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plant metabolomics

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https://www.readbyqxmd.com/read/27917166/temporal-metagenomic-and-metabolomic-characterization-of-fresh-perennial-ryegrass-degradation-by-rumen-bacteria
#1
Olga L Mayorga, Alison H Kingston-Smith, Eun J Kim, Gordon G Allison, Toby J Wilkinson, Matthew J Hegarty, Michael K Theodorou, Charles J Newbold, Sharon A Huws
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27916552/plenty-is-no-plague-streptomyces-symbiosis-with-crops
#2
REVIEW
Thomas Rey, Bernard Dumas
Streptomyces spp. constitute a major clade of the phylum Actinobacteria. These Gram-positive, filamentous prokaryotes are ubiquitous in soils and marine sediments, and are commonly found in the rhizosphere or inside plant roots. Plant-interacting Streptomyces have received limited attention, in contrast to Streptomyces spp. extensively investigated for decades in medicine given their rich potential for secondary metabolite biosynthesis. Recent genomic, metabolomic, and biotechnological advances have produced key insights into Streptomyces spp...
November 5, 2016: Trends in Plant Science
https://www.readbyqxmd.com/read/27903807/concerted-changes-in-the-phosphoproteome-and-metabolome-under-different-co2-o2-gaseous-conditions-in-arabidopsis-rosettes
#3
Cyril Abadie, Samuel Mainguet, Marlène Davanture, Michael Hodges, Michel Zivy, Guillaume Tcherkez
Considerable efforts are currently devoted to understanding the regulation of primary carbon metabolism in plant leaves, which is known to change dramatically with environmental conditions, e.g. during light/dark transitions. Protein phosphorylation is believed to be a key factor in such a metabolic control. In fact, some studies have suggested modifications in the phosphorylation status of key enzymes in the dark compared with the light, or when photosynthesis varies. However, a general view of the phosphoproteome and reciprocal alterations in both the phosphoproteome and metabolome under a wide spectrum of CO2 and O2 conditions so as to vary both gross photosynthesis and photorespiration is currently lacking...
July 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/27895649/-omics-and-plant-responses-to-botrytis-cinerea
#4
REVIEW
Synan F AbuQamar, Khaled Moustafa, Lam-Son P Tran
Botrytis cinerea is a dangerous plant pathogenic fungus with wide host ranges. This aggressive pathogen uses multiple weapons to invade and cause serious damages on its host plants. The continuing efforts of how to solve the "puzzle" of the multigenic nature of B. cinerea's pathogenesis and plant defense mechanisms against the disease caused by this mold, the integration of omic approaches, including genomics, transcriptomics, proteomics and metabolomics, along with functional analysis could be a potential solution...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27894005/uplc-qtof-analysis-reveals-metabolomic-changes-in-the-flag-leaf-of-wheat-triticum-aestivum-l-under-low-nitrogen-stress
#5
Yang Zhang, Xin-Ming Ma, Xiao-Chun Wang, Ji-Hong Liu, Bing-Yan Huang, Xiao-Yang Guo, Shu-Ping Xiong, Gui-Xiao La
Wheat is one of the most important grain crop plants worldwide. Nitrogen (N) is an essential macronutrient for the growth and development of wheat and exerts a marked influence on its metabolites. To investigate the influence of low nitrogen stress on various metabolites of the flag leaf of wheat (Triticum aestivum L.), a metabolomic analysis of two wheat cultivars under different induced nitrogen levels was conducted during two important growth periods based on large-scale untargeted metabolomic analysis using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF)...
November 18, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27892480/metabolic-response-induced-by-parasitic-plant-fungus-interactions-hinder-amino-sugar-and-nucleotide-sugar-metabolism-in-the-host
#6
Dong-Kyu Lee, Soohyun Ahn, Hae Yoon Cho, Hye Young Yun, Jeong Hill Park, Johan Lim, Jeongmi Lee, Sung Won Kwon
Infestation by the biotrophic pathogen Gymnosporangium asiaticum can be devastating for plant of the family Rosaceae. However, the phytopathology of this process has not been thoroughly elucidated. Using a metabolomics approach, we discovered the intrinsic activities that induce disease symptoms after fungal invasion in terms of microbe-induced metabolic responses. Through metabolic pathway enrichment and mapping, we found that the host altered its metabolite levels, resulting in accumulation of tetrose and pentose sugar alcohols, in response to this fungus...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27889524/early-responses-of-mature-arabidopsis-thaliana-plants-to-reduced-water-potential-in-the-agar-based-polyethylene-glycol-infusion-drought-model
#7
Andrej Frolov, Tatiana Bilova, Gagan Paudel, Robert Berger, Gerd U Balcke, Claudia Birkemeyer, Ludger A Wessjohann
Drought is one of the most important environmental stressors resulting in increasing losses of crop plant productivity all over the world. Therefore, development of new approaches to increase the stress tolerance of crop plants is strongly desired. This requires precise and adequate modeling of drought stress. As this type of stress manifests itself as a steady decrease in the substrate water potential (ψw), agar plates infused with polyethylene glycol (PEG) are the perfect experimental tool: they are easy in preparation and provide a constantly reduced ψw, which is not possible in soil models...
November 10, 2016: Journal of Plant Physiology
https://www.readbyqxmd.com/read/27889428/spectroscopic-and-e-tongue-evaluation-of-medicinal-plants-a-taste-of-how-rasa-can-be-studied
#8
Rama Jayasundar, Somenath Ghatak
BACKGROUND: The use of medicinal plants in Ayurveda is based on rasa, generally taken to represent taste as a sensory perception. This chemosensory parameter plays an important role in Ayurvedic pharmacology. OBJECTIVE: The aim is to explore the use of structuro-functional information deduced from analytical techniques for the rasa-based classification of medicinal plants in Ayurveda. MATERIALS AND METHODS: Methods of differential sensing and spectroscopic metabolomics have been used in select medicinal plants from three different taste categories (sweet, pungent and multiple taste): Tribulus terrestris, Vitis vinifera and Glycyrrhiza glabra from sweet category; Piper longum, Cuminum cyminum and Capsicum annum from pungent group; Emblica officinalis with five tastes...
November 23, 2016: Journal of Ayurveda and Integrative Medicine
https://www.readbyqxmd.com/read/27885260/nitric-oxide-triggers-a-transient-metabolic-reprogramming-in-arabidopsis
#9
José León, Álvaro Costa, Mari-Cruz Castillo
Nitric oxide (NO) regulates plant growth and development as well as responses to stress that enhanced its endogenous production. Arabidopsis plants exposed to a pulse of exogenous NO gas were used for untargeted global metabolomic analyses thus allowing the identification of metabolic processes affected by NO. At early time points after treatment, NO scavenged superoxide anion and induced the nitration and the S-nitrosylation of proteins. These events preceded an extensive though transient metabolic reprogramming at 6 h after NO treatment, which included enhanced levels of polyamines, lipid catabolism and accumulation of phospholipids, chlorophyll breakdown, protein and nucleic acid turnover and increased content of sugars...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27883952/recent-applications-of-metabolomics-to-advance-microbial-biofuel-production
#10
REVIEW
Julia I Martien, Daniel Amador-Noguez
Biofuel production from plant biomass is a promising source of renewable energy [1]. However, efficient biofuel production involves the complex task of engineering high-performance microorganisms, which requires detailed knowledge of metabolic function and regulation. This review highlights the potential of mass-spectrometry-based metabolomic analysis to guide rational engineering of biofuel-producing microbes. We discuss recent studies that apply knowledge gained from metabolomic analyses to increase the productivity of engineered pathways, characterize the metabolism of emerging biofuel producers, generate novel bioproducts, enable utilization of lignocellulosic feedstock, and improve the stress tolerance of biofuel producers...
November 21, 2016: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/27883040/effects-of-meja-on-arabidopsis-metabolome-under-endogenous-ja-deficiency
#11
Jingjing Cao, Mengya Li, Jian Chen, Pei Liu, Zhen Li
Jasmonates (JAs) play important roles in plant growth, development and defense. Comprehensive metabolomics profiling of plants under JA treatment provides insights into the interaction and regulation network of plant hormones. Here we applied high resolution mass spectrometry based metabolomics approach on Arabidopsis wild type and JA synthesis deficiency mutant opr3. The effects of exogenous MeJA treatment on the metabolites of opr3 were investigated. More than 10000 ion signals were detected and more than 2000 signals showed significant variation in different genotypes and treatment groups...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27880018/drought-related-secondary-metabolites-of-barley-hordeum-vulgare-l-leaves-and-their-mqtls
#12
Anna Piasecka, Aneta Sawikowska, Anetta Kuczyńska, Piotr Ogrodowicz, Krzysztof Mikołajczak, Karolina Krystkowiak, Kornelia Gudyś, Justyna Guzy-Wróbelska, Paweł Krajewski, Piotr Kachlicki
Determination of the role of plant secondary metabolites in stress conditions is problematic due to diversity of their structures and complexity of interdependence with different biological pathways. Correlation of the metabolomic data with the genetic background provides essential information on the features of metabolites. LC-MS analysis of leaf metabolites from 100 barley recombinant inbred lines (RILs) revealed that 98 traits among 135 detected phenolic and terpenoid compounds significantly changed the level as a result of drought stress...
November 23, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27877182/insights-from-the-cold-transcriptome-and-metabolome-of-dendrobium-officinale-global-reprogramming-of-metabolic-and-gene-regulation-networks-during-cold-acclimation
#13
Zhi-Gang Wu, Wu Jiang, Song-Lin Chen, Nitin Mantri, Zheng-Ming Tao, Cheng-Xi Jiang
Plant cold acclimation (CA) is a genetically complex phenomenon involving gene regulation and expression. Little is known about the cascading pattern of gene regulatroy network and the link between genes and metabolites during CA. Dendrobium officinale (DOKM) is an important medicinal and ornamental plant and hypersensitive to low temperature. Here, we used the large scale metabolomic and transcriptomic technologies to reveal the response to CA in DOKM seedlings based on the physiological profile analyses. Lowering temperature from 4 to -2°C resulted in significant increase (P < 0...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27871150/integrated-proteomics-and-metabolomics-suggests-symbiotic-metabolism-and-multimodal-regulation-in-a-fungal-endobacterial-system
#14
Zhou Li, Qiuming Yao, Stephen P Dearth, Matthew R Entler, Hector F Castro Gonzalez, Jessie K Uehling, Rytas J Vilgalys, Gregory B Hurst, Shawn R Campagna, Jessy L Labbé, Chongle Pan
Many plant-associated fungi host endosymbiotic endobacteria with reduced genomes. While endobacteria play important roles in these tri-partite plant-fungal-endobacterial systems, the active physiology of fungal endobacteria has not been characterized extensively by systems biology approaches. Here, we use integrated proteomics and metabolomics to characterize the relationship between the endobacterium Mycoavidus sp. and the root-associated fungus Mortierella elongata. In nitrogen-poor media, M. elongata had decreased growth but hosted a large and growing endobacterial population...
November 21, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27869667/metabolomics-a-powerful-tool-for-agricultural-research
#15
REVIEW
He Tian, Sin Man Lam, Guanghou Shui
Metabolomics, which is based mainly on nuclear magnetic resonance (NMR), gas-chromatography (GC) or liquid-chromatography (LC) coupled to mass spectrometry (MS) analytical technologies to systematically acquire the qualitative and quantitative information of low-molecular-mass endogenous metabolites, provides a direct snapshot of the physiological condition in biological samples. As complements to transcriptomics and proteomics, it has played pivotal roles in agricultural and food science research. In this review, we discuss the capacities of NMR, GC/LC-MS in the acquisition of plant metabolome, and address the potential promise and diverse applications of metabolomics, particularly lipidomics, to investigate the responses of Arabidopsis thaliana, a primary plant model for agricultural research, to environmental stressors including heat, freezing, drought, and salinity...
November 17, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27856706/osmotic-stress-is-accompanied-by-protein-glycation-in-arabidopsis-thaliana
#16
Gagan Paudel, Tatiana Bilova, Rico Schmidt, Uta Greifenhagen, Robert Berger, Elena Tarakhovskaya, Stefanie Stöckhardt, Gerd Ulrich Balcke, Klaus Humbeck, Wolfgang Brandt, Andrea Sinz, Thomas Vogt, Claudia Birkemeyer, Ludger Wessjohann, Andrej Frolov
Among the environmental alterations accompanying oncoming climate changes, drought is the most important factor influencing crop plant productivity. In plants, water deficit ultimately results in the development of oxidative stress and accumulation of osmolytes (e.g. amino acids and carbohydrates) in all tissues. Up-regulation of sugar biosynthesis in parallel to the increasing overproduction of reactive oxygen species (ROS) might enhance protein glycation, i.e. interaction of carbonyl compounds, reducing sugars and α-dicarbonyls with lysyl and arginyl side-chains yielding early (Amadori and Heyns compounds) and advanced glycation end-products (AGEs)...
December 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27853298/structured-plant-metabolomics-for-the-simultaneous-exploration-of-multiple-factors
#17
Nikolay Vasilev, Julien Boccard, Gerhard Lang, Ulrike Grömping, Rainer Fischer, Simon Goepfert, Serge Rudaz, Stefan Schillberg
Multiple factors act simultaneously on plants to establish complex interaction networks involving nutrients, elicitors and metabolites. Metabolomics offers a better understanding of complex biological systems, but evaluating the simultaneous impact of different parameters on metabolic pathways that have many components is a challenging task. We therefore developed a novel approach that combines experimental design, untargeted metabolic profiling based on multiple chromatography systems and ionization modes, and multiblock data analysis, facilitating the systematic analysis of metabolic changes in plants caused by different factors acting at the same time...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852950/photoperiod-affects-the-phenotype-of-mitochondrial-complex-i-mutants
#18
Pierre Pétriacq, Linda De Bont, Lucie Genestout, Jingfang Hao, Constance Laureau, Igor Florez-Sarasa, Touami Rzigui, Guillaume Queval, Françoise Gilard, Caroline Mauve, Florence Guérard, Marlène Lamothe-Sibold, Jessica Marion, Chantal Fresneau, Spencer Craig Brown, Antoine Danon, Anja Krieger-Liszkay, Richard Berthomé, Miquel Ribas-Carbo, Guillaume G B Tcherkez, Gabriel Cornic, Bernard Pineau, Bertrand Gakiere, Rosine De Paepe
Plant mutants for genes encoding subunits of mitochondrial Complex I (CI, NADH:ubiquinone oxidoreductase), the first enzyme of the respiratory chain, display various phenotypes depending on growth conditions. Here, we examined the impact of photoperiod, a major environmental factor controlling plant development, on two Arabidopsis thaliana CI mutants: a new insertion mutant interrupted in both ndufs8.1 and ndufs8.2 genes encoding the NDUFS8 subunit, and the previously characterized ndufs4 CI mutant. In long day (LD) condition, both ndufs8...
November 16, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27844244/metabolo-transcriptome-profiling-of-barley-reveals-induction-of-chitin-elicitor-receptor-kinase-gene-hvcerk1-conferring-resistance-against-fusarium-graminearum
#19
Shailesh Karre, Arun Kumar, Dhananjay Dhokane, Ajjamada C Kushalappa
We report plausible disease resistance mechanisms induced by barley resistant genotype CI89831 against Fusarium head blight (FHB) based on metabolo-transcriptomics approach. We identified HvCERK1 as a candidate gene for FHB resistance, which is functional in resistant genotype CI9831 but non-functional in susceptible cultivars H106-371 and Zhedar-2. For the first time, we were able to show a hierarchy of regulatory genes that regulated downstream biosynthetic genes that eventually produced resistance related metabolites that reinforce the cell walls to contain the pathogen progress in plant...
November 14, 2016: Plant Molecular Biology
https://www.readbyqxmd.com/read/27843720/proteogenomic-analyses-indicate-bacterial-methylotrophy-and-archaeal-heterotrophy-are-prevalent-below-the-grass-root-zone
#20
Cristina N Butterfield, Zhou Li, Peter F Andeer, Susan Spaulding, Brian C Thomas, Andrea Singh, Robert L Hettich, Kenwyn B Suttle, Alexander J Probst, Susannah G Tringe, Trent Northen, Chongle Pan, Jillian F Banfield
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10-20 cm and 30-40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate...
2016: PeerJ
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