Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A large-scale overexpression screen uncovers two paralogous genes ZCF15 and ZCF26 modulating Candida albicans biofilm gene circuitry (ChIP-seq data)

ABSTRACT: To identify novel genes modulating Candida albicans biofilm formation, a screen of 2451 overexpression strains allowed us to identify 16 genes whose overexpression significantly reduced biofilm formation. Genome-wide expression and binding analyses were conducted upon overexpression of ZCF15 and ZCF26 and wild type planktonic and biofilm cells were performed. A ChIP assays was performed. Briefly, untagged strain (CEC4665) and two replicates each of ZCF15 (CEC5929 and CEC5930) and ZCF26 (CEC5931 and CEC5932) strain were grown in biofilm condition for 18 h and cells were cross-linked with 1% final concentration of formaldehyde for 25 min at 30°C.The DNA was immunoprecipitated with anti-protein A antibodies (Sigma Aldrich Cat. No. P3775). The immunoprecipitated (IP) DNA were used to determine the binding of Zcf15 and Zcf26 across the genome by ChIP-sequencing

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Candida albicans WO-1

SUBMITTER: thomas cokelaer

PROVIDER: E-MTAB-11384 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Biofilm formation is an important virulence trait of the pathogenic yeast Candida albicans. Large-scale genetics strategies aimed at identifying genes involved in biofilm development are hampered by lack of a complete sexual cycle in this diploid yeast in addition to the tedious generation of homozygous gene-deletion mutants. Gene overexpression is an attractive alternative strategy for large-scale phenotypic analyses and gene-function studies. We combined gene overexpression, strain barcoding and microarray profiling to screen a library of 531 C. albicans conditional overexpression strains (~10% of the genome) for genes affecting i) planktonic cell fitness and ii) biofilm development in mixed-population experiments. We found 5 genes whose overexpression affects planktonic strain fitness, including RAD53, RAD51, PIN4, orf19.2781, all encoding (or predicted to encode) regulators of DNA-damage response or cell-cycle progression and SFL2, involved in filamentous growth. We identified 16 and 4 genes (out of 531) whose overexpression respectively increases and decreases strain occupancy within the multi-strain biofilm. Strikingly, strains with increased abundance in the multi-strain biofilm were significantly enriched for genes encoding cell wall proteins (10 genes), including the glycosylphosphatidylinositol (GPI)-anchored proteins Pga15, Pga19, Pga22, Pga59, Pga32 and Pga41. Data validation experiments using either individually- or competitively-grown overexpression and/or the respective knock-out strains revealed that the identified genes differently contribute to biofilm formation during specific stages of biofilm development, including increased or decreased substrate adherence (IHD1, PGA32, PGA37, PGA15, PGA22, PGA59 and PGA19) or biofilm biomass growth and cohesion (PGA15, PGA59 and PGA22). In line with the hypothesis that cell wall genes contribute to biofilm development, we show that strains overexpressing PGA15 or PGA22 display altered cell wall structures. Our study reveals that cell wall proteins are important actors during C. albicans biofilm formation and illustrates the powerful use of signature tagging in conjunction with gene overexpression for the identification of genes involved in processes pertaining to C. albicans virulence. A total of 8 samples are included in this study. For fitness profiling of planktonic cells, 2 biological replicates were analyzed (samples Pool_Fitness_planktonic_rep1 and Pool_Fitness_planktonic_rep2). For quantification of strain abundance during biofilm formation, 6 biological replicates were analyzed (Pool_Biofilm_rep1, Pool_Biofilm_rep2, Pool_Biofilm_rep3, Pool_Biofilm_rep4, Pool_Biofilm_rep5, Pool_Biofilm_rep6). Genomic DNA was purified and used as template to PCR-amplify barcodes, which were then used as probes for microarray hybridization. This experiment was done twice independently. For quantification of strain abundance during multi-strain biofilm formation, strain pools were grown in minimal GHAUM medium with or without doxycycline, each inoculum was then diluted to an OD600 of 1 in fresh minimal GHAUM medium with or without doxycycline and left at room temperature for 30 min, to allow further overexpression. Plastic slides (ThermanoxM-bM-^DM-"; Nunc) were immersed in the inoculum for 30 min at room temperature to allow adhesion of cells to the plastic substrate. The plastic slides were then transferred to the glass vessel of a 40-mL incubation chamber. This vessel has two glass tubes inserted to drive the entry of medium and air, while used medium is evacuated through a third tube. The flow of medium is controlled by a recirculation pump (IsmatecM-BM-.) set at 0.6 mL.min-1 and pushed by pressured air supplied at 105 Pa, conditions minimizing planktonic phase growth and promoting biofilm formation. The chambers with the plastic substrate were incubated at 37C and biofilms were grown for 40h followed by genomic DNA extraction, barcode amplification and differential labeling (dox-treated samples with Cy5, untreated samples with Cy3) and hybridization to barcode microarrays.

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A large-scale overexpression screen uncovers two paralogous genes ZCF15 and ZCF26 modulating Candida albicans biofilm gene circuitry (ChIP-seq data)

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