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Transcriptome analysis of Upland Cotton revealed novel pathways to scavenge reactive oxygen species (ROS) responding to Na2SO4 tolerance

ABSTRACT: Transcriptome analysis of Upland Cotton revealed novel pathways to scavenge reactive oxygen species (ROS) responding to Na2SO4 tolerance

PROVIDER: PRJNA703009 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13746600_1.fastq.gz	Fastqsanger.gz
	SRR13746600_2.fastq.gz	Fastqsanger.gz
	SRR13746601_1.fastq.gz	Fastqsanger.gz
	SRR13746601_2.fastq.gz	Fastqsanger.gz
	SRR13746602_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of Upland Cotton revealed novel pathways to scavenge reactive oxygen species (ROS) responding to Na2SO4 tolerance

Project description:To explore the mechanisms of cotton response to Na2SO4 stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under the treatment of 300 mmol• L-1 Na2SO4 solution at 12 h and the control with water at 12 h. A total of 15,524, 20,409 and 12,146 differentially expressed genes (DEGs) were identified in cotton roots, stems and leaves between treatment and control, 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, plant-pathogen interaction, and Starch and sucrose metabolites were regulated in response to the Na2SO4 stress. We further analyzed genes enriched in ROS (reactive oxygen species) scavenging system including osmotic stress and ion toxicity were significantly up-regulated. In addition, analysis for sulfur metabolism, results in to identification of two rate limiting enzymes APR and OASTL during synthesis of GSH from SO42-. The analysis of the expression profiles of diverse tissues under Na2SO4 stress and identification of relevant key hub genes in a network crosstalk will provide a strong foundation and valuable clues for genetic improvements of cotton in response to various salt stresses.

2021-08-05 | GSE167109 | GEO

Asymmetric cancer cell division regulated by AKT, Reactive Oxygen Species (ROS) high versus ROS low mRNA

Project description:Human tumors often contain slowly proliferating cancer cells that resist treatment but we do not know precisely how these cells arise. We show that rapidly proliferating cancer cells can divide asymmetrically to produce slowly proliferating “G0-like” progeny that are enriched following chemotherapy in breast cancer patients. Asymmetric cancer cell division results from asymmetric suppression of AKT/PKB kinase signaling in one daughter cell during telophase of mitosis. Moreover, inhibition of AKT signaling with small molecule drugs can induce asymmetric cancer cell division and the production of slow proliferators. Cancer cells therefore appear to continuously flux between symmetric and asymmetric division depending on the precise state of their AKT signaling network. This model may have significant implications for understanding how tumors grow, evade treatment, and recur. 3 replicates each of MCF7 Reactive Oxygen Species (ROS) high, HCT116 ROS high, MCF7 ROS low, and HCT116 ROS low.

2011-07-14 | E-GEOD-30465 | biostudies-arrayexpress

Transcriptome analysis of upland cotton revealed novel pathways to scavenge reactive oxygen species (ROS) responding to Na<sub>2</sub>SO<sub>4</sub> tolerance.

Project description:Salinity is an extensive and adverse environmental stress to crop plants across the globe, and a major abiotic constraint responsible for limited crop production threatening the crop security. Soil salinization is a widespread problem across the globe, threatening the crop production and food security. Salinity impairs plant growth and development via reduction in osmotic potential, cytotoxicity due to excessive uptake of ions such as sodium (Na+) and chloride (Cl-), and nutritional imbalance. Cotton, being the most cultivated crop on saline-alkaline soils, it is of great importance to elucidate the mechanisms involved in Na2SO4 tolerance which is still lacking in upland cotton. Zhong 9835, a Na2SO4 resistant cultivar was screened for transcriptomic studies through various levels of Na2SO4 treatments, which results into identification of 3329 differentially expressed genes (DEGs) in roots, stems and leave at 300 mM Na2SO4 stress till 12 h in compared to control. According to gene functional annotation analysis, genes involved in reactive oxygen species (ROS) scavenging system including osmotic stress and ion toxicity were significantly up-regulated, especially GST (glutathione transferase). In addition, analysis for sulfur metabolism, results in to identification of two rate limiting enzymes [APR (Gh_D05G1637) and OASTL (Gh_A13G0863)] during synthesis of GSH from SO42-. Furthermore, we also observed a crosstalk of the hormones and TFs (transcription factors) enriched in hormone signal transduction pathway. Genes related to IAA exceeds the rest of hormones followed by ubiquitin related genes which are greater than TFs. The analysis of the expression profiles of diverse tissues under Na2SO4 stress and identification of relevant key hub genes in a network crosstalk will provide a strong foundation and valuable clues for genetic improvements of cotton in response to various salt stresses.

| S-EPMC8060397 | biostudies-literature

Upland cotton

Project description:Transcriptome data of two upland cottons Raw sequence reads

| PRJNA831595 | ENA

Reactive oxygen species (ROS) production triggers unconventional secretion of antioxidant enzymes

Project description:Nutrient deprivation triggers the release of signal-sequence-lacking antioxidant superoxide dismutase 1 (SOD1). We now report that secreted SOD1 is functionally active and accompanied by export of other antioxidant enzymes such as thioredoxins, (Trx1 and Trx2) and peroxiredoxin Ahp1. Our data reveal that starvation increases mitochondrial activity, which generates higher, but non-toxic, levels of reactive oxygen species (ROS). Inhibiting mitochondrial activity or ROS prevents antioxidants secretion. We suggest that in response to ROS production that can permeate the plasma membrane, the cells respond by secreting antioxidants to prevent ROS-mediated damage in the extracellular space. These findings provide an understanding of why cells secrete signal sequence lacking antioxidant enzymes in response to starvation.

2020-03-26 | PXD016815 | Pride

Reactive oxygen species (ROS) production activates unconventional secretion of antioxidant proteins

Project description:Signal-sequence-lacking superoxide dismutase 1 (SOD1) is secreted upon nutrient starvation, but the physiological relevance of this secretion is unclear. We now report that secreted SOD1 is functionally active. In addition, a secretome analysis has revealed number of other secreted cytoplasmic antioxidant enzymes, including both thioredoxins, (Trx1 and Trx2), and the peroxiredoxin Ahp1. Our data reveal that starvation triggers increased mitochondrial activity, leading to increased production of reactive oxygen species (ROS). Inhibiting mitochondrial activity or ROS, inhibited secretion of the antioxidants. We suggest elevated ROS that evade cytoplasmic antioxidants, can permeate across the plasma membrane to the extracellular space. Cells secrete antioxidants to prevent ROS-mediated damage to the extracellular space. These findings thus provide an understanding of why cells secrete signal sequence lacking proteins like SOD1 and the larger family of antioxidants.

2019-05-14 | PXD010849 | Pride

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

Root Meristem Growth Factor 1 (RGF1) controls root meristem size through reactive oxygen species (ROS) signaling

Project description:Purpose: Although five receptors of RGF1 have recently been identified, the downstream signaling mechanism remains unknown. The goal of this study is to elucidate signaling events following RGF1 action. Methods: mRNA profiles of the root meristematic zone from Arabidopsis seedlings with or without RGF1 treatment were generated by deep sequencing, in triplicate. The sequence reads were analyzed using Tophat and DESeq2. The mutants of selected differentially expressed genes were generated for phenotyping. Results: Our study uncovered a series of signaling events following RGF1 action. The RGF1-receptor pathway controls distribution of reactive oxygen species (ROS) along the developmental zones of the Arabidopsis root. We identify a novel transcription factor, RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 (RITF1), which plays a central role in mediating RGF1 signaling. Manipulating RITF1 expression leads to redistribution of ROS along the root developmental zones. Changes in ROS distribution, in turn, enhance the stability of the PLETHORA2 (PLT2) protein, a master regulator of root stem cells. Conclusions: Our study clearly depicts a signaling cascade initiated by RGF1 and links the RGF1 peptide to ROS regulatory mechanisms.

2019-10-15 | GSE108730 | GEO

cDNA array expression profile of wild-type and fl-mutant upland cotton ovules

Project description:Comparison of gene expression profiles of wild-type and fl-mutant upland cotton ovules Keywords: repeat samples

2006-01-01 | GSE2901 | GEO

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

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

| PRJNA694660 | ENA

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