Ontology highlight
ABSTRACT:
PROVIDER: PRJNA937411 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23580963_1.fastq.gz | Fastqsanger.gz | |||
| SRR23580963_2.fastq.gz | Fastqsanger.gz | |||
| SRR23580964_1.fastq.gz | Fastqsanger.gz | |||
| SRR23580964_2.fastq.gz | Fastqsanger.gz | |||
| SRR23580965_1.fastq.gz | Fastqsanger.gz |
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Project description:The high osmolarity glycerol response (HOG) pathway plays a pivotal role in the stress response, virulence regulation, and differentiation of fungi, including Cryptococcus neoformans that causes fatal meningoencephalitis. Core signaling components of in the HOG pathway, including the Tco-Ypd1-Ssk1 phosphorelay system and the Ssk2-Pbs2-Hog1 MAPK module, have been elucidated but its downstream transcription factors remain unclear. Here we demonstrated that Atf1 with a basic leucine zipper domain is the transcription factor downstream of Hog1 in C. neoformans. We found that ATF1 expression was differentially regulated by oxidative damaging agents, mainly in a Hog1-dependent, but Mpk1-independent, manner. Interestingly, Atf1 not only promoted oxidative stress response and adaptation, but also played an opposing role to Hog1 in the process. Atf1 primarily localized to the nucleus under both unstressed and oxidative stress conditions in a Hog1-independent manner. Our data demonstrated that Atf1 promoted pheromone production and sexual differentiation under negative control by Hog1. Finally, a DNA microarray-based transcriptome analysis of the atf1∆ mutant under unstressed and oxidative stress conditions revealed that Atf1 regulated oxidative stress response genes, including a sulfiredoxin gene (SRX1). Intriguing, the array data further demonstrated that Atf1 modulated basal expression of genes involved in DNA repair and genotoxic stress response. Supporting this, we found that the atf1∆ mutant was highly sensitive to genotoxic agents. In conclusion, this study provided a further insight into the Hog1-dependent oxidative and genotoxic stress response and differentiation mechanism of C. neoformans.
2015-01-13 | GSE64871 | GEO
Project description:The influence of light on living organisms is critical, not only because of its importance as the main source of energy for the biosphere, but also due to its capacity to induce changes in the behaviour and morphology of nearly all forms of life. The common soil fungus Trichoderma atroviride responds to blue-light in a synchronized manner, in time and space, by forming a ring of green conidia at what had been the colony perimeter at the time of exposure (photoconidiation). The complex putatively formed by the BLR-1 and BLR-2 proteins in T. atroviride appears to play an essential role as a sensor and transcriptional regulator in photoconidiation. Expression analyses using microarrays containing 1438 unigenes were carried out in order to identify early light response genes. We found that 2.8% of the genes were light responsive, 2% induced and 0.8% repressed. Exposure of Trichoderma to continuous light allowed us to establish that the light responsive genes are subjected to photoadaptation. Expression analysis in blr deletion mutants allowed us to demonstrate the occurrence of two types of light responses, a blr-independent response in addition to the expected brl-dependent one, as well as a new role of the BLR proteins in repression of transcription. Finally, we show evidence of red light regulated gene expression. Keywords: Light Response, microarrays
2006-08-26 | GSE5578 | GEO
Project description:The high osmolarity glycerol response (HOG) pathway plays a pivotal role in the stress response, virulence regulation, and differentiation of fungi, including Cryptococcus neoformans that causes fatal meningoencephalitis. Core signaling components of in the HOG pathway, including the Tco-Ypd1-Ssk1 phosphorelay system and the Ssk2-Pbs2-Hog1 MAPK module, have been elucidated but its downstream transcription factors remain unclear. Here we demonstrated that Atf1 with a basic leucine zipper domain is the transcription factor downstream of Hog1 in C. neoformans. We found that ATF1 expression was differentially regulated by oxidative damaging agents, mainly in a Hog1-dependent, but Mpk1-independent, manner. Interestingly, Atf1 not only promoted oxidative stress response and adaptation, but also played an opposing role to Hog1 in the process. Atf1 primarily localized to the nucleus under both unstressed and oxidative stress conditions in a Hog1-independent manner. Our data demonstrated that Atf1 promoted pheromone production and sexual differentiation under negative control by Hog1. Finally, a DNA microarray-based transcriptome analysis of the atf1M-bM-^HM-^F mutant under unstressed and oxidative stress conditions revealed that Atf1 regulated oxidative stress response genes, including a sulfiredoxin gene (SRX1). Intriguing, the array data further demonstrated that Atf1 modulated basal expression of genes involved in DNA repair and genotoxic stress response. Supporting this, we found that the atf1M-bM-^HM-^F mutant was highly sensitive to genotoxic agents. In conclusion, this study provided a further insight into the Hog1-dependent oxidative and genotoxic stress response and differentiation mechanism of C. neoformans. There are more than 95% of genome homology between JEC21 and H99. Therefore 6 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligo are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted 2 conditions (with or without treatment of Hydroten peroxide) from H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A), and atf1M-NM-^T). We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy3 as Sample dye and Cy5 as a control dye.
2015-01-13 | E-GEOD-64871 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was to characterize the transcript levels of genes in Drosophila photoreceptor neurons in response to blue light. Using transcriptome profiling of isolated photoreceptor nuclei, we analyzed the changes in gene expression that occur in response to 3h of blue light exposure at 1 or 6 days post-eclosion. We identified sets of genes with both up-regulated and down-regulated expression in response to blue light at either age.
2018-06-20 | GSE106820 | GEO
Project description:We investigated light dependent gene expression changes in the marine ochrophyte Nannochloropsis oceanica CCMP1779. These algae have several putative blue light photoreceptors but appear to lack red light photoreceptors. To study early light signaling in N. oceanica and avoid as much as possible secondary downstream events, we quantified gene expression changes in dark-adapted cells after a short blue or red light pulse. More genes were differentially expressed under blue than under red light. In addition, fold change in expression was smaller for the red light-treated samples. For example, the median fold change of induced genes was 3 for blue light and 2.5 for red light. Moreover, hierarchical cluster analysis showed that gene expression after red light treatment was more similar to the dark control than after blue light treatment.
2022-01-05 | GSE164714 | GEO
Project description:We have studied the transcriptional, metabolic and photo-physiological responses to light of different spectral quality in the marine diatom Phaeodactylum tricornutum through time-series studies of cultures exposed to equal doses of photosynthetically usable radiation of blue, green and red light. The experiments showed that short-term differences in gene expression and profiles are mainly light quality-dependent. Transcription of photosynthesis-associated nuclear genes was activated mainly through a light quality-independent mechanism likely to rely on chloroplast-to-nucleus signaling. In contrast, genes encoding proteins important for photoprotection and PSII repair were highly dependent on a blue light receptor-mediated signal. Changes in energy transfer efficiency by light-harvesting pigments were spectrally dependent; furthermore, a declining trend in photosynthetic efficiency was observed in red light. The combined results suggest that diatoms possess a light quality-dependent ability to activate photoprotection and efficient repair of photodamaged PSII. In spite of approximately equal numbers of PSII-absorbed quanta in blue, green and red light, the spectral quality of light is important for diatom responses to ambient light conditions.
2014-12-22 | GSE55959 | GEO