Relevant bibliographies by topics / Plant specialized metabolome

Academic literature on the topic 'Plant specialized metabolome'

Author: Grafiati
Published: 11 March 2023

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Journal articles on the topic "Plant specialized metabolome"

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Schweiger, Rabea, Eva Castells, Luca Da Sois, Jordi Martínez-Vilalta, and Caroline Müller. "Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum." Cells 10, no. 3 (March 13, 2021): 644. http://dx.doi.org/10.3390/cells10030644.

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Plants show an extraordinary diversity in chemical composition and are characterized by different functional traits. However, relationships between the foliar primary and specialized metabolism in terms of metabolite numbers and composition as well as links with the leaf economics spectrum have rarely been explored. We investigated these relationships in leaves of 20 woody species from the Mediterranean region grown as saplings in a common garden, using a comparative ecometabolomics approach that included (semi-)polar primary and specialized metabolites. Our analyses revealed significant positive correlations between both the numbers and relative composition of primary and specialized metabolites. The leaf metabolomes were highly species-specific but in addition showed some phylogenetic imprints. Moreover, metabolomes of deciduous species were distinct from those of evergreens. Significant relationships were found between the primary metabolome and nitrogen content and carbon/nitrogen ratio, important traits of the leaf economics spectrum, ranging from acquisitive (mostly deciduous) to conservative (evergreen) leaves. A comprehensive understanding of various leaf traits and their coordination in different plant species may facilitate our understanding of plant functioning in ecosystems. Chemodiversity is thereby an important component of biodiversity.
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Li, Dapeng, Rayko Halitschke, Ian T. Baldwin, and Emmanuel Gaquerel. "Information theory tests critical predictions of plant defense theory for specialized metabolism." Science Advances 6, no. 24 (June 2020): eaaz0381. http://dx.doi.org/10.1126/sciadv.aaz0381.

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Different plant defense theories have provided important theoretical guidance in explaining patterns in plant specialized metabolism, but their critical predictions remain to be tested. Here, we systematically explored the metabolomes of Nicotiana attenuata, from single plants to populations, as well as of closely related species, using unbiased tandem mass spectrometry (MS/MS) analyses and processed the abundances of compound spectrum–based MS features within an information theory framework to test critical predictions of optimal defense (OD) and moving target (MT) theories. Information components of plant metabolomes were consistent with the OD theory but contradicted the main prediction of the MT theory for herbivory-induced dynamics of metabolome compositions. From micro- to macroevolutionary scales, jasmonate signaling was confirmed as the master determinant of OD, while ethylene signaling provided fine-tuning for herbivore-specific responses annotated via MS/MS molecular networks.
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Desmet, Sandrien, Kris Morreel, and Rebecca Dauwe. "Origin and Function of Structural Diversity in the Plant Specialized Metabolome." Plants 10, no. 11 (November 6, 2021): 2393. http://dx.doi.org/10.3390/plants10112393.

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The plant specialized metabolome consists of a multitude of structurally and functionally diverse metabolites, variable from species to species. The specialized metabolites play roles in the response to environmental changes and abiotic or biotic stresses, as well as in plant growth and development. At its basis, the specialized metabolism is built of four major pathways, each starting from a few distinct primary metabolism precursors, and leading to distinct basic carbon skeleton core structures: polyketides and fatty acid derivatives, terpenoids, alkaloids, and phenolics. Structural diversity in specialized metabolism, however, expands exponentially with each subsequent modification. We review here the major sources of structural variety and question if a specific role can be attributed to each distinct structure. We focus on the influences that various core structures and modifications have on flavonoid antioxidant activity and on the diversity generated by oxidative coupling reactions. We suggest that many oxidative coupling products, triggered by initial radical scavenging, may not have a function in se, but could potentially be enzymatically recycled to effective antioxidants. We further discuss the wide structural variety created by multiple decorations (glycosylations, acylations, prenylations), the formation of high-molecular weight conjugates and polyesters, and the plasticity of the specialized metabolism. We draw attention to the need for untargeted methods to identify the complex, multiply decorated and conjugated compounds, in order to study the functioning of the plant specialized metabolome.
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Rai, Megha, Amit Rai, Tetsuya Mori, Ryo Nakabayashi, Manami Yamamoto, Michimi Nakamura, Hideyuki Suzuki, Kazuki Saito, and Mami Yamazaki. "Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus." International Journal of Molecular Sciences 22, no. 16 (August 17, 2021): 8835. http://dx.doi.org/10.3390/ijms22168835.

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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.
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Lazcano-Ramírez, Hugo Gerardo, Roberto Gamboa-Becerra, Irving J. García-López, Ricardo A. Chávez Montes, David Díaz-Ramírez, Octavio Martínez de la Vega, José Juan Ordaz-Ortíz, et al. "Effects of the Developmental Regulator BOLITA on the Plant Metabolome." Genes 12, no. 7 (June 29, 2021): 995. http://dx.doi.org/10.3390/genes12070995.

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Transcription factors are important regulators of gene expression. They can orchestrate the activation or repression of hundreds or thousands of genes and control diverse processes in a coordinated way. This work explores the effect of a master regulator of plant development, BOLITA (BOL), in plant metabolism, with a special focus on specialized metabolism. For this, we used an Arabidopsis thaliana line in which the transcription factor activity can be induced. Fingerprinting metabolomic analyses of whole plantlets were performed at different times after induction. After 96 h, all induced replicas clustered as a single group, in contrast with all controls which did not cluster. Metabolomic analyses of shoot and root tissues enabled the putative identification of differentially accumulated metabolites in each tissue. Finally, the analysis of global gene expression in induced vs. non-induced root samples, together with enrichment analyses, allowed the identification of enriched metabolic pathways among the differentially expressed genes and accumulated metabolites after the induction. We concluded that the induction of BOL activity can modify the Arabidopsis metabolome. Future work should investigate whether its action is direct or indirect, and the implications of the metabolic changes for development regulation and bioprospection.
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Mishra, Ajay Kumar, Naganeeswaran Sudalaimuthuasari, Khaled M. Hazzouri, Esam Eldin Saeed, Iltaf Shah, and Khaled M. A. Amiri. "Tapping into Plant–Microbiome Interactions through the Lens of Multi-Omics Techniques." Cells 11, no. 20 (October 17, 2022): 3254. http://dx.doi.org/10.3390/cells11203254.

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This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
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Silva, Sónia, Maria Celeste Dias, Diana C. G. A. Pinto, and Artur M. S. Silva. "Metabolomics as a Tool to Understand Nano-Plant Interactions: The Case Study of Metal-Based Nanoparticles." Plants 12, no. 3 (January 21, 2023): 491. http://dx.doi.org/10.3390/plants12030491.

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Metabolomics is a powerful tool in diverse research areas, enabling an understanding of the response of organisms, such as plants, to external factors, their resistance and tolerance mechanisms against stressors, the biochemical changes and signals during plant development, and the role of specialized metabolites. Despite its advantages, metabolomics is still underused in areas such as nano-plant interactions. Nanoparticles (NPs) are all around us and have a great potential to improve and revolutionize the agri-food sector and modernize agriculture. They can drive precision and sustainability in agriculture as they can act as fertilizers, improve plant performance, protect or defend, mitigate environmental stresses, and/or remediate soil contaminants. Given their high applicability, an in-depth understanding of NPs’ impact on plants and their mechanistic action is crucial. Being aware that, in nano-plant interaction work, metabolomics is much less addressed than physiology, and that it is lacking a comprehensive review focusing on metabolomics, this review gathers the information available concerning the metabolomic tools used in studies focused on NP-plant interactions, highlighting the impact of metal-based NPs on plant metabolome, metabolite reconfiguration, and the reprogramming of metabolic pathways.
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Li, Dapeng, and Emmanuel Gaquerel. "Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity." Annual Review of Plant Biology 72, no. 1 (June 17, 2021): 867–91. http://dx.doi.org/10.1146/annurev-arplant-071720-114836.

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The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity.
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Perez de Souza, Leonardo, Federico Scossa, Sebastian Proost, Elena Bitocchi, Roberto Papa, Takayuki Tohge, and Alisdair R. Fernie. "Multi‐tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome." Plant Journal 97, no. 6 (January 15, 2019): 1132–53. http://dx.doi.org/10.1111/tpj.14178.

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Boutet, Stéphanie, Léa Barreda, François Perreau, Jean‐Chrisologue Totozafy, Caroline Mauve, Bertrand Gakière, Etienne Delannoy, et al. "Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa genotypes." Plant Journal 110, no. 1 (February 6, 2022): 147–65. http://dx.doi.org/10.1111/tpj.15662.

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Dissertations / Theses on the topic "Plant specialized metabolome"

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Xie, Zhengzhi. "Investigation of Plant Specialized Metabolism (Secondary Metabolism) Using Metabolomic and Proteomic Approaches." Diss., The University of Arizona, 2007. http://hdl.handle.net/10150/195218.

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Specialized metabolism (secondary metabolism) in glandular trichomes of sweet basil (Ocimum basilicum L.) and accumulation of specialized metabolites (secondary metabolites) in rhizomes of turmeric (Curcuma longa L.) was investigated using proteomic and metabolomic approaches, respectively. In an effort to further clarify the regulation of metabolism in the glandular trichomes of sweet basil, we utilized a proteomics-based approach that applied MudPIT (multidimensional protein identification technology) and GeLC-MS/MS (gel enhanced LC-MS/MS) to protein samples from isolated trichomes of four different basil lines: MC, SW, SD, and EMX-1. Phosphorylation, ubiquitination and methylation of proteins in these samples were detected using X!tandem. Significant differences in distribution of the 755 non-redundant protein entries demonstrated that the proteomes of the glandular trichomes of the four basil lines were quite distinct. Correspondence between proteomic, EST, and metabolic profiling data demonstrated that both transcriptional regulation and post-transcriptional regulation contribute to the chemical diversity. One very interesting finding was that precursors for different classes of terpenoids, including mono- and sesquiterpenoids, appear to be almost exclusively supplied by the MEP (2-C-methyl-D-erythritol 4- phosphate) pathway, but not the mevolonate pathway, in basil glandular trichomes. Our results suggest that carbon flow can be readily redirected between the phenylpropanoid and terpenoid pathways in this specific cell type. To investigate the impact of genetic, developmental and environmental factors on the accumulation of phytochemicals in rhizomes of turmeric, we performed metabolomic analysis in a 2x2x4 full factorial design experiment using GC-MS, LC-MS, and LC-PDA. Our results showed that growth stage had the largest effect on levels of the three major curcuminoids. Co-regulated metabolite modules were detected, which provided valuable information for identification of phytochemicals and investigation of their biosynthesis. Based on LC-MS/MS data, 4 new diarylheptanoids were tentatively identified in turmeric rhizomes using Tandem-MSASC, a home-made software tool that automatically recognizes spectra of unknown compounds using three approaches. Based on our metabolomic results, we proposed two new strategies, “metabolomics-guided discovery” and “correlation bioassay”, to identify bioactive constituents from plant extracts based on information provided by metabolomic investigation.
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Books on the topic "Plant specialized metabolome"

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Mewis, Inga, Marie-Theres Hauser, Titta Katariina Kotilainen, and Nadja Förster, eds. Effects of Different Light Spectra on Secondary/Specialized Metabolite Accumulation and Plant Resistance Mechanisms. Frontiers Media SA, 2021. http://dx.doi.org/10.3389/978-2-88971-705-7.

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Book chapters on the topic "Plant specialized metabolome"

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Kautsar, Satria A., Hernando G. Suarez Duran, and Marnix H. Medema. "Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH." In Methods in Molecular Biology, 173–88. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7874-8_15.

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Jeyapragash, Danaraj, Ayyappan Saravanakumar, and Mariasingarayan Yosuva. "Seagrass Metabolomics: A New Insight towards Marine Based Drug Discovery." In Metabolomics - Methodology and Applications in Medical Sciences and Life Sciences. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97875.

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Metabolomics is one of the new field of “Omics” approach and the youngest triad of system biology, which provides a broad prospective of how metabolic networks are controlled and indeed emerged as a complementary tool to functional genomics with well-established technologies for genomics, transcriptomics and proteomics. Though, metabolite profiling has been carried out for decades, owing to decisive mechanism of a molecule regulation, the importance of some metabolites in human regimen and their use as diagnostic markers is now being recognized. Plant metabolomics therefore aims to highlight the characterization of metabolite pool of a plant tissue in response to its environment. Seagrassses, a paraphyletic group of marine hydrophilous angiosperms which evolved three to four times from land plants back to the sea. Seagrasses share a number of analogous acquired metabolic adaptations owing to their convergent evolution, but their secondary metabolism varied among the four families that can be considered as true seagrasses. From a chemotaxonomic point of view, numerous specialized metabolites have often been studied in seagrasses. Hence, this chapter focus the metabolome of seagrasses in order to explore their bioactive properties and the recent advancements adopted in analytical technology platforms to study the non-targeted metabolomics of seagrasses using OMICS approach.
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