Transcriptome analysis of Auricularia auricula-judae in response to gamma radiation
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ABSTRACT:
ORGANISM(S): Auricularia auricula-judae
PROVIDER: GSE272180 | GEO | 2024/07/13
REPOSITORIES: GEO
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Project description:The basidiomycetous fungus Cryptococcus has been known as radiation resistant fungi and is found in highly radioactive environments such as the damaged nuclear reactor at Chernobyl. Although Cryptococcus exhibits greater resistant for gamma radiation than the model yeast Saccharomyces cerevisiae, the resistant mechanism of gamma radiation remains elusive. To elucidate a unique regulatory system for radiation-resistance in C. neoformans, we performed genome-wide comparative analysis through DNA microarray analysis using C. neoformans WT strain (serotype A, H99 strain) responding gamma radiation. Based on the transcriptome analysis, genes involved in DNA damage repair systems (RAD51, RDH54, and RAD54) were significantly increased in response to gamma radiation. Actually, rad54∆ and rdh54∆ mutants exhibited sensitivity against both gamma radiation and DNA damage inducers. Furthermore, genes regarding to molecular chaperone and ubiquitination systems were strongly induced. In contrast, expression levels of genes related to protein synthesis, fatty acids/sterols synthesis, and other cellular molecules. Especially, ergosterol homeostasis is required for gamma radiation resistance. Furthermore, radiation-induced genes such as RIG4, RIG5, and RIG6 in C. neoformans play critical roles in gamma radiation resistance. Taken together, the transcriptome analysis contributes to understanding unique molecular mechanism of radiation-resistant fungus C. neoformans.
2016-06-01 | GSE80230 | GEO
Project description:The basidiomycetous fungus Cryptococcus has been known as radiation resistant fungi and is found in highly radioactive environments such as the damaged nuclear reactor at Chernobyl. Although Cryptococcus exhibits greater resistant for gamma radiation than the model yeast Saccharomyces cerevisiae, the resistant mechanism of gamma radiation remains elusive. To elucidate a unique regulatory system for radiation-resistance in C. neoformans, we performed genome-wide comparative analysis through DNA microarray analysis using C. neoformans WT strain (serotype A, H99 strain) responding gamma radiation. Based on the transcriptome analysis, genes involved in DNA damage repair systems (RAD51, RDH54, and RAD54) were significantly increased in response to gamma radiation. Actually, rad54â?? and rdh54â?? mutants exhibited sensitivity against both gamma radiation and DNA damage inducers. Furthermore, genes regarding to molecular chaperone and ubiquitination systems were strongly induced. In contrast, expression levels of genes related to protein synthesis, fatty acids/sterols synthesis, and other cellular molecules. Especially, ergosterol homeostasis is required for gamma radiation resistance. Furthermore, radiation-induced genes such as RIG4, RIG5, and RIG6 in C. neoformans play critical roles in gamma radiation resistance. Taken together, the transcriptome analysis contributes to understanding unique molecular mechanism of radiation-resistant fungus C. neoformans. To elucidate transcriptome change during recovery process post irrdiation, samples were taken at three time interval (30 min, 60 min, and 120 min). The three independent DNA microarry with three independent biological replicates were analyzed to obtain high reliability.
2016-06-01 | E-GEOD-80230 | biostudies-arrayexpress
Project description:We performed comparative RNA sequencing of the early (4 hrs) dose response (0.5 – 200 cGy whole body dose, 10 dose levels) of the mouse aorta to proton and gamma radiation. Total-body proton radiation of conscious animals was performed using a proton beam produced by a cyclotron system, while total-body gamma radiation of animals was performed using a Caesium-137 gamma source. A trend analysis identified genes that showed a dose response, using data permutation to estimate a false discovery rate (q-value) for each gene. We identified 29 and 194 genes (q-value ≤ 0.1) that were upregulated with increasing doses of proton and gamma radiation, respectively. No genes were down-regulated. While fewer genes were dose-responsive to proton radiation, the magnitude of the effect was greater than with gamma radiation. These highly responsive genes were enriched for pathways involved in the response to DNA damage, apoptosis, cellular stress and inflammation (p < 0.01). Gamma radiation responsive genes included the same pathways, but extended to genes in vasculature specific pathways. Genes responsive to both radiation types (19 genes at q-value ≤ 0.1) showed almost perfectly superimposable dose-response relationships. We observed the same superimposable dose response relationship of gamma and proton radiations in a subset of genes validated by quantitative PCR not only in the aorta but also in liver, lung, heart and kidney. Despite a relative similar relative biological effectiveness of protons and gamma photons and the activation of canonical radiation response pathways by both radiation types, we detected marked differences in the genomic response. It seems plausible that these genomic differences translate into differences in the biological processes leading to cardiovascular pathologies.
2019-01-25 | GSE105266 | GEO
Project description:The melanized yeast Exophiala dermatitidis is resistant to many environmental stresses, and is used as a model for understanding the diverse roles of melanin in fungi. To further our understanding resistance mechanism of E. dermatitidis to acute γ-radiation exposure and whether melanin plays a role in this process, we performed RNA-seq on WT and the melanin deficient mutant Δpks1 cultures exposed to γ-radiation at the dose of 1000 Gy, which resulted in ~50% cell deaths in both strains. We observed a dramatic transcriptomic response to γ-radiation that mobilizes pathways involved in morphological development, protein degradation, and DNA repair, and is unaffected by the presence of melanin.
2019-12-19 | GSE142318 | GEO
Project description:In the summer of 2012, one year after the 3.11 accident at Fukushima Daiichi nuclear power plant following the Great Tohoku Earthquake, a project was initiated to examine the effects of low-level gamma radiation on rice plants. The site of the experiment was the highly contaminated Iitate village in Fukushima prefecture of Japan. The basic experimental strategy was to expose healthy rice seedlings to continuous low-dose gamma radiation and examine the morphological and molecular genetic changes therien. Selected gene expression profiles of internal control, DNA replication/repair, oxidative stress, photosynthesis, and defense/stress functions were examined by semi-quantitative RT-PCR. Results revealed that low-level gamma radiation affects the expression of numerous genes, in particular showing the early (6 h) induction in DNA repair/damage-related genes and the late (72 h) induction of a previously described marker gene for defense/stress responses. Based on these results, which confirmed our data from preliminary experiments using detached rice leaves for radiation exposure, we proceeded for DNA microarray analysis. Using the established dye-swap approach, we analyzed the differentially expressed genes at 6 and 72 h time points using a whole rice genome 4 x 44 K custom chip. Obtained results showed that exposure to low-level gamma radiation differentially regulated 4481 (induced) and 3740 (suppressed) and 2291 (induced) and 1474 (suppressed) rice leaf genes at 6 and 72 h post-exposure, respectively, by at least two-fold changes. MapMan bioinformatics tool was also used to produce diagrams of the potential pathways, based on the input gene expression data of highly changed genes, operating downstream of the gamma radiation perception by rice plant.Inventory of a large number of gamma radiation-responsive genes in leaves provide new information and increased knowledge on novel regulatory processes in rice. The highly contaminated Iitate Farm (ITF), which is located 31 Km from the damaged nuclear power plant and having a background radiation level over 100 times (~ 5 microSv/h) than normal, was the designated place for the re-examination of low-level gamma radiation experiments using rice as a model system. As our group had a decade of experience and data on the effects of gamma radiation on leaf segments, the experimental was designed in such a way so as to expose whole rice plants to gamma radiation being emitted from the contaminated ground and examine the morphological and molecular genetic changes in the leaves under a dose-dependent manner.
2013-12-07 | E-GEOD-53055 | biostudies-arrayexpress
Project description:Ionizing radiation-induced changes to the redox balance does not only represent a risk for the cellular homeostasis, but can also induce a drastic modulation in the overall signalling system of cells. In the current study, effects of chronic exposure to ionizing gamma radiation were assessed in the radioresistant nematode Caenorhabditis elegans in order to understand whether antioxidant defences (AODs) could ameliorate radical formation, or if increased ROS levels would cause oxidative damage. This analysis was accompanied by phenotypical as well as molecular investigations, via assessment of reproductive capacity and somatic growth and differential gene expression through RNA sequencing. The use of a fluorescent reporter strain (sod1::gfp) and two ratiometric biosensors (Hyper and Grx1-roGFP2) demonstrated increased ROS production (H2O2) and activation of AODs (SOD1 and GPx) in vivo. The data indicate that at dose-rates ≤10 mGy/h defence mechanisms were able to prevent the manifestation of oxidative stress. In contrast, at dose-rates ≥40 mGy/h the constant formation of radicals induced a redox shift, which lead to oxidative damage responses, including changes in mitochondrial metabolism and functions, protein degradation, lipid metabolism, collagen synthesis and modulation of transcription. Moreover, genotoxic effects were among the most over-represented functions affected by chronic gamma irradiation, as indicated by differential regulation of genes involved in DNA damage, DNA repair, cell-cycle checkpoints, chromosome segregation and chromatin remodelling. Ultimately, the exposure to gamma radiation caused reprotoxic effects, with >20% reduction in the number of offspring per adult hermaphrodite at dose-rates ≥40 mGy/h, accompanied by the down-regulation of more than 300 genes related to reproductive system, meiotic functions and gamete development and fertilization.
2019-10-17 | E-MTAB-8284 | biostudies-arrayexpress
Project description:This study aims to investigate dose-dependent transcriptomic responses of Daphnia magna after chronic exposure to gamma radiation. RNA sequecing was performed after 4 days and 8 days exposure. Differentially expressed genes and major pathways enriched were characerized to provide insights into the chronic effects of gamma radiation.
2023-01-01 | GSE207246 | GEO
Project description:Many brown rot fungi are capable of rapidly degrading wood and are copper-tolerant. To better understand the genes that control these processes, we examined gene expression of Fibroporia radiculosa growing on wood treated with a copper-based preservative that combined copper carbonate with dimethyldidecylammonium carbonate. A global profiling strategy called RNA-Seq was used to quantify gene expression of the fungus at days 31 and 154. At day 31, the preservative was still protecting the wood, which showed no strength loss. At day 154, the effects of the preservative were gone, and the wood exhibited 52% strength loss. Statistical analysis identified 917 genes that were differentially expressed (FDR < 1E-4). Transcripts that showed higher expression levels at the early time point were controlling increased oxalate metabolism, laccase for hydroquinone-driven hydroxyl free radical production, pectin degradation, ATP production, xenobiotic detoxification, copper resistance, and stress response. Transcripts that showed higher expression levels at the late time point were involved in degradation of cellulose, hemicellulose, and pectin, hexose transport, oxalate catabolism, catabolism of laccase substrates, extracellular proton reduction, and remodeling of the fungal cell membrane and cell wall to enhance survival at low pH.
2012-11-26 | GSE35333 | GEO
Project description:Radiation and chemotherapy represent standard-of-care cancer treatments, however most treated patients eventually experience tumor recurrence, treatment failure and metastatic dissemination with fatal consequences. To elucidate molecular mechanisms of resistance to radio- and chemo-therapy, we exposed human cancer cell lines (HeLa, MCF-7, and DU145) to clinically relevant doses of 5-azacytidine or ionizing radiation and compared the transcript profiles of all surviving cell subpopulations including non-adherent fraction. Stress-mobilized non-adherent cell fractions differed from other survivors in deregulation of hundreds of genes including those involved in interferon response. Exposure of cancer cells to interferon-gamma but not interferon-beta resulted in development of a heterogeneous non-adherent fraction comprising, besides apoptotic/necrotic cells, also live cells featuring active Notch signaling and expressing stem cell markers. Interferon-gamma-mediated loss of adhesion and anoikis-resistance required active Erk pathway interlinked with interferon signaling by IRF1, as chemical inhibition of MEK or siRNA-mediated knockdown of Erk1/2 and IRF1 prevented mobilization of the surviving non-adherent population. Noteworthy, among the top scoring genes upregulated in surviving non-adherent tumor cells induced by 5-azacytidine or irradiation was a skin-specific protein suprabasin (SBSN), a recently identified oncoprotein. SBSN expression required the activity of the MEK/Erk pathway, and siRNA-mediated knockdown of SBSN resulted in suppression of the non-adherent fraction in irradiated, interferon-gamma- and 5-azacytidine-treated cells, respectively. Consistently, ectopic expression of SBSN isoforms enhanced the non-adherent phenotype, suggesting functional participation of SBSN in genotoxic stress-induced phenotypic plasticity and stress resistance. The stress-induced expression of skin protein(s) in a subset of cancer cells indicates partial induction of a keratinocyte-like expression program. Overall, we propose that IFN and Erk signaling drive the heterogeneous response of cancer cells to genotoxic therapies and expression of keratinocyte-specific genes as key players in mobilization and survival of cancer stem-like cells, with implications for cancer evolution and therapy resistance.
2018-07-01 | E-MTAB-6062 | biostudies-arrayexpress