1
|
Yousof NSAM, Afzan A, Zainol M, Bakar SIA, Razak MRMA, Jelas NHM, Abdullah NN, Cordell GA, Ismail NH. Molecular networking-based mass spectral identification of Brucea javanica (L.) Merr. metabolites and their selective binding affinities for dengue virus enzymes. Fitoterapia 2024; 175:105955. [PMID: 38604259 DOI: 10.1016/j.fitote.2024.105955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/03/2024] [Accepted: 04/06/2024] [Indexed: 04/13/2024]
Abstract
Brucea javanica, a valued traditional medicinal plant in Malaysia, known for its fever-treating properties yet remains underexplored for its potential antiviral properties against dengue. This study aims to simultaneously identify chemical classes and metabolites within B. javanica using molecular networking (MN), by Global Natural Product Social (GNPS), and SIRIUS in silico annotation. Liquid chromatography-mass spectrometry (LC-MS2)-based MN explores chemical diversity across four plant parts (leaves, roots, fruits, and stem bark), revealing diverse metabolites such as tryptophan-derived alkaloids, terpenoids, and octadecadenoids. Simultaneous LC-MS2 and MN analyses reveal a discriminative capacity for individual plant components, with roots accumulating tryptophan alkaloids, fruits concentrating quassinoids, leaves containing fusidanes, and stem bark primarily characterised by simple indoles. Subsequently, extracts were evaluated for dengue antiviral activity using adenosine triphosphate (ATP) and plaque assays, indicates potent efficacy in the dichloromethane (DCM) extract from roots (EC50 = 0.3 μg/mL, SI = 10). Molecular docking analysis of two major compounds; canthin-6-one (264) and 1-hydroxy-11-methoxycanthin-6-one (275) showed potential binding interactions with active sites of NS5 RNA-dependent RNA polymerase (RdRp) of dengue virus (DENV) protein. Subsequent in vitro evaluation revealed compounds 264 and 275 had a promising dengue antiviral activity with SI value of 63 and 1.85. These identified metabolites emerge as potential candidates for further evaluation in dengue antiviral activities.
Collapse
Affiliation(s)
- Nor Syaidatul Akmal Mohd Yousof
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor, Malaysia; Faculty of Applied Science, UiTM, 40450 Shah Alam, Selangor, Malaysia; Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, No. 1 Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Adlin Afzan
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, No. 1 Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Murizal Zainol
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, No. 1 Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Syahrul Imran Abu Bakar
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor, Malaysia; Faculty of Applied Science, UiTM, 40450 Shah Alam, Selangor, Malaysia
| | - Mohd Ridzuan Mohd Abd Razak
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, No. 1 Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Nur Hana Md Jelas
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, No. 1 Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Nor Nadirah Abdullah
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor, Malaysia; Faculty of Applied Science, UiTM, 40450 Shah Alam, Selangor, Malaysia
| | - Geoffrey A Cordell
- Natural Products Inc., Evanston, IL 60201, USA; College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Nor Hadiani Ismail
- Atta-ur-Rahman Institute for Natural Product Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor, Malaysia; Faculty of Applied Science, UiTM, 40450 Shah Alam, Selangor, Malaysia.
| |
Collapse
|
2
|
Chen J, Tan X, Guo G, Wang P, Zhang H, Lv S, Xu H, Hou D. Cloning and Expression Analysis of Key Enzyme Gene CoGPPS Involved in Iridoid Glycoside Synthesis in Cornus officinalis. DNA Cell Biol 2024; 43:125-131. [PMID: 38350140 DOI: 10.1089/dna.2023.0335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
Cornus iridoid glycosides (CIGs), including loganin and morroniside, are the main active components of Cornus officinalis. As one of the key enzymes in the biosynthesis of CIGs, geranyl pyrophosphate synthase (GPPS) catalyzes the formation of geranyl pyrophosphate, which is the direct precursor of CIGs. In this study, the C. officinalis geranyl pyrophosphate synthase (CoGPPS) sequence was cloned from C. officinalis and analyzed. The cDNA sequence of the CoGPPS gene was 915 bp (GenBank No. OR725699). Phylogenetic analysis showed that CoGPPS was closely related to the GPPS sequence of Actinidia chinensis and Camellia sinensis, but relatively distantly related to Paeonia lactiflora and Tripterygium wilfordii. Results from the quantitative real-time PCR showed the spatiotemporal expression pattern of CoGPPS; that is, CoGPPS was specifically expressed in the fruits. Subcellular localization assay proved that CoGPPS was specifically found in chloroplasts. Loganin and morroniside contents in the tissues were detected by high-performance liquid chromatography, and both compounds were found to be at higher levels in the fruits than in leaves. Thus, this study laid the foundation for further studies on the synthetic pathway of CIGs.
Collapse
Affiliation(s)
- Jiaxi Chen
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center for Evaluation and Innovative Utilization of Homology of Medicine and Food, Luoyang, China
| | - Xinjie Tan
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center for Evaluation and Innovative Utilization of Homology of Medicine and Food, Luoyang, China
| | - Guangyang Guo
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center for Evaluation and Innovative Utilization of Homology of Medicine and Food, Luoyang, China
| | - Panpan Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center for Evaluation and Innovative Utilization of Homology of Medicine and Food, Luoyang, China
| | - Hongxiao Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center for Evaluation and Innovative Utilization of Homology of Medicine and Food, Luoyang, China
| | - Shufang Lv
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center for Evaluation and Innovative Utilization of Homology of Medicine and Food, Luoyang, China
| | - Huawei Xu
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center for Evaluation and Innovative Utilization of Homology of Medicine and Food, Luoyang, China
| | - Dianyun Hou
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center for Evaluation and Innovative Utilization of Homology of Medicine and Food, Luoyang, China
| |
Collapse
|
3
|
Carvalho da Silva TL, Belo Silva VN, Braga ÍDO, Rodrigues Neto JC, Leão AP, Ribeiro JADA, Valadares LF, Abdelnur PV, de Sousa CAF, Souza MT. Integration of metabolomics and transcriptomics data to further characterize Gliricidia sepium (Jacq.) Kunth under high salinity stress. THE PLANT GENOME 2022; 15:e20182. [PMID: 34964552 DOI: 10.1002/tpg2.20182] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Soil salinity is one abiotic stress that threatens agriculture in more than 100 countries. Gliricidia [Gliricidia sepium (Jacq.) Kunth] is a multipurpose tree known for its ability to adapt to a wide range of soils; however, its tolerance limits and responses to salt stress are not yet well understood. In this study, after characterizing the morphophysiological responses of young gliricidia plants to salinity stress, leaf metabolic and transcription profiles were generated and submitted to single and integrated analyses. RNA from leaf samples were subjected to RNA sequencing using an Illumina HiSeq platform and the paired-end strategy. Polar and lipidic fractions from leaf samples were extracted and analyzed on an ultra-high-performance liquid chromatography (UHPLC) coupled with electrospray ionization quadrupole time-of-flight high-resolution mass spectrometry (MS) system. Acquired data were analyzed using the OmicsBox, XCMS Online, MetaboAnalyst, and Omics Fusion platforms. The substrate salinization protocol used allowed the identification of two distinct responses to salt stress: tolerance and adaptation. Single analysis on transcriptome and metabolome data sets led to a group of 5,672 transcripts and 107 metabolites differentially expressed in gliricidia leaves under salt stress. The phenylpropanoid biosynthesis was the most affected pathway, with 15 metabolites and three genes differentially expressed. Results showed that the differentially expressed metabolites and genes from this pathway affect mainly short-term salt stress (STS). The single analysis of the transcriptome identified 12 genes coding for proteins that might play a role in gliricidia response at both STS and long-term salt stress (LTS). Further studies are needed to reveal the mechanisms behind the adaptation response.
Collapse
Affiliation(s)
| | - Vivianny Nayse Belo Silva
- Graduate Program of Plant Biotechnology, Federal Univ. of Lavras, 37200-000, Lavras, MG, CP 3037, Brazil
| | - Ítalo de Oliveira Braga
- Graduate Program of Plant Biotechnology, Federal Univ. of Lavras, 37200-000, Lavras, MG, CP 3037, Brazil
| | | | - André Pereira Leão
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil
| | | | | | - Patrícia Verardi Abdelnur
- Institute of Chemistry, Federal Univ. of Goiás, Campus Samambaia, Goiânia, GO, 74690-900, Brazil
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil
| | | | - Manoel Teixeira Souza
- Graduate Program of Plant Biotechnology, Federal Univ. of Lavras, 37200-000, Lavras, MG, CP 3037, Brazil
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil
| |
Collapse
|
4
|
Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus. Int J Mol Sci 2021; 22:ijms22168835. [PMID: 34445541 PMCID: PMC8396295 DOI: 10.3390/ijms22168835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 02/06/2023] Open
Abstract
Mallotus japonicus is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for M. japonicus to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of M. japonicus represented by 2129 metabolite features. M. japonicus de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in M. japonicus.
Collapse
|
5
|
Dossou SSK, Xu F, Cui X, Sheng C, Zhou R, You J, Tozo K, Wang L. Comparative metabolomics analysis of different sesame (Sesamum indicum L.) tissues reveals a tissue-specific accumulation of metabolites. BMC PLANT BIOLOGY 2021; 21:352. [PMID: 34303354 PMCID: PMC8305604 DOI: 10.1186/s12870-021-03132-0] [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: 04/14/2021] [Accepted: 07/12/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L.) leaves, flowers, especially seeds are used in traditional medicine to prevent or cure various diseases. Its seed's market is expanding. However, the other tissues are still underexploited due to the lack of information related to metabolites distribution and variability in the plant. Herein, the metabolite profiles of five sesame tissues (leaves, fresh seeds, white and purple flowers, and fresh carpels) have been investigated using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics analysis platform. RESULTS In total, 776 metabolites belonging to diverse classes were qualitatively and quantitatively identified. The different tissues exhibited obvious differences in metabolites composition. The majority of flavonoids predominantly accumulated in flowers. Amino acids and derivatives, and lipids were identified predominantly in fresh seeds followed by flowers. Many metabolites, including quinones, coumarins, tannins, vitamins, terpenoids and some bioactive phenolic acids (acteoside, isoacteoside, verbascoside, plantamajoside, etc.) accumulated mostly in leaves. Lignans were principally detected in seeds. 238 key significantly differential metabolites were filtered out. KEGG annotation and enrichment analyses of the differential metabolites revealed that flavonoid biosynthesis, amino acids biosynthesis, and phenylpropanoid biosynthesis were the main differently regulated pathways. In addition to the tissue-specific accumulation of metabolites, we noticed a cooperative relationship between leaves, fresh carpels, and developing seeds in terms of metabolites transfer. Delphinidin-3-O-(6"-O-p-coumaroyl)glucoside and most of the flavonols were up-regulated in the purple flowers indicating they might be responsible for the purple coloration. CONCLUSION This study revealed that the metabolic processes in the sesame tissues are differently regulated. It offers valuable resources for investigating gene-metabolites interactions in sesame tissues and examining metabolic transports during seed development in sesame. Furthermore, our findings provide crucial knowledge that will facilitate sesame biomass valorization.
Collapse
Affiliation(s)
- Senouwa Segla Koffi Dossou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
- Laboratory of Plant Biotechnology and Physiology, University of Lomé, Lomé, 01 BP 1515 Togo
| | - Fangtao Xu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Xianghua Cui
- Zhumadian Academy of Agricultural Sciences, Zhumadian, 4693000 China
| | - Chen Sheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| | - Koffi Tozo
- Laboratory of Plant Biotechnology and Physiology, University of Lomé, Lomé, 01 BP 1515 Togo
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062 China
| |
Collapse
|
6
|
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. Nat Commun 2021; 12:405. [PMID: 33452249 PMCID: PMC7810986 DOI: 10.1038/s41467-020-20508-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.
Collapse
|
7
|
Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020; 19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.
Collapse
Affiliation(s)
- Sandrien Desmet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| |
Collapse
|