Combining chemical and genetic approaches to increase drought resistance in plants
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE101488 | GEO | 2017/08/14
SECONDARY ACCESSION(S): PRJNA394661
REPOSITORIES: GEO
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Project description:Drought stress is a major threat to crop production, but effective methods to mitigate the adverse effects of drought are not available. Here, we report that adding fluorine atoms in the benzyl ring of the abscisic acid (ABA) receptor agonist AM1 optimizes its binding to ABA receptors by increasing the number of hydrogen bonds between the compound and the surrounding amino acid residues in the receptor ligand-binding pocket. The new chemicals, known as AMFs, have long-lasting effects in promoting stomatal closure and inducing the expression of stress-responsive genes. Application of AMFs or transgenic overexpression of the receptor PYL2 in Arabidopsis and soybean plants confers increased drought resistance. The greatest increase in drought resistance is achieved when AMFs are applied to the PYL2-overexpression transgenic plants. Our results demonstrate that the combining of potent chemicals with transgenic overexpression of an ABA receptor is very effective in helping plants combat drought stress.
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Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response
2008-11-19 | GSE9646 | GEO
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response Two-week-old Arabidopsis plants grown on the agar plates were subjected to the stress- or ABA- treatments. The total RNA was prepared from the treated- and untreated- plants, and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.
2008-11-19 | E-GEOD-9646 | biostudies-arrayexpress
Project description:BackgroundThe past decade has seen an upsurge in the number of publications in chemistry. The ever-swelling volume of available documents makes it increasingly hard to extract relevant new information from such unstructured texts. The BioCreative CHEMDNER challenge invites the development of systems for the automatic recognition of chemicals in text (CEM task) and for ranking the recognized compounds at the document level (CDI task). We investigated an ensemble approach where dictionary-based named entity recognition is used along with grammar-based recognizers to extract compounds from text. We assessed the performance of ten different commercial and publicly available lexical resources using an open source indexing system (Peregrine), in combination with three different chemical compound recognizers and a set of regular expressions to recognize chemical database identifiers. The effect of different stop-word lists, case-sensitivity matching, and use of chunking information was also investigated. We focused on lexical resources that provide chemical structure information. To rank the different compounds found in a text, we used a term confidence score based on the normalized ratio of the term frequencies in chemical and non-chemical journals.ResultsThe use of stop-word lists greatly improved the performance of the dictionary-based recognition, but there was no additional benefit from using chunking information. A combination of ChEBI and HMDB as lexical resources, the LeadMine tool for grammar-based recognition, and the regular expressions, outperformed any of the individual systems. On the test set, the F-scores were 77.8% (recall 71.2%, precision 85.8%) for the CEM task and 77.6% (recall 71.7%, precision 84.6%) for the CDI task. Missed terms were mainly due to tokenization issues, poor recognition of formulas, and term conjunctions.ConclusionsWe developed an ensemble system that combines dictionary-based and grammar-based approaches for chemical named entity recognition, outperforming any of the individual systems that we considered. The system is able to provide structure information for most of the compounds that are found. Improved tokenization and better recognition of specific entity types is likely to further improve system performance.
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Project description:Ozone at an elevated level is an important environmental stress factor that limits plant growth and development. To test how O3-induced ROS signalling interacts with the ABA pathway we present a global characterization of O3-responsive genes in the abi1td mutant. To understand better ABA signalling and the interactions between stress-response pathways we also performed a microarray analysis of drought-treated abi1td and WT plants. Since ABA signalling is well known to mediate defined responses based on the WT and different mutants analysis in drought stress conditions, the comparison of the O3 and drought stress response in abi1td enabled the identification of new processes depending on ABA-related pathways in O3-treated plants. Altogether, our findings indicate that ABI1 plays the role of a general signal transducer linking diferrent hormone signalling pathways to O3 stress tolerance.<br><br><br><br>Key words: ROS signalling; ABA signalling; ozone stress; drought stress; environmental stress; gene knockout;
2009-08-27 | E-MEXP-1863 | biostudies-arrayexpress
Project description:Chlorophyll was removed from the veins of the C3 plant Arabidopsis by combining enhancer trap and RNAi approaches. Three independent transgenic lines were created. These were each compared to the parent line, J1511, in a microarray experiment.
2009-12-01 | E-MEXP-1988 | biostudies-arrayexpress
Project description:CBP20 (Cap-Binding Protein 20) encodes a small subunit of the cap-binding complex (CBC), which is involved in the conserved cell processes related to RNA metabolism in plants and, simultaneously, engaged in the signaling network of drought response, which is dependent on ABA. CBP20 (Cap-Binding Protein 20), which encodes a small subunit of the cap-binding complex (CBC). CBC is a heterodimer that is formed by two subunits – a small one that is encoded by CBP20 and a large subunit that is encoded by CBP80 (Cap-Binding Protein 80). Both the nucleotide and amino acid sequences of CBP20 are highly conserved across species from Saccharomyces to Homo sapiens. CBP20 is involved in very conserved cell processes that are related to RNA metabolism such as polyadenylation and splicing, miRNA biogenesis, and according to the most recent reports, to histone methylation (Kuhn et al. 2008; Kim et al. 2008; Gregory et al. 2008; Kmieciak et al. 2002; Laubinger et al. 2008; Li et al. 2016). Most striking, however, is its simultaneous engagement in ABA signaling during seed germination and drought response (Papp et al. 2004; Jäger et al. 2011). It was shown that an Arabidopsis cbp20 mutant exhibited a hypersensitivity to ABA during seed germination and a better performance under water deficit conditions than the WT (Papp et al. 2004; Jäger et al. 2011). Interestingly, the Arabidopsis knockout mutant in CBP80 (Cap-Binding Protein 80; ABA hypersensitive 1) exhibited a similar phenotype when exposed to ABA or drought stress (Hugouvieux et al. 2001; 2002; Daszkowska-Golec et al. 2013). In Solanum tuberosum, an amiR80.2-14 mutant (CBP80 silenced using artificial microRNAs) was also reported to be drought tolerant (Pieczyński et al. 2013). Water-deficiency conditions related gene expression analysis was performed in barley in two genotypes: the wild-type (WT) barley cultivar 'Sebastian’ and hvcbp20.ab mutant; in three time points: (1) optimal water conditions, (2) onset of drought stress and (3) after 10 days of prolonged drought stress in the second leaf; analyses were performed in three biological replicates. Here, we report the enhanced tolerance to drought stress of barley mutant in the HvCBP20 gene.Transcriptome analysis using the Agilent Barley Microarray integrated with observed phenotypic traits allowed to conclude that the hvcbp20.ab mutant exhibited better fitness to stress conditions by its much more efficient and earlier activation of stress-preventing mechanisms. The network hubs involved in the adjustment of hvcbp20.ab mutant to the drought conditions were proposed. These results enabled to make a significant progress in understanding the role of CBP20 in the drought stress response.
2017-08-31 | E-MTAB-5719 | biostudies-arrayexpress
Project description:Pomegranate (Punica granatum L.) is sensitive to drought stress, which largely affects its transplantation survival rate, fruit yield and quality. Abscisic acid (ABA) treatment can reduce the drought-induced adverse impacts on plants. However, no studies have ever applied ABA as an exogenous supply to alleviate the drought stress on pomegranates. In this study, we performed comparative transcriptome analysis between the ABA-treated and untreated pomegranates to reveal the ABA-induced mechanisms in response to drought-stress. Our results showed that exogenous ABA application substantially enhanced pomegranate drought resistance by strengthening metabolic pathways, such as BRs synthesis, peroxisome biogenesis, photosynthesis and hemicelluloses synthesis. Furthermore, treatments with different ABA concentrations may provoke different transcriptional responses and, once the concentration exceeds the optimal (60 μM), it might induce some potential adverse impacts on plant growth and stress resistance.
2020-10-20 | GSE156104 | GEO
Project description:Histone H2B monoubiquitination (H2Bub1) has been implicated in several important physiological and developmental processes, but its role in the regulation of stress responses remains elusive. Here, we report that H2Bub1 is crucially involved in abscisic acid (ABA) signaling and drought response in rice. We found the rice (Oryza sativa) HISTONE MONOUBIQUITINATION2 (OsHUB2), an E3 ligase for H2Bub1, interacted with OsbZIP46, a key transcription factor regulating ABA signaling and drought response in rice. Genetic analyses suggest that OsHUB2, induced by drought and ABA, positively modulates ABA sensitivity and drought resistance. The H2Bub1 levels were increased in the promoters of OsbZIP46 target genes under the drought stress and ABA treatments, and the increased H2Bub1 levels were positively correlated to the increased expression levels of the target genes. Interestingly, MODD, a reported suppressor of ABA signaling and drought resistance through mediation of OsbZIP46 deactivation and degradation, can repress the H2Bub1 level in the promoters of OsbZIP46 target genes by recruiting a putative deubiquitinase OsOTLD1. Suppression of OsOTLD1 in vivo resulted in increased H2Bub1 levels and expression of drought-responsive genes targeted by OsbZIP46. These findings established an elaborate mechanism of histone monoubiquitination in the fine-turning of ABA signaling and drought response via balancing H2Bub1 deposition and removal.
2019-02-09 | GSE117047 | GEO
Project description:Water availability is a key determinant of terrestrial plant productivity. Many climate models predict that water stress will increasingly challenge agricultural yields and exacerbate projected food deficits. To ensure food security and increase agricultural efficiency, crop water productivity must be increased. Research over past decades has established that the phytohormone abscisic acid (ABA) is a central regulator of water use and directly regulates stomatal opening and transpiration. In this study, we investigated whether the water productivity of wheat could be improved by increasing its ABA sensitivity. We show that overexpression of a wheat ABA receptor increases wheat ABA sensitivity, which significantly lowers a plant’s lifetime water consumption. Physiological analyses demonstrated that this water-saving trait is a consequence of reduced transpiration and a concomitant increase in photosynthetic activity, which together boost grain production per liter of water and protect productivity during water deficit. Our findings provide a general strategy for increasing water productivity that should be applicable to other crops because of the high conservation of the ABA signaling pathway.
2019-01-03 | GSE79522 | GEO