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ABSTRACT:
PROVIDER: PRJNA144615 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE30645: Expression analysis of the singlet oxygen resistant 1 (sor1) mutant GSE30646: Response of Chlamydomonas reinhardtii to different oxidative and electrophilic stress conditions Refer to individual Series
2011-07-14 | E-GEOD-30648 | biostudies-arrayexpress
Project description:Acclimation to singlet oxygen was shown to induce various oxidative stress response genes of which some were also strongly overexpressed in the singlet oxygen resistant mutant sor1. Because sor1 was also more tolerant to other oxidative and electrophilic stress conditions, and because many of the sor1 overexpressed genes are known to be involved in the detoxification of reactive electrophile species, the response of the C. reinhardtii wild-type strain to various oxidative and electrophilic stress conditions was determined. Therefore, cultures were exposed to the reactive oxygen species-producing photosensitizer neutral red, the organic hydroperoxide tert-butylhydroperoxide, the photosynthetic herbicide 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB) and the lipophilic electrophile 2(E)-Hexenal for two hours and the global genetic response was analyzed. Cluster analysis revealed the most similar expression pattern between DBMIB and 2(E)-Hexenal and to a lower degree between NR and tBOOH. Still, there were many common induced genes including several of the oxidative stress response and detoxification genes overexpressed in the sor1 mutant.
2011-07-15 | GSE30646 | GEO
Project description:In the KEAP1-NRF2 stress response system, KEAP1 acts as a sensor for oxidative and electrophilic stresses through formation of S-S bond and C-S bond, respectively. Of the many questions left related to the sensor activity, following three appear important; whether these KEAP1 sensor systems are operating in vivo, whether oxidative and electrophilic stresses are sensed by the similar or distinct systems, and how KEAP1 equips highly sensitive mechanisms detecting oxidative and electrophilic stresses in vivo. To address these questions, we conducted a series of analyses utilizing KEAP1-cysteine substitution mutant mice, conditional selenocysteine-tRNA (Trsp) knockout mice, and human cohort whole genome sequence (WGS) data. The Trsp-knockout provokes severe deficiency of selenoproteins and compensatory activation of NRF2. However, mice lacking homozygously a pair of critical oxidative stress sensor cysteine residues of KEAP1 fail to activate NRF2 in the Trsp-knockout livers. Secondly, this study provides evidence for the differential utilization of KEAP1 sensors for oxidative and electrophilic stresses in vivo. Thirdly, theoretical calculations show that the KEAP1 dimer equips quite sensitive sensor machinery in which modification of a single molecule of KEAP1 within the dimer is sufficient to affect the activity. WGS examinations of rare variants identified seven non-synonymous variants in the oxidative stress sensors in human KEAP1, while no variant was found in electrophilic sensor cysteine residues, supporting the fail-safe nature of the KEAP1 oxidative stress sensor activity. These results provide valuable information for our understanding how mammals respond to oxidative and electrophilic stresses efficiently.
2024-10-09 | GSE276818 | GEO
Project description:Response of Chlamydomonas reinhardtii to different oxidative and electrophilic stress conditions
| PRJNA154677 | ENA
Project description:Acclimation to singlet oxygen was shown to induce various oxidative stress response genes of which some were also strongly overexpressed in the singlet oxygen resistant mutant sor1. Because sor1 was also more tolerant to other oxidative and electrophilic stress conditions, and because many of the sor1 overexpressed genes are known to be involved in the detoxification of reactive electrophile species, the response of the C. reinhardtii wild-type strain to various oxidative and electrophilic stress conditions was determined. Therefore, cultures were exposed to the reactive oxygen species-producing photosensitizer neutral red, the organic hydroperoxide tert-butylhydroperoxide, the photosynthetic herbicide 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB) and the lipophilic electrophile 2(E)-Hexenal for two hours and the global genetic response was analyzed. Cluster analysis revealed the most similar expression pattern between DBMIB and 2(E)-Hexenal and to a lower degree between NR and tBOOH. Still, there were many common induced genes including several of the oxidative stress response and detoxification genes overexpressed in the sor1 mutant. The 4A+ wild-type strain was grown mixotrophically in a Tris-acetate phosphate to a density of 2x10^6 cells/ml. Then cultures were split into 20 ml subcultures, and exposed to either of the four chemicals DBMIB (2 µM), 2(E)-Hexenal (0.3 mM), neutral red (NR, 3 µM), tert-butylhydroperoxide (tBOOH, 100 µM) or no chemical (control) for 2 hours, in three independent biological replicates. The cells of each replicate were harvested by centrifugation and total RNA was isolated using the RNeasy Mini Kit (Qiagen). DNA microarrays were performed using the ‘One-Color Microarray-Based Gene Expression Analysis’ system and a custom made 4 × 44 K ‘Chlamydomonas Whole Genome DNA Microarrays’ (Agilent Technologies) containing 15143 specific probes designed based on the Chlamydomonas version 4.0 transcript models provided by the DOE Joint Genome Institute (JGI), with an average of three replicates for each probe
2011-07-14 | E-GEOD-30646 | biostudies-arrayexpress
Project description:In a screen for singlet oxygen resistant mutants, a mutant called sor1 was isolated with increased resistance to different oxidative and electrophilic stress conditions. This mutant was found to have a constitutive high expression of three known singlet oxygen response genes, a glutathione peroxidase GPX5 and two glutathione-S-transferase GSTS1 and GSTS2. The sor1 mutation was mapped to the gene of a 393-amino acid protein for which blast searches revealed only poor homology to other proteins but predicted a putative basic leucine zipper DNA binding domain indicating that it might function as transcription factor to activate gene expression during oxidative stress.Global expression analysis of sor1 compared to the untreated wild-type enabled to identify additional genes differentially regulated in the sor1 mutant including several other genes involved in oxidative stress response and detoxification of endogenous xenobiotics.
2011-07-15 | GSE30645 | GEO
Project description:In a screen for singlet oxygen resistant mutants, a mutant called sor1 was isolated with increased resistance to different oxidative and electrophilic stress conditions. This mutant was found to have a constitutive high expression of three known singlet oxygen response genes, a glutathione peroxidase GPX5 and two glutathione-S-transferase GSTS1 and GSTS2. The sor1 mutation was mapped to the gene of a 393-amino acid protein for which blast searches revealed only poor homology to other proteins but predicted a putative basic leucine zipper DNA binding domain indicating that it might function as transcription factor to activate gene expression during oxidative stress.Global expression analysis of sor1 compared to the untreated wild-type enabled to identify additional genes differentially regulated in the sor1 mutant including several other genes involved in oxidative stress response and detoxification of endogenous xenobiotics. The sor1 mutant and the corresponding wild-type strain 4A+ were grown mixotrophically in a Tris-acetate phosphate in three independent biological replicates. Then the cells of each replicate were harvested by centrifugation and total RNA was isolated using the RNeasy Mini Kit (Qiagen). DNA microarrays were performed using the ‘One-Color Microarray-Based Gene Expression Analysis’ system and a custom made 4 × 44 K ‘Chlamydomonas Whole Genome DNA Microarrays’ (Agilent Technologies) containing 15143 specific probes designed based on the Chlamydomonas version 4.0 transcript models provided by the DOE Joint Genome Institute (JGI), with an average of three replicates for each probe
2011-07-14 | E-GEOD-30645 | biostudies-arrayexpress
Project description:Cellular oxidative and electrophilic stress triggers a protective response in mammals regulated by NRF2 (nuclear factor (erythroid-derived) 2-like; NFE2L2) binding to DNA-regulatory sequences near stress responsive genes. Studies using Nrf2-deficient mice suggest that hundreds of genes may be regulated by NRF2. To identify human NRF2-regulated genes, we conducted ChIP-sequencing experiments in human BEAS-2B cell line treated with the dietary isothiocyanate, sulforaphane (SFN) and carried out follow-up biological experiments on candidates.
2018-06-19 | GSE75812 | GEO
Project description:Old yellow enzymes (OYEs) are widely found in the bacterial, fungal, and plant kingdoms but absent in humans and have been used as biocatalysts for decades. However, OYEs physiological function in bacterial stress response and infection situations remained enigmatic. In the mode of pathogen, the gram-positive bacterium Staphylococcus aureus adapts to numerous stress conditions during pathogenesis. Here we show that in S. aureus genome, two paralogous genes (ofrA and ofrB) encode for two OYEs. We conducted bioinformatic analysis and found that ofrA is conserved among all publicly available representative staphylococcal genomes and some Firmicutes. Expression of ofrA is induced by electrophilic, oxidative, and hypochlorite stress in S. aureus. Furthermore, ofrA contributes to S. aureus survival against reactive electrophilic, oxygen, and chlorine species (RES, ROS, RCS) via thiol-dependent redox homeostasis. At the host-pathogen interface, ofrA mutation affects S. aureus survival in macrophages and whole human blood and the virulence factor staphyloxanthin production. Overall, our results shed the light onto a novel stress response strategy in the bacterial kingdom especially in the important human pathogen S. aureus.
2022-06-03 | GSE196683 | GEO
Project description:Liver-specific depletion of both of the cytosolic NADPH-dependent disulfide reductases, TrxR1 and Gsr, was shown to result in increased activation of Nrf2 as compared to elimination of either of these enzymes alone. Activation of transcription factor Nrf2 and its downstream cytoprotective target genes by oxidative and electrophilic insults can protect cells from potentially carcinogenic damage. However, many cancers have an activated Nrf2 response, which can protect cancer cells from oxidative stress radiation. Gene expression profiles in TrxR1/Gsr-null livers provide a basis for understanding the complex responses to chronically elevated oxidative stress and damage.
2019-05-01 | GSE124445 | GEO