Transcriptome and translatome profiling of Arabidopsis upf1-3 pad4 mutant
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA610184 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11235135.fastq.gz | Fastqsanger.gz | |||
| SRR11235136.fastq.gz | Fastqsanger.gz | |||
| SRR11235137.fastq.gz | Fastqsanger.gz | |||
| SRR11235138.fastq.gz | Fastqsanger.gz | |||
| SRR11235139.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:Goal of the study is to decipher the role of UPF1 in maintaining transcriptome and translatome homeostasis in Arabidopsis
2020-09-09 | GSE146340 | GEO
Project description:We observed inhibition of the hypersensitive response (a typical ETI response) by PTI signaling in an Arabidopsis quadruple mutant dde2 ein2 pad4 sid2 (quad). Thus, we designed an experiment to see the interaction between ETI and PTI signaling at the transcriptome level. The Arabidopsis line dde2 ein2 pad4 sid2 Ed-AvrRpt2 (quadAvrRpt2) was used (Ed-AvrRpt2, estradiol-inducible AvrRpt2 transgene). In this plant line, ETI can be elicited by estradiol (Ed) treatment via in planta expression of AvrRpt2. Transcriptome responses to PTI only, ETI only, and PTI+ETI together were recorded.
2017-08-07 | GSE98075 | GEO
Project description:This experiment was designed to identify transcripts which are changed in plants deficient for evolutionary conserved EST1B gene. A mutation in est1b leads to a constitutive up-regulation of a PAD4-dependent pathogen response pathway. To eliminate secondary effects of the constitutive pathogen response in est1b mutants we will analyze transcriptoms in plants in which lack PAD4. Keywords: Expression profilling by array
2009-11-18 | GSE18979 | GEO
Project description:This experiment was designed to identify transcripts which are changed in plants deficient for evolutionary conserved EST1B gene. A mutation in est1b leads to a constitutive up-regulation of a PAD4-dependent pathogen response pathway. To eliminate secondary effects of the constitutive pathogen response in est1b mutants we will analyze transcriptoms in plants in which lack PAD4. Keywords: Expression profilling by array 6 samples were used in this experiment
2009-11-17 | E-GEOD-18979 | biostudies-arrayexpress
Project description:We examined the possible effects of hypertonic stress on Arabidopsis translatome using polysome profiling. We found that the translatome is partly and rapidly reprogrammed in response to hypertonic stress, and such translatome reprogramming is DCP5-dependent.
2022-01-20 | GSE193804 | GEO
Project description:Arabidopsis Enhanced Disease Susceptibility 1 (EDS1) and its direct partner Phytoalexin Deficient 4 (PAD4) are required for both basal resistance against virulent pathogens and innate immune responses mediated by all tested TIR (Toll-Interleukin-1 Receptors) type nucleotide-binding/leucine-rich-repeat (NLR) receptors. Using transgenic Arabidopsis plants in Col-0 eds1-2 pad4-1 background conditionally expressing PAD4 and constitutively expressing EDS1 (ED-P4E1), an EDS1/PAD4 immune response can be triggered by estradiol treatment and can induce expression of defense-related genes and lead to enhanced basal resistance. In order to capture primary transcriptional changes in response to EDS1/PAD4, we performed RNA-seq gene expression analysis in ED-P4E1 plants after estradiol or mock treatment at three time points: 6, 12 and 24 h.
2016-09-27 | GSE80585 | GEO
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis upf1-1 and upf3-1 mutants. Keywords: untreated condition
2009-01-14 | GSE12101 | GEO
Project description:There is growing evidence that for a comprehensive insight into the function of plant genes it is crucial to assess their functionalities under a wide range of conditions. In this study we examined the role of LESION SIMULATING DISEASE1 (LSD1), ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) in the regulation of photosynthesis, water use efficiency (WUE), ROS/hormonal homeostasis and seed yield in Arabidopsis thaliana grown in the laboratory and in the field. We demonstrate that the LSD1 null mutant (lsd1), which is known to exhibit a runaway cell death in non-permissive conditions, proves to be more tolerant to combined drought and high-light stress than the wild type. Moreover, depending on growing conditions, it shows variations in WUE, salicylic acid and hydrogen peroxide concentrations, photosystem II maximum efficiency and in transcription profiles. However, despite these changes, lsd1 demonstrates similar seed yield under all tested conditions. All of these traits depend on EDS1 and PAD4. The differences in the pathways prevailing in the lsd1 in various growing environments are manifested by the significantly smaller number of transcripts deregulated in the field compared to the laboratory, with only 43 commonly regulated genes. Our data indicate that LSD1, EDS1 and PAD4 participate in the regulation of various molecular and physiological processes that influence Arabidopsis fitness. On the basis of these results we emphasize that the function of such important regulators as LSD1, EDS1 and PAD4 should be studied not only under stable laboratory conditions, but also in the environment abounding in multiple stresses. Six genotypes x two conditions experiment including five-week-old WT (Ws), lsd1, pad4, eds1, eds1lsd1, and pad4lsd1 plants grown in laboratory or field conditions, hybridized in two loop-designs (lab and field). Two biological replicates. In total, 2 x 12 samples were hybridized on 24 Arabidopsis Gene Expression microarrays V4 (Agilent, two-color array) including color swap of replicate samples.
2013-02-07 | E-GEOD-24766 | biostudies-arrayexpress
Project description:There is growing evidence that for a comprehensive insight into the function of plant genes it is crucial to assess their functionalities under a wide range of conditions. In this study we examined the role of LESION SIMULATING DISEASE1 (LSD1), ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) in the regulation of photosynthesis, water use efficiency (WUE), ROS/hormonal homeostasis and seed yield in Arabidopsis thaliana grown in the laboratory and in the field. We demonstrate that the LSD1 null mutant (lsd1), which is known to exhibit a runaway cell death in non-permissive conditions, proves to be more tolerant to combined drought and high-light stress than the wild type. Moreover, depending on growing conditions, it shows variations in WUE, salicylic acid and hydrogen peroxide concentrations, photosystem II maximum efficiency and in transcription profiles. However, despite these changes, lsd1 demonstrates similar seed yield under all tested conditions. All of these traits depend on EDS1 and PAD4. The differences in the pathways prevailing in the lsd1 in various growing environments are manifested by the significantly smaller number of transcripts deregulated in the field compared to the laboratory, with only 43 commonly regulated genes. Our data indicate that LSD1, EDS1 and PAD4 participate in the regulation of various molecular and physiological processes that influence Arabidopsis fitness. On the basis of these results we emphasize that the function of such important regulators as LSD1, EDS1 and PAD4 should be studied not only under stable laboratory conditions, but also in the environment abounding in multiple stresses.
2013-02-07 | GSE24766 | GEO
Project description:Arabidopsis pathogen effector-triggered immunity (ETI) is controlled by a family of three lipase-like proteins EDS1, PAD4 and SAG101 and two sub-families of HET-S/LOB-B (HeLo)-domain “helper” NLRs, ADR1s and NRG1s. EDS1-PAD4 dimers cooperate with ADR1s, and EDS1-SAG101 dimers with NRG1s, in two separate defense-promoting modules. EDS1-PAD4-ADR1 and EDS1- SAG101-NRG1 complexes were detected in immune-activated leaf extracts but the molecular determinants for specific complex formation and function remain unknown. EDS1 signaling is mediated by a C-terminal EP domain (EPD) surface surrounding a cavity formed by the heterodimer. Here we investigated whether the EPDs of PAD4 and SAG101 contribute to EDS1 dimer functions. Using a structure-guided approach, we undertook a comprehensive mutational analysis of Arabidopsis PAD4. We identify two conserved residues (Arg314 and Lys380) lining the PAD4 EPD cavity that are essential for EDS1-PAD4 mediated pathogen resistance, but are dispensible for PAD4 mediated restriction of green peach aphid infestation. Positionally equivalent Met304 and Arg373 at the SAG101 EPD cavity are required for EDS1-SAG101 promotion of ETI-related cell death. In a PAD4 and SAG101 interactome analysis of ETI-activated tissues, PAD4R314A and SAG101M304R EPD variants maintain interaction with EDS1 but lose association, respectively, with helper NLRs ADR1-L1 and NRG1.1, and other immune-related proteins. Our data reveal a fundamental contribution of similar but non-identical PAD4 and SAG101 EPD surfaces to specific EDS1 dimer protein interactions and pathogen immunity.
2022-03-17 | PXD029477 | Pride