Transcript levels of genes in both the wild type SN148 and the crz1/crz1 mutant with or without 0.2M CaCl2 treatment
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ABSTRACT:
PROVIDER: PRJNA507600 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8261870_1.fastq.gz | Fastqsanger.gz | |||
| SRR8261870_2.fastq.gz | Fastqsanger.gz | |||
| SRR8261867_1.fastq.gz | Fastqsanger.gz | |||
| SRR8261867_2.fastq.gz | Fastqsanger.gz | |||
| SRR8261868_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the expression levels of transcripts for two alleles of 6,211 genes in log-phase growing cells of the wild type SN148 and the crz1/crz1 with or without 0.2M CaCl2 treatment.We find that as compared to the wild type cells without 0.2M CaCl2 treatment, there are 828 genes upregulated in the wild type cells with 0.2M CaCl2 treatment.
2018-11-30 | GSE123122 | GEO
Project description:Gene expression was quantified in S. cerevisae cells over a time course of three days of CaCl2 treatment to activate calcineurin. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1. We show that mitochondrial genes are downregulated in both geneotypes over time. Additionally, genes that promote glutathione biosynthesis are upregulated in cells that express calcineurin.
2024-03-19 | GSE254552 | GEO
Project description:Identification of calcineurin-dependent, Crz1-independent gene expression changes in response to chronic CaCl2 stress
| PRJNA1071031 | ENA
Project description:The Ca2+/calcineurin signaling pathway is a central conduit regulating growth, development, and virulence of fungal pathogens infecting plants and human. We have analyzed global gene expression profiles during Ca2+ treatment in the rice blast fungus, Magnaporthe oryzae. An immunosuppressive drug, FK506, and the knock-out mutant of a transcription factor, MoCRZ1, were included to analyze calcineurin- and/or CRZ1-dependent gene expression, respectively. About 1,400 genes were up or down regulated by Ca2+ treatment, while about 200 genes seemed to be up-regulated in a calcineurin/CRZ1-dependent manner. This study analyzes global gene expression dynamics during Ca2+ treatment in the rice blast fungus. We have used Agilent M. grisea 2.0 4×44K Microarrays using a single channel hybridization design. An immunosuppressive drug, FK506, and the knock out mutant of a transcription factor, MoCRZ1, were included to analyze calcineurin- and/or CRZ1-dependent gene expression, respectively. To know the time point at which the gene expression fluctuates most significantly, we treated mycelia with CaCl2 for 0, 15, 30, and 60 min. PMC1 expression level was checked by RT-PCR with the highest expression at 30 min time point. Four biological replicates of wild type and mutant mycelia were harvested after 30 min treatment with chemicals. Pairwise comparisons between Ca2+ treated vs. control and Ca2+ vs. Ca2+/FK506 in wild type (WT), and Ca2+ treated in WT vs. in mutant were conducted.
2010-09-17 | E-GEOD-18185 | biostudies-arrayexpress
Project description:Exposure of the budding Saccharomyces cerevisiae to an alkaline environment produces a robust transcriptional response involving hundreds of genes. Part of this response is triggered by an almost immediate burst of calcium that activates the Ser/Thr protein phosphatase calcineurin. Activated calcineurin dephosphorylates the transcription factor Crz1, which moves to the nucleus and binds to calcineurin/Crz1 responsive gene promoters. In this work we present a genome-wide study of the binding of Crz1 to gene promoters in response to high pH stress. Environmental alkalinization promoted a time-dependent recruitment of Crz1 to 152 intergenic regions, the vast majority between 1 to 5 min upon stress onset. Positional evaluation of the genomic coordinates combined with existing transcriptional studies allowed identifying 139 genes likely responsive to Crz1 regulation. Gene Ontology analysis confirmed the relevant impact of calcineurin/Crz1 on a set of genes involved in glucose utilization, and uncovered novel targets, such as genes responsible for trehalose metabolism. We also identified over a dozen of genes encoding transcription factors that are likely under the control of Crz1, suggesting a possible mechanism for amplification of the signal at the transcription level. Further analysis of the binding sites allowed refining the consensus sequence for Crz1 binding to gene promoters and the effect of chromatin accessibility in the timing of Crz1 recruitment to promoters. The present work defines at the genomic-wide level the kinetics of binding of Crz1 to gene promoters in response to alkaline stress, confirms diverse previously known Crz1 targets and identifies many putative novel ones. Because the relevance of calcineurin/Crz1 in signaling diverse stress conditions, our data will contribute to understand the transcriptional response in other circumstances that also involves calcium signaling, such as exposition to sexual pheromones or saline stress.
2016-06-27 | GSE79342 | GEO
Project description:Calcineurin is a highly conserved Ca2+/calmodulin-dependent serine/threonine-specific protein phosphatase that orchestrates cellular Ca2+ signaling responses. In Cryptococcus neoformans, calcineurin is activated by multiple stresses including high temperature, and is essential for stress adaptation and virulence. The transcription factor Crz1 is a major calcineurin effector in Saccharomyces cerevisiae and other fungi. Calcineurin dephosphorylates Crz1, thereby enabling Crz1 nuclear translocation and transcription of target genes. Here we show that Crz1 is dephosphorylated by calcineurin, and crz1Δ mutants display phenotypes intermediate between wild-type and calcineurin mutants. RNA-sequencing revealed 102 genes that are regulated in a calcineurin/Crz1-dependent manner at 37°C. 99 genes were down-regulated in cna1Δ and crz1Δ mutants, indicating these genes are normally activated by the calcineurin/Crz1 pathway at high temperature. About 58% of calcineurin-Crz1 target genes have unknown functions, while genes with known or predicted functions are involved in cell wall remodeling, calcium transport, and pheromone production. Surprisingly, only five genes have orthologs known to be calcineurin/Crz1-dependent in S. cerevisiae. 393 genes are independently regulated by calcineurin, and Crz1 regulates 59 genes independently of calcineurin. Taken together, these results indicate that the calcineurin/Crz1-dependent pathway controls a transcriptional circuit that has been extensively rewired in C. neoformans compared to S. cerevisiae. Given the intermediate crz1Δ mutant phenotype, and our recent evidence for a calcineurin regulatory network impacting mRNA in P-bodies and stress granules independently of Crz1, calcineurin likely acts on factors beyond Crz1 that govern mRNA expression/stability to operate a branched transcriptional/post-transcriptional stress response network necessary for fungal virulence. Taken together, our findings reveal the core calcineurin-Crz1 stress response cascade is maintained from ascomycetes to a pathogenic basidiomycete fungus, but its output has been extensively rewired to promote fungal virulence.
2017-04-07 | GSE93005 | GEO
Project description:In the industrially relevant yeast Komagataella phaffii, as in other yeasts, alkalinization of the medium results in fast and extensive transcriptional remodeling. This response has been useful to design novel methanol-free, regulatable platforms for heterologous protein expression. However, its molecular bases are fully unknown. Crz1 and Rim101/PacC are transcription factors known to contribute to the alkaline pH transcriptional responses in many fungi. We identified here the transcription factors Crz1 and Rim1 in K. phaffii and used CRISPR/Cas9 techniques to create single and double mutant strains. Phenotypic characterization shows that crz1 cells are strongly sensitive to Ca2+ ions, mildly sensitive to alkaline pH and hypertolerant to SDS. In contrast, rim101 cells are markedly hypersensitive to Na+ and Li+ ions, to alkaline pH and to SDS. RNA-seq transcriptomic analysis revealed that mutation of RIM101 affects 55% of genes whose expression is altered at pH 8.0, whereas lack of Crz1 alters only 11% of these. Thirty-eight genes are co-regulated by both Crz1 and Rim101. The PMC1 vacuolar Ca+2-ATPase is regulated by Crz1, whereas the ENA2 Na+-ATPase, the PHO89 and PHO84 phosphate transporters, and diverse genes involved in iron homeostasis are Rim101-dependent. These effects were confirmed by proteomic analyses after 3 h of alkalinization. Therefore, while Rim101 appears as a major player in the transcriptional response to alkalinization, nearly 40% of the alkaline pH transcriptional response in K. phaffii is controlled still unknown pathways.
2025-09-02 | PXD064682 | Pride
Project description:Gene expression was quantified in S. cerevisae cells after 48 hours of treatment with KCl. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1. We find that calcineurin has very little effect on gene expression in response to KCl.
2024-03-19 | GSE254554 | GEO
Project description:In the industrially relevant yeast Komagataella phaffii, as in other yeasts, alkalinization of the medium results in fast and extensive transcriptional remodeling. This response has been useful to design novel methanol-free, regulatable platforms for heterologous protein expression. However, its molecular bases are fully unknown. Crz1 and Rim101/PacC are transcription factors known to contribute to the alkaline pH transcriptional responses in many fungi. We identified here the transcription factors Crz1 and Rim101 in K. phaffii and used CRISPR/Cas9 techniques to create single and double mutant strains. Phenotypic characterization shows that crz1 cells are strongly sensitive to Ca2+ ions, mildly sensitive to alkaline pH and hypertolerant to SDS. In contrast, rim101 cells are markedly hypersensitive to Na+ and Li+ ions, to alkaline pH and to SDS. RNA-seq transcriptomic analysis revealed that mutation of RIM101 affects 55% of genes whose expression is altered at pH 8.0, whereas lack of Crz1 alters only 11% of these. Thirty-eight genes are co-regulated by both Crz1 and Rim101. The PMC1 vacuolar Ca+2-ATPase is regulated by Crz1, whereas the ENA2 Na+-ATPase, the PHO89 and PHO84 phosphate transporters, and diverse genes involved in iron homeostasis are Rim101-dependent. These effects were confirmed by proteomic analyses after 3 h of alkalinization. Therefore, while Rim101 appears as a major player in the transcriptional response to alkalinization, nearly 40% of the alkaline pH transcriptional response in K. phaffii is controlled still unknown pathways.
2025-09-02 | GSE297128 | GEO
Project description:The Ca2+/calcineurin signaling pathway is a central conduit regulating growth, development, and virulence of fungal pathogens infecting plants and human. We have analyzed global gene expression profiles during Ca2+ treatment in the rice blast fungus, Magnaporthe oryzae. An immunosuppressive drug, FK506, and the knock-out mutant of a transcription factor, MoCRZ1, were included to analyze calcineurin- and/or CRZ1-dependent gene expression, respectively. About 1,400 genes were up or down regulated by Ca2+ treatment, while about 200 genes seemed to be up-regulated in a calcineurin/CRZ1-dependent manner.
2010-09-17 | GSE18185 | GEO