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Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress

ABSTRACT: Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress

PROVIDER: PRJNA694660 | ENA |

REPOSITORIES: ENA

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Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress

Project description:To explore the mechanisms of cotton response to this alkaline stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under NaHCO3 alkaline stress. A total of 18,230 and 11,177 differentially expressed genes (DEGs) were identified in cotton roots and leaves, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, amino acid biosynthesis, and biosynthesis of secondary metabolites were regulated in response to the NaHCO3 stress. We further analyzed genes enriched in secondary metabolic pathways and found that secondary metabolites were regulated to eliminate the reactive oxygen species (ROS) and improve the cotton tolerance to the NaHCO3 stress. In this study, we learned that the toxic effect of NaHCO3 was more profound than that of NaOH at the same pH. Thus, Na+, HCO3- and pH had a great impact on the growth of cotton plant. The novel biological pathways and candidate genes for the cotton tolerance to NaHCO3 stress identified from the study would be useful in the genetic improvement of the alkaline tolerance in cotton.

2022-01-26 | GSE165472 | GEO

Transcriptional profiling of Enterococcus faecalis cells exposed to sodium bicarbonate for 15 minutes in the ate exponential growth phase.

Project description:In an effort to begin to delineate the bicarbonate regulon, we used microarray analysis with cells grown to late exponential growth phase (3 hr) and then submitted to a 15 min exposure with 0.1 M NaHCO3. Our goal was to define the first set of genes affected by the presence of bicarbonate.

2010-01-06 | E-MEXP-2518 | biostudies-arrayexpress

The antibiotics potentiator bicarbonate causes upregulation of tryptophanase and iron acquisition proteins in Escherichia coli

Project description:We have reported that bicarbonate (NaHCO3) potentiates the activity of aminoglycosides in Escherichia coli, but the action mechanism was not identified. To eventually understand how NaHCO3 can potentiate antibiotics, we thought that a rational first step was to examine the effect of NaHCO3 separately and to inspect initial gene expression changes triggered by it. In this work we started by confirming that NaHCO3 can reduce the number of viable E. coli bacteria. We then investigated, via RNAseq, gene expression changes induced by NaHCO3. There were upregulated and downregulated genes, among the top upregulated genes (~10-fold increase in expression) was tnaA, the gene encoding tryptophanase (TnaA), the enzyme that degrades tryptophan to indole. Considering that higher expression of tnaA likely led to increases in indole, we tested the effect of indole and found both growth inhibition and synergy with NaHCO3. We suggest that indole may participate in growth inhibition of E. coli. The RNAseq analysis also revealed upregulation (≥4-fold) of genes encoding proteins for the acquisition of iron and downregulation (≥16-fold) of genes encoding iron-sulfur-holding proteins, hence NaHCO3 apparently triggered also an iron deficit response. We suggest that iron deficiency may also be involved in growth inhibition by NaHCO3.

2018-11-01 | GSE110493 | GEO

A comparative kidney transcriptome analysis of bicarbonate-loaded insrr-null mice

Project description:The maintenance of physiological pH level is critical for the life of all organisms. Well known, that kidney is key organ for acid-base regulation in vertebrates. Metabolic alkalosis is the most common acid-base disorder in hospitalized patients, particularly in the surgical critical care unit. The receptor tyrosine kinase IRR (insulin receptor-related receptor), a receptor like the insulin receptor, is involved in acid-base regulation by kidney due to its ability to autophosphorylate under alkalization of extracellular medium (pH > 7.9). IRR expressed in only β-intercalated cells. In mice with a knockout of the insrr gene, which encoding IRR, bicarbonate secretion to the urine is impaired. Here for the first time, we present analysis of kidney transcriptomes from wild type and insrr gene knockout mice under basal or bicarbonate-loaded conditions by 250 mM NaHCO3 in drinking water. Analysis of NGS sequencing data revealed changes in the expression of a number of genes in the kidney. Using real-time PCR we confirmed change of expression of the slc51b, slc26a4, rps7, slc5a2, aqp6, plcd1, gapdh, rny3, lypd2, kcnk5, slc6a6 , atp6v1g3 genes in IRR knockout mice. Also, we found that expression of kcnk5 gene is increased in wild type mice after bicarbonate loading but didn’t change in knockout mice. Gene set enrichment between the IRR knockout and wildtype samples identified that knockout causes alterations in expression of genes related mostly to the ATP metabolic and electron transport chain processes. Thus, for the first time, we described some details of the functioning of the IRR in the kidneys.

2022-04-13 | GSE200638 | GEO

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

Project description: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

2021-02-10 | GSE164502 | GEO

Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate

Project description:Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate

2013-04-24 | GSE41145 | GEO

Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate

Project description:Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate Two treatments, based on carbon/energy source used for growth: pyruvate and H2/bicarbonate. Triplicate microarrays (biological replicates) were prepared for each treatment. Pyruvate was used as the reference treatment for subsequent analysis. Gene expression changes were compared pair-wise: H2/bicarbonate vs. pyruvate

2013-04-24 | E-GEOD-41145 | biostudies-arrayexpress

mTOR-regulated phosphorylation of electrogenic sodium bicarbonate cotransporter 1, NBCe1, at S255-257 regulates NBCe1 functional expression in mouse cortical astrocyte

Project description:The electrogenic sodium bicarbonate cotransporter 1, NBCe1 (SLC4A4), is the major bicarbonate transporter expressed in astrocytes. It is highly sensitive for bicarbonate, and the main regulator of intracellular-, extracellular-, and synaptic pH, thereby modulating neuronal excitability. However, despite these essential functions, the molecular mechanisms underlying NBCe1-mediated astrocytic response to extracellular pH changes are mostly unknown. Using primary cortical astrocyte cultures we have investigated the effect of long-term extracellular metabolic alkalosis on regulation of NBCe1 using functional assays and phosphoproteomic analysis.

2019-07-15 | PXD014034 | Pride

Bicarbonate induced redox proteome changes in Arabidopsis suspension cells

Project description:Climate change as a consequence of increasing atmospheric CO2 affects plant growth and productivity. CO2 is not only a carbon donor for photosynthesis but also an environmental signal that can perturb cellular redox homeostasis and lead to modifications of redox-sensitive proteins. Although redox regulation of protein functions has emerged as an important mechanism in several biological processes, protein redox modifications and how they function in plant CO2 response remain unclear. Here iodoTMTRAQ proteomics technology was employed to analyze changes in protein redox modifications in Arabidopsis thaliana suspension cells in response to bicarbonate (mimic of elevated CO2) in a time-course study. A total of 47 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism, transport, ROS scavenging, cell structure modulation and protein turnover. This inventory of previously unknown protein redox switches in Arabidopsis thaliana bicarbonate responses lays a foundation for future research toward understanding the molecular mechanisms underlying plant CO2 responses.

2017-02-14 | PXD004963 | Pride

Rescue of chloride and bicarbonate transport by elexacaftor-ivacaftor-tezacaftor in organoid-derived CF intestinal and cholangiocyte monolayers

Project description:In cystic fibrosis (CF), loss of CF transmembrane conductance regulator (CFTR)-dependent bicarbonate secretion precipitates the accumulation of viscous mucus in the lumen of respiratory and gastrointestinal epithelial tissues. We investigated whether the combination of elexacaftor (ELX), ivacaftor (IVA) and tezacaftor (TEZ), apart from its well-documented effect on Phe508del-CFTR-mediated chloride transport, also restores bicarbonate transport.

2021-12-14 | GSE182347 | GEO

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