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Arabidopsis thaliana
51 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Recognition of microbial patterns and host derived damage signals by host pattern recognition receptors is a key step in immune activation in multicellular eukaryotes. Here we show how mutations in ethylene signaling and the coreceptor bak1 affect host immune responses triggered by elicitors.
Publication Title
Layered pattern receptor signaling via ethylene and endogenous elicitor peptides during Arabidopsis immunity to bacterial infection.
Sample Metadata Fields
Treatment, Time
View Samples- Arabidopsis thaliana
- 34 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. The Arabidopsis Toll-related intracellular receptor RPS4 operates inside nuclei to trigger resistance to Pseudomonas bacteria expressing AvrRps4 and defence gene reprogramming through the stress response regulator, EDS1.
Publication Title
Arabidopsis TNL-WRKY domain receptor RRS1 contributes to temperature-conditioned RPS4 auto-immunity.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis SnRK1 is structurally and functionally related to the yeast Snf1 and mammalian AMP-activated kinases, which are activated in response to carbon/glucose limitation and stress conditions causing an imbalance of energy homeostasis increasing the AMP/ATP ratio. Mutations of the SNF4 activating subunit of trimeric Arabidopsis SnRK1 complexes are not transmitted through the male meiosis. Silencing of SNF4 by a -estradiol-inducible artificial microRNA (amiR-SNF4) constructs was used to examine how inhibition of SnRK1 affects transcriptional regulation of different cellular pathways in dark and light grown seedlings. This study shows that amiR-SNF4 silencing of SnRK1 leads to coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/endoplasmic reticulum stress and pathogen defense responses by inducing simultaneous changes in numerous other essential hormonal and metabolic pathways in Arabidopsis.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Serine phosphorylation of conserved Y1S2P3T4S5P6S7 repeats of RNA polymerase II carboxy-terminal domain (RNAPII CTD) plays a central role in the regulation of transcription and co-transcriptional RNA processing. Maintenance of CTD phosphoserine-7 mark in Arabidopsis requires the CDKF;1 kinase, which mediates in vivo activation of downstream-acting CDKD CTD kinase family. Knockout mutations of CDKF;1 lead to over 50% reduction of RNAPII CTD Ser-7 phosphorylation as early as 7 days after germination in seedlings. The transcript profiling experiment aimed at determining how early changes in CTD Ser-7 phosphorylation affect global regulation of transcription.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples
GSE65415- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
TIR-type nucleotide-binding leucine-rich repeat domain proteins (TNLs) constitute one major group of immune receptors in dicotyledonous plants. Under normal conditions, TNLs can detect non-self or modified-self within the plant cytoplasm to activate immune signaling characterized by extensive transcriptional reprogramming and efficiently counteracting pathogen infection. At the same time, TNLs, in negative epistatic interaction with a second endogeneous locus or allele are causal for induction of autoimmunity or hybrid necrosis. Both native, pathogen-induced TNL responses and autoimmunity are fully dependent on the plant-specific lipase-like protein EDS1, which is a central integrator for all TNL-mediated responses. EDS1 signals within structurally similar, but spatially distinct complexes with PAD4 and SAG101. We here analyzed stable transgenic lines expressing an EDS1 fusion with enforced nuclear localization. Even in absence of SAG101, nuclear-localized EDS1-PAD4 complexes are fully sufficient to function in basal and effector-triggered immunity. Furthermore, we show that nuclear EDS1, when expressed to high levels, can induce autoimmuity in combination with an RPP1-like gene cluster from ecotype Ler. RPP1-like genes are also implicated in several cases of hybrid necrosis, and we can identify the RPP1 paralog R8 as causal for autoimmunity induction by nuclear EDS1 and a previously characterized, EMS-induced mutation. This highlights the important role of EDS1-family proteins in the nuclear compartment in different immune-like responses.
Publication Title
Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity.
Sample Metadata Fields
Treatment, Time
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Although bodyguard (bdg), lacerata (lcr) and fiddlehead (fdh) mutations affect three unrelated genes, they trigger similar effects, i.e. ectopic organ fusion, increase of cuticle permeability. After performing cutin and wax analyses on these Arabidopsis thaliana mutants, which did not coincide with the putative enzyme functions, we hypothesised that these mutations trigger a complex response which may be visible at the transcriptional level.
Publication Title
Dissection of the complex phenotype in cuticular mutants of Arabidopsis reveals a role of SERRATE as a mediator.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 21 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Gene expression profiling leading to the identification of novel components in the EDS1/PAD4-regulated defence pathway
Publication Title
Salicylic acid-independent ENHANCED DISEASE SUSCEPTIBILITY1 signaling in Arabidopsis immunity and cell death is regulated by the monooxygenase FMO1 and the Nudix hydrolase NUDT7.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Arabidopsis thaliana
- 29 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We identified a small zinc finger protein, MBS, as a new mediator of singlet oxygen responses in Chlamydomonas and Arabidopsis. MBS is required for induction of singlet oxygen-dependent gene expression and, upon oxidative stress, accumulates in distinct granules in the cytosol of Arabidopsis cells. First, we recorded changes in light stress-regulated gene expression profiles after genetically perturbing MBS function by isolating mutants for the two MBS genes (MBS1 and MBS2) and by overexpression of MBS1 in Arabidopsis thaliana. Then, these light stress-related gene expression profiles were analyzed with respect to genes specifically responding to singlet oxygen and hydrogen peroxide/superoxide. The results indicated that MBS inactivation leads to an impaired response to singlet oxygen signaling under light stress.
Publication Title
A mediator of singlet oxygen responses in Chlamydomonas reinhardtii and Arabidopsis identified by a luciferase-based genetic screen in algal cells.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Saccharomyces cerevisiae
- 23 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Understanding the response processes in cellular systems to external perturbations is a central goal of large-scale molecular profiling experiments. We investigated the molecular response of yeast to increased and lowered temperatures relative to optimal reference conditions across two levels of molecular organization: the transcriptome using a whole yeast genome microarray and the metabolome applying the GC/MS technology with in-vivo stable-isotope labeling for accurate relative quantification of a total of 50 different metabolites. The molecular adaptation of yeast to increased or lowered temperatures relative control conditions at both the metabolic and transcriptional level is dominated by temperature-inverted differential regulation patterns of transcriptional and metabolite responses and the temporal response observed to be biphasic. The set of previously described general environmental stress response (ESR) genes showed particularly strong temperature-inverted response patterns. Among the metabolites measured, trehalose was detected to respond strongest to the temperature stress and with temperature-inverted up and downregulation relative to control, mid-temperature conditions. Although associated with the same principal environmental parameter, the two different temperature regimes caused very distinct molecular response patterns at both the metabolite and the transcript level. While pairwise correlations between different transcripts and between different metabolites were found generally preserved under the various conditions, substantial differences were also observed indicative of changed underlying network architectures or modified regulatory relationships. Gene and associated gene functions were identified that are differentially regulated specifically under the gradual stress induction applied here compared to abrupt stress exposure investigated in previous studies, including genes of as of yet unidentified function and genes involved in protein synthesis and energy metabolism.
Publication Title
No associated publication
Sample Metadata Fields
Time
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using omics technologies. For this purpose a short term sulphate-starvation / re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulphate starvation. Categorization by response behaviors under sulphate-starvation / re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.
Publication Title
Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples