GNPS - Untargeted metabolome using LCMS and GCMS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Agilent 8890-5977B, Waters ACQUITY UPLC I-Class plus/Thermo QE
ORGANISM(S): Triticum Aestivum (ncbitaxon:4565)
SUBMITTER: 
shangshengping
PROVIDER: MSV000097684 | GNPS | Tue Apr 22 00:46:00 BST 2025
REPOSITORIES: GNPS
Similar Datasets
Project description:Detection of the metabolites in the transgenic wheat plants using untargeted metabolics.
2025-04-22 | MSV000097684 | MassIVE
Project description:Detection of the amino acid contents in the transgenic wheat plants.
2025-04-21 | MSV000097681 | MassIVE
Project description:Detection of the amino acid contents in the transgenic wheat plants.
2025-04-21 | MSV000097681 | GNPS
Project description:Background: With the increasing interest in metabolic engineering of plants using various genetic manipulation and gene editing technologies in order to enhance their growth, nutritional value and environmental adaptation, a major concern is the potential of broad and distant effects of manipulating the target gene or the metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these techniques with plant cell cultures to analyze the effects of genetic manipulation of a single step in the biosynthesis of polyamines because of their well-known roles in plant growth, development and stress responses [PMID 19383098] The transcriptomes and metabolomes of a control and a high putrescine producing (HP) cell line of poplar (Populus nigra x maximowiczii) were compared using microarrays and GC/MS. The HP cells expressed an ornithine decarboxylase transgene and accumulated several-fold higher concentrations of putrescine, with only small changes in spermidine and spermine. The results show that up-regulation of a single step in the polyamine biosynthetic pathway (i.e. ornithine→putrescine) altered the expression of a broad spectrum of genes; many of them were involved in transcription, translation, membrane transport, osmoregulation, shock/stress/wounding, and cell wall metabolism. More than half of the 200 detected metabolites were significantly altered (P <0.05) in the HP cells on any day of analysis; the most noteworthy differences were in organic acids, carbohydrates and nitrogen-containing metabolites. The results provide valuable information about the role of polyamines in regulating nitrogen and carbon use pathways in cell cultures of high putrescine producing transgenic cells of poplar vs. their low putrescine counterparts. The results underscore the complexity of cellular responses to genetic perturbation of a single metabolic step related to nitrogen metabolism in plants. Combined with recent studies from our lab regarding increased putrescine production causing an increased flux of glutamate into ornithine, with accompanied increase in glutamate production by additional nitrogen and carbon assimilation; the results may be useful in designing transgenic plants with increased nitrogen use efficiency, especially in plants intended for non-food/feed applications (e.g. increased biomass production or for biofuels).
2016-03-24 | GSE79420 | GEO
Project description:Rust fungi are plant pathogens that cause epidemics which threatens the production of many important plant species, such as wheat, soy, coffee and poplar. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1 184 candidate effectors (CEs), however their functions are poorly known. In this study, we analysed the transcriptome and metabolome of Arabidopsis constitutively expressing CEs of Mlp to discover processes targeted by these fungal proteins. For this purpose, we sequenced the transcriptome and used mass spectrometry to analyse the metabolome of Arabidopsis plants expressing one of 14 selected CEs and of a control line. We found 2 299 deregulated genes in at least one of the 14 transgenic lines. Among the down-regulated genes, the KEGG pathways MAPK signaling pathway and Plant-pathogen interaction were over-represented in six and five of the 14 transgenic lines, respectively. Moreover, the genes down-regulated across the fourteen transgenic lines are related to hormone response and defense. Regarding the metabolome, there were 680 metabolites deregulated across the 14 transgenic lines, with highly unsaturated and phenolic compounds and peptides enriched among down-regulated and up-regulated metabolites, respectively, in almost all transgenic lines. Interestingly, we found that some transgenic lines expressing CEs with no similarity in amino acid sequence had similar patterns of gene and metabolite deregulation, while plants expressing CEs from the same family deregulated different genes and metabolites. Taken together, our results indicate that the sequence of effectors may not be a good predictor of its impact in the plant.
2020-09-24 | GSE158410 | GEO
Project description:Background: With the increasing interest in metabolic engineering of plants using various genetic manipulation and gene editing technologies in order to enhance their growth, nutritional value and environmental adaptation, a major concern is the potential of broad and distant effects of manipulating the target gene or the metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these techniques with plant cell cultures to analyze the effects of genetic manipulation of a single step in the biosynthesis of polyamines because of their well-known roles in plant growth, development and stress responses [PMID 19383098] The transcriptomes and metabolomes of a control and a high putrescine producing (HP) cell line of poplar (Populus nigra x maximowiczii) were compared using microarrays and GC/MS. The HP cells expressed an ornithine decarboxylase transgene and accumulated several-fold higher concentrations of putrescine, with only small changes in spermidine and spermine. The results show that up-regulation of a single step in the polyamine biosynthetic pathway (i.e. ornithineâputrescine) altered the expression of a broad spectrum of genes; many of them were involved in transcription, translation, membrane transport, osmoregulation, shock/stress/wounding, and cell wall metabolism. More than half of the 200 detected metabolites were significantly altered (P <0.05) in the HP cells on any day of analysis; the most noteworthy differences were in organic acids, carbohydrates and nitrogen-containing metabolites. The results provide valuable information about the role of polyamines in regulating nitrogen and carbon use pathways in cell cultures of high putrescine producing transgenic cells of poplar vs. their low putrescine counterparts. The results underscore the complexity of cellular responses to genetic perturbation of a single metabolic step related to nitrogen metabolism in plants. Combined with recent studies from our lab regarding increased putrescine production causing an increased flux of glutamate into ornithine, with accompanied increase in glutamate production by additional nitrogen and carbon assimilation; the results may be useful in designing transgenic plants with increased nitrogen use efficiency, especially in plants intended for non-food/feed applications (e.g. increased biomass production or for biofuels). 12 two-channel arrays directly comparing RNA from control and high putrescine producing (HP) cell lines of Populus nigra x maximowiczii at 3 and 5 days of growth. Three independent biological replicates derived from cells grown in three independent replicate cultures were used. In addition, each sample and time point included dye swap reciprocal two-color experiments for each biological replicate. Thus, six data points per cDNA are included (three biological replicates with two technical replicates each). Please note that experiments were technically carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array; barcode ID for each array is indicated in the sample title and raw data file names) but two idependent raw data files were generated from each slide (one for Cy3, the other for Cy5) and processed as though they are single channel (Cy3 and Cy5 signals are calculated and provided for each sample record). Therfore, each sample record is represented as single channel sample.
2016-03-24 | E-GEOD-79420 | biostudies-arrayexpress
Project description:Small RNAs in transgenic TaNAM-RNAi wheat plants
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Project description:Indian mustard (Brassica juncea; Brassicaceae) is an edible, oilseeds-yielding crop widely consumed as a food spice owing to its richness in nutrients with several health benefits. The current study aims to dissect the B. juncea metabolome heterogeneity among its different organs including leaf, stem, flower, and seed. Moreover, assessing the metabolome differences between two different varieties RH-725 and RH-761 grown at the same conditions. Gas chromatography-mass spectrometry (GC-MS) post-silylation was used to dissect the composition of nutrient metabolites coupled to multivariate data analysis. Variation in sulphur aglycones was measured using headspace-solid phase-microextraction HS-SPME coupled to GC-MS. A total of 101 nutrient metabolites were identified with the abundance of sugars represented by monosaccharides in all organs, except for seeds which were enriched in disaccharides (sucrose). α-Linolenic acid was detected as a marker fatty acid in leaf from RH-725 at 12.5 µg/mg. Malic acid was detected as a significant variant metabolite between the two varieties as detected in the leaf from the RH-725 variety at ca. 128.2 µg/mg compared to traces in RH-761. 7 Volatile sulphur compounds were detected at comparable levels in RH-725 and RH-761, with 3-butenyl isothiocyanate was the most abundant at 0.8-2 ng/mg.
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Project description:TaMYB13 is a transcription factor that has been associated with fructan accumulation in previous studies in wheat (Xue et al. 2011 Plant journal 68: 857 - 870). In this study we aimed to find genes regulated by TaMYB13, through overexpression of this transcription factor in wheat and perform expression analysis by making use of Affymetrix genechip assays. Expression of control plants was compared to transgenic lines, and total RNA was extracted from Flag leaves at anthesis. In this experiment the genome wide gene expression was assessed from wheat flag leaf material harvested at anthesis. Control plants (BW43,BW44,BW45) were compared with transgenic lines that overexpress TaMYB13 (a20, b2, b36).
2013-07-01 | E-GEOD-42000 | biostudies-arrayexpress
Project description:The goal of this study is to compare the differential genes between wild type and TaSIP1 overexpression transgenic wheat plants. We used wild-type (WT) and three independent TaSIP1-∆C overexpressing (∆COE) wheat lines to perform RNA sequencing. As a result, TaSIP overexpression lead to transcriptomic reprogramming. Most of the mitochondrial dysfunction stimulon (MDS) genes, including AtAOX1a, were upregulated substantially by the overexpression of TaSIP1-∆C.
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