all RcTCP genes exhibit a distinct tissue-specific expression pattern and their expression is induced by abiotic stress (including low temperature, abscisic acid, drought, and high salt). Among them, RcTCP01/03/04/08/09/10/14/15/18/19 genes may be excellent stress-responsive genes. CONCLUSION We discovered that RcTCP genes play a crucial role in various activities, including growth and development, the stress response, and transcription. This study provides a basis for studying the function of RcTCP gene in castor.
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Affiliation(s)
- Yanxiao Li
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyang Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyuan Xu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Guishuang Zhu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Dianjun Xiang
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
| | - Peng Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
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Zhu H, Yang JL, Chen W. Epigenetic insights into an epimutant colorless non-ripening: from fruit ripening to stress responses. FRONTIERS IN PLANT SCIENCE 2024; 15:1440120. [PMID: 39015288 PMCID: PMC11250591 DOI: 10.3389/fpls.2024.1440120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 06/12/2024] [Indexed: 07/18/2024]
Abstract
The epigenetic machinery has received extensive attention due to its involvement in plant growth, development, and adaptation to environmental changes. Recent studies often highlight the epigenetic regulatory network by discussing various epigenetic mutants across various plant species. However, a systemic understanding of essential epigenetic regulatory mechanisms remains limited due to a lack of representative mutants involved in multiple biological processes. Colorless Non-ripening (Cnr), a spontaneous epimutant isolated from a commercial population, was initially characterized for its role in fruit ripening regulation. Cnr fruits exhibit an immature phenotype with yellow skin, attributed to hypermethylation of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE-CNR (SlSPL-CNR) promoter, resulting in the repression of gene expression. In addition to DNA methylation, this process also involves histone modification and microRNA, integrating multiple epigenetic regulatory factors. Interestingly, knockout mutants of SlSPL-CNR display phenotypical distinctions from Cnr in fruit ripening, indicating complex genetic and epigenetic control over the non-ripening phenotype in Cnr fruits. Accumulating evidence suggests that Cnr epimutation is pleiotropic, participating in various biological processes such as Cd stress, Fe deficiency, vivipary, and cell death. Therefore, the Cnr epimutant serve as an excellent model for unveiling how epigenetic mechanisms are involved in diverse biological processes. This review paper focuses on recent research advances regarding the Cnr epimutant, delving into its complex genetic and epigenetic regulatory mechanisms, with the aim of enhancing our understanding and facilitating the development of high-quality, high-yield crops through epigenetic modification.
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Affiliation(s)
- Huihui Zhu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Key Laboratory of Vegetable Biology, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Jian Li Yang
- Key Laboratory of Vegetable Biology, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Weiwei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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Williams J, Regedanz E, Lucinda N, Nava Fereira AR, Lacatus G, Berger M, O’Connell N, Coursey T, Ruan J, Bisaro DM, Sunter G. Mutation of the conserved late element in geminivirus CP promoters abolishes Arabidopsis TCP24 transcription factor binding and decreases H3K27me3 levels on viral chromatin. PLoS Pathog 2024; 20:e1012399. [PMID: 39024402 PMCID: PMC11288445 DOI: 10.1371/journal.ppat.1012399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 07/30/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024] Open
Abstract
In geminiviruses belonging to the genus Begomovirus, coat protein (CP) expression depends on viral AL2 protein, which derepresses and activates the CP promoter through sequence elements that lie within the viral intergenic region (IR). However, AL2 does not exhibit sequence-specific DNA binding activity but is instead directed to responsive promoters through interactions with host factors, most likely transcriptional activators and/or repressors. In this study, we describe a repressive plant-specific transcription factor, Arabidopsis thaliana TCP24 (AtTCP24), that interacts with AL2 and recognizes a class II TCP binding site in the CP promoter (GTGGTCCC). This motif corresponds to the previously identified conserved late element (CLE). We also report that histone 3 lysine 27 trimethylation (H3K27me3), an epigenetic mark associated with facultative repression, is enriched over the viral IR. H3K27me3 is deposited by Polycomb Repressive Complex 2 (PRC2), a critical regulator of gene expression and development in plants and animals. Remarkably, mutation of the TCP24 binding site (the CLE) in tomato golden mosaic virus (TGMV) and cabbage leaf curl virus (CaLCuV) CP promoters greatly diminishes H3K27me3 levels on viral chromatin and causes a dramatic delay and attenuation of disease symptoms in infected Arabidopsis and Nicotiana benthamiana plants. Symptom remission is accompanied by decreased viral DNA levels in systemically infected tissue. Nevertheless, in transient replication assays CLE mutation delays but does not limit the accumulation of viral double-stranded DNA, although single-stranded DNA and CP mRNA levels are decreased. These findings suggest that TCP24 binding to the CLE leads to CP promoter repression and H3K27me3 deposition, while TCP24-AL2 interaction may recruit AL2 to derepress and activate the promoter. Thus, a repressive host transcription factor may be repurposed to target a viral factor essential for promoter activity. The presence of the CLE in many begomoviruses suggests a common scheme for late promoter regulation.
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Affiliation(s)
- Jacqueline Williams
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Elizabeth Regedanz
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Natalia Lucinda
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Alba Ruth Nava Fereira
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Gabriela Lacatus
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Mary Berger
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Nels O’Connell
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Tami Coursey
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - David M. Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Garry Sunter
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
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5
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Wang S, Wei S, Deng Y, Wu S, Peng H, Qing Y, Zhai X, Zhou S, Li J, Li H, Feng Y, Yi Y, Li R, Zhang H, Wang Y, Zhang R, Ning L, Yao Y, Fei Z, Zheng Y. HortGenome Search Engine, a universal genomic search engine for horticultural crops. HORTICULTURE RESEARCH 2024; 11:uhae100. [PMID: 38863996 PMCID: PMC11165154 DOI: 10.1093/hr/uhae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/27/2024] [Indexed: 06/13/2024]
Abstract
Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows for the querying of genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 500 horticultural crops. In addition, four commonly used tools, including 'BLAST', 'Batch Query', 'Enrichment analysis', and 'Synteny Viewer' have been developed for efficient mining and analysis of these genomic data.
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Affiliation(s)
- Sen Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shangxiao Wei
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yuling Deng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shaoyuan Wu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Haixu Peng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shijie Zhou
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Jinrong Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hua Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yijian Feng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yating Yi
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Rui Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hui Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yiding Wang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Renlong Zhang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Lu Ning
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
- Library, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
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6
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Gao Y, Regad F, Li Z, Pirrello J, Bouzayen M, Van Der Rest B. Class I TCP in fruit development: much more than growth. FRONTIERS IN PLANT SCIENCE 2024; 15:1411341. [PMID: 38863555 PMCID: PMC11165105 DOI: 10.3389/fpls.2024.1411341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Fruit development can be viewed as the succession of three main steps consisting of the fruit initiation, growth and ripening. These processes are orchestrated by different factors, notably the successful fertilization of flowers, the environmental conditions and the hormones whose action is coordinated by a large variety of transcription factors. Among the different transcription factor families, TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR (TCP) family has received little attention in the frame of fruit biology despite its large effects on several developmental processes and its action as modulator of different hormonal pathways. In this respect, the comprehension of TCP functions in fruit development remains an incomplete puzzle that needs to be assembled. Building on the abundance of genomic and transcriptomic data, this review aims at collecting available TCP expression data to allow their integration in the light of the different functional genetic studies reported so far. This reveals that several Class I TCP genes, already known for their involvement in the cell proliferation and growth, display significant expression levels in developing fruit, although clear evidence supporting their functional significance in this process remains scarce. The extensive expression data compiled in our study provide convincing elements that shed light on the specific involvement of Class I TCP genes in fruit ripening, once these reproductive organs acquire their mature size. They also emphasize their putative role in the control of specific biological processes such as fruit metabolism and hormonal dialogue.
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Affiliation(s)
- Yushuo Gao
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Farid Regad
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Julien Pirrello
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
| | - Mondher Bouzayen
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Benoît Van Der Rest
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
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7
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Pan J, Ju Z, Ma X, Duan L, Jia Z. Genome-wide characterization of TCP family and their potential roles in abiotic stress resistance of oat ( Avena sativa L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1382790. [PMID: 38654900 PMCID: PMC11036127 DOI: 10.3389/fpls.2024.1382790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
The TCP gene family members play multiple functions in plant growth and development and were named after the first three family members found in this family, TB1 (TEOSINTE BRANCHED 1), CYCLOIDEA (CYC), and Proliferating Cell Factor 1/2 (PCF1/2). Nitrogen (N) is a crucial element for forage yield; however, over-application of N fertilizer can increase agricultural production costs and environmental stress. Therefore, the discovery of low N tolerance genes is essential for the genetic improvement of superior oat germplasm and ecological protection. Oat (Avena sativa L.), is one of the world's staple grass forages, but no genome-wide analysis of TCP genes and their roles in low-nitrogen stress has been performed. This study identified the oat TCP gene family members using bioinformatics techniques. It analyzed their phylogeny, gene structure analysis, and expression patterns. The results showed that the AsTCP gene family includes 49 members, and most of the AsTCP-encoded proteins are neutral or acidic proteins; the phylogenetic tree classified the AsTCP gene family members into three subfamilies, and each subfamily has different conserved structural domains and functions. In addition, multiple cis-acting elements were detected in the promoter of the AsTCP genes, which were associated with abiotic stress, light response, and hormone response. The 49 AsTCP genes identified from oat were unevenly distributed on 18 oat chromosomes. The results of real-time quantitative polymerase chain reaction (qRT-PCR) showed that the AsTCP genes had different expression levels in various tissues under low nitrogen stress, which indicated that these genes (such as AsTCP01, AsTCP03, AsTCP22, and AsTCP38) played multiple roles in the growth and development of oat. In conclusion, this study analyzed the AsTCP gene family and their potential functions in low nitrogen stress at the genome-wide level, which lays a foundation for further analysis of the functions of AsTCP genes in oat and provides a theoretical basis for the exploration of excellent stress tolerance genes in oat. This study provides an essential basis for future in-depth studies of the TCP gene family in other oat genera and reveals new research ideas to improve gene utilization.
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Affiliation(s)
| | | | | | | | - Zhifeng Jia
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
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8
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Dong Z, Hao Y, Zhao Y, Tang W, Wang X, Li J, Wang L, Hu Y, Guan X, Gu F, Liu Z, Zhang Z. Genome-Wide Analysis of the TCP Transcription Factor Gene Family in Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:641. [PMID: 38475487 DOI: 10.3390/plants13050641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
TCP transcription factors play a key role in regulating various developmental processes, particularly in shoot branching, flower development, and leaf development, and these factors are exclusively found in plants. However, comprehensive studies investigating TCP transcription factors in pepper (Capsicum annuum L.) are lacking. In this study, we identified 27 CaTCP members in the pepper genome, which were classified into Class I and Class II through phylogenetic analysis. The motif analysis revealed that CaTCPs in the same class exhibit similar numbers and distributions of motifs. We predicted that 37 previously reported miRNAs target 19 CaTCPs. The expression levels of CaTCPs varied in various tissues and growth stages. Specifically, CaTCP16, a member of Class II (CIN), exhibited significantly high expression in flowers. Class I CaTCPs exhibited high expression levels in leaves, while Class II CaTCPs showed high expression in lateral branches, especially in the CYC/TB1 subclass. The expression profile suggests that CaTCPs play specific roles in the developmental processes of pepper. We provide a theoretical basis that will assist in further functional validation of the CaTCPs.
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Affiliation(s)
- Zeyu Dong
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Yupeng Hao
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Yongyan Zhao
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Wenchen Tang
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Xueqiang Wang
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Jun Li
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Luyao Wang
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Yan Hu
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Xueying Guan
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Fenglin Gu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya 572000, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572000, China
| | - Ziji Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Haikou 571101, China
| | - Zhiyuan Zhang
- Hainan Institute, Zhejiang University, Sanya 572000, China
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9
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Liu C, Lv T, Shen Y, Liu T, Liu M, Hu J, Liu S, Jiang Y, Zhang M, Zhao M, Wang K, Wang Y. Genome-wide identification and integrated analysis of TCP genes controlling ginsenoside biosynthesis in Panax ginseng. BMC PLANT BIOLOGY 2024; 24:47. [PMID: 38216888 PMCID: PMC10787463 DOI: 10.1186/s12870-024-04729-x] [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: 04/15/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
Panax ginseng is an important medicinal plant, and ginsenosides are the main bioactive molecules of ginseng. The TCP (TBI, CYC, PCF) family is a group of transcription factors (TFs) that play an important role in plant growth and development, hormone signalling and synthesis of secondary metabolites. In our study, 78 PgTCP transcripts were identified from the established ginseng transcriptome database. A phylogenetic tree analysis showed that the 67 PgTCP transcripts with complete open reading frames were classified into three subfamilies, including CIN, PCF, and CYC/TB1. Protein structure analysis showed that PgTCP genes had bHLH structures. Chromosomal localization analysis showed that 63 PgTCP genes were localized on 17 of the 24 chromosomes of the Chinese ginseng genome. Expression pattern analysis showed that PgTCP genes differed among different lineages and were spatiotemporally specific. Coexpression network analysis indicated that PgTCP genes were coexpressed and involved in plant activities or metabolic regulation in ginseng. The expression levels of PgTCP genes from class I (PCF) were significantly downregulated, while the expression levels of PgTCP genes from class II (CIN and CYC/TB1) were upregulated, suggesting that TCP genes may be involved in the regulation of secondary metabolism in ginseng. As the PgTCP26-02 gene was found to be related to ginsenoside synthesis, its predicted protein structure and expression pattern were further analysed. Our results provide new insights into the origin, differentiation, evolution and function of the PgTCP gene family in ginseng, as well as the regulation of plant secondary metabolism.
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Affiliation(s)
- Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Tingting Lv
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Yanhua Shen
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Tao Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Mingming Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Jian Hu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Sizhang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Yang Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
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10
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Zhang XJ, Wu C, Liu BY, Liang HL, Wang ML, Li H. Transcriptomic and metabolomic profiling reveals the drought tolerance mechanism of Illicium difengpi (Schisandraceae). FRONTIERS IN PLANT SCIENCE 2024; 14:1284135. [PMID: 38259923 PMCID: PMC10800416 DOI: 10.3389/fpls.2023.1284135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Illicium difengpi (Schisandraceae), an endangered medicinal plant endemic to karst areas, is highly tolerant to drought and thus can be used as an ideal material for investigating adaptive mechanism to drought stress. The understanding of the drought tolerance of I. difengpi, especially at the molecular level, is lacking. In the present study, we aimed to clarify the molecular mechanism underlying drought tolerance in endemic I. difengpi plant in karst regions. The response characteristics of transcripts and changes in metabolite abundance of I. difengpi subjected to drought and rehydration were analyzed, the genes and key metabolites responsive to drought and rehydration were screened, and some important biosynthetic and secondary metabolic pathways were identified. A total of 231,784 genes and 632 metabolites were obtained from transcriptome and metabolome analyses, and most of the physiological metabolism in drought-treated I. difengpi plants recovered after rehydration. There were more upregulated genes than downregulated genes under drought and rehydration treatments, and rehydration treatment induced stable expression of 65.25% of genes, indicating that rehydration alleviated drought stress to some extent. Drought and rehydration treatment generated flavonoids, phenolic acids, flavonols, amino acids and their derivatives, as well as metabolites such as saccharides and alcohols in the leaves of I. difengpi plants, which alleviated the injury caused by excessive reactive oxygen species. The integration of transcriptome and metabolome analyses showed that, under drought stress, I. difengpi increased glutathione, flavonoids, polyamines, soluble sugars and amino acids, contributing to cell osmotic potential and antioxidant activity. The results show that the high drought tolerance and recovery after rehydration are the reasons for the normal growth of I. difengpi in karst mountain areas.
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Affiliation(s)
| | - Chao Wu
- *Correspondence: Chao Wu, ; Hui-Ling Liang,
| | | | - Hui-Ling Liang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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11
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Chen C, Zhang Y, Chen Y, Chen H, Gong R. Sweet cherry TCP gene family analysis reveals potential functions of PavTCP1, PavTCP2 and PavTCP3 in fruit light responses. BMC Genomics 2024; 25:3. [PMID: 38166656 PMCID: PMC10759647 DOI: 10.1186/s12864-023-09923-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND TCP proteins are plant specific transcription factors that play important roles in plant growth and development. Despite the known significance of these transcription factors in general plant development, their specific role in fruit growth remains largely uncharted. Therefore, this study explores the potential role of TCP transcription factors in the growth and development of sweet cherry fruits. RESULTS Thirteen members of the PavTCP family were identified within the sweet cherry plant, with two, PavTCP1 and PavTCP4, found to contain potential target sites for Pav-miR159, Pav-miR139a, and Pav-miR139b-3p. Analyses of cis-acting elements and Arabidopsis homology prediction analyses that the PavTCP family comprises many light-responsive elements. Homologs of PavTCP1 and PavTCP3 in Arabidopsis TCP proteins were found to be crucial to light responses. Shading experiments showed distinct correlation patterns between PavTCP1, 2, and 3 and total anthocyanins, soluble sugars, and soluble solids in sweet cherry fruits. These observations suggest that these genes may contribute significantly to sweet cherry light responses. In particular, PavTCP1 could play a key role, potentially mediated through Pav-miR159, Pav-miR139a, and Pav-miR139b-3p. CONCLUSION This study is the first to unveil the potential function of TCP transcription factors in the light responses of sweet cherry fruits, paving the way for future investigations into the role of this transcription factor family in plant fruit development.
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Affiliation(s)
- Chaoqun Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Yao Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Yuanfei Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Hongxu Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Ronggao Gong
- College of Horticulture, Sichuan Agricultural University, Chengdu, 6111130, China.
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12
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Bi M, Wang Z, Cheng K, Cui Y, He Y, Ma J, Qi M. Construction of transcription factor mutagenesis population in tomato using a pooled CRISPR/Cas9 plasmid library. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108094. [PMID: 37995578 DOI: 10.1016/j.plaphy.2023.108094] [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: 05/18/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
Adequate mutant materials are the prerequisite for conducting gene function research or screening novel functional genes in plants. The strategy of constructing a large-scale mutant population using the pooled CRISPR/Cas9-sgRNA library has been implemented in several crops. However, the effective application of this CRISPR/Cas9 large-scale screening strategy to tomato remains to be attempted. Here, we identified 990 transcription factors in the tomato genome, designed and synthesized a CRISPR/Cas9 plasmid library containing 4379 sgRNAs. Using this pooled library, 487 T0 positive plants were obtained, among which 92 plants harbored a single sgRNA sequence, targeting 65 different transcription factors, with a mutation rate of 23%. In the T0 mutant population, the occurrence of homozygous and biallelic mutations was observed at higher frequencies. Additionally, the utilization of a small-scale CRISPR/Cas9 library targeting 30 transcription factors could enhance the efficacy of single sgRNA recognition in positive plants, increasing it from 19% to 42%. Phenotypic characterization of several mutants identified from the mutant population demonstrated the utility of our CRISPR/Cas9 mutant library. Taken together, our study offers insights into the implementation and optimization of CRISPR/Cas9-mediated large-scale knockout library in tomato.
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Affiliation(s)
- Mengxi Bi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Zhijun Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Keyan Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Yiqing Cui
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China
| | - Yi He
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China
| | - Jian Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China.
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13
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Sharma D, Koul A, Bhushan S, Gupta S, Kaul S, Dhar MK. Insights into microRNA-mediated interaction and regulation of metabolites in tomato. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:1142-1153. [PMID: 37681459 DOI: 10.1111/plb.13572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/23/2023] [Indexed: 09/09/2023]
Abstract
microRNAs direct regulation of various metabolic pathways in plants and animals. miRNAs may be useful in developing novel/elite genotypes, with enhanced metabolites and disease resistance. We examined miRNAs in tomato. In tomato, miRNAs in the carotenoid pathway have not been fully elucidated. We examined the potential role of miRNAs in biosynthesis of carotenoids, transcript profiling of miRNAs and their possible targets (genes and transcription factors) at different development stages of tomato using stem-loop PCR and RT-qPCR. We also identified miRNAs targeting key flavonoid genes, such as chalcone isomerase (CHI), and dihydroflavonol-4-reductase (DFR). Distinct expression profiles of miRNAs and their targets were found in fruits of three tomato accessions, suggesting carotenoid regulation by miRNAs at various stages of fruit development. This was also confirmed using HPLC of the carotenoids. The present study may help in understanding possible regulation of carotenoid biosynthesis. The identified miRNAs can be exploited to enhance biosynthesis of different carotenoids in plants.
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Affiliation(s)
- D Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - A Koul
- Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - S Bhushan
- Department of Botany, Central University of Jammu, Bagla (Rahya Suchani), Samba, Jammu, India
| | - S Gupta
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - S Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - M K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
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14
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Zhang M, Agassin RH, Huang Z, Wang D, Yao S, Ji K. Transcriptome-Wide Identification of TCP Transcription Factor Family Members in Pinus massoniana and Their Expression in Regulation of Development and in Response to Stress. Int J Mol Sci 2023; 24:15938. [PMID: 37958919 PMCID: PMC10648340 DOI: 10.3390/ijms242115938] [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: 08/31/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Pinus massoniana is an important coniferous tree species for barren mountain afforestation with enormous ecological and economic significance. It has strong adaptability to the environment. TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors (TFs) play crucial roles in plant stress response, hormone signal transduction, and development processes. At present, TCP TFs have been widely studied in multiple plant species, but research in P. massoniana has not been carried out. In this study, 13 PmTCP TFs were identified from the transcriptomes of P. massoniana. The phylogenetic results revealed that these PmTCP members were divided into two categories: Class I and Class II. Each PmTCP TF contained a conserved TCP domain, and the conserved motif types and numbers were similar in the same subgroup. According to the transcriptional profiling analysis under drought stress conditions, it was found that seven PmTCP genes responded to drought treatment to varying degrees. The qRT-PCR results showed that the majority of PmTCP genes were significantly expressed in the needles and may play a role in the developmental stage. Meanwhile, the PmTCPs could respond to several stresses and hormone treatments at different levels, which may be important for stress resistance. In addition, PmTCP7 and PmTCP12 were nuclear localization proteins, and PmTCP7 was a transcriptional suppressor. These results will help to explore the regulatory factors related to the growth and development of P. massoniana, enhance its stress resistance, and lay the foundation for further exploration of the physiological effects on PmTCPs.
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Affiliation(s)
| | | | | | | | | | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry and Grassland Administration, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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15
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Hu G, Zhang D, Luo D, Sun W, Zhou R, Hong Z, Munir S, Ye Z, Yang C, Zhang J, Wang T. SlTCP24 and SlTCP29 synergistically regulate compound leaf development through interacting with SlAS2 and activating transcription of SlCKX2 in tomato. THE NEW PHYTOLOGIST 2023; 240:1275-1291. [PMID: 37615215 DOI: 10.1111/nph.19221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
The complexity of compound leaves results primarily from the leaflet initiation and arrangement during leaf development. However, the molecular mechanism underlying compound leaf development remains a central research question. SlTCP24 and SlTCP29, two plant-specific transcription factors with the conserved TCP motif, are shown here to synergistically regulate compound leaf development in tomato. When both of them were knocked out simultaneously, the number of leaflets significantly increased, and the shape of the leaves became more complex. SlTCP24 and SlTCP29 could form both homodimers and heterodimers, and such dimerization was impeded by the leaf polarity regulator SlAS2, which interacted with SlTCP24 and SlTCP29. SlTCP24 and SlTCP29 could bind to the TCP-binding cis-element of the SlCKX2 promoter and activate its transcription. Transgenic plants with SlTCP24 and SlTCP29 double-gene knockout had a lowered transcript level of SlCKX2 and an elevated level of cytokinin. This work led to the identification of two key regulators of tomato compound leaf development and their targeted genes involved in cytokinin metabolic pathway. A model of regulation of compound leaf development was proposed based on observations of this study.
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Affiliation(s)
- Guoyu Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Danqiu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Dan Luo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Wenhui Sun
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Rijin Zhou
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Shoaib Munir
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Zhibiao Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Changxian Yang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
| | - Taotao Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, 430070, China
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16
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Wu X, Li J, Wen X, Zhang Q, Dai S. Genome-wide identification of the TCP gene family in Chrysanthemum lavandulifolium and its homologs expression patterns during flower development in different Chrysanthemum species. FRONTIERS IN PLANT SCIENCE 2023; 14:1276123. [PMID: 37841609 PMCID: PMC10570465 DOI: 10.3389/fpls.2023.1276123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
TCP proteins, part of the transcription factors specific to plants, are recognized for their involvement in various aspects of plant growth and development. Nevertheless, a thorough investigation of TCPs in Chrysanthemum lavandulifolium, a prominent ancestral species of cultivated chrysanthemum and an excellent model material for investigating ray floret (RF) and disc floret (DF) development in Chrysanthemum, remains unexplored yet. Herein, a comprehensive study was performed to analyze the genome-wide distribution of TCPs in C. lavandulifolium. In total, 39 TCPs in C. lavandulifolium were identified, showing uneven distribution on 8 chromosomes. Phylogenetic and gene structural analyses revealed that ClTCPs were grouped into classes I and II. The class II genes were subdivided into two subclades, the CIN and CYC/TB1 subclades, with members of each clade having similar conserved motifs and gene structures. Four CIN subclade genes (ClTCP24, ClTCP25, ClTCP26, and ClTCP27) contained the potential miR319 target sites. Promoter analysis revealed that ClTCPs had numerous cis-regulatory elements associated with phytohormone responses, stress responses, and plant growth/development. The expression patterns of ClTCPs during capitulum development and in two different florets were determined using RNA-seq and qRT-PCR. The expression levels of TCPs varied in six development stages of capitula; 25 out of the 36 TCPs genes were specifically expressed in flowers. Additionally, we identified six key ClCYC2 genes, which belong to the class II TCP subclade, with markedly upregulated expression in RFs compared with DFs, and these genes exhibited similar expression patterns in the two florets of Chrysanthemum species. It is speculated that they may be responsible for RFs and DFs development. Subcellular localization and transactivation activity analyses of six candidate genes demonstrated that all of them were localized in the nucleus, while three exhibited self-activation activities. This research provided a better understanding of TCPs in C. lavandulifolium and laid a foundation for unraveling the mechanism by which important TCPs involved in the capitulum development.
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Affiliation(s)
- Xiaoyun Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Junzhuo Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xiaohui Wen
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qiuling Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
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17
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Li X, Tieman D, Alseekh S, Fernie AR, Klee HJ. Natural variations in the Sl-AKR9 aldo/keto reductase gene impact fruit flavor volatile and sugar contents. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1134-1150. [PMID: 37243881 DOI: 10.1111/tpj.16310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/29/2023]
Abstract
The unique flavors of different fruits depend upon complex blends of soluble sugars, organic acids, and volatile organic compounds. 2-Phenylethanol and phenylacetaldehyde are major contributors to flavor in many foods, including tomato. In the tomato fruit, glucose, and fructose are the chemicals that most positively contribute to human flavor preferences. We identified a gene encoding a tomato aldo/keto reductase, Sl-AKR9, that is associated with phenylacetaldehyde and 2-phenylethanol contents in fruits. Two distinct haplotypes were identified; one encodes a chloroplast-targeted protein while the other encodes a transit peptide-less protein that accumulates in the cytoplasm. Sl-AKR9 effectively catalyzes reduction of phenylacetaldehyde to 2-phenylethanol. The enzyme can also metabolize sugar-derived reactive carbonyls, including glyceraldehyde and methylglyoxal. CRISPR-Cas9-induced loss-of-function mutations in Sl-AKR9 significantly increased phenylacetaldehyde and lowered 2-phenylethanol content in ripe fruit. Reduced fruit weight and increased soluble solids, glucose, and fructose contents were observed in the loss-of-function fruits. These results reveal a previously unidentified mechanism affecting two flavor-associated phenylalanine-derived volatile organic compounds, sugar content, and fruit weight. Modern varieties of tomato almost universally contain the haplotype associated with larger fruit, lower sugar content, and lower phenylacetaldehyde and 2-phenylethanol, likely leading to flavor deterioration in modern varieties.
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Affiliation(s)
- Xiang Li
- Horticultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Denise Tieman
- Horticultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Harry J Klee
- Horticultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida, 32611, USA
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18
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Zou Q, Dong Q, Tian D, Mao L, Cao X, Zhu K. Genome-Wide Analysis of TCP Transcription Factors and Their Expression Pattern Analysis of Rose Plants ( Rosa chinensis). Curr Issues Mol Biol 2023; 45:6352-6364. [PMID: 37623220 PMCID: PMC10453170 DOI: 10.3390/cimb45080401] [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: 06/25/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
The plant-specific transcription factor TEOSINTE BRANCHED, CYCLOIDEA, AND PROLIFERATING CELL FACTOR (TCP) gene family plays vital roles in various biological processes, including growth and development, hormone signaling, and stress responses. However, there is a limited amount of information regarding the TCP gene family in roses (Rosa sp.). In this study, we identified 18 TCP genes in the rose genome, which were further classified into two subgroups (Group A and Group B) via phylogenetic analysis. Comprehensive characterization of these TCP genes was performed, including gene structure, motif composition, chromosomal location, and expression profiles. Synteny analysis revealed that a few TCP genes are involved in segmental duplication events, indicating that these genes played an important role in the expansion of the TCP gene family in roses. This suggests that segmental duplication events have caused the evolution of the TCP gene family and may have generated new functions. Our study provides an insight into the evolutionary and functional characteristics of the TCP gene family in roses and lays a foundation for the future exploration of the regulatory mechanisms of TCP genes in plant growth and development.
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Affiliation(s)
| | | | | | | | - Xuerui Cao
- Zhejiang Institute of Landscape Plants and Flowers, Hangzhou 311251, China; (Q.Z.); (Q.D.); (D.T.); (L.M.)
| | - Kaiyuan Zhu
- Zhejiang Institute of Landscape Plants and Flowers, Hangzhou 311251, China; (Q.Z.); (Q.D.); (D.T.); (L.M.)
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19
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Pirona R, Frugis G, Locatelli F, Mattana M, Genga A, Baldoni E. Transcriptomic analysis reveals the gene regulatory networks involved in leaf and root response to osmotic stress in tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1155797. [PMID: 37332696 PMCID: PMC10272567 DOI: 10.3389/fpls.2023.1155797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Introduction Tomato (Solanum lycopersicum L.) is a major horticultural crop that is cultivated worldwide and is characteristic of the Mediterranean agricultural system. It represents a key component of the diet of billion people and an important source of vitamins and carotenoids. Tomato cultivation in open field often experiences drought episodes, leading to severe yield losses, since most modern cultivars are sensitive to water deficit. Water stress leads to changes in the expression of stress-responsive genes in different plant tissues, and transcriptomics can support the identification of genes and pathways regulating this response. Methods Here, we performed a transcriptomic analysis of two tomato genotypes, M82 and Tondo, in response to a PEG-mediated osmotic treatment. The analysis was conducted separately on leaves and roots to characterize the specific response of these two organs. Results A total of 6,267 differentially expressed transcripts related to stress response was detected. The construction of gene co-expression networks defined the molecular pathways of the common and specific responses of leaf and root. The common response was characterized by ABA-dependent and ABA-independent signaling pathways, and by the interconnection between ABA and JA signaling. The root-specific response concerned genes involved in cell wall metabolism and remodeling, whereas the leaf-specific response was principally related to leaf senescence and ethylene signaling. The transcription factors representing the hubs of these regulatory networks were identified. Some of them have not yet been characterized and can represent novel candidates for tolerance. Discussion This work shed new light on the regulatory networks occurring in tomato leaf and root under osmotic stress and set the base for an in-depth characterization of novel stress-related genes that may represent potential candidates for improving tolerance to abiotic stress in tomato.
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Affiliation(s)
- Raul Pirona
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Milano, Italy
| | - Giovanna Frugis
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Rome Unit, Roma, Italy
| | - Franca Locatelli
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Milano, Italy
| | - Monica Mattana
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Milano, Italy
| | - Annamaria Genga
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Milano, Italy
| | - Elena Baldoni
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Milano, Italy
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20
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Wu Y, Zhang J, Li C, Deng X, Wang T, Dong L. Genome-wide analysis of TCP transcription factor family in sunflower and identification of HaTCP1 involved in the regulation of shoot branching. BMC PLANT BIOLOGY 2023; 23:222. [PMID: 37101166 PMCID: PMC10134548 DOI: 10.1186/s12870-023-04211-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Sunflower is an important ornamental plant, which can be used for fresh cut flowers and potted plants. Plant architecture regulation is an important agronomic operation in its cultivation and production. As an important aspect of plant architecture formation, shoot branching has become an important research direction of sunflower. RESULTS TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors are essential in regulating various development process. However, the role of TCPs in sunflowers has not yet been studied. This study, 34 HaTCP genes were identified and classified into three subfamilies based on the conservative domain and phylogenetic analysis. Most of the HaTCPs in the same subfamily displayed similar gene and motif structures. Promoter sequence analysis has demonstrated the presence of multiple stress and hormone-related cis-elements in the HaTCP family. Expression patterns of HaTCPs revealed several HaTCP genes expressed highest in buds and could respond to decapitation. Subcellular localization analysis showed that HaTCP1 was located in the nucleus. Paclobutrazol (PAC) and 1-naphthylphthalamic acid (NPA) administration significantly delayed the formation of axillary buds after decapitation, and this suppression was partially accomplished by enhancing the expression of HaTCP1. Furthermore, HaTCP1 overexpressed in Arabidopsis caused a significant decrease in branch number, indicating that HaTCP1 played a key role in negatively regulating sunflower branching. CONCLUSIONS This study not only provided the systematic analysis for the HaTCP members, including classification, conserved domain and gene structure, expansion pattern of different tissues or after decapitation. But also studied the expression, subcellular localization and function of HaTCP1. These findings could lay a critical foundation for further exploring the functions of HaTCPs.
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Affiliation(s)
- Yu Wu
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Jianbin Zhang
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Chaoqun Li
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Xinyi Deng
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Tian Wang
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Lili Dong
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China.
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21
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Liu X, Pei L, Zhang L, Zhang X, Jiang J. Regulation of miR319b-Targeted SlTCP10 during the Tomato Response to Low-Potassium Stress. Int J Mol Sci 2023; 24:ijms24087058. [PMID: 37108222 PMCID: PMC10138608 DOI: 10.3390/ijms24087058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Potassium deficiency confines root growth and decreases root-to-shoot ratio, thereby limiting root K+ acquisition. This study aimed to identify the regulation network of microRNA319 involved in low-K+ stress tolerance in tomato (Solanum lycopersicum). SlmiR319b-OE roots demonstrated a smaller root system, a lower number of root hairs and lower K+ content under low-K+ stress. We identified SlTCP10 as the target of miR319b using a modified RLM-RACE procedure from some SlTCPs' predictive complementarity to miR319b. Then, SlTCP10-regulated SlJA2 (an NAC transcription factor) influenced the response to low-K+ stress. CR-SlJA2 (CRISPR-Cas9-SlJA2) lines showed the same root phenotype to SlmiR319-OE compared with WT lines. OE-SlJA2(Overexpression-SlJA2) lines showed higher root biomass, root hair number and K+ concentration in the roots under low-K+ conditions. Furthermore, SlJA2 has been reported to promote abscisic acid (ABA) biosynthesis. Therefore, SlJA2 increases low-K+ tolerance via ABA. In conclusion, enlarging root growth and K+ absorption by the expression of SlmiR319b-regulated SlTCP10, mediating SlJA2 in roots, could provide a new regulation mechanism for increasing K+ acquisition efficiency under low-K+ stress.
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Affiliation(s)
- Xin Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry, Shenyang 110866, China
| | - Lingling Pei
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Lingling Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xueying Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Jing Jiang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Protected Horticulture of Education Ministry, Shenyang 110866, China
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22
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Si C, Zhan D, Wang L, Sun X, Zhong Q, Yang S. Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum). Cells 2023; 12:cells12071015. [PMID: 37048089 PMCID: PMC10093338 DOI: 10.3390/cells12071015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/09/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Plant-specific transcription factors such as the TCP family play crucial roles in light responses and lateral branching. The commercial development of S. muricatum has been influenced by the ease with which its lateral branches can be germinated, especially under greenhouse cultivation during the winter with supplemented LED light. The present study examined the TCP family genes in S. muricatum using bioinformatics analysis (whole-genome sequencing and RNA-seq) to explore the response of this family to different light treatments. Forty-one TCP genes were identified through a genome-wide search; phylogenetic analysis revealed that the CYC/TB1, CIN and Class I subclusters contained 16 SmTCP, 11 SmTCP and 14 SmTCP proteins, respectively. Structural and conserved sequence analysis of SmTCPs indicated that the motifs in the same subcluster were highly similar in structure and the gene structure of SmTCPs was simpler than that in Arabidopsis thaliana; 40 of the 41 SmTCPs were localized to 12 chromosomes. In S. muricatum, 17 tandem repeat sequences and 17 pairs of SmTCP genes were found. We identified eight TCPs that were significantly differentially expressed (DETCPs) under blue light (B) and red light (R), using RNA-seq. The regulatory network of eight DETCPs was preliminarily constructed. All three subclusters responded to red and blue light treatment. To explore the implications of regulatory TCPs in different light treatments for each species, the TCP regulatory gene networks and GO annotations for A. thaliana and S. muricatum were compared. The regulatory mechanisms suggest that the signaling pathways downstream of the TCPs may be partially conserved between the two species. In addition to the response to light, functional regulation was mostly enriched with auxin response, hypocotyl elongation, and lateral branch genesis. In summary, our findings provide a basis for further analysis of the TCP gene family in other crops and broaden the functional insights into TCP genes regarding light responses.
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Affiliation(s)
- Cheng Si
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Deli Zhan
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Lihui Wang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
| | - Xuemei Sun
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
| | - Qiwen Zhong
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- Correspondence: (Q.Z.); (S.Y.)
| | - Shipeng Yang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Correspondence: (Q.Z.); (S.Y.)
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Edris S, Abulfaraj AA, Makki RM, Abo-Aba S, Algandaby MM, Sabir J, Jansen RK, El Domyati FM, Bahieldin A. Early Fruit Development Regulation-Related Genes Concordantly Expressed with TCP Transcription Factors in Tomato (Solanum lycopersicum). Curr Issues Mol Biol 2023; 45:2372-2380. [PMID: 36975523 PMCID: PMC10099719 DOI: 10.3390/cimb45030153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/14/2023] Open
Abstract
The tomato (Solanum lycopersicum L.) is considered one of the most important vegetable crops globally, both agronomically and economically; however, its fruit development regulation network is still unclear. The transcription factors serve as master regulators, activating many genes and/or metabolic pathways throughout the entire plant life cycle. In this study, we identified the transcription factors that are coordinated with TCP gene family regulation in early fruit development by making use of the high-throughput sequencing of RNA (RNAseq) technique. A total of 23 TCP-encoding genes were found to be regulated at various stages during the growth of the fruit. The expression patterns of five TCPs were consistent with those of other transcription factors and genes. There are two unique subgroups of this larger family: class I and class II TCPs. Others were directly associated with the growth and/or ripening of fruit, while others were involved in the production of the hormone auxin. Moreover, it was discovered that TCP18 had an expression pattern that was similar to that of the ethylene-responsive transcription factor 4 (ERF4). Tomato fruit set and overall development are under the direction of a gene called auxin response factor 5 (ARF5). TCP15 revealed an expression that was in sync with this gene. This study provides insight into the potential processes that help in acquiring superior fruit qualities by accelerating fruit growth and ripening.
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Affiliation(s)
- Sherif Edris
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- R&D Department, Al Borg Diagnostics, Jeddah 23514, Saudi Arabia
- Correspondence: ; Tel.: +966-59-366-2384
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Rania M. Makki
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Salah Abo-Aba
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- National Research Centre, Department of Microbial Genetics, Genetic Engineering and Biotechnology Division, Giza 12622, Egypt
| | - Mardi M. Algandaby
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jamal Sabir
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Robert K. Jansen
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Fotouh M. El Domyati
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
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24
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Advances in Research on the Regulation of Floral Development by CYC-like Genes. Curr Issues Mol Biol 2023; 45:2035-2059. [PMID: 36975501 PMCID: PMC10047570 DOI: 10.3390/cimb45030131] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number of members that are crucial regulators of floral symmetry. To date, studies on CYC-like genes have mainly focused on plants with actinomorphic and zygomorphic flowers, including Fabaceae, Asteraceae, Scrophulariaceae, and Gesneriaceae species and the effects of CYC-like gene duplication events and diverse spatiotemporal expression patterns on flower development. The CYC-like genes generally affect petal morphological characteristics and stamen development, as well as stem and leaf growth, flower differentiation and development, and branching in most angiosperms. As the relevant research scope has expanded, studies have increasingly focused on the molecular mechanisms regulating CYC-like genes with different functions related to flower development and the phylogenetic relationships among these genes. We summarize the status of research on the CYC-like genes in angiosperms, such as the limited research conducted on CYC1 and CYC3 clade members, the necessity to functionally characterize the CYC-like genes in more plant groups, the need for investigation of the regulatory elements upstream of CYC-like genes, and exploration of the phylogenetic relationships and expression of CYC-like genes with new techniques and methods. This review provides theoretical guidance and ideas for future research on CYC-like genes.
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25
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Hao J, Zheng L, Han Y, Zhang H, Hou K, Liang X, Chen C, Wang Z, Qian J, Lin Z, Wang Z, Zeng H, Shen C. Genome-wide identification and expression analysis of TCP family genes in Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2023; 14:1161534. [PMID: 37123846 PMCID: PMC10130365 DOI: 10.3389/fpls.2023.1161534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Introduction The anti-tumor vindoline and catharanthine alkaloids are naturally existed in Catharanthus roseus (C. roseus), an ornamental plant in many tropical countries. Plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play important roles in various plant developmental processes. However, the roles of C. roseus TCPs (CrTCPs) in terpenoid indole alkaloid (TIA) biosynthesis are largely unknown. Methods Here, a total of 15 CrTCP genes were identified in the newly updated C. roseus genome and were grouped into three major classes (P-type, C-type and CYC/TB1). Results Gene structure and protein motif analyses showed that CrTCPs have diverse intron-exon patterns and protein motif distributions. A number of stress responsive cis-elements were identified in promoter regions of CrTCPs. Expression analysis showed that three CrTCP genes (CrTCP2, CrTCP4, and CrTCP7) were expressed specifically in leaves and four CrTCP genes (CrTCP13, CrTCP8, CrTCP6, and CrTCP10) were expressed specifically in flowers. HPLC analysis showed that the contents of three classic TIAs, vindoline, catharanthine and ajmalicine, were significantly increased by ultraviolet-B (UV-B) and methyl jasmonate (MeJA) in leaves. By analyzing the expression patterns under UV-B radiation and MeJA application with qRT-PCR, a number of CrTCP and TIA biosynthesis-related genes were identified to be responsive to UV-B and MeJA treatments. Interestingly, two TCP binding elements (GGNCCCAC and GTGGNCCC) were identified in several TIA biosynthesis-related genes, suggesting that they were potential target genes of CrTCPs. Discussion These results suggest that CrTCPs are involved in the regulation of the biosynthesis of TIAs, and provide a basis for further functional identification of CrTCPs.
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Affiliation(s)
- Juan Hao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Lijun Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Yidie Han
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Hongshan Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- Kharkiv Institute, Hangzhou Normal University, Hangzhou, China
| | - Kailin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Xueshuang Liang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Cheng Chen
- College of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Zhijing Wang
- College of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Jiayi Qian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Zhihao Lin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Zitong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Kharkiv Institute, Hangzhou Normal University, Hangzhou, China
- *Correspondence: Chenjia Shen, ; Houqing Zeng,
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- Kharkiv Institute, Hangzhou Normal University, Hangzhou, China
- *Correspondence: Chenjia Shen, ; Houqing Zeng,
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26
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Zeng J, Yang M, Deng J, Zheng D, Lai Z, Wang-Pruski G, XuHan X, Guo R. The function of BoTCP25 in the regulation of leaf development of Chinese kale. FRONTIERS IN PLANT SCIENCE 2023; 14:1127197. [PMID: 37143872 PMCID: PMC10151756 DOI: 10.3389/fpls.2023.1127197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/15/2023] [Indexed: 05/06/2023]
Abstract
XG Chinese kale (Brassica oleracea cv. 'XiangGu') is a variety of Chinese kale and has metamorphic leaves attached to the true leaves. Metamorphic leaves are secondary leaves emerging from the veins of true leaves. However, it remains unknown how the formation of metamorphic leaves is regulated and whether it differs from normal leaves. BoTCP25 is differentially expressed in different parts of XG leaves and respond to auxin signals. To clarify the function of BoTCP25 in XG Chinese kale leaves, we overexpressed BoTCP25 in XG and Arabidopsis, and interestingly, its overexpression caused Chinese kale leaves to curl and changed the location of metamorphic leaves, whereas heterologous expression of BoTCP25 in Arabidopsis did not show metamorphic leaves, but only an increase in leaf number and leaf area. Further analysis of the expression of related genes in Chinese kale and Arabidopsis overexpressing BoTCP25 revealed that BoTCP25 could directly bind the promoter of BoNGA3, a transcription factor related to leaf development, and induce a significant expression of BoNGA3 in transgenic Chinese kale plants, whereas this induction of NGA3 did not occur in transgenic Arabidopsis. This suggests that the regulation of Chinese kale metamorphic leaves by BoTCP25 is dependent on a regulatory pathway or elements specific to XG and that this regulatory element may be repressed or absent from Arabidopsis. In addition, the expression of miR319's precursor, a negative regulator of BoTCP25, also differed in transgenic Chinese kale and Arabidopsis. miR319's transcrips were significantly up-regulated in transgenic Chinese kale mature leaves, while in transgenic Arabidopsis, the expression of miR319 in mature leaves was kept low. In conclusion, the differential expression of BoNGA3 and miR319 in the two species may be related to the exertion of BoTCP25 function, thus partially contributing to the differences in leaf phenotypes between overexpressed BoTCP25 in Arabidopsis and Chinese kale.
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Affiliation(s)
- Jiajing Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengyu Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Deng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongyang Zheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gefu Wang-Pruski
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Xu XuHan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Faculté des sciences et de la technologie, Institut de la Recherche Interdiciplinaire de Toulouse (IRIT-ARI), Toulouse, France
| | - Rongfang Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Rongfang Guo,
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Genome-Wide Identification and Characterization of TCP Gene Family Members in Melastoma candidum. Molecules 2022; 27:molecules27249036. [PMID: 36558169 PMCID: PMC9787641 DOI: 10.3390/molecules27249036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
It has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) gene family plays a pivotal role during plant growth and development. M. candidum is a native ornamental species and has a wide range of pharmacodynamic effects. However, there is still a lack of research on TCP’s role in controlling M. candidum’s development, abiotic stress responses and hormone metabolism. A comprehensive description of the TCP gene family in M. candidum is urgently needed. In this study, we used the HMMER search method in conjunction with the BLASTp method to identify the members of the TCP gene family, and a total of 35 TCP genes were identified. A domain analysis further confirmed that all 35 TCPs contained a TCP superfamily, a characteristic involved in dimerization and DNA binding that can be found in most genes from this gene family, suggesting that our identification was effective. As a result of the domain conservation analysis, the 35 TCP genes could be classified into two classes, TCP-P and TCP-C, based on the conservative regions of 55 and 59 amino acids, respectively. Gene-duplication analysis revealed that most TCP genes were present in duplication events that eventually led to TCP gene expansion in M. candidum. All the detected gene pairs had a Ka/Ks value of less than one, suggesting that purification selection is the most important factor that influences the evolution of TCP genes. Phylogenetic analysis of three species displayed the evolutionary relationship of TCP genes across different species and further confirmed our results. The real-time quantitative PCR (qRT-PCR) results showed that McTCP2a, McTCP7a, McTCP10, McTCP11, McTCP12a, McTCP13, McTCP16, McTCP17, McTCP18, McTCP20 and McTCP21 may be involved in leaf development; McTCP4a, McTCP1, McTCP14, McTCP17, McTCP18, McTCP20, McTCP22 and McTCP24 may be involved in flower development; and McTCP2a, McTCP3, McTCP5a, McTCP6, McTCP7a, McTCP9, McTCP11, McTCP14 and McTCP16 may be involved in seed development. Our results dissect the TCP gene family across the genome of M. candidum and provide valuable information for exploring TCP genes to promote molecular breeding and property improvement of M. candidum in the future.
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Damerval C, Claudot C, Le Guilloux M, Conde e Silva N, Brunaud V, Soubigou-Taconnat L, Caius J, Delannoy E, Nadot S, Jabbour F, Deveaux Y. Evolutionary analyses and expression patterns of TCP genes in Ranunculales. FRONTIERS IN PLANT SCIENCE 2022; 13:1055196. [PMID: 36531353 PMCID: PMC9752903 DOI: 10.3389/fpls.2022.1055196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
TCP transcription factors play a role in a large number of developmental processes and are at the crossroads of numerous hormonal biosynthetic and signaling pathways. The complete repertoire of TCP genes has already been characterized in several plant species, but not in any species of early diverging eudicots. We focused on the order Ranunculales because of its phylogenetic position as sister group to all other eudicots and its important morphological diversity. Results show that all the TCP genes expressed in the floral transcriptome of Nigella damascena (Ranunculaceae) are the orthologs of the TCP genes previously identified from the fully sequenced genome of Aquilegia coerulea. Phylogenetic analyses combined with the identification of conserved amino acid motifs suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. We highlight independent duplications in core eudicots and Ranunculales within the class I and class II subfamilies, resulting in different numbers of paralogs within the main subclasses of TCP genes. This has most probably major consequences on the functional diversification of these genes in different plant clades. The expression patterns of TCP genes in Nigella damascena were consistent with the general suggestion that CIN and class I TCP genes may have redundant roles or take part in same pathways, while CYC/TB1 genes have more specific actions. Our findings open the way for future studies at the tissue level, and for investigating redundancy and subfunctionalisation in TCP genes and their role in the evolution of morphological novelties.
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Affiliation(s)
- Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Carmine Claudot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Ludivine Soubigou-Taconnat
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - José Caius
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
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Zhou H, Hwarari D, Ma H, Xu H, Yang L, Luo Y. Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology. Front Genet 2022; 13:1060546. [PMID: 36437962 PMCID: PMC9682074 DOI: 10.3389/fgene.2022.1060546] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/27/2022] [Indexed: 09/29/2023] Open
Abstract
The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.
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Affiliation(s)
- Haiying Zhou
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative In-novation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Delight Hwarari
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hongyu Ma
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Haibin Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative In-novation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
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Li D, Tang X, Dong Y, Wang Y, Shi S, Li S, Liu Y, Ge H, Chen H. Comparative genomic investigation of TCP gene family in eggplant (Solanum melongena L.) and expression analysis under divergent treatments. PLANT CELL REPORTS 2022; 41:2213-2228. [PMID: 36001130 DOI: 10.1007/s00299-022-02918-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The putative TCP genes and their responses to abiotic stress in eggplant were comprehensively characterized, and SmTCP genes (Smechr0202855.1 and Smechr0602431.1) may be involved in anthocyanin synthesis. The Teosinte branched1/Cycloidea/Proliferating cell factors (TCPs), a family of plant-specific transcription factors, plays paramount roles in a plethora of developmental and physiological processes. We here systematically characterized putative TCP genes and their response to abiotic stress in eggplant. In total, 30 SmTCP genes were categorized into two subfamilies based on the classical TCP conserved domains. Chromosomal location analysis illustrated the random distribution of putative SmTCP genes along 12 eggplant chromosomes. Cis-acting elements and miRNA target prediction suggested that versatile and complicated regulatory mechanisms that control SmTCPs gene expression, and 3 miRNAs (miR319a, miR319b, and miR319c-3p) might act as major regulators targeting SmTCPs. Tissue expression profiles indicated divergent spatiotemporal expression patterns of SmTCPs. qRT-PCR assays demonstrated different expression profiles of SmTCP under 4 °C, drought and ABA treatment conditions, suggesting the possible participation of SmTCP genes in multiple signaling pathways. Furthermore, RNA-seq data of eggplant anthocyanin synthesis coupled with yeast one-hybrid and dual-luciferase assays suggested the involvement of SmTCP genes (Smechr0202855.1 and Smechr0602431.1) in the mediation of anthocyanin synthesis. Our study will facilitate further investigation on the putative functional characterization of eggplant TCP genes and lay a solid foundation for the in-depth study of the involvement of SmTCP genes in the regulation of anthocyanin synthesis.
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Affiliation(s)
- Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Xin Tang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yanxiao Dong
- Shanghai Agricultural Science and Technology Service Center, Shanghai, 200335, China
| | - Yingying Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Suli Shi
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Shaohang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Haiyan Ge
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
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31
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Kim HM, Park SH, Park SY, Ma SH, Do JH, Kim AY, Jeon MJ, Shim JS, Joung YH. Identification of essential element determining fruit-specific transcriptional activity in the tomato HISTIDINE DECARBOXYLASE A gene promoter. PLANT CELL REPORTS 2022; 41:1721-1731. [PMID: 35739429 DOI: 10.1007/s00299-022-02886-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
In SlHDC-A promoter, SlHDC-A core-ES is an essential region for fruit-specific expression and interacts with GATA, HSF and AP1. Triplication of essential region was proposed as a minimal fruit-specific promoter. In plant biotechnology, fruit-specific promoter is an important tool for the improvement and utilization of tomato fruit. To expand our understanding on fruit-specific expression, it is necessary to determine the promoter region involved in fruit-specific transcriptional activity and transcriptional regulations of the promoter. In previous study, we isolated a fruit-specific SlHDC-A core promoter specifically expressed during tomato ripening stages. In this study, we identified SlHDC-A promoter region (SlHDC-A core-ES) that is essential for fruit-specific expression of the SlHDC-A. To understand the molecular mechanisms of fruit-specific expression of the SlHDC-A promoter, we first identified the putative transcription factor binding elements in the SlHDC-A core promoter region and corresponding putative transcription factors which are highly expressed during fruit maturation. Yeast one hybrid analysis confirmed that GATA, HSF, and AP1 interact with the SlHDC-A core-ES promoter region. Further transactivation analysis revealed that expression of the three transcription factors significantly activated expression of a reporter gene driven by SlHDC-A core-ES promoter. These results suggest that GATA, HSF, and AP1 are involved in the fruit-specific expression of SlHDC-A promoter. Furthermore, the synthetic promoter composed of three tandem repeats of SlHDC-A core-ES showed relatively higher activity than the constitutive 35S promoter in the transgenic tomato fruits at the orange stage. Taken together, we propose a new synthetic promoter that is specifically expressed during fruit ripening stage.
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Affiliation(s)
- Hyun Min Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Se Hee Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Seo Young Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Sang Hoon Ma
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ju Hui Do
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ah Young Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Mi Jin Jeon
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Young Hee Joung
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Liu DH, Luo Y, Han H, Liu YZ, Alam SM, Zhao HX, Li YT. Genome-wide analysis of citrus TCP transcription factors and their responses to abiotic stresses. BMC PLANT BIOLOGY 2022; 22:325. [PMID: 35790897 PMCID: PMC9258177 DOI: 10.1186/s12870-022-03709-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Citrus is one of the most important fruit crops in the world, and it is worthy to conduct more research on artificially controlling citrus plant growth and development to adapt to different cultivation patterns and environmental conditions. The plant-specific TEOSINTE BRANCHED1, CYCOLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors are crucial regulators controlling plant growth and development, as well as responding to abiotic stresses. However, the information about citrus TCP transcription factors remains unclear. RESULTS In this study, twenty putative TCP genes (CsTCPs) with the TCP domain were explored from Citrus sinensis genome, of which eleven (CsTCP3, - 4, - 5, - 6, - 10, - 11, - 15, - 16, - 18, - 19, - 20), five (CsTCP1, - 2, - 7, - 9, - 13), and four genes (CsTCP8, - 12, - 14, - 17) were unevenly distributed on chromosomes and divided into three subclades. Cis-acting element analysis indicated that most CsTCPs contained many phytohormone- and environment-responsive elements in promoter regions. All of CsTCPs were predominantly expressed in vegetative tissues or organs (stem, leaf, thorn, and bud) instead of reproductive tissues or organs (flower, fruit, and seed). Combined with collinearity analysis, CsTCP3, CsTCP9, and CsTCP13 may take part in leaf development; CsTCP12 and CsTCP14 may function in shoot branching, leaf development, or thorn development; CsTCP15 may participate in the development of stem, leaf, or thorn. In mature leaf, transcript levels of two CsTCPs (CsTCP19, - 20) were significantly increased while transcript levels of eight CsTCPs (CsTCP2, - 5, - 6, - 7, - 8, - 9, - 10, - 13) were significantly decreased by shading; except for two CsTCPs (CsTCP11, - 19), CsTCPs' transcript levels were significantly influenced by low temperature; moreover, transcript levels of two CsTCPs (CsTCP11, - 12) were significantly increased while five CsTCPs' (CsTCP14, - 16, - 18, - 19, - 20) transcript levels were significantly reduced by drought. CONCLUSIONS This study provides significant clues for research on roles of CsTCPs in regulating citrus plant growth and development, as well as responding to abiotic stresses.
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Affiliation(s)
- Dong-Hai Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Yin Luo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Han Han
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Yong-Zhong Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Shariq Mahmood Alam
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Hui-Xing Zhao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Yan-Ting Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)/College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 P.R. China
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Shang X, Han Z, Zhang D, Wang Y, Qin H, Zou Z, Zhou L, Zhu X, Fang W, Ma Y. Genome-Wide Analysis of the TCP Gene Family and Their Expression Pattern Analysis in Tea Plant ( Camellia sinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:840350. [PMID: 35845692 PMCID: PMC9284231 DOI: 10.3389/fpls.2022.840350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors TEOSINTE BRANCHED1/CYCLOIDEA/PCF have been suggested to control the cell growth and proliferation in meristems and lateral organs. A total of 37 CsTCP genes were identified and divided into two classes, class I (PCF, group 1) and class II (CIN CYC/TB1, groups 2, and 3). The residues of TEOSINTE BRANCHED1/CYCLOIDEA/PCF of Camellia sinensis (Tea plant) (CsTCP) proteins between class I and class II were definitely different in the loop, helix I, and helix II regions; however, eighteen conserved tandem was found in bHLH. There are a large number of CsTCP homologous gene pairs in three groups. Additionally, most CsTCP proteins have obvious differences in motif composition. The results illuminated that CsTCP proteins in different groups are supposed to have complementary functions, whereas those in the same class seem to display function redundancies. There is no relationship between the number of CsTCP gene members and genome size, and the CsTCP gene family has only expanded since the divergence of monocots and eudicots. WGD/segmental duplication played a vital role in the expansion of the CsTCP gene family in tea plant, and the CsTCP gene family has expanded a lot. Most CsTCP genes of group 1 are more widely and non-specifically expressed, and the CsTCP genes of group 2 are mainly expressed in buds, flowers, and leaves. Most genes of group 1 and some genes of group 2 were up-/downregulated in varying degrees under different stress, CsTCP genes of group 3 basically do not respond to stress. TCP genes involved in abiotic stress response mostly belong to PCF group. Some CsTCP genes may have the same function as the homologous genes in Arabidopsis, but there is functional differentiation.
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Affiliation(s)
- Xiaowen Shang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhaolan Han
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Dayan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ya Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hao Qin
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Agricultural and Forestry Service Center, Suzhou, China
| | - Zhongwei Zou
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Lin Zhou
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Yang M, He G, Hou Q, Fan Y, Duan L, Li K, Wei X, Qiu Z, Chen E, He T. Systematic analysis and expression profiles of TCP gene family in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stress. BMC Genomics 2022; 23:415. [PMID: 35655134 PMCID: PMC9164426 DOI: 10.1186/s12864-022-08618-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Background As transcription factors, the TCP genes are considered to be promising targets for crop enhancement for their responses to abiotic stresses. However, information on the systematic characterization and functional expression profiles under abiotic stress of TCPs in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) is limited. Results In this study, we identified 26 FtTCPs and named them according to their position on the chromosomes. Phylogenetic tree, gene structure, duplication events, and cis-acting elements were further studied and syntenic analysis was conducted to explore the bioinformatic traits of the FtTCP gene family. Subsequently, 12 FtTCP genes were selected for expression analysis under cold, dark, heat, salt, UV, and waterlogging (WL) treatments by qRT-PCR. The spatio-temporal specificity, correlation analysis of gene expression levels and interaction network prediction revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stresses. Moreover, subcellular localization confirmed that FtTCP15 and FtTCP18 localized in the nucleus function as transcription factors. Conclusions In this research, 26 TCP genes were identified in Tartary buckwheat, and their structures and functions have been systematically explored. Our results reveal that the FtTCP15 and FtTCP18 have special cis-elements in response to abiotic stress and conserved nature in evolution, indicating they could be promising candidates for further functional verification under multiple abiotic stresses. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08618-1.
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Huang F, Shi C, Zhang Y, Hou X. Genome-Wide Identification and Characterization of TCP Family Genes in Pak-Choi [ Brassica campestris (syn. Brassica rapa) ssp. chinensis var. communis]. FRONTIERS IN PLANT SCIENCE 2022; 13:854171. [PMID: 35615139 PMCID: PMC9125175 DOI: 10.3389/fpls.2022.854171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/17/2022] [Indexed: 06/15/2023]
Abstract
The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) gene family, a kind of plant specific transcription factor, is essential for stress response, cell growth, and cell proliferation. However, the characterization of TCP family is still not clear in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis var. communis]. In this study, genome-wide analysis of TCP gene family was performed and 26 TCP genes were identified in Pak-choi. Phylogenetic analysis demonstrated that the 26 BcTCPs were divided into two classes: Class I and Class II. Class II was further classified into two subclasses, CIN and CYC/TB1. The qPCR results suggested that most BcTCPs respond to abiotic stresses. The expressions of BcTCP3, BcTCP12, BcTCP21, and BcTCP22 were significantly changed under ABA and cold treatment. BcTCP3 and BcTCP12 were also up-regulated under osmotic treatment. Subcellular localization showed that BcTCP3 and BcTCP21 were located in the nucleus. Our results will facilitate revealing the functions and regulatory mechanisms of BcTCPs.
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Tang Y, Gao X, Cui Y, Xu H, Yu J. 植物TCP转录因子研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Nie YM, Han FX, Ma JJ, Chen X, Song YT, Niu SH, Wu HX. Genome-wide TCP transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in Pinus tabuliformis. BMC PLANT BIOLOGY 2022; 22:167. [PMID: 35366809 PMCID: PMC8976390 DOI: 10.1186/s12870-022-03554-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/23/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood. RESULTS In the present study, 43 TCP genes were identified from P. tabuliformis genome database. Based on the phylogeny tree and sequence similarity, the 43 TCP genes were classified into four groups. The motif results showed that different subfamilies indeed contained different motifs. Clade II genes contain motif 1, clade I genes contain motif 1, 8, 10 and clade III and IV contain more motifs, which is consistent with our grouping results. The structural analysis of PtTCP genes showed that most PtTCPs lacked introns. The distribution of clade I and clade II on the chromosome is relatively scattered, while clade III and clade IV is relatively concentrated. Co-expression network indicated that PtTCP2, PtTCP12, PtTCP36, PtTCP37, PtTCP38, PtTCP41 and PtTCP43 were co-expressed with clock genes in annual cycle and their annual cycle expression profiles both showed obvious seasonal oscillations. PtTCP2, PtTCP12, PtTCP37, PtTCP38, PtTCP40, PtTCP41, PtTCP42 and PtTCP43 were co-expressed with clock genes in diurnal cycle. Only the expression of PtTCP42 showed diurnal oscillation. CONCLUSIONS The TCP gene family, especially clade II, may play an important role in the regulation of the season and circadian rhythm of P. tabuliformis. In addition, the low temperature in winter may affect the diurnal oscillations.
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Affiliation(s)
- Yu-meng Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Fang-xu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Jing-jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Xi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Yi-tong Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Harry X. Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, SE-901 83 Umeå, Sweden
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Tian C, Zhai L, Zhu W, Qi X, Yu Z, Wang H, Chen F, Wang L, Chen S. Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance. PLANTS (BASEL, SWITZERLAND) 2022; 11:936. [PMID: 35406918 PMCID: PMC9002959 DOI: 10.3390/plants11070936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Plant-specific TCP transcription factors play a key role in plant development and stress responses. Chrysanthemum nankingense shows higher cold tolerance than its ornamental polyploid counterpart. However, whether the TCP gene family plays a role in conferring cold tolerance upon C. nankingense remains unknown. Here, we identified 23 CnTCP genes in C. nankingense, systematically analyzed their phylogenetic relationships and synteny with TCPs from other species, and evaluated their expression profiles at low temperature. Phylogenetic analysis of the protein sequences suggested that CnTCP proteins fall into two classes and three clades, with a typical bHLH domain. However, differences between C. nankingense and Arabidopsis in predicted protein structure and binding sites suggested a unique function of CnTCPs in C. nankingense. Furthermore, expression profiles showed that expression of most CnTCPs were downregulated under cold conditions, suggesting their importance in plant responses to cold stress. Notably, expression of miR319 and of its predicted target genes, CnTCP2/4/14, led to fast responses to cold. Overexpression of Arabidopsis CnTCP4 led to hypersensitivity to cold, suggesting that CnTCP4 might play a negative role in C. nankingense responses to cold stress. Our results provide a foundation for future functional genomic studies on this gene family in chrysanthemum.
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Affiliation(s)
- Chang Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lisheng Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Wenjing Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Xiangyu Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Zhongyu Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Likai Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (C.T.); (L.Z.); (W.Z.); (X.Q.); (Z.Y.); (H.W.); (F.C.)
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Wang S, Shen Y, Guo L, Tan L, Ye X, Yang Y, Zhao X, Nie Y, Deng D, Liu S, Wu W. Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication. FRONTIERS IN PLANT SCIENCE 2022; 13:850064. [PMID: 35356113 PMCID: PMC8959825 DOI: 10.3389/fpls.2022.850064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/27/2022] [Indexed: 05/25/2023]
Abstract
The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family proteins are plant-specific transcription factors that have been well-acknowledged for designing the architectures of plant branch, shoot, and inflorescence. However, evidence for their innovation and emerging role in abiotic stress has been lacking. In this study, we identified a total of 36 TCP genes in Populus trichocarpa, 50% more than that in Arabidopsis (i.e., 24). Comparative intra-genomes showed that such significant innovation was mainly due to the most recent whole genome duplication (rWGD) in Populus lineage around Cretaceous-Paleogene (K-Pg) boundary after the divergence from Arabidopsis. Transcriptome analysis showed that the expressions of PtrTCP genes varied among leaf, stem, and root, and they could also be elaborately regulated by abiotic stresses (e.g., cold and salt). Moreover, co-expression network identified a cold-associated regulatory module including PtrTCP31, PtrTCP10, and PtrTCP36. Of them, PtrTCP10 was rWGD-duplicated from PtrTCP31 and evolved a strong capability of cold induction, which might suggest a neofunctionalization of PtrTCP genes and contribute to the adaptation of Populus lineage during the Cenozoic global cooling. Evidentially, overexpression of PtrTCP10 into Arabidopsis increased freezing tolerance and salt susceptibility. Integrating co-expression network and cis-regulatory element analysis confirmed that PtrTCP10 can regulate the well-known cold- and salt-relevant genes (e.g., ZAT10, GolS2, and SOS1), proving that PtrTCP10 is an evolutionary innovation in P. trichocarpa response to environmental changes. Altogether, our results provide evidence of the rWGD in P. trichocarpa responsible for the innovation of PtrTCP genes and their emerging roles in environmental stresses.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yirong Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xiaoxue Ye
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yanmei Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yuqi Nie
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
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Wang S, Shen Y, Guo L, Tan L, Ye X, Yang Y, Zhao X, Nie Y, Deng D, Liu S, Wu W. Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication. FRONTIERS IN PLANT SCIENCE 2022; 13:850064. [PMID: 35356113 DOI: 10.3389/fpls.2022.850064if] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/27/2022] [Indexed: 06/05/2023]
Abstract
The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family proteins are plant-specific transcription factors that have been well-acknowledged for designing the architectures of plant branch, shoot, and inflorescence. However, evidence for their innovation and emerging role in abiotic stress has been lacking. In this study, we identified a total of 36 TCP genes in Populus trichocarpa, 50% more than that in Arabidopsis (i.e., 24). Comparative intra-genomes showed that such significant innovation was mainly due to the most recent whole genome duplication (rWGD) in Populus lineage around Cretaceous-Paleogene (K-Pg) boundary after the divergence from Arabidopsis. Transcriptome analysis showed that the expressions of PtrTCP genes varied among leaf, stem, and root, and they could also be elaborately regulated by abiotic stresses (e.g., cold and salt). Moreover, co-expression network identified a cold-associated regulatory module including PtrTCP31, PtrTCP10, and PtrTCP36. Of them, PtrTCP10 was rWGD-duplicated from PtrTCP31 and evolved a strong capability of cold induction, which might suggest a neofunctionalization of PtrTCP genes and contribute to the adaptation of Populus lineage during the Cenozoic global cooling. Evidentially, overexpression of PtrTCP10 into Arabidopsis increased freezing tolerance and salt susceptibility. Integrating co-expression network and cis-regulatory element analysis confirmed that PtrTCP10 can regulate the well-known cold- and salt-relevant genes (e.g., ZAT10, GolS2, and SOS1), proving that PtrTCP10 is an evolutionary innovation in P. trichocarpa response to environmental changes. Altogether, our results provide evidence of the rWGD in P. trichocarpa responsible for the innovation of PtrTCP genes and their emerging roles in environmental stresses.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yirong Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xiaoxue Ye
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yanmei Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yuqi Nie
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou, China
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Relaxed selection and the evolution of the chasmogamous flower of Impatiens capensis (Balsaminaceae). Evol Ecol 2022. [DOI: 10.1007/s10682-022-10155-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
Above-ground plant architecture is dictated to a large extent by the fates and growth rates of aerial plant meristems. Shoot apical meristem gives rise to the fundamental plant form by generating new leaves. However, the fates of axillary meristems located in leaf axils have a great influence on plant architecture and affect the harvest index, yield potential and cultural practices. Improving plant architecture by breeding facilitates denser plantations, better resource use efficiency and even mechanical harvesting. Knowledge of the genetic mechanisms regulating plant architecture is needed for precision breeding, especially for determining feasible breeding targets. Fortunately, research in many crop species has demonstrated that a relatively small number of genes has a large effect on axillary meristem fates. In this review, we select a number of important horticultural and agricultural plant species as examples of how changes in plant architecture affect the cultivation practices of the species. We focus specifically on the determination of the axillary meristem fate and review how plant architecture may change even drastically because of altered axillary meristem fate. We also explain what is known about the genetic and environmental control of plant architecture in these species, and how further changes in plant architectural traits could benefit the horticultural sector.
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43
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Sengupta A, Hileman LC. A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales. EvoDevo 2022; 13:3. [PMID: 35093179 PMCID: PMC8801154 DOI: 10.1186/s13227-021-00187-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/18/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND An outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype-Lamiales flower monosymmetry-defined by a developmental program that relies on regulatory interaction among CYCLOIDEA, RADIALIS, DIVARICATA, and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program. RESULTS We found that RADIALIS, DIVARICATA, and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. In addition, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog. CONCLUSION Our results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions.
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Affiliation(s)
- Aniket Sengupta
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.
- St. Albert Hall, 8000 Utopia Pkwy, Room 257, Queens, NY, 11439, USA.
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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Wang C, Hao X, Wang Y, Shi M, Zhou ZG, Kai G. Genome-Wide Identification and Comparative Analysis of the Teosinte Branched 1/Cycloidea/Proliferating Cell Factors 1/2 Transcription Factors Related to Anti-cancer Drug Camptothecin Biosynthesis in Ophiorrhiza pumila. FRONTIERS IN PLANT SCIENCE 2021; 12:746648. [PMID: 34691124 PMCID: PMC8529195 DOI: 10.3389/fpls.2021.746648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/09/2021] [Indexed: 05/27/2023]
Abstract
Ophiorrhiza pumila (O. pumila; Op) is a medicinal herbaceous plant, which can accumulate camptothecin (CPT). CPT and its derivatives are widely used as chemotherapeutic drugs for treating malignant tumors. Its biosynthesis pathway has been attracted significant attention. Teosinte branched 1/cycloidea/proliferating cell factors 1/2 (TCP) transcription factors (TFs) regulate a variety of physiological processes, while TCP TFs are involved in the regulation of CPT biosynthesis remain unclear. In this study, a systematic analysis of the TCP TFs family in O. pumila was performed. A total of 16 O. pumila TCP (OpTCP) genes were identified and categorized into two subgroups based on their phylogenetic relationships with those in Arabidopsis thaliana. Tissue-specific expression patterns revealed that nine OpTCP genes showed the highest expression levels in leaves, while the other seven OpTCPs showed a higher expression level in the stems. Co-expression, phylogeny analysis, and dual-luciferase (Dual-LUC) assay revealed that OpTCP15 potentially plays important role in CPT and its precursor biosynthesis. In addition, the subcellular localization experiment of candidate OpTCP genes showed that they are all localized in the nucleus. Our study lays a foundation for further functional characterization of the candidate OpTCP genes involved in CPT biosynthesis regulation and provides new strategies for increasing CPT production.
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Affiliation(s)
- Can Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, China
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaolong Hao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yao Wang
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Min Shi
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhi-Gang Zhou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Guoyin Kai
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
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Zhang L, Li C, Yang D, Wang Y, Yang Y, Sun X. Genome-Wide Analysis of the TCP Transcription Factor Genes in Dendrobium catenatum Lindl. Int J Mol Sci 2021; 22:ijms221910269. [PMID: 34638610 PMCID: PMC8508941 DOI: 10.3390/ijms221910269] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022] Open
Abstract
Teosinte branched1/cycloidea/proliferating cell factor (TCP) gene family members are plant-specific transcription factors that regulate plant growth and development by controlling cell proliferation and differentiation. However, there are no reported studies on the TCP gene family in Dendrobium catenatum Lindl. Here, a genome-wide analysis of TCP genes was performed in D. catenatum, and 25 TCP genes were identified. A phylogenetic analysis classified the family into two clades: Class I and Class II. Genes in the same clade share similar conserved motifs. The GFP signals of the DcaTCP-GFPs were detected in the nuclei of tobacco leaf epidermal cells. The activity of DcaTCP4, which contains the miR319a-binding sequence, was reduced when combined with miR319a. A transient activity assay revealed antagonistic functions of Class I and Class II of the TCP proteins in controlling leaf development through the jasmonate-signaling pathway. After different phytohormone treatments, the DcaTCP genes showed varied expression patterns. In particular, DcaTCP4 and DcaTCP9 showed opposite trends after 3 h treatment with jasmonate. This comprehensive analysis provides a foundation for further studies on the roles of TCP genes in D. catenatum.
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Affiliation(s)
- Li Zhang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Z.); (C.L.); (D.Y.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Li
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Z.); (C.L.); (D.Y.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Danni Yang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Z.); (C.L.); (D.Y.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhua Wang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Z.); (C.L.); (D.Y.); (Y.W.)
| | - Yongping Yang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Z.); (C.L.); (D.Y.); (Y.W.)
- Correspondence: (Y.Y.); (X.S.); Tel.: +86-871-65230873 (X.S.)
| | - Xudong Sun
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (L.Z.); (C.L.); (D.Y.); (Y.W.)
- Correspondence: (Y.Y.); (X.S.); Tel.: +86-871-65230873 (X.S.)
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Regional Heritability Mapping of Quantitative Trait Loci Controlling Traits Related to Growth and Productivity in Popcorn (Zea mays L.). PLANTS 2021; 10:plants10091845. [PMID: 34579378 PMCID: PMC8466968 DOI: 10.3390/plants10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/17/2022]
Abstract
The method of regional heritability mapping (RHM) has become an important tool in the identification of quantitative trait loci (QTLs) controlling traits of interest in plants. Here, RHM was first applied in a breeding population of popcorn, to identify the QTLs and candidate genes involved in grain yield, plant height, kernel popping expansion, and first ear height, as well as determining the heritability of each significant genomic region. The study population consisted of 98 S1 families derived from the 9th recurrent selection cycle (C-9) of the open-pollinated variety UENF-14, which were genetically evaluated in two environments (ENV1 and ENV2). Seventeen and five genomic regions were mapped by the RHM method in ENV1 and ENV2, respectively. Subsequent genome-wide analysis based on the reference genome B73 revealed associations with forty-six candidate genes within these genomic regions, some of them are considered to be biologically important due to the proteins that they encode. The results obtained by the RHM method have the potential to contribute to knowledge on the genetic architecture of the growth and yield traits of popcorn, which might be used for marker-assisted selection in breeding programs.
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Ren L, Wu H, Zhang T, Ge X, Wang T, Zhou W, Zhang L, Ma D, Wang A. Genome-Wide Identification of TCP Transcription Factors Family in Sweet Potato Reveals Significant Roles of miR319-Targeted TCPs in Leaf Anatomical Morphology. FRONTIERS IN PLANT SCIENCE 2021; 12:686698. [PMID: 34426735 PMCID: PMC8379018 DOI: 10.3389/fpls.2021.686698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/21/2021] [Indexed: 05/08/2023]
Abstract
Plant-specific TCP transcription factors play vital roles in the controlling of growth, development, and the stress response processes. Extensive researches have been carried out in numerous species, however, there hasn't been any information available about TCP genes in sweet potato (Ipomoea batatas L.). In this study, a genome-wide analysis of TCP genes was carried out to explore the evolution and function in sweet potato. Altogether, 18 IbTCPs were identified and cloned. The expression profiles of the IbTCPs differed dramatically in different organs or different stages of leaf development. Furthermore, four CIN-clade IbTCP genes contained miR319-binding sites. Blocking IbmiR319 significantly increased the expression level of IbTCP11/17 and resulted in a decreased photosynthetic rate due to the change in leaf submicroscopic structure, indicating the significance of IbmiR319-targeted IbTCPs in leaf anatomical morphology. A systematic analyzation on the characterization of the IbTCPs together with the primary functions in leaf anatomical morphology were conducted to afford a basis for further study of the IbmiR319/IbTCP module in association with leaf anatomical morphology in sweet potato.
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Affiliation(s)
- Lei Ren
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Haixia Wu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tingting Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xinyu Ge
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tianlong Wang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Wuyu Zhou
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Daifu Ma
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory for Biology and Genetic Breeding of Sweetpotato (Xuzhou), Ministry of Agriculture/Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, China
| | - Aimin Wang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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Li Y, An S, Cheng Q, Zong Y, Chen W, Guo W, Zhang L. Analysis of Evolution, Expression and Genetic Transformation of TCP Transcription Factors in Blueberry Reveal That VcTCP18 Negatively Regulates the Release of Flower Bud Dormancy. FRONTIERS IN PLANT SCIENCE 2021; 12:697609. [PMID: 34305986 PMCID: PMC8299413 DOI: 10.3389/fpls.2021.697609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/15/2021] [Indexed: 05/23/2023]
Abstract
Plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) transcription factors have versatile functions in plant growth, development and response to environmental stress. Despite blueberry's value as an important fruit crop, the TCP gene family has not been systematically studied in this plant. The current study identified blueberry TCP genes (VcTCPs) using genomic data from the tetraploid blueberry variety 'Draper'; a total of 62 genes were obtained. Using multiple sequence alignment, conserved motif, and gene structure analyses, family members were divided into two subfamilies, of which class II was further divided into two subclasses, CIN and TB1. Synteny analysis showed that genome-wide or segment-based replication played an important role in the expansion of the blueberry TCP gene family. The expression patterns of VcTCP genes during fruit development, flower bud dormancy release, hormone treatment, and tissue-specific expression were analyzed using RNA-seq and qRT-PCR. The results showed that the TB1 subclass members exhibited a certain level of expression in the shoot, leaf, and bud; these genes were not expressed during fruit development, but transcript levels decreased uniformly during the release of flower bud dormancy by low-temperature accumulation. The further transgenic experiments showed the overexpression of VcTCP18 in Arabidopsis significantly decreased the seed germination rate in contrast to the wild type. The bud dormancy phenomena as late-flowering, fewer rosettes and main branches were also observed in transgenic plants. Overall, this study provides the first insight into the evolution, expression, and function of VcTCP genes, including the discovery that VcTCP18 negatively regulated bud dormancy release in blueberry. The results will deepen our understanding of the function of TCPs in plant growth and development.
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Affiliation(s)
- Yongqiang Li
- Key Laboratory of Silviculture, Co-Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Shuang An
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Qiangqiang Cheng
- Key Laboratory of Silviculture, Co-Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Yu Zong
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Wenrong Chen
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Weidong Guo
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Lu Zhang
- Key Laboratory of Silviculture, Co-Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, China
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Wei X, Yang J, Lei D, Feng H, Yang Z, Wen G, He Z, Zeng W, Zou J. The SlTCP26 promoting lateral branches development in tomato. PLANT CELL REPORTS 2021; 40:1115-1126. [PMID: 33758995 DOI: 10.1007/s00299-021-02680-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
The SlTCP26 negatively regulated auxin signal to relieve the apical dominance and suppressed abscisic acid signal to remove the lateral bud dormancy, promoting lateral branches development. Lateral branches formation from lateral buds is a complex regulatory process in higher plants, and the interaction between transcription factors and hormones is indispensable during this process. TCP transcription factors have been reported to regulate lateral branches development, while the detailed function, especially interacting with auxin and ABA during this process, was still ambiguous in tomato. In this study, a branch regulatory gene, SlTCP26, was identified in tomato, and its role along with its interaction to hormones during branch development, as investigated. The results indicated that overexpression of SlTCP26 would promote lateral branches development, and could suppress the expressing of the genes associated with IAA signaling, presenting similar effects in decapitated plants. Conversely, the exogenous IAA application could inhibit the expression of SlTCP26. Furthermore, the expressing of the ABA signaling-related genes was inhibited in SlTCP26 overexpressed tomato, similar to that in decapitated tomato. Our findings suggested that SlTCP26 may be a crucial adjuster for synergistic action between ABA and IAA signals during the development of lateral branches, and it could promote the lateral buds grow into lateral shoots, via inhibiting IAA signal to relieve the apical dominance and suppressing ABA signal to remove the lateral bud dormancy. Our study provided some insights for the development of tomato lateral branches to understand the apical dominance regulatory network.
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Affiliation(s)
- Xiaoying Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Jun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Dou Lei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Hao Feng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zhenan Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Guoqin Wen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zhuoyuan He
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Wenjing Zeng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Jian Zou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China.
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50
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Ma Y, Xu D, Yan X, Wu Z, Kayani SI, Shen Q, Fu X, Xie L, Hao X, Hassani D, Li L, Liu H, Pan Q, Lv Z, Liu P, Sun X, Tang K. Jasmonate- and abscisic acid-activated AaGSW1-AaTCP15/AaORA transcriptional cascade promotes artemisinin biosynthesis in Artemisia annua. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1412-1428. [PMID: 33539631 PMCID: PMC8313134 DOI: 10.1111/pbi.13561] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 05/12/2023]
Abstract
Artemisinin, a sesquiterpene lactone widely used in malaria treatment, was discovered in the medicinal plant Artemisia annua. The biosynthesis of artemisinin is efficiently regulated by jasmonate (JA) and abscisic acid (ABA) via regulatory factors. However, the mechanisms linking JA and ABA signalling with artemisinin biosynthesis through an associated regulatory network of downstream transcription factors (TFs) remain enigmatic. Here we report AaTCP15, a JA and ABA dual-responsive teosinte branched1/cycloidea/proliferating (TCP) TF, which is essential for JA and ABA-induced artemisinin biosynthesis by directly binding to and activating the promoters of DBR2 and ALDH1, two genes encoding enzymes for artemisinin biosynthesis. Furthermore, AaORA, another positive regulator of artemisinin biosynthesis responds to JA and ABA, interacts with and enhances the transactivation activity of AaTCP15 and simultaneously activates AaTCP15 transcripts. Hence, they form an AaORA-AaTCP15 module to synergistically activate DBR2, a crucial gene for artemisinin biosynthesis. More importantly, AaTCP15 expression is activated by the multiple reported JA and ABA-responsive TFs that promote artemisinin biosynthesis. Among them, AaGSW1 acts at the nexus of JA and ABA signalling to activate the artemisinin biosynthetic pathway and directly binds to and activates the AaTCP15 promoter apart from the AaORA promoter, which further facilitates formation of the AaGSW1-AaTCP15/AaORA regulatory module to integrate JA and ABA-mediated artemisinin biosynthesis. Our results establish a multilayer regulatory network of the AaGSW1-AaTCP15/AaORA module to regulate artemisinin biosynthesis through JA and ABA signalling, and provide an interesting avenue for future research exploring the special transcriptional regulation module of TCP genes associated with specialized metabolites in plants.
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Affiliation(s)
- Ya‐Nan Ma
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Dong‐Bei Xu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
- Institute of Ecological AgricultureSichuan Agricultural UniversityChengduChina
| | - Xin Yan
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhang‐Kuanyu Wu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Sadaf Ilyas Kayani
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Qian Shen
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xue‐Qing Fu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Li‐Hui Xie
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xiao‐Long Hao
- Laboratory of Medicinal Plant BiotechnologyCollege of PharmacyZhejiang Chinese Medical UniversityHangzhouChina
| | - Danial Hassani
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ling Li
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hang Liu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Qi‐Fang Pan
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zong‐You Lv
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Pin Liu
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xiao‐Fen Sun
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ke‐Xuan Tang
- Joint International Research Laboratory of Metabolic and Developmental SciencesKey Laboratory of Urban Agriculture (South) Ministry of AgriculturePlant Biotechnology Research CenterFudan‐SJTU‐Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
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