Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1304735 | ENA |
REPOSITORIES: ENA
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Project description:Differential gene expression analysis of five different strains of Crabtree-negative Saccharomyces cerevisiae that lack pyruvate decarboxylase activity. The three different acids studied were lactic, malic, and 3-hydroxypropionic acid.
2019-03-01 | E-MTAB-7600 | biostudies-arrayexpress
Project description:This data is part of a study examining the results of increased malic enzyme activity in soybean seeds. The study characterizes changes to oil content and free amino acids when malic enzyme is expressed in different subcellular locations. Malic enzyme was expressed using seed-specific promoters to target activity to the seeds and was also designed to localize into and outside of the chloroplast.
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Project description:Purpose of study was to investigate whole genome expression changes of a strain with deletion of the two-component system TctD-TctE and determine genes dysregulate relative to the parental wildtype to gain insight into possible regulatory targets of TctD-TctE. TctD-TctE is a two-component system in Pseudomonas aeruginosa that responds to and regulates uptake of tricarboxylic acids such as citric acid. It accomplishes this through derepression of the porin encoding the gene opdH, thereby regulating influx of citrate metabolites from the surrounding environment. Deletion of the tctED operon (ΔtctED) resulted in a reduced growth phenotype when citric acid is present in media. In the ΔtctED strain the presence of citric acid was found to have an inhibitory effect on growth. When the alternative carbon source arginine was present, wildtype levels of growth could not be restored. Static cultures of ΔtctED had low cell density in the presence of citric acid but maintained the same levels of biofilm formation compared to conditions when no citric acid was present. This suggests a dysregulation of biofilm formation in the presence of citric acid. In the ΔtctED strain there was also greater accumulation of tobramycin within the biofilm compared to the PA14 wildtype strain. Additionally, analysis of whole-genome expression found that multiple metabolic genes were dysregulated in ΔtctED. Here it is concluded that TctD-TctE is involved in biofilm tolerance to tobramycin in the presence of citrate metabolites.
2018-05-15 | GSE114431 | GEO
Project description:Fusarium graminearum and related species commonly infest grains causing the devastating plant disease Fusarium head blight (FHB) and the formation of trichothecene mycotoxins. The most relevant toxin is deoxynivalenol (DON), which acts as a virulence factor of the pathogen. FHB is difficult to control and resistance to this disease is a polygenic trait, mainly mediated by the quantitative trait loci (QTL) Fhb1 and Qfhs.ifa-5A. In this study we established a targeted GC-MS based metabolomics workflow comprising a standardized experimental setup for growth, treatment and sampling of wheat ears and subsequent GC-MS analysis followed by data processing and evaluation of QC measures using tailored statistical and bioinformatics tools. This workflow was applied to wheat samples of six genotypes with varying levels of Fusarium resistance, treated with either DON or water, and harvested 0, 12, 24, 48 and 96 hours after treatment. The results suggest that the primary carbohydrate metabolism and transport, the citric acid cycle and the primary nitrogen metabolism of wheat are clearly affected by DON treatment. Most importantly significantly elevated levels of amino acids and derived amines were observed. In particular, the concentrations of the three aromatic amino acids phenylalanine, tyrosine, and tryptophan increased. No clear QTL specific difference in the response could be observed except a generally faster increase in shikimate pathway intermediates in genotypes containing Fhb1. The overall workflow proved to be feasible and facilitated to obtain a more comprehensive picture on the effect of DON on the central metabolism of wheat.
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Project description:Soluble pyridine nucleotide transhydrogenase (EcSthA) derived from Escherichia coli was introduced into the L-malic acid producing strain MA009-5 of Pichia kudriavzevii to obtain strain MA009-10. It was found that MA009-10 was superior to MA009-5 in terms of L-malic acid titer, glucose consumption rate, and glucose/L-malic acid conversion rate. To elucidate the effect of EcSthA expression on L-malic acid synthesis, we analyzed the RNA-seq data of both strains.
2023-05-03 | GSE202655 | GEO
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Project description:FaDu treated with citric buffer vs. rCTGF FaDu treated with citric buffer for 24 hours FaDu treated with rCTGF 100 ng/mL for 24 hours
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Project description:The fungus Puccinia striiformis f.sp. tritici (PST) is the causal pathogen of stripe rust in wheat. New highly virulent PST races appeared at the beginning of this century and spread rapidly causing significant yield losses in wheat production worldwide. Race PST-08/21 was isolated in the UK in 2008 Yr1, Yr2, Yr3, Yr4, Yr6, Yr9, Yr17, Yr27, Yr32, YrRob, YrSol. We applied the RNAseq approach to refine the gene prediction in de novo assembled PST 08/21 contigs and to determine which genes are expressed during wheat infections.
2013-08-19 | GSE42496 | GEO
Project description:Fusarium head blight (FHB), caused by Fusarium graminearum is a devastating disease that affects global wheat production. F. graminearum encodes many effector proteins; however, its virulence mechanisms are poorly understood. In this study, we identified a secretory effector candidate protein (FgEC10) that is essential for the virulence of F. graminearum and suppresses the basal immune response. FgEC10 interacted strongly with wheat fumarylacetoacetate hydrolase (TaFAH) and accelerated its degradation via the 26S proteasome pathway. In addition, we showed that TaFAH interacted with TaPSMD, an important component of the 26S proteasome and that FgEC10 enhanced the interaction between TaFAH and TaPSMD. RNA silencing or overexpression of TaFAH in wheat plants showed that TaFAH positively regulated wheat FHB resistance, heading period, and grain yield. Transcriptomic analysis revealed that TaFAH promoted the expression of genes associated with disease resistance and the heading period. Metabolomic analysis revealed that overexpression of TaFAH increased the levels of several amino acids that inhibited F. graminearum growth and enhanced wheat resistance to FHB. Collectively, our study reveals a novel pathogenic mechanism and provides a valuable genetic resource for improving FHB resistance and grain yield in wheat.
2024-08-15 | GSE254427 | GEO