Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA245211 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Endosomal trafficking plays integral roles in various eukaryotic cell activities. In animal cells, a member of the RAB GTPase family, RAB5, is a key regulator of various endosomal functions. In addition to orthologs of animal RAB5, plants harbor the plant-specific RAB5 group, the ARA6 group, which is conserved in land plant lineages. In Arabidopsis thaliana, ARA6 and conventional RAB5 act in distinct endosomal trafficking pathways; ARA6 mediates trafficking from endosomes to the plasma membrane, whereas conventional RAB5 acts in endocytic and vacuolar trafficking pathways. ARA6 is also required for normal salt and osmotic stress tolerance, although the functional link between ARA6 and stress tolerance remains unclear. In this study, we investigated ARA6 function in stress tolerance by monitoring broad-scale changes in gene expression in the ara6 mutant. A comparison of the expression profiles between wild-type and ara6‐1 plants revealed that the expression of the Qua-Quine Starch (QQS) gene was significantly affected by the ara6‐1 mutation. QQS is involved in starch homeostasis, consistent with the starch content decreasing in the ara6 mutants to approximately 60% of that of the wild-type plant. In contrast, the free and total glucose content increased in the ara6 mutants. Moreover, the proliferation of Pseudomonas syringae pv. tomato DC3000 was repressed in ara6 mutants, which could be attributed to the elevated sugar content. These results suggest that ARA6 is responsible for starch and sugar homeostasis, most probably through the function of QQS.
2015-02-18 | GSE57013 | GEO
Project description:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. The presented model is a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. The Petri net formalism was used to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs were applied. Based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism, the core metabolism of Arabidopsis thaliana was formulated. Each reaction (transition) is experimentally proven. The complete Petri net model consists of 134 metabolites, represented by places, and 243 reactions, represented by transitions. Places and transitions are connected via 572 edges.
2020-04-09 | MODEL1801090001 | BioModels
Project description:Photosynthesis is arguably the most important biological process on earth. In plants, energy harvested in photosynthesis is converted into sugar and starch, which are important products from species with agronomic interest. During the photosynthesis in the chloroplast, the intermediate carbon metabolites (triose phosphates) produced by the Calvin cycle can either be exported to the cytosol for sucrose synthesis or stay in the chloroplast for starch synthesis (formation). Two fructose-1,6-bisphosphatase (FBPase) enzymes, the chloroplastidial (cpFBPaseI) and the cytosolic (cyFBPase) isoforms, catalyse the first irreversible step during the conversion of triose phosphate to starch or sucrose, respectively. Recently, another cpFBPase isoform (cpFBPaseII) with unknown function was identified. It has been reported that the reduction of cyFBPase or cpFBPaseI activity leads to an alteration in starch and sucrose content. In our laboratory, Arabidopsis thaliana knock-out mutants for the cyFBPase and cpFBPaseI are now available. The objective this research project is to identify and functionally characterize genes differentially expressed in Arabidopsis thaliana knock-out mutants lacking FBPase genes. We make use of high throughput methodologies, such as the transcriptomic and proteomic analyses which represent invaluable tools to identify new loci responsible for agronomically important traits.
2012-05-04 | GSE32522 | GEO
Project description:Photosynthesis is arguably the most important biological process on earth. In plants, energy harvested in photosynthesis is converted into sugar and starch, which are important products from species with agronomic interest. During the photosynthesis in the chloroplast, the intermediate carbon metabolites (triose phosphates) produced by the Calvin cycle can either be exported to the cytosol for sucrose synthesis or stay in the chloroplast for starch synthesis (formation). Two fructose-1,6-bisphosphatase (FBPase) enzymes, the chloroplastidial (cpFBPaseI) and the cytosolic (cyFBPase) isoforms, catalyse the first irreversible step during the conversion of triose phosphate to starch or sucrose, respectively. Recently, another cpFBPase isoform (cpFBPaseII) with unknown function was identified. It has been reported that the reduction of cyFBPase or cpFBPaseI activity leads to an alteration in starch and sucrose content. In our laboratory, Arabidopsis thaliana knock-out mutants for the cyFBPase and cpFBPaseI are now available. The objective this research project is to identify and functionally characterize genes differentially expressed in Arabidopsis thaliana knock-out mutants lacking FBPase genes. We make use of high throughput methodologies, such as the transcriptomic and proteomic analyses which represent invaluable tools to identify new loci responsible for agronomically important traits. Three independent biological replicates were used for each type of sample. Three hybridizations were performed, representing the three independent biological replicates, being one of them a dye swap
2012-05-03 | E-GEOD-32522 | biostudies-arrayexpress
Project description:The goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.
2021-12-09 | ST002012 | MetabolomicsWorkbench
Project description:● Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SnRK1, a key mediator of responses to low energy. ● We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic, and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. ● In order to get some clues about the role of transcription factor bZIP type bZIP63 in growth and development, we performed a comparative gene expression analysis of bzip63-2 mutant and wild type Ws, harvested at the end of night (EN = ZT 24), immediately before the onset of the light, to maximize the discovery of genes misregulated in bzip63-2. The resulting gene expression profiles revealed 230 upregulated and 117 downregulated genes in bzip63-2 compared to Ws. ● bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants. ● We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.
2021-06-03 | GSE119175 | GEO
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:deOliveiraDalMolin2010 - Genome-scale
metabolic network of Arabidopsis thaliana (AraGEM)
This model is described in the article:
AraGEM, a genome-scale
reconstruction of the primary metabolic network in
Arabidopsis.
de Oliveira Dal'Molin CG, Quek LE,
Palfreyman RW, Brumbley SM, Nielsen LK.
Plant Physiol. 2010 Feb; 152(2):
579-589
Abstract:
Genome-scale metabolic network models have been successfully
used to describe metabolism in a variety of microbial organisms
as well as specific mammalian cell types and organelles. This
systems-based framework enables the exploration of global
phenotypic effects of gene knockouts, gene insertion, and
up-regulation of gene expression. We have developed a
genome-scale metabolic network model (AraGEM) covering primary
metabolism for a compartmentalized plant cell based on the
Arabidopsis (Arabidopsis thaliana) genome. AraGEM is a
comprehensive literature-based, genome-scale metabolic
reconstruction that accounts for the functions of 1,419 unique
open reading frames, 1,748 metabolites, 5,253 gene-enzyme
reaction-association entries, and 1,567 unique reactions
compartmentalized into the cytoplasm, mitochondrion, plastid,
peroxisome, and vacuole. The curation process identified 75
essential reactions with respective enzyme associations not
assigned to any particular gene in the Kyoto Encyclopedia of
Genes and Genomes or AraCyc. With the addition of these
reactions, AraGEM describes a functional primary metabolism of
Arabidopsis. The reconstructed network was transformed into an
in silico metabolic flux model of plant metabolism and
validated through the simulation of plant metabolic functions
inferred from the literature. Using efficient resource
utilization as the optimality criterion, AraGEM predicted the
classical photorespiratory cycle as well as known key
differences between redox metabolism in photosynthetic and
nonphotosynthetic plant cells. AraGEM is a viable framework for
in silico functional analysis and can be used to derive new,
nontrivial hypotheses for exploring plant metabolism.
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2015-07-30 | MODEL1507180028 | BioModels
Project description:Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars. This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source. The functional genomics approach was used to identify sugar responsive genes, which rapidly (within 1 h) respond specifically to low concentration (1 mM) of glucose, fructose and/or sucrose. A habituated A. thaliana cell culture grown in a hormone free full strength MS media in the dark was adapted to growth on xylose as the only carbon source in the media.The cells were subjected to a 1 hour treatment with 1 mM of either Fru, Glc, Suc or Xyl (control). The experiments were carried out in 3 biological repeats per treatment. Whole genome expression analysis was conducted by hybridization of the extracted RNA to the Affymetrix Arabidopsis ATH1 Genome Array.
2014-05-16 | E-GEOD-57751 | biostudies-arrayexpress
Project description:We have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to Arabidopsis thaliana ecotype Ler-0 to infect a set of seven A. thaliana plant ecotypes(Col-0, Ei-2, Wt-1, ler-0, Oy-0, St-0). Each ecotype was inoculated with the same amount of the virus. Using commercial microarrays containing probes Arabidopsis thaliana ssp. Col-0 plant transcripts, we explored the effect of viral infection in the plant transcriptome
2012-07-04 | GSE37269 | GEO