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Zhao Y, Yao Y, Li H, Han Z, Ma X. Integrated transcriptome and metabolism unravel critical roles of carbon metabolism and oxidoreductase in mushroom with Korshinsk peashrub substrates. BMC Genomics 2024; 25:763. [PMID: 39107700 PMCID: PMC11302058 DOI: 10.1186/s12864-024-10666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Edible fungi cultivation serves as an efficient biological approach to transforming agroforestry byproducts, particularly Korshinsk peashrub (KP) branches into valuable mushroom (Lentinus edodes) products. Despite the widespread use of KP, the molecular mechanisms underlying its regulation of mushroom development remain largely unknown. In this study, we conducted a combined analysis of transcriptome and metabolism of mushroom fruiting bodies cultivated on KP substrates compared to those on apple wood sawdust (AWS) substrate. Our aim was to identify key metabolic pathways and genes that respond to the effects of KP substrates on mushrooms. The results revealed that KP induced at least a 1.5-fold increase in protein and fat content relative to AWS, with 15% increase in polysaccharide and total sugar content in mushroom fruiting bodies. There are 1196 differentially expressed genes (DEGs) between mushrooms treated with KP relative to AWS. Bioinformatic analysis show significant enrichments in amino acid metabolic process, oxidase activity, malic enzyme activity and carbon metabolism among the 698 up-regulated DEGs induced by KP against AWS. Additionally, pathways associated with organic acid transport and methane metabolism were significantly enriched among the 498 down-regulated DEGs. Metabolomic analysis identified 439 differentially abundant metabolites (DAMs) in mushrooms treated with KP compared to AWS. Consistent with the transcriptome data, KEGG analysis on metabolomic dataset suggested significant enrichments in carbon metabolism, alanine, aspartate and glutamate metabolism among the up-regulated DAMs by KP. In particular, some DAMs were enhanced by 1.5-fold, including D-glutamine, L-glutamate, glucose and pyruvate in mushroom samples treated with KP relative to AWS. Targeted metabolomic analysis confirmed the contents of DAMs related to glutamate metabolism and energy metabolism. In conclusion, our findings suggest that reprogrammed carbon metabolism and oxidoreductase pathways act critical roles in the enhanced response of mushroom to KP substrates.
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Affiliation(s)
- Yuan Zhao
- Qinghai University, Xining, 810016, China.
- College of Ecol-Environmental Engineering, Qinghai University, Xining, 810016, China.
| | - Youhua Yao
- Qinghai University, Xining, 810016, China
- Academy of Agriculture and Forestry, Qinghai University, Xining, 810016, China
- Qinghai Key Laboratory of Genetic Breeding of Highland Barley/Qinghai Highland Barley Sub- Center of National Wheat Improvement Center, Xining, 810016, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, 810016, China
| | - Hongying Li
- Qinghai University, Xining, 810016, China
- College of Ecol-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Zirui Han
- Qinghai University, Xining, 810016, China
- College of Ecol-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Xuewen Ma
- Qinghai University, Xining, 810016, China
- College of Ecol-Environmental Engineering, Qinghai University, Xining, 810016, China
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Chen C, Wang P, Yan Y, Jiao Z, Xie S, Li Y, Di P. Integrated metabolome and transcriptome analysis provide insight into the biosynthesis of flavonoids in Panax japonicus. FRONTIERS IN PLANT SCIENCE 2024; 15:1432563. [PMID: 39135647 PMCID: PMC11317393 DOI: 10.3389/fpls.2024.1432563] [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: 05/14/2024] [Accepted: 07/01/2024] [Indexed: 08/15/2024]
Abstract
Panax japonicus is an important medicinal plant, and flavonoids are one of its main secondary metabolites. In this study, the main roots, fibrous roots, stems, leaves and flowers of P. japonicus were analyzed using transcriptomics and widely targeted metabolomics. Through correlation analysis of transcription and metabolism, the flavonoid biosynthesis pathway in P. japonicus was analyzed, and the accumulation of flavonoid metabolites and the expression of related genes were investigated. Metabolomics revealed a total of 209 flavonoid metabolites in P. japonicus, among which flavonoids, flavonols, flavanones and flavanonols significantly accumulated in the flowers and leaves. Transcriptome sequencing revealed that key genes in the flavonoid pathway exhibited increased expression in the flowers and leaves. The expression patterns of key genes involved in flavonoid biosynthesis, including PjC4H, Pj4CL, PjCHS, PjCHI, PjF3H, PjF3'H, PjCYP, and PjPAL, are consistent with their upstream and downstream metabolites, demonstrating a significant positive correlation among them. In addition, the PjUGT gene is highly expressed in five tissues of P. japonicus, indicating that PjUGT is one of the key factors for the diversity of flavonoid glycosides. The WGCNA results showed that WRKY transcription factors exist widely in the candidate modules, and it was possible that PjWRKY transcription factors are involved in regulating the expression of key genes involved in flavonoid biosynthesis and the biosynthesis of flavonoid metabolites. This study reveals spatial differences in the accumulation patterns of flavonoid metabolites in different tissues and provides important clues for further understanding the regulatory mechanisms of flavonoid metabolism in P. japonicus, thus contributing to the optimization of germplasm resources of P. japonicus and the promotion of genetic diversity analysis.
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Affiliation(s)
- ChunYu Chen
- Chongqing Three Gorges Medical College, Chongqing, China
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, China
| | - Ping Wang
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Yan Yan
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - ZeWei Jiao
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - ShuHao Xie
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Ye Li
- Chongqing Three Gorges Medical College, Chongqing, China
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, China
| | - Peng Di
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
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Zhou Y, Bai YH, Han FX, Chen X, Wu FS, Liu Q, Ma WZ, Zhang YQ. Transcriptome sequencing and metabolome analysis reveal the molecular mechanism of Salvia miltiorrhiza in response to drought stress. BMC PLANT BIOLOGY 2024; 24:446. [PMID: 38778268 PMCID: PMC11112794 DOI: 10.1186/s12870-024-05006-7] [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: 09/28/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Salvia miltiorrhiza is commonly used as a Chinese herbal medicine to treat different cardiovascular and cerebrovascular illnesses due to its active ingredients. Environmental conditions, especially drought stress, can affect the yield and quality of S. miltiorrhiza. However, moderate drought stress could improve the quality of S. miltiorrhiza without significantly reducing the yield, and the mechanism of this initial drought resistance is still unclear. In our study, transcriptome and metabolome analyses of S. miltiorrhiza under different drought treatment groups (CK, A, B, and C groups) were conducted to reveal the basis for its drought tolerance. We discovered that the leaves of S. miltiorrhiza under different drought treatment groups had no obvious shrinkage, and the malondialdehyde (MDA) contents as well as superoxide dismutase (SOD) and peroxidase (POD) activities dramatically increased, indicating that our drought treatment methods were moderate, and the leaves of S. miltiorrhiza began to initiate drought resistance. The morphology of root tissue had no significant change under different drought treatment groups, and the contents of four tanshinones significantly enhanced. In all, 5213, 6611, and 5241 differentially expressed genes (DEGs) were shared in the A, B, and C groups compared with the CK group, respectively. The results of KEGG and co-expression analysis showed that the DEGs involved in plant-pathogen interactions, the MAPK signaling pathway, phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction responded to drought stress and were strongly correlated with tanshinone biosynthesis. Furthermore, the results of metabolism analysis indicated that 67, 72, and 92 differentially accumulated metabolites (DAMs), including fumarate, ferulic acid, xanthohumol, and phytocassanes, which were primarily involved in phenylpropanoid biosynthesis, flavonoid biosynthesis, and diterpenoid biosynthesis pathways, were detected in these groups. These discoveries provide valuable information on the molecular mechanisms by which S. miltiorrhiza responds to drought stress and will facilitate the development of drought-resistant and high-quality S. miltiorrhiza production.
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Affiliation(s)
- Ying Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yan-Hong Bai
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Feng-Xia Han
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xue Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Fu-Sheng Wu
- Shandong Provincial Center of Forest and Grass, Jinan, China
| | - Qian Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China.
- Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Jinan, China.
| | - Wen-Zhe Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Yong-Qing Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China.
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Bielecka M, Stafiniak M, Pencakowski B, Ślusarczyk S, Jastrzębski JP, Paukszto Ł, Łaczmański Ł, Gharibi S, Matkowski A. Comparative transcriptomics of two Salvia subg. Perovskia species contribute towards molecular background of abietane-type diterpenoid biosynthesis. Sci Rep 2024; 14:3046. [PMID: 38321199 PMCID: PMC10847172 DOI: 10.1038/s41598-024-53510-5] [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: 12/02/2023] [Accepted: 02/01/2024] [Indexed: 02/08/2024] Open
Abstract
Tanshinones, are a group of diterpenoid red pigments present in Danshen - an important herbal drug of Traditional Chinese Medicine which is a dried root of Salvia miltiorrhiza Bunge. Some of the tanshinones are sought after as pharmacologically active natural products. To date, the biosynthetic pathway of tanshinones has been only partially elucidated. These compounds are also present in some of the other Salvia species, i.a. from subgenus Perovskia, such as S. abrotanoides (Kar.) Sytsma and S. yangii B.T. Drew. Despite of the close genetic relationship between these species, significant qualitative differences in their diterpenoid profile have been discovered. In this work, we have used the Liquid Chromatography-Mass Spectrometry analysis to follow the content of diterpenoids during the vegetation season, which confirmed our previous observations of a diverse diterpenoid profile. As metabolic differences are reflected in different transcript profile of a species or tissues, we used metabolomics-guided transcriptomic approach to select candidate genes, which expression possibly led to observed chemical differences. Using an RNA-sequencing technology we have sequenced and de novo assembled transcriptomes of leaves and roots of S. abrotanoides and S. yangii. As a result, 134,443 transcripts were annotated by UniProt and 56,693 of them were assigned as Viridiplantae. In order to seek for differences, the differential expression analysis was performed, which revealed that 463, 362, 922 and 835 genes indicated changes in expression in four comparisons. GO enrichment analysis and KEGG functional analysis of selected DEGs were performed. The homology and expression of two gene families, associated with downstream steps of tanshinone and carnosic acid biosynthesis were studied, namely: cytochromes P-450 and 2-oxoglutarate-dependend dioxygenases. Additionally, BLAST analysis revealed existence of 39 different transcripts related to abietane diterpenoid biosynthesis in transcriptomes of S. abrotanoides and S. yangii. We have used quantitative real-time RT-PCR analysis of selected candidate genes, to follow their expression levels over the vegetative season. A hypothesis of an existence of a multifunctional CYP76AH89 in transcriptomes of S. abrotanoides and S. yangii is discussed and potential roles of other CYP450 homologs are speculated. By using the comparative transcriptomic approach, we have generated a dataset of candidate genes which provides a valuable resource for further elucidation of tanshinone biosynthesis. In a long run, our investigation may lead to optimization of diterpenoid profile in S. abrotanoides and S. yangii, which may become an alternative source of tanshinones for further research on their bioactivity and pharmacological therapy.
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Affiliation(s)
- Monika Bielecka
- Department of Pharmaceutical Biology and Biotechnology, Wroclaw Medical University, Borowska 211A, 50-556, Wrocław, Poland.
| | - Marta Stafiniak
- Department of Pharmaceutical Biology and Biotechnology, Wroclaw Medical University, Borowska 211A, 50-556, Wrocław, Poland
| | - Bartosz Pencakowski
- Department of Pharmaceutical Biology and Biotechnology, Wroclaw Medical University, Borowska 211A, 50-556, Wrocław, Poland
| | - Sylwester Ślusarczyk
- Department of Pharmaceutical Biology and Biotechnology, Wroclaw Medical University, Borowska 211A, 50-556, Wrocław, Poland
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A/113, 10-719, Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-720, Olsztyn, Poland
| | - Łukasz Łaczmański
- Laboratory of Genomics & Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy PAS, Rudolfa Weigla 12, Wrocław, Poland
| | - Shima Gharibi
- Department of Pharmaceutical Biology and Biotechnology, Wroclaw Medical University, Borowska 211A, 50-556, Wrocław, Poland
- Core Research Facilities (CRF), Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
| | - Adam Matkowski
- Department of Pharmaceutical Biology and Biotechnology, Wroclaw Medical University, Borowska 211A, 50-556, Wrocław, Poland
- Botanical Garden of Medicinal Plants, Wroclaw Medical University, Jana Kochanowskiego 14, Wrocław, Poland
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5
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Khodadadi F, Ahmadi FS, Talebi M, Matkowski A, Szumny A, Afshari M, Rahimmalek M. Metabolic and Transcriptomic Approaches of Chitosan and Water Stress on Polyphenolic and Terpenoid Components and Gene Expression in Salvia abrotanoides (Karl.) and S. yangii. Int J Mol Sci 2023; 24:15426. [PMID: 37895107 PMCID: PMC10607810 DOI: 10.3390/ijms242015426] [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: 08/03/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
In this research, a HPLC analysis, along with transcriptomics tools, was applied to evaluate chitosan and water stress for the prediction of phenolic flavonoids patterns and terpenoid components accumulation in Salvia abrotanoides Karel and S. yangii. The results indicated that the tanshinone contents under drought stress conditions increased 4.2-fold with increasing drought stress intensity in both species. The rosmarinic acid content in the leaves varied from 0.038 to 11.43 mg/g DW. In addition, the flavonoid content was increased (1.8 and 1.4-fold) under mild water deficit conditions with a moderate concentration of chitosan (100 mg L-1). The application of foliar chitosan at 100 and 200 mg L-1 under well-watered and mild stress conditions led to increases in hydroxyl cryptotanshinone (OH-CT) and cryptotanshinone (CT) contents as the major terpenoid components in both species. The expressions of the studied genes (DXS2, HMGR, KSL, 4CL, and TAT) were also noticeably induced by water deficit and variably modulated by the treatment with chitosan. According to our findings, both the drought stress and the application of foliar chitosan altered the expression levels of certain genes. Specifically, we observed changes in the expression levels of DXS and HMGR, which are upstream genes in the MEP and MVA pathways, respectively. Additionally, the expression level of KSL, a downstream gene involved in diterpenoid synthesis, was also affected. Finally, the present investigation confirmed that chitosan treatments and water stress were affected in both the methylerythritol phosphate pathway (MEP) and mevalonate (MVA) pathways, but their commitment to the production of other isoprenoids has to be considered and discussed.
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Affiliation(s)
- Farzaneh Khodadadi
- Department of Plant Biotechnology, Ferdowsi University of Mashhad, Mashhad 91779-48974, Iran;
| | - Farajollah Shahriai Ahmadi
- Department of Plant Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Mashhad 91779-48974, Iran;
| | - Majid Talebi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran;
| | - Adam Matkowski
- Department of Pharmaceutical Biology and Botany, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland;
| | - Antoni Szumny
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, 50-375 Wroclaw, Poland
| | - Mahvash Afshari
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan 83111-84156, Iran;
| | - Mehdi Rahimmalek
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, 50-375 Wroclaw, Poland
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran
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Alam SSM, Samanta A, Uddin F, Ali S, Hoque M. Tanshinone IIA targeting cell signaling pathways: a plausible paradigm for cancer therapy. Pharmacol Rep 2023:10.1007/s43440-023-00507-y. [PMID: 37440106 DOI: 10.1007/s43440-023-00507-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Natural compounds originating from plants offer a wide range of pharmacological potential and have traditionally been used to treat a wide range of diseases including cancer. Tanshinone IIA (Tan IIA), a bioactive molecule found in the roots of the Traditional Chinese Medicine (TCM) herb Salvia miltiorrhiza, has been shown to have remarkable anticancer properties through several mechanisms, such as inhibition of tumor cell growth and proliferation, metastasis, invasion, and angiogenesis, as well as induction of apoptosis and autophagy. It has demonstrated excellent anticancer efficacy against cell lines from breast, cervical, colorectal, gastric, lung, and prostate cancer by modulating multiple signaling pathways including PI3K/Akt, JAK/STAT, IGF-1R, and Bcl-2-Caspase pathways. This review focuses on the role of Tan IIA in the treatment of various cancers, as well as the underlying molecular mechanisms.
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Affiliation(s)
| | - Arijit Samanta
- Applied Biochemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata, 700160, India
| | - Faizan Uddin
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
| | - Safdar Ali
- Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah University, Kolkata, 700160, India
| | - Mehboob Hoque
- Applied Biochemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata, 700160, India.
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Wang D, Yu Z, Guan M, Cai Q, Wei J, Ma P, Xue Z, Ma R, Oksman-Caldentey KM, Rischer H. Comparative transcriptome analysis of Veratrum maackii and Veratrum nigrum reveals multiple candidate genes involved in steroidal alkaloid biosynthesis. Sci Rep 2023; 13:8198. [PMID: 37211560 DOI: 10.1038/s41598-023-35429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023] Open
Abstract
Veratrum (Melanthiaceae; Liliales) is a genus of perennial herbs known for the production of unique bioactive steroidal alkaloids. However, the biosynthesis of these compounds is incompletely understood because many of the downstream enzymatic steps have yet to be resolved. RNA-Seq is a powerful method that can be used to identify candidate genes involved in metabolic pathways by comparing the transcriptomes of metabolically active tissues to controls lacking the pathway of interest. The root and leaf transcriptomes of wild Veratrum maackii and Veratrum nigrum plants were sequenced and 437,820 clean reads were assembled into 203,912 unigenes, 47.67% of which were annotated. We identified 235 differentially expressed unigenes potentially involved in the synthesis of steroidal alkaloids. Twenty unigenes, including new candidate cytochrome P450 monooxygenases and transcription factors, were selected for validation by quantitative real-time PCR. Most candidate genes were expressed at higher levels in roots than leaves but showed a consistent profile across both species. Among the 20 unigenes putatively involved in the synthesis of steroidal alkaloids, 14 were already known. We identified three new CYP450 candidates (CYP76A2, CYP76B6 and CYP76AH1) and three new transcription factor candidates (ERF1A, bHLH13 and bHLH66). We propose that ERF1A, CYP90G1-1 and CYP76AH1 are specifically involved in the key steps of steroidal alkaloid biosynthesis in V. maackii roots. Our data represent the first cross-species analysis of steroidal alkaloid biosynthesis in the genus Veratrum and indicate that the metabolic properties of V. maackii and V. nigrum are broadly conserved despite their distinct alkaloid profiles.
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Affiliation(s)
- Dan Wang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
- College of Agricultural Sciences, Yanbian University, Yanji, 133000, Jilin Province, People's Republic of China
| | - Zhijing Yu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Meng Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin, People's Republic of China
| | - Qinan Cai
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Jia Wei
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China
| | - Pengda Ma
- College of Life Sciences, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Zheyong Xue
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Hexing Road 26, Harbin, People's Republic of China
| | - Rui Ma
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, Jilin Province, People's Republic of China.
| | | | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd., P. O. Box 1000, 02044 VTT, Espoo, Finland.
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Wu P, Wang X, Guo J, Zhang S, Li Q, Zhang M, Fang Q, Luo B, Wang H, He W. Analysis of the difference between early-bolting and non-bolting roots of Angelica dahurica based on transcriptome sequencing. Sci Rep 2023; 13:7847. [PMID: 37188680 DOI: 10.1038/s41598-023-34554-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
Angelica dahurica (Fisch. ex Hoffm.) Benth.et Hook.f.var.formosana (Boiss.) Shan et Yuan (A. dahurica) is a well-known medicinal plant that has a wide range of applications in the pharmaceutical, food, cosmetic, and other industries. However, the issue of early bolting has emerged as a major hindrance to its production. This problem not only reduces the yield of A. dahurica, but also has an impact on its active ingredients. To date, the molecular factors that contribute to early bolting and its impact on the growth of A. dahurica have not been thoroughly investigated. Therefore, we conducted a transcriptome study using the Illumina NovaSeq 6000 on two developmental types: early-bolting and non-bolting (normal) roots of A. dahurica. We obtained 2,185 up-regulated and 1,414 down-regulated genes in total. Many of the identified transcripts were related to genes involved in early bolting. The gene ontology analysis revealed several differentially expressed genes that are crucial in various pathways, primarily associated with cellular, molecular, and biological processes. Additionally, the morphological characteristics and coumarin content in the early bolting roots of A. dahurica were significantly altered. This study provides insight into the transcriptomic regulation of early bolting in A. dahurica, which can potentially be utilized to enhance its medicinal properties.
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Affiliation(s)
- Ping Wu
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Xiaoyu Wang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Junxia Guo
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Songli Zhang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Qingmiao Li
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China.
| | - Mei Zhang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Qingmao Fang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Bin Luo
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Hongsu Wang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Weijin He
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis. Int J Mol Sci 2022; 23:ijms232415932. [PMID: 36555572 PMCID: PMC9781956 DOI: 10.3390/ijms232415932] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.
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Meng X, Zhang T, Chen C, Li Q, Liu J. Regulatory network of ginsenoside biosynthesis under Ro stress in the hairy roots of Panax ginseng revealed by RNA sequencing. Front Bioeng Biotechnol 2022; 10:1006386. [PMID: 36394021 PMCID: PMC9659575 DOI: 10.3389/fbioe.2022.1006386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022] Open
Abstract
P. ginseng C.A. Meyer is a valuable Chinese herbal medicine that belongs to the Araliaceae family. Major obstacles to the continuous cropping of ginseng have severely restricted the sustainable development of the ginseng industry. The allelopathic effects of triterpenoid saponins play an important role in disorders related to continuous cropping; however, the mechanisms underlying the allelopathic autotoxicity of triterpenoid ginsenosides remain unknown. In this study, we performed mRNA and miRNA sequencing analyses to identify candidate genes and miRNAs that respond differentially to ginsenoside Ro stress in ginseng and their targets. The growth of the ginseng hairy roots was significantly inhibited under Ro stress (0.5 mg/L, Ro-0.5). The inhibition of root growth and injury to root-tip cells promoted the accumulation of the endogenous hormones indole-3-acetic acid and salicylic acid and inhibited the accumulation of abscisic acid and jasmonate acid. The accumulation of ginsenosides, except Rg3, was significantly inhibited under Ro-0.5 stress. An mRNA analysis of the Ro-0.5 and control groups showed that differentially expressed genes were mostly concentrated in the hormone signal transduction pathway. ARF7 and EFM were upregulated, whereas XTH23 and ZOX1 were downregulated. These genes represent important potential candidates for hormone-responsive continuous cropping diseases. In total, 74 differentially expressed miRNAs were identified based on the miRNA sequencing analysis, of which 22 were upregulated and 52 were downregulated. The target genes of ptc-miR156k_L + 1, mtr-miR156b-5p, gma-miR156a_R + 1, and mtr-miR156e all belonged to TRINITY_DN14567_c0_g4, which is a gene in the plant hormone signal transduction pathway. These four miRNAs were all negatively correlated with mRNA, indicating their likely involvement in the response of ginseng to continuous cropping disorders and the regulation of ginsenoside synthesis. Our findings provide useful insights for removing the barriers to continuous ginseng cropping and have important implications in the genetic engineering of plant stress responses.
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Affiliation(s)
| | - Tao Zhang
- *Correspondence: Tao Zhang, ; Changbao Chen,
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11
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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12
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Resurreccion EP, Fong KW. The Integration of Metabolomics with Other Omics: Insights into Understanding Prostate Cancer. Metabolites 2022; 12:metabo12060488. [PMID: 35736421 PMCID: PMC9230859 DOI: 10.3390/metabo12060488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Our understanding of prostate cancer (PCa) has shifted from solely caused by a few genetic aberrations to a combination of complex biochemical dysregulations with the prostate metabolome at its core. The role of metabolomics in analyzing the pathophysiology of PCa is indispensable. However, to fully elucidate real-time complex dysregulation in prostate cells, an integrated approach based on metabolomics and other omics is warranted. Individually, genomics, transcriptomics, and proteomics are robust, but they are not enough to achieve a holistic view of PCa tumorigenesis. This review is the first of its kind to focus solely on the integration of metabolomics with multi-omic platforms in PCa research, including a detailed emphasis on the metabolomic profile of PCa. The authors intend to provide researchers in the field with a comprehensive knowledge base in PCa metabolomics and offer perspectives on overcoming limitations of the tool to guide future point-of-care applications.
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Affiliation(s)
- Eleazer P. Resurreccion
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
| | - Ka-wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
- Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA
- Correspondence: ; Tel.: +1-859-562-3455
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Wang Z, Peters RJ. Tanshinones: Leading the way into Lamiaceae labdane-related diterpenoid biosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102189. [PMID: 35196638 PMCID: PMC8940693 DOI: 10.1016/j.pbi.2022.102189] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/06/2022] [Accepted: 01/14/2022] [Indexed: 05/06/2023]
Abstract
Tanshinones are the bioactive diterpenoid constituents of the traditional Chinese medicinal herb Danshen (Salvia miltiorrhiza), and are examples of the phenolic abietanes widely found within the Lamiaceae plant family. Due to the significant interest in these labdane-related diterpenoid natural products, their biosynthesis has been intensively investigated. In addition to providing the basis for metabolic engineering efforts, this work further yielded pioneering insights into labdane-related diterpenoid biosynthesis in the Lamiaceae more broadly. This includes stereochemical foreshadowing of aromatization, with novel protein domain loss in the relevant diterpene synthase, as well as broader phylogenetic conservation of the relevant enzymes. Beyond such summary of more widespread metabolism, formation of the furan ring that characterizes the tanshinones also has been recently elucidated. Nevertheless, the biocatalysts for the pair of demethylations remain unknown, and the intriguing potential connection of these reactions to the further aromatization observed in the tanshinones are speculated upon here.
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Affiliation(s)
- Zhibiao Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China; Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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The ease and complexity of identifying and using specialized metabolites for crop engineering. Emerg Top Life Sci 2022; 6:153-162. [PMID: 35302160 PMCID: PMC9023015 DOI: 10.1042/etls20210248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
Plants produce a broad variety of specialized metabolites with distinct biological activities and potential applications. Despite this potential, most biosynthetic pathways governing specialized metabolite production remain largely unresolved across the plant kingdom. The rapid advancement of genetics and biochemical tools has enhanced our ability to identify plant specialized metabolic pathways. Further advancements in transgenic technology and synthetic biology approaches have extended this to a desire to design new pathways or move existing pathways into new systems to address long-running difficulties in crop systems. This includes improving abiotic and biotic stress resistance, boosting nutritional content, etc. In this review, we assess the potential and limitations for (1) identifying specialized metabolic pathways in plants with multi-omics tools and (2) using these enzymes in synthetic biology or crop engineering. The goal of these topics is to highlight areas of research that may need further investment to enhance the successful application of synthetic biology for exploiting the myriad of specialized metabolic pathways.
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LI X, LI J, ISLAM F, NAJEEB U, PAN J, HOU Z, SHOU J, QIN Y, XU L. 5-Aminolevulinic acid could enhance the salinity tolerance by alleviating oxidative damages in Salvia miltiorrhiza. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.103121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Xin LI
- Zhejiang Sci-Tech University, China
| | | | | | | | | | | | - Jianyao SHOU
- Zhuji Municipal Agro-Tech Extension Center, China
| | - Yebo QIN
- Zhejiang Agricultural Technology Extension Center, China
| | - Ling XU
- Zhejiang Sci-Tech University, China
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Wijma M, Lembke CG, Diniz AL, Santini L, Zambotti-Villela L, Colepicolo P, Carneiro MS, Souza GM. Planting Season Impacts Sugarcane Stem Development, Secondary Metabolite Levels, and Natural Antisense Transcription. Cells 2021; 10:cells10123451. [PMID: 34943959 PMCID: PMC8700069 DOI: 10.3390/cells10123451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
To reduce the potentially irreversible environmental impacts caused by fossil fuels, the use of renewable energy sources must be increased on a global scale. One promising source of biomass and bioenergy is sugarcane. The study of this crop's development in different planting seasons can aid in successfully cultivating it in global climate change scenarios. The sugarcane variety SP80-3280 was field grown under two planting seasons with different climatic conditions. A systems biology approach was taken to study the changes on physiological, morphological, agrotechnological, transcriptomics, and metabolomics levels in the leaf +1, and immature, intermediate and mature internodes. Most of the variation found within the transcriptomics and metabolomics profiles is attributed to the differences among the distinct tissues. However, the integration of both transcriptomics and metabolomics data highlighted three main metabolic categories as the principal sources of variation across tissues: amino acid metabolism, biosynthesis of secondary metabolites, and xenobiotics biodegradation and metabolism. Differences in ripening and metabolite levels mainly in leaves and mature internodes may reflect the impact of contrasting environmental conditions on sugarcane development. In general, the same metabolites are found in mature internodes from both "one-year" and "one-and-a-half-year sugarcane", however, some metabolites (i.e., phenylpropanoids with economic value) and natural antisense transcript expression are only detected in the leaves of "one-year" sugarcane.
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Affiliation(s)
- Maryke Wijma
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Luciane Santini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Leonardo Zambotti-Villela
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Pio Colepicolo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Monalisa Sampaio Carneiro
- Centro de Ciências Agrárias, Departamento de Biotecnologia e Produção Vegetal e Animal, Universidade Federal de São Carlos, São Paulo 13600-970, Brazil;
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
- Correspondence:
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Zhang T, Chen Y, Zhang Q, Yu P, Li Q, Qi W, Chen C. Transcriptomic and Metabolomic Differences Between Two Saposhnikovia divaricata (Turcz.) Schischk Phenotypes With Single- and Double-Headed Roots. Front Bioeng Biotechnol 2021; 9:764093. [PMID: 34778235 PMCID: PMC8581353 DOI: 10.3389/fbioe.2021.764093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022] Open
Abstract
Saposhnikovia divaricata is derived from the dried roots of Saposhnikovia divaricata (Turcz.) Schischk and used as a Chinese herbal medicine for treating respiratory, immune, and nervous system diseases. The continuously increasing market demand for traditional Chinese medicine requires the commercial cultivation of Saposhnikovia divaricata using standardized methods and high yielding genotypes, such as double-headed root plants, for achieving consistent quality and a reliable supply. In this study, we aimed to identify the quantitative differences in chromone, a precursor of flavonoid biosynthesis, between plants with single- and double-headed roots using high-performance liquid chromatography and further explore the two phenotypes at the transcriptomic and metabolomic levels. Our results showed that the chromone content was significantly higher in plants with double-headed roots than in those with single-headed roots. Transcriptomic analysis revealed six significantly differentially expressed genes between the two phenotypes, including five key genes in the flavonoid biosynthesis pathway (4-coumarate-CoA ligase, chalcone synthase 1, vinorine synthase, chalcone-flavonone isomerase 1, and flavanone 3 beta-hydroxylase) and one key gene in the abscisic acid biosynthetic pathway (zeaxanthin epoxidase). Moreover, metabolomic analysis showed that the 126 differentially expressed metabolites were mainly enriched in the biosynthesis of secondary metabolites and phytohormones. Overall, our results suggest that plants with double-headed roots have higher medicinal value than those with single-headed roots, probably due to differences in various biosynthetic pathways. These data might help select the genotypes with superior yield and therapeutic properties.
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Affiliation(s)
- Tao Zhang
- Key Laboratory of Chinese Medicine Planting and Development, Changchun University of Chinese Medicine, Changchun, China
| | - Yuqiu Chen
- Key Laboratory of Chinese Medicine Planting and Development, Changchun University of Chinese Medicine, Changchun, China
| | - Qinghe Zhang
- Key Laboratory of Chinese Medicine Planting and Development, Changchun University of Chinese Medicine, Changchun, China
| | - Peng Yu
- Key Laboratory of Chinese Medicine Planting and Development, Changchun University of Chinese Medicine, Changchun, China
| | - Qiong Li
- Key Laboratory of Chinese Medicine Planting and Development, Changchun University of Chinese Medicine, Changchun, China
| | - Weichen Qi
- Key Laboratory of Chinese Medicine Planting and Development, Changchun University of Chinese Medicine, Changchun, China
| | - Changbao Chen
- Key Laboratory of Chinese Medicine Planting and Development, Changchun University of Chinese Medicine, Changchun, China
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Zhou J, Liu R, Shuai M, Yan ZY, Chen X. Comparative transcriptome analyses of different Salvia miltiorrhiza varieties during the accumulation of tanshinones. PeerJ 2021; 9:e12300. [PMID: 34721983 PMCID: PMC8541307 DOI: 10.7717/peerj.12300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/22/2021] [Indexed: 01/07/2023] Open
Abstract
Salvia miltiorrhiza (Labiatae) is an important medicinal plant in traditional Chinese medicine. Tanshinones are one of the main active components of S. miltiorrhiza. It has been found that the intraspecific variation of S. miltiorrhiza is relatively large and the content of tanshinones in its roots of different varieties is also relatively different. To investigate the molecular mechanisms that responsible for the differences among these varieties, the tanshinones content was determined and comparative transcriptomics analysis was carried out during the tanshinones accumulation stage. A total of 52,216 unigenes were obtained from the transcriptome by RNA sequencing among which 23,369 genes were differentially expressed among different varieties, and 2,016 genes including 18 diterpenoid biosynthesis-related genes were differentially expressed during the tanshinones accumulation stage. Functional categorization of the differentially expressed genes (DEGs) among these varieties revealed that the pathway related to photosynthesis, oxidative phosphorylation, secondary metabolite biosynthesis, diterpenoid biosynthesis, terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis are the most differentially regulated processes in these varieties. The six tanshinone components in these varieties showed different dynamic changes in tanshinone accumulation stage. In addition, combined with the analysis of the dynamic changes, 277 DEGs (including one dehydrogenase, three CYP450 and 24 transcription factors belonging to 12 transcription factor families) related to the accumulation of tanshinones components were obtained. Furthermore, the KEGG pathway enrichment analysis of these 277 DEGs suggested that there might be an interconnection between the primary metabolic processes, signaling processes and the accumulation of tanshinones components. This study expands the vision of intraspecific variation and gene regulation mechanism of secondary metabolite biosynthesis pathways in medicinal plants from the “omics” perspective.
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Affiliation(s)
- Jingwen Zhou
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.,Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest, Chengdu, Sichuan, China
| | - Rui Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.,Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest, Chengdu, Sichuan, China
| | - Min Shuai
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.,Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest, Chengdu, Sichuan, China
| | - Zhu-Yun Yan
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.,Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest, Chengdu, Sichuan, China
| | - Xin Chen
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.,Key Laboratory of Characteristic Chinese Medicinal Resources in Southwest, Chengdu, Sichuan, China
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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Lai Z, He J, Zhou C, Zhao H, Cui S. Tanshinones: An Update in the Medicinal Chemistry in Recent 5 Years. Curr Med Chem 2021; 28:2807-2827. [PMID: 32436817 DOI: 10.2174/0929867327666200521124850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 11/22/2022]
Abstract
Tanshinones are an important type of natural products isolated from Salvia miltiorrhiza Bunge with various bioactivities. Tanshinone IIa, cryptotanshinone and tanshinone I are three kinds of tanshinones which have been widely investigated. Particularly, sodium tanshinone IIa sulfonate is a water-soluble derivative of tanshinone IIa and it is used in clinical in China for treating cardiovascular diseases. In recent years, there are increasing interests in the investigation of tanshinones derivatives in various diseases. This article presents a review of the anti-atherosclerotic effects, cardioprotective effects, anticancer activities, antibacterial activities and antiviral activities of tanshinones and structural modification work in recent years.
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Affiliation(s)
- Zhencheng Lai
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jixiao He
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Changxin Zhou
- Institute of Modern Chinese Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Huajun Zhao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Sunliang Cui
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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21
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Yu N, Chen Z, Yang J, Li R, Zou W. Integrated transcriptomic and metabolomic analyses reveal regulation of terpene biosynthesis in the stems of Sindora glabra. TREE PHYSIOLOGY 2021; 41:1087-1102. [PMID: 33372995 DOI: 10.1093/treephys/tpaa168] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Sesquiterpenes are important defensive secondary metabolites that are synthesized in various plant organs. Methyl jasmonate (MeJA) plays a key role in plant defense responses and secondary metabolism. Sindora glabra Merr. ex de Wit produces abundant sesquiterpenes in its trunks, and was subjected to investigation after MeJA treatment in order to characterize the molecular mechanisms underlying the regulation of sesquiterpene biosynthesis in plant stems and further our understanding of oleoresin production in trees. A total of 14 types of sesquiterpenes in the stems of mature S. glabra trees were identified. The levels of two sesquiterpenes, α-copaene and β-caryophyllene, significantly increased after MeJA treatment. Differentially expressed genes involved in terpenoid backbone biosynthesis were significantly enriched over time, while the expression of JAZ genes involved in the jasmonic acid signaling pathway and TGA genes involved in the salicylic acid signaling pathway was significantly enriched at later time points after treatment. Two new terpene synthase genes, SgSTPS4 and SgSTPS5, were also identified. Following MeJA treatment, the expression levels of SgSTPS1, SgSTPS2 and SgSTPS4 decreased, while SgSTPS5 expression increased. The major enzymatic products of SgSTPS4 were identified as β-elemene and cyperene, while SgSTPS5 was identified as a bifunctional mono/sesquiterpene synthase that could catalyze farnesyl pyrophosphate to produce nine types of sesquiterpenes, including α-copaene and β-caryophyllene, while SgSTPS5 could also use geranyl pyrophosphate to produce geraniol. Dramatic changes in the amounts of α-copaene and β-caryophyllene in response to MeJA were correlated with transcriptional expression changes of SgSTPS5 in the wood tissues. In addition, the transcription factors MYB, NAC, ARF, WRKY, MYC, ERF and GRAS were co-expressed with terpene biosynthesis genes and might potentially regulate terpene biosynthesis. Metabolite changes were further investigated with UPLC-TOF/MS following MeJA treatment. These results contribute to the elucidation of the molecular mechanisms of terpene biosynthesis and regulation as well as to the identification of candidate genes involved in these processes.
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Affiliation(s)
- Niu Yu
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou 510520, China
| | - Zhaoli Chen
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou 510520, China
| | - Jinchang Yang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou 510520, China
| | - Rongsheng Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou 510520, China
| | - Wentao Zou
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou 510520, China
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22
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Ranjith GP, Jisha S, Hemanthakumar AS, Saji CV, Shenoi RA, Sabu KK. Impact of potential stimulants on asiaticoside and madecassoside levels and expression of triterpenoid-related genes in axenic shoot cultures of Centella asiatica (L.) Urb. PHYTOCHEMISTRY 2021; 186:112735. [PMID: 33839454 DOI: 10.1016/j.phytochem.2021.112735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The triterpenoid saponins, asiaticoside and madecassoside from Centella asiatica (L.) Urb. are known to have a wide range of applications in pharmaceutical and cosmetic industries. The effect of addition of Potential Metabolite Stimulants (PMSs) - casein acid hydrolysate, meat peptone, salicylic acid, copper sulphate, and silver nitrate, on the concentrations of these saponins and transcript levels of associated genes encoding important biosynthetic enzymes, was assessed in axenic shoot cultures of C. asiatica. Among the stimulants, silver nitrate induced asiaticoside content approximately 6-fold increase in madecassoside levels, after three weeks post-treatment with a decrease in biomass compared to its control. Gene expression analysis of essential genes involved in triterpenoid synthesis such as β-amyrin synthase showed an upregulation of approximately 50-fold at the third week of silver nitrate treatment compared to control. These findings suggest that silver nitrate can act as a metabolite stimulant, to enhance the formation of triterpenoids in axenic shoot culture of C. asiatica, which could be utilized in studying the regulation of terpenoid biosynthesis and biotechnological application for the increased production of these bioactive molecules.
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Affiliation(s)
- Gouri Priya Ranjith
- Division of Biotechnology and Bioinformatics, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 695562, Kerala, India
| | - S Jisha
- Division of Biotechnology and Bioinformatics, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 695562, Kerala, India
| | - Achutan Sudarsanan Hemanthakumar
- Division of Biotechnology and Bioinformatics, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 695562, Kerala, India
| | - Chinthu V Saji
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus, Kottayam, 686009, Kerala, India
| | - Rajesh A Shenoi
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus, Kottayam, 686009, Kerala, India
| | - Kallevettankuzhy Krishnannair Sabu
- Division of Biotechnology and Bioinformatics, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 695562, Kerala, India.
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23
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Hu Z, Liu X, Tian M, Ma Y, Jin B, Gao W, Cui G, Guo J, Huang L. Recent progress and new perspectives for diterpenoid biosynthesis in medicinal plants. Med Res Rev 2021; 41:2971-2997. [PMID: 33938025 DOI: 10.1002/med.21816] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 12/25/2022]
Abstract
Diterpenoids, including more than 18,000 compounds, represent an important class of metabolites that encompass both phytohormones and some industrially relevant compounds. These molecules with complex, diverse structures and physiological activities, have high value in the pharmaceutical industry. Most medicinal diterpenoids are extracted from plants. Major advances in understanding the biosynthetic pathways of these active compounds are providing unprecedented opportunities for the industrial production of diterpenoids by metabolic engineering and synthetic biology. Here, we summarize recent developments in the field of diterpenoid biosynthesis from medicinal herbs. An overview of the pathways and known biosynthetic enzymes is presented. In particular, we look at the main findings from the past decade and review recent progress in the biosynthesis of different groups of ringed compounds. We also discuss diterpenoid production using synthetic biology and metabolic engineering strategies, and draw on new technologies and discoveries to bring together many components into a useful framework for diterpenoid production.
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Affiliation(s)
- Zhimin Hu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiuyu Liu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Pharmaceutical Sciences, Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
| | - Mei Tian
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Ma
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baolong Jin
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Gao
- School of Pharmaceutical, Sciences, Capital Medical University, Beijing, China
| | - Guanghong Cui
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Juan Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Sun H, Ding W, Duan W, Zhou J, Guo L. Proteomic reveals the influences of smoke-water and karrikinolide on the biosynthesis of salvianolic acids and lignins in Salvia miltiorrhiza hairy roots. PLANTA 2021; 253:87. [PMID: 33811528 DOI: 10.1007/s00425-021-03619-y] [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: 12/05/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
The proteins related to the biosynthesis of salvianolic acids and lignins were regulated by smoke-water and karrikinolide in Salvia miltiorrhiza hairy roots. The effects of smoke-water (SW) and karrikinolide (KAR1) on the biosynthesis of salvianolic acids and lignins in Salvia miltiorrhiza hairy roots have been studied using proteomic technology. The results showed that a total of 1290 and 1678 differentially expressed proteins were respectively obtained in SW and KAR1 comparing to the control. Bioinformatics analysis indicated the differentially expressed proteins responding to SW and KAR1 treatments mainly involved in macromolecule metabolic process, cell part, binding, etc., and most of the proteins were located at the cytoplasm and cell membrane, followed by nuclear. In addition, the proteins involved in salvianolic acids biosynthesis were up-regulated, including 4-coumarate-CoA ligase (EC 6.2.1.12) and shikimate O-hydroxycinnamoyl-transferase (EC 2.3.1.133). Enzymes involved in lignins biosynthesis were also identified, e.g. cinnamyl-alcohol dehydrogenase (EC 1.1.1.195) and peroxidase (EC 1.11.1.7). The results indicated that proteins related to the biosynthesis of salvianolic acids and lignins were regulated by SW and KAR1 in S. miltiorrhiza hairy roots. This study will enhance our understanding of the mechanism by which SW and KAR1 on the biosynthesis of salvianolic acids and lignins in S. miltiorrhiza hairy roots.
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Affiliation(s)
- Hui Sun
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Weina Ding
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Wanying Duan
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jie Zhou
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
| | - Lanping Guo
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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25
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Song W, Zhuang Y, Liu T. CYP82AR Subfamily Proteins Catalyze C-1' Hydroxylations of Deoxyshikonin in the Biosynthesis of Shikonin and Alkannin. Org Lett 2021; 23:2455-2459. [PMID: 33728922 DOI: 10.1021/acs.orglett.1c00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Shikonin and S-enantiomer alkannin are important naphthoquinone derivatives present in many Boraginaceae species. We report that cytochrome P450 monooxygenases (CYPs) from a new CYP82AR subfamily catalyzed hydroxylations of deoxyshikonin at C-1' position of isoprenoid side chain. Two homologues were discovered from each species of the four Boraginaceae plants. One CYP preferred converting deoxyshikonin into shikonin, and the other stereoselectively hydroxylated deoxyshikonin into alkannin. The discovery might be a general feature of shikonin/alkannin-producing Boraginaceae plants.
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Affiliation(s)
- Wan Song
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yibin Zhuang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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26
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Wei G, Chen Y, Guo X, Wei J, Dong L, Chen S. Biosyntheses characterization of alkaloids and flavonoids in Sophora flavescens by combining metabolome and transcriptome. Sci Rep 2021; 11:7388. [PMID: 33795823 PMCID: PMC8016917 DOI: 10.1038/s41598-021-86970-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Sophora flavescens are widely used for their pharmacological effects. As its main pharmacological components, alkaloids and flavonoids are distributed in the root tissues wherein molecular mechanisms remain elusive. In this study, metabolite profiles are analyzed using metabolomes to obtain biomarkers detected in different root tissues. These biomarkers include alkaloids, phenylpropanoids, and flavonoids. The high-performance liquid chromatography analysis results indicate the differences in principal component contents. Oxymatrine, sophoridine, and matrine contents are the highest in the phloem, whereas trifolirhizin, maackiain, and kushenol I contents are the highest in the xylem. The transcript expression profiles also show tissue specificity in the roots. A total of 52 and 39 transcripts involved in alkaloid and flavonoid syntheses are found, respectively. Among them, the expression levels of LYSA1, LYSA2, AO2, AO6, PMT1, PMT17, PMT34, and PMT35 transcripts are highly and positively correlated with alkaloids contents. The expression levels of 4CL1, 4CL3, 4CL12, CHI5, CHI7, and CHI9 transcripts are markedly and positively correlated with flavonoids contents. Moreover, the quantitative profiles of alkaloids and flavonoids are provided, and the pivotal genes regulating their distribution in S. flavescens are determined. These results contribute to the existing data for the genetic improvement and target breeding of S. flavescens.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yongzhong Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaotong Guo
- College of Agriculture, Ludong University, Yantai, 264025, China
| | - Jianhe Wei
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, 570311, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- , No.16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China.
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27
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Wu S, Zhu B, Qin L, Rahman K, Zhang L, Han T. Transcription Factor: A Powerful Tool to Regulate Biosynthesis of Active Ingredients in Salvia miltiorrhiza. FRONTIERS IN PLANT SCIENCE 2021; 12:622011. [PMID: 33719294 PMCID: PMC7943460 DOI: 10.3389/fpls.2021.622011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/22/2021] [Indexed: 05/28/2023]
Abstract
Salvia miltiorrhiza Bunge is a common Chinese herbal medicine, and its major active ingredients are phenolic acids and tanshinones, which are widely used to treat vascular diseases. However, the wild form of S. miltiorrhiza possess low levels of these important pharmaceutical agents; thus, improving their levels is an active area of research. Transcription factors, which promote or inhibit the expressions of multiple genes involved in one or more biosynthetic pathways, are powerful tools for controlling gene expression in biosynthesis. Several families of transcription factors have been reported to participate in regulating phenolic acid and tanshinone biosynthesis and influence their accumulation. This review summarizes the current status in this field, with focus on the transcription factors which have been identified in recent years and their functions in the biosynthetic regulation of phenolic acids and tanshinones. Otherwise, the new insight for further research is provided. Finally, the application of the biosynthetic regulation of active ingredients by the transcription factors in S. miltiorrhiza are discussed, and new insights for future research are explored.
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Affiliation(s)
- Sijia Wu
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Bo Zhu
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Luping Qin
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Khalid Rahman
- Faculty of Science, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Lei Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Ting Han
- School of Pharmacy, Second Military Medical University, Shanghai, China
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28
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Ma Y, Cui G, Chen T, Ma X, Wang R, Jin B, Yang J, Kang L, Tang J, Lai C, Wang Y, Zhao Y, Shen Y, Zeng W, Peters RJ, Qi X, Guo J, Huang L. Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza. Nat Commun 2021; 12:685. [PMID: 33514704 PMCID: PMC7846762 DOI: 10.1038/s41467-021-20959-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/01/2021] [Indexed: 11/09/2022] Open
Abstract
Tanshinones are the bioactive nor-diterpenoid constituents of the Chinese medicinal herb Danshen (Salvia miltiorrhiza). These groups of chemicals have the characteristic furan D-ring, which differentiates them from the phenolic abietane-type diterpenoids frequently found in the Lamiaceae family. However, how the 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly of Danshen using a highly homozygous genotype. We identify a cytochrome P450 (CYP71D) tandem gene array through gene expansion analysis. We show that CYP71D373 and CYP71D375 catalyze hydroxylation at carbon-16 (C16) and 14,16-ether (hetero)cyclization to form the D-ring, whereas CYP71D411 catalyzes upstream hydroxylation at C20. In addition, we discover a large biosynthetic gene cluster associated with tanshinone production. Collinearity analysis indicates a more specific origin of tanshinones in Salvia genus. It illustrates the evolutionary origin of abietane-type diterpenoids and those with a furan D-ring in Lamiaceae.
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Affiliation(s)
- Ying Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guanghong Cui
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Tong Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaohui Ma
- College of Pharmaceutical Science, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Ruishan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baolong Jin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jian Yang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Liping Kang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jinfu Tang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Changjiangsheng Lai
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yujun Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ye Shen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wen Zeng
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Reuben J Peters
- Roy J. Carver Dep. of Biochem., Biophys. & Mol. Biol., Iowa State University, Ames, IA, USA
| | - Xiaoquan Qi
- Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
| | - Juan Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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Zhu W, Han H, Liu A, Guan Q, Kang J, David L, Dufresne C, Chen S, Tian J. Combined ultraviolet and darkness regulation of medicinal metabolites in Mahonia bealei revealed by proteomics and metabolomics. J Proteomics 2020; 233:104081. [PMID: 33352312 DOI: 10.1016/j.jprot.2020.104081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022]
Abstract
Roots of Mahonia bealei have been used as traditional Chinese medicine with antibacterial, antioxidant and anti-inflammatory properties due to its high alkaloid content. Previously, we reported that alkaloid and flavonoid contents in the M. bealei leaves could be increased by the combined ultraviolet B and dark treatment (UV+D). To explore the underlying metabolic pathways and networks, proteomic and metabolomic analyses of the M. bealei leaves were conducted. Proteins related to tricarboxylic acid cycle, transport and signaling varied greatly under the UV + D. Among them, calmodulin involved in calcium signaling and ATP-binding cassette transporter involved in transport of berberine were increased. Significantly changed metabolites were overrepresented in phenylalanine metabolism, nitrogen metabolism, phenylpropanoid, flavonoid and alkaloid biosynthesis. In addition, the levels of salicylic acid and gibberellin decreased in the UV group and increased in the UV + D group. These results indicate that multi-hormone crosstalk may regulate the biosynthesis of flavonoids and alkaloids to alleviate oxidative stress caused by the UV + D treatment. Furthermore, protoberberine alkaloids may be induced through calcium signaling crosstalk with reaction oxygen species and transported to leaves. SIGNIFICANCE: Mahonia bealei root and stem, not leaf, were used as traditional medicine for a long history because of the high contents of active components. In the present study, UV-B combined with dark treatments induced the production of alkaloids and flavonoids in the M. bealei leaf, especially protoberberine alkaloids such as berberine. Multi-omics analyses indicated that multi-hormone crosstalk, enhanced tricarboxylic acid cycle and active calcium signaling were involved. The study informs a strategy for utilization of the leaves, and improves understanding of the functions of secondary metabolites in M. bealei.
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Affiliation(s)
- Wei Zhu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China; Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA; Changsu Qiushi Technology Co., Ltd, Suzhou 215500, PR China
| | - Haote Han
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China
| | - Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China
| | - Qijie Guan
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China; Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA
| | - Jianing Kang
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA; College of Life Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Lisa David
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA
| | - Craig Dufresne
- Thermo Fisher Scientific, West Palm Beach, FL 33407, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida Genetics Institute, Gainesville, FL 32610, USA; Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, PR China.
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30
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Zhang B, Li X, Li X, Lu Z, Cai X, Ou Yang Q, Ma P, Dong J. Lipopolysaccharide Enhances Tanshinone Biosynthesis via a Ca 2+-Dependent Manner in Salvia miltiorrhiza Hairy Roots. Int J Mol Sci 2020; 21:ijms21249576. [PMID: 33339149 PMCID: PMC7765610 DOI: 10.3390/ijms21249576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/13/2023] Open
Abstract
Tanshinones, the major bioactive components in Salvia miltiorrhiza Bunge (Danshen), are synthesized via the mevalonic acid (MVA) pathway or the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway and the downstream biosynthesis pathway. In this study, the bacterial component lipopolysaccharide (LPS) was utilized as a novel elicitor to induce the wild type hairy roots of S. miltiorrhiza. HPLC analysis revealed that LPS treatment resulted in a significant accumulation of cryptotanshinone (CT) and dihydrotanshinone I (DTI). qRT-PCR analysis confirmed that biosynthesis genes such as SmAACT and SmHMGS from the MVA pathway, SmDXS and SmHDR from the MEP pathway, and SmCPS, SmKSL and SmCYP76AH1 from the downstream pathway were markedly upregulated by LPS in a time-dependent manner. Furthermore, transcription factors SmWRKY1 and SmWRKY2, which can activate the expression of SmDXR, SmDXS and SmCPS, were also increased by LPS. Since Ca2+ signaling is essential for the LPS-triggered immune response, Ca2+ channel blocker LaCl3 and CaM antagonist W-7 were used to investigate the role of Ca2+ signaling in tanshinone biosynthesis. HPLC analysis demonstrated that both LaCl3 and W-7 diminished LPS-induced tanshinone accumulation. The downstream biosynthesis genes including SmCPS and SmCYP76AH1 were especially regulated by Ca2+ signaling. To summarize, LPS enhances tanshinone biosynthesis through SmWRKY1- and SmWRKY2-regulated pathways relying on Ca2+ signaling. Ca2+ signal transduction plays a key role in regulating tanshinone biosynthesis in S. miltiorrhiza.
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Affiliation(s)
- Bin Zhang
- College of Life Sciences, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, China; (B.Z.); (X.L.); (Z.L.); (Q.O.Y.); (P.M.)
| | - Xueying Li
- College of Life Sciences, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, China; (B.Z.); (X.L.); (Z.L.); (Q.O.Y.); (P.M.)
| | - Xiuhong Li
- College of Forestry, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, China;
| | - Zhigang Lu
- College of Life Sciences, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, China; (B.Z.); (X.L.); (Z.L.); (Q.O.Y.); (P.M.)
| | - Xiaona Cai
- College of Innovation and Experiment, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, China;
| | - Qing Ou Yang
- College of Life Sciences, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, China; (B.Z.); (X.L.); (Z.L.); (Q.O.Y.); (P.M.)
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, China; (B.Z.); (X.L.); (Z.L.); (Q.O.Y.); (P.M.)
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, China; (B.Z.); (X.L.); (Z.L.); (Q.O.Y.); (P.M.)
- Correspondence: ; Tel.: +86-029-8709-2262
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Mao R, He Z. Pinellia ternata (Thunb.) Breit: A review of its germplasm resources, genetic diversity and active components. JOURNAL OF ETHNOPHARMACOLOGY 2020; 263:113252. [PMID: 32798614 DOI: 10.1016/j.jep.2020.113252] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 07/15/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The medicinal plant Pinellia ternata has been widely used in China, Korea, and Japan and has been demonstrated to be highly effective for treating cough, vomiting, infection, and inflammatory diseases. Modern pharmacological investigations have demonstrated its multiple activities, such as antitussive, expectorant, antiemetic, antitumor, antibacterial, and sedative-hypnotic activities. AIM OF THE REVIEW This review aims to summarize the information about the biological traits, genetic diversity, active components, and continuous cropping obstacle of P. ternata in order to improve its use. MATERIALS AND METHODS In this review, the relevant literature was gathered by using Pinellia ternata, genetic diversity, active components, and continuous cropping obstacle as the keywords from Google Scholar, PubMed, Springer Link, the Wiley online library, SciFinder, SCOPUS, Baidu Scholar, China national knowledge infrastructure (CNKI), and WANFANF DATA (up to April 2020). RESULTS P. ternata is the most widely used herb in the Pinellia genus to treat several diseases. The genetic diversity of P. ternata has been extensively studied, and its high genetic diversity level in China has been demonstrated. Modern pharmacological research has indicated that amino acids, alkaloids, and polysaccharides are the main active components supporting P. ternata's medicinal effects. However, an efficient method for determining its active components is still unavailable. The method used to evaluate Pinelliae Rhizoma (PR) quality standards should be further optimized. The continuous cropping obstacle has a significant effect on the quantity and quality of P. ternata. The underlying mechanism of the continuous cropping obstacle needs to be further explored. CONCLUSIONS P. ternata has emerged as a valuable source of traditional medicine. Some uses of P. ternata in medicine have been validated by pharmacological investigations. However, a more efficient analytical method should be established to evaluate the quality of PR based on multiple quality markers. Furthermore, high-performance liquid chromatography (HPLC) and DNA barcoding should be introduced to identify the authenticity of PR. In addition, the genes involved in the metabolic synthesis pathways of the main active components, population genetic relationships, the quality control of processed PR, and the continuous cropping obstacle need to be further elucidated. We hope this review will allow for better utilization of this valuable herb.
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Affiliation(s)
- Renjun Mao
- College of Life Sciences & Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China.
| | - Zhigui He
- School of Leisure and Health, Guilin Tourism University, Guilin, 541006, Guangxi, China.
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Hairy root culture technology: applications, constraints and prospect. Appl Microbiol Biotechnol 2020; 105:35-53. [PMID: 33226470 DOI: 10.1007/s00253-020-11017-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022]
Abstract
Hairy root (HR) culture, a successful biotechnology combining in vitro tissue culture with recombinant DNA machinery, is intended for the genetic improvement of plants. This technology has been put to use since the last three decades for genetic advancement of medicinal and aromatic plants and also to harvest the economical products in the form of secondary metabolites that are significantly important for their ethnobotanical and pharmacological properties. It also provides an efficient way out for the quicker extraction and quantification of the valuable phytochemicals. The current review provides an account of the in vitro HR culture technology and its wide-scale applications in the field of research as well as in pharmaceutical industries. Different facets of HR with respect to the culture establishment, phytochemical production as well as research investigations concerning the areas of gene manipulation, biotransformation of the secondary metabolites, phytoremediation, their industrial utilisations and different problems encountered during the application of this technology have been covered in this appraisal. Eventually, an idea has been provided on HR about the recent trends on the progress of this technology that may open up newer prospects in near future and calls for further research and explorations in this field. KEY POINTS: • Genetic engineering-based HR culture aims towards enhanced secondary metabolite production. • This review explores an insight in the HR technology and its multi-faceted approaches. • Up-to-date ground-breaking research applications and constraints of HR culture are discussed.
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Shi M, Liao P, Nile SH, Georgiev MI, Kai G. Biotechnological Exploration of Transformed Root Culture for Value-Added Products. Trends Biotechnol 2020; 39:137-149. [PMID: 32690221 DOI: 10.1016/j.tibtech.2020.06.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 02/09/2023]
Abstract
Medicinal plants produce valuable secondary metabolites with anticancer, analgesic, anticholinergic or other activities, but low metabolite levels and limited available tissue restrict metabolite yields. Transformed root cultures, also called hairy roots, provide a feasible approach for producing valuable secondary metabolites. Various strategies have been used to enhance secondary metabolite production in hairy roots, including increasing substrate availability, regulating key biosynthetic genes, multigene engineering, combining genetic engineering and elicitation, using transcription factors (TFs), and introducing new genes. In this review, we focus on recent developments in hairy roots from medicinal plants, techniques to boost production of desired secondary metabolites, and the development of new technologies to study these metabolites. We also discuss recent trends, emerging applications, and future perspectives.
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Affiliation(s)
- Min Shi
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, China
| | - Pan Liao
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907-2063, USA
| | - Shivraj Hariram Nile
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, China
| | - Milen I Georgiev
- Laboratory of Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 139 Ruski Blvd, 4000 Plovdiv, Bulgaria; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Guoyin Kai
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, China.
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Wang Y, Shahid MQ, Ghouri F, Baloch FS. De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers. Biochem Genet 2020; 58:914-934. [DOI: 10.1007/s10528-020-09983-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/25/2020] [Indexed: 02/08/2023]
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Song W, Zhuang Y, Liu T. Potential role of two cytochrome P450s obtained from Lithospermum erythrorhizon in catalyzing the oxidation of geranylhydroquinone during Shikonin biosynthesis. PHYTOCHEMISTRY 2020; 175:112375. [PMID: 32305685 DOI: 10.1016/j.phytochem.2020.112375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Shikonin is a natural naphthoquinone derivative that specifically occurs in boraginaceous plants, and the major active ingredient of the medicinal plant Lithospermum erythrorhizon. Previously, a cytochrome P450 oxygenase (CYP) CYP76B74 catalyzing 3″-hydroxylation of geranylhydroquinone (GHQ) - a key intermediate of shikonin biosynthesis, was identified from cultured cells of Arnebia euchroma. However, the enzymes catalyzing oxidation of the geranyl side-chain of GHQ from L. erythrorhizon remain unknown. In this study, we performed transcriptome analysis of different tissues (red roots and green leaves/stems) from L. erythrorhizon using RNA sequencing technology. Highly expressed CYP genes found in the roots were then heterologously expressed in Saccharomyces cerevisiae and functionally screened with GHQ as the substrate. As the result, two CYPs of CYP76B subfamily catalyzing the oxidation of GHQ were characterized. CYP76B100 catalyzed the hydroxylation of the geranyl side-chain of GHQ at the C-3″ position to form 3″-hydroxyl geranylhydroquinone (GHQ-3″-OH). The enzyme CYP76B101 carried out oxidation reaction of GHQ at the C-3″ position to produce a 3″-carboxylic acid derivative of GHQ (GHQ-3″-COOH) as well as GHQ-3″-OH. This enzyme-catalyzed oxidation reaction with GHQ as the substrate is reported for the first time. This study implicates CYP76B100 and CYP76B101 as having a potential role in shikonin biosynthesis in L. erythrorhizon.
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Affiliation(s)
- Wan Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yibin Zhuang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Li A, Li A, Deng Z, Guo J, Wu H. Cross-Species Annotation of Expressed Genes and Detection of Different Functional Gene Modules Between 10 Cold- and 10 Hot-Propertied Chinese Herbal Medicines. Front Genet 2020; 11:532. [PMID: 32625232 PMCID: PMC7314971 DOI: 10.3389/fgene.2020.00532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/04/2020] [Indexed: 12/11/2022] Open
Abstract
According to the traditional Chinese medicine (TCM) system, Chinese herbal medicines (HMs) can be divided into four categories: hot, warm, cold, and cool. A cool nature usually is categorized as a cold nature, and a warm nature is classified as a hot nature. However, the detectable characteristics of the gene expression profile associated with the cold and hot properties have not been studied. To address this question, a strategy for the cross-species annotation of conserved genes was established in the present study by using transcriptome data of 20 HMs with cold and hot properties. Functional enrichment analysis was performed on group-specific expressed genes inferred from the functional genome of the reference species (i.e., Arabidopsis). Results showed that metabolic pathways relevant to chrysoeriol, luteolin, paniculatin, and wogonin were enriched for cold-specific genes, and pathways of inositol, heptadecane, lauric acid, octanoic acid, hexadecanoic acid, and pentadecanoic acid were enriched for hot-specific genes. Six functional modules were identified in the HMs with the cold property: nucleotide biosynthetic process, peptidy-L-cysteine S-palmitoylation, lipid modification, base-excision repair, dipeptide transport, and response to endoplasmic reticulum stress. For the hot HMs, another six functional modules were identified: embryonic meristem development, embryonic pattern specification, axis specification, regulation of RNA polymerase II transcriptional preinitiation complex assembly, mitochondrial RNA modification, and cell redox homeostasis. The research provided a new insight into HMs’ cold and hot properties from the perspective of the gene expression profile of plants.
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Affiliation(s)
- Arong Li
- Guangzhou Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pharmacy, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Aqian Li
- Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, School of Psychology, South China Normal University, Guangzhou, China
| | - Zhijun Deng
- Department of Pharmacy, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Jiewen Guo
- Guangzhou Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pharmacy, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Hongkai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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Liang J, Li W, Jia X, Zhang Y, Zhao J. Transcriptome sequencing and characterization of Astragalus membranaceus var. mongholicus root reveals key genes involved in flavonoids biosynthesis. Genes Genomics 2020; 42:901-914. [PMID: 32519170 DOI: 10.1007/s13258-020-00953-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/15/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Astragalus membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao is a traditional medicinal herb of Leguminosae since it contains bioactive compounds such as flavonoids, which have significant pharmacological effects on immunity and antioxidant. However, the scanty genomic and transcriptome resources of Astragalus membranaceus have hindered further exploration of its biosynthesis and accumulation mechanism. OBJECTIVE This project aim to further improve our understanding of the relationship between transcriptional behavior and flavonoids content of A. mongholicus. METHODS The accumulation of flavonoids and related gene expression in five different developmental stages (A: vegetative, B: florescence, C: fruiting, D: fruit ripening and E: defoliating stages) of A. mongholicus root were studied by combining UV spectrophotometry and transcriptomic techniques. The de novo assembly, annotation and functional evaluation of the contigs were performed with bioinformatics tools. RESULTS After screening and assembling the raw data, there were a total of 158,123 unigenes with an average length of 644.89 bp were finally obtained, which has 8362 unigenes could be jointly annotated by NR, SwissProt, eggNOG, GO, KEGG and Pfam databases. KEGG enrichment analysis was performed on differentially expressed genes(DEGs)in the four groups (A vs. B, B vs. C, C vs. D, D vs. E). The results showed that many DEGs in each group were significantly enriched to flavonoids biosynthesis related pathways. Among them, a number of 86 were involved in the biosynthesis of isoflavonoid (12), flavonoid (5) and phenylpropanoid (69). Further analysis of these DEGs revealed that the expression levels of key genes such as PAL, 4CL, CCR, COMT, DFR, etc. were all down-regulated at the fruiting stage, and then raised at the fruit ripening stage. This expression pattern was similar to the accumulation trend of total flavonoids content. CONCLUSIONS In summary, this comprehensive transcriptome dataset allowed the identification of genes associated with flavonoids metabolic pathways. The results laid a foundation for the biosynthesis and regulation of flavonoids. It also provided a scientific basis for the most suitable harvest time and resource utilization of A. mongholicus.
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Affiliation(s)
- Jianping Liang
- Department of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Wenqian Li
- Department of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xiaoyun Jia
- Department of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Ying Zhang
- Department of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Jianping Zhao
- Experiment mangement center, Shanxi University of Chinese Medicine, Jinzhong, 030619, Shanxi, China
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Wei T, Deng K, Gao Y, Chen L, Song W, Zhang Y, Wang C, Chen C. SmKSL overexpression combined with elicitor treatment enhances tanshinone production from Salvia miltiorrhiza hairy roots. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Chen Y, Pan W, Jin S, Lin S. Combined metabolomic and transcriptomic analysis reveals key candidate genes involved in the regulation of flavonoid accumulation in Anoectochilus roxburghii. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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40
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Teimoori-Boghsani Y, Ganjeali A, Cernava T, Müller H, Asili J, Berg G. Endophytic Fungi of Native Salvia abrotanoides Plants Reveal High Taxonomic Diversity and Unique Profiles of Secondary Metabolites. Front Microbiol 2020; 10:3013. [PMID: 32010087 PMCID: PMC6978743 DOI: 10.3389/fmicb.2019.03013] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022] Open
Abstract
Endophytic fungi are often embedded in their host's metabolic networks, which can result in alterations of metabolite production and higher amounts of active compounds in medicinal plants. This study reports the occurrence, diversity, and secondary metabolite profiles of endophytic fungi isolated from Salvia abrotanoides plants obtained from three geographically distinct sites in Iran. A total of 56 endophytic fungi were isolated from roots and leaves of S. abrotanoides; site-specificity and root-dominated colonization was found to be a general characteristic of the endophytes. Based on molecular identification, the endophytic fungi were classified into 15 genera. Mycelial extracts of these isolates were subjected to high-resolution mass spectrometry analyses and revealed a broad spectrum of secondary metabolites. Our results demonstrated that Penicillium canescens, P. murcianum, Paraphoma radicina, and Coniolariella hispanica are producers of cryptotanshinone, which is a main bioactive compound of S. abrotanoides. Moreover, it was shown that it can be produced independent of the host plant. The effect of exogenous gibberellin on S. abrotanoides and endophytic fungi was shown to have a positive effect on increasing the cryptotanshinone production in the plant as well as in endophytic fungi cultivated under axenic conditions. Our findings provide further evidence that endophytic fungi play an important role in the production plant bioactive metabolites. Moreover, they provide an exploitable basis to increase cryptotanshinone production in S. abrotanoides.
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Affiliation(s)
| | - Ali Ganjeali
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Javad Asili
- Department of Pharmacognosy, Faculty of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Zhang C, Xing B, Yang D, Ren M, Guo H, Yang S, Liang Z. SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots. PHYTOCHEMISTRY 2020; 169:112183. [PMID: 31704239 DOI: 10.1016/j.phytochem.2019.112183] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/15/2019] [Accepted: 10/19/2019] [Indexed: 05/24/2023]
Abstract
Phenolic acids and tanshinones are the two groups of pharmaceutically active metabolites in Salvia miltiorrhiza Bunge. Their contents are the key quality indicator to evaluate S. miltiorrhiza. bHLH transcription factors have important roles in regulation of plant specialised metabolism. In this study, an endogenous bHLH transcription factor, SmbHLH3, was identified and functionally analyzed. SmbHLH3 was presented in all the six tissues and mostly expressed in fibrous roots and flowers. It was localized to the nucleus. Overexpression of SmbHLH3 decreased both phenolic acids and tanshinones contents. Contents of caffeic acid and rosmarinic acid were both decreased to 50% of the control. And accumulation of salvianolic acid B was decreased as much as 62%. Content of cryptotanshinone, dihydrotanshinone I, tanshinone I and tanshinone IIA in SmbHLH3-overexpression lines were reduced 97%, 62%, 86% and 91%, respectively. In the transgenic lines, expression of C4H1, TAT and HPPR in phenolic acids pathways were reduced to about 43%, 66% and 77% of the control, respectively. For tanshinone biosynthetic pathways, transcripts of DXS3, DXR, HMGR1, KSL1, CPS1 and CYP76AH1 were reduced to 46%, 65%, 78%, 57%, 27% and 62% of the control, respectively. There was an E/G-box specific binding site in SmbHLH3, which may bind the E/G-box present in promoter region of these biosynthetic pathway genes. Y1H results indicated that SmbHLH3 could bind the promoter of TAT, HPPR, KSL1 and CYP76AH1. These findings indicated that SmbHLH3 downregulate both phenolic acids and tanshinone accumulation through directly suppressing the transcription of key enzyme genes.
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Affiliation(s)
- Chenlu Zhang
- College of Biological Sciences & Engineering, Shaanxi University of Technology, Hanzhong, 723001, China.
| | - Bingcong Xing
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, 712100, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dongfeng Yang
- College of Life Sciences, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Min Ren
- Xinxiang University, Xinxiang, 453003, China
| | - Hui Guo
- Xinxiang University, Xinxiang, 453003, China
| | - Shushen Yang
- College of Biological Sciences & Engineering, Shaanxi University of Technology, Hanzhong, 723001, China
| | - Zongsuo Liang
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, 712100, China; College of Life Sciences, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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Integrated Metabolomics and Transcriptomics Unravel the Metabolic Pathway Variations for Different Sized Beech Mushrooms. Int J Mol Sci 2019; 20:ijms20236007. [PMID: 31795288 PMCID: PMC6928633 DOI: 10.3390/ijms20236007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 11/23/2022] Open
Abstract
Beech mushrooms (Hypsizygus marmoreus) are largely relished for their characteristic earthy flavor, chewy-texture, and gustatory and nutritional properties in East Asian societies. Intriguingly, the aforementioned properties of beech mushroom can be subsumed under its elusive metabolome and subtle transcriptome regulating its various stages of growth and development. Herein, we carried out an integrated metabolomic and transcriptomic profiling for different sized beech mushrooms across spatial components (cap and stipe) to delineate their signature pathways. We observed that metabolite profiles and differentially expressed gene (DEGs) displayed marked synergy for specific signature pathways according to mushroom sizes. Notably, the amino acid, nucleotide, and terpenoid metabolism-related metabolites and genes were more abundant in small-sized mushrooms. On the other hand, the relative levels of carbohydrates and TCA intermediate metabolites as well as corresponding genes were linearly increased with mushroom size. However, the composition of flavor-related metabolites was varying in different sized beech mushrooms. Our study explores the signature pathways associated with growth, development, nutritional, functional and organoleptic properties of different sized beech mushrooms.
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Yuan Y, Zhang J, Kallman J, Liu X, Meng M, Lin J. Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues. BMC PLANT BIOLOGY 2019; 19:521. [PMID: 31775630 PMCID: PMC6882186 DOI: 10.1186/s12870-019-2138-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/14/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Dendrobium moniliforme (Linnaeus) Swartz is a well-known plant used in traditional Chinese medicine due to bioactive constituents. Polysaccharides are the main medicinal ingredients, yet no studies have been published on polysaccharide biosynthesis in D. moniliforme. To comprehensively investigate the polysaccharide at the transcription level, we performed de novo transcriptome sequencing for the first time to produce a comprehensive transcriptome of D. moniliforme. RESULTS In our study, a database of 562,580 unigenes (average length = 1115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, we identified 1204 carbohydrate-active related unigenes against CAZy database, including 417 glycosyltransferase genes (GTs), 780 glycoside hydrolases (GHs), 19 carbohydrate esterases (CEs), 75 carbohydrate-binding modules (CBMs), and 44 polysaccharide lyases (PLs). In the cellulose synthase family, 21 differential expression genes (DEGs) related to polysaccharide were identified. Subsequently, the tissue-specific expression patterns of the genes involved in polysaccharide pathway were investigated, which provide understanding of the biosynthesis and regulation of DMP at the molecular level. The two key enzyme genes (Susy and SPS) involved in the polysaccharide pathway were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR. CONCLUSIONS We determined the content of polysaccharides from Dendrobium moniliforme under different tissues, and we obtained a large number of differential genes by transcriptome sequencing. This database provides a pool of candidate genes involved in biosynthesis of polysaccharides in D. moniliforme. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb.
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Affiliation(s)
- Yingdan Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
- Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037 China
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
- Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037 China
| | | | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
- Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037 China
| | - Miaojing Meng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
- Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037 China
| | - Jie Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
- Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, 210037 China
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Chang Y, Wang M, Li J, Lu S. Transcriptomic analysis reveals potential genes involved in tanshinone biosynthesis in Salvia miltiorrhiza. Sci Rep 2019; 9:14929. [PMID: 31624328 PMCID: PMC6797793 DOI: 10.1038/s41598-019-51535-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022] Open
Abstract
Tanshinones are important bioactive components in Salvia miltiorrhiza and mainly accumulate in the periderms of mature roots. Tanshinone biosynthesis is a complicated process, and little is known about the third stage of the pathway. To investigate potential genes that are responsible for tanshinone biosynthesis, we conducted transcriptome profiling analysis of two S. miltiorrhiza cultivars. Differential expression analysis provided 2,149 differentially expressed genes (DEGs) for further analysis. GO and KEGG analysis showed that the DEGs were mainly associated with the biosynthesis of secondary metabolites. Weighted gene coexpression network analysis (WGCNA) was further performed to identify a “cyan” module associated with tanshinone biosynthesis. In this module, 25 cytochromes P450 (CYPs), three 2-oxoglutarate-dependent dioxygenases (2OGDs), one short-chain alcohol dehydrogenases (SDRs) and eight transcription factors were found to be likely involved in tanshinone biosynthesis. Among these CYPs, 14 CYPs have been reported previously, and 11 CYPs were identified in this study. Expression analysis showed that four newly identified CYPs were upregulated upon application of MeJA, suggesting their possible roles in tanshinone biosynthesis. Overall, this study not only identified candidate genes involved in tanshinone biosynthesis but also provided a basis for characterization of genes involved in important active ingredients of other traditional Chinese medicinal plants.
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Affiliation(s)
- Yujie Chang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.,Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Metabolome and transcriptome analyses reveal quality change in the orange-rooted Salvia miltiorrhiza (Danshen) from cultivated field. Chin Med 2019; 14:42. [PMID: 31592267 PMCID: PMC6775661 DOI: 10.1186/s13020-019-0265-6] [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: 08/22/2019] [Accepted: 09/23/2019] [Indexed: 01/10/2023] Open
Abstract
Background The dry root and rhizome of Salvia miltiorrhiza Bunge, or Danshen, is a well-known, traditional Chinese medicine. Tanshinones are active compounds that accumulate in the periderm, resulting in red-colored roots. However, lines with orange roots have been observed in cultivated fields. Here, we performed metabolome and transcriptome analyses to investigate the changes of orange-rooted Danshen. Methods Metabolome analysis was performed by ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-Tof–MS) to investigate the metabolites variation between orange Danshen and normal Danshen. RNA sequencing and KEGG enrichment analysis were performed to analyzing the differentially expressed genes between orange-rooted and normal Danshen. Results In total, 40 lipophilic components were detected in metabolome analysis, and seven compounds were significantly decreased in the orange Danshen, including the most abundant active compounds, tanshinone IIA and tanshinone I in normal Danshen. Systematic analysis of transcriptome profiles revealed that the down-regulated genes related to catalytic dehydrogenation was not detected. However, two genes related to stress resistance, and four genes related to endoplasmic reticulum (ER)-associated degradation of proteins were up-regulated in orange Danshen. Conclusions Decreases in the content of dehydrogenated furan ring tanshinones such as tanshinone IIA resulted in phenotypic changes and quality degradation of Danshen. Transcriptome analysis indicated that incorrect folding and ER-associated degradation of corresponding enzymes, which could catalyze C15-C16 dehydrogenase, might be contributed to the decrease in dehydrogenated furan ring tanshinones, rather than lower expression of the relative genes. This limited dehydrogenation of cryptotanshinone and dihydrotanshinone I into tanshinones IIA and I products, respectively, led to a reduced quality of Danshen in cultivated fields.
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Zheng X, Li P, Lu X. Research advances in cytochrome P450-catalysed pharmaceutical terpenoid biosynthesis in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4619-4630. [PMID: 31037306 DOI: 10.1093/jxb/erz203] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Terpenoids, the biggest class of plant secondary metabolites, have a wide range of significant physiological roles, while many of them are important natural drugs. Biosynthesis of pharmaceutical terpenoids in plants is a fairly complex process, most of which involves cytochrome P450 (CYP450) monooxygenases. CYP450 enzymes are versatile biocatalysts that play critical roles in terpenoid skeleton modification and structural diversity. Therefore, the discovery and identification of CYP450 genes is significant for elucidating the terpenoid biosynthetic pathway. This review summarizes the progress and cloning strategies relating to CYP450s in pharmaceutical terpenoid biosynthesis of the past decade.
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Affiliation(s)
- Xiaoyan Zheng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
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Rahnamaie-Tajadod R, Goh HH, Mohd Noor N. Methyl jasmonate-induced compositional changes of volatile organic compounds in Polygonum minus leaves. JOURNAL OF PLANT PHYSIOLOGY 2019; 240:152994. [PMID: 31226543 DOI: 10.1016/j.jplph.2019.152994] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/10/2019] [Accepted: 06/10/2019] [Indexed: 05/19/2023]
Abstract
Polygonum minus Huds. is a medicinal aromatic plant rich in terpenes, aldehydes, and phenolic compounds. Methyl jasmonate (MeJA) is a plant signaling molecule commonly applied to elicit stress responses to produce plant secondary metabolites. In this study, the effects of exogenous MeJA treatment on the composition of volatile organic compounds (VOCs) in P. minus leaves were investigated by using a metabolomic approach. Time-course changes in the leaf composition of VOCs on days 1, 3, and 5 after MeJA treatment were analyzed through solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS). The VOCs found in MeJA-elicited leaves were similar to those found in mock-treated leaves but varied in quantity at different time points. We focused our analysis on the content and composition of monoterpenes, sesquiterpenes, and green leaf volatiles (GLVs) within the leaf samples. Our results suggest that MeJA enhances the activity of biosynthetic pathways for aldehydes and terpenes in P. minus. Hence, the production of aromatic compounds in this medicinal herb can be increased by MeJA elicitation. Furthermore, the relationship between MeJA elicitation and terpene biosynthesis in P. minus was shown through SPME-GC-MS analysis of VOCs combined with transcriptomic analysis of MeJA-elicited P. minus leaves from our previous study.
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Affiliation(s)
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia.
| | - Normah Mohd Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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48
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Zhang B, Wang C, Yang W, Zhang H, Meng Q, Shi B, Shan A. Transcriptome analysis of the effect of pyrroloquinoline quinone disodium (PQQ·Na 2) on reproductive performance in sows during gestation and lactation. J Anim Sci Biotechnol 2019; 10:62. [PMID: 31406573 PMCID: PMC6685232 DOI: 10.1186/s40104-019-0369-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023] Open
Abstract
Background Pyrroloquinoline quinone (PQQ), which is a water soluble, thermo-stable triglyceride-quinone, is widely distributed in nature and characterized as a mammalian vitamin-like redox cofactor. The objective of this study was to investigate the effects of pyrroloquinoline quinone disodium (PQQ·Na2) on reproductive performance in sows. Results Dietary supplementation with PQQ·Na2 significantly increased the total number of piglets born, the number of piglets born alive and the born alive litter weight. It also increased the antioxidant status in the placenta, plasma and milk. The concentration of NO was significantly increased in the plasma and placenta. RNA-seq analysis showed that 462 unigenes were differentially expressed between the control (Con) treatment and PQQ treatment groups. Among these unigenes, 199 were upregulated, while 263 unigenes were downregulated. The assigned functions of the unigenes covered a broad range of GO categories. Reproduction (27, 7.03%) and the reproduction process (27, 7.03%) were assigned to the biological process category. By matching DEGs to the KEGG database, we identified 29 pathways. Conclusions In conclusion, dietary supplementation with PQQ·Na2 in gestating and lactating sows had positive effects on their reproductive performance. Electronic supplementary material The online version of this article (10.1186/s40104-019-0369-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Boru Zhang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Chenxi Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Wei Yang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Hongyun Zhang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Qingwei Meng
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Baoming Shi
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
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Liu X, Jin M, Zhang M, Li T, Sun S, Zhang J, Dai J, Wang Y. The application of combined 1H NMR-based metabolomics and transcriptomics techniques to explore phenolic acid biosynthesis in Salvia miltiorrhiza Bunge. J Pharm Biomed Anal 2019; 172:126-138. [PMID: 31035094 DOI: 10.1016/j.jpba.2019.04.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022]
Abstract
Salvia miltiorrhiza Bunge is a traditional Chinese medicine, and its water-soluble phenolic acid active compounds have very important medicinal value; however, the synthesis pathways of the main active ingredients remain unknown. Here, we employed nuclear magnetic resonance (NMR)-based metabolomics and transcriptomics techniques to study the biosynthesis mechanism of salvianolic acids. High-performance liquid chromatography (HPLC) combined with NMR showed an improvement over traditional techniques, and 54 metabolites were detected. The results of the multivariate statistical analysis showed that salvianolic acid B (SAB), rosmarinic acid (RA), caffeic acid, succinate, and citrate were among the multiple compounds that were increased in the methyl jasmonate (MeJA)-elicited group; the levels of sucrose, fructose, glutamine, and tyrosine were decreased. Combined with the differentially expressed genes (DEGs) found by transcriptome sequencing, we speculate that the synthesis of RA after MeJA treatment mostly occurred through caffeic acid and bypassed 4-hydroxyphenyllactic acid. This provides useful information for the study of salvianolic acids synthesis.
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Affiliation(s)
- Xia Liu
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Mengxia Jin
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Min Zhang
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Tianqi Li
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Shanshan Sun
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Jinyue Zhang
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Jungui Dai
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Yinghong Wang
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China.
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Contreras A, Leroy B, Mariage PA, Wattiez R. Proteomic analysis reveals novel insights into tanshinones biosynthesis in Salvia miltiorrhiza hairy roots. Sci Rep 2019; 9:5768. [PMID: 30962498 PMCID: PMC6453882 DOI: 10.1038/s41598-019-42164-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 03/26/2019] [Indexed: 12/29/2022] Open
Abstract
Salvia miltiorrhiza is a medicinal plant highly appreciated by its content of tanshinones and salvianolic acids. Tanshinones are of particular relevance for their anti-oxidant, anti-tumoral and anti-inflammatory properties. Abiotic and biotic agents as silver nitrate and yeast extract have shown efficiently to stimulate tanshinone accumulation, but the underlying molecular mechanism remains essentially unknown. By using hairy roots as experimental material and the elicitors mentioned, were obtained up to 22 mg of tanshinones per gram of dry weight. Differential label-free quantitative proteomic analysis was applied to study the proteins involved in tanshinone biosynthesis. A total of 2650 proteins were identified in roots extracts, of which 893 showed statistically (p < 0.05) significant change in relative abundance compared to control roots, 251 proteins were upregulated and 642 downregulated. Among the upregulated proteins the predominant functional categories were metabolism (47%), stress defense (18%) and redox homeostasis (10%). Within the metabolism category, isoprenoid metabolism enzymes, cytochromes P450 and FAD-binding berberine proteins showed abundance profile linked to tanshinone concentration. The results presented here allowed to propose 5 new cytochromes P450 and 5 berberine enzymes as candidates to be involved into tanshinone biosynthesis, a novel finding that opens new avenues to improve tanshinone production through biotechnological approaches.
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Affiliation(s)
- Angela Contreras
- Proteomics and Microbiology department, Research center for Biosciences, University of Mons, 20 place du Parc, Mons, 7000, Belgium
| | - Baptiste Leroy
- Proteomics and Microbiology department, Research center for Biosciences, University of Mons, 20 place du Parc, Mons, 7000, Belgium
| | | | - Ruddy Wattiez
- Proteomics and Microbiology department, Research center for Biosciences, University of Mons, 20 place du Parc, Mons, 7000, Belgium.
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