Expression data of ahg2-1, ahg2-1abi1-1, ahg2-1sid2-2, and WT Arabidopsis plants grown under normal growth conditions.
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE16913 | GEO | 2009/11/27
SECONDARY ACCESSION(S): PRJNA117703
REPOSITORIES: GEO
Similar Datasets
Project description:Arabidopsis ABA hypersensitive germination2-1 mutant shows an enhanced sensitivity to ABA. This mutant has higher levels of endogenous ABA. This mutant also exhibited SA hypersensitivity and dwarf phenotype. Regarding SA hypersensitivity, ahg2-1 exhibits higher endogenous SA level and an enhanced resistance to pathogenic bacteria. Since AHG2 encodes the Arabidopsis polyA specific ribonuclease that is involved in mRNA degradation, presumably abnormal accumulation of some mRNAs confers the unique phenotype. Transcriptome analyses are expected to offer information on the target of AHG2. In order to eliminate secondary effects of higher levels of ABA and SA, ahg2-1abi1-1 and ahg2-1sid2-2 double mutants were also examined. The transcriptome data revealed that; ahg2-1 confers unique gene expression profiles, ABA and SA affect the expression profiles of this mutant but many genes are independent of those plant hormone responses. Comparing with expression profiles of other mutants indicated that the ahg2-1 might affect mitochondrial function. Keywords: strain comparison, ABA, SA To investigate the whole genome transcription profiles of an ABA and SA hypersensitive mutant ahg2-1, transcriptome analysis for wild type, ahg2-1, ahg2-1abi1-1, ahg2-1sid2-2 plants were conducted. The plants of those lines were grown on MS-pplante containing 0,2% sucrose for three weeks under normal conditions. Comparing the data among those four lines, the direct targets of the ahg2-1 mutation were analyzed using R. In addition, the deduced data were compared with transcriptome data of various mutants or stimuli deposited in public database.
2009-11-26 | E-GEOD-16913 | biostudies-arrayexpress
Project description:Plant hormones involved in environmental stresses, namely abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), have been shown to interact with each other in a complex manner. To address the network of the hormone interactions, we have investigated the changes in expression under multiple hormone treatments, ABA+SA and ABA+JA. We chose cultured cells to remove the difference in the response to hormones among developmental cells or tissues. The cells were treated for 3hr and 24hr to see the rapid or transient response and steady-state response. The obtained data indicate that ABA and SA affect antagonistically, but these hormones affected many genes collaboratively. Indeed, according to the microarray data, there are many genes that responded only to ABA+SA. In addition, the ABA+SA responsive genes also responded to ABA+JA. These data suggest that hormone crosstalk is more complicated than expected and that more systematic analysis is required to untangle the hormone crosstalk network. To investigate the hormonal interactions, Arabidopsis T87 cultured cells were exposed to ABA, SA, or JA alone, or two hormones simultaneously, ABA+SA or ABA+JA, for 3hr and 24 hr. Comparing the data among those treatments, the relationships among these hormones were deduced.
2011-12-01 | E-GEOD-28600 | biostudies-arrayexpress
Project description:Plant hormones involved in environmental stresses, namely abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), have been shown to interact with each other in a complex manner. To address the network of the hormone interactions, we have investigated the changes in expression under multiple hormone treatments, ABA+SA and ABA+JA. We chose cultured cells to remove the difference in the response to hormones among developmental cells or tissues. The cells were treated for 3hr and 24hr to see the rapid or transient response and steady-state response. The obtained data indicate that ABA and SA affect antagonistically, but these hormones affected many genes collaboratively. Indeed, according to the microarray data, there are many genes that responded only to ABA+SA. In addition, the ABA+SA responsive genes also responded to ABA+JA. These data suggest that hormone crosstalk is more complicated than expected and that more systematic analysis is required to untangle the hormone crosstalk network.
2011-12-01 | GSE28600 | GEO
Project description:Plants adapt to abiotic and biotic stresses by activating abscisic acid-mediated (ABA) abiotic stress-responsive and salicylic acid-(SA) or jasmonic acid-mediated (JA) biotic stress-responsive pathways, respectively. Although the abiotic stress-responsive pathway interacts antagonistically with the biotic stress-responsive pathways, the mechanisms that regulate these pathways remain largely unknown. In this study, we provide insight into the function of vascular plant one-zinc-finger proteins (VOZs) that modulate various stress responses in Arabidopsis. The expression of many stress-responsive genes was changed in the voz1voz2 double mutant under normal growth conditions. Consistent with altered stress-responsive gene expression, freezing- and drought-stress tolerances were increased in the voz1voz2 double mutant. In contrast, resistance to a fungal pathogen, Colletotrichum higginsianum, and to a bacterial pathogen, Pseudomonas syringae, was severely impaired. Thus, impairing VOZ function simultaneously conferred increased abiotic tolerance and biotic stress susceptibility. In a chilling stress condition, both the VOZ1 and VOZ2 mRNA expression levels and the VOZ2 protein level gradually decreased. VOZ2 degradation during cold exposure was completely inhibited by the addition of the 26S proteasome inhibitor, MG132, a finding that suggested that VOZ2 degradation is dependent on the ubiquitin/26S proteasome system. In voz1voz2, ABA-inducible transcription factor CBF4 expression was enhanced significantly even under normal growth conditions, despite an unchanged endogenous ABA content. A finding that suggested that VOZs negatively affect CBF4 expression in an ABA-independent manner. These results suggest that VOZs function as both negative and positive regulators of the abiotic and biotic stress-responsive pathways, and control Arabidopsis adaptation to various stress conditions.
2012-11-19 | GSE24741 | GEO
Project description:Arabidopsis ABA3 is an enzyme involved in the synthesis of the sulfurated form of the molybdenum (Mo) cofactor (MoCo), which is required for the enzymatic activity of so-called Mo enzymes such as aldehyde oxidase (AO) and xanthine dehydrogenase (XDH). It has been reported that AO and XDH are essential for the biosynthesis of the bioactive compounds, ABA and allantoin, respectively. However, aba3 mutants often exhibit pleiotropic phenotypes that are not explained by defects in ABA and/or allantoin biosynthesis, leading us to hypothesize that ABA3 regulates additional metabolic pathways. To reveal the currently unidentified functions of ABA3 we compared transcriptome and metabolome of the Arabidopsis aba3 mutant with those of wild type and a typical ABA-deficient mutant aba2. We found that endogenous levels of anthocyanins, members of the flavonoid group, were significantly lower in the aba3 mutant than in the wild type or the aba2 mutant under oxidative stress. In contrast, mutants defective in the AO and XDH holoenzymes accumulated significantly higher levels of anthocyanins when compared with aba3 mutant under the same conditions. Our findings shed light on a key role of ABA3 in the ABA- and allantoin-independent accumulation of anthocyanins during stress responses.
2018-11-13 | GSE110079 | GEO
Project description:Several phytohormones and other small molecules have been demonstrated to be involved in iron (Fe) homeostasis. However, how salicylic acid (SA), an essential hormone in plant immunity and defense responses, participates in Fe-deficiency responses in plants is largely unknown. Here, we took advantage of a SA biosynthesis defect mutant phytoalexin deficient 4 (pad4: T-DNA Salk_089936) to explore the possible effects of endogenous SA on the morphological and physiological responses to Fe deprivation. Under a Fe-deficiency treatment, Col-0 showed more severe leaf chlorosis and root growth inhibition compared with the pad4 mutant. The soluble Fe concentrations were significant higher in pad4 than Col-0 under the Fe-deficiency treatment, suggesting that a mutation in the PAD4 gene may alleviate the Fe-deficiency-induced symptoms by regulating the soluble Fe concentrations. Furthermore, a SA signaling maker line (PR1promoter: GUS) was used to investigate how Fe deficiency affects endogenous SA biosynthesis and metabolism. The data showed that Fe deficiency significantly induced SA accumulation in Col-0, and the loss function of PAD4 blocked this process. The requirement of endogenous SA accumulation for Fe-deficiency responses was confirmed using a series of SA biosynthetic mutants and transgenic lines.
2016-10-01 | GSE74515 | GEO
Project description:Pokhilko2013 - TOC1 signalling in Arabidopsis
circadian clock
In this model, Pokhilko
et al. has incorporated the negative transcriptional
regulations of the core clock genes by TOC1 and the up-regulation
of TOC1 expression by ABA signalling, to their previous model
BIOMD0000000412
This model is described in the article:
Modelling the widespread
effects of TOC1 signalling on the plant circadian clock and its
outputs.
Pokhilko A, Mas P, Millar AJ.
BMC Syst Biol 2013; 7: 23
Abstract:
BACKGROUND: 24-hour biological clocks are intimately
connected to the cellular signalling network, which complicates
the analysis of clock mechanisms. The transcriptional regulator
TOC1 (TIMING OF CAB EXPRESSION 1) is a founding component of
the gene circuit in the plant circadian clock. Recent results
show that TOC1 suppresses transcription of multiple target
genes within the clock circuit, far beyond its
previously-described regulation of the morning transcription
factors LHY (LATE ELONGATED HYPOCOTYL) and CCA1 (CIRCADIAN
CLOCK ASSOCIATED 1). It is unclear how this pervasive effect of
TOC1 affects the dynamics of the clock and its outputs. TOC1
also appears to function in a nested feedback loop that
includes signalling by the plant hormone Abscisic Acid (ABA),
which is upregulated by abiotic stresses, such as drought. ABA
treatments both alter TOC1 levels and affect the clock's timing
behaviour. Conversely, the clock rhythmically modulates
physiological processes induced by ABA, such as the closing of
stomata in the leaf epidermis. In order to understand the
dynamics of the clock and its outputs under changing
environmental conditions, the reciprocal interactions between
the clock and other signalling pathways must be integrated.
RESULTS: We extended the mathematical model of the plant clock
gene circuit by incorporating the repression of multiple clock
genes by TOC1, observed experimentally. The revised model more
accurately matches the data on the clock's molecular profiles
and timing behaviour, explaining the clock's responses in TOC1
over-expression and toc1 mutant plants. A simplified
representation of ABA signalling allowed us to investigate the
interactions of ABA and circadian pathways. Increased ABA
levels lengthen the free-running period of the clock,
consistent with the experimental data. Adding stomatal closure
to the model, as a key ABA- and clock-regulated downstream
process allowed to describe TOC1 effects on the rhythmic gating
of stomatal closure. CONCLUSIONS: The integrated model of the
circadian clock circuit and ABA-regulated environmental sensing
allowed us to explain multiple experimental observations on the
timing and stomatal responses to genetic and environmental
perturbations. These results crystallise a new role of TOC1 as
an environmental sensor, which both affects the pace of the
central oscillator and modulates the kinetics of downstream
processes.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000445.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000445 | BioModels
Project description:Loss of the seed-specific WRKY transcription factor WRKY43 confers enhanced tolerance towards high salt, high osmolarity and low temperature with respect to seed germination. wrky43 loss of function lines display increased inhibition of seed germination in response to exogenous ABA, while WRKY43 overexpression lines are more tolerant towards exogenous ABA. The opposing effect of the wrky43 mutant on salt and ABA tolerance is reminiscent of fatty acid desaturase mutants. Loss of WRKY43 enhances polyunsaturated fatty acid content, particularly 18:2 and 18:3 in TAGs and Phospholipids. Gene chip arrays show that ABA-induced regulation of FUSCA3, ZAT10 and seed storage proteins are absent in the wrky43 mutant. Promoter-Luciferase studies confirm direct regulation of ZAT10 by WRKY43 and suggest indirect regulation of FUS3 and SSPs. In summary WRKY43 acts as a positive regulator of ABA-dependent gene regulation and of fatty acid desaturation that finally results in enhanced tolerance to abiotic stress. 2 biological replicates of Arabidopsis thaliana Ler-0 wildtype and wrky43 muatnt seeds were compared after incubation in liquid 0.5 MS media with 2 µM ABA for 4 days
2016-08-16 | E-GEOD-72154 | biostudies-arrayexpress
Project description:ZFP3, a nuclear C2H2 zinc finger protein acts as a negative regulator of ABA- suppressed germination. Regulated over-expression of ZFP3 and closely related ZFP1, ZFP4, ZFP6 and ZFP7 confers ABA insensitivity to seed germination while the zfp3,zfp4 double mutant displays enhanced ABA susceptibility. Reduced expression of a large set of ABA-induced genes such as RAB18 and transcription factors ABI3, ABI4, ABI5 and RGL2 in ZFP3ox seedling suggests that ZFP3 indeed negatively regulates ABA signaling. Analysis of ZFP3ox plants revealed multiple phenotypic alterations such as semidwarf growth habit, defects in fertility and enhanced sensitivity of hypocotyl elongation to red but not to far-red or blue light. Analysis of genetic interactions with phytochrome and abi mutants suggested that ZFP3 amplifies red light signals perceived by photoreceptors other than phyB, and controlled by ABI5 downstream of ZFP3. Comparison of ZFP3 overexpressing and wild type Arabidopsis seedlings
2014-01-01 | E-GEOD-48661 | biostudies-arrayexpress
Project description:NPR1 is a central positive regulator of salicylic-acid (SA)-mediated defense signaling in Arabidopsis. Here, we report characterization of OsNPR1, an Oryzae sativa (rice) ortholog of NPR1, focusing on its role in blast disease resistance and identification of OsNPR1-regulated genes followed by their comparison with NPR1-regulated genes in Arabidopsis. Blast resistance tests using OsNPR1–knockdown and –overexpressing rice lines indicated that OsNPR1 plays an essential role in benzothiadiazole-induced blast resistance. Genome-wide transcript profiling using OsNPR1–knockdown lines revealed that 358 genes out of 1,228 BTH-upregulated genes and 724 genes out of 1,069 BTH-downregulated genes were OsNPR1 dependent with respect to their BTH responsiveness, indicating that OsNPR1 plays a major role in the downregulation. Inspection of OsNPR1-dependent genes revealed that many genes involved in photosynthesis and chloroplastic translation and transcription were downregulated by BTH in an OsNPR1 dependent manner, indicating that photosynthesis and chloroplast activities is coordinately suppressed by OsNPR1 in response to BTH-induced activation of SA-signaling pathway. ABA-responsive genes were also OsNPR1-dependently downregulated, suggesting antagonistic interaction of SA signaling on ABA signaling. None of 11 BTH-upregulated genes for WRKY transcription factors was OsNPR1 dependent, whereas most of those are NPR1-dependently upregulated in Arabidopsis, indicating that the role of OsNPR1 is distinct from that of NPR1 in Arabidopsis. We discuss the significance of OsNPR1-regulated gene expression in SA-regulated defense program and the role of OsNPR1 in rice SA-signaling pathway that is branched to OsNPR1- and rice WRKY45-dependent sub-pathways.
2010-12-24 | GSE16144 | GEO