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Expression data from Arabidopsis grown in perlite and compost

ABSTRACT: Composts are the products obtained after the aerobic degradation of different types of organic matter wastes and can be used as substrates or substrate/soil amendments. There are a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost as growing medium compared to standard substrates. The purpose of this study was to unravel the gene expression alteration produced by the compost to gain knowledge about the mechanisms involved in the compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis compared to the standard substrate perlite. Microarray analyses revealed that 178 genes were differently expressed with a fold change cut off of 1 from which 155 were upregulated and 23 were down regulated in compost-grown compared to perlite-grown plants. Functional enrichment study of up regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched terms as well as immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA dependent/independent abiotic stress responses.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE42149 | GEO | 2012/11/09

SECONDARY ACCESSION(S): PRJNA179209

REPOSITORIES: GEO

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Expression data from Arabidopsis grown in perlite and compost

Project description:Composts are the products obtained after the aerobic degradation of different types of organic matter wastes and can be used as substrates or substrate/soil amendments. There are a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost as growing medium compared to standard substrates. The purpose of this study was to unravel the gene expression alteration produced by the compost to gain knowledge about the mechanisms involved in the compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis compared to the standard substrate perlite. Microarray analyses revealed that 178 genes were differently expressed with a fold change cut off of 1 from which 155 were upregulated and 23 were down regulated in compost-grown compared to perlite-grown plants. Functional enrichment study of up regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched terms as well as immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA dependent/independent abiotic stress responses. Global gene expression of plants grown in compost (3 biological replicates) versus plants grown in perlite (2 biological replicates) was studied.

2012-11-09 | E-GEOD-42149 | biostudies-arrayexpress

AtBRO1, BRO1-like domain-containing protein, modulates growth and abiotic stress responses in Arabidopsis

Project description:Plants physiological mechanisms are affected by Abscisic acid (ABA) via changing gene expression and empowers plants to adapt in numerous environments. Plants have evolved their protection mechanisms for seed germination and abiotic environments to deal with critical harsh conditions. Here, we have explored those changes in Arabidopsis thaliana plants subjected to multiple abiotic stresses. AtBro1 transcripts showed up-regulation in the presence of salt, ABA and mannitol stress conditions. AtBRO1 over-expression lines exhibited robust tolerance to drought and salt stress. Further, ABA elicits resistance responses in loss-of-function bro1-1 mutant plants and AtBro1 positively regulates drought resistance in Arabidopsis. Promoter of AtBro1 fused with GUS showed GUS expression mainly in the rosette leaves and floral clusters, especially in anthers. AtBro1 protein was found to be localized in the plasma membrane of Arabidopsis at the subcellular level by using AtBro1::GFP fusion. Using a broad RNA-sequencing analysis, we observed that early transcriptional responses prompted by ABA induction exhibit specific quantitative differences at different time points, suggesting that ABA stimulates resistance responses in bro1-1 mutant plants. Additionally, transcripts levels of MOP9.5, MRD1, HEI10, and MIOX4 were altered in loss-of-function mutant plants which are involved in different stress conditions. Collectively, our results have shown that AtBro1 is involved in a significant role by regulating plant transcriptional response to ABA and induction of resistance response against abiotic stress.

2023-04-18 | GSE225062 | GEO

JAZ1 attenuates drought resistance by regulating JA and ABA signaling in rice

Project description:Jasmonates (JA) and abscisic acid (ABA) are phytohormones known to play important roles in plant response and adaptation to various abiotic stresses including salinity, drought, wounding, and cold. JAZ (JASMONATE ZIM-domain) proteins have been reported to play negative roles in JA signaling. However, direct evidence is still lacking that JAZ proteins regulate drought resistance. In this study, OsJAZ1 was investigated for its role in drought resistance in rice. Expression of OsJAZ1 was strongly responsive to JA treatment, and it was slightly responsive to ABA, salicylic acid, and abiotic stresses including drought, salinity, and cold. The OsJAZ1-overexpression rice plants were more sensitive to drought stress treatment than the wild-type rice Zhonghua 11 (ZH11) at both the seedling and reproductive stages, while the jaz1 T-DNA insertion mutant plants showed increased drought tolerance compared to the wild-type plants. The OsJAZ1-overexpression plants were hyposensitive to MeJA and ABA, whereas the jaz1 mutant plants were hypersensitive to MeJA and ABA. In addition, there were significant differences in shoot and root length between the OsJAZ1 transgenic and wild-type plants under the MeJA and ABA treatments. A subcellular localization assay indicated that OsJAZ1 was localized in both the nucleus and cytoplasm. Transcriptome profiling analysis by RNA-seq revealed that the expression levels of many genes in the ABA and JA signaling pathways exhibited significant differences between the OsJAZ1-overexpression plants and wild-type ZH11 under drought stress treatment. Quantitative real-time PCR confirmed the expression profiles of some of the differentially expressed genes, including OsNCED4, OsLEA3, RAB21, OsbHLH006, OsbHLH148, OsDREB1A, OsDREB1B, SNAC1, and OsCCD1. These results together suggest that OsJAZ1 plays a role in regulating the drought resistance of rice partially via the ABA and JA pathways.

2018-02-28 | GSE107425 | GEO

WRKY33 binding sites in Arabidopsis upon Botrytis cinerea 2100 inoculation

Project description:The Arabidopsis thaliana mutant wrky33 is highly susceptible to the necrotrophic fungus Botrytis cinerea. We identified by ChIP-seq >1680 high-confidence WRKY33 binding sites associated with 1576 genes within the Arabidopsis genome, with all of them being dependent on rapid activation of WRKY33 expression by Botrytis cinerea strain 2100. Genome-wide transcriptional analysis defined 318 genes as direct functional targets at 14 h post inoculation. Comparison between resistant wild-type Columbia-0 and susceptible wrky33 mutant plants revealed that expression of 75% of all WRKY33 regulated targets were down-regulated upon infection, indicating that WRKY33 predominately acts as a repressor. However, WRKY33 appears to possess dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. Our genome-wide analysis confirmed known WRKY33 targets involved in ethylene and jasmonic acid hormone signaling and phytoalexin biosynthesis, but also uncovered a previously unknown role of abscisic acid (ABA) biosynthesis in the complex regulatory circuitry affecting resistance towards Botrytis. Analysis of transgenic plants expressing WRKY33-HA under its native promoter post inoculation with spores of Botrytis cinerea 2100

2015-06-15 | E-GEOD-66289 | biostudies-arrayexpress

Expression data of sound vibration-treated Arabidopsis thaliana during Botrytis cinerea infection

Project description:Sound vibration (SV), a mechanical stimulus, can trigger various molecular and physiological changes in plants. Herein, we investigated the effect of SV pre-treatment on Arabidopsis immunity to measure the priming potential of SV. Arabidopsis plants (fourteen-day-old) were treated with sound vibration (1000 Hz, 100 dB) for daily 3 hours up to 10 days in a soundproof chamber. The control plants were kept in a similar sound-proof chamber without SV exposure (daily 3 h) up to 10 days. After that, control and SV-treated plants were challenged with Botrytis cinerea spores. The result showed that SV pre-treatment increases the disease resistance of Arabidopsis against B. cinerea. Samples from three different time points were analyzed through microarray: (1) right after the 10th day of 3h SV treatment (0 h time point), and (2) after Botrytis spore inoculation (12 and 24 hpi time points). RNA was isolated from rosette leaves.

2017-04-29 | E-MTAB-4077 | biostudies-arrayexpress

RNA-seq analysis of Arabidopsis treated with abscisic acid (ABA) and its derivatives

Project description:Transcriptome of chemical-treated plants were investigated for the evaluation of ABA derivatives. Abscisic acid and its derivatives up-regulated mainly abiotic stress responsive genes.

2020-03-01 | GSE127910 | GEO

Chitosan primes plant defence mechanisms against Botrytis cinerea including Avr9/Cf-9 rapidly-elicited genes

Project description:Current protection strategies against the fungal pathogen Botrytis cinerea rely on a combination of conventional fungicides and host genetic resistance. Defence elicitors can stimulate plant defence mechanisms through a phenomenon known as priming. Priming results on a faster and/or stronger expression of resistance upon pathogen attack. This work aims to study priming of a commercial formulation of the elicitor Chitosan. Treatments with Chitosan result in induced resistance in solanaceous and brassicaceous plants. Large-scale transcriptomic analysis in this study revealed that Chitosan primes gene expression at early time-points after infection. Four conditions were analysed using microarrays: (i) water-treated and non-infected plants (Water + Mock); (ii) Chitosan-treated and non-infected plants (Chitosan + Mock); (iii) water-treated and B. cinerea-infected plants (Water + B. cinerea); (iv) Chitosan-treated and B. cinerea-infected plants (Chitosan + B. cinerea). Inoculations were performed four days after treatment with Chitosan, and leaf discs from four independent plants (biological replicates) per treatment were sampled at 6 h, 9 h and 12 h post-inoculation (hpi) with water mock or B. cinerea spores.

2020-07-01 | E-MTAB-8868 | biostudies-arrayexpress

Identification of ABA regulated genes in sunflower

Project description:Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. We studied in parallel microRNA profiles on the same samples and we will try to identify sunflower microRNA regulated genes in response to ABA. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.-The experiment consisted of 3 repeats of four 12-day-old-plantlets of sunflower genotype SF193 (INRA code: XRQ) grown in growth chamber conditions and submitted to a 6-hour-treatment of 10 µM absissic acid or not. Growth conditions were 14h light at 23°C and 10h night at 20°C under fluorescent bulbs. Plants were grown in 6 hydroponic boxes containing 20 litres of aerated liquid culture medium (as described in Massonneau et al., 2001 Planta). Leaves (not cotyledons) 1 to 4 were harvested 4 hours after light onset and frozen immediately in liquid nitrogen.

2012-12-09 | GSE22519 | GEO

The C-terminal domains SnRK2-box and ABA-box have a role in sugarcane SnRK2s auto-activation and activity

Project description:Resistance to drought stress is fundamental to plant survival and development. Abscisic acid (ABA) is one of the major hormones involved in different types of abiotic and biotic stress responses. ABA intracellular signaling has been extensively explored in Arabidopsis thaliana and occurs via a phosphorylation cascade mediated by three related protein kinases, denominated SnRK2s (SNF1-related protein kinases). However, the role of ABA signaling and the biochemistry of SnRK2 in crop plants remains underexplored. Considering the importance of the ABA hormone in abiotic stress tolerance, here we investigated the regulatory mechanism of sugarcane SnRK2s - known as SAPKs (Stress/ABA-activated Protein Kinases). The crystal structure of ScSAPK10 revealed the characteristic SnRK2 family architecture, in which the regulatory SnRK2-box interacts with the kinase domain αC helix. To study sugarcane SnRK2 regulation, we produced a series of mutants for the protein regulatory domains SnRK2-box and ABA-box. Surprisingly, mutations in the SnRK2-box did not drastically affect sugarcane SnRK2 activity, in contrast to previous observations for the homologous proteins in Arabidopsis. Also, we found that the ABA-box might have a role in SnRK2 activation in the absence of PP2C phosphatase. Taken together, our results demonstrate that both C-terminal domains of sugarcane SnRK2 proteins play a role in protein activation and activity.

2019-11-13 | PXD014298 | Pride

Barley Systemic Immunity: Dataset Induced challenged

Project description:Leaf-to-leaf, systemic immune signaling known as systemic acquired resistance (SAR) is poorly understood in monocotyledonous plants. Here, we characterize systemic immunity in barley (Hordeum vulgare) triggered after primary leaf infection with either Pseudomonas syringae pathovar japonica (Psj) or Xanthomonas translucens pathovar cerealis (Xtc). Both pathogens induced resistance in systemic, uninfected leaves against a subsequent challenge infection with Xtc. In contrast to SAR in Arabidopsis thaliana, systemic immunity in barley was not associated with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 or the local or systemic accumulation of salicylic acid (SA). Instead, we documented a moderate local but not systemic induction of abscisic acid (ABA) after infection of leaves with Psj. In contrast to SA or its functional analog benzothiadiazole, local applications of the jasmonic acid methyl ester or ABA triggered systemic immunity to Xtc. RNA-seq analysis of local and systemic transcript accumulation revealed unique gene expression changes in response to both Psj and Xtc and a clear separation of local from systemic responses. The systemic response appeared relatively modest and quantitative RT-PCR associated systemic immunity with the local and systemic induction of two WRKY and two ETHYLENE RESPONSIVE FACTOR-like transcription factors. Systemic immunity against Xtc was further associated with transcriptional changes after a secondary/systemic Xtc challenge infection; these changes were dependent on the primary treatment. Taken together, bacteria-induced systemic immunity in barley may be mediated in part by WRKY and ERF-like transcription factors possibly facilitating transcriptional reprogramming to potentiate immunity.

2014-11-24 | E-MTAB-3056 | biostudies-arrayexpress

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