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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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Yu S, Li J, Peng T, Ni S, Feng Y, Wang Q, Wang M, Chu X, Fan Z, Li X, Yin H, Ge W, Liu W. Identification of Chalcone Isomerase Family Genes and Roles of CnCHI4 in Flavonoid Metabolism in Camellia nitidissima. Biomolecules 2022; 13:biom13010041. [PMID: 36671426 PMCID: PMC9855375 DOI: 10.3390/biom13010041] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Camellia nitidissima is a woody plant with high ornamental value, and its golden-yellow flowers are rich in a variety of bioactive substances, especially flavonoids, that are beneficial to human health. Chalcone isomerases (CHIs) are key enzymes in the flavonoid biosynthesis pathway; however, there is a scarcity of information regarding the CHI family genes of C. nitidissima. In this study, seven CHI genes of C. nitidissima were identified and divided into three subfamilies by phylogenetic analysis. The results of multiple sequence alignment revealed that, unlike CnCHI1/5/6/7, CnCHI2/3/4 are bona fide CHIs that contain all the active site and critical catalytic residues. Analysis of the expression patterns of CnCHIs and the total flavonoid content of the flowers at different developmental stages revealed that CnCHI4 might play an essential role in the flavonoid biosynthesis pathway of C. nitidissima. CnCHI4 overexpression significantly increased flavonoid production in Nicotiana tabacum and C. nitidissima. The results of the dual-luciferase reporter assay and yeast one-hybrid system revealed that CnMYB7 was the key transcription factor that governed the transcription of CnCHI4. The study provides a comprehensive understanding of the CHI family genes of C. nitidissima and performed a preliminary analysis of their functions and regulatory mechanisms.
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Affiliation(s)
- Suhang Yu
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- School of Marine Sciences, Ningbo University, Ningbo 315800, China
- Jinhua Moxian Horticultural Engineering Co., Ltd., Jinhua 321000, China
| | - Jiyuan Li
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Jinhua Moxian Horticultural Engineering Co., Ltd., Jinhua 321000, China
| | - Ting Peng
- College of Agriculture, Guizhou University, Guiyang 550525, China
| | - Sui Ni
- School of Marine Sciences, Ningbo University, Ningbo 315800, China
| | - Yi Feng
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Qiushi Wang
- Changchun GeneScience Pharmaceuticals Co., Ltd., Changchun 130103, China
| | - Minyan Wang
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xian Chu
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhengqi Fan
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Jinhua Moxian Horticultural Engineering Co., Ltd., Jinhua 321000, China
| | - Xinlei Li
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Hengfu Yin
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Wanchuan Ge
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Weixin Liu
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Correspondence:
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Identification of a major-effect QTL associated with pre-harvest sprouting in cucumber (Cucumis sativus L.) using the QTL-seq method. BMC Genomics 2021; 22:249. [PMID: 33827431 PMCID: PMC8028694 DOI: 10.1186/s12864-021-07548-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
Background Cucumber (Cucumis sativus L.) is cultivated worldwide, and it is essential to produce enough high-quality seeds to meet demand. Pre-harvest sprouting (PHS) in cucumber is a critical problem and causes serious damage to seed production and quality. Nevertheless, the genetic basis and molecular mechanisms underlying cucumber PHS remain unclear. QTL-seq is an efficient approach for rapid quantitative trait loci (QTL) identification that simultaneously takes advantage of bulked-segregant analysis (BSA) and whole-genome resequencing. In the present research, QTL-seq analysis was performed to identify QTLs associated with PHS in cucumber using an F2 segregating population. Results Two QTLs that spanned 7.3 Mb on Chromosome 4 and 0.15 Mb on Chromosome 5 were identified by QTL-seq and named qPHS4.1 and qPHS5.1, respectively. Subsequently, SNP and InDel markers selected from the candidate regions were used to refine the intervals using the extended F2 populations grown in the 2016 and 2017 seasons. Finally, qPHS4.1 was narrowed to 0.53 Mb on chromosome 4 flanked by the markers SNP-16 and SNP-24 and was found to explain 19–22% of the phenotypic variation in cucumber PHS. These results reveal that qPHS4.1 is a major-effect QTL associated with PHS in cucumber. Based on gene annotations and qRT-PCR expression analyses, Csa4G622760 and Csa4G622800 were proposed as the candidate genes. Conclusions These results provide novel insights into the genetic mechanism controlling PHS in cucumber and highlight the potential for marker-assisted selection of PHS resistance breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07548-8.
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