Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA179046 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Isoleucine (Ile) is one of the branched-chain amino acids (BCAAs) that are essential substrates for protein synthesis in all organisms. In this study, we characterized an Arabidopsis mutant, lib (low isoleucine biosynthesis), that has defects in both cell proliferation and cell expansion processes during root development. This mutant carries a mutation in OMR1 gene that encodes a threonine deaminase/dehydratase (TD) which results in a defect in isoleucine production. Microarray analysis indicated that the partial deficiency of Ile in the lib mutant triggers a decrease in transcript levels of the genes encoding the major enzymes involved in the BCAA degradation pathway; the analysis also indicated that many genes involved in the biosynthesis of methionine-derived glucosinolates are up-regulated.
2012-11-07 | GSE42060 | GEO
Project description:Isoleucine (Ile) is one of the branched-chain amino acids (BCAAs) that are essential substrates for protein synthesis in all organisms. In this study, we characterized an Arabidopsis mutant, lib (low isoleucine biosynthesis), that has defects in both cell proliferation and cell expansion processes during root development. This mutant carries a mutation in OMR1 gene that encodes a threonine deaminase/dehydratase (TD) which results in a defect in isoleucine production. Microarray analysis indicated that the partial deficiency of Ile in the lib mutant triggers a decrease in transcript levels of the genes encoding the major enzymes involved in the BCAA degradation pathway; the analysis also indicated that many genes involved in the biosynthesis of methionine-derived glucosinolates are up-regulated. Total RNAs were isolated from three replicate samples of the root tissues of 8-day-old wild type (w) and lib mutant (m)seedlings grown on 1/2 MS medium and hybridized on Affymetrix ATH1 microarrays. The changes of gene expression in the lib mutant (m) was compared with the wild type (w). The corrected P value of <0.05 was used to select the genes for comparison, and only those genes whose expression was two-fold higher or lower in lib than in the WT were used for analysis.
2012-11-07 | E-GEOD-42060 | biostudies-arrayexpress
Project description:Postoperative insulin resistance refers to the phenomenon that the body’s glucose uptake stimulated by insulin is reduced due to stress effects such as trauma or the inhibitory effect of insulin on liver glucose output is weakened after surgery.
There is a clear link between postoperative insulin resistance and poor perioperative prognosis. Therefore, exploring interventions to reduce postoperative stress insulin resistance, stabilize postoperative blood glucose, and reduce postoperative complications are clinical problems that need to be solved urgently. In recent years, research on branched-chain amino acids and metabolic diseases has become a hot spot. Studies have found that in the rat model, preoperatively given a high branched-chain amino acid diet can inhibit postoperative insulin resistance and stabilize blood glucose levels. This research plan is to try to add branched-chain amino acids before surgery to observe the occurrence of postoperative insulin resistance in patients.
| 2744698 | ecrin-mdr-crc
Project description:Mice were put on either a control or low isoleucine diet and their liver transcriptomic expression was measured in both the fasting and fed state. This was to discover the impact of reducing a single branched chain amino acid on the metabolism of the liver.
2021-04-21 | GSE168588 | GEO
Project description:Objective: Insulin regulates amino acid metabolism. We investigated whether glycemia and 43 genetic risk variants for hyperglycemia/type 2 diabetes affect amino acid levels in a large population-based cohort. Subjects and Methods: A total of 9,371 non-diabetic or newly-diagnosed type 2 diabetic Finnish men from the population-based METSIM Study were studied. Proton NMR spectroscopy was used to measure plasma levels of 8 amino acids. Genotyping of 42 SNPs and mRNA microarray analysis from 200 subcutaneous adipose tissue samples were performed. Results: Increasing fasting and/or 2-hour plasma glucose levels were associated with increasing levels of alanine, valine, leucine, isoleucine, phenylalanine and tyrosine, and decreasing levels of histidine and glutamine. We also found significant correlations between insulin sensitivity (Matsuda ISI) and expression of genes regulating amino acid metabolism. Only one SNP (rs780094 in GCKR) of the 42 risk SNPs for type 2 diabetes or hyperglycemia was significantly associated with the levels of alanine, isoleucine, and glutamine. Conclusions : We observed that the levels of branched-chain, aromatic amino acids and alanine increased and the levels of glutamine and histidine decreased with increasing glycemia. These associations seemed to be mediated by insulin resistance, at least in part. GCKR rs780094 was significantly associated with several amino acids. Total RNA was obtained from subcutaneous fat biopsies from 200 people participating in the METSIM study (4 samples were replicated for a total of 204 arrays).
2012-04-01 | E-GEOD-32512 | biostudies-arrayexpress
Project description:Objective: Insulin regulates amino acid metabolism. We investigated whether glycemia and 43 genetic risk variants for hyperglycemia/type 2 diabetes affect amino acid levels in a large population-based cohort. Subjects and Methods: A total of 9,371 non-diabetic or newly-diagnosed type 2 diabetic Finnish men from the population-based METSIM Study were studied. Proton NMR spectroscopy was used to measure plasma levels of 8 amino acids. Genotyping of 42 SNPs and mRNA microarray analysis from 200 subcutaneous adipose tissue samples were performed. Results: Increasing fasting and/or 2-hour plasma glucose levels were associated with increasing levels of alanine, valine, leucine, isoleucine, phenylalanine and tyrosine, and decreasing levels of histidine and glutamine. We also found significant correlations between insulin sensitivity (Matsuda ISI) and expression of genes regulating amino acid metabolism. Only one SNP (rs780094 in GCKR) of the 42 risk SNPs for type 2 diabetes or hyperglycemia was significantly associated with the levels of alanine, isoleucine, and glutamine. Conclusions : We observed that the levels of branched-chain, aromatic amino acids and alanine increased and the levels of glutamine and histidine decreased with increasing glycemia. These associations seemed to be mediated by insulin resistance, at least in part. GCKR rs780094 was significantly associated with several amino acids.
2012-04-02 | GSE32512 | GEO
Project description:Transcriptional regulation of branched-chain amino acid metabolism in Saccharomyces cerevisiae involves two key regulator proteins, Leu3p and Gcn4p. Leu3p is a pathway-specific regulator, known to regulate six genes involved in branched-chain amino acid metabolism and one gene in nitrogen assimilation. Gcn4p is a global regulator, involved in the general response to amino acid and purine starvation. To investigate the contribution of Leu3p in regulation of gene expression, a leu3D strain was compared to an isogenic reference strain using DNA-microarray analysis. This comparison was performed for both glucose-grown, ammonium-limited and ethanol-limited, ammonium-excess chemostat cultures. In ethanol-limited cultures, absence of Leu3p led to reduced transcript levels of six of the seven established Leu3p target genes, but did not affect key physiological parameters. In ammonium-limited cultures, absence of Leu3p caused a drastic decrease in storage carbohydrate content. mRNA levels of genes involved in storage carbohydrate metabolism were also found reduced. Under N-limited conditions, the leu3D genotype elicited an amino-acid starvation response, leading to increased transcript levels of many amino acid biosynthesis genes. By combining the transcriptome data with data from earlier studies that measured DNA binding of Leu3p both in vitro and in vivo, BAT1, GAT1 and OAC1 were identified as additional Leu3p-regulated genes. This study demonstrates that unravelling of transcriptional regulation networks should preferably include several cultivation conditions and requires a combination of experimental approaches.
2007-07-07 | E-GEOD-2076 | biostudies-arrayexpress
Project description:Gene expression profiling of Blastobotrys raffinosifermentans LS3 cells based on 6.025 annotated chromosomal Blastobotrys raffinosifermentans LS3 sequences and 36 putative mitochondrial gene oligos was performed following exposure to gallic acid. Microarray data were successfully used to identify expression changes of main candidate genes involved in tannic acid degradation, protocatechuic acid degradation, β-oxidation, the glyoxylate cycle, the methyl citrate cycle and the catabolism of the branched-chain amino acids valine, leucine and isoleucine.
2022-02-03 | GSE195801 | GEO
Project description:Gene expression profiling of Blastobotrys raffinosifermentans LS3 cells based on 6.025 annotated chromosomal Blastobotrys raffinosifermentans LS3 sequences and 36 putative mitochondrial gene oligos was performed following exposure to protocatechuic acid. Microarray data were successfully used to identify expression changes of main candidate genes involved in tannic acid degradation, protocatechuic acid degradation, β-oxidation, the glyoxylate cycle, the methyl citrate cycle and the catabolism of the branched-chain amino acids valine, leucine and isoleucine.
2022-02-03 | GSE195808 | GEO
Project description:Transcriptional regulation of branched-chain amino acid metabolism in Saccharomyces cerevisiae involves two key regulator proteins, Leu3p and Gcn4p. Leu3p is a pathway-specific regulator, known to regulate six genes involved in branched-chain amino acid metabolism and one gene in nitrogen assimilation. Gcn4p is a global regulator, involved in the general response to amino acid and purine starvation. To investigate the contribution of Leu3p in regulation of gene expression, a leu3D strain was compared to an isogenic reference strain using DNA-microarray analysis. This comparison was performed for both glucose-grown, ammonium-limited and ethanol-limited, ammonium-excess chemostat cultures. In ethanol-limited cultures, absence of Leu3p led to reduced transcript levels of six of the seven established Leu3p target genes, but did not affect key physiological parameters. In ammonium-limited cultures, absence of Leu3p caused a drastic decrease in storage carbohydrate content. mRNA levels of genes involved in storage carbohydrate metabolism were also found reduced. Under N-limited conditions, the leu3D genotype elicited an amino-acid starvation response, leading to increased transcript levels of many amino acid biosynthesis genes. By combining the transcriptome data with data from earlier studies that measured DNA binding of Leu3p both in vitro and in vivo, BAT1, GAT1 and OAC1 were identified as additional Leu3p-regulated genes. This study demonstrates that unravelling of transcriptional regulation networks should preferably include several cultivation conditions and requires a combination of experimental approaches. Keywords: ordered
2004-12-17 | GSE2076 | GEO