The Candida albicans regulator ZCF21 controls the expression of cell wall components
ABSTRACT: We report that a transcriptional regulator that originated in the lineage that gave rise to multiple host-associated Candida species is a key component of the circuitry that governs the C. albicans cell surface composition. Specifically, we show that the transcription regulator ZCF21 controls the expression of genes encoding multiple cell surface proteins and cell wall modifying enzymes. Transcriptome (RNA-seq) analysis of 2 Candida albicans strains (reference strain and zcf21 deletion mutant) grown under 4 culture conditions (YPD broth at 30°C for 24h; YPD broth at 30°C in the presence of 15 mM caffeine for 24h; Todd-Hewitt agar at 37°C for 24h; Todd-Hewitt agar at 37°C for 24h in the presence of 5 mM caffeine).
Project description:Transcriptome analysis of wild type and set3-deficient Candida albicans cells in yeast and hyphal morphological phases RNA Sequencing was performed of wild type and set3-deficient Candida albicans strains in two morphological phases (yeast and hypha). Yeast-phase cells were grown to the exponential phase in YPD at 30oC. Hyphal differentiation was induced by resuspending the cells in YPD+20% Fetal Calf Serum and a shift of the growth temperature to 37oC. Induction was performed for 30 minutes. Three biological replicates of both genotypes in each morphological phases were analyzed.
Project description:The dataset contains ChIP-Seq data of the Set3 and Hos2 proteins in Candida albicans, assayed in two morphological phases (yeast and hypha). The Set3 and Hos2 proteins in the respective strains carry 9myc epitopes and ChIP was performed with an anti-myc antibody. Included samples are the following: 1 input and 1 ChIP sample of an untagged wild type strain as negative control assayed in the yeast phase, 1 input and 3 ChIP biological replicates of the Set3-9myc strain in the yeast phase, 1 input and 2 ChIP biological replicates of the Set3-9myc strain in the hypha phase, 1 input and 2 ChIP biological replicates of the Hos2-9myc strain in the yeast phase, 1 input and 2 ChIP biological replicates of the Hos2-9myc strain in the hypha phase, 1 input and 3 ChIP biological replicates of Set3-9myc in a set1delta/delta background in the yeast phase. ChIP-Seq was performed of Candida albicans strains in two morphological phases (yeast and hypha). Yeast-phase cells were grown to the exponential phase in YPD at 30C. Hyphal differentiation was induced by resuspending the cells in YPD+20% Fetal Calf Serum and a shift of the growth temperature to 37C. Induction was performed for 30 minutes. Cells were crosslinked with 1% formaldehyde for 15 minutes at room temperature.
Project description:RNA sequencing was performed on Candida albicans wild type cells (JC50) grown to exponential phase on YPD , YPD plus Nitrosative Stress 2.5mM DPTA NONOate, and compared to exponential Candida albicans hog1 deletion mutant cells grown on on YPD , YPD plus Nitrosative Stress 2.5mM DPTA NONOate. Three independent experiments were performed.
Project description:Recent studies have shown that the transcriptional landscape of the pleiomorphic fungus Candida albicans is highly dependent upon growth conditions. Here using a dual RNA-seq approach we identified 299 C. albicans and 72 Streptococcus gordonii genes that were either up- or down-regulated specifically as a result of co-culturing these human oral cavity microorganisms. Seventy five C. albicans genes involved in responses to chemical stimuli, regulation, homeostasis, protein modification and cell cycle were statistically (P ≤0.05) upregulated, while 36 genes mainly involved in transport and translation were down-regulated. Upregulation of filamentation-associated TEC1 and FGR42 genes, and of ALS1 adhesin gene, concurred with previous evidence that the C. albicans yeast to hypha transition is promoted by S. gordonii. Increased expression of genes required for arginine biosynthesis in C. albicans was potentially indicative of a novel oxidative stress response. The transcriptional response of S. gordonii to C. albicans was less dramatic, with only eight S. gordonii genes significantly (P ≤0.05) up-regulated ≥ twofold (glpK, rplO, celB, rplN, rplB, rpsE, ciaR, and gat). The expression patterns suggest that signals from S. gordonii cause a positive filamentation response in C. albicans, while S. gordonii appears to be transcriptionally less influenced by C. albicans. Five Samples; Sample 1 - Candida albicans cells grown in hypha inducing conditions for two hours; Sample 2 - Candida albicans cells grown in hypha-inducing conditions for two hours before co-culture with Streptococcus gordonii cells for one hour in a 2:1 rato; Sample 3 - Candida albicans cells grown in hypha-inducing conditions for two hours before culture in Streptococcus gordonii media for one hour; Sample 4 - Candida albicans cells grown in hypha inducing conditions for two hours, filtered to remove Candida albicans cells and media added to Streptococcus gordonii cells for one hour; Sample 5 - Streptococcus gordonii cells alone for one hour. All samples extracted and sequenced in biological triplicate using Illumina HiSeq2500. Samples 1, 2 and 3 aligned to the reference genome for Candida albicans and Samples 2, 4 and 5 aligned to the reference genome for Streptococcus gordonii.
Project description:To delineate the functional role of ZCF32 in Candida albicans biology, we carried out the genome wide expression analysis of wild-type and zcf32 null mutants by global expression array. We analysed the gene expression profiles of YPK102/1 and YPK102/2 and the parent wild type (SC5314) strain grown in YPD liquid medium at 30°C till the start of the stationary phase. In the microarray analysis, a total of 607 genes were found to be differentially expressed (fold change < 1.5 at p-value < 0.05) between the wild type and two zcf32 null mutants. Out of the 607 differentially expressed genes, 438 genes were up-regulated whereas 169 genes were down-regulated. Gene ontology (GO) analysis of up-regulated and down-regulated genes suggests that biofilm, filamentation, iron homeostasis, cell wall biogenesis, oxidation, and cell cycle are the major pathways altered in zcf32 null mutant. Overall design: Organism : Candida albicans , Agilent Custom Candida albicans Gene Expression 8x15k Array (AMADID: 026377) designed by Genotypic Technology Private Limited.
Project description:Mms21 deletion in Candida albicans resulted in invasveness and filamentatation in YPD media at 30 degrees Celsius. Wild type SN148 do not make any Filaments in YPD at 30 degrees Celsius. The aim was to look for transcription profiling mms21 dleleted mutant against wild type to find genes up and down regulated in the mutant especially thoseones critical for filamentation Overall design: 2 samples were analyzed. Cells were grown in YPD media at 30 degrees celcius to OD 0.8. MMS21 deleted strain (mms21Δ/Δ) vs wild type (SN148)
Project description:The diploid fungal pathogen Candida albicans is a highly heterozygous organism, with numerous non-synonymous substitutions often seen within two alleles. RNA-sequencing of the wild-type strain SC5314 has revealed 233 genes with significant levels of allelic expression imbalance. Overall percentage protein identity comparisons were significantly lower in these differentially expressed alleles. This suggests that two different, perhaps functionally divergent, proteins are being expressed at significantly different quantities by the two alleles of a single gene. Previously, gene expression levels have been correlated with structural factors such as GC content, ORF length and codon usage. Here, these factors were first correlated with overall gene expression data to decipher the relationship they have with gene expression in Candida albicans. These relationships were then used to assess the contribution of these factors to allelic expression imbalance. GC content and codon usage did not differ significantly in differentially expressed alleles whereas ORF length was found to be significantly lower in the allele with lowest expression. This surprising result goes against the overall trend observed between length and gene expression. Differences in GC content and ORF length between alleles correlated strongly with percentage protein identity, suggesting an indirect link between these factors and allelic expression imbalance. One sample (SC5314: wild-type strain) assessed in triplicate and compared to the reference diploid genome