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Wei G, Zhang G, Li M, Zheng Y, Zheng W, Wang B, Zhang Z, Zhang X, Huang Z, Wei T, Shi L, Chen S, Dong L. Panax notoginseng: panoramagram of phytochemical and pharmacological properties, biosynthesis, and regulation and production of ginsenosides. HORTICULTURE RESEARCH 2024; 11:uhae170. [PMID: 39135729 PMCID: PMC11317898 DOI: 10.1093/hr/uhae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/12/2024] [Indexed: 08/15/2024]
Abstract
Panax notoginseng is a famous perennial herb widely used as material for medicine and health-care food. Due to its various therapeutic effects, research work on P. notoginseng has rapidly increased in recent years, urging a comprehensive review of research progress on this important medicinal plant. Here, we summarize the latest studies on the representative bioactive constituents of P. notoginseng and their multiple pharmacological effects, like cardiovascular protection, anti-tumor, and immunomodulatory activities. More importantly, we emphasize the biosynthesis and regulation of ginsenosides, which are the main bioactive ingredients of P. notoginseng. Key enzymes and transcription factors (TFs) involved in the biosynthesis of ginsenosides are reviewed, including diverse CYP450s, UGTs, bHLH, and ERF TFs. We also construct a transcriptional regulatory network based on multi-omics data and predicted candidate TFs mediating the biosynthesis of ginsenosides. Finally, the current three major biotechnological approaches for ginsenoside production are highlighted. This review covers advances in the past decades, providing insights into quality evaluation and perspectives for the rational utilization and development of P. notoginseng resources. Modern omics technologies facilitate the exploration of the molecular mechanisms of ginsenoside biosynthesis, which is crucial to the breeding of novel P. notoginseng varieties. The identification of functional enzymes for biosynthesizing ginsenosides will lead to the formulation of potential strategies for the efficient and large-scale production of specific ginsenosides.
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Affiliation(s)
- Guangfei Wei
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Guozhuang Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Mengzhi Li
- Nanyang Institute of Technology, Nanyang, No.80, Changjiang Road, Wulibao Street, Wancheng District, 473000, China
| | - Yuqing Zheng
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, No. 1 Amber Road, Xiangcheng District, Zhangzhou, Fujian, 363099, China
| | - Wenke Zheng
- Tianjin University of Traditional Chinese Medicine, No. 312, Anshan West Road, Nankai District, Tianjin, 301617, China
| | - Bo Wang
- Hubei Institute for Drug Control, No.54, Dingziqiao Road, Zhongnan Road, Wuchang District, Wuhan, 430012, China
| | - Zhaoyu Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Xiao Zhang
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, No. 1 Amber Road, Xiangcheng District, Zhangzhou, Fujian, 363099, China
| | - Ziying Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Tengyun Wei
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, No. 1 Amber Road, Xiangcheng District, Zhangzhou, Fujian, 363099, China
| | - Liping Shi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
| | - Shilin Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, No. 37, 12 Qiao Road, Jinniu District, Chengdu, 611137, China
| | - Linlin Dong
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16 Nanxiaojie, Dongzhimennei Ave., Beijing, 100700, China
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Rahman H, Vikram P, Hu Y, Asthana S, Tanaji A, Suryanarayanan P, Quadros C, Mehta L, Shahid M, Gkanogiannis A, Thushar S, Balazadeh S, Mueller-Roeber B, Becerra Lopez-Lavalle LA, Wei T, Singh RK. Mining genomic regions associated with agronomic and biochemical traits in quinoa through GWAS. Sci Rep 2024; 14:9205. [PMID: 38649738 PMCID: PMC11035704 DOI: 10.1038/s41598-024-59565-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Quinoa (Chenopodium quinoa Willd.), an Andean crop, is a facultative halophyte food crop recognized globally for its high nutritional value and plasticity to adapt to harsh conditions. We conducted a genome-wide association study on a diverse set of quinoa germplasm accessions. These accessions were evaluated for the following agronomic and biochemical traits: days to 50% flowering (DTF), plant height (PH), panicle length (PL), stem diameter (SD), seed yield (SY), grain diameter (GD), and thousand-grain weight (TGW). These accessions underwent genotyping-by-sequencing using the DNBSeq-G400R platform. Among all evaluated traits, TGW represented maximum broad-sense heritability. Our study revealed average SNP density of ≈ 3.11 SNPs/10 kb for the whole genome, with the lowest and highest on chromosomes Cq1B and Cq9A, respectively. Principal component analysis clustered the quinoa population in three main clusters, one clearly representing lowland Chilean accessions, whereas the other two groups corresponded to germplasm from the highlands of Peru and Bolivia. In our germplasm set, we estimated linkage disequilibrium decay to be ≈ 118.5 kb. Marker-trait analyses revealed major and consistent effect associations for DTF on chromosomes 3A, 4B, 5B, 6A, 7A, 7B and 8B, with phenotypic variance explained (PVE) as high as 19.15%. Nine associations across eight chromosomes were also found for saponin content with 20% PVE by qSPN5A.1. More QTLs were identified for PL and TGW on multiple chromosomal locations. We identified putative candidate genes in the genomic regions associated with DTF and saponin content. The consistent and major-effect genomic associations can be used in fast-tracking quinoa breeding for wider adaptation across marginal environments.
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Affiliation(s)
- Hifzur Rahman
- International Center for Biosaline Agriculture, Dubai, UAE.
| | - Prashant Vikram
- International Center for Biosaline Agriculture, Dubai, UAE
- SGT University, Gurugram, Haryana, India
| | - Yulan Hu
- BGI-Research, 518083, Shenzhen, China
- BGI Research, 430074, Wuhan, China
| | | | - Abhinav Tanaji
- Birla Institute of Technology and Science Pilani, Dubai Campus, Dubai, UAE
| | | | - Chris Quadros
- Birla Institute of Technology and Science Pilani, Dubai Campus, Dubai, UAE
| | - Lovely Mehta
- International Center for Biosaline Agriculture, Dubai, UAE
| | | | | | | | - Salma Balazadeh
- Institute of Biology Leiden, Sylvius Laboratory, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
| | | | - Tong Wei
- International Center for Biosaline Agriculture, Dubai, UAE.
- BGI-Research, 518083, Shenzhen, China.
- BGI Research, 430074, Wuhan, China.
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Kochan E, Sienkiewicz M, Szmajda-Krygier D, Balcerczak E, Szymańska G. Carvacrol as a Stimulant of the Expression of Key Genes of the Ginsenoside Biosynthesis Pathway and Its Effect on the Production of Ginseng Saponins in Panax quinquefolium Hairy Root Cultures. Int J Mol Sci 2024; 25:909. [PMID: 38255986 PMCID: PMC10815547 DOI: 10.3390/ijms25020909] [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: 12/15/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The accumulation of ginsenosides (triterpenic saponins) was determined in Panax quinquefolium hairy root cultures subjected to an elicitation process using carvacrol at 5, 10, 25, 50, 100, 250, and 500 μM concentrations during 24 and 72 h exposure. This study was the first one in which carvacrol was applied as an elicitor. The content of eight ginsenosides, Rb1, Rb2, Rb3, Rc, Rd, Rg1, Rg2, and Re, was determined using HPLC analysis. Moreover, the quantitative RT-PCR method was applied to assess the relative expression level of farnesyl diphosphate synthase, squalene synthase, and dammarenediol synthase genes in the studied cultures. The addition of carvacrol (100 μM) was an effective approach to increase the production of ginsenosides. The highest content and productivity of all detected saponins were, respectively, 20.01 mg∙g-1 d.w. and 5.74 mg∙L-1∙day-1 after 72 h elicitation. The production profile of individual metabolites in P. quinquefolium cultures changed under the influence of carvacrol. The biosynthesis of most examined protopanaxadiol derivatives was reduced under carvacrol treatment. In contrast, the levels of ginsenosides belonging to the Rg group increased. The strongest effect of carvacrol was noticed for Re metabolites, achieving a 7.72-fold increase in comparison to the control. Saponin Rg2, not detected in untreated samples, was accumulated after carvacrol stimulation, reaching its maximum concentration after 72 h exposure to 10 μM elicitor.
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Affiliation(s)
- Ewa Kochan
- Department of Pharmaceutical Biotechnology, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
| | - Monika Sienkiewicz
- Department of Pharmaceutical Microbiology and Microbiological Diagnostics, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland;
| | - Dagmara Szmajda-Krygier
- Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (D.S.-K.); (E.B.)
| | - Ewa Balcerczak
- Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (D.S.-K.); (E.B.)
| | - Grażyna Szymańska
- Department of Pharmaceutical Biotechnology, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
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Yang Z, Dong D, Qi Z, Jia C, Han L, Chao Y. Genome-wide identification, expression analysis, and transcriptome analysis of the IAA gene family in Zoysia japonica. Mol Biol Rep 2023; 50:4385-4394. [PMID: 36961632 DOI: 10.1007/s11033-022-08154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/23/2022] [Indexed: 03/25/2023]
Abstract
BACKGROUND AUX/IAA is an essential signaling molecule and has great physiological importance in various plants, but its function in Zoysia japonica remains unknown. METHODS AND RESULTS Genome-wide identification and analysis of AUX/IAA genes used bioinformatics methods to investigate the ZjIAA genes' expression of exogenous IAA hydroponics treatment for 2 h by qRT-PCR, control and exogenous IAA treated zoysia were subjected to transcriptome sequencing. ZjIAAs were distributed across the 13 subfamilies by phylogenetic analysis with Oryza sativa and Arabidopsis thaliana. Multiple sequence alignment revealed that the majority of genes were non-canonical ZjIAAs with incomplete domain. The optimal growth concentration of the IAA hormone was 0.05 mM, and the qRT-PCR analysis revealed that eight ZjIAAs were differentially expressed, with seven genes considerably upregulating and one gene significantly downregulating. The result of transcriptome sequencing revealed that 515 differentially expressed genes (DEGs) were identified, with 344 upregulated genes and 171 downregulated genes. A total of 18 genes were annotated as involved in the plant hormone signal transduction pathway. And 8 ZjIAAs exhibited distinct expressions, 7 upregulated, and only one downregulated, according to the qRT-PCR study. CONCLUSIONS Genome-wide identification and analysis increased the understanding of the evolution and function of the IAA family in zoysia. DEGs of control and treatment with 0.05 mM exogenous IAA hormone were investigated by transcriptome sequencing. ZjIAAs had substantial variations in the expression of associated genes, with the majority of genes upregulated and 18 genes implicated in plant hormone signal transduction.
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Affiliation(s)
- Zhuoxiong Yang
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Di Dong
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Zewen Qi
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Chenyan Jia
- Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd, Hohhot, 010010, Inner Mongolia, China
| | - Liebao Han
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
| | - Yuehui Chao
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
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Wadapurkar RM, Sivaram A, Vyas R. Computational studies reveal co-occurrence of two mutations in IL7R gene of high-grade serous carcinoma patients. J Biomol Struct Dyn 2022; 40:13310-13324. [PMID: 34657565 DOI: 10.1080/07391102.2021.1987326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Major cause of mortality in ovarian cancer can be attributed to a lack of specific and sensitive biomarkers for diagnosis and prognosis of the disease. Uncovering the mutations in genes involved in crucial oncogenic pathways is a key step in discovery and development of novel biomarkers. Whole exome sequencing (WES) is a powerful method for the detection of cancer driver mutations. The present work focuses on identifying functionally damaging mutations in patients with high-grade serous ovarian carcinoma (HGSC) through computational analysis of WES. In this study, WES data of HGSC patients was retrieved from the genomic literature available in sequence read archive, the variants were identified and comprehensive structural and functional analysis was performed. Interestingly, I66T and V138I mutations were found to be co-occurring in the IL7R gene in four out of five HGSC patient samples investigated in this study. The V138I mutation was located in the fibronectin type-3 domain and computationally assessed to be causing disruptive effects on the structure and dynamics of IL7R protein. This mutation was found to be co-occurring with the neutral I66T mutation in the same domain which compensated the disruptive effects of V138I variant. These comprehensive studies point to a hitherto unexplored significant role of the IL7R gene in ovarian carcinoma. It is envisaged that the work will lay the foundation for the development of a novel biomarker with potential application in molecular profiling and in estimation of the disease prognosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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Tyagi P, Singh D, Mathur S, Singh A, Ranjan R. Upcoming progress of transcriptomics studies on plants: An overview. FRONTIERS IN PLANT SCIENCE 2022; 13:1030890. [PMID: 36589087 PMCID: PMC9798009 DOI: 10.3389/fpls.2022.1030890] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and developmental stages. RNA-Seq is a significant technique for identifying gene predictions and mining functional analysis that improves gene ontology understanding mechanisms of biological processes, molecular functions, and cellular components, but there is limited information available on this topic. Transcriptomics research on different types of plants can assist researchers to understand functional genes in better ways and regulatory processes to improve breeding selection and cultivation practices. In recent years, several advancements in RNA-Seq technology have been made for the characterization of the transcriptomes of distinct cell types in biological tissues in an efficient manner. RNA-Seq technologies are briefly introduced and examined in terms of their scientific applications. In a nutshell, it introduces all transcriptome sequencing and analysis techniques, as well as their applications in plant biology research. This review will focus on numerous existing and forthcoming strategies for improving transcriptome sequencing technologies for functional gene mining in various plants using RNA- Seq technology, based on the principles, development, and applications.
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Jiang Z, Gao H, Liu R, Xia M, Lu Y, Wang J, Chen X, Zhang Y, Li D, Tong Y, Liu P, Liu Y, Luo Y, Gao J, Yin Y, Huang L, Gao W. Key Glycosyltransferase Genes of Panax notoginseng: Identification and Engineering Yeast Construction of Rare Ginsenosides. ACS Synth Biol 2022; 11:2394-2404. [PMID: 35687875 DOI: 10.1021/acssynbio.2c00094] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Panax notoginseng is one of the most famous valuable medical plants in China, and its broad application in clinical treatment has an inseparable relationship with the active molecules, ginsenosides. Ginsenosides are glycoside compounds that have varied structures for the diverse sugar chain. Although extensive work has been done, there are still unknown steps in the biosynthetic pathway of ginsenosides. Here, we screened candidate glycosyltransferase genes based on the previous genome and transcriptome data of P. notoginseng and cloned the full length of 27 UGT genes successfully. Among them, we found that PnUGT33 could catalyze different ginsenoside substrates to produce higher polarity rare ginsenosides by extending the sugar chain. We further analyzed the enzymatic kinetics and predicted the catalytic mechanism of PnUGT33 by simulating molecular docking. After that, we reconstructed the biosynthetic pathway of rare ginsenoside Rg3 and gypenoside LXXV in yeast. By combining the Golden Gate method and overexpressing the UDPG biosynthetic genes, we further improved the yield of engineering yeast strain. Finally, the shake-flask culture yield of Rg3 reached 51 mg/L and the fed-batch fermentation yield of gypenoside LXXV reached 94.5 mg/L, which was the first and highest record.
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Affiliation(s)
- Zhouqian Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Haiyun Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Rong Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Meng Xia
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Jiadian Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Xiaochao Chen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yifeng Zhang
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, People's Republic of China
| | - Dan Li
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, People's Republic of China
| | - Panting Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yunfeng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Jie Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yan Yin
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, People's Republic of 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 100700, People's Republic of China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, People's Republic of China
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Chauhan N, Porte S, Joshi V, Shah K. Plants' steroidal saponins - A review on its pharmacology properties and analytical techniques. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/2311-8571.353503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Bai Y, Liu H, Pan J, Zhang S, Guo Y, Xian Y, Sun Z, Zhang Z. Transcriptomics and Metabolomics Changes Triggered by Inflorescence Removal in Panax notoginseng (Burk.). FRONTIERS IN PLANT SCIENCE 2021; 12:761821. [PMID: 34868157 PMCID: PMC8636121 DOI: 10.3389/fpls.2021.761821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
The root of Panax notoginseng (Burk.), in which saponins are the major active components, is a famous traditional Chinese medicine used to stop bleeding and to decrease inflammation and heart disease. Inflorescence removal increases the yield and quality of P. notoginseng, but the underlying molecular mechanisms are unknown. Here, the differences between inflorescence-removal treatment and control groups of P. notoginseng were compared using transcriptomics and metabolomics analyses. Illumina sequencing of cDNA libraries prepared from the rhizomes, leaves and roots of the two groups independently identified 6,464, 4,584, and 7,220 differentially expressed genes (DEG), respectively. In total, 345 differentially expressed transcription factors (TFs), including MYB and WRKY family members, were induced by the inflorescence-removal treatment. Additionally, 215 DEGs involved in saponin terpenoid backbone biosynthetic pathways were identified. Most genes involved in the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways were activated by inflorescence removal. The co-expression analysis showed that the low expression levels of flavonoid biosynthesis-related genes (e.g., C4H and F3H) decreased the biosynthesis and accumulation of some flavonoids after inflorescence removal. The results not only provide new insights into the fundamental mechanisms underlying the poorly studied inflorescence-removal process in P. notoginseng and other rhizome crops, but they also represent an important resource for future research on gene functions during inflorescence-removal treatments and the reproductive stage.
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Tien NQD, Ma X, Man LQ, Chi DTK, Huy NX, Nhut DT, Rombauts S, Ut T, Loc NH. De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng ( Panax vietnamensis Ha et Grushv.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2215-2229. [PMID: 34744362 PMCID: PMC8526660 DOI: 10.1007/s12298-021-01076-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 05/04/2023]
Abstract
UNLABELLED Vietnamese ginseng (Panax vietnamensis Ha et Grushv.), also known as Ngoc Linh ginseng, is a high-value herb in Vietnam. Vietnamese ginseng has been proven to be effective in enhancing the immune system, human memory, anti-stress, anti-inflammatory, anti-cancer, and prevent aging. The present study reports the first draft whole-genome of Vietnamese ginseng and the identification of potential genes involved in the triterpenoid metabolic pathway. De novo whole-genome assembly was performed successfully from a data of approximately 139 Gbps of 394,802,120 high quality reads to generate 9815 scaffolds with an N50 value of 572,722 bp from the leaf of Vietnamese ginseng. The assembled genome of Vietnamese ginseng is 3,001,967,204 bp long containing 79,374 gene models. Among them, there are 55,012 genes (69.30%) were annotated by various public molecular biology databases. The potential genes involved in triterpenoid saponin biosynthesis in Vietnamese ginseng and their metabolic pathway were also predicted." Three genes encoding squalene monooxygenase isozymes in Vietnamese ginseng were cloned, sequenced and characterized. Moreover, expression levels of several key genes involved in terpenoid biosynthesis in different parts of Vietnamese ginseng were also analyzed. The SSR markers were detected by various programs from both of assembly full dataset of Vietnamese ginseng genome and predicted genes. The present work provided important data of the draft whole-genome of Vietnamese ginseng for further studies to understand the role of genes involved in ginsenoside biosynthesis and their metabolic pathway at the molecular level of this rare medicinal species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01076-1.
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Affiliation(s)
- Nguyen Quang Duc Tien
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
- Department of Biology, Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | - Xiao Ma
- VIB-UGent Center for Plant Systems Biology, Ghent University, 9000 Ghent, Belgium
| | - Le Quang Man
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | - Duong Thi Kim Chi
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | | | - Duong-Tan Nhut
- Tay Nguyen Institute of Scientific Research, Vietnam Academy of Science and Technology, Dalat, 670000 Vietnam
| | - Stephane Rombauts
- VIB-UGent Center for Plant Systems Biology, Ghent University, 9000 Ghent, Belgium
| | - Tran Ut
- Ngoc Linh Ginseng and Medicinal Materials Development Center, Quang Nam Quang Ngai, 51000 Vietnam
| | - Nguyen Hoang Loc
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
- Department of Biology, Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
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Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng. Int J Mol Sci 2021; 22:ijms22168694. [PMID: 34445398 PMCID: PMC8395461 DOI: 10.3390/ijms22168694] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Gibberellins (GAs) are an important group of phytohormones associated with diverse growth and developmental processes, including cell elongation, seed germination, and secondary growth. Recent genomic and genetic analyses have advanced our knowledge of GA signaling pathways and related genes in model plant species. However, functional genomics analyses of GA signaling pathways in Panax ginseng, a perennial herb, have rarely been carried out, despite its well-known economical and medicinal importance. Here, we conducted functional characterization of GA receptors and investigated their physiological roles in the secondary growth of P. ginseng storage roots. We found that the physiological and genetic functions of P. ginseng gibberellin-insensitive dwarf1s (PgGID1s) have been evolutionarily conserved. Additionally, the essential domains and residues in the primary protein structure for interaction with active GAs and DELLA proteins are well-conserved. Overexpression of PgGID1s in Arabidopsis completely restored the GA deficient phenotype of the Arabidopsis gid1a gid1c (atgid1a/c) double mutant. Exogenous GA treatment greatly enhanced the secondary growth of tap roots; however, paclobutrazol (PCZ), a GA biosynthetic inhibitor, reduced root growth in P. ginseng. Transcriptome profiling of P. ginseng roots revealed that GA-induced root secondary growth is closely associated with cell wall biogenesis, the cell cycle, the jasmonic acid (JA) response, and nitrate assimilation, suggesting that a transcriptional network regulate root secondary growth in P. ginseng. These results provide novel insights into the mechanism controlling secondary root growth in P. ginseng.
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Guo J, Huang Z, Sun J, Cui X, Liu Y. Research Progress and Future Development Trends in Medicinal Plant Transcriptomics. FRONTIERS IN PLANT SCIENCE 2021; 12:691838. [PMID: 34394145 PMCID: PMC8355584 DOI: 10.3389/fpls.2021.691838] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/29/2021] [Indexed: 05/17/2023]
Abstract
Transcriptomics is one of the most popular topics in biology in recent times. Transcriptome sequencing (RNA-Seq) is a high-throughput, high-sensitivity, and high-resolution technique that can be used to study model and non-model organisms. Transcriptome sequencing is also an important method for studying the genomes of medicinal plants, a topic on which limited information is available. The study of medicinal plants through transcriptomics can help researchers analyze functional genes and regulatory mechanisms of medicinal plants and improve breeding selection and cultivation techniques. This article analyzes and compares the applications of transcriptome sequencing in medicinal plants over the past decade and briefly introduces the methods of transcriptome sequencing and analysis, their applications in medicinal plant research, and potential development trends. We will focus on the research and application progress of transcriptome sequencing in the following four areas: the mining of functional genes in medicinal plants, development of molecular markers, biosynthetic pathways of secondary metabolites, and developmental mechanisms of medicinal plants. Our review will provide ideas for the mining of functional genes of medicinal plants and breeding new varieties.
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Affiliation(s)
- Junda Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Zhen Huang
- Yuxi Walvax Biotechnology Co., Ltd., Yuxi, China
| | - Jialing Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
- Key Laboratory of Panax Notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
- Key Laboratory of Panax Notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
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13
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Chopra P, Chhillar H, Kim YJ, Jo IH, Kim ST, Gupta R. Phytochemistry of ginsenosides: Recent advancements and emerging roles. Crit Rev Food Sci Nutr 2021; 63:613-640. [PMID: 34278879 DOI: 10.1080/10408398.2021.1952159] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ginsenosides, a group of tetracyclic saponins, accounts for the nutraceutical and pharmaceutical relevance of the ginseng (Panax sp.) herb. Owing to the associated therapeutic potential of ginsenosides, their demand has been increased significantly in the last two decades. However, a slow growth cycle, low seed production, and long generation time of ginseng have created a gap between the demand and supply of ginsenosides. The biosynthesis of ginsenosides involves an intricate network of pathways with multiple oxidation and glycosylation reactions. However, the exact functions of some of the associated genes/proteins are still not completely deciphered. Moreover, ginsenoside estimation and extraction using analytical techniques are not feasible with high efficiency. The present review is a step forward in recapitulating the comprehensive aspects of ginsenosides including their distribution, structural diversity, biotransformation, and functional attributes in both plants and animals including humans. Moreover, ginsenoside biosynthesis in the potential plant sources and their metabolism in the human body along with major regulators and stimulators affecting ginsenoside biosynthesis have also been discussed. Furthermore, this review consolidates biotechnological interventions to enhance the biosynthesis of ginsenosides in their potential sources and advancements in the development of synthetic biosystems for efficient ginsenoside biosynthesis to meet their rising industrial demands.
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Affiliation(s)
- Priyanka Chopra
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Himanshu Chhillar
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - Ick Hyun Jo
- Department of Herbal Crop Research, Rural Development Administration, Eumseong, South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - Ravi Gupta
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India.,Department of Forestry, Environment, and Systems, College of Science and Technology, Kookmin University, Seoul, South Korea
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14
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Wang M, Qiu X, Pan X, Li C. Transcriptional Factor-Mediated Regulation of Active Component Biosynthesis in Medicinal Plants. Curr Pharm Biotechnol 2021; 22:848-866. [PMID: 32568019 DOI: 10.2174/1389201021666200622121809] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/06/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022]
Abstract
Plants produce thousands of chemically diverse secondary metabolites, many of which have valuable pharmaceutical properties. There is much interest in the synthesis of these pharmaceuticallyvaluable compounds, including the key enzymes and the transcription factors involved. The function and regulatory mechanism of transcription factors in biotic and abiotic stresses have been studied in depth. However, their regulatory roles in the biosynthesis of bioactive compounds, especially in medicinal plants, have only begun. Here, we review what is currently known about how transcription factors contribute to the synthesis of bioactive compounds (alkaloids, terpenoids, flavonoids, and phenolic acids) in medicinal plants. Recent progress has been made in the cloning and characterization of transcription factors in medicinal plants on the genome scale. So far, several large transcription factors have been identified in MYB, WRKY, bHLH, ZIP, AP2/ERF transcription factors. These transcription factors have been predicted to regulate bioactive compound production. These transcription factors positively or negatively regulate the expression of multiple genes encoding key enzymes, and thereby control the metabolic flow through the biosynthetic pathway. Although the research addressing this niche topic is in its infancy, significant progress has been made, and advances in high-throughput sequencing technology are expected to accelerate the discovery of key regulatory transcription factors in medicinal plants. This review is likely to be useful for those interested in the synthesis of pharmaceutically- valuable plant compounds, especially those aiming to breed or engineer plants that produce greater yields of these compounds.
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Affiliation(s)
- Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xian Pan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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Kim YK, Sathasivam R, Kim YB, Kim JK, Park SU. Transcriptomic Analysis, Cloning, Characterization, and Expression Analysis of Triterpene Biosynthetic Genes and Triterpene Accumulation in the Hairy Roots of Platycodon grandiflorum Exposed to Methyl Jasmonate. ACS OMEGA 2021; 6:12820-12830. [PMID: 34056433 PMCID: PMC8154235 DOI: 10.1021/acsomega.1c01202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/27/2021] [Indexed: 05/17/2023]
Abstract
Platycodon grandiflorum is a perennial plant that has been used for medicinal purposes. Specifically, it is widely used in Northern China and Korea for the treatment of various diseases. Terpenoids belong to a group called secondary metabolites and have attracted a wide range of interest. Here, we determined the expressed sequence tag (EST) library of the methyl jasmonate (MeJA)-treated hairy root of P. grandiflorum. In total, 5760 ESTs were obtained, but after deleting the vector sequences and removing poor-quality sequences, a total of 2536 ESTs were attained. Of these, 811 contigs and 1725 singletons were annotated. The data were further analyzed with a focus on the gene families of the terpenoid biosynthetic pathway (TBP). We identified and characterized four TBP genes; among these were three full-length cDNAs encoding PgHMGS, PgMK, and PgMVD, whereas PgHMGR had a partial sequence based on the EST library database. Phylogenetic analysis and a pairwise identity matrix showed that these identified genes were closely related to those of other higher plants. Moreover, the tertiary structure and multiple alignment analysis showed that several distinct conserved motifs were present. Quantitative reverse transcription-polymerase chain reaction results revealed that TBP genes were constitutively expressed in all organs of P. grandiflorum, while the expression of transcript levels of these genes varied distinctly among the organs. Additionally, the total amount of platycosides was highly detected in the root, accumulating in concentrations 7.8 and 2.6 times higher than in the hairy root and stem, respectively, and 1.4 times higher than in the leaf and flower. The highest amount of total phytosterols was found to accumulate in the leaves at 9.3, 9.1, 1.8, and 1.6 times higher than that of the stem, root, hairy root, and flower, respectively. After the hairy root was exposed to the MeJA treatment, the transcript levels of PgHMGS, PgHMGR, PgMK, and PgMVD had significantly increased. The highest level of transcript accumulation occurred at 3 h after initial exposure for most of the genes. Meanwhile, triterpene saponin accumulation increased with the increase in the time of exposure, and at 48 h after initial exposure, the total saponin content was the highest recorded.
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Affiliation(s)
- Yong-Kyoung Kim
- Division
of Safety Analysis, Experiment and Research Institute, National Agricultural Products Quality Management
Service, Gimcheon 39660, Republic of Korea
| | - Ramaraj Sathasivam
- Department
of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic
of Korea
| | - Yeon Bok Kim
- Department
of Medicinal and Industrial Crops, Korea
National College of Agriculture and Fisheries, Jeonju 54874, Republic of Korea
| | - Jae Kwang Kim
- Division
of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro,
Yeonsu-gu, Incheon 22012, Republic of Korea
- . Phone: +82-32-835-8241. Fax: +82-32-835-0763
| | - Sang Un Park
- Department
of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic
of Korea
- Department
of Smart Agriculture Systems, Chungnam National
University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- . Phone: +82-42-821-5730. Fax: +82-42-822-2631
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Su L, Li S, Qiu H, Wang H, Wang C, He C, Xu M, Zhang Z. Full-Length Transcriptome Analyses of Genes Involved in Triterpenoid Saponin Biosynthesis of Psammosilene tunicoides Hairy Root Cultures With Exogenous Salicylic Acid. Front Genet 2021; 12:657060. [PMID: 33854529 PMCID: PMC8039526 DOI: 10.3389/fgene.2021.657060] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/09/2021] [Indexed: 11/13/2022] Open
Abstract
Triterpenoid saponins constitute a diverse class of bioactive compounds in medicinal plants. Salicylic acid (SA) is an efficient elicitor for secondary metabolite production, but a transcriptome-wide regulatory network of SA-promoted triterpenoid saponin biosynthesis remains little understood. In the current study, we described the establishment of the hairy root culture system for Psammosilene tunicoides, a triterpenoid saponin-producing medicinal herb in China, using genetic transformation by Agrobacterium rhizogenes. Compared to controls, we found that total saponin content was dramatically increased (up to 2.49-fold) by the addition of 5 mg/L SA in hairy roots for 1 day. A combination of single-molecule real-time (SMRT) and next-generation sequencing (Illumina RNA-seq) was generated to analyze the full-length transcriptome data for P. tunicoides, as well as the transcript profiles in treated (8 and 24 h) and non-treated (0 h) groups with 5 mg/L SA in hairy roots. A total of 430,117 circular consensus sequence (CCS) reads, 16,375 unigenes and 4,678 long non-coding RNAs (lncRNAs) were obtained. The average length of unigenes (2,776 bp) was much higher in full-length transcriptome than that derived from single RNA-seq (1,457 bp). The differentially expressed genes (DEGs) were mainly enriched in the metabolic process. SA up-regulated the unigenes encoding SA-binding proteins and antioxidant enzymes in comparison with controls. Additionally, we identified 89 full-length transcripts encoding enzymes putatively involved in saponin biosynthesis. The candidate transcription factors (WRKY, NAC) and structural genes (AACT, DXS, SE, CYP72A) might be the key regulators in SA-elicited saponin accumulation. Their expression was further validated by quantitative real-time PCR (qRT-PCR). These findings preliminarily elucidate the regulatory mechanisms of SA on triterpenoid saponin biosynthesis in the transcriptomic level, laying a foundation for SA-elicited saponin augmentation in P. tunicoides.
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Affiliation(s)
- Lingye Su
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Shufang Li
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.,School of Biology Engineering, Dalian Polytechnic University, Dalian, China
| | - Hanhan Qiu
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.,School of Biology Engineering, Dalian Polytechnic University, Dalian, China
| | - Hongfeng Wang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Congcong Wang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Chunmei He
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Mingfeng Xu
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Zongshen Zhang
- School of Biology Engineering, Dalian Polytechnic University, Dalian, China
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17
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Jiang Z, Tu L, Yang W, Zhang Y, Hu T, Ma B, Lu Y, Cui X, Gao J, Wu X, Tong Y, Zhou J, Song Y, Liu Y, Liu N, Huang L, Gao W. The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis. PLANT COMMUNICATIONS 2021; 2:100113. [PMID: 33511345 PMCID: PMC7816079 DOI: 10.1016/j.xplc.2020.100113] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/25/2020] [Accepted: 09/17/2020] [Indexed: 05/13/2023]
Abstract
Panax notoginseng, a perennial herb of the genus Panax in the family Araliaceae, has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects. Here, we report a high-quality reference genome of P. notoginseng, with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb, produced with third-generation PacBio sequencing technology. This is the first chromosome-level genome assembly for the genus Panax. Through genome evolution analysis, we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis. We performed a detailed transcriptional analysis of P. notoginseng and explored gene-level mechanisms that regulate the formation of characteristic tubercles. Next, we studied the biosynthesis and regulation of saponins at temporal and spatial levels. We combined multi-omics data to identify genes that encode key enzymes in the P. notoginseng terpenoid biosynthetic pathway. Finally, we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P. notoginseng. The genetic information obtained in this study provides a resource for further exploration of the growth characteristics, cultivation, breeding, and saponin biosynthesis of P. notoginseng.
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Affiliation(s)
- Zhouqian Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | | | - Yifeng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Tianyuan Hu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Baowei Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jie Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xiaoyi Wu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Jiawei Zhou
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yadi Song
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Nan Liu
- School of Traditional Chinese Medicine, Capital Medical University, 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
- Corresponding author
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
- Corresponding author
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Sun R, Gao JL, Chen H, Liu S, Tang ZZ. CbCYP716A261, a New β-Amyrin 28-Hydroxylase Involved in Conyzasaponin Biosynthesis from Conyza blinii. Mol Biol 2020. [DOI: 10.1134/s002689332005009x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis. BMC Genomics 2020; 21:639. [PMID: 32933468 PMCID: PMC7493163 DOI: 10.1186/s12864-020-07056-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/06/2020] [Indexed: 12/15/2022] Open
Abstract
Background Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness and remarkable anti-inflammatory activities. Triterpenoid saponins are the major bioactive compounds of Entada phaseoloides. However, genomic or transcriptomic technologies have not been used to study the triterpenoid saponin biosynthetic pathway in this plant. Results We performed comparative transcriptome analysis of the root, stem, and leaf tissues of Entada phaseoloides with three independent biological replicates and obtained a total of 53.26 Gb clean data and 116,910 unigenes, with an average N50 length of 1218 bp. Putative functions could be annotated to 42,191 unigenes (36.1%) based on BLASTx searches against the Non-redundant, Uniprot, KEGG, Pfam, GO, KEGG and COG databases. Most of the unigenes related to triterpenoid saponin backbone biosynthesis were specifically upregulated in the stem. A total of 26 cytochrome P450 and 17 uridine diphosphate glycosyltransferase candidate genes related to triterpenoid saponin biosynthesis were identified. The differential expressions of selected genes were further verified by qPT-PCR. Conclusions The dataset reported here will facilitate the research about the functional genomics of triterpenoid saponin biosynthesis and genetic engineering of Entada phaseoloides.
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Vu DD, Shah SNM, Pham MP, Bui VT, Nguyen MT, Nguyen TPT. De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. BMC PLANT BIOLOGY 2020; 20:358. [PMID: 32727354 PMCID: PMC7391578 DOI: 10.1186/s12870-020-02571-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 07/23/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. RESULTS In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. CONCLUSION Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.
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Affiliation(s)
- Dinh Duy Vu
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University Dera Ismail Khan, Dera Ismail Khan, Pakistan
| | - Mai Phuong Pham
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Van Thang Bui
- College of Forestry Biotechnology, Vietnam National University of Forestry, Xuan Mai, Hanoi, Vietnam
| | - Minh Tam Nguyen
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi Phuong Trang Nguyen
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, , Cau Giay, Hanoi, Vietnam.
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Lin T, Du J, Zheng X, Zhou P, Li P, Lu X. Comparative transcriptome analysis of MeJA-responsive AP2/ERF transcription factors involved in notoginsenosides biosynthesis. 3 Biotech 2020; 10:290. [PMID: 32550109 DOI: 10.1007/s13205-020-02246-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/05/2020] [Indexed: 10/24/2022] Open
Abstract
Differential transcriptome analysis is an effective method for gene selection of triterpene saponin biosynthetic pathways. MeJA-induced differential transcriptome of Panax notoginseng has not been analyzed yet. In this study, comparative transcriptome analysis of P. notoginseng roots and methyl jasmonate (MeJA)-induced roots revealed 83,532 assembled unigenes and 21,947 differentially expressed unigenes. Sixteen AP2/ERF transcription factors, which were significantly induced by MeJA treatment in the root of P. notoginseng, were selected for further analysis. Real-time quantitative PCR (RT-qPCR) and co-expression network analysis of the 16 AP2/ERF transcription factors showed that PnERF2 and PnERF3 had significant correlation with dammarenediol II synthase gene (DS) and squalene epoxidase gene (SE), which are key genes in notoginsenoside biosynthesis, in different tissues and MeJA-induced roots. A phylogenetic tree was conducted to analyze the 16 candidate AP2/ERF transcription factors and other 38 transcription factors. The phylogenetic tree analysis showed PnERF2, AtERF3, AtERF7, TcERF12 and other seven transcriptional factors are in same branch, while PnERF3 had close evolutionary relationships with AtDREB1A, GhERF38 and TcAP2. The results of comparative transcriptomes and AP2/ERF transcriptional factors analysis laid a solid foundation for further investigations of disease resistance and notoginsenoside biosynthesis in P. notoginseng.
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22
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Long G, Zhao C, Zhao P, Zhou C, Ntirenganya E, Zhou Y. Transcriptomic response to cold of thermophilous medicinal plant Marsdenia tenacissima. Gene 2020; 742:144602. [PMID: 32199947 DOI: 10.1016/j.gene.2020.144602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/11/2020] [Accepted: 03/16/2020] [Indexed: 12/18/2022]
Abstract
Extracts from Marsdenia tenacissima, involving tenacissoside H, I and G, have been used as remedies of cancer, inflammation and asthma. Low temperature serves as one of the main factors constrain the planting expansion and quality of M. tenacissima, but its functional mechanism has been known scarcely for the lack of genomic information and transcriptional profile. Here we investigated the transcriptomic responses of M. tenacissima under cold stress to gain insight into the molecular mechanism of low temperature sensitivity. Total RNAs were collected from samples obtained at 4-time points (after 0, 3, 6 and 48 h cold treatments with 4 °C, respectively), then used for library construction and sequenced on the Illumina Hiseq™ 4000 platform. Passing quality assessments, 500794 transcripts, and 206137 unigenes were de novo assembly out in Trinity v2.4.0, holding contig N50 of 2566 bp and unigene mean length of 754 bp. 44.20% of assembled unigenes were annotated to the well-known public protein database on a basis of sequence similarity. Using statistical comparison of the fragments per kilo base of transcript per million reads mapped (FPKM) values between conditions, 6082 group-specific differentially expressed genes (DEGs) were identified and considered as cold-responsive genes, which contained copious transcription factors and active secondary metabolism. Among them, 43 unigenes were constantly up-regulated expression along with cold time, which mainly implicated in the biosynthesis of secondary metabolites, carbon metabolism, RNA and DNA metabolism. Conversely, 21 unigenes involved in photosynthesis, cell wall, protein degradation, and transporters were downregulated continually with cold timescale. Experimentally, MtEF1α was chosen as the best housekeeping gene. Functional enrichments found that damaging of cold stress on M. tenacissima may be ascribed to inability of photosynthesis, ribsome processing, flavonoid biosynthesis and terpenoids degradation. Correlation analysis between cold induced transcription factors and tenacissoside biosynthesis-related genes indicated that 3β-HSD significant positively correlated with bHLH51, and 4-MSO with NF-YB, GRAS3, Trihelix, FAR1, MYB60, MYBS1, bZIP43. Further promoter clone found MYB-binding site in the promoter of 4-MSO. In view of the reported cold tolerance of MYB60, it is recommended as a potential candidate suitable for future molecular design of exaptation cultivation with high bioactive constituents.
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Affiliation(s)
- Guangqiang Long
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan 650201, China
| | - Changhong Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan 650201, China
| | - Ping Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan 650201, China
| | - Chengli Zhou
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; School of Information Science and Engineering, Yunnan University, Kunming, Yunnan 650201, China
| | - Elie Ntirenganya
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yanli Zhou
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Till 2018: a survey of biomolecular sequences in genus Panax. J Ginseng Res 2020; 44:33-43. [PMID: 32095095 PMCID: PMC7033366 DOI: 10.1016/j.jgr.2019.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Ginseng is popularly known to be the king of ancient medicines and is used widely in most of the traditional medicinal compositions due to its various pharmaceutical properties. Numerous studies are being focused on this plant's curative effects to discover their potential health benefits in most human diseases, including cancer- the most life-threatening disease worldwide. Modern pharmacological research has focused mainly on ginsenosides, the major bioactive compounds of ginseng, because of their multiple therapeutic applications. Various issues on ginseng plant development, physiological processes, and agricultural issues have also been studied widely through state-of-the-art, high-throughput sequencing technologies. Since the beginning of the 21st century, the number of publications on ginseng has rapidly increased, with a recent count of more than 6,000 articles and reviews focusing notably on ginseng. Owing to the implementation of various technologies and continuous efforts, the ginseng plant genomes have been decoded effectively in recent years. Therefore, this review focuses mainly on the cellular biomolecular sequences in ginseng plants from the perspective of the central molecular dogma, with an emphasis on genomes, transcriptomes, and proteomes, together with a few other related studies.
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Chu LL, Montecillo JAV, Bae H. Recent Advances in the Metabolic Engineering of Yeasts for Ginsenoside Biosynthesis. Front Bioeng Biotechnol 2020; 8:139. [PMID: 32158753 PMCID: PMC7052115 DOI: 10.3389/fbioe.2020.00139] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/11/2020] [Indexed: 01/03/2023] Open
Abstract
Ginsenosides are a group of glycosylated triterpenes isolated from Panax species. Ginsenosides are promising candidates for the prevention and treatment of cancer as well as food additives. However, owing to a lack of efficient approaches for ginsenoside production from plants and chemical synthesis, ginsenosides may not yet have reached their full potential as medicinal resources. In recent years, an alternative approach for ginsenoside production has been developed using the model yeast Saccharomyces cerevisiae and non-conventional yeasts such as Yarrowia lipolytica and Pichia pastoris. In this review, various metabolic engineering strategies, including heterologous gene expression, balancing, and increasing metabolic flux, and enzyme engineering, have been described as recent advanced engineering techniques for improving ginsenoside production. Furthermore, the usefulness of a systems approach and fermentation strategy has been presented. Finally, the present challenges and future research direction for industrial cell factories have been discussed.
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Affiliation(s)
- Luan Luong Chu
- Department of Biotechnology, Yeungnam University, Gyeongsan-si, South Korea
| | | | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan-si, South Korea
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25
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Mining genes associated with furanocoumarin biosynthesis in an endangered medicinal plant, Glehnia littoralis. J Genet 2020. [DOI: 10.1007/s12041-019-1170-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Song J, Luo H, Xu Z, Zhang Y, Xin H, Zhu D, Zhu X, Liu M, Wang W, Ren H, Chen H, Gao T. Mining genes associated with furanocoumarin biosynthesis in an endangered medicinal plant, Glehnia littoralis. J Genet 2020; 99:11. [PMID: 32089530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The endangered medicinal plant Glehnia littoralis is one of the important natural source of furanocoumarin, which has been used as mucolytic, antitussive, antitumour and antibacterial. However, the genetic information of furanocoumarin biosynthesis in G. littoralis is scarce at present. The objective of this study was to mine the putative candidate genes involved in the biosynthesis pathwayof furanocoumarin and provide references for gene identification, and functional genomics of G. littoralis. We carried out the transcriptome analysis of leaves and roots in G. littoralis, which provided a dataset for gene mining. Psoralen, imperatorin and isoimperatorin were detected in G. littoralis by high performance liquid chromatography analysis. Candidate key genes were mined based on the annotations and local BLAST with homologous sequences using BioEdit software. The relative expression of genes was analysed using quantitative real-time polymerase chain reaction. Further, the CYP450 genes were mined using phylogenetic analyses using MEGA 6.0 software. Atotal of 156,949 unigenes were generated, of which 9021 were differentially-expressed between leaves and roots. A total of 82 unigenes encoding eight enzymes in furanocoumarin biosynthetic pathway were first obtained. Seven genes that encoded key enzymes in the downstream furanocoumarin biosynthetic pathway and expressed more in roots than leaves were screened. Twenty-six candidate CYP450 unigenes expressed abundantly in roots and were chiefly concentrated in CYP71, CYP85 and CYP72 clans. Finally, we filtered 102 differentially expressed transcription factors (TFs) unigenes. The transcriptome of G. littoralis was characterized which would help to elucidate the furanocoumarin biosynthetic pathway in G. littoralis and provide an invaluable resource for further study of furanocoumarin.
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Affiliation(s)
- Jiejie Song
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China.
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Xia P, Zheng Y, Liang Z. Structure and Location Studies on Key Enzymes in Saponins Biosynthesis of Panax notoginseng. Int J Mol Sci 2019; 20:ijms20246121. [PMID: 31817263 PMCID: PMC6940827 DOI: 10.3390/ijms20246121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/19/2019] [Accepted: 12/03/2019] [Indexed: 11/16/2022] Open
Abstract
Panax notoginseng is one of the most widely used traditional herbs for the treatment of various diseases, in which saponins were the main active components. At present, the research of P. notoginseng mainly focused on the discovery of new compounds and pharmacology. However, there were few studies on the molecular mechanism of the synthesis of secondary metabolites of P. notoginseng. In our study, four coding sequences (CDS) encoding the key enzymes involved in saponin biosynthesis were cloned, namely farnesyl diphosphate synthase (FPS), squalene synthase (SS), squalene epoxidase (SE), and dammarenediol-II synthase (DS), which contained open reading frame (ORF) of 1029 bp, 1248 bp, 1614 bp, and 2310 bp, and coded 342, 415, 537, and 769 amino acids, respectively. At the same time, their domains, secondary structures, three-dimensional structures, and phylogenetics trees were analyzed by kinds of bioinformatics tools. Their phylogenetics relationships were also analyzed. In addition, GFP (Green fluorescent protein) fusion genes were constructed by the plasmid transformation system to determine the subcellular localization. The results of subcellular localization showed that FPS, SE, and DS were mainly located in cytomembrane and its surrounding, while SS was located both in cytoplasm and cytomembrane. Our findings provided data demonstrating the expression patterns of genes involved in saponin biosynthesis and would facilitate efforts to further elucidate the biosynthesis of the bioactive components in P. notoginseng.
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Affiliation(s)
- Pengguo Xia
- Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China;
- State Key Laboratory of Membrane Biology, Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Correspondence: (P.X.); (Z.L.); Tel./Fax: +86-571-86843301 (Z.L.)
| | - Yujie Zheng
- Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China;
| | - Zongsuo Liang
- Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China;
- Correspondence: (P.X.); (Z.L.); Tel./Fax: +86-571-86843301 (Z.L.)
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28
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Wang DD, Kim YJ, Baek NI, Mathiyalagan R, Wang C, Jin Y, Xu XY, Yang DC. Glycosyltransformation of ginsenoside Rh2 into two novel ginsenosides using recombinant glycosyltransferase from Lactobacillus rhamnosus and its in vitro applications. J Ginseng Res 2019; 45:48-57. [PMID: 33437156 PMCID: PMC7790896 DOI: 10.1016/j.jgr.2019.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/18/2019] [Accepted: 11/01/2019] [Indexed: 11/30/2022] Open
Abstract
Background Ginsenoside Rh2 is well known for many pharmacological activities, such as anticancer, antidiabetes, antiinflammatory, and antiobesity properties. Glycosyltransferases (GTs) are ubiquitous enzymes present in nature and are widely used for the synthesis of oligosaccharides, polysaccharides, glycoconjugates, and novel derivatives. We aimed to synthesize new ginsenosides from Rh2 using the recombinant GT enzyme and investigate its cytotoxicity with diverse cell lines. Methods We have used a GT gene with 1,224-bp gene sequence cloned from Lactobacillus rhamnosus (LRGT) and then expressed in Escherichia coli BL21 (DE3). The recombinant GT protein was purified and demonstrated to transform Rh2 into two novel ginsenosides, and they were characterized by nuclear magnetic resonance (NMR) techniques and evaluated by 3-(4, 5-dimethylthiazol-2-yl)-2-5-diphenyltetrazolium bromide assay. Results Two novel ginsenosides with an additional glucopyranosyl (6→1) and two additional glucopyranosyl (6→1) linked with the C-3 position of the substrate Rh2 were synthesized, respectively. Cell viability assay in the lung cancer (A549) cell line showed that glucosyl ginsenoside Rh2 inhibited cell viability more potently than ginsenoside Rg3 and Rh2 at a concentration of 10 μM. Furthermore, glucosyl ginsenoside Rh2 did not exhibit any cytotoxic effect in murine macrophage cells (RAW264.7), mouse embryo fibroblasts cells (3T3-L1), and skin cells (B16BL6) at a concentration of 10 μM compared with ginsenoside Rh2 and Rg3. Conclusion This is the first report on the synthesis of two novel ginsenosides, namely, glucosyl ginsenoside Rh2 and diglucosyl ginsenoside Rh2 from Rh2 by using recombinant GT isolated from L. rhamnosus. Moreover, diglucosyl ginsenoside Rh2 might be a new candidate for treatment of inflammation, obesity, and skin whiting, and especially for anticancer.
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Affiliation(s)
- Dan-Dan Wang
- School of Life Sciences, Yantai University, Yantai, China
| | - Yeon-Ju Kim
- Department of Oriental Medicinal Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, Republic of Korea.,Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin Republic of Korea
| | - Nam In Baek
- Department of Oriental Medicinal Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, Republic of Korea
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin Republic of Korea
| | - Chao Wang
- Department of Oriental Medicinal Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, Republic of Korea
| | - Yan Jin
- Department of Oriental Medicinal Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, Republic of Korea
| | - Xing Yue Xu
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin Republic of Korea
| | - Deok-Chun Yang
- Department of Oriental Medicinal Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, Republic of Korea.,Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin Republic of Korea
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29
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Liu D, Zhao Q, Cui X, Chen R, Li X, Qiu B, Ge F. A transcriptome analysis uncovers Panax notoginseng resistance to Fusarium solani induced by methyl jasmonate. Genes Genomics 2019; 41:1383-1396. [PMID: 31493262 DOI: 10.1007/s13258-019-00865-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/27/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND Panax notoginseng is a famous Chinese herbal medicine, but the root rot disease mainly caused by Fusarium solani severely reduces the yield and quality of its medicinal materials. OBJECTIVE The defense priming in P. notoginseng through exogenous application of signaling molecule will supply theoretical support for the exogenous regulation of disease resistance in P. notoginseng. METHODS In this study, the exogenous application of methyl jasmonate (MeJA) increased P. notoginseng's resistance to F. solani. Furthermore, the P. notoginseng transcriptome during F. solani infection was investigated through next-generation sequencing to uncover the resistance mechanism of P. notogingseng induced by MeJA. RESULTS The de novo assembly of transcriptome sequences produced 80,551 unigenes, and 36,771 of these unigenes were annotated by at least one database. A differentially expressed gene analysis revealed that a large number of genes related to terpenoid backbone biosynthesis, phenylalanine metabolism, and plant-pathogen interactions were predominantly up-regulated by MeJA. Moreover, jasmonic acid (JA) biosynthesis-related genes and the JA signaling pathway genes, such as linoleate 13S-lipoxygenase, allene oxide cyclase, allene oxide synthase, TIFY, defensin, and pathogenesis-related proteins, showed increased transcriptional levels after inoculation with F. solani. Notably, according to the gene expression analysis, JA and ethylene signaling pathways may act synergistically to positively regulate the defense responses of P. notoginseng to F. solani. CONCLUSION JA signaling appears to play a vital role in P. notoginseng responses to F. solani infection, which will be helpful in improving the disease resistance of P. notoginseng cultivars as well as in developing an environmentally friendly biological control method for root rot disease.
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Affiliation(s)
- Diqiu Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Number 727 Jing Ming South Road, Chenggong District, Kunming, 650500, Yunnan, China. .,Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, Yunnan, China.
| | - Qin Zhao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Number 727 Jing Ming South Road, Chenggong District, Kunming, 650500, Yunnan, China.,Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, Yunnan, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Number 727 Jing Ming South Road, Chenggong District, Kunming, 650500, Yunnan, China.,Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, Yunnan, China
| | - Rui Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Number 727 Jing Ming South Road, Chenggong District, Kunming, 650500, Yunnan, China.,Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, Yunnan, China
| | - Xin Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Number 727 Jing Ming South Road, Chenggong District, Kunming, 650500, Yunnan, China.,Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, Yunnan, China
| | - Bingling Qiu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Number 727 Jing Ming South Road, Chenggong District, Kunming, 650500, Yunnan, China.,Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, Yunnan, China
| | - Feng Ge
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Number 727 Jing Ming South Road, Chenggong District, Kunming, 650500, Yunnan, China.,Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, Yunnan, China
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Li J, Guan XK, Liu RX. Role of Chinese Herbal Medicines in Regulation of Energy Metabolism in Treating Cardiovascular Diseases. Chin J Integr Med 2019; 25:307-315. [PMID: 31236891 DOI: 10.1007/s11655-018-2943-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2018] [Indexed: 02/06/2023]
Abstract
Recently, studying myocardial energy metabolism pathways or improving myocardial metabolism through drugs is another effective strategy for treating ischemic heart disease. Many active components of Chinese herbal medicines (CHMs) have been found to modulate energy metabolism in myocardial cells, cerebral vascular cells, endothelial cells and tumour cells. This paper reviews the advances in studies on the active components of CHMs that modulating energy metabolism in treating cardiovascular diseases over the past five years.
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Affiliation(s)
- Jie Li
- Department of Cardiology, Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Xuan-Ke Guan
- Department of Cardiology, Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Ru-Xiu Liu
- Department of Cardiology, Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, Beijing, 100053, China.
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Hussain M, Debnath B, Qasim M, Bamisile BS, Islam W, Hameed MS, Wang L, Qiu D. Role of Saponins in Plant Defense Against Specialist Herbivores. Molecules 2019; 24:E2067. [PMID: 31151268 PMCID: PMC6600540 DOI: 10.3390/molecules24112067] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/25/2019] [Accepted: 05/27/2019] [Indexed: 11/25/2022] Open
Abstract
The diamondback moth (DBM), Plutella xylostella (Lepidoptera: Plutellidae) is a very destructive crucifer-specialized pest that has resulted in significant crop losses worldwide. DBM is well attracted to glucosinolates (which act as fingerprints and essential for herbivores in host plant recognition) containing crucifers such as wintercress, Barbarea vulgaris (Brassicaceae) despite poor larval survival on it due to high-to-low concentration of saponins and generally to other plants in the genus Barbarea. B. vulgaris build up resistance against DBM and other herbivorous insects using glucosinulates which are used in plant defense. Aside glucosinolates, Barbarea genus also contains triterpenoid saponins, which are toxic to insects and act as feeding deterrents for plant specialist herbivores (such as DBM). Previous studies have found interesting relationship between the host plant and secondary metabolite contents, which indicate that attraction or resistance to specialist herbivore DBM, is due to higher concentrations of glucosinolates and saponins in younger leaves in contrast to the older leaves of Barbarea genus. As a response to this phenomenon, herbivores as DBM has developed a strategy of defense against these plant biochemicals. Because there is a lack of full knowledge in understanding bioactive molecules (such as saponins) role in plant defense against plant herbivores. Thus, in this review, we discuss the role of secondary plant metabolites in plant defense mechanisms against the specialist herbivores. In the future, trials by plant breeders could aim at transferring these bioactive molecules against herbivore to cash crops.
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Affiliation(s)
- Mubasher Hussain
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou 350002, China.
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fuzhou 350002, China.
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Biswojit Debnath
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China.
| | - Muhammad Qasim
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou 3100058, China.
| | - Bamisope Steve Bamisile
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fuzhou 350002, China.
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Geography, Fujian Normal University, Fuzhou 350007, China.
| | - Muhammad Salman Hameed
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Faculty of Agricultural Sciences, Department of Plant Protection, Ghazi University, Dera Ghazi Khan 32200, Pakistan.
| | - Liande Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou 350002, China.
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fuzhou 350002, China.
- Institute of Applied Ecology and Research Centre for Biodiversity and Eco-Safety, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dongliang Qiu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 35002, China.
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Wei G, Yang F, Wei F, Zhang L, Gao Y, Qian J, Chen Z, Jia Z, Wang Y, Su H, Dong L, Xu J, Chen S. Metabolomes and transcriptomes revealed the saponin distribution in root tissues of Panax quinquefolius and Panax notoginseng. J Ginseng Res 2019; 44:757-769. [PMID: 33192118 PMCID: PMC7655499 DOI: 10.1016/j.jgr.2019.05.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/09/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022] Open
Abstract
Background Panax quinquefolius and Panax notoginseng are widely used and well known for their pharmacological effects. As main pharmacological components, saponins have different distribution patterns in the root tissues of Panax plants. Methods In this study, the representative ginsenosides were detected and quantified by desorption electrospray ionization mass spectrometry and high-performance liquid chromatography analysis to demonstrate saponin distribution in the root tissues of P. quinquefolius and P. notoginseng, and saponin metabolite profiles were analyzed by metabolomes to obtain the biomarkers of different root tissues. Finally, the transcriptome analysis was performed to demonstrate the molecular mechanisms of saponin distribution by gene profiles. Results There was saponin distribution in the root tissues differed between P. quinquefolius and P. notoginseng. Eight-eight and 24 potential biomarkers were detected by metabolome analysis, and a total of 340 and 122 transcripts involved in saponin synthesis that were positively correlated with the saponin contents (R > 0.6, P < 0.05) in the root tissues of P. quinquefolius and P. notoginseng, respectively. Among them, GDPS1, CYP51, CYP64, and UGT11 were significantly correlated with the contents of Rg1, Re, Rc, Rb2, and Rd in P. quinquefolius. UGT255 was markedly related to the content of R1; CYP74, CYP89, CYP100, CYP103, CYP109, and UGT190 were markedly correlated with the Rd content in P. notoginseng. Conclusions These results provided the visual and quantitative profiles of and confirmed the pivotal transcripts of CYPs and UGTs regulating the saponin distribution in the root tissues of P. quinquefolius and P. notoginseng.
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Key Words
- AACT, Acetoacetyl-CoA acyltransferase
- DS, Dammarenediol-II synthase
- DXPR, 1-deoxy-o-xylulose 5-phosphate reductoisomerase
- DXPS, 1-deoxy-o-xylulose 5-phosphate synthase
- FDR, False discovery rate
- FPP, Farnesyl diphosphate
- FPS, Farnesyl pyrophosphate synthase
- GDPS, Gerenyl diphosphatesynthase
- GO, Gene Ontology
- HDS, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatesynthase
- HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase
- HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase
- HPLC-UV, High-performance liquid chromatography-ultraviolet detection
- IPP, Isoprenyl diphosphate
- IPPI, Isopentenyl pyrophosphate isomerase
- ISPD, 2-C-methylerythritol 4-phosphatecytidyl transferase
- ISPE, 4-(cytidine-5′-diphospho)-2-C-methylerythritol kinase
- ISPH, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
- MALDI-MS, Matrix-assisted laser desorption/ionization–mass spectrometry
- MECPS, 2-C-methylerythritol-2,4-cyclophosphate synthase
- MEP, 2-C-methyl-D-erythritol-4-phosphate
- MVA, Mevalonate acid
- MVD, Mevalonate diphosphate decarboxylase
- MVK, Mevalonate kinase
- Metabolome
- NCBI Nr, NCBI Non-redundant protein
- OPLS-DA, Orthogonal partial least squares-discriminant analysis
- ORF, Open read frame
- P450, P450-monooxygenase
- PMK, Phosphomevalonate kinase
- Panax plants
- Root tissues
- SE, Squalene epoxidase
- SS, Squalene synthase
- Saponin distribution
- Transcriptome
- UGTs, UDP-glycosyltransferases
- UPLC-MS, Ultrahigh-performance liquid chromatography quadrupole time of flight-mass spectrometry
- WGCNA, Weighted gene coexpression network analysis
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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, China
| | - Feng Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd., Wenshan, China
| | - Lianjuan Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Jun Qian
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - Zhengwei Jia
- Waters Corporation Shanghai Science & Technology Co Ltd, Shanghai, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - He Su
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 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, China
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 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, China
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Rahimi S, Kim J, Mijakovic I, Jung KH, Choi G, Kim SC, Kim YJ. Triterpenoid-biosynthetic UDP-glycosyltransferases from plants. Biotechnol Adv 2019; 37:107394. [PMID: 31078628 DOI: 10.1016/j.biotechadv.2019.04.016] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/20/2019] [Accepted: 04/30/2019] [Indexed: 01/22/2023]
Abstract
Triterpenoid saponins are naturally occurring structurally diverse glycosides of triterpenes that are widely distributed among plant species. Great interest has been expressed by pharmaceutical and agriculture industries for the glycosylation of triterpenes. Such modifications alter their taste and bio-absorbability, affect their intra-/extracellular transport and storage in plants, and induce novel biological activities in the human body. Uridine diphosphate (UDP)-glycosyltransferases (UGTs) catalyze glycosylation using UDP sugar donors. These enzymes belong to a multigene family and recognize diverse natural products, including triterpenes, as the acceptor molecules. For this review, we collected and analyzed all of the UGT sequences found in Arabidopsis thaliana as well as 31 other species of triterpene-producing plants. To identify potential UGTs with novel functions in triterpene glycosylation, we screened and classified those candidates based on similarity with UGTs from Panax ginseng, Glycine max, Medicago truncatula, Saponaria vaccaria, and Barbarea vulgaris that are known to function in glycosylate triterpenes. We highlight recent findings on UGT inducibility by methyl jasmonate, tissue-specific expression, and subcellular localization, while also describing their catalytic activity in terms of regioselectivity for potential key UGTs dedicated to triterpene glycosylation in plants. Discovering these new UGTs expands our capacity to manipulate the biological and physicochemical properties of such valuable molecules.
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Affiliation(s)
- Shadi Rahimi
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea; Intelligent Synthetic Biology Center, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea; Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden.
| | - Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea; Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Sun-Chang Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea; Intelligent Synthetic Biology Center, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
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Zhang X, Yu Y, Jiang S, Yu H, Xiang Y, Liu D, Qu Y, Cui X, Ge F. Oleanane-Type Saponins Biosynthesis in Panax notoginseng via Transformation of β-Amyrin Synthase Gene from Panax japonicus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1982-1989. [PMID: 30742432 DOI: 10.1021/acs.jafc.8b07183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Oleanane-type saponins considered as the main medicinal ingredients in Panax japonicus are not found in Panax notoginseng. β-Amyrin synthase (βAS) was recognized as the first key enzyme in the biosynthetic branch of oleanane-type saponins. In this study, βAS gene from P. japonicus ( PjβAS) was transferred into P. notoginseng cells. Along with PjβAS expression in the transgenic cells, the expression levels of several key enzyme genes related to triterpenoid saponins biosynthesis and the content of P. notoginseng saponins were also increased. Two oleanane-type saponins, chikusetsusaponin IV and chikusetsusaponin IVa, contained in P. japonicus were first discovered in transgenic P. notoginseng cells. This study successfully constructed a biosynthetic pathway of oleanane-type saponins in P. notoginseng by introducing just one gene into the species. On the basis of this discovery and previous studies, the common biosynthetic pathway of triterpenoid saponins in Panax genus may be unified to some extent.
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Affiliation(s)
- Xiang Zhang
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
| | - Yilin Yu
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
| | - Sen Jiang
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
| | - Hong Yu
- School of Life Science , Yunnan University , Kunming 650500 , China
| | - Yingying Xiang
- Department of Stomatology , Yan'an Hospital Affiliated to Kunming Medical University , Kunming 650031 , China
| | - Diqiu Liu
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
- Yunnan Key Laboratory of Panax notoginseng , Kunming University of Science and Technology , Kunming 650500 , China
| | - Yuan Qu
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
- Yunnan Key Laboratory of Panax notoginseng , Kunming University of Science and Technology , Kunming 650500 , China
| | - Xiuming Cui
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
- Yunnan Key Laboratory of Panax notoginseng , Kunming University of Science and Technology , Kunming 650500 , China
| | - Feng Ge
- Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming 650500 , China
- Yunnan Key Laboratory of Panax notoginseng , Kunming University of Science and Technology , Kunming 650500 , China
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Tang QY, Chen G, Song WL, Fan W, Wei KH, He SM, Zhang GH, Tang JR, Li Y, Lin Y, Yang SC. Transcriptome analysis of Panax zingiberensis identifies genes encoding oleanolic acid glucuronosyltransferase involved in the biosynthesis of oleanane-type ginsenosides. PLANTA 2019; 249:393-406. [PMID: 30219960 DOI: 10.1007/s00425-018-2995-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/28/2018] [Indexed: 05/26/2023]
Abstract
Oleanolic acid glucuronosyltransferase (OAGT) genes synthesizing the direct precursor of oleanane-type ginsenosides were discovered. The four recombinant proteins of OAGT were able to transfer glucuronic acid at C-3 of oleanolic acid that yields oleanolic acid 3-O-β-glucuronide. Ginsenosides are the primary active components in the genus Panax, and great efforts have been made to elucidate the mechanisms underlying dammarane-type ginsenoside biosynthesis. However, there is limited information on oleanane-type ginsenosides. Here, high-performance liquid chromatography analysis demonstrated that oleanane-type ginsenosides (particularly ginsenoside Ro and chikusetsusaponin IV and IVa) are the abundant ginsenosides in Panax zingiberensis, an extremely endangered Panax species in southwest China. These ginsenosides are derived from oleanolic acid 3-O-β-glucuronide, which may be formed from oleanolic acid catalyzed by an unknown oleanolic acid glucuronosyltransferase (OAGT). Transcriptomic analysis of leaves, stems, main roots, and fibrous roots of P. zingiberensis was performed, and a total of 46,098 unigenes were obtained, including all the identified homologous genes involved in ginsenoside biosynthesis. The most upstream genes were highly expressed in the leaves, and the UDP-glucosyltransferase genes were highly expressed in the roots. This finding indicated that the precursors of ginsenosides are mainly synthesized in the leaves and transported to different parts for the formation of particular ginsenosides. For the first time, enzyme activity assay characterized four genes (three from P. zingiberensis and one from P. japonicus var. major, another Panax species with oleanane-type ginsenosides) encoding OAGT, which particularly transfer glucuronic acid at C-3 of oleanolic acid to form oleanolic acid 3-O-β-glucuronide. Taken together, our study provides valuable genetic information for P. zingiberensis and the genes responsible for synthesizing the direct precursor of oleanane-type ginsenosides.
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Affiliation(s)
- Qing-Yan Tang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Geng Chen
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Wan-Ling Song
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Kun-Hua Wei
- Guangxi Medicinal Resources Protection and Genetic Improvement Laboratory, Guangxi Botanical Garden of Medicinal Plant, Nanning, 530023, China
| | - Si-Mei He
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Guang-Hui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Rong Tang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Ying Li
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yuan Lin
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Sheng-Chao Yang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China.
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Jung JH, Kim HY, Kim HS, Jung SH. Transcriptome analysis of Panax ginseng response to high light stress. J Ginseng Res 2019; 44:312-320. [PMID: 32148414 PMCID: PMC7031748 DOI: 10.1016/j.jgr.2018.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/18/2018] [Accepted: 12/24/2018] [Indexed: 11/28/2022] Open
Abstract
Background Ginseng (Panax ginseng Meyer) is an essential source of pharmaceuticals and functional foods. Ginseng productivity has been compromised by high light (HL) stress, which is one of the major abiotic stresses during the ginseng cultivation period. The genetic improvement for HL tolerance in ginseng could be facilitated by analyzing its genetic and molecular characteristics associated with HL stress. Methods Genome-wide analysis of gene expression was performed under HL and recovery conditions in 1-year-old Korean ginseng (P. ginseng cv. Chunpoong) using the Illumina HiSeq platform. After de novo assembly of transcripts, we performed expression profiling and identified differentially expressed genes (DEGs). Furthermore, putative functions of identified DEGs were explored using Gene Ontology terms and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis. Results A total of 438 highly expressed DEGs in response to HL stress were identified and selected from 29,184 representative transcripts. Among the DEGs, 326 and 114 transcripts were upregulated and downregulated, respectively. Based on the functional analysis, most upregulated and a significant number of downregulated transcripts were related to stress responses and cellular metabolic processes, respectively. Conclusion Transcriptome profiling could be a strategy to comprehensively elucidate the genetic and molecular mechanisms of HL tolerance and susceptibility. This study would provide a foundation for developing breeding and metabolic engineering strategies to improve the environmental stress tolerance of ginseng.
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Affiliation(s)
- Je Hyeong Jung
- Center for Natural Products Convergence Research, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Ho-Youn Kim
- Convergence Research Center for Smart Farm Solution, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Hyoung Seok Kim
- Center for Natural Products Convergence Research, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea.,Convergence Research Center for Smart Farm Solution, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Sang Hoon Jung
- Center for Natural Products Convergence Research, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
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Trends in herbgenomics. SCIENCE CHINA-LIFE SCIENCES 2018; 62:288-308. [PMID: 30128965 DOI: 10.1007/s11427-018-9352-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Abstract
From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networks of herbs to clarify their molecular mechanism in the prevention and treatment of human diseases. The main theoretical system includes genomics, functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, metagenomics, synthetic biology, pharmacogenomics of TCM, and bioinformatics, among other fields. Herbgenomics is mainly applicable to the study of medicinal model plants, genomic-assisted breeding, herbal synthetic biology, protection and utilization of gene resources, TCM quality evaluation and control, and TCM drug development. Such studies will accelerate the application of cutting-edge technologies, revitalize herbal research, and strongly promote the development and modernization of TCM.
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Kang KB, Jayakodi M, Lee YS, Nguyen VB, Park HS, Koo HJ, Choi IY, Kim DH, Chung YJ, Ryu B, Lee DY, Sung SH, Yang TJ. Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng. Sci Rep 2018; 8:11744. [PMID: 30082711 PMCID: PMC6078999 DOI: 10.1038/s41598-018-30262-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022] Open
Abstract
Ginsenosides are dammarane-type or triterpenoidal saponins that contribute to the various pharmacological activities of the medicinal herb Panax ginseng. The putative biosynthetic pathway for ginsenoside biosynthesis is known in P. ginseng, as are some of the transcripts and enzyme-encoding genes. However, few genes related to the UDP-glycosyltransferases (UGTs), enzymes that mediate glycosylation processes in final saponin biosynthesis, have been identified. Here, we generated three replicated Illumina RNA-Seq datasets from the adventitious roots of P. ginseng cultivar Cheongsun (CS) after 0, 12, 24, and 48 h of treatment with methyl jasmonate (MeJA). Using the same CS cultivar, metabolomic data were also generated at 0 h and every 12-24 h thereafter until 120 h of MeJA treatment. Differential gene expression, phylogenetic analysis, and metabolic profiling were used to identify candidate UGTs. Eleven candidate UGTs likely to be involved in ginsenoside glycosylation were identified. Eight of these were considered novel UGTs, newly identified in this study, and three were matched to previously characterized UGTs in P. ginseng. Phylogenetic analysis further asserted their association with ginsenoside biosynthesis. Additionally, metabolomic analysis revealed that the newly identified UGTs might be involved in the elongation of glycosyl chains of ginsenosides, especially of protopanaxadiol (PPD)-type ginsenosides.
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Affiliation(s)
- Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Van Binh Nguyen
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun Jo Koo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ik Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Gangwon-do, 24341, Republic of Korea
| | - Dae Hyun Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - You Jin Chung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byeol Ryu
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong Young Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Wei G, Wei F, Yuan C, Chen Z, Wang Y, Xu J, Zhang Y, Dong L, Chen S. Integrated Chemical and Transcriptomic Analysis Reveals the Distribution of Protopanaxadiol- and Protopanaxatriol-Type Saponins in Panax notoginseng. Molecules 2018; 23:molecules23071773. [PMID: 30029488 PMCID: PMC6099965 DOI: 10.3390/molecules23071773] [Citation(s) in RCA: 11] [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: 07/05/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 02/04/2023] Open
Abstract
Panax notoginseng is famous for its important therapeutic effects and commonly used worldwide. The active ingredients saponins have distinct contents in different tissues of P. notoginseng, and they may be related to the expression of key genes in the synthesis pathway. In our study, high-performance liquid chromatography results indicated that the contents of protopanaxadiol-(Rb1, Rc, Rb2, and Rd) and protopanaxatriol-type (R1, Rg1, and Re) saponins in below ground tissues were higher than those in above ground tissues. Clustering dendrogram and PCA analysis suggested that the below and above ground tissues were clustered into two separate groups. A total of 482 and 882 unigenes were shared in the below and above ground tissues, respectively. A total of 75 distinct expressions of CYPs transcripts (RPKM ≥ 10) were detected. Of these transcripts, 38 and 37 were highly expressed in the below ground and above ground tissues, respectively. RT-qPCR analysis showed that CYP716A47 gene was abundantly expressed in the above ground tissues, especially in the flower, whose expression was 31.5-fold higher than that in the root. CYP716A53v2 gene was predominantly expressed in the below ground tissues, especially in the rhizome, whose expression was 20.1-fold higher than that in the flower. Pearson's analysis revealed that the CYP716A47 expression was significantly correlated with the contents of ginsenoside Rc and Rb2. The CYP716A53v2 expression was associated with the saponin contents of protopanaxadiol-type (Rb1 and Rd) and protopanaxatriol-type (R1, Rg1, and Re). Results indicated that the expression patterns of CYP716A47 and CYP716A53v2 were correlated with the distribution of protopanaxadiol-type and protopanaxatriol-type saponins in P. notoginseng. This study identified the pivotal genes regulating saponin distribution and provided valuable information for further research on the mechanisms of saponin synthesis, transportation, and accumulation.
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Affiliation(s)
- Guangfei Wei
- Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
- 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.
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology Co., Ltd., Wenshan 663000, China.
| | - Can Yuan
- 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.
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China.
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China.
| | - Jiang Xu
- 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.
| | - Yongqing Zhang
- Shandong University of Traditional Chinese Medicine, Jinan 250355, 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.
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Integrated metabolomic and transcriptomic analyses revealed the distribution of saponins in Panax notoginseng. Acta Pharm Sin B 2018; 8:458-465. [PMID: 29881685 PMCID: PMC5989832 DOI: 10.1016/j.apsb.2017.12.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/16/2017] [Accepted: 12/19/2017] [Indexed: 12/04/2022] Open
Abstract
Panax notoginseng is famous for its important therapeutic effects. Saponins are bioactive compounds found in different parts and developmental stages of P. notoginseng plants. Thus, it is urgently to study saponins distribution in different parts and growth ages of P. notoginseng plants. In this study, potential biomarkers were found, and their chemical characteristic differences were revealed through metabolomic analysis. High-performance liquid chromatography data indicated the higher content of saponins (i.e., Rg1, Re, Rd, and Rb1) in the underground parts than that in the aerial parts. 20(S)-Protopanaxadiol saponins were mainly distributed in the aerial parts. Additionally, the total saponin content in the 3-year-old P. notoginseng plant (188.0 mg/g) was 1.4-fold higher than that in 2-year-old plant (130.5 mg/g). The transcriptomic analysis indicated the tissue-specific transcription expression of genes, namely, PnFPS, PnSS, PnSE1, PnSE2, and PnDS, which encoded critical synthases in saponin biosyntheses. These genes showed similar expression patterns among the parts of P. notoginseng plants. The expression levels of these genes in the flowers and leaves were 5.2fold higher than that in the roots and fibrils. These results suggested that saponins might be actively synthesized in the aerial parts and transformed to the underground parts. This study provides insights into the chemical and genetic characteristics of P. notoginseng to facilitate the synthesis of its secondary metabolites and a scientific basis for appropriate collection and rational use of this plant.
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Key Words
- AACT, acetoacetyl-CoA acyltransferase
- DS, dammarenediol-II synthase
- DXPR, 1-deoxy-d-xylulose 5-phosphate reductoisomerase
- DXPS, 1-deoxy-d-xylulose 5-phosphate synthase
- FPP, farnesyl diphosphate
- FPS, farnesyl pyrophosphate synthase
- GDPS, gerenyl diphosphatesynthase
- Gene expression
- Growth years
- HDS, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase
- HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase
- HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase
- HPLC—UV, high-performance liquid chromatography-ultraviolet detection
- IPP, isoprenyl diphosphate
- IPPI, isopentenyl pyrophosphate isomerase
- ISPD, 2-C-methylerythritol 4-phosphatecytidyl transferase
- ISPE, 4-(cytidine-5′-diphospho)-2-C-methylerythritol kinase
- ISPH, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
- MECPS, 2-C-methylerythritol-2,4-cyclophosphate synthase
- MEP, 2-C-methyl-d-erythritol-4-phosphate
- MVA, mevalonate
- MVDD, mevalonate diphosphate decarboxylase
- MVK, mevalonate kinase
- Metabolomic analyses
- OPLS-DA, orthogonal partial least-squares discrimination analysis
- P450, P450-monooxygenase
- PCA, principal component analysis
- PDS, 20(S)-protopanaxadiol saponins
- PMK, phosphomevalonate kinase
- PTS, 20(S)-protopanaxatriol saponins
- Panax notoginseng
- SE, squalene epoxidase
- SS, squalene synthase
- Saponin
- UGTs, UDP-glycosyltransferases
- UPLC—MS, ultrahigh-performance liquid chromatography–mass spectrometry
- VIP, variable importance in projection
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Progress on the Studies of the Key Enzymes of Ginsenoside Biosynthesis. Molecules 2018; 23:molecules23030589. [PMID: 29509695 PMCID: PMC6017814 DOI: 10.3390/molecules23030589] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 12/31/2022] Open
Abstract
As the main bioactive constituents of Panax species, ginsenosides possess a wide range of notable medicinal effects such as anti-cancer, anti-oxidative, antiaging, anti-inflammatory, anti-apoptotic and neuroprotective activities. However, the increasing medical demand for ginsenosides cannot be met due to the limited resource of Panax species and the low contents of ginsenosides. In recent years, biotechnological approaches have been utilized to increase the production of ginsenosides by regulating the key enzymes of ginsenoside biosynthesis, while synthetic biology strategies have been adopted to produce ginsenosides by introducing these genes into yeast. This review summarizes the latest research progress on cloning and functional characterization of key genes dedicated to the production of ginsenosides, which not only lays the foundation for their application in plant engineering, but also provides the building blocks for the production of ginsenosides by synthetic biology.
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Li MR, Shi FX, Li YL, Jiang P, Jiao L, Liu B, Li LF. Genome-Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer). Genome Biol Evol 2018; 9:2159-2169. [PMID: 28922794 PMCID: PMC5737880 DOI: 10.1093/gbe/evx160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2017] [Indexed: 11/15/2022] Open
Abstract
Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions. In complement, the 45s rDNA, chloroplast and mitochondrial genomes were included to perform phylogenetic and population genetic analyses. The observed spatial genetic structure between northern cultivated ginseng (NCG) and southern cultivated ginseng (SCG) accessions suggested multiple independent origins of cultivated ginseng. Genome-wide scanning further demonstrated that NCG and SCG have undergone distinct selection pressures during the domestication process, with more genes identified in the NCG (97 genes) than in the SCG group (5 genes). Functional analyses revealed that these genes are involved in diverse pathways, including DNA methylation, lignin biosynthesis, and cell differentiation. These findings suggested that the SCG and NCG groups have distinct demographic histories. Candidate genes identified are useful for future molecular breeding of cultivated ginseng.
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Affiliation(s)
- Ming-Rui Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Feng-Xue Shi
- Northeast Normal University Natural History Museum, Changchun, China
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lili Jiao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Del Vecchio F, Mastroiaco V, Di Marco A, Compagnoni C, Capece D, Zazzeroni F, Capalbo C, Alesse E, Tessitore A. Next-generation sequencing: recent applications to the analysis of colorectal cancer. J Transl Med 2017; 15:246. [PMID: 29221448 PMCID: PMC5723063 DOI: 10.1186/s12967-017-1353-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Since the establishment of the Sanger sequencing method, scientists around the world focused their efforts to progress in the field to produce the utmost technology. The introduction of next-generation sequencing (NGS) represents a revolutionary step and promises to lead to massive improvements in our understanding on the role of nucleic acids functions. Cancer research began to use this innovative and highly performing method, and interesting results started to appear in colorectal cancer (CRC) analysis. Several studies produced high-quality data in terms of mutation discovery, especially about actionable or less frequently mutated genes, epigenetics, transcriptomics. Analysis of results is unveiling relevant perspectives aiding to evaluate the response to therapies. Novel evidences have been presented also in other directions such as gut microbiota or CRC circulating tumor cells. However, despite its unquestioned potential, NGS poses some issues calling for additional studies. This review intends to offer a view of the state of the art of NGS applications to CRC through examination of the most important technologies and discussion of recent published results.
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Affiliation(s)
- Filippo Del Vecchio
- Division of Cancer Sciences, University of Southampton, Southampton, Hampshire, SO16 6YD UK
| | - Valentina Mastroiaco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Antinisca Di Marco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Daria Capece
- Department of Medicine, Centre for Cell Signaling and Inflammation, Imperial College London, London, W12 0NN UK
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, La Sapienza University, Rome, 00161 Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
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Jo IH, Lee J, Hong CE, Lee DJ, Bae W, Park SG, Ahn YJ, Kim YC, Kim JU, Lee JW, Hyun DY, Rhee SK, Hong CP, Bang KH, Ryu H. Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes (Basel) 2017; 8:E228. [PMID: 28914759 PMCID: PMC5615361 DOI: 10.3390/genes8090228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/17/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022] Open
Abstract
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.
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Affiliation(s)
- Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chi Eun Hong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | | | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Sin-Gi Park
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Yong Ju Ahn
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Young Chang Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jang Uk Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jung Woo Lee
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Dong Yun Hyun
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea.
| | | | - Kyong Hwan Bang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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Wang N, Wang L, Qi L, Lu X. Construct a gene-to-metabolite network to screen the key genes of triterpene saponin biosynthetic pathway in Panax notoginseng. Biotechnol Appl Biochem 2017; 65:119-127. [PMID: 28779486 DOI: 10.1002/bab.1580] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 01/01/2023]
Abstract
Triterpene saponins are main active constituents of Panax notoginseng. Metabolites profiling of 12 triterpene saponins was analyzed by high-performance liquid chromatography-mass spectrometry in leaf, petiole, and root extracts of P. notoginseng. Most of the 20(S)-protopanaxatriol (PPT) type saponins, except ginsenoside Re, were mainly distributed in roots, while 20(S)-protopanaxadiol (PPD) type saponins were detected among various tissues. The total content of PPD-type saponins decreased in the order of leaf, petiole, and root. The expression patterns of four key genes (PnFPS, PnSQS, PnDS, and PnSE) in the triterpene saponin biosynthetic pathway were measured by real-time quantitative PCR (RT-qPCR). All the four investigated genes showed high expression levels in leaf. A gene-to-metabolite network was constructed through canonical correlation analysis. The results indicated that the expression levels of PnFPS, PnSQS, PnDS, and PnSE had high correlation with PPD-type saponins ginsenoside Rb2 , Rb3 , and Rc, while PnSQS was also highly correlated with Rb1 . Combining metabolic profiling, RT-qPCR, and gene-to-metabolite network, we inferred that the leaf of P. notoginseng was the main biosynthesis site of PPD-type saponins Rb2 , Rb3 , and Rc. The contribution to the biosynthesis of ginsenosides Rb2 , Rb3 , and Rc was in the order of PnSE > PnDS > PnSQS > PnFPS. PnSE and PnDS should be the preferred targets to regulate the production of PPD-type saponins Rb2 , Rb3 , and Rc in P. notoginseng by plant metabolic engineering.
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Affiliation(s)
- Ning Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Long Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Lianwen Qi
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Xu Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
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Abdelrahman M, El-Sayed M, Sato S, Hirakawa H, Ito SI, Tanaka K, Mine Y, Sugiyama N, Suzuki M, Yamauchi N, Shigyo M. RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines. PLoS One 2017; 12:e0181784. [PMID: 28800607 PMCID: PMC5553718 DOI: 10.1371/journal.pone.0181784] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/06/2017] [Indexed: 01/06/2023] Open
Abstract
The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium’s defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosome from the shallot (A. cepa Aggregatum group, AA) are powerful genetic resources that enable us to understand many physiological traits of Allium. In the present study, we were able to isolate and identify Alliospiroside A saponin compound in A. fistulosum with extra chromosome 2A from shallot (FF2A) and its role in the defense mechanism against Fusarium pathogens. Furthermore, to gain molecular insight into the Allium saponin biosynthesis pathway, high-throughput RNA-Seq of the root, bulb, and leaf of AA, MALs, and FF was carried out using Illumina's HiSeq 2500 platform. An open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp) was generated based on RNA-Seq data. The resulting assembled transcripts were functionally annotated, revealing 50 unigenes involved in saponin biosynthesis. Differential gene expression (DGE) analyses of AA and MALs as compared with FF (as a control) revealed a strong up-regulation of the saponin downstream pathway, including cytochrome P450, glycosyltransferase, and beta-glucosidase in chromosome 2A. An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance.
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Affiliation(s)
- Mostafa Abdelrahman
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Japan
- Botany Department, Faculty of Science, Aswan University, Aswan, Egypt
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Magdi El-Sayed
- Botany Department, Faculty of Science, Aswan University, Aswan, Egypt
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | | | - Shin-ichi Ito
- Laboratory of Molecular Plant Pathology, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Japan
| | - Keisuke Tanaka
- The NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Yoko Mine
- Department of Agriculture, Faculty of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Nobuo Sugiyama
- Department of Agriculture, Faculty of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Minoru Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Naoki Yamauchi
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Japan
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Japan
- * E-mail:
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Transcriptome analysis of Cinnamomum longepaniculatum by high-throughput sequencing. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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Jeena GS, Fatima S, Tripathi P, Upadhyay S, Shukla RK. Comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri identifies potential genes related to triterpenoid saponin biosynthesis. BMC Genomics 2017; 18:490. [PMID: 28659188 PMCID: PMC5490213 DOI: 10.1186/s12864-017-3865-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/15/2017] [Indexed: 12/02/2022] Open
Abstract
Background Bacopa monnieri commonly known as Brahmi is utilized in Ayurveda to improve memory and many other human health benefits. Bacosides enriched standardized extract of Bacopa monnieri is being marketed as a memory enhancing agent. In spite of its well known pharmacological properties it is not much studied in terms of transcripts involved in biosynthetic pathway and its regulation that controls the secondary metabolic pathway in this plant. The aim of this study was to identify the potential transcripts and provide a framework of identified transcripts involved in bacosides production through transcriptome assembly. Results We performed comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri in two independent biological replicate and obtained 22.48 million and 22.0 million high quality processed reads in shoot and root respectively. After de novo assembly and quantitative assessment total 26,412 genes got annotated in root and 18,500 genes annotated in shoot sample. Quality of raw reads was determined by using SeqQC-V2.2. Assembled sequences were annotated using BLASTX against public database such as NR or UniProt. Searching against the KEGG pathway database indicated that 37,918 unigenes from root and 35,130 unigenes from shoot were mapped to 133 KEGG pathways. Based on the DGE data we found that most of the transcript related to CYP450s and UDP-glucosyltransferases were specifically upregulated in shoot tissue as compared to root tissue. Finally, we have selected 43 transcripts related to secondary metabolism including transcription factor families which are differentially expressed in shoot and root tissues were validated by qRT-PCR and their expression level were monitored after MeJA treatment and wounding for 1, 3 and 5 h. Conclusions This study not only represents the first de novo transcriptome analysis of Bacopa monnieri but also provides information about the identification, expression and differential tissues specific distribution of transcripts related to triterpenoid sapogenin which is one of the most important pharmacologically active secondary metabolite present in Bacopa monnieri. The identified transcripts in this study will establish a foundation for future studies related to carrying out the metabolic engineering for increasing the bacosides biosynthesis and its regulation for human health benefits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3865-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gajendra Singh Jeena
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Shahnoor Fatima
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Pragya Tripathi
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Swati Upadhyay
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Rakesh Kumar Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India.
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De novo assembly and annotation of the Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) transcriptome in different growth stages. Sci Rep 2017; 7:3616. [PMID: 28620183 PMCID: PMC5472570 DOI: 10.1038/s41598-017-03937-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/05/2017] [Indexed: 12/28/2022] Open
Abstract
Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) is a traditional medicinal herb in the family Liliaceae that has significant pharmacological effects on immunity and cardiovascular disease. In this study, three different growth stages of Zhe-Maidong were investigated using RNA-seq, and a total of 16.4 Gb of raw data was obtained. After filtering and assembling, 96,738 unigenes with an average length of 605.3 bp were ultimately generated. A total of 77,300 unigenes were annotated using information from five databases, including the NT, NR, SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. Additionally, the mechanisms of flavonoid, saponin and polysaccharide biosynthesis and of accumulation at different stages of tuber development were also characterized. From the first to third years, the contents of flavonoids, saponins and polysaccharides all increased, whereas the expression levels of related genes decreased in the flavonoid and saponin pathways and first increased and then decreased in the polysaccharide pathway. The results of this study provide the most comprehensive expressed sequence resource for Zhe-Maidong and will expand the available O. japonicus gene library and facilitate further genome-wide research and analyses of this species.
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Chen W, Kui L, Zhang G, Zhu S, Zhang J, Wang X, Yang M, Huang H, Liu Y, Wang Y, Li Y, Zeng L, Wang W, He X, Dong Y, Yang S. Whole-Genome Sequencing and Analysis of the Chinese Herbal Plant Panax notoginseng. MOLECULAR PLANT 2017; 10:899-902. [PMID: 28315474 DOI: 10.1016/j.molp.2017.02.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/24/2017] [Accepted: 02/27/2017] [Indexed: 05/21/2023]
Affiliation(s)
- Wei Chen
- Biological Big Data College, Yunnan Agricultural University, Kunming 650201, China; Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanghui Zhang
- National-Local Joint Engineering Research Center on Germplasm Utilization and Innovation of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jing Zhang
- NOWBIO Technology Co. Ltd, Kunming 650202, China
| | - Xiao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Huichuan Huang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yixiang Liu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yong Wang
- Institute of Panax notoginseng, Wenshan University, Wenshan 663000, China
| | - Yahe Li
- Longjing Pharmaceutical Co. Ltd, Kunming 650228, China
| | - Lipin Zeng
- Farlong Pharmaceutical, Walnut, CA 91789, USA
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
| | - Yang Dong
- Biological Big Data College, Yunnan Agricultural University, Kunming 650201, China; Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China; Institute of Panax notoginseng, Wenshan University, Wenshan 663000, China; College of Life Science, Kunming University of Science and Technology, Kunming 650504, China.
| | - Shengchao Yang
- National-Local Joint Engineering Research Center on Germplasm Utilization and Innovation of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China.
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