ChIP-chip and gene expression model of the MoCRZ1 mediated circuit for Ca2+/calcineurin signaling in rice blast fungus
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ABSTRACT:
ORGANISM(S): Magnaporthe oryzae
SUBMITTER: Soonok Kim
PROVIDER: E-GEOD-18193 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:CRZ1 (Calcineurin Responsive Zinc finger 1) is a conserved transcription factor that relays Ca2+/calcineurin signals within the cell. To catalog genome wide locations that MoCRZ1 binds to, we have conducted chromatin immunoprecipitation coupled with microarray (ChIP-chip) in the rice blast fungus, Magnaporthe oryzae. Fungal mycelia were treated with 200mM CaCl2 to activate translocation of MoCRZ1 to the nucleus, thereby binding to the promoter regions of downstream genes, and CaCl2 together with 10ug/ml FK506 to block these phenomena. Using ChIP-chip, we were able to identify over 100 direct targets of MoCRZ1 which include well known downstream genes as well as previously unknown genes. Fungal mycelia expressing MoCRZ1::GFP under its native promoter were treated with 200mM CaCl2. MoCRZ1 bound DNA fragments which were immunoprecipitated with antiGFP-antibody were compared with 30% input DNA. Mycelia treated with 200mM CaCl2 and 10ug/ml FK506 were processed as the same way and used as negative control treatment.
2010-09-17 | E-GEOD-18080 | biostudies-arrayexpress
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.
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Project description:Gene BbSNF1 playes an essential role in mediating metabolism and cell development during conidation, a determinant to the biocontrol potential of entomopathogenic fungi. The genome-wide exprssion analysis involved in fungal conidiation was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in deveopment of fungal conida. . Total RNA obtained from BbSNF1 disruption mutant were compared to that of wild type strain (WT) grown on SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar).
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Project description:The induction of genes in response to exposure of T. reesei to wheat straw was explored using genome-wide RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to the lignocellulose. After 24 h of exposure to straw, transcript levels of known and predicted lignocellulose-degrading enzymes increased to around 8% of total cellular mRNA in T. reesei, which was much less when compared to A. niger. The bulk of enzymes used to deconstruct wheat straw is similar in both fungi. Other, non-plant cell wall-degrading enzymes which may aid in lignocellulose degradation were also uncovered in T. reesei and similar to those described in A. niger. Antisense transcripts were also shown to be present in T. reesei and their expession can be regulated by the respective growth condition. Triplicate samples of T. reesei cultivated in each of the three following conditions were taken: 1) After 48 h growth in glucose-based minimal media; 2) After transfer of mycelia from glucose-based media into media containing wheat straw as a sole carbon source and 3) 5 h after addition of glucose to straw cultures.
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Project description:In order to identify calcineurin pathway-regulated genes, we compared the genome-wide expression profile of wild-type with FK506-treated wild-type, cna1, and crz1 mutants. We expect that FK506-treated wild-type will have similar expression profile with that of the cna1 mutant. In response to calcineurin inhibitor FK506, the up- and down-regulated by FK506 were 113 and 87 genes, respectively (cutoff q < 0.001). The genes regulated by FK506 are largely overlapped (90%, 180/200) with those of cna1 mutant. Interestingly, FK506 induced 20 distinct genes other than that of the cna1 mutant. These genes encode proteins involved in plasma membrane ATP-bindding cassette (ABC) multidrug transporters (PDR15, PDR5, and YOR1), amino acid transporters (ALP1 and YBT1), and transcription factors (CUP2 and INO2). We also identified 34 genes regulated by calcineurin and Crz1. These genes encode proteins involved in cell wall biosynthesis (YPS5, YPS1, YSR3, YPC1, PIR1, HOR7, and NTE1), heat shock protein responses (SBA1 and GRE2), regulator of calcineurin (RCN2), and other functions. 5 sample wheel hybridization design with dye swaps totaling 10 arrays replicated 2 times to include an additional set of biological replicates. 20 arrays total.
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Project description:Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips were harvested after 6 months and used for RNA extraction. Reads of 100 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 6. mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips and free-living mycelium were generated by Illumina HiSeq2000 sequencing (100bp). Ttwo biological replicates were sequenced for mycorrhizal and mycelium samples.
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Project description:BbMBF1 played crucial roles in mediating response the prolonged thermal stress, a determinant to the environmental fitness of fungal entomopathogens. We characterized for the first time that disruption of BbMBF1 reduced the mycelial tolerance to the 9-h thermal stress under 40°C. The global transcriptome involved in the response to the thermal stress was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in fungal response to the themal stress. 1. Total RNA obtained from BbMBF1 disruption mutant were compared to that of wild type strain under control conditin (free of thermal stress); 2. Total RNA obtained from BbMBF1 disruption mutant were compared to that of WT strain under 9-h thermal stress at 40°C.
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