To analyze the effect of deletion of RTA3 on the transcriptome in Candida albicans
Ontology highlight
ABSTRACT:
ORGANISM(S): Candida albicans
PROVIDER: GSE77774 | GEO | 2017/01/05
SECONDARY ACCESSION(S): PRJNA311902
REPOSITORIES: GEO
Similar Datasets
Project description:Pheromone-induced biofilm arrays in the planktonic and pheromone-induced biofilm growth conditions
| PRJNA190005 | ENA
Project description:Biofilm formation on medically implanted devices by Candida albicans poses a significant clinical challenge. Here we compared biofilm-associated gene expression in two clinical C. albicans isolates, SC5314 and WO-1, to identify shared gene regulatory responses that may be functionally relevant. Among the 50 genes most highly expressed in biofilms relative to planktonic (suspension-grown) cells, we were able to recover insertion mutations in 25 genes. We observed that 20 of the 25 mutants have altered biofilm-related properties, including cell-substrate adherence, cell-cell signaling, and azole susceptibility. We focused on the most highly up-regulated gene in biofilms, RHR2, which specifies the glycerol biosynthetic enzyme glycerol-3-phosphate phosphatase. Glycerol is 5-fold more abundant in biofilm cells than planktonic cells, and an rhr2D/D strain accumulates 2-fold less biofilm glycerol than the wild type. Under in vitro growth conditions, the rhr2D/D mutant has reduced biofilm biomass and reduced adherence to silicone. The rhr2D/D mutant is severely defective in biofilm formation in vivo, in a rat catheter infection model. Expression profiling of the rhr2D/D mutant indicates that it has reduced expression of cell surface adhesin genes ALS1, ALS3, and HWP1, as well as a large fraction of all other biofilm up-regulated genes. Reduced adhesin expression is the cause of the rhr2D/D mutant biofilm defect, because overexpression of ALS1, ALS3, or HWP1 restores biofilm formation ability to the mutant in vitro and in vivo. Our findings indicate that internal glycerol has a regulatory role in biofilm gene expression, and that adhesin genes are among the main functional Rhr2-regulated genes.
2013-04-12 | GSE45141 | GEO
Project description:Candida albicans can form biofilm on the surface of indwelling medical devices. Biofilm formation is an importanat clinical problem because biofilm-grown cells have decreased susceptibility to antifungal agents. Microarray technology was used to identify changes in gene expression during biofilm development. Two biofilm substrates (denture and catheter) were used, with two C. albicans strains tested on each substrate. Three phases of biofilm development were studies: early (6 h), intermediate (12 h), and mature (48 h). Planktonic specimens were collected at the same time points. Comparison between biofilm and planktonic cell transcriptional profiles at each time point showed differential expression of approximately 3% of the genome in biofilm. Fewer than half of these genes were up-regulated in biofilm, compared to planktonic cells. Transcriptional profiles were also analyzed over the time course of biofilm development. Genes up-regulated during the early phase (6 h) primarily were involved in glycolytic and non-glycolytic carbohydrate assimilation, and amino acid metabolism. The largest number of differentially expressed genes were identified at the intermediate phase (12 h) of biofilm development where the largest increase in biofilm biomass occurs. Genes up-regulated at 12 h were involved in transcription, protein synthesis/translation, energy generation, cellular transport, and nucleotide metabolism. At mature phase (48 h), few genes were up-regulated compared to the 12 h time point. These data define phase-dependent changes in gene expression that occur during biofilm development and show how genes belong to different, but interconnected, functional categories regulate the morphology and phenotype of C. albicans biofilm Keywords: phase-dependent gene expression; comparative genomic hybridization; cell type comparison
2007-08-01 | GSE7825 | GEO
Project description:Biofilm formation on medically implanted devices by Candida albicans poses a significant clinical challenge. Here we compared biofilm-associated gene expression in two clinical C. albicans isolates, SC5314 and WO-1, to identify shared gene regulatory responses that may be functionally relevant. Among the 50 genes most highly expressed in biofilms relative to planktonic (suspension-grown) cells, we were able to recover insertion mutations in 25 genes. We observed that 20 of the 25 mutants have altered biofilm-related properties, including cell-substrate adherence, cell-cell signaling, and azole susceptibility. We focused on the most highly up-regulated gene in biofilms, RHR2, which specifies the glycerol biosynthetic enzyme glycerol-3-phosphate phosphatase. Glycerol is 5-fold more abundant in biofilm cells than planktonic cells, and an rhr2D/D strain accumulates 2-fold less biofilm glycerol than the wild type. Under in vitro growth conditions, the rhr2D/D mutant has reduced biofilm biomass and reduced adherence to silicone. The rhr2D/D mutant is severely defective in biofilm formation in vivo, in a rat catheter infection model. Expression profiling of the rhr2D/D mutant indicates that it has reduced expression of cell surface adhesin genes ALS1, ALS3, and HWP1, as well as a large fraction of all other biofilm up-regulated genes. Reduced adhesin expression is the cause of the rhr2D/D mutant biofilm defect, because overexpression of ALS1, ALS3, or HWP1 restores biofilm formation ability to the mutant in vitro and in vivo. Our findings indicate that internal glycerol has a regulatory role in biofilm gene expression, and that adhesin genes are among the main functional Rhr2-regulated genes. Gene expression profiles, in duplicate; (1) for biofilm vs. planktonic growth conditions for the two wild-type clinical isolates of Candida albicans (SC5314 and WO1-white/WO1-opaque), and (2) for rhr2M-NM-^T/M-NM-^T mutant and complemented strain, via RNA-deep sequencing using Illumina GA2 and HiSeq2000 platforms, respectively
2013-04-12 | E-GEOD-45141 | biostudies-arrayexpress
Project description:Transcriptional profile of Candida albicans DAY286 culture without ketoconazole versus DAY286 culture with 0.04 μg/ml ketoconazole, both at 20% oxygen (normoxia).
| PRJNA133661 | ENA
Project description:We obtained ketoconazole tolerant mutants in Candida albicans after exposing the strain SC5314 to inhibitory concentration of ketoconazole. We did RNA-Seq to compare the transcriptomes of the aneuploid strains versus the parent euploid strain.
2020-03-30 | E-MTAB-8671 | biostudies-arrayexpress
Project description:The cyclic AMP-protein kinase A pathway has a central role in the biology of Candida albicans, a prominent fungal pathogen of humans. The two catalytic subunits for cyclic AMP-dependent protein kinase, Tpk1 (orf19.4892) and Tpk2 (orf19.2277), have divergent roles, and most studies indicate a more pronounced role for Tpk2. Here we dissect two Tpk1-responsive properties: adherence and cell wall integrity. Homozygous tpk1/tpk1 mutants are hyperadherent, and a Tpk1 defect enables biofilm formation in the absence of Bcr1, a central transcriptional regulator of biofilm adhesins. Microarray analysis revealed an enrichment for cell wall and surface functions among Tpk1-repressed genes, and overexpression of individual target genes indicates that cell surface proteins Als1, Als2, Als4, Csh1, and Csp37 contribute to Tpk1-regulated adherence. Tpk1 is also required for cell wall integrity, but has no role in the cell wall integrity gene expression response. Interestingly, increased expression of the adhesin gene ALS2 conferred a cell wall defect, as manifested in hypersensitivity to the cell wall inhibitor caspofungin and a shallow cell wall structure. Our findings indicate that Tpk1 has a central role in C. albicans cell wall properties that is exerted through repression of select cell surface protein genes. Two-color microarrays using a closed-loop experimental design to determine the effects of a M-bM-^HM-^Ftpk1 deletion in the absence or presence of the antifungal Caspofungin (CF)
2012-08-06 | E-GEOD-38846 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE24073: Transcriptional profile of Candida albicans during Hypoxic conditions. GSE24074: Transcriptional profile of Candida albicans DAY286 culture without ketoconazole versus DAY286 culture with 0.04 μg/ml ketoconazole, both at 20% oxygen (normoxia). GSE24075: Transcriptional profile of Candida albicans DAY286 versus UPC2 delete, both at 1% oxygen (hypoxia). Refer to individual Series
2010-11-15 | E-GEOD-24076 | biostudies-arrayexpress
Project description:Expression profiles of five caspofungin adapted candida albicans strains were analysed from their parental strains
2022-11-05 | GSE217094 | GEO
Project description:RNA-seq analysis of Caspofungin sensitive gene expression in Candida albicans.
| PRJNA693694 | ENA