Journal articles: 'Metabolomics, elicitors, secondary metabolism'

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Iula, Giusy, Begoña Miras-Moreno, Youssef Rouphael, Luigi Lucini, and Marco Trevisan. "The Complex Metabolomics Crosstalk Triggered by Four Molecular Elicitors in Tomato." Plants 11, no. 5 (March 1, 2022): 678. http://dx.doi.org/10.3390/plants11050678.

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The elicitation of plant secondary metabolism may offer interesting opportunities in the framework of sustainable approaches in plant science and in terms of their ability to prime resistance to biotic and abiotic stressors. The broad metabolic reprogramming triggered by different molecular elicitors, namely salicylate (SA), polyamines (PAs), and chitosan, was comprehensively investigated using a metabolomics approach and the tomato (Solanum lycopersicum L.) as the model crop. Six different treatments were compared: a negative control (no treatments), a second negative control treated with 1 M acetic acid (the reference for chitosan, since chitosan was solubilized in acetic acid), and four molecular elicitors, 1 mM 2,1,3-benzothiadiazole (BTH, a positive control), 10 mg/mL chitosan, 0.01 mM SA, and a 0.1 mM PA (putrescine, spermidine, and spermine). All treatments determined a slight increase in biomass, in particular following PA treatment. A broad reprogramming of secondary metabolism could be observed, including membrane lipid remodeling, phenylpropanoid antioxidants, and phytohormone crosstalk. Overall, our results suggest that PAs, SA, and BTH shared a systemic acquired resistance (SAR)-related response, whereas chitosan induced a more distinct induced systemic resistance (ISR)-like jasmonate-related response. These results pave the way towards the possible use of elicitors as a sustainable tool in plant science and agriculture by increasing crop resilience to biotic and abiotic stressors without detrimental effects on plant biomass.

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de Felício, Rafael, Patricia Ballone, Cristina Freitas Bazzano, Luiz F. G. Alves, Renata Sigrist, Gina Polo Infante, Henrique Niero, et al. "Chemical Elicitors Induce Rare Bioactive Secondary Metabolites in Deep-Sea Bacteria under Laboratory Conditions." Metabolites 11, no. 2 (February 12, 2021): 107. http://dx.doi.org/10.3390/metabo11020107.

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Bacterial genome sequencing has revealed a vast number of novel biosynthetic gene clusters (BGC) with potential to produce bioactive natural products. However, the biosynthesis of secondary metabolites by bacteria is often silenced under laboratory conditions, limiting the controlled expression of natural products. Here we describe an integrated methodology for the construction and screening of an elicited and pre-fractionated library of marine bacteria. In this pilot study, chemical elicitors were evaluated to mimic the natural environment and to induce the expression of cryptic BGCs in deep-sea bacteria. By integrating high-resolution untargeted metabolomics with cheminformatics analyses, it was possible to visualize, mine, identify and map the chemical and biological space of the elicited bacterial metabolites. The results show that elicited bacterial metabolites correspond to ~45% of the compounds produced under laboratory conditions. In addition, the elicited chemical space is novel (~70% of the elicited compounds) or concentrated in the chemical space of drugs. Fractionation of the crude extracts further evidenced minor compounds (~90% of the collection) and the detection of biological activity. This pilot work pinpoints strategies for constructing and evaluating chemically diverse bacterial natural product libraries towards the identification of novel bacterial metabolites in natural product-based drug discovery pipelines.

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Zulak, Katherine G., Aalim M. Weljie, Hans J. Vogel, and Peter J. Facchini. "Quantitative 1H NMR metabolomics reveals extensive metabolic reprogramming of primary and secondary metabolism in elicitor-treated opium poppy cell cultures." BMC Plant Biology 8, no. 1 (2008): 5. http://dx.doi.org/10.1186/1471-2229-8-5.

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Lauchli, Ryan, and Wilhelm Boland. "Indanoyl amino acid conjugates: Tunable elicitors of plant secondary metabolism." Chemical Record 3, no. 1 (January 2003): 12–21. http://dx.doi.org/10.1002/tcr.10043.

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Breitling, Rainer, Ana Ceniceros, Andris Jankevics, and Eriko Takano. "Metabolomics for Secondary Metabolite Research." Metabolites 3, no. 4 (November 11, 2013): 1076–83. http://dx.doi.org/10.3390/metabo3041076.

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Nguyen, Quoc-Thai, Maria E. Merlo, Marnix H. Medema, Andris Jankevics, Rainer Breitling, and Eriko Takano. "Metabolomics methods for the synthetic biology of secondary metabolism." FEBS Letters 586, no. 15 (February 15, 2012): 2177–83. http://dx.doi.org/10.1016/j.febslet.2012.02.008.

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Mafakheri, Saeideh, and Akbar Karami. "Integrated Metabolomics and Phytochemical Genomics Approaches for Studies on St. John’s Wort." Natural Products Journal 10, no. 3 (June 16, 2020): 188–92. http://dx.doi.org/10.2174/2210315508666180723154923.

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Metabolomics is widely applied for investigation of the correlation between metabolites and genes responsible for the synthesis of the particular sets of metabolites. In this review, we discuss metabolomics research on Hypericum perforatum (St. John’s Wort) to elucidate the overall regulation of the metabolism related to the mechanisms of natural variations and environmental stresses such as fungal infections, light stresses, and chemical elicitors. We also focus on phytochemical genomics and genomic information. St. John’s Wort is a medicinal plant with high potential of producing hypericin used for mild depression remedy, so knowledge on the biosynthetic pathway of unique metabolites is fundamental for their biotechnological commercial production. These metabolites have often complex biosynthetic pathway and it is challenging to identify all of the catalyzing enzymes. The development of metabolic systems biology could open new channels for high-speed construction and evaluation of hypotheses for cellular regulatory systems.

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Nemat Alla, M., Amira El-Falla, and Madeha Hamed. "SECONDARY METABOLISM, ENZYMATIC ANTIOXIDANTS AND ANTIBACTERIAL ACTIVITIES AS SIGNALING TO SOME STRESS ELICITORS." Journal of Plant Production 3, no. 1 (January 1, 2012): 17–31. http://dx.doi.org/10.21608/jpp.2012.84025.

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Engelberth, Jürgen, Thomas Koch, Frank Kühnemann, and Wilhelm Boland. "Channel-Forming Peptaibols Are Potent Elicitors of Plant Secondary Metabolism and Tendril Coiling." Angewandte Chemie International Edition 39, no. 10 (May 15, 2000): 1860–62. http://dx.doi.org/10.1002/(sici)1521-3773(20000515)39:10<1860::aid-anie1860>3.0.co;2-f.

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Alcalde, Miguel Angel, Edgar Perez-Matas, Ainoa Escrich, Rosa M. Cusido, Javier Palazon, and Mercedes Bonfill. "Biotic Elicitors in Adventitious and Hairy Root Cultures: A Review from 2010 to 2022." Molecules 27, no. 16 (August 17, 2022): 5253. http://dx.doi.org/10.3390/molecules27165253.

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One of the aims of plant in vitro culture is to produce secondary plant metabolites using plant cells and organ cultures, such as cell suspensions, adventitious, and hairy roots (among others). In cases where the biosynthesis of a compound in the plant is restricted to a specific organ, unorganized systems, such as plant cell cultures, are sometimes unsuitable for biosynthesis. Then, its production is based on the establishment of organ cultures such as roots or aerial shoots. To increase the production in these biotechnological systems, elicitors have been used for years as a useful tool since they activate secondary biosynthetic pathways that control the flow of carbon to obtain different plant compounds. One important biotechnological system for the production of plant secondary metabolites or phytochemicals is root culture. Plant roots have a very active metabolism and can biosynthesize a large number of secondary compounds in an exclusive way. Some of these compounds, such as tropane alkaloids, ajmalicine, ginsenosides, etc., can also be biosynthesized in undifferentiated systems, such as cell cultures. In some cases, cell differentiation and organ formation is necessary to produce the bioactive compounds. This review analyses the biotic elicitors most frequently used in adventitious and hairy root cultures from 2010 to 2022, focusing on the plant species, the target secondary metabolite, the elicitor and its concentration, and the yield/productivity of the target compounds obtained. With this overview, it may be easier to work with elicitors in in vitro root cultures and help understand why some are more effective than others.

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Stockman, Gastón, and Ricardo Boland. "Integration of Plasma Membrane and Nuclear Signaling in Elicitor Regulation of Plant Secondary Metabolism." Natural Product Communications 3, no. 8 (August 2008): 1934578X0800300. http://dx.doi.org/10.1177/1934578x0800300803.

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The plant kingdom represents a valuable source of natural products of commercial interest. These compounds, named secondary metabolites, are not essential for the survival of plants, but confer them some advantages that allow adaptation to changes in their environment. Nevertheless, yields of secondary metabolites are low for commercial purposes, so it has become important to design strategies for increasing their production. Plants manage to adapt to physical changes in their environment, defending themselves against pathogen attack or herbivore wounding. Such aggressive stimuli, also known as elicitors, initiate signaling metabolic cascades that induce accumulation of certain secondary metabolites. Progress has been recently achieved in the understanding of signaling events originating from elicitation and related transcriptional regulation. These advances will allow maneuvering expression of key enzymes implicated in biosynthetic pathways of secondary metabolites, thereby enhancing their accumulation.

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Podgórska, Beata, Marta Wielogórska-Partyka, Joanna Godzień, Julia Siemińska, Michał Ciborowski, Małgorzata Szelachowska, Adam Krętowski, and Katarzyna Siewko. "Applications of Metabolomics in Calcium Metabolism Disorders in Humans." International Journal of Molecular Sciences 23, no. 18 (September 8, 2022): 10407. http://dx.doi.org/10.3390/ijms231810407.

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The pathogenesis of the disorders of calcium metabolism is not fully understood. This review discusses the studies in which metabolomics was applied in this area. Indeed, metabolomics could play an essential role in discovering biomarkers and elucidating pathological mechanisms. Despite the limited bibliography, the present review highlights the potential of metabolomics in identifying the biomarkers of some of the most common endocrine disorders, such as primary hyperparathyroidism (PHPT), secondary hyperparathyroidism (SHPT), calcium deficiency, osteoporosis and vitamin D supplementation. Metabolites related to above-mentioned diseorders were grouped into specific classes and mapped into metabolic pathways. Furthermore, disturbed metabolic pathways can open up new directions for the in-depth exploration of the basic mechanisms of these diseases at the molecular level.

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Benincasa, Paolo, Roberto D’Amato, Beatrice Falcinelli, Elisabetta Troni, Maria Chiara Fontanella, Sarah Frusciante, Marcello Guiducci, Gian Maria Beone, Daniela Businelli, and Gianfranco Diretto. "Grain Endogenous Selenium and Moderate Salt Stress Work as Synergic Elicitors in the Enrichment of Bioactive Compounds in Maize Sprouts." Agronomy 10, no. 5 (May 20, 2020): 735. http://dx.doi.org/10.3390/agronomy10050735.

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Salt stress and selenium are known to elicitate the production of plant secondary metabolites with antioxidant properties. On this basis, maize grains obtained from mother plants fertilized or not fertilized with selenium were sprouted at different levels of salinity (0, 25, and 50 mM NaCl) to evaluate the effects on the sprout yield, inorganic and organic Se species, minerals, and secondary metabolites, as revealed by a metabolomics analysis. Grain endogenous selenium (135 mg kg−1 vs. 0.19 mg kg−1 of the non-enriched grain) and salinity affected the sprout yield and composition, with salinity having the greatest effect on secondary metabolites. Most of the Se in sprouts was in an inorganic form, despite Se-enriched grains only containing organic Se. Some synergic effect was observed between Se and salinity. The best combination was obtained with Se-enriched grains sprouted at 25 mM NaCl, since this provided a good yield (not lower than in the untreated control), while sprout shoots were enriched in selenocystine and pro-nutritional semipolar compounds with antioxidant properties. Therefore, using grains from Se-fertilized crops and sprouting them under mild salt stress might represent a promising technique for improving the nutritional value of sprouts.

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Yang, Dongfeng, Xuhong Du, Zongqi Yang, Zongsuo Liang, Zhixin Guo, and Yan Liu. "Transcriptomics, proteomics, and metabolomics to reveal mechanisms underlying plant secondary metabolism." Engineering in Life Sciences 14, no. 5 (April 17, 2014): 456–66. http://dx.doi.org/10.1002/elsc.201300075.

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Garcia-Mier, Lina, Sandra Neli Jimenez-Garcia, Ramon Gerardo Guevara-González, Ana Angelica Feregrino-Perez, Luis Miguel Contreras-Medina, and Irineo Torres-Pacheco. "Elicitor Mixtures Significantly Increase Bioactive Compounds, Antioxidant Activity, and Quality Parameters in Sweet Bell Pepper." Journal of Chemistry 2015 (2015): 1–8. http://dx.doi.org/10.1155/2015/269296.

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Sweet bell peppers are greatly appreciated for their taste, color, pungency, and aroma. Additionally, they are good sources of bioactive compounds with antioxidant activity, which can be improved by the use of elicitors. Elicitors act as metabolite-inducing factors (MIF) by mimic stress conditions. Since plants rarely experience a single stress condition one by one but are more likely to be exposed to simultaneous stresses, it is important to evaluate the effect of elicitors on plant secondary metabolism as mixtures. Jasmonic acid (JA), hydrogen peroxide (HP), and chitosan (CH) were applied to fruits and plants of bell pepper as mixtures. Bioactive compounds, antioxidant activity, and quality parameters were evaluated. The assessed elicitor cocktail leads to an increase in the variables evaluated (P≤ 0.05) when applied to mature fruits after harvest, whereas the lowest values were observed in the treatment applied to immature fruits. Therefore, the application of the elicitor cocktail to harvested mature fruits is recommended in order to improve bioactive compounds and the antioxidant activity of sweet bell peppers.

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Neill, Steven J., John R. Lenton, and Mark S. Wibberley. "Differential effects of elicitors on secondary metabolism in hairy root cultures of tobacco (Nicotiana tabacum)." Biochemical Society Transactions 22, no. 2 (May 1, 1994): 383–88. http://dx.doi.org/10.1042/bst0220383.

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Cai, Zhenzhen, Heidi Riedel, Nay Min Min Thaw Saw, Inga Mewis, Kai Reineke, Dietrich Knorr, and Iryna Smetanska. "Effects of elicitors and high hydrostatic pressure on secondary metabolism of Vitis vinifera suspension culture." Process Biochemistry 46, no. 7 (July 2011): 1411–16. http://dx.doi.org/10.1016/j.procbio.2011.03.015.

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Delfin, Jay C., Mutsumi Watanabe, and Takayuki Tohge. "Understanding the function and regulation of plant secondary metabolism through metabolomics approaches." Theoretical and Experimental Plant Physiology 31, no. 1 (November 29, 2018): 127–38. http://dx.doi.org/10.1007/s40626-018-0126-1.

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Mañero, F. Javier Gutiérrez, Elena Algar, María Soledad Martín Gómez, María Dolores Saco Sierra, and Beatriz Ramos Solano. "Elicitation of secondary metabolism inHypericum perforatumby rhizosphere bacteria and derived elicitors in seedlings and shoot cultures." Pharmaceutical Biology 50, no. 10 (August 20, 2012): 1201–9. http://dx.doi.org/10.3109/13880209.2012.664150.

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Duan, Shuyan, Yusen Wu, Ruifeng Fu, Lei Wang, Yujin Chen, Wenping Xu, Caixi Zhang, Chao Ma, Jianxin Shi, and Shiping Wang. "Comparative Metabolic Profiling of Grape Skin Tissue along Grapevine Berry Developmental Stages Reveals Systematic Influences of Root Restriction on Skin Metabolome." International Journal of Molecular Sciences 20, no. 3 (January 28, 2019): 534. http://dx.doi.org/10.3390/ijms20030534.

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This research aimed to comparatively evaluate the influences of root restriction (RR) cultivation and traditional cultivation (RC) on grape berry skin metabolomics using a non-targeted metabolomics method. Two-hundred-and-ninety-one metabolites were annotated and the kinetics analyses showed that berry skin metabolome is stage- and cultivation-dependent. Our results showed that RR influences significantly the metabolomes of berry skin tissues, particularly on secondary metabolism, and that this effect is more obvious at pre-veraison stage, which was evidenced by the early and fast metabolic shift from primary to secondary metabolism. Altogether, this study provided an insight into metabolic adaptation of berry skin to RR stress and expanded general understanding of berry development.

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Chen, Yunqiu, Michelle Unger, Ioanna Ntai, Ryan A. McClure, Jessica C. Albright, Regan J. Thomson, and Neil L. Kelleher. "Gobichelin A and B: mixed-ligandsiderophores discovered using proteomics." MedChemComm 4, no. 1 (2013): 233–38. http://dx.doi.org/10.1039/c2md20232h.

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Rivero-Montejo, Samantha de Jesus, Marcela Vargas-Hernandez, and Irineo Torres-Pacheco. "Nanoparticles as Novel Elicitors to Improve Bioactive Compounds in Plants." Agriculture 11, no. 2 (February 6, 2021): 134. http://dx.doi.org/10.3390/agriculture11020134.

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Bioactive compounds (e.g., flavonoids, phenolics acids, alkaloids and carotenoids) are commercially-valued products, due to their wide array of applications in the medical, pharmacological, cosmetic, agriculture and food industry. A strategy applied to increase or enhancing bioactive compounds production in plants is controlled elicitation. In recent years, many researchers have studied the role of nanoparticles (NPs) as a novel elicitor for the biosynthesis of bioactive compounds shown that the NPs could affect the plant’s secondary metabolism in plant and culture systems. In this sense, recent studies have highlighted the potential applications of nanotechnology in crop production by improving the nutraceutical and nutritional quality of plants. In this review, we present studies about the application of NPs to enhance the production of bioactive plant metabolites. The aforementioned studies in ex vitro as in vitro, in addition to the effect of post-harvest by NPs application.

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Liu, Xin-Guang, Xu Lu, Ji-Xin Wang, Bin Wu, Lin Lin, Hui-Ying Wang, Ru-Zhou Guo, Ping Li, and Hua Yang. "Combining paired analytical metabolomics and common garden trial to study the metabolism and gene variation of Ginkgo biloba L. cultivated varieties." RSC Advances 7, no. 87 (2017): 55309–17. http://dx.doi.org/10.1039/c7ra06229j.

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Núñez-Montero, Kattia, Damián Quezada-Solís, Zeinab G. Khalil, Robert J. Capon, Fernando D. Andreote, and Leticia Barrientos. "Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds." Biomolecules 10, no. 5 (April 27, 2020): 673. http://dx.doi.org/10.3390/biom10050673.

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Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new “-omics” comparative approaches for drug discovery.

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Wijma, Maryke, Carolina Gimiliani Lembke, Augusto Lima Diniz, Luciane Santini, Leonardo Zambotti-Villela, Pio Colepicolo, Monalisa Sampaio Carneiro, and Glaucia Mendes Souza. "Planting Season Impacts Sugarcane Stem Development, Secondary Metabolite Levels, and Natural Antisense Transcription." Cells 10, no. 12 (December 8, 2021): 3451. http://dx.doi.org/10.3390/cells10123451.

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To reduce the potentially irreversible environmental impacts caused by fossil fuels, the use of renewable energy sources must be increased on a global scale. One promising source of biomass and bioenergy is sugarcane. The study of this crop’s development in different planting seasons can aid in successfully cultivating it in global climate change scenarios. The sugarcane variety SP80-3280 was field grown under two planting seasons with different climatic conditions. A systems biology approach was taken to study the changes on physiological, morphological, agrotechnological, transcriptomics, and metabolomics levels in the leaf +1, and immature, intermediate and mature internodes. Most of the variation found within the transcriptomics and metabolomics profiles is attributed to the differences among the distinct tissues. However, the integration of both transcriptomics and metabolomics data highlighted three main metabolic categories as the principal sources of variation across tissues: amino acid metabolism, biosynthesis of secondary metabolites, and xenobiotics biodegradation and metabolism. Differences in ripening and metabolite levels mainly in leaves and mature internodes may reflect the impact of contrasting environmental conditions on sugarcane development. In general, the same metabolites are found in mature internodes from both “one-year” and “one-and-a-half-year sugarcane”, however, some metabolites (i.e., phenylpropanoids with economic value) and natural antisense transcript expression are only detected in the leaves of “one-year” sugarcane.

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Oh, Mira, SeonJu Park, Hun Kim, Gyung Ja Choi, and Seung Hyun Kim. "Application of UPLC-QTOF-MS Based Untargeted Metabolomics in Identification of Metabolites Induced in Pathogen-Infected Rice." Plants 10, no. 2 (January 22, 2021): 213. http://dx.doi.org/10.3390/plants10020213.

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Metabolomics is a useful tool for comparing metabolite changes in plants. Because of its high sensitivity, metabolomics combined with high-resolution mass spectrometry (HR-MS) is the most widely accepted metabolomics tools. In this study, we compared the metabolites of pathogen-infected rice (Oryza sativa) with control rice using an untargeted metabolomics approach. We profiled the mass features of two rice groups using a liquid chromatography quadrupole time-of-flight mass spectrometry (QTOF-MS) system. Twelve of the most differentially induced metabolites in infected rice were selected through multivariate data analysis and identified through a mass spectral database search. The role of these compounds in metabolic pathways was finally investigated using pathway analysis. Our study showed that the most frequently induced secondary metabolites are prostanoids, a subclass of eicosanoids, which are associated with plant defense metabolism against pathogen infection. Herein, we propose a new untargeted metabolomics approach for understanding plant defense system at the metabolic level.

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Meng, Li, Ruyue Zhou, Jialong Lin, Qingji Wang, Panmeng Wang, Wei Wang, Li Wang, and Zhuang Li. "Integrated Transcriptomics and Nontargeted Metabolomics Analysis Reveal Key Metabolic Pathways in Ganoderma lucidum in Response to Ethylene." Journal of Fungi 8, no. 5 (April 28, 2022): 456. http://dx.doi.org/10.3390/jof8050456.

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Ganoderic acid (GA) is an important secondary metabolite of Ganoderma lucidum with a diverse array of pharmacological properties. In this study, we found that exogenous ethylene increased the production of endogenous ethylene and ganoderic acid in G. lucidum. However, the mechanism by which ethylene is regulated remains unclear. As a result, we performed a combined transcriptomics and nontargeted metabolomics analysis to evaluate the regulatory mechanism of ethylene. A total of 4070 differentially expressed genes (1835 up-regulated and 2235 down-regulated) and 378 differentially accumulated metabolites (289 up-regulated and 89 down-regulated) were identified in all groups. The transcriptomics and nontargeted metabolomics data revealed that genes involved in the tricarboxylic acid (TCA) cycle, polyamine metabolic pathway, acetyl-CoA carboxylase (ACC) pathway, and triterpenoid metabolism were up-regulated, whereas the metabolic intermediates involved in these metabolic pathways were down-regulated. These findings imply that ethylene potentially accelerates normal glucose metabolism, hence increasing the number of intermediates available for downstream biological processes, including polyamine metabolism, ethylene synthesis pathway, and ganoderic acid biosynthesis. The findings will contribute significantly to our understanding of secondary metabolites biosynthesis in fungi.

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Iula, Giusy, Begoña Miras-Moreno, Luigi Lucini, and Marco Trevisan. "The Mycorrhiza-and Trichoderma-Mediated Elicitation of Secondary Metabolism and Modulation of Phytohormone Profile in Tomato Plants." Horticulturae 7, no. 10 (October 12, 2021): 394. http://dx.doi.org/10.3390/horticulturae7100394.

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Arbuscular mycorrhiza and Trichoderma are well-known beneficial fungi whose plant growth promotion and defense elicitation effects are known. However, the molecular and biochemical processes underlying the beneficial effects of these priming microorganisms have not been fully elucidated yet. On this basis, the present work aimed to use metabolomics to dissect comprehensively the modulation of secondary metabolism induced by mycorrhiza and Trichoderma, using tomato as a model plant. To this aim, either mycorrhiza or Trichoderma were applied to tomato roots at transplanting using a commercial formulation and then harvested once the mutualistic relationship was well established. Shoots were analyzed using an MS-based untargeted metabolomics approach, and differential metabolites identified by multivariate statistics were subjected to pathway analysis. Together with promoting plant growth, the treatments induced a broad molecular reprogramming with the phenylpropanoid biosynthetic pathway (including defense phenolics like coumarins and glycosylated anthocyanins) being strongly elicited. An accumulation of auxins, cytokinins, and jasmonate (especially after treatment with Trichoderma) could be observed concerning phytohormone profiles. Overall, the broad and distinctive effects triggered by mycorrhiza and Trichoderma in tomato secondary metabolism supported both plant growth promotion and immunity.

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Gálvez Ranilla, Lena. "The Application of Metabolomics for the Study of Cereal Corn (Zea mays L.)." Metabolites 10, no. 8 (July 23, 2020): 300. http://dx.doi.org/10.3390/metabo10080300.

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Corn (Zea mays L.) is an important cereal crop indigenous to the Americas, where its genetic biodiversity is still preserved, especially among native populations from Mesoamerica and South America. The use of metabolomics in corn has mainly focused on understanding the potential differences of corn metabolomes under different biotic and abiotic stresses or to evaluate the influence of genetic and environmental factors. The increase of diet-linked non-communicable diseases has increased the interest to optimize the content of bioactive secondary metabolites in current corn breeding programs to produce novel functional foods. This review provides perspectives on the role of metabolomics in the characterization of health-relevant metabolites in corn biodiversity and emphasizes the integration of metabolomics in breeding strategies targeting the enrichment of phenolic bioactive metabolites such as anthocyanins in corn kernels.

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Li, Dapeng, Sven Heiling, Ian T. Baldwin, and Emmanuel Gaquerel. "Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory." Proceedings of the National Academy of Sciences 113, no. 47 (November 7, 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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Mordaunt, Dylan, David Cox, and Maria Fuller. "Metabolomics to Improve the Diagnostic Efficiency of Inborn Errors of Metabolism." International Journal of Molecular Sciences 21, no. 4 (February 11, 2020): 1195. http://dx.doi.org/10.3390/ijms21041195.

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Early diagnosis of inborn errors of metabolism (IEM)—a large group of congenital disorders—is critical, given that many respond well to targeted therapy. Newborn screening programs successfully capture a proportion of patients enabling early recognition and prompt initiation of therapy. For others, the heterogeneity in clinical presentation often confuses diagnosis with more common conditions. In the absence of family history and following clinical suspicion, the laboratory diagnosis typically begins with broad screening tests to circumscribe specialised metabolite and/or enzyme assays to identify the specific IEM. Confirmation of the biochemical diagnosis is usually achieved by identifying pathogenic genetic variants that will also enable cascade testing for family members. Unsurprisingly, this diagnostic trajectory is too often a protracted and lengthy process resulting in delays in diagnosis and, importantly, therapeutic intervention for these rare conditions is also postponed. Implementation of mass spectrometry technologies coupled with the expanding field of metabolomics is changing the landscape of diagnosing IEM as numerous metabolites, as well as enzymes, can now be measured collectively on a single mass spectrometry-based platform. As the biochemical consequences of impaired metabolism continue to be elucidated, the measurement of secondary metabolites common across groups of IEM will facilitate algorithms to further increase the efficiency of diagnosis.

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Alsoufi, Abdulwadood Shakir Mahmood, Cezary Pączkowski, Marek Długosz, and Anna Szakiel. "Influence of Selected Abiotic Factors on Triterpenoid Biosynthesis and Saponin Secretion in Marigold (Calendula officinalis L.) in Vitro Hairy Root Cultures." Molecules 24, no. 16 (August 10, 2019): 2907. http://dx.doi.org/10.3390/molecules24162907.

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The aim of the study was the evaluation of the efficiency of selected abiotic elicitors, i.e., silver and cadmium ions, ultrasound, and UV-C irradiation, in the stimulation of triterpenoid biosynthesis, accumulation, and saponin secretion in Calendula officinalis hairy root cultures. Apart from the possible enhancement of triterpenoid production, the relationship between primary and secondary metabolism (represented respectively by sterols and pentacyclic triterpenes), modifications of the sterol compositional profile, and fluctuations in the total triterpenoid content were monitored in the performed experiments. The main phenomenon observed as a response to heavy metal treatment was the stimulation (up to 12-fold) of the secretion of saponins, accompanied by significant changes in sterol composition. Ultrasound stimulated the secretion of saponins (up to 11-fold); however, it exerted diverse influences on the triterpenoid content in hairy root tissue (stimulating or decreasing) depending on the duration of the exposure to the elicitor. UV-C radiation caused a slight increase in the content of both sterols and saponins in hairy root tissue, and stimulated saponin secretion up to 8.5-fold. The expected symptoms of the competition between the biosynthetic pathways of sterols and pentacyclic triterpenoids were less evident in reactions to abiotic stressors than those reported previously for biotic elicitors.

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Gómez-Cebrián, Nuria, Ayelén Rojas-Benedicto, Arturo Albors-Vaquer, Beatriz Bellosillo, Carlos Besses, Joaquín Martínez-López, Antonio Pineda-Lucena, and Leonor Puchades-Carrasco. "Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients." Cancers 13, no. 3 (January 27, 2021): 482. http://dx.doi.org/10.3390/cancers13030482.

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Most common myeloproliferative neoplasms (MPNs) include polycythemia vera (PV) and essential thrombocythemia (ET). Accurate diagnosis of these disorders remains a clinical challenge due to the lack of specific clinical or molecular features in some patients enabling their discrimination. Metabolomics has been shown to be a powerful tool for the discrimination between different hematological diseases through the analysis of patients’ serum metabolic profiles. In this pilot study, the potential of NMR-based metabolomics to characterize the serum metabolic profile of MPNs patients (PV, ET), as well as its comparison with the metabolic profile of healthy controls (HC) and secondary thrombocytosis (ST) patients, was assessed. The metabolic profile of PV and ET patients, compared with HC, exhibited higher levels of lysine and decreased levels of acetoacetic acid, glutamate, polyunsaturated fatty acids (PUFAs), scyllo-inositol and 3-hydroxyisobutyrate. Furthermore, ET patients, compared with HC and ST patients, were characterized by decreased levels of formate, N-acetyl signals from glycoproteins (NAC) and phenylalanine, while the serum profile of PV patients, compared with HC, showed increased concentrations of lactate, isoleucine, creatine and glucose, as well as lower levels of choline-containing metabolites. The overall analysis revealed significant metabolic alterations mainly associated with energy metabolism, the TCA cycle, along with amino acid and lipid metabolism. These results underscore the potential of metabolomics for identifying metabolic alterations in the serum of MPNs patients that could contribute to improving the clinical management of these diseases.

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Salzer, Liesa, and Michael Witting. "Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the Nematode." Metabolites 11, no. 5 (April 29, 2021): 284. http://dx.doi.org/10.3390/metabo11050284.

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Metabolomics and lipidomics recently gained interest in the model organism Caenorhabditis elegans (C. elegans). The fast development, easy cultivation and existing forward and reverse genetic tools make the small nematode an ideal organism for metabolic investigations in development, aging, different disease models, infection, or toxicology research. The conducted type of analysis is strongly depending on the biological question and requires different analytical approaches. Metabolomic analyses in C. elegans have been performed using nuclear magnetic resonance (NMR) spectroscopy, direct infusion mass spectrometry (DI-MS), gas-chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) or combinations of them. In this review we provide general information on the employed techniques and their advantages and disadvantages in regard to C. elegans metabolomics. Additionally, we reviewed different fields of application, e.g., longevity, starvation, aging, development or metabolism of secondary metabolites such as ascarosides or maradolipids. We also summarised applied bioinformatic tools that recently have been used for the evaluation of metabolomics or lipidomics data from C. elegans. Lastly, we curated metabolites and lipids from the reviewed literature, enabling a prototypic collection which serves as basis for a future C. elegans specific metabolome database.

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Liu, Yu, Merja Rossi, Xu Liang, Hui Zhang, Li Zou, and Choon Nam Ong. "An Integrated Metabolomics Study of Glucosinolate Metabolism in Different Brassicaceae Genera." Metabolites 10, no. 8 (July 31, 2020): 313. http://dx.doi.org/10.3390/metabo10080313.

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Glucosinolates are a group of plant secondary metabolites that can be hydrolyzed into a variety of breakdown products such as isothiocyanates, thiocyanates, and nitriles. These breakdown products can facilitate plant defense and function as attractants to natural enemies of insect pests. As part of the diet, some of these compounds have shown cancer-preventing activities, and the levels of these metabolites in the edible parts of the plants are of interest. In this study, we systematically examined variations in glucosinolates, their precursors, and their breakdown products in 12 commonly consumed vegetables of the Brassicaceae family with gas chromatography—quadrupole time-of-flight mass spectrometer (GC-Q-TOF/MS), liquid chromatography–quadrupole time-of-flight mass spectrometer (LC-Q-TOF/MS), and liquid chromatography—triple quadrupole mass spectrometer (LC-QQQ/MS), using both untargeted and targeted approaches. The findings were integrated with data from literature to provide a comprehensive map of pathways for biosynthesis of glucosinolates and isothiocyanates. The levels of precursor glucosinolates are found to correlate well with their downstream breakdown products. Further, the types and abundances of glucosinolates among different genera are significantly different, and these data allow the classification of plants based on morphological taxonomy. Further validation on three genera, which are grown underground, in damp soil, and above ground, suggests that each genus has its specific biosynthetic pathways and that there are variations in some common glucosinolate biosynthesis pathways. Our methods and results provide a good starting point for further investigations into specific aspects of glucosinolate metabolism in the Brassica vegetables.

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Feng, Ju, Nancy Isern, Sarah Burton, and Jian Hu. "Studies of Secondary Melanoma on C57BL/6J Mouse Liver Using 1H NMR Metabolomics." Metabolites 3, no. 4 (October 31, 2013): 1011–35. http://dx.doi.org/10.3390/metabo3041011.

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Martin-Rivilla, Helena, F. Javier Gutierrez-Mañero, Ana Gradillas, Miguel O. P. Navarro, Galdino Andrade, and José A. Lucas. "Identifying the Compounds of the Metabolic Elicitors of Pseudomonas fluorescens N 21.4 Responsible for Their Ability to Induce Plant Resistance." Plants 9, no. 8 (August 12, 2020): 1020. http://dx.doi.org/10.3390/plants9081020.

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In this work, the metabolic elicitors extracted from the beneficial rhizobacterium Pseudomonas fluorescens N 21.4 were sequentially fragmented by vacuum liquid chromatography to isolate, purify and identify the compounds responsible for the extraordinary capacities of this strain to induce systemic resistance and to elicit secondary defensive metabolism in diverse plant species. To check if the fractions sequentially obtained were able to increase the synthesis of isoflavones and if, therefore, they still maintained the eliciting capacity of the live strain, rapid and controlled experiments were done with soybean seeds. The optimal action concentration of the fractions was established and all of them elicited isoflavone secondary metabolism—the fractions that had been extracted with n-hexane being more effective. The purest fraction was the one with the highest eliciting capacity and was also tested in Arabidopsis thaliana seedlings to induce systemic resistance against the pathogen Pseudomonas syringae pv. tomato DC 3000. This fraction was then analyzed by UHPLC/ESI–QTOF–MS, and an alkaloid, two amino lipids, three arylalkylamines and a terpenoid were tentatively identified. These identified compounds could be part of commercial plant inoculants of biological and sustainable origin to be applied in crops, due to their potential to enhance the plant immune response and since many of them have putative antibiotic and/or antifungal potential.

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Khan, Tariq, Bilal Haider Abbasi, and Mubarak Ali Khan. "The interplay between light, plant growth regulators and elicitors on growth and secondary metabolism in cell cultures of Fagonia indica." Journal of Photochemistry and Photobiology B: Biology 185 (August 2018): 153–60. http://dx.doi.org/10.1016/j.jphotobiol.2018.06.002.

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Espinoza, Christian, Benoît Bascou, Christophe Calvayrac, and Cédric Bertrand. "Deciphering Prunus Responses to PPV Infection: A Way toward the Use of Metabolomics Approach for the Diagnostic of Sharka Disease." Metabolites 11, no. 7 (July 19, 2021): 465. http://dx.doi.org/10.3390/metabo11070465.

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Sharka disease, caused by Plum pox virus (PPV), induces several changes in Prunus. In leaf tissues, the infection may cause oxidative stress and disrupt the photosynthetic process. Moreover, several defense responses can be activated after PPV infection and have been detected at the phytohormonal, transcriptomic, proteomic, and even translatome levels. As proposed in this review, some responses may be systemic and earlier to the onset of symptoms. Nevertheless, these changes are highly dependent among species, variety, sensitivity, and tissue type. In the case of fruit tissues, PPV infection can modify the ripening process, induced by an alteration of the primary metabolism, including sugars and organic acids, and secondary metabolism, including phenolic compounds. Interestingly, metabolomics is an emerging tool to better understand Prunus–PPV interactions mainly in primary and secondary metabolisms. Moreover, through untargeted metabolomics analyses, specific and early candidate biomarkers of PPV infection can be detected. Nevertheless, these candidate biomarkers need to be validated before being selected for a diagnostic or prognosis by targeted analyses. The development of a new method for early detection of PPV-infected trees would be crucial for better management of the outbreak, especially since there is no curative treatment.

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Li, Anran, Bethany K. Okada, Paul C. Rosen, and Mohammad R. Seyedsayamdost. "Piperacillin triggers virulence factor biosynthesis via the oxidative stress response in Burkholderia thailandensis." Proceedings of the National Academy of Sciences 118, no. 26 (June 25, 2021): e2021483118. http://dx.doi.org/10.1073/pnas.2021483118.

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Natural products have been an important source of therapeutic agents and chemical tools. The recent realization that many natural product biosynthetic genes are silent or sparingly expressed during standard laboratory growth has prompted efforts to investigate their regulation and develop methods to induce their expression. Because it is difficult to intuit signals that induce a given biosynthetic locus, we recently implemented a forward chemical-genetic approach to identify such inducers. In the current work, we applied this approach to nine silent biosynthetic loci in the model bacterium Burkholderia thailandensis to systematically screen for elicitors from a library of Food and Drug Administration–approved drugs. We find that β-lactams, fluoroquinolones, antifungals, and, surprisingly, calcimimetics, phenothiazine antipsychotics, and polyaromatic antidepressants are the most effective global inducers of biosynthetic genes. Investigations into the mechanism of stimulation of the silent virulence factor malleicyprol by the β-lactam piperacillin allowed us to elucidate the underlying regulatory circuits. Low-dose piperacillin causes oxidative stress, thereby inducing redox-sensing transcriptional regulators, which activate malR, a pathway-specific positive regulator of the malleicyprol gene cluster. Malleicyprol is thus part of the OxyR and SoxR regulons in B. thailandensis, allowing the bacterium to initiate virulence in response to oxidative stress. Our work catalogs a diverse array of elicitors and a previously unknown regulatory input for secondary metabolism in B. thailandensis.

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Jiang, Ai-Liang, Yong-Nan Liu, Rui Liu, Ang Ren, Hong-Yu Ma, Lie-Bo Shu, Liang Shi, Jing Zhu, and Ming-Wen Zhao. "Integrated Proteomics and Metabolomics Analysis Provides Insights into Ganoderic Acid Biosynthesis in Response to Methyl Jasmonate in Ganoderma Lucidum." International Journal of Molecular Sciences 20, no. 24 (December 4, 2019): 6116. http://dx.doi.org/10.3390/ijms20246116.

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Ganoderma lucidum is widely recognized as a medicinal basidiomycete. It was previously reported that the plant hormone methyl jasmonate (MeJA) could induce the biosynthesis of ganoderic acids (GAs), which are the main active ingredients of G. lucidum. However, the regulatory mechanism is still unclear. In this study, integrated proteomics and metabolomics were employed on G. lucidum to globally identify differences in proteins and metabolites under MeJA treatment for 15 min (M15) and 24 h (M24). Our study successfully identified 209 differential abundance proteins (DAPs) in M15 and 202 DAPs in M24. We also identified 154 metabolites by GC–MS and 70 metabolites by LC–MS in M24 that are involved in several metabolic pathways. With an in-depth analysis, we found some DAPs and metabolites that are involved in the oxidoreduction process, secondary metabolism, energy metabolism, transcriptional and translational regulation, and protein synthesis. In particular, our results reveal that MeJA treatment leads to metabolic rearrangement that inhibited the normal glucose metabolism, energy supply, and protein synthesis of cells but promoted secondary metabolites, including GAs. In conclusion, our proteomics and metabolomics data further confirm the promoting effect of MeJA on the biosynthesis of GAs in G. lucidum and will provide a valuable resource for further investigation of the molecular mechanisms of MeJA signal response and GA biosynthesis in G. lucidum and other related species.

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Derntl, Christian, Bernhard Kluger, Christoph Bueschl, Rainer Schuhmacher, Robert L. Mach, and Astrid R. Mach-Aigner. "Transcription factor Xpp1 is a switch between primary and secondary fungal metabolism." Proceedings of the National Academy of Sciences 114, no. 4 (January 10, 2017): E560—E569. http://dx.doi.org/10.1073/pnas.1609348114.

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Fungi can produce a wide range of chemical compounds via secondary metabolism. These compounds are of major interest because of their (potential) application in medicine and biotechnology and as a potential source for new therapeutic agents and drug leads. However, under laboratory conditions, most secondary metabolism genes remain silent. This circumstance is an obstacle for the production of known metabolites and the discovery of new secondary metabolites. In this study, we describe the dual role of the transcription factor Xylanase promoter binding protein 1 (Xpp1) in the regulation of both primary and secondary metabolism of Trichoderma reesei. Xpp1 was previously described as a repressor of xylanases. Here, we provide data from an RNA-sequencing analysis suggesting that Xpp1 is an activator of primary metabolism. This finding is supported by our results from a Biolog assay determining the carbon source assimilation behavior of an xpp1 deletion strain. Furthermore, the role of Xpp1 as a repressor of secondary metabolism is shown by gene expression analyses of polyketide synthases and the determination of the secondary metabolites of xpp1 deletion and overexpression strains using an untargeted metabolomics approach. The deletion of Xpp1 resulted in the enhanced secretion of secondary metabolites in terms of diversity and quantity. Homologs of Xpp1 are found among a broad range of fungi, including the biocontrol agent Trichoderma atroviride, the plant pathogens Fusarium graminearum and Colletotrichum graminicola, the model organism Neurospora crassa, the human pathogen Sporothrix schenckii, and the ergot fungus Claviceps purpurea.

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Pastore, Chiara, Gianluca Allegro, Gabriele Valentini, Emilia Colucci, Fabrizio Battista, and Ilaria Filippetti. "Biochemical and molecular effects of yeast extract applications on anthocyanin accumulation in cv. Sangiovese." BIO Web of Conferences 13 (2019): 03005. http://dx.doi.org/10.1051/bioconf/20191303005.

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The effect of biotic and abiotic elicitors on the secondary metabolism in grapevine is gaining a lot of interest, as it has been shown that they can increase the accumulation of phenolic compounds and anthocyanins in particular. The aim of this research was to verify the biochemical and molecular effects of the application of LalVigne™ MATURE (Lallemand, St. Simon, France), 100% inactivated natural yeast (Saccharomyces cerevisiae) on the anthocyanin accumulation in potted plants of Sangiovese. In both years, LVM plants did not differ from C in technological ripening at harvest. A significant increase in anthocyanin concentration and the expression of genes involved in their biosynthesis was found in 2016 in LVM grapes compared to C, while in 2017, a year with extremely warm temperatures, the anthocyanins of C and LVM were comparable, despite a slight increase in LVM after the second treatment.

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Lu, Hengqian, Shuai Wang, Tiantian Gu, Liangyin Sun, and Yongzhong Wang. "Roles of the Fungal-Specific Lysine Biosynthetic Pathway in the Nematode-Trapping Fungus Arthrobotrys oligospora Identified through Metabolomics Analyses." Journal of Fungi 9, no. 2 (February 5, 2023): 206. http://dx.doi.org/10.3390/jof9020206.

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In higher fungi, lysine is biosynthesized via the α-aminoadipate (AAA) pathway, which differs from plants, bacteria, and lower fungi. The differences offer a unique opportunity to develop a molecular regulatory strategy for the biological control of plant parasitic nematodes, based on nematode-trapping fungi. In this study, in the nematode-trapping fungus model Arthrobotrys oligospora, we characterized the core gene in the AAA pathway, encoding α-aminoadipate reductase (Aoaar), via sequence analyses and through comparing the growth, and biochemical and global metabolic profiles of the wild-type and Aoaar knockout strains. Aoaar not only has α-aminoadipic acid reductase activity, which serves fungal L-lysine biosynthesis, but it also is a core gene of the non-ribosomal peptides biosynthetic gene cluster. Compared with WT, the growth rate, conidial production, number of predation rings formed, and nematode feeding rate of the ΔAoaar strain were decreased by 40–60%, 36%, 32%, and 52%, respectively. Amino acid metabolism, the biosynthesis of peptides and analogues, phenylpropanoid and polyketide biosynthesis, and lipid metabolism and carbon metabolism were metabolically reprogrammed in the ΔAoaar strains. The disruption of Aoaar perturbed the biosynthesis of intermediates in the lysine metabolism pathway, then reprogrammed amino acid and amino acid-related secondary metabolism, and finally, it impeded the growth and nematocidal ability of A. oligospora. This study provides an important reference for uncovering the role of amino acid-related primary and secondary metabolism in nematode capture by nematode-trapping fungi, and confirms the feasibility of Aoarr as a molecular target to regulate nematode-trapping fungi to biocontrol nematodes.

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Pei, Jiying, Shiguo Chen, Kefu Yu, Junjie Hu, Yitong Wang, Jingjing Zhang, Zhenjun Qin, et al. "Metabolomics Characterization of Scleractinia Corals with Different Life-History Strategies: A Case Study about Pocillopora meandrina and Seriatopora hystrix in the South China Sea." Metabolites 12, no. 11 (November 8, 2022): 1079. http://dx.doi.org/10.3390/metabo12111079.

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Life-history strategies play a critical role in susceptibility to environmental stresses for Scleractinia coral. Metabolomics, which is capable of determining the metabolic responses of biological systems to genetic and environmental changes, is competent for the characterization of species’ biological traits. In this study, two coral species (Pocillopora meandrina and Seriatopora hystrix in the South China Sea) with different life-history strategies (“competitive” and “weedy”) were targeted, and untargeted mass spectrometry metabolomics combined with molecular networking was applied to characterize their differential metabolic pathways. The results show that lyso-platelet activating factors (lyso-PAFs), diacylglyceryl carboxyhydroxymethylcholine (DGCC), aromatic amino acids, and sulfhydryl compounds were more enriched in P. meandrina, whereas new phospholipids, dehydrated phosphoglycerol dihydroceramide (de-PG DHC), monoacylglycerol (MAG), fatty acids (FA) (C < 18), short peptides, and guanidine compounds were more enriched in S. hystrix. The metabolic pathways involved immune response, energy metabolism, cellular membrane structure regulation, oxidative stress system, secondary metabolite synthesis, etc. While the immune system (lysoPAF) and secondary metabolite synthesis (aromatic amino acids and sulfhydryl compounds) facilitates fast growth and resistance to environmental stressors of P. meandrina, the cell membrane structure (structural lipids), energy storage (storage lipids), oxidative stress system (short peptides), and secondary metabolite synthesis (guanidine compounds) are beneficial to the survival of S. hystrix in harsh conditions. This study contributes to the understanding of the potential molecular traits underlying life-history strategies of different coral species.

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Liu, Rui-ying, Jing Deng, Xiu-Lian Lin, Ya-mei Li, Yan Lin, Bo-hou Xia, and Li-mei Lin. "Metabolomics Reveals Distinct Metabolites between Lonicera japonica and Lonicera macranthoides Based on GC-MS." Journal of Chemistry 2020 (September 21, 2020): 1–12. http://dx.doi.org/10.1155/2020/6738571.

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Lonicera japonica Thunb. (LJ) and Lonicera macranthoides Hand. -Mazz. (LM) have been widely used in Chinese medicine for thousands of years. Although the morphological characteristics of LJ and LM are quite similar, there are significant distinctions of medicinal ingredients (mainly the secondary metabolites) and clinical indications between them. However, the in-depth differences of primary metabolites have not thoroughly been studied yet. Therefore, gas chromatography-mass spectrometry- (GC-MS-) based metabolomics method combined with chemometric methods were performed to analyze the distinction in this study. The results showed that LJ and LM were obviously classified into two groups. 10 metabolites were obtained as biomarkers on account of their p values, pcorr values, and differing variable importance in projection (VIP) values. Metabolic pathway analysis showed that the galactose metabolism and starch and sucrose metabolism gathered as potential pathways caused these extraordinary differences of primary metabolites between LJ and LM. Further, we found that the differences of main medicinal ingredients between LJ and LM could be interpreted from these metabolites according to the analysis of mainly related pathways. The metabolites involved in the starch and sucrose metabolism presented upregulated in LJ, while almost all metabolites in the galactose metabolism, the TCA cycle, and the phenolic acid part of phenylpropanoid metabolism were downregulated in LJ. Therefore, the energy stored in the starch and sucrose metabolism may be saved to produce flavonoid, which could be the reason that the level of flavonoid of phenylpropanoid metabolism is higher in LJ compared to LM. Consequently, this study presented an effective tool for quality evaluation of LJ and LM and laid a foundation for further studies of the metabolic mechanisms and high-quality manufacturing of them.

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Papantoniou, Dimitra, Fredd Vergara, Alexander Weinhold, Teresa Quijano, Bekzod Khakimov, David I. Pattison, Søren Bak, Nicole M. van Dam, and Ainhoa Martínez-Medina. "Cascading Effects of Root Microbial Symbiosis on the Development and Metabolome of the Insect Herbivore Manduca sexta L." Metabolites 11, no. 11 (October 25, 2021): 731. http://dx.doi.org/10.3390/metabo11110731.

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Root mutualistic microbes can modulate the production of plant secondary metabolites affecting plant–herbivore interactions. Still, the main mechanisms underlying the impact of root mutualists on herbivore performance remain ambiguous. In particular, little is known about how changes in the plant metabolome induced by root mutualists affect the insect metabolome and post-larval development. By using bioassays with tomato plants (Solanum lycopersicum), we analyzed the impact of the arbuscular mycorrhizal fungus Rhizophagus irregularis and the growth-promoting fungus Trichoderma harzianum on the plant interaction with the specialist insect herbivore Manduca sexta. We found that root colonization by the mutualistic microbes impaired insect development, including metamorphosis. By using untargeted metabolomics, we found that root colonization by the mutualistic microbes altered the secondary metabolism of tomato shoots, leading to enhanced levels of steroidal glycoalkaloids. Untargeted metabolomics further revealed that root colonization by the mutualists affected the metabolome of the herbivore, leading to an enhanced accumulation of steroidal glycoalkaloids and altered patterns of fatty acid amides and carnitine-derived metabolites. Our results indicate that the changes in the shoot metabolome triggered by root mutualistic microbes can cascade up altering the metabolome of the insects feeding on the colonized plants, thus affecting the insect development.

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Lozada, Dennis N., Sahithi Reddy Pulicherla, and Francisco Omar Holguin. "Widely Targeted Metabolomics Reveals Metabolite Diversity in Jalapeño and Serrano Chile Peppers (Capsicum annuum L.)." Metabolites 13, no. 2 (February 16, 2023): 288. http://dx.doi.org/10.3390/metabo13020288.

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Chile peppers (Capsicum annuum L.) are good sources of vitamins and minerals that can be included in the diet to mitigate nutritional deficiencies. Metabolomics examines the metabolites involved in biological pathways to understand the genes related to complex phenotypes such as the nutritional quality traits. The current study surveys the different metabolites present in jalapeño (‘NuMex Pumpkin Spice’) and serrano (‘NuMex LotaLutein’) type chile peppers grown in New Mexico using a widely targeted metabolomics approach, with the ‘NuMex LotaLutein’ as control. A total of 1088 different metabolites were detected, where 345 metabolites were differentially expressed; 203 (59%) were downregulated and 142 (41%) were upregulated (i.e., relative metabolite content is higher in ‘NuMex Pumpkin Spice’). The upregulated metabolites comprised mostly of phenolic acids (42), flavonoids (22), and organic acids (13). Analyses of principal component (PC) and orthogonal partial least squares demonstrated clustering based on cultivars, where at least 60% of variation was attributed to the first two PCs. Pathway annotation identified 89 metabolites which are involved in metabolic pathways and the biosynthesis of secondary metabolites. Altogether, metabolomics provided insights into the different metabolites present which can be targeted for breeding and selection towards the improvement of nutritional quality traits in Capsicum.

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Li, Wen-Long, Jia-Li Hong, Jin-Qiang Lu, Shan-Gong Tong, Li Ni, Bin Liu, and Xu-Cong Lv. "Comparative Transcriptomic and Metabolomic Analyses Reveal the Regulatory Effect and Mechanism of Tea Extracts on the Biosynthesis of Monascus Pigments." Foods 11, no. 20 (October 11, 2022): 3159. http://dx.doi.org/10.3390/foods11203159.

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Monascus pigments (MPs) are natural edible pigments with high safety and strong function, which have been widely used in food and health products. In this study, different types of tea extracts (rich in polyphenols) were used to regulate the biosynthesis of MPs. The results showed that 15% ethanol extract of pu-erh tea (T11) could significantly increase MPs production in liquid fermentation of Monaco’s purpureus M3. Comparative transcriptomic and metabolomic analyses combined with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) were used to further explore the regulatory mechanism of T11 on the biosynthesis of MPs. Comparative transcriptomic analysis showed that there were 1503 differentially expressed genes (DEGs) between the Con group and the T11 group, which were mainly distributed in carbohydrate metabolism, amino acid metabolism, energy metabolism, lipid metabolism, metabolism of terpenoids and polyketides, etc. A total of 115 differential metabolites (DMs) identified by metabolomics between the Con and T11 groups were mainly enriched in glutathione metabolism, starch and sucrose metabolism, alanine, aspartic acid and glutamate metabolism and glycine, serine and threonine metabolism, etc. The results of metabolomics were basically consistent with those of gene transcriptomics, indicating that the regulatory effect of T11 on the biosynthesis of MPs is mainly achieved through affecting the primary metabolic pathway, providing sufficient energy and more biosynthetic precursors for secondary metabolism. In this study, tea extracts with low economic value and easy access were used as promoters of MPs biosynthesis, which may be conducive to the application of MPs in large-scale industrial production. At the same time, a more systematic understanding of the molecular regulatory mechanism of Monascus metabolism was obtained through multi-omics analysis.

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Tshikhudo, Phumudzo, Khayalethu Ntushelo, Fhatuwani Mudau, Bahare Salehi, Mehdi Sharifi-Rad, Natália Martins, Miquel Martorell, and Javad Sharifi-Rad. "Understanding Camellia sinensis using Omics Technologies along with Endophytic Bacteria and Environmental Roles on Metabolism: A Review." Applied Sciences 9, no. 2 (January 14, 2019): 281. http://dx.doi.org/10.3390/app9020281.

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Camellia sinensis is the most consumed beverage worldwide. It contains a wide variety of secondary metabolites, such as alkaloids, saponins, tannins, catechins, and polyphenols, generated through a condensation reaction of cinnamic acid with three malonyl-CoA groups. In addition to the metabolic processes occurring within this plant, there are also some plant-associated bacterial endophytes. These bacteria reside in the living tissues of the host plants without causing any harmful effect to them, thereby stimulating secondary metabolite production with a diverse range of biological effects. Omics technologies reveal understanding of the biological phenomena of transcriptomics, proteomics, and metabolomics. In this sense, the present review aims to provide a comprehensive review of various methods used to identify distinct plant compounds, namely transcriptomic, proteomic, and metabolomic analysis. The role of endophytic bacteria in C. sinensis metabolism, and C. sinensis antioxidant and antimicrobial effects, are also carefully highlighted.

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Journal articles on the topic 'Metabolomics, elicitors, secondary metabolism'

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