E-MTAB-8326
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-8326 | ExpressionAtlas | 2019-10-04
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-8326-analysis-methods.tsv | Tabular | |||
| E-MTAB-8326-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-8326-configuration.xml | Xml | |||
| E-MTAB-8326-percentile-ranks.tsv | Tabular | |||
| E-MTAB-8326.condensed-sdrf.tsv | Tabular |
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Project description:Agrobacterium tumefaciens is a special plant pathogen causing crown gall disease. This pathogen is well known for the technology Agrobacterium-mediated transformation. As a pathogen, Agrobacterium triggers plant immunity, and this affects transformation. But the signaling components and pathways in plant immunity to Agrobacterium remain elusive. We demonstrate two Arabidopsis MAPKKs MKK4/MKK5 and their downstream MAPKs MPK3/MPK6 play a major role in both Agrobacterium-triggered immunity and Agrobacterium-mediated transformation. Agrobacteria induce MPK3/MPK6 activity and plant defense responsive genes expression in a very early stage. This process is dependent on MKK4/MKK5 function. Loss of function of MKK4 and MKK5 or their downstream MPK3 and MPK6 abolishes plant immunity to agrobacteria, and increases the transformation frequency, while activation of MKK4 and MKK5 enhances the plant immunity and represses the transformation. Global transcriptome indicates agrobacteria induce various plant defense pathways, including ROS production, ethylene and SA-mediated defense responses, and MKK4/MKK5 is essential for these pathways induction. Activation of MKK4 and MKK5 promotes ROS production and cell death in agrobacteria infection process. Ethylene and SA act bypass of MKK4/MKK5 signaling to regulate transformation. Based on these results, we propose MKK4/5-MPK3/6 cascade is an essential signaling pathway to regulate Agrobacterium-mediated transformation by modulating Agrobacterium-triggered plant immunity.
2021-10-20 | GSE179628 | GEO
Project description:VIP2 is a transcription regulator and the C-terminal NOT2 domain of VIP2 interacts with VirE2. However, AtVIP2 overexpressor lines in Arabidopsis did not show an improvement in Agrobacterium-mediated stable root transformation. To investigate the role of VIP2 in Agrobacterium-plant interaction, we carried out transcriptome profiling by comparing a homozygous Arabidopsis AtVIP2 overexpressor line with wild-type Col-0 plants following Agrobacterium infection.
2019-09-26 | E-MTAB-8326 | biostudies-arrayexpress
Project description:The pathogen Agrobacterium tumefaciens infects a broad range of plants, introducing the T-DNA into their genome. Contrary to all known bacterial phyto-pathogens, Agrobacterium lacks the hypersensitive response-inducing HRP genes although it introduces numerous proteins into the plant cell through a type IV secretion system. To understand the timing and extent of the plant transcriptional response to this unusual pathogen, we used an Arabidopsis 26-thousand gene oligonucleotide microarray. We inoculated Arabidopsis cell cultures with an oncogenic strain of Agrobacterium and analyzed four biological replicates to identify two robust sets of regulated genes, one induced and the other suppressed. In both cases, the response was distinct at 48 hours after infection, but not at 24 hours or earlier. The induced set includes genes encoding known defense proteins, the repressed set is enriched with genes characteristic of cell proliferation even though a growth arrest was not visible in the inoculated cultures. The analysis of the repressed genes revealed that the conserved upstream regulatory elements Frankiebox (a.k.a. “site II”) and Telobox are associated with the suppression of gene expression. The regulated gene sets should be useful in dissecting the signaling pathways in this plant-pathogen interaction. Keywords: Time-course of Agrobacterium infection
2006-01-31 | GSE4116 | GEO
Project description:WARNING: This library was yield low amount of material and it was over-amplified by PCR. This libraries are used study the robustness of several statitical methods against PCR artifacts. ChIP experiments were performed on Arabidopsis wildtype inflorescences using an antibody raised against a C-terminal peptide of SEP3. ArrayExpress Release Date: 2011-04-27 Publication Title: ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions Publication Author List: Jose M. Muino, Kerstin Kaufmann, Roeland C. H. J. van Ham, Gerco C. Angenent, and Pawel Krajewski Person Roles: submitter Person Last Name: Muino Person First Name: Jose Person Mid Initials: M. Person Email: jose.muino@wur.nl Person Phone: 0317-481122 Person Address: Droevendaalsesteeg 1, P.O. Box 16, 6700 AA Wageningen, The Netherlands Person Affiliation: Plant Research International B.V.
2011-07-14 | GSE30616 | GEO
Project description:Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs) were analyzed in wheat callus cells co-cultured with Agrobacterium by using RNA sequencing (RNA-seq). Note: All samples in SRA were assigned the same sample accession (SRS417803). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2013-05-07 | E-MTAB-4272 | biostudies-arrayexpress
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 roots in response to A. tumefaciens C58 for the identification of differentially expressed genes.
2014-10-28 | GSE62750 | GEO
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 leafs in response to A. tumefaciens C58 for the identification of differentially expressed genes.
2014-10-28 | GSE62749 | GEO
Project description:Analysis of the effect of heterologous expression of a soybean DREB2 gene (GmDREB2A;2)on the transcriptome of transgenic Arabidopsis plants. For the genetic modification of Arabidopsis, we introduced gene casettes that express our genes of interest into the genome viaT-DNA transfer using Agrobacterium tumefaciens.
2012-12-04 | E-MEXP-3692 | biostudies-arrayexpress
Project description:During Agrobacterium-mediated transformation of plant cells a part of the tumour inducing plasmid, the T-DNA, is integrated into the host genome. In addition, a number of virulence proteins are translocated into the host cell. The virulence protein VirE3 binds to the Arabidopsis thaliana pBrp protein, a plant-specific general transcription factor of the TFIIB family. To study a possible role of VirE3 in transcriptional regulation, we stably expressed virE3 in A. thaliana under control of a tamoxifen-inducible promoter. By RNA sequencing we showed that upon expression of virE3 the RNA levels of 607 genes were increased more than three-fold and those of 132 genes decreased more than three-fold.
2018-04-18 | GSE68130 | GEO
Project description:The intention of these gene expression analysis was to study host responses to an infection with Agrobacterium tumefaciens at different stages of crown gall development. Therefore the transcriptome of infected inflorescence stalk tissue and mature crown galls of Arabidopsis thaliana (WS-2) was determined of three different time points. These were compared with the transcriptome of mock-infected inflorescence stalk tissue (reference) of the same age. The following time points were analyzed: (i) three hours post inoculation, before the T-DNA is integrated into the host genome (ii) six days after inoculation when the T-DNA is present in the nucleus and the oncogenes are expressed in the host cell, and (iii) 35 days after inoculation when a mature tumors has developed. For the three-hour- (3hpi) and six-day- time point (6dpi) plants were infected with the virulent strain C58, harboring a T-DNA, or with strain GV3101, containing a disarmed Ti-plasmid. This allows discrimination between signals which derive from the bacterial pathogen and the T-DNA encoded oncogenes. This SuperSeries is composed of the following subset Series:; GSE13929: Arabidopsis thaliana three hours after infection with Agrobacterium tumefaciens; GSE13930: Arabidopsis thaliana six days after infection with Agrobacterium tumefaciens; GSE13927: Transcriptome of mature A. thaliana crown galls. Experiment Overall Design: Refer to individual Series
2009-12-02 | E-GEOD-14106 | biostudies-arrayexpress