1
|
Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2023:elad050. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
Collapse
Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| |
Collapse
|
2
|
Kaur G, Arya SK, Singh B, Singh S, Sushmita, Saxena G, Verma PC, Ganjewala D. Comparative transcriptional analysis of metabolic pathways and mechanisms regulating essential oil biosynthesis in four elite Cymbopogon spp. Int J Biol Macromol 2023; 229:943-951. [PMID: 36621735 DOI: 10.1016/j.ijbiomac.2022.12.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/19/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
Cymbopogon is an important aromatic and medicinal grass with several species of ethnopharmaceutical importance. The genus is extremely rich in secondary metabolites, monoterpenes like geraniol and citral being principal constituents, also used as biomarker for classification and identification of Cymbopogon chemotypes. In the light of this, present study involved RNA sequencing and comparison of expression profiles of four contrasting Cymbopogon species namely C. flexuosus var. Chirharit (citral rich and frost resistant), C. martinii var. PRC-1 (geraniol rich), C. pendulus var. Praman (the most stable and citral-rich genotype), and Jamrosa (a hybrid of C. nardus var. confertiflorus × C. jwarancusa (rich in geraniol and geranyl acetate). The transcriptome profiles revealed marked differences in gene expression patterns of 28 differentially expressed genes (DEGs) of terpenoid metabolic pathways between the four Cymbopogon sp. The major DEGs were Carotenoid Cleavage Dioxygenases (CCD), Aspartate aminotransferase (ASP amino), Mevalonate E-4 hydroxy, AKR, GGPS, FDPS, and AAT. In addition, few TFs related to different regulatory pathways were also identified. The gene expression profiles of DEGs were correlated to the EO yield and their monoterpene compositions. Overall, the PRC-1 (C. martinii) shows distinguished gene expression profiles from all other genotypes. Thus, the transcriptome sequence database expanded our understanding of terpenoid metabolism and its molecular regulation in Cymbopogon species. Additionally, this data also serves as an important source of knowledge for enhancing oil yield and quality in Cymbopogon and closely related taxa. KEY MESSAGE: Unfolding the new secretes surrounding EO biosynthesis and regulation in four contrasting Cymbopogon species.
Collapse
Affiliation(s)
- Gurminder Kaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida 201303, UP, India
| | - Surjeet Kumar Arya
- CSIR-National Botanical Research Institute (Council of Scientific and Industrial Research), Rana Pratap Marg, Lucknow, UP 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Babita Singh
- CSIR-National Botanical Research Institute (Council of Scientific and Industrial Research), Rana Pratap Marg, Lucknow, UP 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sanchita Singh
- CSIR-National Botanical Research Institute (Council of Scientific and Industrial Research), Rana Pratap Marg, Lucknow, UP 226001, India; Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh 226007, India
| | - Sushmita
- CSIR-National Botanical Research Institute (Council of Scientific and Industrial Research), Rana Pratap Marg, Lucknow, UP 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Gauri Saxena
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh 226007, India
| | - Praveen C Verma
- CSIR-National Botanical Research Institute (Council of Scientific and Industrial Research), Rana Pratap Marg, Lucknow, UP 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Deepak Ganjewala
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida 201303, UP, India.
| |
Collapse
|
3
|
Gao XC, Zhang NX, Shen JM, Lv JW, Zhang KY, Sun Y, Li H, Wang YL, Cheng DD, Zhao MY, Zhang H, Li CN, Sun JM. Screening of the Active Compounds against Neural Oxidative Damage from Ginseng Phloem Using UPLC-Q-Exactive-MS/MS Coupled with the Content-Effect Weighted Method. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27249061. [PMID: 36558193 PMCID: PMC9781605 DOI: 10.3390/molecules27249061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
The neuroprotective properties of ginsenosides have been found to reverse the neurological damage caused by oxidation in many neurodegenerative diseases. However, the distribution of ginsenosides in different tissues of the main root, which was regarded as the primary medicinal portion in clinical practice was different, the specific parts and specific components against neural oxidative damage were not clear. The present study aims to screen and determine the potential compounds in different parts of the main root in ginseng. Comparison of the protective effects in the main root, phloem and xylem of ginseng on hydrogen peroxide-induced cell death of SH-SY5Y neurons was investigated. UPLC-Q-Exactive-MS/MS was used to quickly and comprehensively characterize the chemical compositions of the active parts. Network pharmacology combined with a molecular docking approach was employed to virtually screen for disease-related targets and potential active compounds. By comparing the changes before and after Content-Effect weighting, the compounds with stronger anti-nerve oxidative damage activity were screened out more accurately. Finally, the activity of the selected monomer components was verified. The results suggested that the phloem of ginseng was the most effective part. There were 19 effective compounds and 14 core targets, and enriched signaling pathway and biological functions were predicted. After Content-Effect weighting, compounds Ginsenosides F1, Ginsenosides Rf, Ginsenosides Rg1 and Ginsenosides Rd were screened out as potential active compounds against neural oxidative damage. The activity verification study indicated that all four predicted ginsenosides were effective in protecting SH-SY5Y cells from oxidative injury. The four compounds can be further investigated as potential lead compounds for neurodegenerative diseases. This also provides a combined virtual and practical method for the simple and rapid screening of active ingredients in natural products.
Collapse
Affiliation(s)
- Xiao-Chen Gao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Nan-Xi Zhang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Jia-Ming Shen
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Jing-Wei Lv
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Kai-Yue Zhang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Yao Sun
- School of Chemistry and Life Sciences, Changchun University of Technology, Changchun 130012, China
| | - Hang Li
- School of Chemistry and Life Sciences, Changchun University of Technology, Changchun 130012, China
| | - Yue-Long Wang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Duan-Duan Cheng
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Meng-Ya Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Hui Zhang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
- Correspondence: (H.Z.); (C.-N.L.); (J.-M.S.); Tel.: +86-431-86763809 (J.-M.S.)
| | - Chun-Nan Li
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
- Correspondence: (H.Z.); (C.-N.L.); (J.-M.S.); Tel.: +86-431-86763809 (J.-M.S.)
| | - Jia-Ming Sun
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
- Correspondence: (H.Z.); (C.-N.L.); (J.-M.S.); Tel.: +86-431-86763809 (J.-M.S.)
| |
Collapse
|
4
|
Yao L, Zhang H, Liu Y, Ji Q, Xie J, Zhang R, Huang L, Mei K, Wang J, Gao W. Engineering of triterpene metabolism and overexpression of the lignin biosynthesis gene PAL promotes ginsenoside Rg 3 accumulation in ginseng plant chassis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1739-1754. [PMID: 35731022 DOI: 10.1111/jipb.13315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/20/2022] [Indexed: 05/28/2023]
Abstract
The ginsenoside Rg3 found in Panax species has extensive pharmacological properties, in particular anti-cancer effects. However, its natural yield in Panax plants is limited. Here, we report a multi-modular strategy to improve yields of Rg3 in a Panax ginseng chassis, combining engineering of triterpene metabolism and overexpression of a lignin biosynthesis gene, phenylalanine ammonia lyase (PAL). We first performed semi-rational design and site mutagenesis to improve the enzymatic efficiency of Pq3-O-UGT2, a glycosyltransferase that directly catalyzes the biosynthesis of Rg3 from Rh2 . Next, we used clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing to knock down the branch pathway of protopanaxatriol-type ginsenoside biosynthesis to enhance the metabolic flux of the protopanaxadiol-type ginsenoside Rg3 . Overexpression of PAL accelerated the formation of the xylem structure, significantly improving ginsenoside Rg3 accumulation (to 6.19-fold higher than in the control). We combined overexpression of the ginsenoside aglycon synthetic genes squalene epoxidase, Pq3-O-UGT2, and PAL with CRISPR/Cas9-based knockdown of CYP716A53v2 to improve ginsenoside Rg3 accumulation. Finally, we produced ginsenoside Rg3 at a yield of 83.6 mg/L in a shake flask (7.0 mg/g dry weight, 21.12-fold higher than with wild-type cultures). The high-production system established in this study could be a potential platform to produce the ginsenoside Rg3 commercially for pharmaceutical use.
Collapse
Affiliation(s)
- Lu Yao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Yirong Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Qiushuang Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Jing Xie
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ru Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, 325000, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
5
|
Oberc C, Sedighi A, Li PCH. The genetic authentication of Panax ginseng and Panax quinquefolius based on using single nucleotide polymorphism (SNP) conducted in a nucleic acid test chip. Anal Bioanal Chem 2022; 414:3987-3998. [PMID: 35385984 DOI: 10.1007/s00216-022-04044-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 11/26/2022]
Abstract
Panax ginseng and Panax quinquefolius, which are commonly called Chinese ginseng and American ginseng respectively, have different medicinal properties and market values; however, these samples can be difficult to differentiate from one another based on physical appearances of the samples especially when they are in powdery or granular forms. A molecular technique is thus needed to overcome this difficulty; this technique is based on the nucleic acid test (NAT) conducted on the microfluidic chip surface. Three single nucleotide polymorphism (SNP) sites (i.e. N1, N2, N3) on the Panax genome that differ between P. ginseng (G) and P. quinquefolius (Q) have been selected to design probes for the NAT. Primers were designed to amplify the antisense strands by asymmetric PCR. We have developed three different NAT methodologies involving surface immobilization and subsequent (stop flow or dynamic) hybridization of probes (i.e. N1G, N1Q, N2G, N2Q, N3Q) to the antisense strands. These NAT methods consist of two steps, namely immobilization and hybridization, and each method is distinguished by what is immobilized on the microfluidic chip surface in the first step (i.e. probe, target or capture strand). These three NATs developed are called probe-target method 1, target-probe method 2 and three-strand complex method 3. Out of the three methods, it was found that the capture strand-target-probe method 3 provided the best differentiation of the ginseng species, in which a 3' NH2 capture strand is first immobilized and the antisense PCR strand is then bound, while N2G and N3Q probes are used for detection of P. ginseng (G) and P. quinquefolius (Q) respectively.
Collapse
Affiliation(s)
- Christopher Oberc
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Abootaleb Sedighi
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Paul C H Li
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
| |
Collapse
|
6
|
Xiao S, Chu Y, Chen Y, Zhao Q, Liao B, Zhang J, Gao Y, Xu J, Chen S. Genome-wide identification and transcriptional profiling analysis of PIN/PILS auxin transporter gene families in Panax ginseng. CHINESE HERBAL MEDICINES 2021; 14:48-57. [PMID: 36120122 PMCID: PMC9476816 DOI: 10.1016/j.chmed.2021.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/12/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yang Chu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yanjun Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qinghe Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Yuan Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Corresponding author.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| |
Collapse
|
7
|
Xu R, Zhang J, You J, Gao L, Li Y, Zhang S, Zhu W, Shu S, Xiong C, Xiong H, Chen P, Guo J, Liu Z. Full-length transcriptome sequencing and modular organization analysis of oleanolic acid- and dammarane-type saponins related gene expression patterns in Panax japonicus. Genomics 2020; 112:4137-4147. [PMID: 32653517 DOI: 10.1016/j.ygeno.2020.06.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/15/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
The saponins found in Panax japonicus, a traditional medicinal herb in Asia, exhibit high degrees of structural and functional similarity. In this study, metabolite analysis revealed that oleanolic acid-type and dammarane-type saponins were distributed unevenly in three tissues (rhizome_Y, rhizome_O, and secRoot) of P. japonicus. Single-molecule real-time (SMRT) sequencing and next generation sequencing (NGS) data revealed distinct and tissue-specific transcriptomic patterns relating to the production of these two types of saponins. In the co-expression network and hierarchical clustering analyses, one 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) and two 1-deoxy-D-xylulose-5-phosphate synthase (DXS) etc. transcripts were found to be key genes associated with the biosynthesis of oleanolic acid and dammarane-type saponins in P. japonicus, respectively. In addition, cytochrome p450 (CYP) and UDP-glucuronosyltransferase (UGT) family proteins that serve as regulators of saponin biosynthesis-related genes were also found to exhibit tissue-specific expression patterns. Together these results offer a comprehensive metabolomic and transcriptomic overview of P. japonicus.
Collapse
Affiliation(s)
- Ran Xu
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jiao Zhang
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jingmao You
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China
| | - Limei Gao
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Yongchang Li
- Kansas City University of Medicine and Biosciences, Joplin 64804, USA
| | - Shaopeng Zhang
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Wenjun Zhu
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Shaohua Shu
- School of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao Xiong
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hui Xiong
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Ping Chen
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jie Guo
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China.
| | - Zhiguo Liu
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| |
Collapse
|
8
|
Xu R, Xu J, Li YC, Dai YT, Zhang SP, Wang G, Liu ZG, Dong LL, Chen SL. Integrated chemical and transcriptomic analyses unveils synthetic characteristics of different medicinal root parts of Angelica sinensis. CHINESE HERBAL MEDICINES 2020; 12:19-28. [PMID: 36117566 PMCID: PMC9476730 DOI: 10.1016/j.chmed.2019.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/27/2019] [Accepted: 07/20/2019] [Indexed: 02/06/2023] Open
Abstract
Objective Why are different medicinal parts including heads, bodies and tails of Angelicae Sinensis Radix (ASR) distinct in pharmaceutical activities? Here we explored their discrepancy in chemical constituents and transcriptome. Methods ASR were separated into three medicinal parts: heads (rootstocks with petiole traces of ASR), bodies (taproots of ASR) and tails (lateral roots of ASR), and chemical and transcriptomic analyses were conducted simultaneously. Results High performance liquid chromatography (HPLC) fingerprint results showed that five widely used active ingredients (ferulic acid, senkyunolide H, senkyunolide A, n-butylphathlide, and ligustilide) were distributed unevenly in the three ASR medicinal parts. Partial least squares-discriminant analysis (PLS-DA) demonstrated that the heads can be differentiated from the two other root parts due to different amounts of the main components. However, the content of ferulic acid (a main quality marker) was significantly higher in tails than in the heads and bodies. The transcriptome analysis found that 25,062, 10,148 and 29,504 unigenes were specifically expressed in the heads, bodies and tails, respectively. WGCNA analysis identified 17 co-expression modules, which were constructed from the 19,198 genes in the nine samples of ASR. Additionally, we identified 28 unigenes involved in two phenylpropanoid biosynthesis (PB) pathways about ferulic acid metabolism pathways, of which 17 unigenes (60.7%) in the PB pathway were highly expressed in the tails. The expression levels of PAL, C3H, and CQT transcripts were significantly higher in the tails than in other root parts. RT-qPCR analysis confirmed that PAL, C3H, and CQT genes were predominantly expressed in the tail parts, especially PAL, whose expression was more than doubled as compared with that in other root parts. Conclusion Chemical and transcriptomic analyses revealed the distribution contents and pivotal transcripts of the ferulic acid biosynthesis-related pathways. The spatial gene expression pattern partially explained the discrepancy of integral medicinal activities of three medicinal root parts.
Collapse
|
9
|
Huang P, Lin F, Li B, Zheng Y. Hybrid-Transcriptome Sequencing and Associated Metabolite Analysis Reveal Putative Genes Involved in Flower Color Difference in Rose Mutants. PLANTS (BASEL, SWITZERLAND) 2019; 8:E267. [PMID: 31387222 PMCID: PMC6724100 DOI: 10.3390/plants8080267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/21/2019] [Accepted: 07/29/2019] [Indexed: 02/04/2023]
Abstract
Gene mutation is a common phenomenon in nature that often leads to phenotype differences, such as the variations in flower color that frequently occur in roses. With the aim of revealing the genomic information and inner mechanisms, the differences in the levels of both transcription and secondary metabolism between a pair of natural rose mutants were investigated by using hybrid RNA-sequencing and metabolite analysis. Metabolite analysis showed that glycosylated derivatives of pelargonidin, e.g., pelargonidin 3,5 diglucoside and pelargonidin 3-glucoside, which were not detected in white flowers (Rosa 'Whilte Mrago Koster'), constituted the major pigments in pink flowers. Conversely, the flavonol contents of petal, such as kaempferol-3-glucoside, quercetin 3-glucoside, and rutin, were higher in white flowers. Hybrid RNA-sequencing obtained a total of 107,280 full-length transcripts in rose petal which were annotated in major databases. Differentially expressed gene (DEG) analysis showed that the expression of genes involved in the flavonoid biosynthesis pathway was significantly different, e.g., CHS, FLS, DFR, LDOX, which was verified by qRT-PCR during flowering. Additionally, two MYB transcription factors were found and named RmMYBAN2 and RmMYBPA1, and their expression patterns during flowering were also analyzed. These findings indicate that these genes may be involved in the flower color difference in the rose mutants, and competition between anthocyanin and flavonol biosynthesis is a primary cause of flower color variation, with its regulation reflected by transcriptional and secondary metabolite levels.
Collapse
Affiliation(s)
- Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| |
Collapse
|
10
|
Chen X, Li J, Wang X, Zhong L, Tang Y, Zhou X, Liu Y, Zhan R, Zheng H, Chen W, Chen L. Full-length transcriptome sequencing and methyl jasmonate-induced expression profile analysis of genes related to patchoulol biosynthesis and regulation in Pogostemon cablin. BMC PLANT BIOLOGY 2019; 19:266. [PMID: 31221095 PMCID: PMC6585090 DOI: 10.1186/s12870-019-1884-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/12/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Pogostemon cablin (Blanco) Benth. (Patchouli) is an important aromatic and medicinal plant and widely used in traditional Chinese medicine as well as in the perfume industry. Patchoulol is the primary bioactive component in P. cablin, its biosynthesis has attracted widespread interests. Previous studies have surveyed the putative genes involved in patchoulol biosynthesis using next-generation sequencing method; however, technical limitations generated by short-read sequencing restrict the yield of full-length genes. Additionally, little is known about the expression pattern of genes especially patchoulol biosynthesis related genes in response to methyl jasmonate (MeJA). Our understanding of patchoulol biosynthetic pathway still remained largely incomplete to date. RESULTS In this study, we analyzed the morphological character and volatile chemical compounds of P. cablin cv. 'Zhanxiang', and 39 volatile chemical components were detected in the patchouli leaf using GC-MS, most of which were sesquiterpenes. Furthermore, high-quality RNA isolated from leaves and stems of P. cablin were used to generate the first full-length transcriptome of P. cablin using PacBio isoform sequencing (Iso-Seq). In total, 9.7 Gb clean data and 82,335 full-length UniTransModels were captured. 102 transcripts were annotated as 16 encoding enzymes involved in patchouli alcohol biosynthesis. Accorded with the uptrend of patchoulol content, the vast majority of genes related to the patchoulol biosynthesis were up-regulated after MeJA treatment, indicating that MeJA led to an increasing synthesis of patchoulol through activating the expression level of genes involved in biosynthesis pathway of patchoulol. Moreover, expression pattern analysis also revealed that transcription factors participated in JA regulation of patchoulol biosynthesis were differentially expressed. CONCLUSIONS The current study comprehensively reported the morphological specificity, volatile chemical compositions and transcriptome characterization of the Chinese-cultivated P. cablin cv. 'Zhanxiang', these results contribute to our better understanding of the physiological and molecular features of patchouli, especially the molecular mechanism of biosynthesis of patchoulol. Our full-length transcriptome data also provides a valuable genetic resource for further studies in patchouli.
Collapse
Affiliation(s)
- Xiuzhen Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Junren Li
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Xiaobing Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Liting Zhong
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Yun Tang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Xuanxuan Zhou
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Yanting Liu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Hai Zheng
- Guangdong Institute of Traditional Chinese Medicine, Guangzhou, 510520 People’s Republic of China
| | - Weiwen Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| | - Likai Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006 People’s Republic of China
| |
Collapse
|
11
|
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.
Collapse
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
Collapse
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
| |
Collapse
|
12
|
Herbgenomics: A stepping stone for research into herbal medicine. SCIENCE CHINA-LIFE SCIENCES 2019; 62:913-920. [DOI: 10.1007/s11427-018-9472-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022]
|
13
|
Genome-Wide Identification and Comparative Analysis for OPT Family Genes in Panax ginseng and Eleven Flowering Plants. Molecules 2018; 24:molecules24010015. [PMID: 30577553 PMCID: PMC6337337 DOI: 10.3390/molecules24010015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/06/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023] Open
Abstract
Herb genomics and comparative genomics provide a global platform to explore the genetics and biology of herbs at the genome level. Panax ginseng C.A. Meyer is an important medicinal plant for a variety of bioactive chemical compounds of which the biosynthesis may involve transport of a wide range of substrates mediated by oligopeptide transporters (OPT). However, information about the OPT family in the plant kingdom is still limited. Only 17 and 18 OPT genes have been characterized for Oryza sativa and Arabidopsisthaliana, respectively. Additionally, few comprehensive studies incorporating the phylogeny, gene structure, paralogs evolution, expression profiling, and co-expression network between transcription factors and OPT genes have been reported for ginseng and other species. In the present study, we performed those analyses comprehensively with both online tools and standalone tools. As a result, we identified a total of 268 non-redundant OPT genes from 12 flowering plants of which 37 were from ginseng. These OPT genes were clustered into two distinct clades in which clade-specific motif compositions were considerably conservative. The distribution of OPT paralogs was indicative of segmental duplication and subsequent structural variation. Expression patterns based on two sources of RNA-Sequence datasets suggested that some OPT genes were expressed in both an organ-specific and tissue-specific manner and might be involved in the functional development of plants. Further co-expression analysis of OPT genes and transcription factors indicated 141 positive and 11 negative links, which shows potent regulators for OPT genes. Overall, the data obtained from our study contribute to a better understanding of the complexity of the OPT gene family in ginseng and other flowering plants. This genetic resource will help improve the interpretation on mechanisms of metabolism transportation and signal transduction during plant development for Panax ginseng.
Collapse
|
14
|
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.
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Chu Y, Xiao S, Su H, Liao B, Zhang J, Xu J, Chen S. Genome-wide characterization and analysis of bHLH transcription factors in Panax ginseng. Acta Pharm Sin B 2018; 8:666-677. [PMID: 30109190 PMCID: PMC6089850 DOI: 10.1016/j.apsb.2018.04.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/24/2018] [Accepted: 03/14/2018] [Indexed: 11/24/2022] Open
Abstract
Ginseng (Panax ginseng C.A. Meyer) is one of the best-selling herbal medicines, with ginsenosides as its main pharmacologically active constituents. Although extensive chemical and pharmaceutical studies of these compounds have been performed, genome-wide studies of the basic helix-loop-helix (bHLH) transcription factors of ginseng are still limited. The bHLH transcription factor family is one of the largest transcription factor families found in eukaryotic organisms, and these proteins are involved in a myriad of regulatory processes. In our study, 169 bHLH transcription factor genes were identified in the genome of P. ginseng, and phylogenetic analysis indicated that these PGbHLHs could be classified into 24 subfamilies. A total of 21 RNA-seq data sets, including two sequencing libraries for jasmonate (JA)-responsive and 19 reported libraries for organ-specific expression analyses were constructed. Through a combination of gene-specific expression patterns and chemical contents, 6 PGbHLH genes from 4 subfamilies were revealed to be potentially involved in the regulation of ginsenoside biosynthesis. These 6 PGbHLHs, which had distinct target genes, were further divided into two groups depending on the absence of MYC-N structure. Our results would provide a foundation for understanding the molecular basis and regulatory mechanisms of bHLH transcription factor action in P. ginseng.
Collapse
Affiliation(s)
- Yang Chu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - He Su
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jingjing Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Corresponding authors.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Corresponding authors.
| |
Collapse
|
17
|
Liu J, Gao F, Ren J, Lu X, Ren G, Wang R. A Novel AP2/ERF Transcription Factor CR1 Regulates the Accumulation of Vindoline and Serpentine in Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2017; 8:2082. [PMID: 29270185 PMCID: PMC5724233 DOI: 10.3389/fpls.2017.02082] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/21/2017] [Indexed: 05/23/2023]
Abstract
As one type of the most important alkaloids in the world, terpenoid indole alkaloids (TIAs) show a wide range of pharmaceutical activities that are beneficial for clinical treatments. Catharanthus roseus produces approximately 130 identified TIAs and is considered to be a model plant to study TIA biosynthesis. In order to increase the production of high medical value metabolites whose yields are extremely low in C. roseus, genetic engineering combined with transcriptional regulation has been applied in recent years. By using bioinformatics which is based on RNA sequencing (RNA-seq) data from methyl jasmonate (MeJA)-treated C. roseus as well as phylogenetic analysis, the present work aims to screen candidate genes that may be involved in the regulation of TIA biosynthesis, resulting in a novel AP2/ERF transcription factor, CR1 (Catharanthus roseus 1). Subsequently, virus-induced gene silencing (VIGS) of CR1 was carried out to identify the involvement of CR1 in the accumulations of several TIAs and quantitative real-time PCR (qRT-PCR) was then applied to detect the expression levels of 7 genes in the related biosynthetic pathway in silenced plants. The results show that all the 7 genes were upregulated in CR1-silenced plants. Furthermore, metabolite analyses indicate that silencing CR1 could increase the accumulations of vindoline and serpentine in C. roseus. These results suggest a novel negative regulator which may be involved in the TIAs biosynthetic pathway.
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|