Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: MSV000079641
PROVIDER: PRJNA360931 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5167790.fastq.gz | Fastqsanger.gz | |||
| SRR5167800.fastq.gz | Fastqsanger.gz | |||
| SRR5167810.fastq.gz | Fastqsanger.gz | |||
| SRR5167820.fastq.gz | Fastqsanger.gz | |||
| SRR5167830.fastq.gz | Fastqsanger.gz |
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Project description:We report global gene expression profilies of Brassinosteroid related Arabidopsis mutants in response to dehydration and fixed-carbon starvation stresses by RNA-seq
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Project description:We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) wild type plants under phosphate starvation stress and in plants with altered PHR1(-like) activity, comparing mutants of phr1 and phr1-phl1 grown in phosphate-lacking medium. Results show the central role of PHR1 and functionally redundant members of its family in the control of transcriptional responses to Pi starvation.
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Project description:Large-scale identification of transcripts with large cross-genotype differences in abundance provides a genome-wide approach to identify natural variation in gene function. Transcript profiling was performed in 20 Arabidopsis accessions at dusk, dawn and after a 6h extension of the night. Individual genes with a high variance in transcript abundances across accessions were identified by inspection at each individual time point and by ANOVA across all three time points. Up to 40% of genes show significant changes in transcript abundance between accessions, with over-enrichment for biotic resistance, including pathogenesis resistance proteins and glucosinolate metabolism, cell wall modification, minor carbohydrate metabolism, amino acid degradation, brassinosteroid metabolism, redox and abiotic stress and underrepresentation of photosynthesis, DNA synthesis, RNA processing, regulation of transcription, protein synthesis and protein targeting. Some functional classes were enriched at all three time points. Genes related to carbon starvation-responses were enriched specifically at dawn, when their transcript abundance varied independently of carbohydrate levels, pointing to genetic variation in the sensitivity with which low carbon is sensed. Cross-accession correlation networks were generated at each time point to identify sets of genes whose transcripts show coordinated change in abundance between accessions. A cluster that was highly enriched for cold-response genes was found at dusk and after an extension of the night. Another cluster found at all three time points was highly enriched for glucosinolate biosynthesis, and correlated with glucosinolate content. We conclude that genes involved in stress and defense related processes show especially large and coordinated natural variation in transcript abundance.
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Project description:Arabidopsis plants that have experienced stress from water withdrawal show an improved ability to tolerate subsequent exposures as a ‘memory’ from the previous stress. This physiological stress memory is associated with ‘transcriptional memory’ illustrated by a subset of dehydrations stress responding genes that produce significantly different transcript amounts during repeated dehydration stresses relative to their response in the first. Here we report the genome-wide representation of dehydration stress transcriptional memory genes in A. thaliana. We identify four novel transcription patterns in response to repeated dehydration stress treatments. The nature of the proteins encoded by genes from each type of memory-response pattern is analyzed and the consequences of the genes’ memory behavior are considered in the context of possible biological relevance. The memory behavior of genes co-regulated by the dehydration/ABA and other abiotic stress and hormone responding pathways suggested that the crosstalk at the transcriptional level between them was affected as well. The intensity and the nature of specific biochemical, membrane, chloroplast, and stress response-related interactions during multiple exposures to dehydration stress are different from the responses to a single dehydration stress. The results reveal additional, hitherto unknown, levels of complexity of the plants’ transcriptional behavior when adjusting and adapting to recurring water deficits.
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Project description:Background: Polycyclic aromatic hydrocarbons (PAHs) are toxic, widely-distributed, environmentally persistent, and carcinogenic byproducts of carbon-based fuel combustion. Previously, plant studies have shown that PAHs induce oxidative stress, reduce growth, and cause leaf deformation as well as tissue necrosis. To understand the transcriptional changes that occur during these processes, we performed microarray experiments on Arabidopsis thaliana L. under phenanthrene treatment, and compared the results to published Arabidopsis microarray data representing a variety of stress and hormone treatments. In addition, to probe hormonal aspects of PAH stress, we assayed transgenic ethylene-inducible reporter plants as well as ethylene pathway mutants under phenanthrene treatment. Results: Microarray results revealed numerous perturbations in signaling and metabolic pathways that regulate reactive oxygen species (ROS) and responses related to pathogen defense. A number of glutathione S-transferases that may tag xenobiotics for transport to the vacuole were upregulated. Comparative microarray analyses indicated that the phenanthrene response was closely related to other ROS conditions, including pathogen defense conditions. The ethylene-inducible transgenic reporters were activated by phenanthrene. Mutant experiments showed that PAH inhibits growth through an ethylene-independent pathway, as PAH-treated ethylene-insensitive etr1-4 mutants exhibited a greater growth reduction than WT. Further, phenanthrene-treated, constitutive ethylene signaling mutants had longer roots than the untreated control plants, indicating that the PAH inhibits parts of the ethylene signaling pathway. Conclusions: This study identified major physiological systems that participate in the PAH-induced stress response in Arabidopsis. At the transcriptional level, the results identify specific gene targets that will be valuable in finding lead compounds and engineering increased tolerance. Collectively, the results open a number of new avenues for researching and improving plant resilience and PAH phytoremediation.
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Project description:Arabidopsis thaliana plants that have experienced an initial exposure to dehydration stress (“trained plants”) have an increased ability to maintain leaf relative water content (RWC) during subsequent stresses than plants experiencing the stress for the first time and transcription of selected dehydration response genes is altered during successive exposures to dehydration stress. This physiological and transcriptional behavior of trained plants is consistent with a “memory “of an earlier stress. It is unknown whether such memory is present in other Angiosperm lineages and whether it is an evolutionarily conserved response to stress. Here, we analyzed the behavior and transcriptomes of maize (Zea mays) plants experiencing multiple dehydration stresses and compare them with responses of the evolutionarily distant A. thaliana. We found structurally related genes in maize that displayed the same memory-type responses as in A. thaliana, providing evidence of the conservation of function and transcriptional memory in the evolution of plants’ dehydration stress response systems. Similar to A. thaliana, trained Z. mays plants retained higher RWC during dehydration stress than untrained plants, due in part to maintaining reduced stomatal conductance, despite full recovery of RWC, after the first stress. Divergent transcriptional memory responses were also expressed, suggesting diversification of function among stress memory genes. Some dehydration stress memory genes were also shared with other stress and hormone responding pathways, indicating complex and dynamic interactions between different plant signaling networks. The results provide new insight into how plants respond to multiple dehydration stresses and provide a platform for studies of the functions of memory genes in adaptive responses to water deficit in monocot and eudicot plants .
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Project description:Arabidopsis mutants in the PMP/PNP oxidase PDX3 show abberant growth and development.RNA sequencing reveals strong induction of stress-related genes in pdx3, particularly those associated with biotic stress.
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