Similar Datasets
Project description:The target of rapamycin (TOR) kinase is a central regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions. Although the TOR pathway is conserved among eukaryotes, plants developed unique adaptations to this pathway to cope with their autotrophic and sessile nature. Here, we captured for the first time a proteome-wide view of the plant TOR phosphorylation and interaction landscape. After sampling four biological repeats, proteins were extracted, digested and phosphopeptides were enriched. In total, 8302 phosphopeptides on 2558 proteins were identified from all samples. After label free quantitative analysis, a filtered dataset of 5500 phosphopeptides on 2056 proteins was retained. To identify TOR-dependent sites, the control-, AZD8055- and rapamycin-treated samples were statistically analyzed using a linear mixed model to evaluate the effect of the treatment, time and the interaction between both. For T10, T20 and T40, the sucrose control samples were compared to the AZD8055 or rapamycin samples. In addition, the AZD8055 samples were compared to the rapamycin samples, and the sucrose control samples (T10, T20, T40) were compared to T0. Overall, the strongest effect occurred with AZD8055. Therefore, an additional filter was applied retrieving only phosphopeptides that changed at least two-fold upon AZD8055 treatment. In total, 96 unambiguous TOR-dependent phosphosites were detected on 66 proteins, linking TOR to a plethora of biological processes.
2019-07-17 | PXD008355 | Pride
Project description:The goal of this experiment was to explore the molecular network of glucose-TOR signaling in Arabidopsis seedling autotrophic transition stage. We used the whole-genome microarrays to detail the global program of gene expression mediated by glucose and TOR.
2013-04-05 | GSE40245 | GEO
Project description:The goal of this experiment was to explore the molecular network of glucose-TOR signaling in Arabidopsis seedling autotrophic transition stage. We used the whole-genome microarrays to detail the global program of gene expression mediated by glucose and TOR. Arabidopsis WT and estradiol inducible RNAi-tor seedlings were germinated in low light condition for 3 days to deplete seed nutrient supply. Fifteen mM glucose was adding back to reactivate the quiescent seedlings and the samples were harvested for RNA isolation. Transcript profiles were analyzed and compared between with and without glucose treatment to identify early glucose-TOR target genes. Each experimental condition was repeated three times and total 12 samples were generated.
2013-04-05 | E-GEOD-40245 | biostudies-arrayexpress
Project description:Rapamycin-sensitive transgenic Arabidopsis lines (BP12) expressing yeast FK506 Binding Protein12 (FKBP12) were developed. Inhibition of TOR in BP12 plants by rapamycin resulted in slower overall root, leaf and shoot growth and development leading to poor nutrient uptake and light energy utilization. Genetic and physiological studies together with RNA-Seq and metabolite analysis of TOR-suppressed lines revealed that TOR regulates development and lifespan in Arabidopsis by restructuring cell growth, carbon and nitrogen metabolism, gene expression, ribosomal RNA and protein synthesis.
2012-12-18 | GSE42968 | GEO
Project description:ngs2018_05_tor-analysis of arabidopsis mutants tor/lst8/yak1/maktor-Analysis of Arabidopsis insertion and suppressor mutants linked to the TOR signaling pathway.-Comparison of in vitro grown plantlets for lst8, yak1 mutants and double mutants corresponding to suppressor lines. Comparison of in vitro grown plantlets for mutants affected in LST8 interacting proteins (MAKTOR) compared to wild type.
2019-05-23 | GSE120003 | GEO
Project description:Upon illumination, etiolated seedlings experience a transition from heterotrophic to photoautotrophic growth. During this process, the tetrapyrrole biosynthesis pathway provides chlorophyll for photosynthesis. This pathway has to be tightly controlled to prevent the accumulation of photoreactive metabolites and to provide stoichiometric amounts of chlorophyll for its incorporation into photosynthetic protein complexes. Therefore, plants have evolved regulatory mechanisms to synchronize the biosynthesis of chlorophyll and chlorophyll-binding proteins. Two phytochrome-interacting factors (PIF1 and PIF3) and the DELLA proteins, which are controlled by the gibberellin pathway, are key regulators of this process. Here, we show that impairment of TARGET OF RAPAMYCIN (TOR) activity in Arabidopsis (Arabidopsis thaliana), either by mutation of the TOR complex component RAPTOR1B or by treatment with TOR inhibitors, leads to a significantly reduced accumulation of the photoreactive chlorophyll precursor protochlorophyllide in darkness but an increased greening rate of etiolated seedlings after exposure to light. Detailed profiling of metabolic, transcriptomic, and physiological parameters revealed that the TOR-repressed lines not only grow slower, they grow in a nutrient-saving mode, which allows them to resist longer periods of low nutrient availability. Our results also indicated that RAPTOR1B acts upstream of the gibberellin-DELLA pathway and its mutation complements the repressed greening phenotype of pif1 and pif3 after etiolation.
2018-07-17 | GSE114639 | GEO
Project description:gnp_blan06_torpten - rnai tor time course - The impact of the TOR pathway on growth and stress responses. Modification of translational and transcriptional profiles in Tor-inducible RNAi mutants and identification of TOR targets.
2011-01-07 | GSE25701 | GEO
Project description:Rapamycin-sensitive transgenic Arabidopsis lines (BP12) expressing yeast FK506 Binding Protein12 (FKBP12) were developed. Inhibition of TOR in BP12 plants by rapamycin resulted in slower overall root, leaf and shoot growth and development leading to poor nutrient uptake and light energy utilization. Genetic and physiological studies together with RNA-Seq and metabolite analysis of TOR-suppressed lines revealed that TOR regulates development and lifespan in Arabidopsis by restructuring cell growth, carbon and nitrogen metabolism, gene expression, ribosomal RNA and protein synthesis. Arabidopsis WT (Col)and BP12-2 (TOR knockdown line) seedlings at 15 DAG were treated with rapamycin for 3 days by transferring from 0.5 MS medium to 0.5 MS+10 ug/ml rapamycin. Triplicate samples of rapamycin treated WT and BP12-2 seedlings were used for RNA-Seq analysis (Illumina Hiseq 2000). Paired-end alignments were obtained through aligning short reads onto the reference Arabidopsis Genome (TAIR9) using Bowtie. More than 80% of the reads mapped onto the genome. Htseq-count was used to count the reads from the Bowtie derived output files. Differential expressed genes were identified using edgeR. The FDR-corrected P value for differential expression was set to be <=0.05.
2012-12-18 | E-GEOD-42968 | biostudies-arrayexpress
Project description:We performed targeted purification of polysomal mRNA (TRAP-Seq, Vragović et al, 2015 - http://dx.doi.org/10.1073/pnas.1417947112) using a transgenic line ubiquitously expressing a GFP-tagged RPL18 (Mustroph et al, 2009 - https://doi.org/10.1073/pnas.0906131106) 6h after the synchronous induction of lateral root formation by auxin treatment (IAA) upon inhibition of TOR activity (AZD8055 treatment, AZD). To correct for abundance of mRNA, bulk RNA-Seq was performed on the same samples and used to normalise the reads purified with the ribosomes.
2022-03-23 | GSE199203 | GEO
Project description:Expression of the EXS domain of PHO1 in the Arabidopsis thaliana pho1 mutant leads to improved shoot growth in comparison to the parental pho1 mutant. We have used RNAseq to study the gene expression profile in the roots and shoots of the pho1 mutant, two independent transgenic lines of pho1 expressing the EXS domain of PHO1 (lines EXS32 and EXS34) as well as a pho1 mutant transformed with the full length PHO1 gene (complemented line).
2016-01-15 | GSE73067 | GEO