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
Project description:This study aims at investigating the link between internalized inorganic or methyl Hg and the global expression of genes, obtained by high-throughput sequencing (RNA-Seq), in the microalga Chlamydomonas reinhardtii. Algal cells were exposed two hours in a simplified artificial medium spiked with series of inorganic Hg concentrations (0.1, 1, 100 nM Hg) or series of methyl Hg concentrations (0.05, 0.5, 5, 50 nM CH3Hg). Three biological replicates were assessed for each of the 8 tested conditions: Control, 3 Hg concentrations, 4 CH3Hg concentrations.
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
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
Project description:To identify components involved in the signal transduction and activation of the singlet oxygen-mediated response, a mutant selection was performed. This led to the isolation of the singlet oxygen resistant 1 (sor1) mutant, which is more tolerant to singlet oxygen-producing chemicals and shows a constitutively higher expression of GPXH and GSTS1. Map-based cloning revealed that the SOR1 gene encodes a novel bZIP transcription factor, which seems to control its own expression as well as that of a large number of oxidative stress response and detoxification genes. In the promoter region of many of these genes a highly conserved 8-bp palindromic sequence element was found to be enriched. This element was shown to be essential for GSTS1 overexpression in sor1 and for induction by increased levels of lipophilic reactive electrophile species (RES) suggesting that it functions as an electrophile response element (ERE). RES can be formed after singlet oxygen-induced lipid peroxidation, indicating that a RES-stimulated and SOR1-mediated response of detoxification genes is part of the singlet oxygen-induced acclimation process in C. reinhardtii. The sor1 mutant isolated in a screen for singlet oxygen resistant mutants and the corresponding wild-type strain 4A+ were grown in a 12 h light dark cycle for several days before total RNA was extracted 6 h after the light came on.
Project description:This SuperSeries is composed of the following subset Series: GSE20859: Change in gene expression in Chlamydomonas reinhardtii upon heat shock GSE20860: Change in gene expression in Chlamydomonas reinhardtii upon feeding with hemin and Mg-protoporphyrin Refer to individual Series
Project description:The toxicity of silver and zinc oxide nanoparticles is hypothesised to be mediated by dissolved metal ions and cerium dioxide nanoparticles (CeO2 NPs) are hypothesised to induce toxicity specifically by oxidative stress dependant on their surface redox state. To test these hypotheses, RNAseq was applied to characterise the molecular responses of cells to metal nanoparticle and metal ion exposures. The human epithelial lung carcinoma cell line A549 was exposed to different CeO2 NPs with different surface charges, micron-sized and nano-sized silver particles and silver ions, micron-sized and nano-sized zinc oxide particles and zinc ions, or control conditions, for 1 hour, 6 hours and 24 hours. Concentrations were the lower of either EC20 or 128 micrograms/mL. Transcriptional responses were characterised by RNAseq transcriptomics using an Illumina HiSeq2500 .
Project description:Past studies have shown that the photosynthetic apparatus of a psychrophilic alga C. sp. UWO241 is remodeled to support high rates of Photosystem I (PSI)-associated cyclic electron flow (CEF). Iron levels in ELB are in the nanomolar range; therefore, we hypothesized that PSI restructuring in C. sp. UWO241 may reflect a strategy to survive long-term Fe-deficiency. We studied the effect of Fe availability in C. sp. UWO241, a mesophile, C. reinhardtii, and a second ELB psychrophile, Chlamydomonas sp. ICE-MDV. Under Fe-deficient conditions (2 µM Fe), abundance of the PSI reaction center protein, PsaA, as well as levels of photooxidizable P700 (ΔA820/A820) were significantly reduced in both psychrophiles relative to C. reinhardtii. In response to increased Fe, C. sp. ICE-MDV exhibited increases in PSI 77K Chl a fluorescence and ΔA820/A820 which matched that of C. reinhardtii, while C. sp. UWO241 exhibited moderate restoration of PSI function. Our results indicate that PSI functional organization in C. sp. UWO241 is unique. The unique physiological traits in PSI photochemistry exhibited by the psychrophiles may reflect adaptation to the stratified physicochemical conditions present the shallow vs. deep photic zones of a chemically Antarctic lake.
Project description:We have employed a whole genome microarray for gene expression profilling to understand the global view of the cellular mechanism and metabolic response of B. cereus B3711 exposed to 1 mM silver nitrate. RNA was extracted from B. cereus grown under silver treated and untreated set of conditions in duplicates at two different time points (30 & 60 min). Comparing the transcript profile of the control and treated cells, several differentially expressed genes were identified. These includes genes involved in various metabolic pathways, such as arginine and alanine metabolism, membrane transport system and alternate respiratory proteins such as arsenate reductase, stress related proteins, proteins of transcriptional regulators, hypothetical proteins and protein of two-component systems. Agilent one-color experiment,Organism: Bacillus cereus ,Agilent-023971 Genotypic designed Custom Bacillus cereus 8x15k , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)