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Journal articles on the topic 'Exo-metabolome'

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Author: Grafiati

Published: 10 March 2023

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1

Vilhauer, Laura, Judith Jervis, W. Keith Ray, and Richard F. Helm. "The exo-proteome and exo-metabolome of Nostoc punctiforme (Cyanobacteria) in the presence and absence of nitrate." Archives of Microbiology 196, no. 5 (March 19, 2014): 357–67. http://dx.doi.org/10.1007/s00203-014-0974-2.

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2

Gutiérrez-Sánchez, Angélica, Javier Plasencia, Juan L. Monribot-Villanueva, José B. Rodríguez-Haas, Jose Abel López-Buenfil, Clemente J. García-Ávila, Eliel Ruiz-May, Diana Sánchez-Rangel, and José A. Guerrero-Analco. "Characterization of the Exo-Metabolome of the Emergent Phytopathogen Fusarium kuroshium sp. nov., a Causal Agent of Fusarium Dieback." Toxins 13, no. 4 (April 9, 2021): 268. http://dx.doi.org/10.3390/toxins13040268.

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Fusarium kuroshium is the fungal symbiont associated with the ambrosia beetle Euwallacea kuroshio, a plague complex that attacks avocado, among other hosts, causing a disease named Fusarium dieback (FD). However, the contribution of F. kuroshium to the establishment of this disease remains unknown. To advance the understanding of F. kuroshium pathogenicity, we profiled its exo-metabolome through metabolomics tools based on accurate mass spectrometry. We found that F. kuroshium can produce several key metabolites with phytotoxicity properties and other compounds with unknown functions. Among the metabolites identified in the fungal exo-metabolome, fusaric acid (FA) was further studied due to its phytotoxicity and relevance as a virulence factor. We tested both FA and organic extracts from F. kuroshium at various dilutions in avocado foliar tissue and found that they caused necrosis and chlorosis, resembling symptoms similar to those observed in FD. This study reports for first-time insights regarding F. kuroshium associated with its virulence, which could lead to the potential development of diagnostic and management tools of FD disease and provides a basis for understanding the interaction of F. kuroshium with its host plants.

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3

Barreto, M. C., J. C. Frisvad, T. O. Larsen, J. Mogensen, and Maria Vitória San-Romão. "Exo-metabolome of some fungal isolates growing on cork-based medium." European Food Research and Technology 232, no. 4 (January 20, 2011): 575–82. http://dx.doi.org/10.1007/s00217-011-1426-8.

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4

García, Carlos J., Verónica Alacid, Francisco A. Tomás-Barberán, Carlos García, and Pedro Palazón. "Untargeted Metabolomics to Explore the Bacteria Exo-Metabolome Related to Plant Biostimulants." Agronomy 12, no. 8 (August 16, 2022): 1926. http://dx.doi.org/10.3390/agronomy12081926.

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The control and development of plant growth promoters is a key factor for the agro-nomy industry in its economic performance. Different genera of bacteria are widely used as natural biostimulants with the aim of enhancing nutrition efficiency, abiotic stress tolerance and/or crop quality traits, regardless of their nutrients content. However, the complete exo-metabolome of the bacteria responsible for the biostimulant effect is still unknown and needs to be investigated. Three bacteria with different biostimulant effects were studied by untargeted metabolomics in order to describe the metabolites responsible for this effect. The pentose phosphate pathway, tryptophan metabolism, zeatin biosynthesis, vitamin B6 metabolism and amino acid metabolism were the highlighted pathways related to bacteria biostimulant activity. These results are related to the plant hormones biosynthesis pathway for auxins and zeatins biosynthesis. Fourteen metabolites were identified as biomarkers of the biostimulant activity. The results suggest a greater relevance of auxins than cytokinin pathways due the importance of the precursors identified. The results show a clear trend of using indole-3-pyruvate and 3-Indoleglycolaldehyde pathways to produce auxins by bacteria. The results demonstrate for the first time that 4-Pyridoxic acid, the fructosamines N-(1-Deoxy-1-fructosyl)phenylalanine and N-(1-Deoxy-1-fructosyl)isoleucine and the tripeptides diprotin A and B are metabolites related to biostimulant capabilities. This study shows how untargeted metabolomic approaches can be useful tools to investigate the bacteria exo-metabolomes related to biostimulant effects.

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5

Palama, T. L., I. Canard, G. J. P. Rautureau, C. Mirande, S. Chatellier, and B. Elena-Herrmann. "Identification of bacterial species by untargeted NMR spectroscopy of the exo-metabolome." Analyst 141, no. 15 (2016): 4558–61. http://dx.doi.org/10.1039/c6an00393a.

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6

Zhour, Houssein, Fabrice Bray, Israa Dandache, Guillaume Marti, Stéphanie Flament, Amélie Perez, Maëlle Lis, et al. "Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition." International Journal of Molecular Sciences 23, no. 23 (December 3, 2022): 15248. http://dx.doi.org/10.3390/ijms232315248.

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Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.

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7

Jung, Eun Sung, Hye Min Park, Seung Min Hyun, Jong Cheol Shon, Digar Singh, Kwang-Hyeon Liu, Tae Woong Whon, Jin-Woo Bae, Jae Sung Hwang, and Choong Hwan Lee. "The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure." PLOS ONE 12, no. 11 (November 8, 2017): e0187154. http://dx.doi.org/10.1371/journal.pone.0187154.

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8

Petitgonnet, Clément, Géraldine L. Klein, Chloé Roullier-Gall, Philippe Schmitt-Kopplin, Beatriz Quintanilla-Casas, Stefania Vichi, Diane Julien-David, and Hervé Alexandre. "Influence of cell-cell contact between L. thermotolerans and S. cerevisiae on yeast interactions and the exo-metabolome." Food Microbiology 83 (October 2019): 122–33. http://dx.doi.org/10.1016/j.fm.2019.05.005.

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9

Romano, Stefano, Thorsten Dittmar, Vladimir Bondarev, Ralf J. M. Weber, Mark R. Viant, and Heide N. Schulz-Vogt. "Exo-Metabolome of Pseudovibrio sp. FO-BEG1 Analyzed by Ultra-High Resolution Mass Spectrometry and the Effect of Phosphate Limitation." PLoS ONE 9, no. 5 (May 2, 2014): e96038. http://dx.doi.org/10.1371/journal.pone.0096038.

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10

Ileri, N., and P. Calik. "Effects of pH Strategy on endo- and exo-Metabolome Profiles and Sodium Potassium Hydrogen Ports of β-Lactamase-Producing Bacillus licheniformis." Biotechnology Progress 22, no. 2 (April 7, 2006): 411–19. http://dx.doi.org/10.1021/bp050373+.

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11

Cabezas, Ricardo, Cynthia Martin-Jiménez, Martha Zuluaga, Andrés Pinzón, George E. Barreto, and Janneth González. "Integrated Metabolomics and Lipidomics Reveal High Accumulation of Glycerophospholipids in Human Astrocytes under the Lipotoxic Effect of Palmitic Acid and Tibolone Protection." International Journal of Molecular Sciences 23, no. 5 (February 23, 2022): 2474. http://dx.doi.org/10.3390/ijms23052474.

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Lipotoxicity is a metabolic condition resulting from the accumulation of free fatty acids in non-adipose tissues which involves a series of pathological responses triggered after chronic exposure to high levels of fatty acids, severely detrimental to cellular homeostasis and viability. In brain, lipotoxicity affects both neurons and other cell types, notably astrocytes, leading to neurodegenerative processes, such as Alzheimer (AD) and Parkinson diseases (PD). In this study, we performed for the first time, a whole lipidomic characterization of Normal Human Astrocytes cultures exposed to toxic concentrations of palmitic acid and the protective compound tibolone, to establish and identify the set of potential metabolites that are modulated under these experimental treatments. The study covered 3843 features involved in the exo- and endo-metabolome extracts obtained from astrocytes with the mentioned treatments. Through multivariate statistical analysis such as PCA (principal component analysis), partial least squares (PLS-DA), clustering analysis, and machine learning enrichment analysis, it was possible to determine the specific metabolites that were affected by palmitic acid insult, such as phosphoethanolamines, phosphoserines phosphocholines and glycerophosphocholines, with their respective metabolic pathways impact. Moreover, our results suggest the importance of tibolone in the generation of neuroprotective metabolites by astrocytes and may be relevant to the development of neurodegenerative processes.

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12

Rossouw, Debra, Tormod Næs, and Florian F. Bauer. "Linking gene regulation and the exo-metabolome: A comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast." BMC Genomics 9, no. 1 (2008): 530. http://dx.doi.org/10.1186/1471-2164-9-530.

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13

Piampiano, Elisa, Francesco Pini, Natascia Biondi, Carlos J. Garcia, Francesca Decorosi, Francisco A. Tomàs-Barberàn, Luciana Giovannetti, and Carlo Viti. "Tetraselmis suecica F&M-M33 phycosphere: associated bacteria and exo-metabolome characterisation." European Journal of Phycology, June 17, 2020, 1–11. http://dx.doi.org/10.1080/09670262.2020.1765024.

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14

Mashabela, Manamele D., Fidele Tugizimana, Paul A. Steenkamp, Lizelle A. Piater, Ian A. Dubery, and Msizi I. Mhlongo. "Untargeted metabolite profiling to elucidate rhizosphere and leaf metabolome changes of wheat cultivars (Triticum aestivum L.) treated with the plant growth-promoting rhizobacteria Paenibacillus alvei (T22) and Bacillus subtilis." Frontiers in Microbiology 13 (August 25, 2022). http://dx.doi.org/10.3389/fmicb.2022.971836.

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The rhizosphere is a highly complex and biochemically diverse environment that facilitates plant–microbe and microbe–microbe interactions, and this region is found between plant roots and the bulk soil. Several studies have reported plant root exudation and metabolite secretion by rhizosphere-inhabiting microbes, suggesting that these metabolites play a vital role in plant–microbe interactions. However, the biochemical constellation of the rhizosphere soil is yet to be fully elucidated and thus remains extremely elusive. In this regard, the effects of plant growth-promoting rhizobacteria (PGPR)–plant interactions on the rhizosphere chemistry and above ground tissues are not fully understood. The current study applies an untargeted metabolomics approach to profile the rhizosphere exo-metabolome of wheat cultivars generated from seed inoculated (bio-primed) with Paenibacillus (T22) and Bacillus subtilis strains and to elucidate the effects of PGPR treatment on the metabolism of above-ground tissues. Chemometrics and molecular networking tools were used to process, mine and interpret the acquired mass spectrometry (MS) data. Global metabolome profiling of the rhizosphere soil of PGPR-bio-primed plants revealed differential accumulation of compounds from several classes of metabolites including phenylpropanoids, organic acids, lipids, organoheterocyclic compounds, and benzenoids. Of these, some have been reported to function in plant–microbe interactions, chemotaxis, biocontrol, and plant growth promotion. Metabolic perturbations associated with the primary and secondary metabolism were observed from the profiled leaf tissue of PGPR-bio-primed plants, suggesting a distal metabolic reprograming induced by PGPR seed bio-priming. These observations gave insights into the hypothetical framework which suggests that PGPR seed bio-priming can induce metabolic changes in plants leading to induced systemic response for adaptation to biotic and abiotic stress. Thus, this study contributes knowledge to ongoing efforts to decipher the rhizosphere metabolome and mechanistic nature of biochemical plant–microbe interactions, which could lead to metabolome engineering strategies for improved plant growth, priming for defense and sustainable agriculture.

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15

Varsha, Kontham Kulangara, Mitzi Nagarkatti, and Prakash Nagarkatti. "Role of Gut Microbiota in Cannabinoid-Mediated Suppression of Inflammation." Advances in Drug and Alcohol Research 2 (July 14, 2022). http://dx.doi.org/10.3389/adar.2022.10550.

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Cannabinoids and the endocannabinoid system have been well established to play a crucial role in the regulation of the immune response. Also, emerging data from numerous investigations unravel the imperative role of gut microbiota and their metabolites in the maintenance of immune homeostasis and gut barrier integrity. In this review, we concisely report the immunosuppressive mechanisms triggered by cannabinoids, and how they are closely associated with the alterations in the gut microbiome and metabolome following exposure to endogenous or exogenous cannabinoids. We discuss how cannabinoid-mediated induction of microbial secondary bile acids, short chain fatty acids, and indole metabolites, produced in the gut, can suppress inflammation even in distal organs. While clearly, more clinical studies are necessary to establish the cross talk between exo- or endocannabinoid system with the gut microbiome and the immune system, the current evidence opens a new avenue of cannabinoid-gut-microbiota-based therapeutics to regulate immunological disorders.

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16

Gupta, Rachit, Kathy Y. Rhee, Sarah D. Beagle, Ravi Chawla, Nicolas Perdomo, Steve W. Lockless, and Pushkar P. Lele. "Indole modulates cooperative protein-protein interactions in the flagellar motor." PNAS Nexus, April 30, 2022. http://dx.doi.org/10.1093/pnasnexus/pgac035.

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Abstract Indole is a major component of the bacterial exo-metabolome, and the mechanisms for its wide-ranging effects on bacterial physiology are biomedically significant although they remain poorly understood. Here, we determined how indole modulates the functions of a widely-conserved motility apparatus, the bacterial flagellum. Our experiments in Escherichia coli revealed that indole influences the rotation rates and reversals in the flagellum's direction of rotation via multiple mechanisms. At concentrations higher than 1 mM, indole decreased the membrane potential to dissipate the power available for the rotation of the motor that operates the flagellum. Below 1 mM, indole did not dissipate the membrane potential. Instead, experiments and modeling indicated that indole weakens cooperative protein interactions within the flagellar complexes to inhibit motility. The metabolite also induced reversals in the rotational direction of the motor to promote a weak chemotactic response, even when the chemotaxis response regulator, CheY, was lacking. Experiments further revealed that Indole does not require the transporter Mtr to cross the membrane and influence motor functions. Based on these findings, we propose that indole modulates intra- and inter-protein interactions in the cell to influence several physiological functions.

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