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Zhou H, Jiang M, Li J, Xu Y, Li C, Lu S. Genome-Wide Identification and Functional Analysis of Salvia miltiorrhiza MicroRNAs Reveal the Negative Regulatory Role of Smi-miR159a in Phenolic Acid Biosynthesis. Int J Mol Sci 2024; 25:5148. [PMID: 38791194 PMCID: PMC11121111 DOI: 10.3390/ijms25105148] [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: 03/29/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs in plants. They play critical functions in various biological processes during plant growth and development. Salvia miltiorrhiza is a well-known traditional Chinese medicinal plant with significant medicinal, economic, and academic values. In order to elucidate the role of miRNAs in S. miltiorrhiza, six small RNA libraries from mature roots, young roots, stems, mature leaves, young leaves and flowers of S. miltiorrhiza and one degradome library from mixed tissues were constructed. A total of 184 miRNA precursors, generating 137 known and 49 novel miRNAs, were genome-widely identified. The identified miRNAs were predicted to play diversified regulatory roles in plants through regulating 891 genes. qRT-PCR and 5' RLM-RACE assays validated the negative regulatory role of smi-miR159a in SmMYB62, SmMYB78, and SmMYB80. To elucidate the function of smi-miR159a in bioactive compound biosynthesis, smi-miR159a transgenic hairy roots were generated and analyzed. The results showed that overexpression of smi-miR159a caused a significant decrease in rosmarinic acid and salvianolic acid B contents. qRT-PCR analysis showed that the targets of smi-miR159a, including SmMYB62, SmMYB78, and SmMYB80, were significantly down-regulated, accompanied by the down-regulation of SmPAL1, SmC4H1, Sm4CL1, SmTAT1, SmTAT3, SmHPPR1, SmRAS, and SmCYP98A14 genes involved in phenolic acid biosynthesis. It suggests that smi-miR159a is a significant negative regulator of phenolic acid biosynthesis in S. miltiorrhiza.
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Affiliation(s)
- Hong Zhou
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- 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
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Maochang Jiang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- 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
| | - Jiang Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- 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
| | - Yayun Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- 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
| | - Caili Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- 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
| | - Shanfa Lu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (H.Z.); (M.J.); (J.L.); (Y.X.)
- 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
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Ren X, Lin C, Huang Y, Su T, Guo J, Yang L. Miltiradiene Production by Cytoplasmic Metabolic Engineering in Nicotiana benthamiana. Metabolites 2023; 13:1188. [PMID: 38132870 PMCID: PMC10745046 DOI: 10.3390/metabo13121188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Plant natural products are important sources of innovative drugs, but the extraction and isolation of medicinal natural products from plants is challenging as these compounds have complex structures that are difficult to synthesize chemically. Therefore, utilizing heterologous expression systems to produce medicinal natural products in plants is a novel, environmentally friendly, and sustainable method. In this study, Nicotiana benthamiana was used as the plant platform to successfully produce miltiradiene, the key intermediate of tanshinones, which are the bioactive constituents of the Chinese medicinal plant Salvia miltiorrhiza. The yield of miltiradiene was increased through cytoplasmic engineering strategies combined with the enhancement of isoprenoid precursors. Additionally, we discovered that overexpressing SmHMGR alone accelerated apoptosis in tobacco leaves. Due to the richer membrane systems and cofactors in tobacco compared to yeast, tobacco is more conducive to the expression of plant enzymes. Therefore, this study lays the foundation for dissecting the tanshinone biosynthetic pathway in tobacco, which is essential for subsequent research. Additionally, it highlights the potential of N. benthamiana as an alternative platform for the production of natural products in plants.
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Affiliation(s)
- Xiangxiang Ren
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (X.R.); (T.S.)
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (C.L.); (Y.H.)
| | - Chuhang Lin
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (C.L.); (Y.H.)
| | - Yanbo Huang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (C.L.); (Y.H.)
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (X.R.); (T.S.)
| | - Juan Guo
- State Key Laboratory of Dao-Di Herbs, Beijing 100700, China;
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (C.L.); (Y.H.)
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Zeeshan Ul Haq M, Yu J, Yao G, Yang H, Iqbal HA, Tahir H, Cui H, Liu Y, Wu Y. A Systematic Review on the Continuous Cropping Obstacles and Control Strategies in Medicinal Plants. Int J Mol Sci 2023; 24:12470. [PMID: 37569843 PMCID: PMC10419402 DOI: 10.3390/ijms241512470] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Continuous cropping (CC) is a common practice in agriculture, and usually causes serious economic losses due to soil degeneration, decreased crop yield and quality, and increased disease incidence, especially in medicinal plants. Continuous cropping obstacles (CCOs) are mainly due to changes in soil microbial communities, nutrient availability, and allelopathic effects. Recently, progressive studies have illustrated the molecular mechanisms of CCOs, and valid strategies to overcome them. Transcriptomic and metabolomics analyses revealed that identified DEGs (differently expressed genes) and metabolites involved in the response to CCOs are involved in various biological processes, including photosynthesis, carbon metabolism, secondary metabolite biosynthesis, and bioactive compounds. Soil improvement is an effective strategy to overcome this problem. Soil amendments can improve the microbial community by increasing the abundance of beneficial microorganisms, soil fertility, and nutrient availability. In this review, we sum up the recent status of the research on CCOs in medicinal plants, the combination of transcriptomic and metabolomics studies, and related control strategies, including uses of soil amendments, crop rotation, and intercropping. Finally, we propose future research trends for understanding CCOs, and strategies to overcome these obstacles and promote sustainable agriculture practices in medicinal plants.
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Affiliation(s)
| | | | | | | | | | | | | | - Ya Liu
- Sanya Nanfan Research Institute of Hainan University, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Yougen Wu
- Sanya Nanfan Research Institute of Hainan University, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
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Wang Y, Liu K, Zhou Y, Chen Y, Jin C, Hu Y. Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of Polygonatum odoratum. PLANTS (BASEL, SWITZERLAND) 2023; 12:943. [PMID: 36840290 PMCID: PMC9962977 DOI: 10.3390/plants12040943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Polygonatum odoratum (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root rot in CC. To better understand the phenolic acid biosynthesis of P. odoratum roots in response to CC, this study performed a combined microRNA (miRNA)-seq and RNA-seq analysis. The phenolic acid contents of the first cropping (FC) soil and CC soil were determined by HPLC analysis. The results showed that CC soils contained significantly higher levels of p-coumaric acid, phenylacetate, and caffeic acid than FC soil, except for cinnamic acid and sinapic acid. Transcriptome identification and miRNA sequencing revealed 15,788 differentially expressed genes (DEGs) and 142 differentially expressed miRNAs (DEMs) in roots from FC and CC plants. Among them, 28 DEGs and eight DEMs were involved in phenolic acid biosynthesis. Meanwhile, comparative transcriptome and microRNA-seq analysis demonstrated that eight miRNAs corresponding to five target DEGs related to phenolic acid synthesis were screened. Among them, ath-miR172a, ath-miR172c, novel_130, sbi-miR172f, and tcc-miR172d contributed to phenylalanine synthesis. Osa-miR528-5p and mtr-miR2673a were key miRNAs that regulate syringyl lignin biosynthesis. Nta-miR156f was closely related to the shikimate pathway. These results indicated that the key DEGs and DEMs involved in phenolic acid anabolism might play vital roles in phenolic acid secretion from roots of P. odoratum under the CC system. As a result of the study, we may have a better understanding of phenolic acid biosynthesis during CC of roots of P. odoratum.
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Affiliation(s)
- Yan Wang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha 410082, China
| | - Kaitai Liu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yunyun Zhou
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yong Chen
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Chenzhong Jin
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yihong Hu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
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Yan W, Cao S, Wu Y, Ye Z, Zhang C, Yao G, Yu J, Yang D, Zhang J. Integrated Analysis of Physiological, mRNA Sequencing, and miRNA Sequencing Data Reveals a Specific Mechanism for the Response to Continuous Cropping Obstacles in Pogostemon cablin Roots. FRONTIERS IN PLANT SCIENCE 2022; 13:853110. [PMID: 35432413 PMCID: PMC9010791 DOI: 10.3389/fpls.2022.853110] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/07/2022] [Indexed: 06/02/2023]
Abstract
Pogostemon cablin (patchouli) is a commercially important medicinal and industrial crop grown worldwide for its medicinal and aromatic properties. Patchoulol and pogostone, derived from the essential oil of patchouli, are considered valuable components in the cosmetic and pharmaceutical industries. Due to its high application value in the clinic and industry, the demand for patchouli is constantly growing. Unfortunately, patchouli cultivation has suffered due to severe continuous cropping obstacles, resulting in a significant decline in yield and quality. Moreover, the physiological and transcriptional changes in patchouli in response to continuous cropping obstacles remain unclear. This has greatly restricted the development of the patchouli industry. To explore the mechanism underlying the rapid response of patchouli roots to continuous cropping stress, integrated analysis of the transcriptome and miRNA profiles of patchouli roots under continuous and noncontinuous cropping conditions in different growth periods was conducted using RNA sequencing (RNA-seq) and miRNA-seq and complemented with physiological data. The physiological and biochemical results showed that continuous cropping significantly inhibited root growth, decreased root activity, and increased the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) and the levels of osmoregulators (malondialdehyde, soluble protein, soluble sugar, and proline). Subsequently, we found 4,238, 3,494, and 7,290 upregulated and 4,176, 3,202, and 8,599 downregulated differentially expressed genes (DEGs) in the three growth periods of continuously cropped patchouli, many of which were associated with primary carbon and nitrogen metabolism, defense responses, secondary metabolite biosynthesis, and transcription factors. Based on miRNA-seq, 927 known miRNAs and 130 novel miRNAs were identified, among which 67 differentially expressed miRNAs (DEMIs) belonging to 24 miRNA families were induced or repressed by continuous cropping. By combining transcriptome and miRNA profiling, we obtained 47 miRNA-target gene pairs, consisting of 18 DEMIs and 43 DEGs, that likely play important roles in the continuous cropping response of patchouli. The information provided in this study will contribute to clarifying the intricate mechanism underlying the patchouli response to continuous cropping obstacles. In addition, the candidate miRNAs and genes can provide a new strategy for breeding continuous cropping-tolerant patchouli.
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Pu C, Ge Y, Yang G, Zheng H, Guan W, Chao Z, Shen Y, Liu S, Chen M, Huang L. Arbuscular mycorrhizal fungi enhance disease resistance of Salvia miltiorrhiza to Fusarium wilt. FRONTIERS IN PLANT SCIENCE 2022; 13:975558. [PMID: 36531366 PMCID: PMC9753693 DOI: 10.3389/fpls.2022.975558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/20/2022] [Indexed: 05/04/2023]
Abstract
Salvia miltiorrhiza Bunge (Danshen in Chinese) is vulnerable to Fusarium wilt, which severely affects the quality of the crude drug. Mycorrhizal colonization enhances resistance to fungal pathogens in many plant species. In this study, pre-inoculation of S. miltiorrhiza with the arbuscular mycorrhizal fungi (AMF) Glomus versiforme significantly alleviated Fusarium wilt caused by Fusarium oxysporum. Mycorrhizal colonization protected S. miltiorrhiza from pathogen infection, thereby preventing a loss of biomass and photosynthesis. There were greater defense responses induced by pathogen infection in AMF pre-inoculated plants than those in non-treated plants. AMF pre-inoculation resulted in systemic responses upon pathogen inoculation, including significant increases in the protein content and activities of phenylalanine ammonia-lyase (PAL), chitinase, and β-1,3-glucanase in S. miltiorrhiza roots. In addition, mycorrhizal pre-inoculation caused upregulation of defense-related genes, and jasmonic acid (JA) and salicylic acid (SA) signaling pathway genes after pathogen infection. The above findings indicate that mycorrhizal colonization enhances S. miltiorrhiza resistance against F. oxysporum infection by enhancing photosynthesis, root structure, and inducing the expression of defense enzymes and defense-related genes on the other hand.
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Affiliation(s)
- Chunjuan Pu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yang Ge
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guang Yang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Han Zheng
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Guan
- State Key Laboratory for Biology of Plant Diseases and Insert Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Ye Shen
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sha Liu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Meilan Chen
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Meilan Chen, ; Luqi Huang,
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Meilan Chen, ; Luqi Huang,
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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Jiang M, Chen H, Liu J, Du Q, Lu S, Liu C. Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza. Sci Rep 2021; 11:4769. [PMID: 33637790 PMCID: PMC7910453 DOI: 10.1038/s41598-021-83520-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/29/2021] [Indexed: 01/01/2023] Open
Abstract
Salvia miltiorrhiza is one of the most widely used traditional medicines. Natural antisense transcripts (NATs) are a class of long noncoding RNAs that can regulate gene expression. Here, we identified 812 NATs, including 168 cis-NATs and 644 trans-NATs from twelve root, flower, and leaf samples of S. miltiorrhiza using RNA-seq. The expression profiles for 41 of 50 NATs and their sense transcripts (STs) obtained from RNA-Seq were validated using qRT-PCR. The expression profiles of 17 NATs positively correlated with their STs. GO and KEGG pathway analyses mapped the STs for cis-NATs to pathways for biosynthesis of secondary metabolites. We characterized four NATs in detail, including NAT0001, NAT0002, NAT0004, and NAT00023. Their STs are kaurene synthase-like 1 and the homologs of UDP-glucose flavonoid 3-O-glucosyltransferase 6, UDP-glycosyltransferase 90A1, and beta-glucosidase 40, respectively. The first gene is involved in the biosynthesis of bioactive tanshinones, the next two are involved in anthocyanin biosynthesis, whereas the last is involved in phenylpropanoid biosynthesis. Besides, we found seven STs that are potential targets of miRNAs. And we found two miRNAs including miR156a and miR7208, might originate from NATs, NAT0112 and NAT0086. The results suggest that S. miltiorrhiza NATs might interact with STs, produce miRNAs, and be regulated by miRNAs. They potentially play significant regulatory roles in the biosynthesis of bioactive compounds.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Qing Du
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.,College of Pharmacy, Key Laboratory of Plant Resources of Qinghai-Tibet Plateau in Chemical Research, Qinghai Nationalities University, Xining, 810007, Qinghai, People's Republic of China
| | - Shanfa Lu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
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Zheng X, Li H, Chen M, Zhang J, Tan R, Zhao S, Wang Z. smi-miR396b targeted SmGRFs, SmHDT1, and SmMYB37/4 synergistically regulates cell growth and active ingredient accumulation in Salvia miltiorrhiza hairy roots. PLANT CELL REPORTS 2020; 39:1263-1283. [PMID: 32607753 DOI: 10.1007/s00299-020-02562-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
MIR396b had been cloned and overexpressed in Salvia miltiorrhiza hairy roots. MiR396b targets SmGRFs, SmHDT1, and SmMYB37/4 to regulate cell growth and secondary metabolism in S. miltiorrhiza hairy roots. Danshen (Salvia miltiorrhiza Bunge) is a valuable medicinal herb with two kinds of clinically used natural products, salvianolic acids and tanshinones. miR396 is a conserved microRNA and plays extensive roles in plants. However, it is still unclear how miR396 works in S. miltiorrhiza. In this study, an smi-MIR396b has been cloned from S. miltiorrhiza. Overexpression of miR396b in danshen hairy roots inhibited hairy root growth, reduced salvianolic acid concentration, but enhanced tanshinone accumulation, resulting in the biomass and total salvianolic acids respectively reduced to 55.5 and 72.1% of the control and total tanshinones increased up to 1.91-fold of the control. Applied degradome sequencing, 5'RLM-RACE, and qRT-PCR, 13 targets for miR396b were identified including seven conserved SmGRF1-7 and six novel ones. Comparative transcriptomics and microRNomics analysis together with qRT-PCR results confirmed that miR396b targets SmGRFs, SmHDT1, and SmMYB37/4 to mediate the phytohormone, especially gibberellin signaling pathways and consequentially resulted in the phenotype variation of miR396b-OE hairy roots. Furthermore, miR396b could be activated by methyl jasmonate, abscisic acid, gibberellin, salt, and drought stresses. The findings in this study indicated that smi-miR396b acts as an upstream and central regulator in cell growth and the biosynthesis of tanshinones and salvianolic acids, shedding light on the coordinated regulation of plant growth and biosynthesis of active ingredients in S. miltiorrhiza.
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Affiliation(s)
- Xiaoyu Zheng
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Hang Li
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Min Chen
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Jinjia Zhang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Ronghui Tan
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China.
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China.
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10
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Zhao T, Xu X, Wang M, Li C, Li C, Zhao R, Zhu S, He Q, Chen J. Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application. BMC Genomics 2019; 20:421. [PMID: 31138116 PMCID: PMC6537205 DOI: 10.1186/s12864-019-5760-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 05/02/2019] [Indexed: 12/18/2022] Open
Abstract
Background Cotton is the most essential textile crop worldwide, and phytohormones are critical for cotton fiber development. One example is the role of auxin in fiber initiation, but we know little molecular basis. MicroRNAs (miRNAs) have a significant function in cotton development; nevertheless their role in fiber initiation remains unclear. Here, exogenous IAA was applied to cotton plant before anthesis. Utilizing small RNA sequencing, the mechanism underlying miRNA-mediated regulation of fiber initiation under exogenous IAA treatment was investigated. Results With exogenous IAA application, the endogenous IAA and GA contents of IAA treated (IT) ovules were higher than control (CK) ovules at the fiber initiation stage, while endogenous ABA content was lower in IT than CK. Using scanning electron microscopy, we found the fiber number and size were significantly promoted in IT at 0 DPA. Fiber quality analysis showed that fiber length, uniformity, strength, elongation, and micronaire of IT were higher than CK, though not statistically significant, while lint percent was significantly higher in IT. We generated six small RNA libraries using − 3, 0, and 3 DPA ovules of IT and CK, and identified 58 known miRNAs and 83 novel miRNAs together with the target genes. The differential expressed miRNAs number between IT and CK at − 3, 0, 3 DPA was 34, 16 and 24, respectively. Gene ontology and KEGG pathway enrichment analyses for the target genes of the miRNAs expressed in a differential manner showed that they were significantly enriched in 30 terms and 8 pathways. QRT-PCR for those identified miRNAs and the target genes related to phytohormones and fiber development was performed, and results suggested a potential role of these miRNAs in fiber initiation. Conclusions The exogenous IAA application affected the relative phytohormone contents in ovule and promoted fiber initiation in cotton. Identification and profiling of miRNAs and their targets at the fiber initiation stage provided insights for miRNAs’ regulation function of fiber initiation. These findings not only shed light on the regulatory network of fiber growth but also offer clues for cotton fiber amelioration strategies in cotton. Electronic supplementary material The online version of this article (10.1186/s12864-019-5760-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianlun Zhao
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Xiaojian Xu
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Min Wang
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Cheng Li
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Cong Li
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Rubing Zhao
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Shuijin Zhu
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Qiuling He
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, Zhejiang Sci-Tech University, Zhejiang, 310018, Hangzhou, China.
| | - Jinhong Chen
- Department of Agronomy, Zhejiang University, Zhejiang, 310058, Hangzhou, China.
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11
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Li J, Li C, Lu S. Systematic analysis of DEMETER-like DNA glycosylase genes shows lineage-specific Smi-miR7972 involved in SmDML1 regulation in Salvia miltiorrhiza. Sci Rep 2018; 8:7143. [PMID: 29739980 PMCID: PMC5940787 DOI: 10.1038/s41598-018-25315-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/09/2018] [Indexed: 11/09/2022] Open
Abstract
DEMETER-like DNA glycosylases (DMLs) initiate the base excision repair-dependent DNA demethylation to regulate a wide range of biological processes in plants. Six putative SmDML genes, termed SmDML1-SmDML6, were identified from the genome of S. miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies. Integrated analysis of gene structures, sequence features, conserved domains and motifs, phylogenetic analysis and differential expression showed the conservation and divergence of SmDMLs. SmDML1, SmDML2 and SmDML4 were significantly down-regulated by the treatment of 5Aza-dC, a general DNA methylation inhibitor, suggesting involvement of SmDMLs in genome DNA methylation change. SmDML1 was predicted and experimentally validated to be target of Smi-miR7972. Computational analysis of forty whole genome sequences and almost all of RNA-seq data from Lamiids revealed that MIR7972s were only distributed in some plants of the three orders, including Lamiales, Solanales and Boraginales, and the number of MIR7972 genes varied among species. It suggests that MIR7972 genes underwent expansion and loss during the evolution of some Lamiids species. Phylogenetic analysis of MIR7972s showed closer evolutionary relationships between MIR7972s in Boraginales and Solanales in comparison with Lamiales. These results provide a valuable resource for elucidating DNA demethylation mechanism in S. miltiorrhiza.
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Affiliation(s)
- Jiang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151 Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151 Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151 Malianwa North Road, Haidian District, Beijing, 100193, China.
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12
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Li C, Li D, Li J, Shao F, Lu S. Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza. Sci Rep 2017; 7:44622. [PMID: 28304398 PMCID: PMC5356337 DOI: 10.1038/srep44622] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/10/2017] [Indexed: 12/11/2022] Open
Abstract
Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes. Expression patterns of eighteen SmPPOs were significantly altered under MeJA treatment, and twelve were yeast extract and Ag+-responsive, suggesting the majority of SmPPOs are stress-responsive. Analysis of high-throughput small RNA sequences and degradome data showed that miR1444-mediated regulation of PPOs existing in P. trichocarpa is absent from S. miltiorrhiza. Instead, a subset of SmPPOs was posttranscriptionally regulated by a novel miRNA, termed Smi-miR12112. It indicates the specificity and significance of miRNA-mediated regulation of PPOs. The results shed light on the regulation of SmPPO expression and suggest the complexity of SmPPO-associated phenolic acid biosynthesis and metabolism.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Dongqiao Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jiang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Fenjuan Shao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
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