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Younkin GC, Alani ML, Züst T, Jander G. Four enzymes control natural variation in the steroid core of Erysimum cardenolides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588904. [PMID: 38645095 PMCID: PMC11030354 DOI: 10.1101/2024.04.10.588904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Plants commonly produce families of structurally related metabolites with similar defensive functions. This apparent redundancy raises the question of underlying molecular mechanisms and adaptive benefits of such chemical variation. Cardenolides, a class defensive compounds found in the wallflower genus Erysimum (L., Brassicaceae) and scattered across other plant families, show substantial structural variation, with glycosylation and hydroxylation being common modifications of a steroid core, which itself may vary in terms of stereochemistry and saturation. Through a combination of chemical mutagenesis and analysis of gene coexpression networks, we identified four enzymes involved in cardenolide biosynthesis in Erysimum that work together to determine stereochemistry at carbon 5 of the steroid core: Ec3βHSD, a 3β-hydroxysteroid dehydrogenase, Ec3KSI, a ketosteroid isomerase, EcP5βR2, a progesterone 5β-reductase, and EcDET2, a steroid 5α-reductase. We biochemically characterized the activity of these enzymes in vitro and generated CRISPR/Cas9 knockout lines to confirm activity in vivo. Cardenolide biosynthesis was not eliminated in any of the knockouts. Instead, mutant plants accumulated cardenolides with altered saturation and stereochemistry of the steroid core. Furthermore, we found variation in carbon 5 configuration among the cardenolides of 44 species of Erysimum, where the occurrence of some 5β-cardenolides is associated with the expression and sequence of P5βR2. This may have allowed Erysimum species to fine-tune their defensive profiles to target specific herbivore populations over the course of evolution. SIGNIFICANCE STATEMENT Plants use an array of toxic compounds to defend themselves from attack against insects and other herbivores. One mechanism through which plants may evolve more toxic compounds is through modifications to the structure of compounds they already produce. In this study, we show how plants in the wallflower genus Erysimum use four enzymes to fine-tune the structure of toxic metabolites called cardenolides. Natural variation in the sequence and expression of a single enzyme called progesterone 5β-reductase 2 partly explains the variation in cardenolides observed across the Erysimum genus. These alterations to cardenolide structure over the course of evolution suggests that there may be context-dependent benefits to Erysimum to invest in one cardenolide variant over another.
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Affiliation(s)
- Gordon C. Younkin
- Boyce Thompson Institute, Ithaca, New York 14853
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | | | - Tobias Züst
- Institute of Systematic and Evolutionary Botany, University of Zurich, 8008 Zürich, Switzerland
| | - Georg Jander
- Boyce Thompson Institute, Ithaca, New York 14853
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Cuello C, Jansen HJ, Abdallah C, Zamar Mbadinga DL, Birer Williams C, Durand M, Oudin A, Papon N, Giglioli-Guivarc'h N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism. Heliyon 2024; 10:e28078. [PMID: 38533072 PMCID: PMC10963385 DOI: 10.1016/j.heliyon.2024.e28078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Specialized metabolites possess diverse interesting biological activities and some cardenolides- and monoterpene indole alkaloids- (MIAs) derived pharmaceuticals are currently used to treat human diseases such as cancers or hypertension. While these two families of biocompounds are produced by specific subfamilies of Apocynaceae, one member of this medicinal plant family, the succulent tree Pachypodium lamerei Drake (also known as Madagascar palm), does not produce such specialized metabolites. To explore the evolutionary paths that have led to the emergence and loss of cardenolide and MIA biosynthesis in Apocynaceae, we sequenced and assembled the P. lamerei genome by combining Oxford Nanopore Technologies long-reads and Illumina short-reads. Phylogenomics revealed that, among the Apocynaceae whose genomes have been sequenced, the Madagascar palm is so far the species closest to the common ancestor between MIA producers/non-MIA producers. Transposable elements, constituting 72.48% of the genome, emerge as potential key players in shaping genomic architecture and influencing specialized metabolic pathways. The absence of crucial MIA biosynthetic genes such as strictosidine synthase in P. lamerei and non-Rauvolfioideae species hints at a transposon-mediated mechanism behind gene loss. Phylogenetic analysis not only showcases the evolutionary divergence of specialized metabolite biosynthesis within Apocynaceae but also underscores the role of transposable elements in this intricate process. Moreover, we shed light on the low conservation of enzymes involved in the final stages of MIA biosynthesis in the distinct MIA-producing plant families, inferring independent gains of these specialized enzymes along the evolution of these medicinal plant clades. Overall, this study marks a leap forward in understanding the genomic dynamics underpinning the evolution of specialized metabolites biosynthesis in the Apocynaceae family, with transposons emerging as potential architects of genomics restructuring and gene loss.
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Affiliation(s)
- Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Hans J. Jansen
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Cécile Abdallah
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | | | - Ron P. Dirks
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
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Amani S, Alinejad S, Asadi N, Yousefi E, Khademvatan S, Howarth GS. Anti-Leishmania major activity of Calotropis procera extract by increasing ROS production and upregulating TNF-α, IFN-γ and iNOS mRNA expression under in vitro conditions. Trop Med Health 2024; 52:16. [PMID: 38303082 PMCID: PMC10832188 DOI: 10.1186/s41182-024-00578-4] [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: 10/30/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Leishmaniasis, caused by protozoan parasites of the genus Leishmania, is a neglected tropical disease with 700,000 to 1,000,000 global new cases annually. Adverse effects associated with expense, long-term treatment and drug resistance have made conventional therapies unfavorable, encouraging the search for alternative drugs based on plant products. In this study, the effect of Calotropis procera (Asclepiadaceae) extract against viability of promastigotes and amastigotes of Leishmania major was evaluated in vitro. METHODS The extract from the leaves of C. procera seedlings was prepared using a methanol maceration method. The colorimetric cell viability 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was used to determine the growth-inhibitory effect of the extract on promastigotes. The level of reactive oxygen species (ROS) in promastigote cultures was determined after treatment with the extract using the 2',7'-dichlorofluorescein diacetate (DCFH-DA) method and compared with untreated cultures (control). After exposure to the extract the expression levels of tumor necrosis factor-α (TNF-α), interferon gamma (IFN-γ) and inducible nitric oxide synthase (iNOS) genes were determined and compared to control in peripheral blood mononuclear cells (PBMCs) infected with L. major. RESULTS Based on the MTT assay, the C. procera extract significantly reduced the proliferation of L. major promastigotes with IC50 values of 377.28 and 222.44 μg/mL for 24 and 72 h, respectively (p < 0.01). After treatment with 222.44 and 377.28 μg/mL of C. procera extract, ROS production in L. major promastigote cultures increased 1.2- to 1.65-fold and 2- to 4-fold compared to the control, respectively (p < 0.05). C. procera extract induced significant increases in gene expression of TNF-α (2.76-14.83 fold), IFN-γ (25.63-threefold) and iNOS (16.32-3.97 fold) in infected PBMCs compared to control (p < 0.01). CONCLUSIONS On the basis of its anti-leishmanial activity, C. procera can be considered as a promising new plant source for the potential treatment of leishmaniasis.
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Affiliation(s)
- Shahla Amani
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute & Department of Medical Parasitology and Mycology, Urmia University of Medical Sciences, Urmia, Iran
| | - Soheila Alinejad
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute & Department of Medical Parasitology and Mycology, Urmia University of Medical Sciences, Urmia, Iran
| | - Negar Asadi
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute & Department of Medical Parasitology and Mycology, Urmia University of Medical Sciences, Urmia, Iran
| | - Elham Yousefi
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute & Department of Medical Parasitology and Mycology, Urmia University of Medical Sciences, Urmia, Iran
| | - Shahram Khademvatan
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute & Department of Medical Parasitology and Mycology, Urmia University of Medical Sciences, Urmia, Iran.
| | - Gordon Stanley Howarth
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
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Kunert M, Langley C, Lucier R, Ploss K, Rodríguez López CE, Serna Guerrero DA, Rothe E, O'Connor SE, Sonawane PD. Promiscuous CYP87A enzyme activity initiates cardenolide biosynthesis in plants. NATURE PLANTS 2023; 9:1607-1617. [PMID: 37723202 PMCID: PMC10581899 DOI: 10.1038/s41477-023-01515-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/16/2023] [Indexed: 09/20/2023]
Abstract
Cardenolides are specialized, steroidal metabolites produced in a wide array of plant families1,2. Cardenolides play protective roles in plants, but these molecules, including digoxin from foxglove (Digitalis spp.), are better known for treatment of congenital heart failure, atrial arrhythmia, various cancers and other chronic diseases3-9. However, it is still unknown how plants synthesize 'high-value', complex cardenolide structures from, presumably, a sterol precursor. Here we identify two cytochrome P450, family 87, subfamily A (CYP87A) enzymes that act on both cholesterol and phytosterols (campesterol and β-sitosterol) to form pregnenolone, the first committed step in cardenolide biosynthesis in the two phylogenetically distant plants Digitalis purpurea and Calotropis procera. Arabidopsis plants overexpressing these CYP87A enzymes ectopically accumulated pregnenolone, whereas silencing of CYP87A in D. purpurea leaves by RNA interference resulted in substantial reduction of pregnenolone and cardenolides. Our work uncovers the key entry point to the cardenolide pathway, and expands the toolbox for sustainable production of high-value plant steroids via synthetic biology.
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Affiliation(s)
- Maritta Kunert
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Chloe Langley
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Rosalind Lucier
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Kerstin Ploss
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Carlos E Rodríguez López
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Delia A Serna Guerrero
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Eva Rothe
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Prashant D Sonawane
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
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Hassan S, Atef A, Ali HM, Alshamrani R, Ramadan A. Calotropis procera accumulates Uzarigenin and Calotropagenin in response to environmental lighting and drought. Saudi J Biol Sci 2023; 30:103622. [PMID: 36950364 PMCID: PMC10025005 DOI: 10.1016/j.sjbs.2023.103622] [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: 01/19/2023] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023] Open
Abstract
Calotropis procera (C. procera) was evaluated as a pharmaceutically useful plant and for its therapeutic effects in the most significant studies. Uzarigenin and Calotropagenin are significant components of this plant that have pharmacological effects on certain systems, including the digestive, immunological, and focal, and peripheral sensory systems. In this study, pathway genes are extracted from high throughput data acc.no. SRR1554320. Seven critical enzymes are involved in studying the effects of sunlight on the formation of Uzaragenin and Calotropagenin in C. procera before and after irrigation. Molecular identification and NCBI submission of six enzyme genes were successful; HSD (acc.no. OQ091761) for 3β-hydroxystroid dehydrogenase, OR (acc.no. OQ091762) for 5beta-pregnan oxidoreductase, MO (acc.no. OQ091763) for Pregnan monooxygenase, HOX (acc.no. OQ091764) for Steroid hydroxylase, MAT (acc.no. OQ091765) for Melonyletransferase, UHOX (acc.no. OQ091766) for Uzarigenin hydroxylase. During dawn after irrigation, the Uzargenin pathway showed the highest activity, however midday after irrigation was the lowest. The most period that showed high activity for the Uzargenin pathway was dawn after irrigation, however, midday after irrigation was the lowest. This data is confirmed by chromatography analysis (UPLC) to calculate the accumulation of Uzarigenin and Calotropagenin in different periods.
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Affiliation(s)
- Sabah Hassan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Ahmed Atef
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani M. Ali
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rahma Alshamrani
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Ramadan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Plant Molecular Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
- Corresponding author at: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
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6
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Raghavan I, Ravi Gopal B, Carroll E, Wang ZQ. Cardenolide Increase in Foxglove after 2,1,3-Benzothiadiazole Treatment Reveals a Potential Link between Cardenolide and Phytosterol Biosynthesis. PLANT & CELL PHYSIOLOGY 2023; 64:107-116. [PMID: 36222367 DOI: 10.1093/pcp/pcac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Cardenolides are steroidal metabolites in Digitalis lanata with potent cardioactive effects on animals. In plants, cardenolides are likely involved in various stress responses. However, the molecular mechanism of cardenolide increase during stresses is mostly unknown. Additionally, cardenolides are proposed to arise from cholesterol, but indirect results show that phytosterols may also be substrates for cardenolide biosynthesis. Here, we show that cardenolides increased after methyl jasmonate (MJ), sorbitol, potassium chloride (KCl) and salicylic acid analog [2,1,3-benzothiadiazole (BTH)] treatments. However, the expression of three known genes for cardenolide biosynthesis did not correlate well with these increases. Specifically, the expression of progesterone-5β-reductases (P5βR and P5βR2) did not correlate with the cardenolide increase. The expression of 3β-hydroxysteroid dehydrogenase (3βHSD) correlated with changes in cardenolide levels only during the BTH treatment. Mining the D. lanata transcriptome identified genes involved in cholesterol and phytosterol biosynthesis: C24 sterol sidechain reductase 1 (SSR1), C4 sterol methyl oxidase 1, and 3 (SMO1 and SMO3). Surprisingly, the expression of all three genes correlated well with the cardenolide increase after the BTH treatment. Phylogenetic analysis showed that SSR1 is likely involved in both cholesterol and phytosterol biosynthesis. In addition, SMO1 is likely specific to phytosterol biosynthesis, and SMO3 is specific to cholesterol biosynthesis. These results suggest that stress-induced increase of cardenolides in foxglove may correlate with cholesterol and phytosterol biosynthesis. In summary, this work shows that cardenolides are important for stress responses in D. lanata and reveals a potential link between phytosterol and cardenolide biosynthesis.
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Affiliation(s)
- Indu Raghavan
- Department of Biological Sciences, University at Buffalo, The State University of New York, 109 Cooke Hall, Buffalo, NY 14260, USA
| | - Baradwaj Ravi Gopal
- Department of Biological Sciences, University at Buffalo, The State University of New York, 109 Cooke Hall, Buffalo, NY 14260, USA
| | - Emily Carroll
- Department of Biological Sciences, University at Buffalo, The State University of New York, 109 Cooke Hall, Buffalo, NY 14260, USA
| | - Zhen Q Wang
- Department of Biological Sciences, University at Buffalo, The State University of New York, 109 Cooke Hall, Buffalo, NY 14260, USA
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Rattan S, Kumar P, Kaur E, Sood A, Acharya V, Warghat AR. Comparative transcriptome and tissue-specific expression analysis of genes reveal tissue-cultured plants as an alternative source for phenylethanoids and phenylpropanoids in Rhodiola imbricata (Edgew.). Gene X 2022; 836:146672. [PMID: 35714804 DOI: 10.1016/j.gene.2022.146672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 11/29/2022] Open
Abstract
Rhodiola imbricata (Crassulaceae) is a traditional trans-Himalayan endangered medicinal herb with immense therapeutic applications. Over the years, over-exploitation, un-managed harvesting, and lack of captive cultivation procedures persuaded threat to its wild habitat. Plant tissue culture and RNA-Seq-based molecular bioprospection of key regulatory genes aid the understanding of molecular dynamics involved in specialized metabolites (phenylethanoids and phenylpropanoids) biosynthesis and its sustainable production. Hence, comparative transcriptomic analysis was performed using leaf and root tissues from the wild and tissue-cultured plants, revealing tissue-specific production of salidroside and rosavin. The transcriptome profiling resulted in 345 million high-quality reads yielding 92,380 unique transcripts with an N50 of 1260 bp. Tissue-specific gene expression analysis revealed that both phenylethanoids and phenylpropanoids biosynthesis are predominantly associated with the shikimate pathway. In addition to RNA-Seq data, the downstream biosynthesis pathways genes viz., phospho-2-dehydro-3-deoxyheptonate aldolase (DAHPS), 3-dehydroquinate synthase (DHQS), shikimate kinase (SK), chorismate mutase (CM), arogenate dehydrogenase (TYRAAT), aromatic-L-amino-acid decarboxylase (TDC), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4-CL), cinnamoyl-CoA reductase (CCR), and cinnamyl alcohol dehydrogenase (CAD) showed higher expression pattern in wild plant tissues compared to tissue-cultured plants. The transcript fold expression determined by RT-qPCR results followed similar patterns as those observed in RNA-seq and targeted metabolite profiling data. Salidroside and rosavin content in wild plants exhibited 2.40 fold and 1.77 fold increase accumulation compared to the tissue-cultured plant. The present investigation explained the tissue and condition-specific significant differences between the expression of proposed biosynthetic pathway genes and salidroside and rosavin content. Additionally, NAC, bHLH, and ARF were the most abundant transcription factor families found in the transcriptomic analysis of R. imbricata. The generated transcriptome dataset provides a valuable gene(s)/transcription factors hub that can be used for the sustainable production of salidroside and rosavin in R. imbricata under tissue culture conditions.
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Affiliation(s)
- Shiv Rattan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pankaj Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Ekjot Kaur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Archit Sood
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Vishal Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashish R Warghat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Li G, An T, Li Y, Yue J, Huang R, Huang J, Liang J, Yao W, Huang L, Chen Y, Zhang R, Ji A, Duan L. Transcriptome Analysis and Identification of the Cholesterol Side Chain Cleavage Enzyme BbgCYP11A1 From Bufo bufo gargarizans. Front Genet 2022; 13:828877. [PMID: 35480310 PMCID: PMC9037069 DOI: 10.3389/fgene.2022.828877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/16/2022] [Indexed: 11/18/2022] Open
Abstract
Bufo bufo gargarizans Cantor are precious medicinal animals in traditional Chinese medicine (TCM). Bufadienolides as the major pharmacological components are generated from the venomous glands of B. bufo gargarizans. Bufadienolides are one type of cardiac aglycone with a six-member lactone ring and have properties of antitumor, cardiotonic, tonsillitis, and anti-inflammatory. The biosynthesis of bufadienolides is complex and unclear. This study explored the transcriptome of three different tissues (skin glands, venom glands, and muscles) of B. bufo gargarizans by high-throughput sequencing. According to the gene tissue–specific expression profile, 389 candidate genes were predicted possibly participating in the bufadienolides biosynthesis pathway. Then, BbgCYP11A1 was identified as a cholesterol side chain cleaving the enzyme in engineering yeast producing cholesterol. Furthermore, the catalytic activity of BbgCYP11A1 was studied with various redox partners. Interestingly, a plant NADPH-cytochrome P450 reductase (CPR) from Anemarrhena asphodeloides showed notably higher production than BbgAdx-2A-BbgAdR from B. bufo gargarizans. These results will provide certainly molecular research to reveal the bufadienolides biosynthesis pathway in B. bufo gargarizans.
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Affiliation(s)
- Guangli Li
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Tianyue An
- School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yanta, China
| | - Yu Li
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jinyang Yue
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruoshi Huang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jia Huang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jincai Liang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Yao
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liufang Huang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yidu Chen
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Rongrong Zhang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Aijia Ji
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lixin Duan
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
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Firneno TJ, Ramesh B, Maldonado JA, Hernandez-Briones AI, Emery AH, Roelke CE, Fujita MK. Transcriptomic analysis reveals potential candidate pathways and genes involved in toxin biosynthesis in true toads. J Hered 2022; 113:311-324. [PMID: 35325156 DOI: 10.1093/jhered/esac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Synthesized chemical defenses have broadly evolved across countless taxa and are important in shaping evolutionary and ecological interactions within ecosystems. However, the underlying genomic mechanisms by which these organisms synthesize and utilize their toxins are relatively unknown. Herein, we use comparative transcriptomics to uncover potential toxin synthesizing genes and pathways, as well as interspecific patterns of toxin synthesizing genes across ten species of North American true toads (Bufonidae). Upon assembly and annotation of the ten transcriptomes, we explored patterns of relative gene expression and possible protein-protein interactions across the species to determine what genes and/or pathways may be responsible for toxin synthesis. We also tested our transcriptome dataset for signatures of positive selection to reveal how selection may be acting upon potential toxin producing genes. We assembled high quality transcriptomes of the bufonid parotoid gland, a tissue not often investigated in other bufonid related RNAseq studies. We found several genes involved in metabolic and biosynthetic pathways (e.g. steroid biosynthesis, terpenoid backbone biosynthesis, isoquinoline biosynthesis, glucosinolate biosynthesis) that were functionally enriched and/or relatively expressed across the ten focal species that may be involved in the synthesis of alkaloid and steroid toxins, as well as other small metabolic compounds that cause distastefulness in bufonids. We hope that our study lays a foundation for future studies to explore the genomic underpinnings and specific pathways of toxin synthesis in toads, as well as at the macroevolutionary scale across numerous taxa that produce their own defensive toxins.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | - Balan Ramesh
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | - Jose A Maldonado
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | | | - Alyson H Emery
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | - Corey E Roelke
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
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10
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Pan Y, Zhao X, Wang Y, Tan J, Chen DX. Metabolomics integrated with transcriptomics reveals the distribution of iridoid and crocin metabolic flux in Gardenia jasminoides Ellis. PLoS One 2021; 16:e0256802. [PMID: 34506519 PMCID: PMC8432746 DOI: 10.1371/journal.pone.0256802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Gardenia jasminoides Ellis (G. jasminoides) fruits are used as a resource for obtaining natural colorants and in traditional Chinese herbal medicine. However, G. jasminoides presents a relatively long flowering period and different ripening periods, so there are significant differences in the accumulation of metabolites in fruits of different colors. In addition, the complete metabolic pathways of iridoidsand crocins, which are used as medicinal composition of G. jasminoides, are poorly understood at present. In this research, we comprehensively compared the transcriptome and metabolites profiles of the developmental stages and locations of iridoid and crocin biosynthesis. A large number of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were detected in four groups of samples, and clear variation in the pattern of metabolite abundance and gene expression were observed among different fruit colors and parts. Geniposide and gardenoside mainly accumulated in the sarcocarp of green fruit (GFS) and the sarcocarp of red fruit (FS), respectively. Crocin mainly accumulated in the peel and sarcocarp of red fruits. In the iridoid pathway, we hypothesized that there was a transport mechanism from the sarcocarp to the peel of G. jasminoides because of the inconsistent expression of G8O, 10-HGO and IS associated with differences in fruit ripening. UGTs play an important role in the biosynthesis of the active components of G. jasminoides. Combined transcriptome and metabonomics analysis showed a negative correlation between the biosynthesis of geniposide and crocin. The redirection of the metabolic flux and the regulation of key enzymes may be the main reasons for the changes in the biosynthesis of iridoid and crocin in G. jasminoides fruit. Our study expended valuable information for functional genomic library and provided new insights for metabolic engineering of secondary metabolite in G. Jasminoides.
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Affiliation(s)
- Yuan Pan
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Xiao Zhao
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Yu Wang
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Jun Tan
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Da-xia Chen
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- * E-mail:
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11
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Olajuyin AM, Olajuyin AK, Wang Z, Zhao X, Xu Z, Zhang Q, Zhang X. Anti-proliferative, antioxidant effects of methanol extract of Calotropis procera leaf on lung cancer cells (H1299) and its ameliorative effect on expression of CD146 on blood cells. CLINICAL PHYTOSCIENCE 2021. [DOI: 10.1186/s40816-021-00289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Abstract
Background
Calotropis procera leaf is one of the plants commonly utilized in phytomedicine in Nigeria. The present investigation explored the use of the extracts on cell viability and apoptosis respectively. In this study, the expression of the Cluster of differentiation 146 (CD146) in the blood of lung cancer patients on regulatory T cells (Tregs) was determined. The antioxidant and anti-proliferative effects of methanol extracts of Caloropis procera leaf on lung cancer cell H1299 were investigated.
Methods
From the flow cytometry, the expression of the CD146+ in the T cells were evaluated using the healthy patient, adenocarcinoma, squamous, and small cell lung cancer respectively. The apoptosis of granulocytes, monocytes, lymphocytes, CD4+, and Treg were determined by 7-amino-actinomycin D/Annexin V-Allophycocyanin (APC) staining during the resting stage and after 24 h respectively. Immunofluorescence was conducted. Cell viability assay, hydroxyl (OH), hydrogen peroxide (H2O2) and nitric oxide (NO) scavenging radicals were conducted. Reducing power and flavonoid content of Calotropis procera were investigated. The effect of the Calotropis procera at different concentrations at 24hrs was determined.
Results
From the flow cytometry, the expression of the CD146+ on the T cells includes 4.60 % in healthy patients, 10.10, 12.20, 9.80 % in adenocarcinoma, squamous and small cell lung cancer. The apoptosis of granulocytes, monocytes, lymphocytes, CD4+ and Treg were determined by 7-amino-actinomycin D/Annexin V-APC staining during the resting stage and after 24 h which indicate that apoptosis also occurred on Treg. Immunofluorescence shows the presence of CD146 in lung cancer patient’s tissues. The methanol extracts of Calotropis procera leaf have antioxidant and anti-proliferative effects. Methanol extract of Calotropis procera leaf reduced CD146 expression on blood cells at 24 h.
Conclusion
Increased CD146 expression in the Treg of lung cancer patients indicates that it may be a possible target for the treatment of lung cancer by utilizing potent immunotherapy or natural products such as methanol extract of Calotropis procera leaf which may ameliorate the expression of CD146. Calotropis procera has antioxidant, inhibitory capacity on H1299 lung cancer cells, and the ability to scavenge OH, H2O2, and NO radicals. Hence, this investigation strengthens the phyto-medicinal properties of Calotropis procera.
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12
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Rabelo AC, Borghesi J, Carreira ACO, Hayashi RG, Bessa F, Barreto RDSN, da Costa RP, Cantanhede Filho AJ, Carneiro FJC, Miglino MA. Calotropis procera (Aiton) Dryand (Apocynaceae) as an anti-cancer agent against canine mammary tumor and osteosarcoma cells. Res Vet Sci 2021; 138:79-89. [PMID: 34119813 DOI: 10.1016/j.rvsc.2021.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 05/10/2021] [Accepted: 06/03/2021] [Indexed: 12/01/2022]
Abstract
Our goal was to evaluate phytochemical characterization and the antitumor potential of Calotropis procera. The phytochemical constitution of the crude extract (CE) revealed the presence of flavonoids, glycosides and cardenolide. The MTT assay was used to evaluate the cytotoxicity of CE, methanolic (MF) and ethyl acetate fractions (EAF) of C. procera in canine osteosarcoma cells (OST), canine mammary tumor (CMT), and canine skin fibroblasts (non-tumor cell). Doxorubicin was also used as a positive control. Results showed that CE, MF and EAF promoted a decrease in the viability of OST and CMT cells and did not alter the fibroblasts viability. C. procera also decreased the number of cells, corroborating to the decrease in proliferation and the cell cycle arrest in the G0/G1 phase. It was also evaluated the cell morphology by light and fluorescence microscopy, being demonstrated a reduction in cytoplasmic and cell rounding characteristic of programmed cell death. Moreover, flow cytometry data demonstrated that CE treatment promoted increase of caspase-3 and p53, showing that the cell death was activated in OST cells. In addition, there was a decrease in CD31, VEGF, osteopontin and TGF-β after CE treatment, suggesting that CE exerts its antitumor effect by reducing angiogenesis and tumor progression in OST cells. Moreover, CMT cells showed a reduction in PCNA after treatment with MF and CE. Analyzing the data together, C. procera, especially CE, showed an antitumor potential in both OST and CMT cells, encouraging us to continue investigating its use in cancer therapy.
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Affiliation(s)
- Ana CarolinaSilveira Rabelo
- Laboratory of Stem Cell, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508 270, Brazil.
| | - Jéssica Borghesi
- Laboratory of Stem Cell, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508 270, Brazil
| | - Ana Claudia O Carreira
- Laboratory of Stem Cell, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508 270, Brazil; Center for Cellular and Molecular Therapy (NUCEL), School of Medicine, University of São Paulo (USP), São Paulo 05360-130, Brazil
| | - Rafael Gonçalves Hayashi
- Laboratory of Stem Cell, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508 270, Brazil
| | - Fernanda Bessa
- Laboratory of Stem Cell, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508 270, Brazil
| | - Rodrigo da Silva Nunes Barreto
- Laboratory of Stem Cell, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508 270, Brazil
| | - Romário Pereira da Costa
- Department of Chemistry, Federal University of São Carlos (UFSCar), São Carlos 13560-970, Brazil
| | | | - Fernando José Costa Carneiro
- Department of Chemistry, Federal Institute of Education, Science and Technology of Maranhão, Campus São Luís, Monte Castelo, Maranhão 65030-005, Brazil
| | - Maria Angélica Miglino
- Laboratory of Stem Cell, Faculty of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo 05508 270, Brazil
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RNA Sequencing-based Transcriptomic profiles of HeLa, MCF-7 and A549 cancer cell lines treated with Calotropis gigantea leaf extracts. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Haddaji F, Papetti A, Noumi E, Colombo R, Deshpande S, Aouadi K, Adnan M, Kadri A, Selmi B, Snoussi M. Bioactivities and in silico study of Pergularia tomentosa L. phytochemicals as potent antimicrobial agents targeting type IIA topoisomerase, TyrRS, and Sap1 virulence proteins. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:25349-25367. [PMID: 33454827 DOI: 10.1007/s11356-020-11946-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Pergularia tomentosa L. (P. tomentosa) has been largely used in Tunisian folk medicine as remedies against skin diseases, asthma, and bronchitis. The main objectives of this study were to identify phytochemical compounds that have antioxidant and antimicrobial properties from the stem, leaves, and fruit crude methanolic extracts of P. tomentosa, and to search for tyrosyl-tRNA synthetase (TyrRS), topoisomerase type IIA, and Candidapepsin-1 (SAP1) enzyme inhibitors through molecular docking study. Phytochemical quantification revealed that fruit and leaves extracts displayed the highest total flavonoids (582 mg QE/g Ex; 219 mg QE/g Ex) and tannins content (375 mg TAE/g Ex; 216 mg TAE/g Ex), also exhibiting significant scavenging activity to decrease free radicals for ABTS, DPPH, β-carotene, and FRAP assay with IC50 values (> 1 mg/mL). Additionally, promising antimicrobial activities towards different organs have been observed against several bacteria and Candida strains. From the liquid chromatography-mass spectrometry (LC-MS) analysis, five polyphenolic compounds, namely digitoxigenin, digitonin glycoside and calactina in the leaves, kaempferol in the fruit, and calotropagenin in the stems, were identified. They were also analyzed for their drug likeliness, based on computational methods. Molecular docking study affirmed that the binding affinity of calactin and actodigin to the active site of TyrRS, topoisomerase type IIA, and SAP1 target virulence proteins was the highest among the examined dominant compounds. Therefore, this study indicated that P. tomentosa methanolic extracts displayed great potential to become a potent antimicrobial agent and might be a promising source for therapeutic and nutritional functions. These phytocompounds could be further promoted as a candidate for drug discovery and development.
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Affiliation(s)
- Fatma Haddaji
- Laboratory of Genetics, Biodiversity and Valorization of Bio-resources (LR11ES41), University of Monastir, Higher Institute of Biotechnology of Monastir, Avenue Tahar Haddad, BP74, 5000, Monastir, Tunisia
| | - Adele Papetti
- Nutraceutical & Food Chemical-Toxicological Analysis Laboratory, Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Emira Noumi
- Department of Biology, College of Science, University of Ha'il, P.O. 2440, Hail, Saudi Arabia
- Laboratory of Bioressources: Integrative Biology and Valorization, (LR14-ES06), University of Monastir, Higher Institute of Biotechnology of Monastir, Avenue Tahar Haddad, BP 74, 5000, Monastir, Tunisia
| | - Raffaella Colombo
- Nutraceutical & Food Chemical-Toxicological Analysis Laboratory, Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Sumukh Deshpande
- Central Biotechnology Services, College of Biomedical and Life Sciences, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Kaïss Aouadi
- Faculty of Science and Arts in Baljurashi, Albaha University, P.O. Box 1988, Albaha, Saudi Arabia
- Faculty of Science of Monastir, Laboratory of Hetrocyclic Chemistry, Natural Products and Reactivity, Avenue of the Environment, University of Monastir, 5019, Monastir, Tunisia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, P.O. 2440, Hail, Saudi Arabia
| | - Adel Kadri
- Faculty of Science of Sfax, Department of Chemistry, University of Sfax, B.P. 1171, 3000, Sfax, Tunisia
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Boulbaba Selmi
- Laboratory of Bioressources: Integrative Biology and Valorization, (LR14-ES06), University of Monastir, Higher Institute of Biotechnology of Monastir, Avenue Tahar Haddad, BP 74, 5000, Monastir, Tunisia
| | - Mejdi Snoussi
- Department of Biology, College of Science, University of Ha'il, P.O. 2440, Hail, Saudi Arabia.
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Dreisbach D, Petschenka G, Spengler B, Bhandari DR. 3D-surface MALDI mass spectrometry imaging for visualising plant defensive cardiac glycosides in Asclepias curassavica. Anal Bioanal Chem 2021; 413:2125-2134. [PMID: 33544161 PMCID: PMC7943518 DOI: 10.1007/s00216-021-03177-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/22/2022]
Abstract
Mass spectrometry-based imaging (MSI) has emerged as a promising method for spatial metabolomics in plant science. Several ionisation techniques have shown great potential for the spatially resolved analysis of metabolites in plant tissue. However, limitations in technology and methodology limited the molecular information for irregular 3D surfaces with resolutions on the micrometre scale. Here, we used atmospheric-pressure 3D-surface matrix-assisted laser desorption/ionisation mass spectrometry imaging (3D-surface MALDI MSI) to investigate plant chemical defence at the topographic molecular level for the model system Asclepias curassavica. Upon mechanical damage (simulating herbivore attacks) of native A. curassavica leaves, the surface of the leaves varies up to 700 μm, and cardiac glycosides (cardenolides) and other defence metabolites were exclusively detected in damaged leaf tissue but not in different regions of the same leaf. Our results indicated an increased latex flow rate towards the point of damage leading to an accumulation of defence substances in the affected area. While the concentration of cardiac glycosides showed no differences between 10 and 300 min after wounding, cardiac glycosides decreased after 24 h. The employed autofocusing AP-SMALDI MSI system provides a significant technological advancement for the visualisation of individual molecule species on irregular 3D surfaces such as native plant leaves. Our study demonstrates the enormous potential of this method in the field of plant science including primary metabolism and molecular mechanisms of plant responses to abiotic and biotic stress and symbiotic relationships.
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Affiliation(s)
- Domenic Dreisbach
- Institute for Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Georg Petschenka
- Institute of Phytomedicine, University of Hohenheim, Otto-Sander-Straße 5, 70599, Stuttgart, Germany
| | - Bernhard Spengler
- Institute for Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Dhaka R Bhandari
- Institute for Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany.
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16
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Systematic Phytochemical Screening of Different Organs of Calotropis procera and the Ovicidal Effect of Their Extracts to the Foodstuff Pest Cadra cautella. Molecules 2021; 26:molecules26040905. [PMID: 33572107 PMCID: PMC7916075 DOI: 10.3390/molecules26040905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/27/2022] Open
Abstract
In developing countries, crop deterioration is mainly caused by inappropriate storage conditions that promote insect infestation. Synthetic pesticides are associated with serious adverse effects on humans and the environment. Thus, finding alternative “green” insecticides is a very pressing need. Calotropis procera (Aiton) Dryand (Apocynaceae) growing in Saudi Arabia was selected for this purpose. LC-MS/MS analysis was applied to investigate the metabolic composition of different C. procera extracts. Particularly, C. procera latex and leaves showed a high presence of cardenolides including calactin, uscharidin, 15β-hydroxy-calactin, 16β-hydroxy-calactin, and 12β-hydroxy-calactin. The ovicidal activity of the extracts from different plant organs (flowers, leaves, branches, roots), and of the latex, against Cadra cautella (Walker) (Lepidoptera, Pyralidae) was assessed. Extracts of C. procera roots displayed the most potent activity with 50% of C. cautella eggs not hatching at 10.000 ppm (1%).
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17
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Ünlü ES, Kaya Ö, Eker İ, Gürel E. Sequencing, de novo assembly and annotation of Digitalis ferruginea subsp. schischkinii transcriptome. Mol Biol Rep 2021; 48:127-137. [PMID: 33403559 DOI: 10.1007/s11033-020-05982-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 11/05/2020] [Indexed: 11/24/2022]
Abstract
There is an increasing demand for elucidating the biosynthetic pathway of medicinal plants, which are capable of producing several metabolites with great potentials for industrial drug production. Digitalis species are important medicinal plants for the production of cardenolide compounds. Advancement on culture techniques is strictly related to our understanding of the genomic background of species. There are a limited number of genomic studies on Digitalis species. The goal of this study is to contribute to the genomic data of Digitalis ferruginea subsp. schischkinii by presenting transcriptome annotation. Digitalis ferruginea subsp. schischkinii has a limited distribution in Turkey and Transcaucasia, and has a high level of lanatoside C, an important cardenolide. In the study, we sequenced the cDNA library prepared from RNA pools of D. ferruginea subsp. schischkinii tissues treated with various stress conditions. Comprehensive bioinformatics approaches were used for de novo assembly and functional annotation of D. ferruginea subsp. schischkinii transcriptome sequence data along with TF families predictions and phylogenetic analysis. In the study, 58,369 unigenes were predicted and unigenes were annotated by analyzing the sequence data in the non-redundant (NR) protein database, the non-redundant nucleotide (NT) database, Gene Orthology (GO), EuKaryotic Orthologous Groups (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt, and InterPro databases. This study is the first transcriptome data for D. ferruginea subsp. schischkinii.
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Affiliation(s)
- Ercan Selçuk Ünlü
- Department of Chemistry, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey.
| | - Özge Kaya
- Department of Biology, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey
| | - İsmail Eker
- Department of Biology, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey
| | - Ekrem Gürel
- Department of Biology, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey
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18
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Yang Y, Yang Y, Qiu H, Ju Z, Shi Y, Wang Z, Yang L. Localization of constituents for determining the age and parts of ginseng through ultraperfomance liquid chromatography quadrupole/time of flight-mass spectrometry combined with desorption electrospray ionization mass spectrometry imaging. J Pharm Biomed Anal 2020; 193:113722. [PMID: 33171337 DOI: 10.1016/j.jpba.2020.113722] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/08/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
Ginseng has been used for prevention and treatment of disease for thousands of years in China and many other Asian countries. Phytochemical studies have indicated that ginsenosides, polysaccharides, alkaloids, and phenolic acids are the active constituents of ginseng. Main and branch roots of ginseng exhibit distinct bioactive behavior. Furthermore, the bioactive behavior of ginseng depends on its age. Traditional analysis is complex preparation and provides inadequate of chemical information of the original distribution of analytes. Therefore, in this study, ultraperformance liquid chromatography quadrupole/time of flight-mass spectrometry (UPLC-QTOF MS) and desorption electrospray ionization mass spectrometry imaging (DESI-MSI) combined with orthogonal partial least squares discriminant analysis were used to discriminate ginseng in different age and parts of ginseng, and profiled distribution of selected markers. The results indicated that UPLC-QTOF-MS and DESI-MSI could be used to determine the parts and age of ginseng. Fifteen variables including five of protopanaxatriol (PPT), four of protopanaxadiol (PPD), and six of other types were assumed as markers for different parts of ginseng. Moreover, four variables of PPT, four of PPD, and ten of other types were used to determine the age of ginseng samples. An analysis of localization of markers indicated that malonyl ginsenoside, including malonyl-ginsenoside Rb1, Rb2, Rc, and Rd was mainly distributed in the corks. Neutral ginsenoside Rg1, yesanchinoisde D, and chikusetsusaponin Iva were mainly distributed in the cork and phloem. Non-ginsenoside castanoside H, 20(S)-protopanaxatriol, unknown 2, saponin III and cistanoside C were distributed in all tissues. Ethyloleate, unknown 1 and monolinolein were distributed in the cork.
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Affiliation(s)
- Yuangui Yang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yingbo Yang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Kanion Pharmaceutical Co. Ltd., Lianyungang, 222001, China
| | - Hao Qiu
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengcai Ju
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yanchao Shi
- Waters Corporation Shanghai Science & Technology Co. Ltd., Shanghai 201206, China
| | - Zhengtao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Shanghai R&D Center for Standardization of Chinese Medicines, Shanghai 201203, China.
| | - Li Yang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Shanghai R&D Center for Standardization of Chinese Medicines, Shanghai 201203, China.
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Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis. BMC Genomics 2020; 21:639. [PMID: 32933468 PMCID: PMC7493163 DOI: 10.1186/s12864-020-07056-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/06/2020] [Indexed: 12/15/2022] Open
Abstract
Background Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness and remarkable anti-inflammatory activities. Triterpenoid saponins are the major bioactive compounds of Entada phaseoloides. However, genomic or transcriptomic technologies have not been used to study the triterpenoid saponin biosynthetic pathway in this plant. Results We performed comparative transcriptome analysis of the root, stem, and leaf tissues of Entada phaseoloides with three independent biological replicates and obtained a total of 53.26 Gb clean data and 116,910 unigenes, with an average N50 length of 1218 bp. Putative functions could be annotated to 42,191 unigenes (36.1%) based on BLASTx searches against the Non-redundant, Uniprot, KEGG, Pfam, GO, KEGG and COG databases. Most of the unigenes related to triterpenoid saponin backbone biosynthesis were specifically upregulated in the stem. A total of 26 cytochrome P450 and 17 uridine diphosphate glycosyltransferase candidate genes related to triterpenoid saponin biosynthesis were identified. The differential expressions of selected genes were further verified by qPT-PCR. Conclusions The dataset reported here will facilitate the research about the functional genomics of triterpenoid saponin biosynthesis and genetic engineering of Entada phaseoloides.
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Long G, Zhao C, Zhao P, Zhou C, Ntirenganya E, Zhou Y. Transcriptomic response to cold of thermophilous medicinal plant Marsdenia tenacissima. Gene 2020; 742:144602. [PMID: 32199947 DOI: 10.1016/j.gene.2020.144602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/11/2020] [Accepted: 03/16/2020] [Indexed: 12/18/2022]
Abstract
Extracts from Marsdenia tenacissima, involving tenacissoside H, I and G, have been used as remedies of cancer, inflammation and asthma. Low temperature serves as one of the main factors constrain the planting expansion and quality of M. tenacissima, but its functional mechanism has been known scarcely for the lack of genomic information and transcriptional profile. Here we investigated the transcriptomic responses of M. tenacissima under cold stress to gain insight into the molecular mechanism of low temperature sensitivity. Total RNAs were collected from samples obtained at 4-time points (after 0, 3, 6 and 48 h cold treatments with 4 °C, respectively), then used for library construction and sequenced on the Illumina Hiseq™ 4000 platform. Passing quality assessments, 500794 transcripts, and 206137 unigenes were de novo assembly out in Trinity v2.4.0, holding contig N50 of 2566 bp and unigene mean length of 754 bp. 44.20% of assembled unigenes were annotated to the well-known public protein database on a basis of sequence similarity. Using statistical comparison of the fragments per kilo base of transcript per million reads mapped (FPKM) values between conditions, 6082 group-specific differentially expressed genes (DEGs) were identified and considered as cold-responsive genes, which contained copious transcription factors and active secondary metabolism. Among them, 43 unigenes were constantly up-regulated expression along with cold time, which mainly implicated in the biosynthesis of secondary metabolites, carbon metabolism, RNA and DNA metabolism. Conversely, 21 unigenes involved in photosynthesis, cell wall, protein degradation, and transporters were downregulated continually with cold timescale. Experimentally, MtEF1α was chosen as the best housekeeping gene. Functional enrichments found that damaging of cold stress on M. tenacissima may be ascribed to inability of photosynthesis, ribsome processing, flavonoid biosynthesis and terpenoids degradation. Correlation analysis between cold induced transcription factors and tenacissoside biosynthesis-related genes indicated that 3β-HSD significant positively correlated with bHLH51, and 4-MSO with NF-YB, GRAS3, Trihelix, FAR1, MYB60, MYBS1, bZIP43. Further promoter clone found MYB-binding site in the promoter of 4-MSO. In view of the reported cold tolerance of MYB60, it is recommended as a potential candidate suitable for future molecular design of exaptation cultivation with high bioactive constituents.
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Affiliation(s)
- Guangqiang Long
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan 650201, China
| | - Changhong Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan 650201, China
| | - Ping Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China; National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan 650201, China
| | - Chengli Zhou
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; School of Information Science and Engineering, Yunnan University, Kunming, Yunnan 650201, China
| | - Elie Ntirenganya
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yanli Zhou
- Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Gharat SA, Shinde BA, Mule RD, Punekar SA, Dholakia BB, Jayaramaiah RH, Ramaswamy G, Giri AP. High-throughput metabolomic and transcriptomic analyses vet the potential route of cerpegin biosynthesis in two varieties of Ceropegia bulbosa Roxb. PLANTA 2019; 251:28. [PMID: 31802261 DOI: 10.1007/s00425-019-03319-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
Exploration with high-throughput transcriptomics and metabolomics of two varieties of Ceropegia bulbosa identifies candidate genes, crucial metabolites and a potential cerpegin biosynthetic pathway. Ceropegia bulbosa is an important medicinal plant, used in the treatment of various ailments including diarrhea, dysentery, and syphilis. This is primarily attributed to the presence of pharmaceutically active secondary metabolites, especially cerpegin. As this plant belongs to an endemic threatened category, genomic resources are not available hampering exploration on the molecular basis of cerpegin accumulation till now. Therefore, we undertook high-throughput metabolomic and transcriptomic analyses using different tissues from two varieties namely, C. bulbosa var. bulbosa and C. bulbosa var. lushii. Metabolomic analysis revealed spatial and differential accumulation of various metabolites. We chemically synthesized and characterized the cerpegin and its derivatives by liquid chromatography tandem-mass spectrometry (LC-MS/MS). Importantly, these comparisons suggested the presence of cerpegin and 5-allyl cerpegin in all C. bulbosa tissues. Further, de novo transcriptome analysis indicated the presence of significant transcripts for secondary metabolic pathways through the Kyoto encyclopedia of genes and genomes database. Tissue-specific profiling of transcripts and metabolites showed a significant correlation, suggesting the intricate mechanism of cerpegin biosynthesis. The expression of potential candidate genes from the proposed cerpegin biosynthetic pathway was further validated by qRT-PCR and NanoString nCounter. Overall, our findings propose a potential route of cerpegin biosynthesis. Identified transcripts and metabolites have built a foundation as new molecular resources that could facilitate future research on biosynthesis, regulation, and engineering of cerpegin or other important metabolites in such non-model plants.
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Affiliation(s)
- Sachin A Gharat
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Balkrishna A Shinde
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Department of Biotechnology, Shivaji University, Vidyanagar, Kolhapur, 416004, India
| | - Ravindra D Mule
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sachin A Punekar
- Biospheres, Eshwari, 52/403, Lakshmi nagar, Parvati, Pune, 411009, India
| | - Bhushan B Dholakia
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Ramesha H Jayaramaiah
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Theracues Innovations Private Limited, Sahakar nagar, Bangalore, 560092, India
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | | | - Ashok P Giri
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.
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22
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Olajuyin AM, Olajuyin AK, Wang Z, Zhao X, Zhang X. CD146 T cells in lung cancer: its function, detection, and clinical implications as a biomarker and therapeutic target. Cancer Cell Int 2019; 19:247. [PMID: 31572064 PMCID: PMC6761715 DOI: 10.1186/s12935-019-0969-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
CD146 alternatively called melanoma cell adhesion molecule (MCAM), is a biomarker and therapeutic target of clinical significance. It is found on different cells including the endothelial cells and lymphocytes which participate in heterotypic and homotypic ligand-receptor. This review concentrated on the CD146 expression T cells (or lymphocytes) centering on Treg in lung cancer. Here, we have also considered the vigorous investigation of CD146 mainly acknowledged new roles, essential mechanisms and clinical implications of CD146 in cancer. CD146 has progressively become a significant molecule, particularly recognized as a novel biomarker, prognosis and therapy for cancer. Hence, targeting CD146 expression by utilization of methanol extracts of Calotropis procera leaf may be useful for the treatment of carcinogenesis.
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Affiliation(s)
- Ayobami Matthew Olajuyin
- Department of Respiratory and Critical Care Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, 450003 Henan China
| | - Adefunke Kafayat Olajuyin
- Department of Respiratory and Critical Care Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, 450003 Henan China
| | - Ziqi Wang
- Department of Respiratory and Critical Care Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, 450003 Henan China
| | - Xingru Zhao
- Department of Respiratory and Critical Care Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, 450003 Henan China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, 450003 Henan China
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Weitemier K, Straub SC, Fishbein M, Bailey CD, Cronn RC, Liston A. A draft genome and transcriptome of common milkweed ( Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PeerJ 2019; 7:e7649. [PMID: 31579586 PMCID: PMC6756140 DOI: 10.7717/peerj.7649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
Milkweeds (Asclepias) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present a transcriptome and draft nuclear genome assembly of the common milkweed, Asclepias syriaca. This reconstruction of the nuclear genome is augmented by linkage group information, adding to existing chloroplast and mitochondrial genomic resources for this member of the Apocynaceae subfamily Asclepiadoideae. The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated. A large proportion of gene space is represented in the assembly, with 96.7% of Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Scaffolds covering 75 Mbp of the Asclepias assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in Coffea found that six chromosomes show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. The progesterone 5β-reductase gene family, a key component of cardenolide production, is likely reduced in Asclepias relative to other Apocynaceae. The genome and transcriptome of common milkweed provide a rich resource for future studies of the ecology and evolution of a charismatic plant family.
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Affiliation(s)
- Kevin Weitemier
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | | | - Mark Fishbein
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, USA
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Richard C. Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, USA
| | - Aaron Liston
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
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24
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Coêlho MRV, Rivas R, Ferreira-Neto JRC, Pandolfi V, Bezerra-Neto JP, Benko-Iseppon AM, Santos MG. Reference genes selection for Calotropis procera under different salt stress conditions. PLoS One 2019; 14:e0215729. [PMID: 30998798 PMCID: PMC6472812 DOI: 10.1371/journal.pone.0215729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 04/08/2019] [Indexed: 02/04/2023] Open
Abstract
Calotropis procera is a perennial Asian shrub with significant adaptation to adverse climate conditions and poor soils. Given its increased salt and drought stress tolerance, C. procera stands out as a powerful candidate to provide alternative genetic resources for biotechnological approaches. The qPCR (real-time quantitative polymerase chain reaction), widely recognized among the most accurate methods for quantifying gene expression, demands suitable reference genes (RGs) to avoid over- or underestimations of the relative expression and incorrect interpretation. This study aimed at evaluating the stability of ten RGs for normalization of gene expression of root and leaf of C. procera under different salt stress conditions and different collection times. The selected RGs were used on expression analysis of three target genes. Three independent experiments were carried out in greenhouse with young plants: i) Leaf100 = leaf samples collected 30 min, 2 h, 8 h and 45 days after NaCl-stress (100 mM NaCl); ii) Root50 and iii) Root200 = root samples collected 30 min, 2 h, 8 h and 1day after NaCl-stress (50 and 200 mM NaCl, respectively). Stability rank among the three algorithms used showed high agreement for the four most stable RGs. The four most stable RGs showed high congruence among all combination of collection time, for each software studied, with minor disagreements. CYP23 was the best RG (rank of top four) for all experimental conditions (Leaf100, Root50, and Root200). Using appropriated RGs, we validated the relative expression level of three differentially expressed target genes (NAC78, CNBL4, and ND1) in Leaf100 and Root200 samples. This study provides the first selection of stable reference genes for C. procera under salinity. Our results emphasize the need for caution when evaluating the stability RGs under different amplitude of variable factors.
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Affiliation(s)
- Maria R. V. Coêlho
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
| | - Rebeca Rivas
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
| | - José Ribamar C. Ferreira-Neto
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Valesca Pandolfi
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - João P. Bezerra-Neto
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Ana Maria Benko-Iseppon
- Universidade Federal de Pernambuco, Departamento de Genética, Laboratório Genética e Biotecnologia Vegetal, Recife, PE, Brazil
| | - Mauro G. Santos
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil
- * E-mail:
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25
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Mohana Kumara P, Uma Shaanker R, Pradeep T. UPLC and ESI-MS analysis of metabolites of Rauvolfia tetraphylla L. and their spatial localization using desorption electrospray ionization (DESI) mass spectrometric imaging. PHYTOCHEMISTRY 2019; 159:20-29. [PMID: 30562679 DOI: 10.1016/j.phytochem.2018.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 05/22/2023]
Abstract
Rauvolfia tetraphylla L. (family Apocynaceae), often referred to as the wild snakeroot plant, is an important medicinal plant and produces a number of indole alkaloids in its seeds and roots. The plant is often used as a substitute for Ravuolfia serpentine (L.) Benth. ex Kurz known commonly as the Indian snakeroot plant or sarphagandha in the preparation of Ayurvedic formulations for a range of diseases including hypertension. In this study, we examine the spatial localization of the various indole alkaloids in developing fruits and plants of R. tetraphylla using desorption electrospray ionization mass spectrometry imaging (DESI-MSI). A semi-quantitative analysis of the various indole alkaloids was performed using UPLC-ESI/MS. DESI-MS images showed that the distribution of ajmalcine, yohimbine, demethyl serpentine and mitoridine are largely localized in the fruit coat while that for ajmaline is restricted to mesocarp of the fruit. At a whole plant level, the ESI-MS intensities of many of the ions were highest in the roots and lesser in the shoot region. Within the root tissue, except sarpagine and ajmalcine, all other indole alkaloids occurred in the epidermal and cortex tissues. In leaves, only serpentine, ajmalcine, reserpiline and yohimbine were present. Serpentine was restricted to the petiolar region of leaves. Principal component analysis based on the presence of the indole alkaloids, clearly separated the four tissues (stem, leaves, root and fruits) into distinct clusters. In summary, the DESI-MSI results indicated a clear tissue localization of the various indole alkaloids, in fruits, leaves and roots of R. tetraphylla. While it is not clear of how such localization is attained, we discuss the possible pathways of indole alkaloid biosynthesis and translocation during fruit and seedling development in R. tetraphylla. We also briefly discuss the functional significance of the spatial patterns in distribution of metabolites.
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Affiliation(s)
- P Mohana Kumara
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India; Center for Ayurveda Biology and Holistic Nutrition, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, 560064, India.
| | - R Uma Shaanker
- School of Ecology and Conservation, Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India
| | - T Pradeep
- DST Unit of Nanoscience and Thematic Unit of Excellence, Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India.
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26
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Mao J, He Z, Hao J, Liu T, Chen J, Huang S. Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine ( Pinus taeda L.) based on transcriptome analyses. PeerJ 2019; 7:e6124. [PMID: 30723613 PMCID: PMC6360084 DOI: 10.7717/peerj.6124] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/18/2018] [Indexed: 01/30/2023] Open
Abstract
Loblolly pine (Pinus taeda L.) is one of the most important species for oleoresin (a mixture of terpenoids) in South China. The high oleoresin content of loblolly pine is associated with resistance to bark beetles and other economic benefits. In this study, we conducted transcriptome analyses of loblolly pine secondary xylem to gain insight into the genes involved in terpenoid biosynthesis. A total of 372 unigenes were identified as being critical for oleoresin production, including genes for ATP-binding cassette (ABC) transporters, the cytochrome P450 (CYP) protein family, and terpenoid backbone biosynthesis enzymes. Six key genes involved in terpenoid biosynthetic pathways were selected for multiple sequence alignment, conserved motif prediction, and phylogenetic and expression profile analyses. The protein sequences of all six genes exhibited a higher degree of sequence conservation, and upstream genes were relatively more conserved than downstream genes in terpenoid biosynthetic pathways. The N-terminal regions of these sequences were less conserved than the C-terminal ends, as the N-terminals were quite diverse in both length and composition. The phylogenetic analyses revealed that most genes originated from gene duplication after species divergence, and partial genes exhibited incomplete lineage sorting. In addition, the expression profile analyses showed that all six genes exhibited high expression levels during the high-oleoresin-yielding phase.
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Affiliation(s)
- Jipeng Mao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zidi He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jing Hao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Tianyi Liu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiehu Chen
- Science Corporation of Gene, Guangzhou, Guangdong, China
| | - Shaowei Huang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
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27
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Du F, Zou Y, Hu Q, Jing Y, Yang X. Metabolic Profiling of Pleurotus tuoliensis During Mycelium Physiological Maturation and Exploration on a Potential Indicator of Mycelial Maturation. Front Microbiol 2019; 9:3274. [PMID: 30687265 PMCID: PMC6333644 DOI: 10.3389/fmicb.2018.03274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/17/2018] [Indexed: 12/20/2022] Open
Abstract
Pleurotus tuoliensis is a valuable and rare edible fungus with extremely high nutritional and medicinal value. However, the relative immaturity of P. tuoliensis cultivation technology leads to fluctuating yields and quality. The main difficulty in P. tuoliensis cultivation is estimate of mycelial maturity. There is currently no measurable indicator that clearly characterizes the physiological maturation of mycelia. The aim of this study was to identify potential indicators of physiological maturation for P. tuoliensis mycelia by using metabolomics approach. A metabolite profiling strategy involving gas chromatography-mass spectrometry (GC/MS) was used to analyze changes to extracellular metabolites in mycelia collected at mycelium physiological maturation period (MPMP) day 0, MPMP day 35 at 17°C and MPMP day 35 at 29°C. 72 differential metabolites (37.8% up-regulated and 62.2% down-regulated) were identified based on the selected criteria [variable important in projection (VIP) greater than 1.0 and p < 0.01]. Metabolic pathways enrichment analysis showed that these metabolites are involved in glycolysis, organic acid metabolism, amino acid metabolism, tricarboxylic acid cycle (TCA), sugar metabolism, nicotinate and nicotinamide metabolism, and oxidative phosphorylation. In addition, the pyrimidine synthesis pathway was significantly activated during mycelium physiological maturation of P. tuoliensis. The abundance of N-carbamoyl-L-aspartate (CA-asp), a component of this pathway, was significantly increased at MPMP day 35, which motivated us to explore its potential as an indicator for physiological maturation of mycelia. The content of CA-asp in mycelia changed in a consistent manner during physiological maturation. The feasibility of using CA-asp as an indicator for mycelial maturation requires further investigation.
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Affiliation(s)
- Fang Du
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yajie Zou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingxiu Hu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunge Jing
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohong Yang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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28
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Ramadan AM, Azeiz AA, Baabad S, Hassanein S, Gadalla NO, Hassan S, Algandaby M, Bakr S, Khan T, Abouseadaa HH, Ali HM, Al-Ghamdi A, Osman G, Edris S, Eissa H, Bahieldin A. Control of β-sitosterol biosynthesis under light and watering in desert plant Calotropis procera. Steroids 2019; 141:1-8. [PMID: 30414421 DOI: 10.1016/j.steroids.2018.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/23/2018] [Accepted: 11/02/2018] [Indexed: 01/13/2023]
Abstract
Most scientific studies on Calotropis procera refer to the plant as an important source of pharmaceutical compounds and its valuable benefits in medicine. One of the most important substances in this plant is the potential immunostimulant β-sitosterol (BS) that acts in improving human health. This study focused on the effects of lighting before and after irrigation on the BS accumulation pathway namely steroid biosynthesis. Studying the enzymes in BS biosynthetic pathway indicated the upregulation at dawn and predusk of the SMT2 and SMO2 genes encoding sterol methyltransferase 2 and methylsterol monooxygenase, two key enzymes in BS accumulation in C. procera. The results almost indicated no regulation at the different time points of the CYP710A gene encoding sterol 22-desaturase, an enzyme that acts in depleting β-sitosterol towards the biosynthesis of stigmasterol. RNA-Seq data was validated via quantitative RT-PCR and results were positive. The data of ultra-performance liquid chromatography-tandem mass spectrometry analysis with regard to BS accumulation also aligned with those of RNA-Seq analysis. We focused on the effects of light before and after watering on BS accumulation in C. procera. Our results show that BS accumulation is high at dawn in both dehydrated and well-watered condition. While, the BS was dramatically decrease at midday in well-watered plants. This increase/decrease in BS content is correlated with rates of expression of SMT 2 gene. This gene is a key convertor between the different branches in the cardiac glycoside biosynthesis. Accordingly, it could be suggested that BS (or one of the descendent product) may play an important role in C. procera tolerance to drought/light intensity conditions.
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Affiliation(s)
- Ahmed M Ramadan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Plant Molecular Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
| | - Ahmed Abdel Azeiz
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt
| | - Saeed Baabad
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sameh Hassanein
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt; Bioinformatics Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center(ARC), Giza, Egypt
| | - Nour O Gadalla
- Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia; Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt
| | - Sabah Hassan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Mardi Algandaby
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Salwa Bakr
- Department of Clinical Pathology, Hematology, College of Medicine, Fayoum University, Fayoum, Egypt; College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Thana Khan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heba H Abouseadaa
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Hani Mohammed Ali
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Areej Al-Ghamdi
- Physics Department, Faculty of Science, Jeddah University, Jeddah, Saudi Arabia
| | - Gamal Osman
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia; Department of Microbial genetics, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
| | - Sherif Edris
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Hala Eissa
- Plant Molecular Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt; College of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt
| | - Ahmed Bahieldin
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
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Kumar VL, Pandey A, Verma S, Das P. Protection afforded by methanol extract of Calotropis procera latex in experimental model of colitis is mediated through inhibition of oxidative stress and pro-inflammatory signaling. Biomed Pharmacother 2018; 109:1602-1609. [PMID: 30551414 DOI: 10.1016/j.biopha.2018.10.187] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/27/2018] [Accepted: 10/31/2018] [Indexed: 12/14/2022] Open
Abstract
Calotropis procera, a latex producing plant is known to possess medicinal properties including its beneficial effect in gastrointestinal disorders. The anti-inflammatory effect of its latex in various experimental models is noteworthy and in light of this the present study was carried out with an objective to evaluate its efficacy in ulcerative colitis, an inflammatory condition of the colon. Colitis was induced in rats by acetic acid and the rats were divided into four groups where one group served as experimental control and the other groups were treated with two doses of methanol extract of dried latex of C. procera (MeDL; 50 and 150 mg/kg) and mesalazine (MSZ; 300 mg/kg). The study also included normal control (NC) group for comparison of various parameters related to colon like macroscopic changes, ulcer score, adherent mucus content, weight/length ratio, small intestinal transit, oxidative stress and inflammatory markers, tissue histology and immunoreactivity of cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS) and nuclear factor kappa beta (NFκB) subunit p65. Treatment of colitic rats with MeDL produced a significant reduction in colonic mucosal damage as revealed by macroscopic and microscopic evaluation and normalization of tissue levels of oxidative stress markers and pro-inflammatory mediators. The protection afforded by MeDL was also evident from its restorative effect on tissue histology and expression of COX-2, iNOS and NFκB(p65). This study shows that by targeting oxidative stress and NFκB(p65) mediated pro-inflammatory signaling, the latex of C. procera affords protection in colitis and its effect was comparable to that of mesalazine. This study suggests that latex of C. procera could serve as a promising therapeutic option for treating inflammatory conditions of the colon.
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Affiliation(s)
- Vijay L Kumar
- Department of Pharmacology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India.
| | - Abhimanu Pandey
- Department of Pharmacology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Sneh Verma
- Department of Pharmacology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Prasenjit Das
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
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De novo transcriptome analysis deciphered polyoxypregnane glycoside biosynthesis pathway in Gymnema sylvestre. 3 Biotech 2018; 8:381. [PMID: 30148031 DOI: 10.1007/s13205-018-1389-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022] Open
Abstract
Gymnema sylvestre is an important medicinal plant containing antidiabetic activity. Through de novo transcriptomic study, the pathways of polyoxypregnane glycosides were explored and candidate genes of these pathways were identified in G. sylvestre. High-quality raw reads were assembled into transcripts which resulted in 193,615 unigenes. These unigenes further decoded 58,274 coding DNA sequences (CDSs). Functional annotation of predicted CDSs was carried out using the protein databases, i.e., NCBI's non-redundant, Uniprot and Pfam. Eukaryotic orthologous group (KOG) classification and transcription factor analysis has revealed most CDS-enriched categories as "Signal transduction mechanism" and "Basic Helix loop helix" (bHLH) transcription factor family, respectively. A total of 16,569 CDSs were assigned minimum one Gene Ontology (GO) term. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis disclosed 235 CDSs which represented total 27 genes of pregnane glycoside pathways and 19 CDSs represented 10 important enzymes of polyoxypregnane glycoside biosynthesis, i.e., sterol 24-C-methyltransferase, cycloeucalenol cycloisomerase, Δ14-sterol reductase, C-8,7 sterol isomerase, sterol methyltransferase 2, C-5 sterol desaturase, sterol Δ7 reductase, Δ24 sterol reductase, 3β-hydroxysteroid dehydrogenase and progesterone 5β reductase (5βPOR). This transcriptome analysis provided an important resource for future functional genomic studies in G. sylvestre.
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Hou DY, Shi LC, Yang MM, Li J, Zhou S, Zhang HX, Xu HW. De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform. PLoS One 2018; 13:e0192610. [PMID: 29451882 PMCID: PMC5815590 DOI: 10.1371/journal.pone.0192610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/27/2018] [Indexed: 01/06/2023] Open
Abstract
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization. Hence, enriching its genomic data and information is very important. In recent years, the fast-growing technology of next generation sequencing has provided an effective path to gain genomic information from nonmodel species. This study is the first to explore the leaf and fruit tissue transcriptome of C. officinalis using the Illumina HiSeq 4000 platform. A total of 57,954,134 and 60,971,652 clean reads from leaf and fruit were acquired, respectively (GenBank number SRP115440). The pooled reads from all two libraries were assembled into 56,392 unigenes with an average length 856 bp. Among these, 41,146 unigenes matched with sequences in the NCBI nonredundant protein database. The Gene Ontology database assigned 24,336 unigenes with biological process (83.26%), cellular components (53.58%), and molecular function (83.93%). In addition, 10,808 unigenes were assigned a KOG functional classification by the KOG database. Searching against the KEGG pathway database indicated that 18,435 unigenes were mapped to 371 KEGG pathways. Moreover, the edgeR database identified 4,585 significant differentially expressed genes (DEGs), of which 1,392 were up-regulated and 3,193 were down-regulated in fruit tissue compared with leaf tissue. Finally, we explored 581 transcription factors with 50 transcription factor gene families. Most DEGs and transcription factors were related to terpene biosynthesis and secondary metabolic regulation. This study not only represented the first de novo transcriptomic analysis of C. officinalis but also provided fundamental information on its genes and biosynthetic pathway. These findings will help us explore the molecular metabolism mechanism of terpene biosynthesis in C. officinalis.
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Affiliation(s)
- Dian-Yun Hou
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
- * E-mail:
| | - Lin-Chun Shi
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Meng-Meng Yang
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Jiong Li
- Chinese Medicinal Materials Production Technology Service Center, Department of Agriculture of Henan Province, Zhengzhou, Henan Province, China
| | - Shuang Zhou
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Hong-Xiao Zhang
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Hua-Wei Xu
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
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Hoopes GM, Hamilton JP, Kim J, Zhao D, Wiegert-Rininger K, Crisovan E, Buell CR. Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides. G3 (BETHESDA, MD.) 2018; 8:385-391. [PMID: 29237703 PMCID: PMC5919723 DOI: 10.1534/g3.117.300331] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/10/2017] [Indexed: 12/02/2022]
Abstract
Calotropis gigantea produces specialized secondary metabolites known as cardenolides, which have anticancer and antimalarial properties. Although transcriptomic studies have been conducted in other cardenolide-producing species, no nuclear genome assembly for an Asterid cardenolide-producing species has been reported to date. A high-quality de novo assembly was generated for C. gigantea, representing 157,284,427 bp with an N50 scaffold size of 805,959 bp, for which quality assessments indicated a near complete representation of the genic space. Transcriptome data in the form of RNA-sequencing libraries from a developmental tissue series was generated to aid the annotation and construction of a gene expression atlas. Using an ab initio and evidence-driven gene annotation pipeline, 18,197 high-confidence genes were annotated. Homologous and syntenic relationships between C. gigantea and other species within the Apocynaceae family confirmed previously identified evolutionary relationships, and suggest the emergence or loss of the specialized cardenolide metabolites after the divergence of the Apocynaceae subfamilies. The C. gigantea genome assembly, annotation, and RNA-sequencing data provide a novel resource to study the cardenolide biosynthesis pathway, especially for understanding the evolutionary origin of cardenolides and the engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications.
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Affiliation(s)
- Genevieve M Hoopes
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Jeongwoon Kim
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Dongyan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | | | - Emily Crisovan
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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Wen C, Huang W, Zhu XL, Li XS, Zhang F, Jiang RW. UGT74AN1, a Permissive Glycosyltransferase from Asclepias curassavica for the Regiospecific Steroid 3-O-Glycosylation. Org Lett 2018; 20:534-537. [DOI: 10.1021/acs.orglett.7b03619] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Chao Wen
- Guangdong Province Key Laboratory
of Pharmacodynamic Constituents of TCM and New Drugs Research, Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Wei Huang
- Guangdong Province Key Laboratory
of Pharmacodynamic Constituents of TCM and New Drugs Research, Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Xue-Lin Zhu
- Guangdong Province Key Laboratory
of Pharmacodynamic Constituents of TCM and New Drugs Research, Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Xiao-San Li
- Guangdong Province Key Laboratory
of Pharmacodynamic Constituents of TCM and New Drugs Research, Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Fan Zhang
- Guangdong Province Key Laboratory
of Pharmacodynamic Constituents of TCM and New Drugs Research, Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Ren-Wang Jiang
- Guangdong Province Key Laboratory
of Pharmacodynamic Constituents of TCM and New Drugs Research, Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
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Mutwakil MZ, Hajrah NH, Atef A, Edris S, Sabir MJ, Al-Ghamdi AK, Sabir MJSM, Nelson C, Makki RM, Ali HM, El-Domyati FM, Al-Hajar ASM, Gloaguen Y, Al-Zahrani HS, Sabir JSM, Jansen RK, Bahieldin A, Hall N. Transcriptomic and metabolic responses of Calotropis procera to salt and drought stress. BMC PLANT BIOLOGY 2017; 17:231. [PMID: 29202709 PMCID: PMC5716246 DOI: 10.1186/s12870-017-1155-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 11/08/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Calotropis procera is a wild plant species in the family Apocynaceae that is able to grow in harsh, arid and heat stressed conditions. Understanding how this highly adapted plant persists in harsh environments should inform future efforts to improve the hardiness of crop and forage plant species. To study the plant response to droμght and osmotic stress, we treated plants with polyethylene glycol and NaCl and carried out transcriptomic and metabolomics measurements across a time-course of five days. RESULTS We identified a highly dynamic transcriptional response across the time-course including dramatic changes in inositol signaling, stress response genes and cytokinins. The resulting metabolome changes also involved sharp increases of myo-inositol, a key signaling molecule and elevated amino acid metabolites at later times. CONCLUSIONS The data generated here provide a first glimpse at the expressed genome of C. procera, a plant that is exceptionally well adapted to arid environments. We demonstrate, through transcriptome and metabolome analysis that myo-inositol signaling is strongly induced in response to drought and salt stress and that there is elevation of amino acid concentrations after prolonged osmotic stress. This work should lay the foundations of future studies in adaptation to arid environments.
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Affiliation(s)
- Mohammed Z Mutwakil
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Nahid H Hajrah
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Ahmed Atef
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Sherif Edris
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Mernan J Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Areej K Al-Ghamdi
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Meshaal J S M Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Charlotte Nelson
- Centre for Genomic Research, The University of Liverpool, Liverpool, L170AH, UK
| | - Rania M Makki
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Hani M Ali
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Fotouh M El-Domyati
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Abdulrahman S M Al-Hajar
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Yoann Gloaguen
- College of MVLS, Glasgow Polyomics, University of Glasgow, Glasgow, UK
| | - Hassan S Al-Zahrani
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Jamal S M Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
| | - Robert K Jansen
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ahmed Bahieldin
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Neil Hall
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah, 21589, Saudi Arabia.
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK.
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Jeena GS, Fatima S, Tripathi P, Upadhyay S, Shukla RK. Comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri identifies potential genes related to triterpenoid saponin biosynthesis. BMC Genomics 2017; 18:490. [PMID: 28659188 PMCID: PMC5490213 DOI: 10.1186/s12864-017-3865-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/15/2017] [Indexed: 12/02/2022] Open
Abstract
Background Bacopa monnieri commonly known as Brahmi is utilized in Ayurveda to improve memory and many other human health benefits. Bacosides enriched standardized extract of Bacopa monnieri is being marketed as a memory enhancing agent. In spite of its well known pharmacological properties it is not much studied in terms of transcripts involved in biosynthetic pathway and its regulation that controls the secondary metabolic pathway in this plant. The aim of this study was to identify the potential transcripts and provide a framework of identified transcripts involved in bacosides production through transcriptome assembly. Results We performed comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri in two independent biological replicate and obtained 22.48 million and 22.0 million high quality processed reads in shoot and root respectively. After de novo assembly and quantitative assessment total 26,412 genes got annotated in root and 18,500 genes annotated in shoot sample. Quality of raw reads was determined by using SeqQC-V2.2. Assembled sequences were annotated using BLASTX against public database such as NR or UniProt. Searching against the KEGG pathway database indicated that 37,918 unigenes from root and 35,130 unigenes from shoot were mapped to 133 KEGG pathways. Based on the DGE data we found that most of the transcript related to CYP450s and UDP-glucosyltransferases were specifically upregulated in shoot tissue as compared to root tissue. Finally, we have selected 43 transcripts related to secondary metabolism including transcription factor families which are differentially expressed in shoot and root tissues were validated by qRT-PCR and their expression level were monitored after MeJA treatment and wounding for 1, 3 and 5 h. Conclusions This study not only represents the first de novo transcriptome analysis of Bacopa monnieri but also provides information about the identification, expression and differential tissues specific distribution of transcripts related to triterpenoid sapogenin which is one of the most important pharmacologically active secondary metabolite present in Bacopa monnieri. The identified transcripts in this study will establish a foundation for future studies related to carrying out the metabolic engineering for increasing the bacosides biosynthesis and its regulation for human health benefits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3865-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gajendra Singh Jeena
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Shahnoor Fatima
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Pragya Tripathi
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Swati Upadhyay
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India
| | - Rakesh Kumar Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, P.O. CIMAP, Lucknow, 226015, India.
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