Expression data from PSARK::IPT Nicotiana and wildtype plants
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana Solanum lycopersicum
PROVIDER: GSE19787 | GEO | 2010/01/09
SECONDARY ACCESSION(S): PRJNA121927
REPOSITORIES: GEO
Similar Datasets
Project description:Stress-induced leaf senescence could be delayed in transgenic plants expressing isopentenyltransferase (IPT), an enzyme that catalyzes the rate-limiting step in CK synthesis under the control of SARK, a maturation- and stress-inducible promoter (Rivero et al., 2007). Increased CK production resulted in enhanced drought tolerance of the transgenic PSARK::IPT plants, with minimal yield loss (Rivero et al., 2007). We have used a large-scale expression profiling approach to investigate the effects of PSARK::IPT on gene expression to elucidate the molecular events associated with the CK-induced drought tolerance displayed by the PSARK::IPT plants. We used tomato genechips to capture the differential transcriptional responses of WT and PSARK::IPT plants under control and water stress conditions Leaf samples from well watered (1000 mL per day) and water stressed (300 mL per day) plants were collected for RNA extraction and hybridization on Affymetrix microarrays after 45 days of stress.
2010-01-09 | E-GEOD-19787 | biostudies-arrayexpress
Project description:Transgenic rice plants expressing isopentenyltransferase (IPT), an enzyme that catalyzes the rate-limiting step in CK synthesis under the control of SARK, a maturation- and stress-inducible promoter. Increased CK production resulted in sink source alteration and enhanced drought tolerance of the transgenic plants.
2011-10-27 | GSE23211 | GEO
Project description:Transgenic rice plants expressing isopentenyltransferase (IPT), an enzyme that catalyzes the rate-limiting step in CK synthesis under the control of SARK, a maturation- and stress-inducible promoter. Increased CK production resulted in sink source alteration and enhanced drought tolerance of the transgenic plants. Flag leaf samples from well-watered (control) and water-stressed (3 days of withholding water) plants were collected for RNA extraction and hybridization on Affymetrix rice microarrays chip.
2011-10-26 | E-GEOD-23211 | biostudies-arrayexpress
Project description:In rice, gene expression profiling under different stresses have been carried out earlier through microarrays and SAGE (Kawasaki et al., 2001; Rabbani et al., 2003,;. Yazaki et al., 2003, 2004; Walia et al., 2005; Zhou et al., 2005; Jiao et al., 2005; Zhou, 2007; Wang, et al., 2007)). The results reported so far were mostly derived from different stress treatments, array formats, species, tissue types, and time courses, which make it difficult for direct comparison among studies. Also, most of the stress experiments on expression profiles were conducted under laboratory, growth chamber or field grown plants subjected to stress in laboratory conditions, usually by inducing stress with exogenous compounds such as abscisic acid (ABA) or gibberellin (GA) genes (Yazaki et al., 2003, 2004; Rabbani et al., 2003), salt (Kawasaki et al., 2001; Rabbani et al., 2003; Walia et al., 2005), organ specific gene expression under high salinity (Jiao et al., 2005) and drought (Zhou et al., 2007), comparison with different cultivars (Wang et al., 2007) and other environmental stresses such as cold and drought (Rabbani et al., 2003; Zhou et al., 2005). However, such laboratory, growth chamber grown plants or field grown plants subjected to stress under laboratory conditions significantly differ from the field stress conditions and therefore the resultant plant response may not truly represent the actual stress conditions prevailing on field. This has been extensively reviewed by Mittler, 2006 and the need for utilizing data from multiple stress experiments for developing plants resistant to stress has been focused. The review also focuses on evaluating farmers experiences in stress management and kinds of stress that a plant is subjected prior to taking up research on stress resistances has been of significant importance. In the present study, to bridge the gap between the available data on drought stress and the gene regulation under field drought conditions has been paid attention. The outcome of this data will give new leads for breeders to design strategies to develop plants resistant to drought without much loss in yield. In the present study experiments were conducted under different field capacities using a rainout shelter to minimizing the effects of drought induction due to rains. The microarray analysis is thus expected to throw light on stress responsive gene expression in field drought conditions. Till now, to our knowledge there have been no reports on gene expression in rice under field drought conditions. Further, there is no data available on gene expression profiling during various stages of plant growth in leaf and panicle tissues under different levels of water stress. Here, we have focused on generating stress responsive gene (SRG) expression profiles in field drought conditions through the entire life cycle of rice plant. Optimal drought simulation was achieved by conducting a drought stress experiment and validated by a series of dry runs. The main reason for evaluating gene expression under drought in field condition is as drought itself is not limited to water stress but various other factors, such as heat, humidity, hot winds, and long day lengths effect the gene regulation. All these are likely to trigger common pathways that are also a part of drought stress response and therefore significantly affect the expression profiles. In the present study, field drought stress was initiated from 31 days after germination and transplantation to the field at 100%, 60%, 40% and 15% field capacities designated as A1, A2, A3, and A4. It took 7 days for the onset of the actual drought for the experimental plots to reach to their designated field capacities from 100% FC. Samples were collected from 7 days after drought stress to 33 days after drought stress to evaluate different drought stress regimes based on the developmental stages of the plant. At all the tested stress levels the data points were Hierarchically grouped and clustered sets of genes were examined and an approximate number of clusters to be formed were estimated. Finding a group of genes showing a similar pattern of gene expression by means of expression data from microarray analysis is the basis for identification of genes and pathways controlling a specific trait. We have followed unsupervised classification and clustered the genes hierarchically after normalizing expression data to obtain a set of co-regulated genes. Analysis of data revealed that there are at least 3 to 4 clusters which show differential regulation under each stress regime. The annotated genes falling in these clusters interestingly include a number of novel genes from N22 library along with some known candidate genes for drought tolerance which were earlier identified in our study (Markandeya et al., 2007). Expression pattern of these genes from 7 days after drought stress to 33 days after drought stress with their fold changes were evaluated in the present study. In particular, it is observed that many genes of unknown function are also co-regulated in an interesting pattern along with known genes.
2011-11-27 | GSE31974 | GEO
Project description:Growth retardation and stress-induced premature plant senescence are accompanied by a severe yield reduction and raise a major agro-economic concern. To improve biomass and yield in agricultural crops under mild stress conditions, the survival must be changed to productivity mode. Our previous successful attempts to delay premature senescence and growth inhibition under abiotic stress conditions by autoregulation of cytokinins (CKs) levels constitute a generic technology toward the development of highly productive plants. Since this technology is based on the induction of CKs synthesis during the age-dependent senescence phase by a senescence-specific promoter (SARK), which is not necessarily regulated by abiotic stress conditions, we developed autoregulating transgenic plants expressing the IPT gene specifically under abiotic stress conditions. The Arabidopsis promoter of the stress-induced metallothionein gene (AtMT) was isolated, fused to the IPT gene and transformed into tobacco plants. The MT::IPT transgenic tobacco plants displayed comparable elevated biomass productivity and maintained growth under drought conditions. To decipher the role and the molecular mechanisms of CKs in reverting the survival transcriptional program to a sustainable plant growth program, we performed gene expression analysis of candidate stress-related genes and found unexpectedly clear downregulation in the CK-overproducing plants. We also investigated kinase activity after applying exogenous CKs to tobacco cell suspensions that were grown in salinity stress. In-gel kinase activity analysis demonstrated CK-dependent deactivation of several stress-related kinases including two of the MAPK components, SIPK and WIPK and the NtOSAK, a member of SnRK2 kinase family, a key component of the ABA signaling cascade. A comprehensive phosphoproteomics analysis of tobacco cells, treated with exogenous CKs under salinity-stress conditions indicated that >50% of the identified phosphoproteins involved in stress responses were dephosphorylated by CKs. We hypothesize that upregulation of CK levels under stress conditions desensitize stress signaling cues through deactivation of kinases that are normally activated under stress conditions. CK-dependent desensitization of environmental stimuli is suggested to attenuate various pathways of the avoidance syndrome including the characteristic growth arrest and the premature senescence while allowing normal growth and metabolic maintenance.
2021-09-09 | PXD019418 | Pride
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:Drought stress is the main environmental factor influencing hemp growth and yield. However, little is known about the response mechanism of hemp to drought stress. A total of 44.10 M tags and 8.91G bases were sequenced in the control hemp (CK) and drought stress hemp (DS) libraries. A total of 1292 differentially expressed genes (DEGs), including 883 up-regulated genes and 409 down-regulated genes, were identified. These results may contribute toward improving our understanding about the drought stress regulatory mechanism of hemp, and improving its drought tolerance ability.
2017-04-22 | GSE56964 | GEO
Project description:Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, miRNAs, and key miRNA-target pairs in M. ruthenica under drought and re-watering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed between the re-watering (RW) vs. drought (DS) comparison and control (CK) groups. The degradome sequencing analysis revealed that 348 miRNAs (37 novel and 311 conserved miRNAs) were identified with 6,912 target transcripts, forming 11,390 miRNA-target pairs in the three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21,18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.
2021-08-03 | GSE169022 | GEO
Project description:Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, miRNAs, and key miRNA-target pairs in M. ruthenica under drought and re-watering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed between the re-watering (RW) vs. drought (DS) comparison and control (CK) groups. The degradome sequencing analysis revealed that 348 miRNAs (37 novel and 311 conserved miRNAs) were identified with 6,912 target transcripts, forming 11,390 miRNA-target pairs in the three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21,18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.
2021-08-03 | GSE168920 | GEO
Project description:Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, miRNAs, and key miRNA-target pairs in M. ruthenica under drought and re-watering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed between the re-watering (RW) vs. drought (DS) comparison and control (CK) groups. The degradome sequencing analysis revealed that 348 miRNAs (37 novel and 311 conserved miRNAs) were identified with 6,912 target transcripts, forming 11,390 miRNA-target pairs in the three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21,18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.
2021-08-03 | GSE179927 | GEO