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Xie C, Tian Q, Qiu H, Wang R, Wang L, Yue Y, Yang X. Methylation Modification in Ornamental Plants: Impact on Floral Aroma and Color. Int J Mol Sci 2024; 25:8267. [PMID: 39125834 PMCID: PMC11311783 DOI: 10.3390/ijms25158267] [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: 06/12/2024] [Revised: 07/24/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
Methylation represents a crucial class of modification that orchestrates a spectrum of regulatory roles in plants, impacting ornamental characteristics, growth, development, and responses to abiotic stress. The establishment and maintenance of methylation involve the coordinated actions of multiple regulatory factors. Methyltransferases play a pivotal role by specifically recognizing and methylating targeted sites, which induces alterations in chromatin structure and gene expression, subsequently influencing the release of volatile aromatic substances and the accumulation of pigments in plant petals. In this paper, we review the regulatory mechanisms of methylation modification reactions and their effects on the changes in aromatic substances and pigments in plant petals. We also explore the potential of methylation modifications to unravel the regulatory mechanisms underlying aroma and color in plant petals. This aims to further elucidate the synthesis, metabolism, and regulatory mechanisms of various methylation modifications related to the aroma and color substances in plant petals, thereby providing a theoretical reference for improving the aroma and color of plant petals.
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Affiliation(s)
- Chenchen Xie
- Key Laboratory of Landscape Architecture, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; (C.X.); (Q.T.); (H.Q.); (R.W.); (L.W.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qingyin Tian
- Key Laboratory of Landscape Architecture, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; (C.X.); (Q.T.); (H.Q.); (R.W.); (L.W.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hanruo Qiu
- Key Laboratory of Landscape Architecture, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; (C.X.); (Q.T.); (H.Q.); (R.W.); (L.W.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Rui Wang
- Key Laboratory of Landscape Architecture, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; (C.X.); (Q.T.); (H.Q.); (R.W.); (L.W.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Lianggui Wang
- Key Laboratory of Landscape Architecture, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; (C.X.); (Q.T.); (H.Q.); (R.W.); (L.W.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanzheng Yue
- Key Laboratory of Landscape Architecture, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; (C.X.); (Q.T.); (H.Q.); (R.W.); (L.W.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiulian Yang
- Key Laboratory of Landscape Architecture, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China; (C.X.); (Q.T.); (H.Q.); (R.W.); (L.W.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Jia Y, Yin X, Yang H, Xiang Y, Ding K, Pan Y, Jiang B, Yong X. Transcriptome Analyses Reveal the Aroma Terpeniods Biosynthesis Pathways of Primula forbesii Franch. and the Functional Characterization of the PfDXS2 Gene. Int J Mol Sci 2023; 24:12730. [PMID: 37628910 PMCID: PMC10454305 DOI: 10.3390/ijms241612730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Primula forbesii Franch. is a unique biennial herb with a strong floral fragrance, making it an excellent material for studying the aroma characteristics of the genus Primula. The floral scent is an important ornamental trait that facilitates fertilization. However, the molecular mechanism regulating the floral scent in Primula is unknown. In order to better understand the biological mechanisms of floral scents in this species, this study used RNA sequencing analysis to discuss the first transcriptome sequence of four flowering stages of P. forbesii, which generated 12 P. forbesii cDNA libraries with 79.64 Gb of clean data that formed 51,849 unigenes. Moreover, 53.26% of the unigenes were annotated using public databases. P. forbesii contained 44 candidate genes covering all known enzymatic steps for the biosynthesis of volatile terpenes, the major contributor to the flower's scent. Finally, 1-deoxy-d-xylulose 5-phosphate synthase gene of P. forbesii (PfDXS2, MK370094), the first key enzyme gene in the 2-c-methyl-d-erythritol 4-phosphate (MEP) pathway of terpenoids, was cloned and functionally verified using virus-induced gene silencing (VIGs). The results showed that PfDXS2-silencing significantly reduced the relative concentrations of main volatile terpenes. This report is the first to present molecular data related to aroma metabolites biosynthesis pathways and the functional characterization of any P. forbesii gene. The data on RNA sequencing provide comprehensive information for further analysis of other plants of the genus Primula.
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Affiliation(s)
- Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (H.Y.); (Y.X.); (K.D.); (Y.P.); (B.J.); (X.Y.)
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Li J, Li C, Deng Y, Wei H, Lu S. Characteristics of Salvia miltiorrhiza methylome and the regulatory mechanism of DNA methylation in tanshinone biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad114. [PMID: 37577393 PMCID: PMC10419789 DOI: 10.1093/hr/uhad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/21/2023] [Indexed: 08/15/2023]
Abstract
Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value. Its roots produce a group of diterpenoid lipophilic bioactive components, termed tanshinones. Biosynthesis and regulation of tanshinones has attracted widespread interest. However, the methylome of S. miltiorrhiza has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely unknown. Here we report single-base resolution DNA methylomes from roots and leaves. Comparative analysis revealed differential methylation patterns for CG, CHG, and CHH contexts and the association between DNA methylation and the expression of genes and small RNAs. Lowly methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in S. miltiorrhiza. DNA methylation variation analysis showed that CHH methylation contributed mostly to the difference. Go enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_root. Tanshinone biosynthesis-related enzyme genes, such as DXS2, CMK, IDI1, HMGR2, DXR, MDS, CYP76AH1, 2OGD25, and CYP71D373, were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in March. Consistently, gene expression was up-regulated in S. miltiorrhiza roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone production. It suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in S. miltiorrhiza through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.
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Affiliation(s)
- Jiang Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Caili Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yuxing Deng
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Shanfa Lu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution. Int J Mol Sci 2022; 23:ijms23158299. [PMID: 35955429 PMCID: PMC9368846 DOI: 10.3390/ijms23158299] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 01/06/2023] Open
Abstract
DNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation.
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