Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differentially regulated genes in TOR knockdown Arabidopsis lines

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE42968 | GEO | 2012/12/18

SECONDARY ACCESSION(S): PRJNA183972

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Differentially regulated genes in TOR knockdown Arabidopsis lines

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

Inhibition of TOR Represses Nutrient Consumption, Which Improves Greening after Extended Periods of Etiolation

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

Chemical Genetics of TOR Identifies an SCF Family E3 Ubiquitin Ligase Inhibitor

2011-06-30 | GSE22272 | GEO

Analysis of arabidopsis mutants tor/lst8/yak1/maktor

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

Identification of new target genes of TOR during growth in MDN

Project description:To identify novel targets of TOR when prototrophic strain S288c is grown in MDN media. Arrays compare growth in MDN with and without addition of rapamycin. For comparison, growth in YPD versus MDN as well as SCD versus MDN were examined as well.

2010-06-30 | E-GEOD-3157 | biostudies-arrayexpress

Exploring the scope of TOR/PKA co-regulation in MDN

Project description:To identify genes co-regulated by TOR and PKA during growth in MDN BCY1, bcy1 deletion, TPK, and tpk1-3 deletion strains were grown in MDN with and without rapamycin treatment. Different combinations of these samples were examined.

2010-07-01 | E-GEOD-3160 | biostudies-arrayexpress

rnai tor time course - The signalization way TOR/PTEN in Arabidopsis

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

TOR early response genes in plant shoots

Project description:We identified TOR target genes using three different TOR active site inhbitors AZD8055, TORIN1 and KU63749 in Arabidopsis thaliana shoots

2023-02-01 | GSE197099 | GEO

Chemical Genetics of TOR Identifies an SCF Family E3 Ubiquitin Ligase Inhibitor

Project description:The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyper-activation of the mTOR pathway in human cancers, novel strategies to enhance TOR pathway inhibition are highly desirable. We used a yeast-based high-throughput chemical genetic screen to identify small-molecule enhancers of rapamycin (SMERs) and used whole genome expression analysis to identify their mechanisms of action. This SuperSeries is composed of the following subset Series: GSE22270: Expression data from Saccharomyces cerevisiae Met30 temperature-sensitive strain GSE22271: Expression data from Saccharomyces cerevisiae temperature-sensitive strains specific for SCF core components (Skp1, Cullin (Cdc53), E2 enzyme (Cdc34)) and the F-box protein Cdc4. Refer to individual Series

2011-06-30 | E-GEOD-22272 | biostudies-arrayexpress

Post-translational regulation of photosynthetic activity via the TOR kinase in plants.

Project description:Chloroplasts are the powerhouse of the plant cell, and their activity must be matched to plant growth to avoid photo-oxidative damage. We have identified a post-translational mechanism linking the conserved Target of Rapamycin (TOR) kinase that promotes growth and the guanosine tetraphosphate (ppGpp) signaling pathway that regulates chloroplast activity, and photosynthesis in particular. We find that RelA SpoT Homologue 3 (RSH3), a nuclear-encoded enzyme responsible for ppGpp biosynthesis, interacts directly with the TOR complex via a plant-specific N-terminal region which is phosphorylated in a TOR-dependent manner. Downregulating TOR activity increases ppGpp synthesis by RSH3, and reduces photosynthetic capacity. The TOR-RSH3 signaling axis therefore regulates chloroplast activity to match plant growth, and sets a new precedent for the regulation of organellar function by TOR.

2024-05-03 | PXD047124 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data