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Dong J, Zhao X, Song X, Wang S, Zhao X, Liang B, Long Y, Xing Z. Identification of Eleutherococcus senticosus NAC transcription factors and their mechanisms in mediating DNA methylation of EsFPS, EsSS, and EsSE promoters to regulate saponin synthesis. BMC Genomics 2024; 25:536. [PMID: 38816704 PMCID: PMC11140872 DOI: 10.1186/s12864-024-10442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND The formation of pharmacologically active components in medicinal plants is significantly impacted by DNA methylation. However, the exact mechanisms through which DNA methylation regulates secondary metabolism remain incompletely understood. Research in model species has demonstrated that DNA methylation at the transcription factor binding site within functional gene promoters can impact the binding of transcription factors to target DNA, subsequently influencing gene expression. These findings suggest that the interaction between transcription factors and target DNA could be a significant mechanism through which DNA methylation regulates secondary metabolism in medicinal plants. RESULTS This research conducted a comprehensive analysis of the NAC family in E. senticosus, encompassing genome-wide characterization and functional analysis. A total of 117 EsNAC genes were identified and phylogenetically divided into 15 subfamilies. Tandem duplications and chromosome segment duplications were found to be the primary replication modes of these genes. Motif 2 was identified as the core conserved motif of the genes, and the cis-acting elements, gene structures, and expression patterns of each EsNAC gene were different. EsJUB1, EsNAC047, EsNAC098, and EsNAC005 were significantly associated with the DNA methylation ratio in E. senticosus. These four genes were located in the nucleus or cytoplasm and exhibited transcriptional self-activation activity. DNA methylation in EsFPS, EsSS, and EsSE promoters significantly reduced their activity. The methyl groups added to cytosine directly hindered the binding of the promoters to EsJUB1, EsNAC047, EsNAC098, and EsNAC005 and altered the expression of EsFPS, EsSS, and EsSE genes, eventually leading to changes in saponin synthesis in E. senticosus. CONCLUSIONS NAC transcription factors that are hindered from binding by methylated DNA are found in E. senticosus. The incapacity of these NACs to bind to the promoter of the methylated saponin synthase gene leads to subsequent alterations in gene expression and saponin synthesis. This research is the initial evidence showcasing the involvement of EsNAC in governing the impact of DNA methylation on saponin production in E. senticosus.
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Affiliation(s)
- Jing Dong
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xuelei Zhao
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xin Song
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Shuo Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xueying Zhao
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Baoxiang Liang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yuehong Long
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
| | - Zhaobin Xing
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
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Cao X, Guo Z, Wang P, Lu S, Li W, Ma Z, Mao J, Chen B. MdbZIP44-MdCPRF2-like- Mdα-GP2 regulate starch and sugar metabolism in apple under nitrogen supply. HORTICULTURE RESEARCH 2024; 11:uhae072. [PMID: 38725457 PMCID: PMC11079487 DOI: 10.1093/hr/uhae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 05/12/2024]
Abstract
Nitrogen (N) is regarded as an essential macronutrient and is tightly associated with carbon (C) metabolism in plants. The transcriptome data obtained from this study showed that the expression level of the apple basic leucine zipper (bZIP) transcription factor (TF) MdbZIP44 was up-regulated in 'Oregon Spur Delicious' (Malus domestica Borkh.) apple fruits under nitrogen supply. MdbZIP44 bound to the promoter of Mdα-GP2 gene and inhibited its expression, thereby promoting starch accumulation and decreasing glucose content in apple and tomato fruits. Besides, overexpression of MdbZIP44 promoted sucrose accumulation by regulating the activities of sucrose metabolism-related enzymes and the expression of sugar metabolism-related genes in apple callus and tomato fruits. Furthermore, biochemical assays indicated that MdbZIP44 directly interacted with MdCPRF2-like, another bZIP gene in apple. Meanwhile, this study found that MdCPRF2-like, along with the MdbZIP44 and MdCPRF2-like complex, could activate the expression of Mdα-GP2, respectively. In conclusion, this study provides a new reference for potential mechanisms underlying that MdbZIP44-MdCPRF2-like-Mdα-GP2 regulates starch and sugar metabolism under nitrogen supply.
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Affiliation(s)
- Xuejing Cao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhigang Guo
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui 741000, China
| | - Ping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenfang Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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Wang S, Zhao X, Li C, Dong J, Ma J, Long Y, Xing Z. DNA methylation regulates the secondary metabolism of saponins to improve the adaptability of Eleutherococcus senticosus during drought stress. BMC Genomics 2024; 25:330. [PMID: 38565995 PMCID: PMC10986080 DOI: 10.1186/s12864-024-10237-x] [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: 12/18/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Plant growth and development can be significantly impacted by drought stress. Plants will adjust the synthesis and accumulation of secondary metabolites to improve survival in times of water constraint. Simultaneously, drought stress can lead to modifications in the DNA methylation status of plants, and these modifications can directly impact gene expression and product synthesis by changing the DNA methylation status of functional genes involved in secondary metabolite synthesis. However, further research is needed to fully understand the extent to which DNA methylation modifies the content of secondary metabolites to mediate plants' responses to drought stress, as well as the underlying mechanisms involved. Our study found that in Eleutherococcus senticosus (E. senticosus), moderate water deprivation significantly decreased DNA methylation levels throughout the genome and at the promoters of EsFPS, EsSS, and EsSE. Transcription factors like EsMYB-r1, previously inhibited by DNA methylation, can re-bind to the EsFPS promotor region following DNA demethylation. This process promotes gene expression and, ultimately, saponin synthesis and accumulation. The increased saponin levels in E. senticosus acted as antioxidants, enhancing the plant's adaptability to drought stress.
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Affiliation(s)
- Shuo Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - XueLei Zhao
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Chang Li
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jing Dong
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - JiaCheng Ma
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - YueHong Long
- College of Life Sciences, North China University of Science and Technology, Tangshan, China.
| | - ZhaoBin Xing
- College of Life Sciences, North China University of Science and Technology, Tangshan, China.
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Cao Y, Mei Y, Zhang R, Zhong Z, Yang X, Xu C, Chen K, Li X. Transcriptional regulation of flavonol biosynthesis in plants. HORTICULTURE RESEARCH 2024; 11:uhae043. [PMID: 38623072 PMCID: PMC11017525 DOI: 10.1093/hr/uhae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 02/02/2024] [Indexed: 04/17/2024]
Abstract
Flavonols are a class of flavonoids that play a crucial role in regulating plant growth and promoting stress resistance. They are also important dietary components in horticultural crops due to their benefits for human health. In past decades, research on the transcriptional regulation of flavonol biosynthesis in plants has increased rapidly. This review summarizes recent progress in flavonol-specific transcriptional regulation in plants, encompassing characterization of different categories of transcription factors (TFs) and microRNAs as well as elucidation of different transcriptional mechanisms, including direct and cascade transcriptional regulation. Direct transcriptional regulation involves TFs, such as MYB, AP2/ERF, and WRKY, which can directly target the key flavonol synthase gene or other early genes in flavonoid biosynthesis. In addition, different regulation modules in cascade transcriptional regulation involve microRNAs targeting TFs, regulation between activators, interaction between activators and repressors, and degradation of activators or repressors induced by UV-B light or plant hormones. Such sophisticated regulation of the flavonol biosynthetic pathway in response to UV-B radiation or hormones may allow plants to fine-tune flavonol homeostasis, thereby balancing plant growth and stress responses in a timely manner. Based on orchestrated regulation, molecular design strategies will be applied to breed horticultural crops with excellent health-promoting effects and high resistance.
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Affiliation(s)
- Yunlin Cao
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Hangzhou, 310058, China
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China
| | - Yuyang Mei
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Hangzhou, 310058, China
| | - Ruining Zhang
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Hangzhou, 310058, China
| | - Zelong Zhong
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaochun Yang
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China
| | - Changjie Xu
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Hangzhou, 310058, China
| | - Kunsong Chen
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Hangzhou, 310058, China
| | - Xian Li
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Manipulation, Zhejiang University, Hangzhou, 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China
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Kan J, Yuan N, Lin J, Li H, Yang Q, Wang Z, Shen Z, Ying Y, Li X, Cao F. Seed Germination and Growth Improvement for Early Maturing Pear Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:4120. [PMID: 38140447 PMCID: PMC10747775 DOI: 10.3390/plants12244120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
Breeding early maturing cultivars is one of the most important objectives in pear breeding. Very early maturing pears provide an excellent parental material for crossing, but the immature embryo and low seed germination of their hybrid progenies often limit the selection and breeding of new early maturing pear cultivars. In this study, we choose a very early maturing pear cultivar 'Pearl Pear' as the study object and investigate the effects of cold stratification, the culture medium, and the seed coat on the germination and growth of early maturing pear seeds. Our results show that cold stratification (4 °C) treatment could significantly improve the germination rates of early maturing pear seeds. A total of 100 days of cold-temperature treatment in 4 °C and in vitro germination on White medium increased the germination rate to 84.54%. We also observed that seed coat removal improved the germination of early maturing pear seeds, with middle seed coat removal representing the optimal method, with a high germination rate and low contamination. The results of our study led to the establishment of an improved protocol for the germination of early maturing pear, which will greatly facilitate the breeding of new very early maturing pear cultivars.
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Affiliation(s)
- Jialiang Kan
- Institute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.K.); (N.Y.); (J.L.); (H.L.); (Q.Y.); (Z.W.); (Z.S.)
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
| | - Na Yuan
- Institute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.K.); (N.Y.); (J.L.); (H.L.); (Q.Y.); (Z.W.); (Z.S.)
| | - Jing Lin
- Institute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.K.); (N.Y.); (J.L.); (H.L.); (Q.Y.); (Z.W.); (Z.S.)
| | - Hui Li
- Institute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.K.); (N.Y.); (J.L.); (H.L.); (Q.Y.); (Z.W.); (Z.S.)
| | - Qingsong Yang
- Institute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.K.); (N.Y.); (J.L.); (H.L.); (Q.Y.); (Z.W.); (Z.S.)
| | - Zhonghua Wang
- Institute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.K.); (N.Y.); (J.L.); (H.L.); (Q.Y.); (Z.W.); (Z.S.)
| | - Zhijun Shen
- Institute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.K.); (N.Y.); (J.L.); (H.L.); (Q.Y.); (Z.W.); (Z.S.)
| | - Yeqing Ying
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
| | - Xiaogang Li
- Institute of Pomology, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.K.); (N.Y.); (J.L.); (H.L.); (Q.Y.); (Z.W.); (Z.S.)
| | - Fuliang Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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