Microarray analysis of gene expression in rice lacking cytosolic glutamine synthetase 1;1 and 1;2 grown under the ammonium sufficient condition
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ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Japonica Group
PROVIDER: GSE49789 | GEO | 2020/04/20
REPOSITORIES: GEO
Similar Datasets
Project description:Goal of the study is to characterize distinct function(s) of two cytosolic glutamine synthetase (GS) in rice plants. We grew rice lacking GS1;1 and GS1;2 under the ammonium sufficient condition. We harvested roots from the two mutants as well as those of the corresponding control.
2019-04-01 | E-MTAB-6303 | biostudies-arrayexpress
Project description:Goal of the study is to characterize specific function(s) of the cytosolic glutamine synthetase (GS) 1;2 for apical meristem induction in rice plants. To address the issue, we conducted transcript profiling toward basal parts of the knockout mutant lacking GS1;2. We used microarrays conduct transcript profiling of gs1;2 plants. Wild-type samples were used as control.
2014-11-28 | GSE62124 | GEO
Project description:Rice grown in paddy fields prefers to use ammonium ions as a major source of inorganic nitrogen. Glutamine synthetase (GS) catalyzes the conversion of ammonium ions to glutamine. In three cytosolic GS in rice, OsGS1;1 has the critical role for normal growth and grain filling. To understand a role of GS1;1, we performed transcriptional profiling of wild type Nipponbare and GS1;1 mutant plants in seedling using the Agilent Rice Oligo Microarray.
2010-03-01 | GSE15122 | GEO
Project description:Glutamine synthetase (GS) catalyzes a reaction that incorporates ammonium into glutamate and yields glutamine in the cytosol and chloroplasts. Although the enzymatic characteristics of the GS1 isozymes are well known, their physiological functions in ammonium assimilation and regulation in roots remain unclear. In this study we show evidence that two cytosolic GS1 isozymes (GLN1;2 and GLN1;3) contribute to ammonium assimilation in Arabidopsis roots. Arabidopsis T-DNA insertion lines for GLN1;2 and GLN1;3 (i.e. gln1;2 and gln1;3 single-mutants), the gln1;2:gln1;3 double-mutant, and the wild-type accession (Col-0) were grown in hydroponic culture with variable concentrations of ammonium to compare their growth, and their content of nitrogen, carbon, ammonium, and amino acids. GLN1;2 and GLN1;3 promoter-dependent green fluorescent protein was observed under conditions with or without ammonium supply. Loss of GLN1;2 caused significant suppression of plant growth and glutamine biosynthesis under ammonium-replete conditions. In contrast, loss of GLN1;3 caused slight defects in growth and Gln biosynthesis that were only visible based on a comparison of the gln1;2 single- and gln1;2:gln1;3 double-mutants. GLN1;2, being the most abundantly expressed GS1 isozyme, markedly increased following ammonium supply and its promoter activity was localized at the cortex and epidermis, while GLN1;3 showed only low expression at the pericycle, suggesting their different physiological contributions to ammonium assimilation in roots. The GLN1;2 promoter-deletion analysis identified regulatory sequences required for controlling ammonium-responsive gene expression of GLN1;2 in Arabidopsis roots. These results shed light on GLN1 isozyme-specific regulatory mechanisms in Arabidopsis that allow adaptation to an ammonium-replete environment.
| S-EPMC5441914 | biostudies-literature
Project description:Rice aleurone cytosolic proteome was fractionized by SEC and analyzed by LC-MSMS.
2021-06-17 | PXD021450 | Pride
Project description:Nitrogen is major nutrient for plant growth. Two forms for inorganic nitrogen are available for plant, ammonium and nitrate. External status of them affects largely plant growth and production. Generally, root is a sole organ to uptake nitrogen. Hence, identifying regulatory genes depend on nitrogen status in roots is important to improve sustainable production or rice. To isolate the candidate gene, array experiments were performed. Consequently, we isolated genes which showed marked accumulation in deficient and sufficient concentrations of ammonium in roots.
2018-01-24 | GSE66807 | GEO
Project description:Plant cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes involved in Cys biosynthesis and located in different subcellular compartments. These enzymes are made up of a complex variety of isoforms resulting in different subcellular Cys pools. To unravel the contribution of cytosolic Cys to plant metabolism, we characterized the knockout oas-a1.1 and osa-a1.2 mutants, deficient in the most abundant cytosolic OASTL isoform in Arabidposis thaliana. Total intracellular Cys and glutathione concentrations were reduced, and the glutathione redox state was shifted in favour of its oxidized form. Interestingly, the capability of the mutants to chelate heavy metals did not differ from that of the wild type, but the mutants have an enhanced sensitivity to Cd. With the aim of establishing the metabolic network most influenced by the cytosolic Cys pool, we used the ATH1 GeneChip for evaluation of differentially expressed genes in the oas-a1.1 mutant grown under non-stress conditions. The transcriptomic footprints of mutant plants had predicted functions associated with various physiological responses that are dependent on reactive oxygen species and suggested that the mutant was oxidatively stressed. To further elucidate the specific function(s) of the OAS-A1 isoform in the adaptation response to cadmium we extended the trasncriptome experiment to the wild type and oas-a1.1 mutant plants exposed to Cd. The comparison of transcriptomic profiles showed a higher proportion of genes with altered expression in the mutant than in the wild type, highlighting up-regulated genes identified as of the general oxidative stress response rather than metal-responsive genes. Wild type and oas-a1.1 mutant plants were grown hydroponically and, after a two-week acclimation period, the roots and shoots were harvested separately. Total RNA was then prepared and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array. Three biological replicates were performed for each sample. We made two different comparisons to classify the differently expressed genes in the mutant plant: oas-a1.1 roots versus wild-type roots and oas-a1.1 shoots versus wild-type shoots. Hydroponically-grown wild type and oas-a1.1 mutant plants were further treated with 50µM CdCl2 and 18h-treated-roots and 24h-treated-shoots were harvested. Total RNA was then prepared and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array. Three biological replicates were performed for each sample. Different comparisons were performed as follows: 18h Cd-treated wild type roots versus untreated wild type roots; 24h Cd-treated wild type shoots versus untreated wild type shoots; 18h Cd-treated oas-a1.1 roots versus untreated oas-a1.1 roots; 24h Cd-treated oas-a1.1 shoots versus untreated oas-a1.1 shoots; 18h Cd-treated oas-a1.1 roots versus 18h Cd-treated wild type roots; 24h Cd-treated oas-a1.1 shoots versus 24h Cd-treated wild type shoots
2010-10-01 | E-GEOD-19245 | biostudies-arrayexpress
Project description:Cytosolic acetyl-coenzyme A is a precursor for many biotechnologically relevant compounds produced by Saccharomyces cerevisiae. In this yeast, cytosolic acetyl-CoA synthesis and growth strictly depend on expression of either the Acs1 or Acs2 isoenzyme of acetyl-CoA synthetase (ACS). Since hydrolysis of ATP to AMP and pyrophosphate in the ACS reaction constrains maximum yields of acetyl-CoA-derived products, this study explores replacement of ACS by two ATP-independent pathways for acetyl-CoA synthesis. After evaluating expression of different bacterial genes encoding acetylating acetaldehyde dehydrogenase (A-ALD) and pyruvate-formate lyase (PFL), acs1M-NM-^T acs2M-NM-^T S. cerevisiae strains were constructed in which A-ALD or PFL successfully replaced ACS. In A-ALD-dependent strains, aerobic growth rates of up to 0.27 h-1 were observed, while anaerobic growth rates of PFL-dependent S. cerevisiae (0.21 h-1) were stoichiometrically coupled to formate production. In glucose-limited chemostat cultures, intracellular metabolite analysis did not reveal major differences between A-ALD-dependent and reference strains. However, biomass yields on glucose of A-ALD- and PFL-dependent strains were lower than those of the reference strain. Transcriptome analysis suggested that reduced biomass yields were caused by acetaldehyde and formate in A-ALD- and PFL-dependent strains, respectively. Transcript profiles also indicated that a previously proposed role of Acs2 in histone acetylation is probably linked to cytosolic acetyl-CoA levels rather than to direct involvement of Acs2 in histone acetylation. While, for the first time, demonstrating that yeast ACS can be fully replaced by alternative reactions, this study demonstrates that further modifications are needed to achieve optimal in vivo efficiencies of the supply of acetyl-CoA as product precursor. To investigate the impact of introduced changes in native pathway of cytosolic acetyl-CoA formation in S. cerevisiae, a DNA microarray-based transcriptome analysis was performed on aerobic or anaerobic, glucose-limited chemostat cultures.
2013-11-21 | E-GEOD-47983 | biostudies-arrayexpress
Project description:Trace concentrations of vanadium (V) have several benefits for plant growth, but high concentrations are toxic. To help characterize the cellular mechanisms underlying the toxic effects of V in plants, we present the first large-scale analysis of rice root responding to V during the early stages (1 and 3 h) of toxicity. Exposure to V triggered changes in the transcript levels of several genes related to cellular metabolic process, response to stimulus and transporters. Gene expression profiling revealed upregulated levels of genes associated with signaling and biosynthesis of auxin, abscisic acid (ABA) and jasmonic acid (JA) in V-treated rice roots. In addition, V upregulated the expression of ATP-dependent GSH-conjugated transport, ATP binding cassette (ABC) transporter, and markedly downregulated of the expression of divalent cation transporters, drug/metabolite transporter (DMT) and zinceiron permease (ZIP). Among the V-specific responsive transcription factors and protein kinases, the most predominant families were NAC (NAM, ATAF, CUC) transcription factor, receptor-like cytoplasmic kinase VII (RLCK-VII) and leucinerich repeat kinase VIII (LRR-VIII). These microarray data provide a new insight into the molecular mechanism of the rice roots response to V toxicity. Trace concentrations of vanadium (V) have several benefits for plant growth, but high concentrations are toxic. To help characterize the cellular mechanisms underlying the toxic effects of V in plants, we present the first large-scale analysis of rice root responding to V during the early stages (1 and 3 h) of toxicity. Exposure to V triggered changes in the transcript levels of several genes related to cellular metabolic process, response to stimulus and transporters. Gene expression profiling revealed upregulated levels of genes associated with signaling and biosynthesis of auxin, abscisic acid (ABA) and jasmonic acid (JA) in V-treated rice roots. In addition, V upregulated the expression of ATP-dependent GSH-conjugated transport, ATP binding cassette (ABC) transporter, and markedly downregulated of the expression of divalent cation transporters, drug/metabolite transporter (DMT) and zinceiron permease (ZIP). Among the V-specific responsive transcription factors and protein kinases, the most predominant families were NAC (NAM, ATAF, CUC) transcription factor, receptor-like cytoplasmic kinase VII (RLCK-VII) and leucinerich repeat kinase VIII (LRR-VIII). These microarray data provide a new insight into the molecular mechanism of the rice roots response to V toxicity.
2014-11-11 | GSE63152 | GEO
Project description:Acetyl-Coenzyme A (acetyl-CoA) is a central metabolite and the acetyl source for protein acetylation, particularly histone acetylation that promotes gene expression. However, the effect of acetyl-CoA levels on histone acetylation status in plants remains unknown. Here, we show that malfunctioned cytosolic acetyl-CoA carboxylase1 (ACC1) in Arabidopsis leads to elevated levels of acetyl-CoA and promotes histone hyperacetylation predominantly at lysine 27 of histone H3 (H3K27). The increase of H3K27 acetylation (H3K27ac) is dependent on ATP-citrate lyase which cleaves citrate to acetyl-CoA in the cytoplasm, and requires histone acetyltransferase GCN5. A comprehensive analysis of the transcriptome and metabolome in combination with the genome-wide H3K27ac profiles of acc1 mutants, demonstrate the dynamic changes of H3K27ac, gene transcripts and metabolites occurring in the cell by the increased levels of acetyl-CoA. This study suggests that H3K27ac is an important link between cytosolic acetyl-CoA level and gene expression in response to the dynamic metabolic environments in plants.
2017-09-25 | GSE79524 | GEO