Artículos de revistas: "Plant specialized metabolome"

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Schweiger, Rabea, Eva Castells, Luca Da Sois, Jordi Martínez-Vilalta y Caroline Müller. "Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum". Cells 10, n.º 3 (13 de marzo de 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 y Emmanuel Gaquerel. "Information theory tests critical predictions of plant defense theory for specialized metabolism". Science Advances 6, n.º 24 (junio de 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 y Rebecca Dauwe. "Origin and Function of Structural Diversity in the Plant Specialized Metabolome". Plants 10, n.º 11 (6 de noviembre de 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 y Mami Yamazaki. "Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus". International Journal of Molecular Sciences 22, n.º 16 (17 de agosto de 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, n.º 7 (29 de junio de 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 y Khaled M. A. Amiri. "Tapping into Plant–Microbiome Interactions through the Lens of Multi-Omics Techniques". Cells 11, n.º 20 (17 de octubre de 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 y Artur M. S. Silva. "Metabolomics as a Tool to Understand Nano-Plant Interactions: The Case Study of Metal-Based Nanoparticles". Plants 12, n.º 3 (21 de enero de 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 y Emmanuel Gaquerel. "Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity". Annual Review of Plant Biology 72, n.º 1 (17 de junio de 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 y 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, n.º 6 (15 de enero de 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, n.º 1 (6 de febrero de 2022): 147–65. http://dx.doi.org/10.1111/tpj.15662.

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11

Zhou, Shaoqun, Karl A. Kremling, Nonoy Bandillo, Annett Richter, Ying K. Zhang, Kevin R. Ahern, Alexander B. Artyukhin et al. "Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites". Plant Cell 31, n.º 5 (28 de marzo de 2019): 937–55. http://dx.doi.org/10.1105/tpc.18.00772.

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12

Quer, Elodie, Susana Pereira, Thomas Michel, Mathieu Santonja, Thierry Gauquelin, Guillaume Simioni, Jean-Marc Ourcival et al. "Amplified Drought Alters Leaf Litter Metabolome, Slows Down Litter Decomposition, and Modifies Home Field (Dis)Advantage in Three Mediterranean Forests". Plants 11, n.º 19 (30 de septiembre de 2022): 2582. http://dx.doi.org/10.3390/plants11192582.

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In Mediterranean ecosystems, the projected rainfall reduction of up to 30% may alter plant–soil interactions, particularly litter decomposition and Home Field Advantage (HFA). We set up a litter transplant experiment in the three main forests encountered in the northern part of the Medi-terranean Basin (dominated by either Quercus ilex, Quercus pubescens, or Pinus halepensis) equipped with a rain exclusion device, allowing an increase in drought either throughout the year or concentrated in spring and summer. Senescent leaves and needles were collected under two precipitation treatments (natural and amplified drought plots) at their “home” forest and were left to decompose in the forest of origin and in other forests under both drought conditions. MS-based metabolomic analysis of litter extracts combined with multivariate data analysis enabled us to detect modifications in the composition of litter specialized metabolites, following amplified drought treatment. Amplified drought altered litter quality and metabolomes, directly slowed down litter decomposition, and induced a loss of home field (dis)advantage. No indirect effect mediated by a change in litter quality on decomposition was observed. These results may suggest major alterations of plant–soil interactions in Mediterranean forests under amplified drought conditions.

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Weed, Rebecca A., Kyryll G. Savchenko, Leandro M. Lessin, Lori M. Carris y David R. Gang. "Untargeted Metabolomic Investigation of Wheat Infected with Stinking Smut Tilletia caries". Phytopathology® 111, n.º 12 (diciembre de 2021): 2343–54. http://dx.doi.org/10.1094/phyto-09-20-0383-r.

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Tilletia caries infection of wheat (Triticum aestivum) has become an increasing problem in organic wheat agriculture throughout the world. Little is known about how this pathogen alters host metabolism to ensure a successful infection. We investigated how T. caries allocates resources from wheat for its growth over the life cycle of the pathogen. An untargeted metabolomics approach that combined gas chromatography time-of-flight mass spectrometry and ultraperformance liquid chromatography tandem mass spectrometry platforms was used to determine which primary or specialized metabolite pathways are targeted and altered during T. caries infection. We found that T. caries does not dramatically alter the global metabolome of wheat but instead alters key metabolites for its own nutrient uptake and to antagonize host defenses by reducing wheat’s sweet immunity response and other related pathways. Our results highlight metabolic characteristics needed for selecting wheat varieties that are resistant to T. caries infection for organic agriculture. In addition, several wheat metabolites were identified that could be used in developing a diagnostic tool for early detection of T. caries infection.

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Li, Dapeng, Sven Heiling, Ian T. Baldwin y Emmanuel Gaquerel. "Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory". Proceedings of the National Academy of Sciences 113, n.º 47 (7 de noviembre de 2016): E7610—E7618. http://dx.doi.org/10.1073/pnas.1610218113.

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Secondary metabolite diversity is considered an important fitness determinant for plants’ biotic and abiotic interactions in nature. This diversity can be examined in two dimensions. The first one considers metabolite diversity across plant species. A second way of looking at this diversity is by considering the tissue-specific localization of pathways underlying secondary metabolism within a plant. Although these cross-tissue metabolite variations are increasingly regarded as important readouts of tissue-level gene function and regulatory processes, they have rarely been comprehensively explored by nontargeted metabolomics. As such, important questions have remained superficially addressed. For instance, which tissues exhibit prevalent signatures of metabolic specialization? Reciprocally, which metabolites contribute most to this tissue specialization in contrast to those metabolites exhibiting housekeeping characteristics? Here, we explore tissue-level metabolic specialization in Nicotiana attenuata, an ecological model with rich secondary metabolism, by combining tissue-wide nontargeted mass spectral data acquisition, information theory analysis, and tandem MS (MS/MS) molecular networks. This analysis was conducted for two different methanolic extracts of 14 tissues and deconvoluted 895 nonredundant MS/MS spectra. Using information theory analysis, anthers were found to harbor the most specialized metabolome, and most unique metabolites of anthers and other tissues were annotated through MS/MS molecular networks. Tissue–metabolite association maps were used to predict tissue-specific gene functions. Predictions for the function of two UDP-glycosyltransferases in flavonoid metabolism were confirmed by virus-induced gene silencing. The present workflow allows biologists to amortize the vast amount of data produced by modern MS instrumentation in their quest to understand gene function.

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Blatt-Janmaat, Kaitlyn L., Steffen Neumann, Jörg Ziegler y Kristian Peters. "Host Tree and Geography Induce Metabolic Shifts in the Epiphytic Liverwort Radula complanata". Plants 12, n.º 3 (27 de enero de 2023): 571. http://dx.doi.org/10.3390/plants12030571.

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Bryophytes are prolific producers of unique, specialized metabolites that are not found in other plants. As many of these unique natural products are potentially interesting, for example, pharmacological use, variations in the production regarding ecological or environmental conditions have not often been investigated. Here, we investigate metabolic shifts in the epiphytic Radula complanata L. (Dumort) with regard to different environmental conditions and the type of phorophyte (host tree). Plant material was harvested from three different locations in Sweden, Germany, and Canada and subjected to untargeted liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) and data-dependent acquisition (DDA-MS). Using multivariate statistics, variable selection methods, in silico compound identification, and compound classification, a large amount of variation (39%) in the metabolite profiles was attributed to the type of host tree and 25% to differences in environmental conditions. We identified 55 compounds to vary significantly depending on the host tree (36 on the family level) and 23 compounds to characterize R. complanata in different environments. Taken together, we found metabolic shifts mainly in primary metabolites that were associated with the drought response to different humidity levels. The metabolic shifts were highly specific to the host tree, including mostly specialized metabolites suggesting high levels of ecological interaction. As R. complanata is a widely distributed generalist species, we found it to flexibly adapt its metabolome according to different conditions. We found metabolic composition to also mirror the constitution of the habitat, which makes it interesting for conservation measures.

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Benninghaus, Vincent Alexander, Nicole van Deenen, Boje Müller, Kai-Uwe Roelfs, Ines Lassowskat, Iris Finkemeier, Dirk Prüfer y Christian Schulze Gronover. "Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology". Journal of Experimental Botany 71, n.º 4 (19 de noviembre de 2019): 1278–93. http://dx.doi.org/10.1093/jxb/erz512.

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Abstract Taraxacum koksaghyz has been identified as one of the most promising alternative rubber crops. Its high-quality rubber is produced in the latex of laticifers, a specialized cell type that is organized in a network of elongated tubules throughout the entire plant body. In order to gain insights into the physiological role(s) of latex and hence laticifer biology, we examine the effects of barnase-induced latex RNA degradation on the metabolite and protein compositions in the roots. We established high-quality datasets that enabled precise discrimination between cellular and physiological processes in laticifers and non-laticifer cell types of roots at different vegetative stages. We identified numerous latex-specific proteins, including a perilipin-like protein that has not been studied in plants yet. The barnase-expressing plants revealed a phenotype that did not exude latex, which may provide a valuable genetic basis for future studies of plant–environment interactions concerning latex and also help to clarify the evolution and arbitrary distribution of latex throughout the plant kingdom. The overview of temporal changes in composition and protein abundance provided by our data opens the way for a deeper understanding of the molecular interactions, reactions, and network relationships that underlie the different metabolic pathways in the roots of this potential rubber crop.

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Padilla-González, Guillermo F., Mauricio Diazgranados y Fernando B. Da Costa. "Effect of the Andean Geography and Climate on the Specialized Metabolism of Its Vegetation: The Subtribe Espeletiinae (Asteraceae) as a Case Example". Metabolites 11, n.º 4 (4 de abril de 2021): 220. http://dx.doi.org/10.3390/metabo11040220.

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The Andean mountains are ‘center stage’ to some of the most spectacular examples of plant diversifications, where geographic isolation and past climatic fluctuations have played a major role. However, the influence of Andean geography and climate as drivers of metabolic variation in Andean plants is poorly elucidated. Here, we studied the influence of those factors on the metabolome of the subtribe Espeletiinae (Asteraceae) using liquid chromatography coupled to high-resolution mass spectrometry data of over two hundred samples from multiple locations. Our results demonstrate that metabolic profiles can discriminate Espeletiinae taxa at different geographic scales, revealing inter- and intraspecific metabolic variations: at the country level, segregation between Colombian and Venezuelan taxa was observed; regionally, between páramo massifs; and locally, between páramo complexes. Metabolic differences in Espeletiinae were mainly explained by geographic isolation, although differences in taxonomic genera, temperature, and elevation, were also important. Furthermore, we found that different species inhabiting the same páramo complex showed stronger chemical similarities than the same species at different locations, corroborating that geographic isolation represents the main driver of metabolic change in Espeletiinae. The current study serves as a starting point to fill in the gaps in how Andean geography and climate have shaped the metabolism of its vegetation and reveal the potential of untargeted metabolomics to study the environmental physiology of plants.

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Ramabulana, Anza-Tshilidzi, Paul A. Steenkamp, Ntakadzeni E. Madala y Ian A. Dubery. "Application of Plant Growth Regulators Modulates the Profile of Chlorogenic Acids in Cultured Bidens pilosa Cells". Plants 10, n.º 3 (25 de febrero de 2021): 437. http://dx.doi.org/10.3390/plants10030437.

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Plant cell culture offers an alternative to whole plants for the production of biologically important specialised metabolites. In cultured plant cells, manipulation by auxin and cytokinin plant growth regulators (PGRs) may lead to in vitro organogenesis and metabolome changes. In this study, six different combination ratios of 2,4-dichlorophenoxyacetic acid (2,4-D) and benzylaminopurine (BAP) were investigated with the aim to induce indirect organogenesis from Bidens pilosa callus and to investigate the associated induced changes in the metabolomes of these calli. Phenotypic appearance of the calli and total phenolic contents of hydromethanolic extracts indicated underlying biochemical differences that were investigated using untargeted metabolomics, based on ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC–qTOF–MS), combined with multivariate data analysis. The concentration and combination ratios of PGRs were shown to induce differential metabolic responses and, thus, distinct metabolomic profiles, dominated by chlorogenic acids consisting of caffeoyl- and feruloyl-derivatives of quinic acid. Although organogenesis was not achieved, the results demonstrate that exogenous application PGRs can be used to manipulate the metabolome of B. pilosa for in vitro production of specialised metabolites with purported pharmacological properties.

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Dhaou, Dounia, Virginie Baldy, Dao Van Tan, Jean-Rémi Malachin, Nicolas Pouchard, Anaïs Roux, Sylvie Dupouyet et al. "Allelopathic Potential of Mangroves from the Red River Estuary against the Rice Weed Echinochloa crus-galli and Variation in Their Leaf Metabolome". Plants 11, n.º 19 (21 de septiembre de 2022): 2464. http://dx.doi.org/10.3390/plants11192464.

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Mangroves are the only forests located at the sea–land interface in tropical and subtropical regions. They are key elements of tropical coastal ecosystems, providing numerous ecosystem services. Among them is the production of specialized metabolites by mangroves and their potential use in agriculture to limit weed growth in cultures. We explored the in vitro allelopathic potential of eight mangrove species’ aqueous leaf extracts (Avicennia marina, Kandelia obovata, Bruguiera gymnorhiza, Sonneratia apetala, Sonneratia caseolaris, Aegiceras corniculatum, Lumnitzera racemosa and Rhizophora stylosa) on the germination and growth of Echinochloa crus-galli, a weed species associated with rice, Oryza sativa. Leaf methanolic extracts of mangrove species were also studied via UHPLC-ESI/qToF to compare their metabolite fingerprints. Our results highlight that A. corniculatum and S. apetala negatively affected E. crus-galli development with a stimulating effect or no effect on O. sativa. Phytochemical investigations of A. corniculatum allowed us to putatively annotate three flavonoids and two saponins. For S. apetala, three flavonoids, a tannin and two unusual sulfated ellagic acid derivatives were found. Some of these compounds are described for the first time in these species. Overall, A. corniculatum and S. apetala leaves are proposed as promising natural alternatives against E. crus-galli and should be further assessed under field conditions.

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Raghuvanshi, Ruma, Allyssa G. Grayson, Isabella Schena, Onyebuchi Amanze, Kezia Suwintono y Robert A. Quinn. "Microbial Transformations of Organically Fermented Foods". Metabolites 9, n.º 8 (10 de agosto de 2019): 165. http://dx.doi.org/10.3390/metabo9080165.

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Fermenting food is an ancient form of preservation ingrained many in human societies around the world. Westernized diets have moved away from such practices, but even in these cultures, fermented foods are seeing a resurgent interested due to their believed health benefits. Here, we analyze the microbiome and metabolome of organically fermented vegetables, using a salt brine, which is a common ‘at-home’ method of food fermentation. We found that the natural microbial fermentation had a strong effect on the food metabolites, where all four foods (beet, carrot, peppers and radishes) changed through time, with a peak in molecular diversity after 2–3 days and a decrease in diversity during the final stages of the 4-day process. The microbiome of all foods showed a stark transition from one that resembled a soil community to one dominated by Enterobacteriaceae, such as Erwinia spp., within a single day of fermentation and increasing amounts of Lactobacillales through the fermentation process. With particular attention to plant natural products, we observed significant transformations of polyphenols, triterpenoids and anthocyanins, but the degree of this metabolism depended on the food type. Beets, radishes and peppers saw an increase in the abundance of these compounds as the fermentation proceeded, but carrots saw a decrease through time. This study showed that organically fermenting vegetables markedly changed their chemistry and microbiology but resulted in high abundance of Enterobacteriaceae which are not normally considered as probiotics. The release of beneficial plant specialized metabolites was observed, but this depended on the fermented vegetable.

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Stilo, Federico, Giulia Tredici, Carlo Bicchi, Albert Robbat, Joshua Morimoto y Chiara Cordero. "Climate and Processing Effects on Tea (Camellia sinensis L. Kuntze) Metabolome: Accurate Profiling and Fingerprinting by Comprehensive Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry". Molecules 25, n.º 10 (24 de mayo de 2020): 2447. http://dx.doi.org/10.3390/molecules25102447.

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This study applied an untargeted–targeted (UT) fingerprinting approach, based on comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOF MS), to assess the effects of rainfall and temperature (both seasonal and elevational) on the tea metabolome. By this strategy, the same compound found in multiple samples need only to be identified once, since chromatograms and mass spectral features are aligned in the data analysis process. Primary and specialized metabolites of leaves from two Chinese provinces, Yunnan (pu′erh) and Fujian (oolong), and a farm in South Carolina (USA, black tea) were studied. UT fingerprinting provided insight into plant metabolism activation/inhibition, taste and trigeminal sensations, and antioxidant properties, not easily attained by other analytical approaches. For example, pu′erh and oolong contained higher relative amounts of amino acids, organic acids, and sugars. Conversely, black tea contained less of all targeted compounds except fructose and glucose, which were more similar to oolong tea. Findings revealed compounds statistically different between spring (pre-monsoon) and summer (monsoon) in pu′erh and oolong teas as well as compounds that exhibited the greatest variability due to seasonal and elevational differences. The UT fingerprinting approach offered unique insights into how differences in growing conditions and commercial processing affect the nutritional benefits and sensory characteristics of tea beverages.

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Sekhohola-Dlamini, Lerato M., Olajide M. Keshinro, Wiya L. Masudi y A. Keith Cowan. "Elaboration of a Phytoremediation Strategy for Successful and Sustainable Rehabilitation of Disturbed and Degraded Land". Minerals 12, n.º 2 (19 de enero de 2022): 111. http://dx.doi.org/10.3390/min12020111.

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Humans are dependent upon soil which supplies food, fuel, chemicals, medicine, sequesters pollutants, purifies and conveys water, and supports the built environment. In short, we need soil, but it has little or no need of us. Agriculture, mining, urbanization and other human activities result in temporary land-use and once complete, used and degraded land should be rehabilitated and restored to minimize loss of soil carbon. It is generally accepted that the most effective strategy is phyto-remediation. Typically, phytoremediation involves re-invigoration of soil fertility, physicochemical properties, and its microbiome to facilitate establishment of appropriate climax cover vegetation. A myco-phytoremediation technology called Fungcoal was developed in South Africa to achieve these outcomes for land disturbed by coal mining. Here we outline the contemporary and expanded rationale that underpins Fungcoal, which relies on in situ bio-conversion of carbonaceous waste coal or discard, in order to explore the probable origin of humic substances (HS) and soil organic matter (SOM). To achieve this, microbial processing of low-grade coal and discard, including bio-liquefaction and bio-conversion, is examined in some detail. The significance, origin, structure, and mode of action of coal-derived humics are recounted to emphasize the dynamic equilibrium, that is, humification and the derivation of soil organic matter (SOM). The contribution of plant exudate, extracellular vesicles (EV), extra polymeric substances (EPS), and other small molecules as components of the dynamic equilibrium that sustains SOM is highlighted. Arbuscular mycorrhizal fungi (AMF), saprophytic ectomycorrhizal fungi (EMF), and plant growth promoting rhizobacteria (PGPR) are considered essential microbial biocatalysts that provide mutualistic support to sustain plant growth following soil reclamation and restoration. Finally, we posit that de novo synthesis of SOM is by specialized microbial consortia (or ‘humifiers’) which use molecular components from the root metabolome; and, that combinations of functional biocatalyst act to re-establish and maintain the soil dynamic. It is concluded that a bio-scaffold is necessary for functional phytoremediation including maintenance of the SOM dynamic and overall biogeochemistry of organic carbon in the global ecosystem

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23

Luo, Lei, Ying Wang, Lu Qiu, Xingpei Han, Yaqian Zhu, Lulu Liu, Mingwu Man, Fuguang Li, Maozhi Ren y Yadi Xing. "MYC2: A Master Switch for Plant Physiological Processes and Specialized Metabolite Synthesis". International Journal of Molecular Sciences 24, n.º 4 (9 de febrero de 2023): 3511. http://dx.doi.org/10.3390/ijms24043511.

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The jasmonic acid (JA) signaling pathway plays important roles in plant defenses, development, and the synthesis of specialized metabolites synthesis. Transcription factor MYC2 is a major regulator of the JA signaling pathway and is involved in the regulation of plant physiological processes and specialized metabolite synthesis. Based on our understanding of the mechanism underlying the regulation of specialized metabolite synthesis in plants by the transcription factor MYC2, the use of synthetic biology approaches to design MYC2-driven chassis cells for the synthesis of specialized metabolites with high medicinal value, such as paclitaxel, vincristine, and artemisinin, seems to be a promising strategy. In this review, the regulatory role of MYC2 in JA signal transduction of plants to biotic and abiotic stresses, plant growth, development and specialized metabolite synthesis is described in detail, which will provide valuable reference for the use of MYC2 molecular switches to regulate plant specialized metabolite biosynthesis.

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24

Nagel, Raimund. "Pyrethrin Biosynthesis: From a Phytohormone to Specialized Metabolite". Plant Physiology 181, n.º 3 (noviembre de 2019): 836–37. http://dx.doi.org/10.1104/pp.19.01210.

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25

Panda, Sayantan, Yana Kazachkova y Asaph Aharoni. "Catch-22 in specialized metabolism: balancing defense and growth". Journal of Experimental Botany 72, n.º 17 (22 de julio de 2021): 6027–41. http://dx.doi.org/10.1093/jxb/erab348.

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Abstract Plants are unsurpassed biochemists that synthesize a plethora of molecules in response to an ever-changing environment. The majority of these molecules, considered as specialized metabolites, effectively protect the plant against pathogens and herbivores. However, this defense most probably comes at a great expense, leading to reduction of growth (known as the ‘growth–defense trade-off’). Plants employ several strategies to reduce the high metabolic costs associated with chemical defense. Production of specialized metabolites is tightly regulated by a network of transcription factors facilitating its fine-tuning in time and space. Multifunctionality of specialized metabolites—their effective recycling system by re-using carbon, nitrogen, and sulfur, thus re-introducing them back to the primary metabolite pool—allows further cost reduction. Spatial separation of biosynthetic enzymes and their substrates, and sequestration of potentially toxic substances and conversion to less toxic metabolite forms are the plant’s solutions to avoid the detrimental effects of metabolites they produce as well as to reduce production costs. Constant fitness pressure from herbivores, pathogens, and abiotic stressors leads to honing of specialized metabolite biosynthesis reactions to be timely, efficient, and metabolically cost-effective. In this review, we assess the costs of production of specialized metabolites for chemical defense and the different plant mechanisms to reduce the cost of such metabolic activity in terms of self-toxicity and growth.

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26

Chambard, Marie, Mohamed Amine Ben Mlouka, Lun Jing, Carole Plasson, Pascal Cosette, Jérôme Leprince, Marie-Laure Follet-Gueye, Azeddine Driouich, Eric Nguema-Ona y Isabelle Boulogne. "Elicitation of Roots and AC-DC with PEP-13 Peptide Shows Differential Defense Responses in Multi-Omics". Cells 11, n.º 16 (21 de agosto de 2022): 2605. http://dx.doi.org/10.3390/cells11162605.

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The root extracellular trap (RET) has emerged as a specialized compartment consisting of root AC-DC and mucilage. However, the RET’s contribution to plant defense is still poorly understood. While the roles of polysaccharides and glycoproteins secreted by root AC-DC have started to be elucidated, how the low-molecular-weight exudates of the RET contribute to root defense is poorly known. In order to better understand the RET and its defense response, the transcriptomes, proteomes and metabolomes of roots, root AC-DC and mucilage of soybean (Glycine max (L.) Merr, var. Castetis) upon elicitation with the peptide PEP-13 were investigated. This peptide is derived from the pathogenic oomycete Phytophthora sojae. In this study, the root and the RET responses to elicitation were dissected and sequenced using transcriptional, proteomic and metabolomic approaches. The major finding is increased synthesis and secretion of specialized metabolites upon induced defense activation following PEP-13 peptide elicitation. This study provides novel findings related to the pivotal role of the root extracellular trap in root defense.

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27

Wu, Sheng, Alexander E. Wilson, Lijing Chang y Li Tian. "Exploring the Phytochemical Landscape of the Early-Diverging Flowering Plant Amborella trichopoda Baill." Molecules 24, n.º 21 (23 de octubre de 2019): 3814. http://dx.doi.org/10.3390/molecules24213814.

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Although the evolutionary significance of the early-diverging flowering plant Amborella (Amborella trichopoda Baill.) is widely recognized, its metabolic landscape, particularly specialized metabolites, is currently underexplored. In this work, we analyzed the metabolomes of Amborella tissues using liquid chromatography high-resolution electrospray ionization mass spectrometry (LC-HR-ESI-MS). By matching the mass spectra of Amborella metabolites with those of authentic phytochemical standards in the publicly accessible libraries, 63, 39, and 21 compounds were tentatively identified in leaves, stems, and roots, respectively. Free amino acids, organic acids, simple sugars, cofactors, as well as abundant glycosylated and/or methylated phenolic specialized metabolites were observed in Amborella leaves. Diverse metabolites were also detected in stems and roots, including those that were not identified in leaves. To understand the biosynthesis of specialized metabolites with glycosyl and methyl modifications, families of small molecule UDP-dependent glycosyltransferases (UGTs) and O-methyltransferases (OMTs) were identified in the Amborella genome and the InterPro database based on conserved functional domains. Of the 17 phylogenetic groups of plant UGTs (A–Q) defined to date, Amborella UGTs are absent from groups B, N, and P, but they are highly abundant in group L. Among the 25 Amborella OMTs, 7 cluster with caffeoyl-coenzyme A (CCoA) OMTs involved in lignin and phenolic metabolism, whereas 18 form a clade with plant OMTs that methylate hydroxycinnamic acids, flavonoids, or alkaloids. Overall, this first report of metabolomes and candidate metabolic genes in Amborella provides a starting point to a better understanding of specialized metabolites and biosynthetic enzymes in this basal lineage of flowering plants.

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28

Chen, Si, Jun Lin, Huihui Liu, Zhihong Gong, Xiaxia Wang, Meihong Li, Asaph Aharoni, Zhenbiao Yang y Xiaomin Yu. "Insights into Tissue-specific Specialized Metabolism in Tieguanyin Tea Cultivar by Untargeted Metabolomics". Molecules 23, n.º 7 (21 de julio de 2018): 1817. http://dx.doi.org/10.3390/molecules23071817.

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Tea plants produce extremely diverse and abundant specialized metabolites, the types and levels of which are developmentally and environmentally regulated. However, little is known about how developmental cues affect the synthesis of many of these molecules. In this study, we conducted a comparative profiling of specialized metabolites from six different tissues in a premium oolong tea cultivar, Tieguanyin, which is gaining worldwide popularity due to its uniquely rich flavors and health benefits. UPLC-QTOF MS combined with multivariate analyses tentatively identified 68 metabolites belonging to 11 metabolite classes, which exhibited sharp variations among tissues. Several metabolite classes, such as flavonoids, alkaloids, and hydroxycinnamic acid amides were detected predominantly in certain plant tissues. In particular, tricoumaroyl spermidine and dicoumaroyl putrescine were discovered as unique tea flower metabolites. This study offers novel insights into tissue-specific specialized metabolism in Tieguanyin, which provides a good reference point to explore gene-metabolite relationships in this cultivar.

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Yactayo-Chang, Jessica P., Hoang V. Tang, Jorrel Mendoza, Shawn A. Christensen y Anna K. Block. "Plant Defense Chemicals against Insect Pests". Agronomy 10, n.º 8 (8 de agosto de 2020): 1156. http://dx.doi.org/10.3390/agronomy10081156.

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Insect pests cause significant global agricultural damage and lead to major financial and environmental costs. Crops contain intrinsic defenses to protect themselves from such pests, including a wide array of specialized secondary metabolite-based defense chemicals. These chemicals can be induced upon attack (phytoalexins) or are constitutive (phytoanticipins), and can have a direct impact on the pests or be used indirectly to attract their natural enemies. They form part of a global arms race between the crops and their insect pests, with the insects developing methods of suppression, avoidance, detoxification, or even capture of their hosts defensive chemicals. Harnessing and optimizing the chemical defense capabilities of crops has the potential to aid in the continuing struggle to enhance or improve agricultural pest management. Such strategies include breeding for the restoration of defense chemicals from ancestral varieties, or cross-species transfer of defense metabolite production.

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30

Muhich, Anna Jo, Amanda Agosto-Ramos y Daniel J. Kliebenstein. "The ease and complexity of identifying and using specialized metabolites for crop engineering". Emerging Topics in Life Sciences 6, n.º 2 (18 de marzo de 2022): 153–62. http://dx.doi.org/10.1042/etls20210248.

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Plants produce a broad variety of specialized metabolites with distinct biological activities and potential applications. Despite this potential, most biosynthetic pathways governing specialized metabolite production remain largely unresolved across the plant kingdom. The rapid advancement of genetics and biochemical tools has enhanced our ability to identify plant specialized metabolic pathways. Further advancements in transgenic technology and synthetic biology approaches have extended this to a desire to design new pathways or move existing pathways into new systems to address long-running difficulties in crop systems. This includes improving abiotic and biotic stress resistance, boosting nutritional content, etc. In this review, we assess the potential and limitations for (1) identifying specialized metabolic pathways in plants with multi-omics tools and (2) using these enzymes in synthetic biology or crop engineering. The goal of these topics is to highlight areas of research that may need further investment to enhance the successful application of synthetic biology for exploiting the myriad of specialized metabolic pathways.

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31

Lockhart, Jennifer. "Chasing Scattered Genes: Identifying Specialized Metabolite Pathway Genes through Global Coexpression Analysis". Plant Cell 29, n.º 5 (13 de abril de 2017): 915. http://dx.doi.org/10.1105/tpc.17.00303.

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32

Soriano, Gabriele, Claudia Petrillo, Marco Masi, Mabrouka Bouafiane, Aminata Khelil, Angela Tuzi, Rachele Isticato, Mónica Fernández-Aparicio y Alessio Cimmino. "Specialized Metabolites from the Allelopathic Plant Retama raetam as Potential Biopesticides". Toxins 14, n.º 5 (28 de abril de 2022): 311. http://dx.doi.org/10.3390/toxins14050311.

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To cope with the rising food demand, modern agriculture practices are based on the indiscriminate use of agrochemicals. Although this strategy leads to a temporary solution, it also severely damages the environment, representing a risk to human health. A sustainable alternative to agrochemicals is the use of plant metabolites and plant-based pesticides, known to have minimal environmental impact compared to synthetic pesticides. Retama raetam is a shrub growing in Algeria’s desert areas, where it is commonly used in traditional medicine because of its antiseptic and antipyretic properties. Furthermore, its allelopathic features can be exploited to effectively control phytopathogens in the agricultural field. In this study, six compounds belonging to isoflavones and flavones subgroups have been isolated from the R. raetam dichloromethane extract and identified using spectroscopic and optical methods as alpinumisoflavone, hydroxyalpinumisoflavone, laburnetin, licoflavone C, retamasin B, and ephedroidin. Their antifungal activity was evaluated against the fungal phytopathogen Stemphylium vesicarium using a growth inhibition bioassay on PDA plates. Interestingly, the flavonoid laburnetin, the most active metabolite, displayed an inhibitory activity comparable to that exerted by the synthetic fungicide pentachloronitrobenzene, in a ten-fold lower concentration. The allelopathic activity of R. raetam metabolites against parasitic weeds was also investigated using two independent parasitic weed bioassays to discover potential activities on either suicidal stimulation or radicle growth inhibition of broomrapes. In this latter bioassay, ephedroidin strongly inhibited the growth of Orobanche cumana radicles and, therefore, can be proposed as a natural herbicide.

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33

Wong, Darren C. J., Eran Pichersky y Rod Peakall. "Many different flowers make a bouquet: Lessons from specialized metabolite diversity in plant–pollinator interactions". Current Opinion in Plant Biology 73 (junio de 2023): 102332. http://dx.doi.org/10.1016/j.pbi.2022.102332.

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34

Hamberger, Björn y Søren Bak. "Plant P450s as versatile drivers for evolution of species-specific chemical diversity". Philosophical Transactions of the Royal Society B: Biological Sciences 368, n.º 1612 (19 de febrero de 2013): 20120426. http://dx.doi.org/10.1098/rstb.2012.0426.

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The irreversible nature of reactions catalysed by P450s makes these enzymes landmarks in the evolution of plant metabolic pathways. Founding members of P450 families are often associated with general (i.e. primary) metabolic pathways, restricted to single copy or very few representatives, indicative of purifying selection. Recruitment of those and subsequent blooms into multi-member gene families generates genetic raw material for functional diversification, which is an inherent characteristic of specialized (i.e. secondary) metabolism. However, a growing number of highly specialized P450s from not only the CYP71 clan indicate substantial contribution of convergent and divergent evolution to the observed general and specialized metabolite diversity. We will discuss examples of how the genetic and functional diversification of plant P450s drives chemical diversity in light of plant evolution. Even though it is difficult to predict the function or substrate of a P450 based on sequence similarity, grouping with a family or subfamily in phylogenetic trees can indicate association with metabolism of particular classes of compounds. Examples will be given that focus on multi-member gene families of P450s involved in the metabolic routes of four classes of specialized metabolites: cyanogenic glucosides, glucosinolates, mono- to triterpenoids and phenylpropanoids.

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35

Strauch, Renee C., Elisabeth Svedin, Brian Dilkes, Clint Chapple y Xu Li. "Discovery of a novel amino acid racemase through exploration of natural variation inArabidopsis thaliana". Proceedings of the National Academy of Sciences 112, n.º 37 (31 de agosto de 2015): 11726–31. http://dx.doi.org/10.1073/pnas.1503272112.

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Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. As an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions ofArabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite–gene associations led to the identification ofN-malonyl-d-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5′-phosphate for its activity. This study thus identifies a newd-amino acid racemase gene family and advances our knowledge of plantd-amino acid metabolism that is currently largely unexplored. It also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.

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36

Buitrago-Villanueva, Ivon, Ricardo Barbosa-Cornelio y Ericsson Coy-Barrera. "Influence of the Culture System and Harvest Time on the Specialized Metabolite Composition of Rocket Salad (Eruca sativa) Leaves". Horticulturae 9, n.º 2 (9 de febrero de 2023): 235. http://dx.doi.org/10.3390/horticulturae9020235.

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Eruca sativa is a leafy vegetable widely consumed fresh in salads and recognized for the presence of bioactive compounds, such as glucosinolates (GLS) and flavonols. This plant is traditionally cultivated in soils but adapts well to soilless cultures, such as hydroponics and aquaponics. However, despite the good results in the literature on E. sativa cultivation in soilless systems, the influence of the culture systems and harvest time on the specialized metabolite-based chemical composition of E. sativa leaves is not entirely understood. Based on the above, this study aimed to evaluate the specialized metabolite composition of three different cultivation types, i.e., using soil (SCS), nutrient film technique (NFT)-based hydroponic (HCS), and aquaponic (ACS) culture systems, along three growing cycles, and collected at two commercial harvest times, i.e., 21 days after transplanting (DAT) to get early plant material, namely “baby leaf”, and 42 DAT as the traditional harvest time. The chemical composition was obtained by liquid chromatography coupled with mass spectrometry (LC-MS), and multivariate statistics supported the analysis of the whole dataset. The SCS was characterized to promote an important accumulation of two antioxidant flavonols, i.e., (kaempferol and isorhamnetin diglucopyranosides) in young leaves (21 DAT). The hydroponically-grown plants exhibited a smaller number of various compounds. The ACS-cultivated leaves accumulated indole-containing glucosinolates and a marker associated with harvest time, spirobrassinin, a cruciferous oxindoline phytoalexin. These findings constitute the first report of those compounds relevantly accumulated by the effect of soilless cultures and a starting point for further studies related to the metabolite regulation of E. sativa under hydroponics and aquaponics.

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37

Arya, Sagar S., James E. Rookes, David M. Cahill y Sangram K. Lenka. "Next-generation metabolic engineering approaches towards development of plant cell suspension cultures as specialized metabolite producing biofactories". Biotechnology Advances 45 (diciembre de 2020): 107635. http://dx.doi.org/10.1016/j.biotechadv.2020.107635.

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38

Patyra, Andrzej, Marta Katarzyna Dudek y Anna Karolina Kiss. "LC-DAD–ESI-MS/MS and NMR Analysis of Conifer Wood Specialized Metabolites". Cells 11, n.º 20 (21 de octubre de 2022): 3332. http://dx.doi.org/10.3390/cells11203332.

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Many species from the Pinaceae family have been recognized as a rich source of lignans, flavonoids, and other polyphenolics. The great common occurrence of conifers in Europe, as well as their use in the wood industry, makes both plant material and industrial waste material easily accessible and inexpensive. This is a promising prognosis for both discovery of new active compounds as well as for finding new applications for wood and its industry waste products. This study aimed to analyze and phytochemically profile 13 wood extracts of the Pinaceae family species, endemic or introduced in Polish flora, using the LC-DAD–ESI-MS/MS method and compare their respective metabolite profiles. Branch wood methanolic extracts were phytochemically profiled. Lignans, stilbenes, flavonoids, diterpenes, procyanidins, and other compounds were detected, with a considerable variety of chemical content among distinct species. Norway spruce (Picea abies (L.) H.Karst.) branch wood was the most abundant source of stilbenes, European larch (Larix decidua Mill.) mostly contained flavonoids, while silver fir (Abies alba Mill.) was rich in lignans. Furthermore, 10 lignans were isolated from the studied material. Our findings confirm that wood industry waste materials, such as conifer branches, can be a potent source of different phytochemicals, with the plant matrix being relatively simple, facilitating future isolation of target compounds.

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39

Watson, Alison A., Ana L. Winters, Sarah A. Corbet, Catherine Tiley y Robert J. Nash. "Selective Metabolism of Glycosidase Inhibitors by a Specialized Moth Feeding on Hyacinthoides non-scripta Flowers". Natural Product Communications 3, n.º 1 (enero de 2008): 1934578X0800300. http://dx.doi.org/10.1177/1934578x0800300109.

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The British moth Eana incanana (Tortricidae) has been found to selectively metabolize the glycosidase inhibitor 2 R, 3 R, 4 R, 5 R-2,5-dihydroxymethyl-3,4-dihydroxypyrrolidine (DMDP), whereas it excretes related alkaloids from Hyacinthoides non-scripta (Hyacinthaceae). Very few native animals feed on H. non-scripta, but the larvae of E. incanana are specialized herbivores feeding just on the buds and flowers destroying the ovary. DMDP is the major glucosidase inhibitor of H. non-scripta and the moth may overcome inhibition of digestive glucosidases by metabolizing the DMDP. The glucosidase enzymes of the caterpillar are inhibited by DMDP. The caterpillar excretes the other glycosidase inhibitors produced by this plant and the frass has increased concentrations of these alkaloids.

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40

Dokwal, Dhiraj, Jean-Christophe Cocuron, Ana Paula Alonso y Rebecca Dickstein. "Metabolite shift in Medicago truncatula occurs in phosphorus deprivation". Journal of Experimental Botany 73, n.º 7 (31 de diciembre de 2021): 2093–111. http://dx.doi.org/10.1093/jxb/erab559.

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Abstract Symbiotic nitrogen (N) fixation entails successful interaction between legume hosts and rhizobia that occur in specialized organs called nodules. N-fixing legumes have a higher demand for phosphorus (P) than legumes grown on mineral N. Medicago truncatula is an important model plant for characterization of effects of P deficiency at the molecular level. Hence, a study was carried out to address the alteration in metabolite levels of M. truncatula grown aeroponically and subjected to 4 weeks of P stress. First, GC-MS-based untargeted metabolomics initially revealed changes in the metabolic profile of nodules, with increased levels of amino acids and sugars and a decline in amounts of organic acids. Subsequently, LC-MS/MS was used to quantify these compounds including phosphorylated metabolites in the whole plant. Our results showed a drastic reduction in levels of organic acids and phosphorylated compounds in –P leaves, with a moderate reduction in –P roots and nodules. Additionally, sugars and amino acids were elevated in the whole plant under P deprivation. These findings provide evidence that N fixation in M. truncatula is mediated through a N feedback mechanism that in parallel is related to carbon and P metabolism.

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41

Kopsell, Dean A., Carl E. Sams y Robert C. Morrow. "Blue Wavelengths from LED Lighting Increase Nutritionally Important Metabolites in Specialty Crops". HortScience 50, n.º 9 (septiembre de 2015): 1285–88. http://dx.doi.org/10.21273/hortsci.50.9.1285.

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Light is one of the most important environmental stimuli impacting plant growth and development. Plants have evolved specialized pigment-protein complexes, commonly referred to as photoreceptors, to capture light energy to drive photosynthetic processes, as well as to respond to changes in light quality and quantity. Blue light can act as a powerful environmental signal regulating phototropisms, suppression of stem elongation, chloroplast movements, stomatal regulation, and cell membrane transport activity. An emerging application of light-emitting diode (LED) technology is for horticultural plant production in controlled environments. Work by our research group is measuring important plant responses to different wavelengths of light from LEDs. We have demonstrated positive impacts of blue wavelengths on primary and secondary metabolism in microgreen and baby leafy green brassica crops. Results show significant increases in shoot tissue pigments, glucosinolates, and essential mineral elements following exposure to higher percentages of blue wavelengths from LED lighting. The perception of energy-rich blue light by specialized plant photoreceptors appears to trigger a cascade of metabolic responses, which is supported by current research showing stimulation of primary and secondary metabolite biosynthesis following exposure to blue wavelengths. Management of the light environment may be a viable means to improve concentrations of nutritionally important primary and secondary metabolites in specialty vegetable crops.

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42

McKee, Michelle C., Sarah A. Wilson y Susan C. Roberts. "The Interface amongst Conserved and Specialized Pathways in Non-Paclitaxel and Paclitaxel Accumulating Taxus Cultures". Metabolites 11, n.º 10 (7 de octubre de 2021): 688. http://dx.doi.org/10.3390/metabo11100688.

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Plant cell cultures derived from Taxus are used to produce valuable metabolites like paclitaxel, a chemotherapeutic drug. Methyl jasmonate elicitation enhances paclitaxel accumulation, but also inhibits culture growth and increases phenylpropanoid biosynthesis, two side effects that detract from taxane accumulation. To understand the connection between all of these processes, a systems approach is applied to investigate cell-wide metabolism in Taxus. Non-paclitaxel and paclitaxel accumulating cultures were elicited over single and multi-generational periods, and subsequent changes in conserved and specialized metabolism were quantified. Methyl jasmonate typically resulted in decreased growth and increased metabolite content in paclitaxel accumulating cultures. Conversely, elicitation typically resulted in either no change or decrease in accumulation of metabolites in the non-paclitaxel accumulating cultures. In both sets of cultures, variability was seen in the response to methyl jasmonate across generations of cell growth. Consolidation of these data determined that paclitaxel accumulation and basal levels of phenolic and flavonoid compounds are indirectly correlated with aggregate size. These approaches assess alternative metabolic pathways that are linked to paclitaxel biosynthesis and provide a comprehensive strategy to both understand the relationship between conserved and specialized metabolism in plants and in the design of strategies to increase natural product yields in plant cell culture.

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Li, Guangjin, Tong Chen, Zhanquan Zhang, Boqiang Li y Shiping Tian. "Roles of Aquaporins in Plant-Pathogen Interaction". Plants 9, n.º 9 (1 de septiembre de 2020): 1134. http://dx.doi.org/10.3390/plants9091134.

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Aquaporins (AQPs) are a class of small, membrane channel proteins present in a wide range of organisms. In addition to water, AQPs can facilitate the efficient and selective flux of various small solutes involved in numerous essential processes across membranes. A growing body of evidence now shows that AQPs are important regulators of plant-pathogen interaction, which ultimately lead to either plant immunity or pathogen pathogenicity. In plants, AQPs can mediate H2O2 transport across plasma membranes (PMs) and contribute to the activation of plant defenses by inducing pathogen-associated molecular pattern (PAMP)-triggered immunity and systemic acquired resistance (SAR), followed by downstream defense reactions. This involves the activation of conserved mitogen-activated protein kinase (MAPK) signaling cascades, the production of callose, the activation of NPR1 and PR genes, as well as the opening and closing of stomata. On the other hand, pathogens utilize aquaporins to mediate reactive oxygen species (ROS) signaling and regulate their normal growth, development, secondary or specialized metabolite production and pathogenicity. This review focuses on the roles of AQPs in plant immunity, pathogenicity, and communications during plant-pathogen interaction.

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44

Rico-Chávez, Amanda Kim, Jesus Alejandro Franco, Arturo Alfonso Fernandez-Jaramillo, Luis Miguel Contreras-Medina, Ramón Gerardo Guevara-González y Quetzalcoatl Hernandez-Escobedo. "Machine Learning for Plant Stress Modeling: A Perspective towards Hormesis Management". Plants 11, n.º 7 (2 de abril de 2022): 970. http://dx.doi.org/10.3390/plants11070970.

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Plant stress is one of the most significant factors affecting plant fitness and, consequently, food production. However, plant stress may also be profitable since it behaves hormetically; at low doses, it stimulates positive traits in crops, such as the synthesis of specialized metabolites and additional stress tolerance. The controlled exposure of crops to low doses of stressors is therefore called hormesis management, and it is a promising method to increase crop productivity and quality. Nevertheless, hormesis management has severe limitations derived from the complexity of plant physiological responses to stress. Many technological advances assist plant stress science in overcoming such limitations, which results in extensive datasets originating from the multiple layers of the plant defensive response. For that reason, artificial intelligence tools, particularly Machine Learning (ML) and Deep Learning (DL), have become crucial for processing and interpreting data to accurately model plant stress responses such as genomic variation, gene and protein expression, and metabolite biosynthesis. In this review, we discuss the most recent ML and DL applications in plant stress science, focusing on their potential for improving the development of hormesis management protocols.

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45

Sugiyama, Ryosuke, Rui Li, Ayuko Kuwahara, Ryo Nakabayashi, Naoyuki Sotta, Tetsuya Mori, Takehiro Ito et al. "Retrograde sulfur flow from glucosinolates to cysteine in Arabidopsis thaliana". Proceedings of the National Academy of Sciences 118, n.º 22 (25 de mayo de 2021): e2017890118. http://dx.doi.org/10.1073/pnas.2017890118.

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Specialized (secondary) metabolic pathways in plants have long been considered one-way routes of leading primary metabolite precursors to bioactive end products. Conversely, endogenous degradation of such “end” products in plant tissues has been observed following environmental stimuli, including nutrition stress. Therefore, it is of general interest whether specialized metabolites can be reintegrated into primary metabolism to recover the invested resources, especially in the case of nitrogen- or sulfur-rich compounds. Here, we demonstrate that endogenous glucosinolates (GLs), a class of sulfur-rich plant metabolites, are exploited as a sulfur source by the reallocation of sulfur atoms to primary metabolites such as cysteine in Arabidopsis thaliana. Tracer experiments using 34S- or deuterium-labeled GLs depicted the catabolic processing of GL breakdown products in which sulfur is mobilized from the thioglucoside group in GL molecules, potentially accompanied by the release of the sulfate group. Moreover, we reveal that beta-glucosidases BGLU28 and BGLU30 are the major myrosinases that initiate sulfur reallocation by hydrolyzing particular GL species, conferring sulfur deficiency tolerance in A. thaliana, especially during early development. The results delineate the physiological function of GL as a sulfur reservoir, in addition to their well-known functions as defense chemicals. Overall, our findings demonstrate the bidirectional interaction between primary and specialized metabolism, which enhances our understanding of the underlying metabolic mechanisms via which plants adapt to their environments.

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Tralamazza, Sabina Moser, Liliana Oliveira Rocha, Ursula Oggenfuss, Benedito Corrêa y Daniel Croll. "Complex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex". Genome Biology and Evolution 11, n.º 11 (14 de octubre de 2019): 3106–22. http://dx.doi.org/10.1093/gbe/evz225.

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Abstract Fungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss, and neofunctionalization are largely unknown. We analyzed the Fusarium graminearum species complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. We de novo assembled genomes of previously uncharacterized FGSC members (two strains of F. austroamericanum, F. cortaderiae, and F. meridionale). Our analyses of 8 species of the FGSC in addition to 15 other Fusarium species identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and the Fusarium genus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.

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Castro-Moretti, Fernanda R., Irene N. Gentzel, David Mackey y Ana P. Alonso. "Metabolomics as an Emerging Tool for the Study of Plant–Pathogen Interactions". Metabolites 10, n.º 2 (29 de enero de 2020): 52. http://dx.doi.org/10.3390/metabo10020052.

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Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant–microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.

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Brown, Stephanie, Marc Clastre, Vincent Courdavault y Sarah E. O’Connor. "De novo production of the plant-derived alkaloid strictosidine in yeast". Proceedings of the National Academy of Sciences 112, n.º 11 (9 de febrero de 2015): 3205–10. http://dx.doi.org/10.1073/pnas.1423555112.

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The monoterpene indole alkaloids are a large group of plant-derived specialized metabolites, many of which have valuable pharmaceutical or biological activity. There are ∼3,000 monoterpene indole alkaloids produced by thousands of plant species in numerous families. The diverse chemical structures found in this metabolite class originate from strictosidine, which is the last common biosynthetic intermediate for all monoterpene indole alkaloid enzymatic pathways. Reconstitution of biosynthetic pathways in a heterologous host is a promising strategy for rapid and inexpensive production of complex molecules that are found in plants. Here, we demonstrate how strictosidine can be produced de novo in a Saccharomyces cerevisiae host from 14 known monoterpene indole alkaloid pathway genes, along with an additional seven genes and three gene deletions that enhance secondary metabolism. This system provides an important resource for developing the production of more complex plant-derived alkaloids, engineering of nonnatural derivatives, identification of bottlenecks in monoterpene indole alkaloid biosynthesis, and discovery of new pathway genes in a convenient yeast host.

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Ntana, Fani, Wajid W. Bhat, Sean R. Johnson, Hans J. L. Jørgensen, David B. Collinge, Birgit Jensen y Björn Hamberger. "A Sesquiterpene Synthase from the Endophytic Fungus Serendipita indica Catalyzes Formation of Viridiflorol". Biomolecules 11, n.º 6 (16 de junio de 2021): 898. http://dx.doi.org/10.3390/biom11060898.

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Interactions between plant-associated fungi and their hosts are characterized by a continuous crosstalk of chemical molecules. Specialized metabolites are often produced during these associations and play important roles in the symbiosis between the plant and the fungus, as well as in the establishment of additional interactions between the symbionts and other organisms present in the niche. Serendipita indica, a root endophytic fungus from the phylum Basidiomycota, is able to colonize a wide range of plant species, conferring many benefits to its hosts. The genome of S. indica possesses only few genes predicted to be involved in specialized metabolite biosynthesis, including a putative terpenoid synthase gene (SiTPS). In our experimental setup, SiTPS expression was upregulated when the fungus colonized tomato roots compared to its expression in fungal biomass growing on synthetic medium. Heterologous expression of SiTPS in Escherichia coli showed that the produced protein catalyzes the synthesis of a few sesquiterpenoids, with the alcohol viridiflorol being the main product. To investigate the role of SiTPS in the plant-endophyte interaction, an SiTPS-over-expressing mutant line was created and assessed for its ability to colonize tomato roots. Although overexpression of SiTPS did not lead to improved fungal colonization ability, an in vitro growth-inhibition assay showed that viridiflorol has antifungal properties. Addition of viridiflorol to the culture medium inhibited the germination of spores from a phytopathogenic fungus, indicating that SiTPS and its products could provide S. indica with a competitive advantage over other plant-associated fungi during root colonization.

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Kang, Kyo Bin, Sunmin Woo, Madeleine Ernst, Justin J. J. van der Hooft, Louis-Félix Nothias, Ricardo R. da Silva, Pieter C. Dorrestein, Sang Hyun Sung y Mina Lee. "Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow". Phytochemistry 173 (mayo de 2020): 112292. http://dx.doi.org/10.1016/j.phytochem.2020.112292.

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