Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Title: Leaf transcriptomics of Catalan A. thaliana demes under alkaline and carbonated stress at 3h and 48 hours.

ABSTRACT: Purpose: High carbonate and bicarbonate concentrations of calcareous soils with high pH can affect crop performance due to different constraints. The goal of this study is to perform a comparative transcriptomic analysis using demes moderate-tolerance and sensitive under alkaline stress ( high pH 8.3 and 10 mM NaHCO3) Methods: Transcriptomic analysis was performed on two naturally selected Arabidopsis thaliana demes. Carbon soil tolerant A1(c+) and the sensitive T6(c-). Plants 15 day-old were exposed for 3 or 48 h to either pH stress alone (pH 5.9 vs pH 8.3 adjusted by BTP and MES buffers) or to alkaline stress (pH 8.3) caused by 10 mM of Results Shoot transcriptome analysis revealed that bicarbonate quickly (3 h) induced Fe-deficiency related genes in T6(c-) leaves, while in A1 (c+) main initial changes were found in receptor-like proteins (RPL), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolate (GS), Sulphur starvation, starch degradation, and cell cycle. Conclusions: Our results suggest that leaves of carbonate tolerant plants do not sense iron deficiency as fast as sensitive ones. This is in line with the ability to translocate more iron to aerial parts, producing a higher biomass and maintaining silique production. In leaves of A1(c+) plants, the activation of other genes related to apoplastic stress perception, signal transduction, GS, sulphur acquisition, and cell cycle regu-lation precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE164502 | GEO | 2021/02/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CRISPR/Cas9 screen identifies oxidative phosphorylation as essential for cancer cell survival at low extracellular pH

Project description:Unlike most cell types, many cancer cells survive at low extracellular pH (pHe), a chemical signature of tumors. Genes that facilitate survival under acid stress are therefore potential targets for cancer therapies. We performed a genome-wide CRISPR/Cas9 cell viability screen at physiological and acidic conditions to systematically identify gene knockouts associated with pH-related fitness defects in colorectal cancer cells. Knockouts of genes involved in oxidative phosphorylation (NDUFS1) and iron-sulfur cluster biogenesis (IBA57, NFU1) grew well at physiological pHe, but underwent profound cell death under acidic conditions. We identified several small-molecule inhibitors of mitochondrial metabolism that can kill cancer cells at low pHe only. Xenografts established from NDUFS1-/- cells grew considerably slower than their wild-type controls, but growth could be stimulated with systemic bicarbonate therapy which lessens the tumoral acid stress. These findings raise the possibility of therapeutically targeting mitochondrial metabolism in combination with acid stress as a cancer treatment option.

2022-02-26 | GSE195484 | GEO

Complex regulatory mechanisms underlying mineral nutrient acquisition in soybean roots responsive to low pH stress

Project description:Proton toxicity is one of the major environmental stresses limiting crop production, and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrient accumulation and global transcriptome changes in soybean (Glycine max) in response to long-term acid stress were investigated. Results showed that acid stress significantly inhibited soybean root growth, but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acid stress, mainly dependent on soybean organs and mineral nutrient types. The concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N) and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased, respectively. Whereas, the concentrations of calcium (Ca), sulfate (S) and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identifying 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrient transportation. Among them, all the detected five GmPTs and GmZIPs, two GmAMTs and GmKUP genes, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5 and GmHKT1, were significantly suppressed. Moreover, the genes encoding transcription factors (e.g., GmSTOP2s and a GmPHL1), and genes involved in pH stat metabolic pathways were significantly up-regulated by low pH stress in soybean roots. Taken together, it strongly suggested that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acid stress, which might be regulated by a complex signaling network.

2019-06-24 | GSE129320 | GEO

Chemical potentiator of copper-accumulation and -toxicity: Probing iron- regulons of Saccharomyces cerevisiae

Project description:RNA-seq was used to assess mRNA transcript abundance in wild type and fra2Δ S. cerevisiae (BY4741) cells treated with 2-(6-benzyl-2-pyridyl)quinazoline (BPQ) and CuSO4. BPQ potentiates copper toxicity and in yeast, in common with other organisms, a major cause of copper toxicity is damage of iron-sulphur clusters. Iron sensing within yeast relies on mitochondrial iron-sulphur cluster biosynthesis and therefore treatment with BPQ and copper can be used to mimic iron deficiency. Fra2 is known to be a key component of the iron sensing mechanism; however, this mechanism can operate, to an extent, independently of Fra2. BPQ (+CuSO4) treatment was used with the aim of probing the regulation of the iron regulon of S. cerevisiae and the role of Fra2 in the suppression of the low iron response. This study has uncovered nine new Cth2 target-transcripts, plus a new Aft1 target-gene and paralogous non-target. Fra2 dominates basal repression of the iron regulon in iron-replete cultures, however, Fra2-independent control of the iron regulon is also observed with CTH2 appearing to be atypically Fra2-dependent. Transcripts from untreated and CuSO4 treated cells were included as controls.

2014-06-04 | GSE54045 | GEO

Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress

Project description:Alkalinity stress is considered to be one of the major stressors for fish in saline-alkali water. Thus, it is of great significance from both aquaculture and physiological viewpoint to understand the molecular genetic response of aquatic organisms to alkalinity stress. The objective of this study is to determine genome-wide gene expression profiles to better understand the physiology response of medaka (Oryzias latipes) to high carbonate alkalinity stress. In lab-based cultures, adult fish were exposed to freshwater and high carbonate alkalinity water .We designed a microarray containing 26429 oligonucleotides and describe our experimental results for measuring gene expression changes in the gill of carbonate alkalinity stress exposed fish. The fish were exposed to freshwater (FW) and high carbonate alkalinity water (AW) for 96h, each with three replicates.

2014-01-24 | E-GEOD-27298 | biostudies-arrayexpress

Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress

2014-01-24 | GSE27298 | GEO

Chemical potentiator of copper-accumulation and -toxicity: Probing iron- regulons of Saccharomyces cerevisiae

Project description:RNA-seq was used to assess mRNA transcript abundance in wild type and fra2M-NM-^T S. cerevisiae (BY4741) cells treated with 2-(6-benzyl-2-pyridyl)quinazoline (BPQ) and CuSO4. BPQ potentiates copper toxicity and in yeast, in common with other organisms, a major cause of copper toxicity is damage of iron-sulphur clusters. Iron sensing within yeast relies on mitochondrial iron-sulphur cluster biosynthesis and therefore treatment with BPQ and copper can be used to mimic iron deficiency. Fra2 is known to be a key component of the iron sensing mechanism; however, this mechanism can operate, to an extent, independently of Fra2. BPQ (+CuSO4) treatment was used with the aim of probing the regulation of the iron regulon of S. cerevisiae and the role of Fra2 in the suppression of the low iron response. This study has uncovered nine new Cth2 target-transcripts, plus a new Aft1 target-gene and paralogous non-target. Fra2 dominates basal repression of the iron regulon in iron-replete cultures, however, Fra2-independent control of the iron regulon is also observed with CTH2 appearing to be atypically Fra2-dependent. Transcripts from untreated and CuSO4 treated cells were included as controls. Three independent biological replicates were analysed for each condition (BPQ and CuSO4 treated wild type and fra2M-NM-^T cells, CuSO4 treated wild type and fra2M-NM-^T cells and untreated wild type and fra2M-NM-^T cells)

2014-06-04 | E-GEOD-54045 | biostudies-arrayexpress

Approaching absolute quantification using label-free approaches and external proteins standards in yeast cultures

Project description:Protein extracts of Saccharomyces cerevisiae CEN.PK113-7D cultivated in chemostats under different conditions. Representative samples containing aliquots of all conditions were spiked with UPS2 standard (Sigma) to estimate absolute values in fmol. The conditions for Saccharomyces cerevisiae CEN.PK113-7D are: T2- Standard condition : 30°C, pH 5.5 T3- High temperature: 36°C, pH 5.5 T4- Low pH: 30°C, pH 3.5 T5- Osmotic stress : 30°C, pH 5.5, 1M KCl T6- Anaerobic condition Furthermore, representative samples pooling aliquots of each condition are indicated as "bulk" samples. These samples were spiked with UPS proteins. A validation step was carried out by spiking 4 external proteins at known concentrations within the yeast and UPS proteins mixture

2022-02-15 | PXD014765 | Pride

Project description:Low pH (acidity) stress responsive transcriptome of rice leaves

| PRJNA746766 | ENA

Differential expression of transcriptome under copper stress in Microcystis aeruginosa. PCC 7806

Project description:The cyanobacterium Microcystis aeruginosa PCC 7806 was used for a systematic survey of the relationship between copper and microcystins synthesis. Here we have used microarrays to interrogate the global responses to copper additions at 0.5 micromolar (µM) and 3 µM of copper. From the gene level, microarray studies (3 µM copper supplementation) showed effects on iron, sulfur, glutaredoxin and dehydratase homeostasis gene expression. However, in 0.5 µM groups, those genes that significantly enriched in 3 µM groups regulatory were not all found. In the microarray data for copper stress (3 µM) revealed a broad effect on the expression of iron-sulphur cluster associated pathways, such as cysteine biosynthesis. All of these data indicate that Fe / S cluster biogenesis and/or repair were affected by copper in M. aeruginosa.

2018-12-21 | GSE108380 | GEO

Molecular and Physiological Responses of Citrus sinensis Leaves to Long-term Low pH Revealed by RNA-Seq Integrated with Targeted Metabolomics

Project description:Low pH-induced alterations in gene expression profiles and organic acids (OAs) and free amino acids (FAAs) abundances were investigated in Citrus sinensis leaves. We identified 503 downreg-ulated and 349 upregulated genes in low pH-treated leaves. Further analysis indicated that low pH impaired light reaction and carbon fixation in photosynthetic organisms, thereby lowering photosynthesis in leaves. Low pH reduced carbon and carbohydrate metabolisms, OAs biosyn-thesis and ATP production in leaves. Low pH downregulated the biosynthesis of nitrogen com-pounds, proteins and FAAs in leaves, which might be conducive to maintaining energy homeo-stasis during ATP deprivation. Low pH-treated leaves displayed some adaptive responses, in-cluding phosphate recycling, lipid remodeling and phosphate transport. Low pH upregulated the expression of some reactive oxygen species (ROS) and aldehyde detoxifying enzyme (peroxidase and superoxidase) genes and the concentrations of some antioxidants (L-tryptophan, L-proline, nicotinic acid, pantothenic acid and pyroglutamic acid), but it impaired pentose phosphate pathway, VE and secondary metabolite biosynthesis, downregulated the expression of some ROS and aldehyde detoxifying enzyme (ascorbate peroxidase, aldo-keto reductase and 2-alkenal re-ductase) genes and the concentrations of some antioxidants (pyridoxine and γ-aminobutyric acid), thus disturbing the balance between production and detoxification of ROS and aldehydes and causing oxidative damage to leaves.

2018-05-12 | GSE114369 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data