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Ahmed U, Ong SK, Tan KO, Khan KM, Khan NA, Siddiqui R, Alawfi BS, Anwar A. Alpha-Mangostin and its nano-conjugates induced programmed cell death in Acanthamoeba castellanii belonging to the T4 genotype. Int Microbiol 2024; 27:1063-1081. [PMID: 38015290 DOI: 10.1007/s10123-023-00450-1] [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: 09/13/2023] [Revised: 10/26/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
Acanthamoeba are free living amoebae that are the causative agent of keratitis and granulomatous amoebic encephalitis. Alpha-Mangostin (AMS) is a significant xanthone; that demonstrates a wide range of biological activities. Here, the anti-amoebic activity of α-Mangostin and its silver nano conjugates (AMS-AgNPs) were evaluated against pathogenic A. castellanii trophozoites and cysts in vitro. Amoebicidal assays showed that both AMS and AMS-AgNPs inhibited the viability of A. castellanii dose-dependently, with an IC50 of 88.5 ± 2.04 and 20.2 ± 2.17 μM, respectively. Both formulations inhibited A. castellanii-mediated human keratinocyte cell cytopathogenicity. Functional assays showed that both samples caused apoptosis through the mitochondrial pathway and reduced mitochondrial membrane potential and ATP production, while increasing reactive oxygen species (ROS) and nicotinamide adenine dinucleotide phosphate (NADPH) cytochrome-c reductase in the cytosol. Whole transcriptome sequencing of A. castellanii showed the expression of 826 genes, with 447 genes being up-regulated and 379 genes being down-regulated post treatment. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the majority of genes were linked to apoptosis, autophagy, RAP1, AGE-RAGE and oxytocin signalling pathways. Seven genes (PTEN, H3, ARIH1, SDR16C5, PFN, glnA GLUL, and SRX1) were identified as the most significant (Log2 (FC) value 4) for molecular mode of action in vitro. Future in vivo studies with AMS and nanoconjugates are needed to realize the clinical potential of this work.
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Affiliation(s)
- Usman Ahmed
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, 47500, Subang Jaya, Selangor, Malaysia
| | - Seng-Kai Ong
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, 47500, Subang Jaya, Selangor, Malaysia
| | - Kuan Onn Tan
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, 47500, Subang Jaya, Selangor, Malaysia
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Naveed Ahmed Khan
- Microbiota Research Center, Istinye University, Istanbul, 34010, Turkey.
| | - Ruqaiyyah Siddiqui
- Microbiota Research Center, Istinye University, Istanbul, 34010, Turkey
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Bader Saleem Alawfi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, 42353, Madinah, Saudi Arabia
| | - Ayaz Anwar
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, 47500, Subang Jaya, Selangor, Malaysia.
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Ahmed U, Ong SK, Khan KM, Siddiqui R, Khan NA, Shaikh MF, Alawfi BS, Anwar A. Effect of embelin on inhibition of cell growth and induction of apoptosis in Acanthamoeba castellanii. Arch Microbiol 2023; 205:360. [PMID: 37898989 DOI: 10.1007/s00203-023-03698-3] [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: 08/23/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023]
Abstract
Acanthamoeba castellanii is the causative agent of fatal encephalitis and blinding keratitis. Current therapies remain a challenge, hence there is a need to search for new therapeutics. Here, we tested embelin (EMB) and silver nanoparticles doped with embelin (EMB-AgNPs) against A. castellanii. Using amoebicidal assays, the results revealed that both compounds inhibited the viability of Acanthamoeba, having an IC50 of 27.16 ± 0.63 and 13.63 ± 1.08 μM, respectively, while causing minimal cytotoxicity against HaCaT cells in vitro. The findings suggest that both samples induced apoptosis through the mitochondria-mediated pathway. Differentially expressed genes analysis showed that 652 genes were uniquely expressed in treated versus untreated cells, out of which 191 were significantly regulated in the negative control vs. conjugate. Combining the analysis, seven genes (ARIH1, RAP1, H3, SDR16C5, GST, SRX1, and PFN) were highlighted as the most significant (Log2 (FC) value ± 4) for the molecular mode of action in vitro. The KEGG analysis linked most of the genes to apoptosis, the oxidative stress signaling pathway, cytochrome P450, Rap1, and the oxytocin signaling pathways. In summary, this study provides a thorough framework for developing therapeutic agents against microbial infections using EMB and EMB-AgNPs.
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Affiliation(s)
- Usman Ahmed
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya, 47500, Selangor, Malaysia
| | - Seng-Kai Ong
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya, 47500, Selangor, Malaysia
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Naveed Ahmed Khan
- Microbiota Research Center, Istinye University, 34010, Istanbul, Turkey.
| | - Mohd Farooq Shaikh
- Neuropharmacology Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500, Bandar Sunway, Malaysia
- School of Dentistry and Medical Sciences, Charles Sturt University, Orange, New South Wales, Australia
| | - Bader Saleem Alawfi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, 42353, Madinah, Saudi Arabia
| | - Ayaz Anwar
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya, 47500, Selangor, Malaysia.
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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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Su F, Sun Y, Zhu W, Bai C, Zhang W, Luo Y, Yang B, Kuang H, Wang Q. A comprehensive review of research progress on the genus Arisaema: Botany, uses, phytochemistry, pharmacology, toxicity and pharmacokinetics. JOURNAL OF ETHNOPHARMACOLOGY 2022; 285:114798. [PMID: 34780984 DOI: 10.1016/j.jep.2021.114798] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/07/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The genus Arisaema belongs to the family Araceae, which includes Chinese herbal medicines with wide-ranging pharmacological functions, including those useful for the treatment of stubborn phlegm, cough, epilepsy, tetanus, snakebite, rheumatoid arthritis, and other ailments. AIM OF THE STUDY The current study aimed to comprehensively review the botany, uses, phytochemistry, pharmacology, toxicity, quality control and pharmacokinetics of plants in the genus Arisaema and to provide novel insights to develop future research in this field. MATERIALS AND METHODS Relevant information on the genus Arisaema was obtained from published scientific materials (including materials from PubMed, Elsevier, Web of Science, Google Scholar, Baidu Scholar, CNKI, and Wiley) and other literature sources (e.g., the Chinese Pharmacopoeia, 2020 edition; Chinese herbal books and PhD and MSc thesis). RESULTS The application information complied with this review and included processing techniques, traditional uses, clinical applications and classic prescriptions. Approximately 260 compounds, including flavonoids, alkaloids, saccharides, steroids, fatty acids, amino acids and volatile oils, have been separated and identified from the genus Arisaema. The isolated compounds exhibit wide-ranging pharmacological activities such as antitumor activity, analgesic and sedative activity, antioxidant activity and anti-inflammatory activity. The toxicity and irritant impacts, quality control, and pharmacokinetics are also discussed in this review. CONCLUSIONS Plants in the genus Arisaema are valuable resources with therapeutic potential for a broad spectrum of ailments. Based on the limited literature, this review comprehensively and systematically summarizes current knowledge regarding the genus Arisaema for the first time. However, there have been insufficient studies on the active ingredients and germplasm and insufficient in-depth mechanistic studies. Therefore, isolation and identification of additional effective components and through research on the germplasm, pharmacodynamic mechanisms, and toxicology should be conducted to assess effectiveness and safety and to ensure the quality of the related drugs.
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Affiliation(s)
- Fazhi Su
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Yanping Sun
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Wenbo Zhu
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Chenxi Bai
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Wensen Zhang
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Yumeng Luo
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Bingyou Yang
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China
| | - Haixue Kuang
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China.
| | - Qiuhong Wang
- Key Laboratory of Chinese Material Medica (Ministry of Education), Heilongjiang University of Chinese Medicine, 24 Heping Road, Xiangfang District, Harbin, 150040, China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, 232 Outer Ring Road, University Town, Guangzhou, 510006, China.
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Feng T, Jiang Y, Jia Q, Han R, Wang D, Zhang X, Liang Z. Transcriptome Analysis of Different Sections of Rhizome in Polygonatum sibiricum Red. and Mining Putative Genes Participate in Polysaccharide Biosynthesis. Biochem Genet 2022; 60:1547-1566. [DOI: 10.1007/s10528-022-10183-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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Yi S, Xu T, Song X, Wang W, Yu W, Han B. Sequencing and phylogenetic analysis of the complete chloroplast genome of Arisaema heterophyllum Blume. Mitochondrial DNA B Resour 2021; 6:3297-3299. [PMID: 34712816 PMCID: PMC8547874 DOI: 10.1080/23802359.2021.1993460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Arisaema heterophyllum Blume is a perennial medicinal herb widely distributed in China, Korea and Japan. In this study, the complete chloroplast genome sequence of A. heterophyllum was assembled and characterized based on high-throughput sequencing data. The whole chloroplast genome is 170,610 bp in length and contains 95,485 bp large single-copy (LSC) and 22,605 bp small single-copy (SSC) regions separated by a pair of 26,260 bp inverted repeat (IR) regions. It contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, with an overall GC content of 34.5%. A phylogenetic tree reconstructed by 30 chloroplast genomes reveals that A. heterophyllum is mostly related to the same genus A. ringens, A. franchetianum and A. erubescens. The complete chloroplast genome of A. heterophyllum was the firstly reported and deposited at GenBank under accession number MZ424448.
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Affiliation(s)
- Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Xiangwen Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
| | - Wangyang Yu
- Anhui Qiansouyan Biotechnology Co., Ltd, Lu'an, P.R. China
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, P.R. China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, P.R. China
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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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Zhang S, Zhao L, Shan C, Shi Y, Ma K, Wu J. Exploring the biosynthetic pathway of lignin in Acorus tatarinowii Schott using de novo leaf and rhizome transcriptome analysis. Biosci Rep 2021; 41:BSR20210006. [PMID: 34076245 PMCID: PMC8200657 DOI: 10.1042/bsr20210006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 01/02/2023] Open
Abstract
Acorus tatarinowii Schott is a well-known Chinese traditional herb. Lignin is the major biologically active ingredient and exerts a broad range of pharmacological effects: it is an antitumor, antioxidant and bacteriostatic agent, and protects the cardiovascular system. In the present study, the transcriptomes of the leaf and rhizome tissues of A. tatarinowii Schott were obtained using the BGISEQ-500 platform. A total of 141777 unigenes were successfully assembled, of which 76714 were annotated in public databases. Further analysis of the lignin biosynthesis pathway revealed a total of 107 unigenes encoding 8 key enzymes, which were involved in this pathway. Furthermore, the expression of the key genes involved in lignin synthesis in different tissues was identified by quantitative real-time PCR. Analysis of the differentially expressed genes (DEGs) showed that most of the up-regulated unigenes were enriched in rhizome tissues. In addition, 2426 unigenes were annotated to the transcriptome factor (TF) family. Moreover, 16 TFs regulating the same key enzyme (peroxidase) were involved in the lignin synthesis pathway. The alignment of peroxidase amino acid sequences and the analysis of the structural characteristics revealed that the key peroxidase enzyme had well-conserved sequences, spatial structures, and active sites. The present study is the first to provide comprehensive genetic information on A. tatarinowii Schott at the transcriptional level, and will facilitate our understanding of the lignin biosynthesis pathway.
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Affiliation(s)
- Shengxiang Zhang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Liqiang Zhao
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Chunmiao Shan
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Yuanyuan Shi
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Kelong Ma
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China
- Clinical College of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei 230012, China
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10
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Wang C, Xu N, Cui S. Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis. PeerJ 2021; 9:e10885. [PMID: 33665027 PMCID: PMC7906042 DOI: 10.7717/peerj.10885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pueraria lobata (Willd.) Ohwi is a valuable herb used in traditional Chinese medicine. Isoflavonoids are the major bioactive compounds in P. lobata, namely puerarin, daidzin, glycitin, genistin, daidzein, and glycitein, which have pharmacological properties of anti-cardiovascular, anti-hypertension, anti-inflammatory, and anti-arrhythmic. METHODS To characterize the corresponding genes of the compounds in the isoflavonoid pathway, RNA sequencing (RNA-Seq) analyses of roots, stems, and leaves of P. lobata were carried out on the BGISEQ-500 sequencing platform. RESULTS We identified 140,905 unigenes in total, of which 109,687 were annotated in public databases, after assembling the transcripts from all three tissues. Multiple genes encoding key enzymes, such as IF7GT and transcription factors, associated with isoflavonoid biosynthesis were identified and then further analyzed. Quantitative real-time PCR (qRT-PCR) results of some genes encoding key enzymes were consistent with our RNA-Seq analysis. Differentially expressed genes (DEGs) were determined by analyzing the expression profiles of roots compared with other tissues (leaves and stems). This analysis revealed numerous DEGs that were either uniquely expressed or up-regulated in the roots. Finally, quantitative analyses of isoflavonoid metabolites occurring in the three P. lobata tissue types were done via high-performance liquid-chromatography and tandem mass spectrometry methodology (HPLC-MS/MS). Our comprehensive transcriptome investigation substantially expands the genomic resources of P. lobata and provides valuable knowledge on both gene expression regulation and promising candidate genes that are involved in plant isoflavonoid pathways.
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Affiliation(s)
- Chenkai Wang
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
- Anhui University, Hefei, China
- Anhui University of Chinese Medicine, Hefei, China
| | - Nenggui Xu
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuai Cui
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
- Anhui University of Chinese Medicine, Hefei, China
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Chen Y, Yao L, Pan W, Guo B, Lin S, Wei Y. An integrated analysis of metabolomic and transcriptomic profiles reveals flavonoid metabolic differences between Anoectochilus roxburghii and Anoectochilus formosanus. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Shi Y, Zhang S, Peng D, Shan C, Zhao L, Wang B, Wu J. De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis. PeerJ 2020; 8:e10157. [PMID: 33194397 PMCID: PMC7651471 DOI: 10.7717/peerj.10157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 09/21/2020] [Indexed: 01/12/2023] Open
Abstract
Cnidium monnieri (L.) Cuss (C. monnieri) is one of the most widely used traditional herbal medicines, exhibiting a wide range of pharmacological functions for treating asynodia, trichomonas vaginitis, and osphyalgia. Its important medicinal value comes from its abundance of coumarins. To identify genes involved in coumarin biosynthesis and accumulation, we analyzed transcriptome data from flower, leaf, root and stem tissues of C. monnieri. A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of these, 119,177 unigenes were annotated in public databases. We identified differentially expressed genes (DEGs) based on expression profile analysis. These DEGs exhibited higher expression levels in flower tissue than in leaf, stem or root tissues. We identified and analyzed numerous genes encoding enzymes involved in coumarin biosynthesis, and verified genes encoding key enzymes using quantitative real-time PCR. Our transcriptome data will make great contributions to research on C. monnieri and provide clues for identifying candidate genes involved in coumarin metabolic pathways.
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Affiliation(s)
- Yuanyuan Shi
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Shengxiang Zhang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Daiyin Peng
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China.,Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, China
| | - Chunmiao Shan
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Liqiang Zhao
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Bin Wang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China.,Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, China
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Zhang S, Shi Y, Huang L, Wang C, Zhao D, Ma K, Wu J, Peng D. Comparative transcriptomic analysis of rhizomes, stems, and leaves of Polygonatum odoratum (Mill.) Druce reveals candidate genes associated with polysaccharide synthesis. Gene 2020; 744:144626. [PMID: 32224272 DOI: 10.1016/j.gene.2020.144626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/19/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
Polygonatum odoratum (Mill.) Druce is a well-known traditional Chinese herb. Polysaccharides are major bioactive components of Polygonatum odoratum, which can improve immunity, and are used to treat rheumatic heart disease, cardiovascular disease, and diabetes. This study identified potential genes and transcription factors (TFs) that regulate polysaccharide synthesis in Polygonatum odoratum (Mill.) Druce using RNA sequencing data from leaf, stem, and rhizome tissues. 76,714 unigenes were annotated in public databases. Analysis of KEGG annotations identified 18 key enzymes responsible for polysaccharide biosynthesis and the most of the upregulated expressed unigenes were enriched in rhizome tissue compared with leaf or stem tissue. 73 TFs involved in polysaccharide synthesis were predicted. In addition, key enzyme genes were verified by quantitative real-time PCR. This study substantially enlarged the public transcriptome datasets of this species, and provided insight into detection of novel genes involved in synthesis of polysaccharides and other secondary metabolites.
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Affiliation(s)
- Shengxiang Zhang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038
| | - Yuanyuan Shi
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038
| | - Luqi Huang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China; State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chenkai Wang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038
| | - Derui Zhao
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038
| | - Kelong Ma
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China; Clinical College of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038; Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei 230012, China.
| | - Daiyin Peng
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei 230038, China; Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei 230012, China.
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14
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De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway. Sci Rep 2019; 9:14876. [PMID: 31619732 PMCID: PMC6795813 DOI: 10.1038/s41598-019-51355-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/16/2019] [Indexed: 01/06/2023] Open
Abstract
Gymnema sylvestre is a highly valuable medicinal plant in traditional Indian system of medicine and used in many polyherbal formulations especially in treating diabetes. However, the lack of genomic resources has impeded its research at molecular level. The present study investigated functional gene profile of G. sylvestre via RNA sequencing technology. The de novo assembly of 88.9 million high quality reads yielded 23,126 unigenes, of which 18116 were annotated against databases such as NCBI nr database, gene ontology (GO), KEGG, Pfam, CDD, PlantTFcat, UniProt & GreeNC. Total 808 unigenes mapped to 78 different Transcription Factor families, whereas 39 unigenes assigned to CYP450 and 111 unigenes coding for enzymes involved in the biosynthesis of terpenoids including transcripts for synthesis of important compounds like Vitamin E, beta-amyrin and squalene. Among them, presence of six important enzyme coding transcripts were validated using qRT-PCR, which showed high expression of enzymes involved in methyl-erythritol phosphate (MEP) pathway. This study also revealed 1428 simple sequence repeats (SSRs), which may aid in molecular breeding studies. Besides this, 8 putative long non-coding RNAs (lncRNAs) were predicted from un-annotated sequences, which may hold key role in regulation of essential biological processes in G. sylvestre. The study provides an opportunity for future functional genomic studies and to uncover functions of the lncRNAs in G. sylvestre.
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