CgEfg1 and CgTec1 transcription factors controlling biofilm formation in Candida glabrata
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ABSTRACT:
PROVIDER: PRJNA589660 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10447404_1.fastq.gz | Fastqsanger.gz | |||
| SRR10447404_2.fastq.gz | Fastqsanger.gz | |||
| SRR10447405_1.fastq.gz | Fastqsanger.gz | |||
| SRR10447405_2.fastq.gz | Fastqsanger.gz | |||
| SRR10447406_1.fastq.gz | Fastqsanger.gz |
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Project description:This work reports the transcriptome-wide changes of C. glabrata cells (RNA-seq) upon 24h of biofilm formation on polystyerene surface, comparatively to planktonic conditions. The role of CgEfg1 and CgTec1 transcription factors is explored through the comparison of the transcriptome profiles of WT and CgEfg1 mutant cells, as well as the comparison between the profile of WT and CgTec1 mutant cells, in planktonic and 24h of biofilm conditions. mRNA profiles of WT and deletion mutant cells were generated by deep sequencing, in duplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed with TopHat followed by HTSeq. RNA-seq data allowed to identify genes whose expression is altered upon 24h of biofilm comparatively to planktonic conditions (1567 upregulated and 1505 downregulated). RNA-seq data allowed to identify genes regulated by the CgEfg1 (650 positively regulated and 514 negatively regulated) and CgTec1 (487 positively regulated and 595 negatively regulated) transcription factors in biofilm conditions. In all cases a log2fold change ≥1 and p value <0.01 was considered. The transcriptomics data was then used to guide further work to detail the function of each transcription factor in regulating biofilm formation.
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Project description:Transcriptional profiling of Candida glabrata zap1Δ and zap1Δ::ZAP1 strains, comparing cells grown under planktonic and biofilm-inducing conditions. Goal was to analyse the effect of ZAP1 deletion in the transcriptomic profile of C. glabrata biofilm cells (in comparision to planktonic cells), under acidic conditions, in order to study the function of the Zap1 transcription factor in C. glabrata biofilm matrix production.
2024-08-08 | GSE226915 | GEO
Project description:Aim: of the study was to compare the transcriptomic profiling of planktonic and biofilm growth phase of clinical isolate of Candida glabrata Methodology: RNA was extracted using Hi-PurA yeast RNA purification kit from biofilm and planktonic growth phase and sequenced by Illumina Hi-Seq 2500 platform with 250bp paired chemistry Results: we got 959 significantly Differential Expressed Genes DEGs (logFC => 1.5) acconts for 18.11 % in which 596 (11.26 %) are getting downregulated and 363 (6.85%) upregulated in the biofilm growth mode. We validated 8 genes by qPCR Conclusion: Comprehensive analysis of the large expression gene sets generated from experimental conditions (Planktonic vs Biofilm) by RNA Seq revealed the unique network of genes associated with this intricate and complex process. We observed that Differentially Expressed Genes (DEGs) associated with Glyoxylate and Dicarboxylate metabolism, Carbon-Carbon lyase activity
2021-06-09 | GSE152789 | GEO
Project description:Candida spp. are commensal opportunistic fungal pathogens that often colonize and infect mucosal surfaces of the human body. Candida, along with other microbes in the microbiota, generally grow as biofilms in a polymicrobial environment. Due to the nature of cellular growth in a biofilm (such as production of a protective extracellular matrix) and the recalcitrance of biofilms, infections involving biofilms are very difficult to treat with antibiotics and perpetuate the cycle of infection. The two most commonly isolated Candida spp. from Candida infections are Candida albicans and Candida glabrata, and the presence of both of these species results in increased patient inflammation and overall biofilm formation. This work aims to investigate the interspecies interactions between C. albicans (Ca) and C. glabrata (Cg) in co-culture through transcriptome analysis over the course of biofilm growth. We report that during co-culture, lipid biosynthesis and transporter genes were significantly modulated in both Ca and Cg. Differentially expressed genes in Ca during co-culture growth included putative transporter genes (C2_02180W_A and C1_09210C_B; up-regulated), amino acid biosynthesis (ARO7; up-regulated most in Ca:Cg 1:3), and lipid-related genes (LIP3 and IPT1; down-regulated). Differentially expressed genes in Cg in co-culture included putative transmembrane transporters (CAGL0H03399g and CAGL0K04609g; up-regulated), an oxidative stress response gene (CAGL0E04114g; down-regulated most in Ca:Cg 1:3), genes involved in the TCA cycle (LYS12 and CAGL0J06402g; down-regulated), and several genes involved in cell wall/membrane biosynthesis (SEC53, GAS2, VIG9; down-regulated). Additionally, confocal microscopy was utilized for membrane lipid analysis between monoculture and co-culture biofilms. Through filipin-stained lipid analysis, we found that there was a significant increase in cell membrane lipid content in Ca:Cg 1:3 biofilms compared to Ca and Ca:Cg 3:1 biofilms. These results suggest substantial modifications of both cell wall, cell membrane, and transporters in both Ca and Cg during the time course of co-culture growth, which allows for increased biofilm formation and virulence in Candida co-culture biofilms.
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Project description:In this study we performed a whole-transcriptome analysis of C. glabrata biofilm cells exposed to different environmental conditions and constraints in order to identify the molecular pathways involved in fluconazole resistance and understand how acidic pH niches, associated with the presence of acetic acid, are able to modulate these responses.
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2018-12-26 | GSE114175 | GEO
Project description:Candida glabrata is a human-associated opportunistic fungal pathogen. It shares its niche with Lactobacillus spp. in the gastrointestinal and vaginal tract. In fact, Lactobacillus species are thought to competitively prevent Candida overgrowth. We investigated the molecular aspects of this antifungal effect by analyzing the interaction of C. glabrata strains with Limosilactobacillus fermentum. From a collection of clinical C. glabrata isolates, we identified strains with different sensitivities to L. fermentum in coculture. We analyzed the variation of their expression pattern to isolate the specific response to L. fermentum. C. glabrata-L. fermentum coculture induced genes associated with ergosterol biosynthesis, weak acid stress, and drug/chemical stress. L. fermentum coculture depleted C. glabrata ergosterol. The reduction of ergosterol was dependent on the Lactobacillus species, even in coculture with different Candida species. We found a similar ergosterol-depleting effect with other lactobacillus strains (Lactobacillus crispatus and Lactobacillus rhamosus) on Candida albicans, Candida tropicalis, and Candida krusei. The addition of ergosterol improved C. glabrata growth in the coculture. Blocking ergosterol synthesis with fluconazole increased the susceptibility against L. fermentum, which was again mitigated by the addition of ergosterol. In accordance, a C. glabrata Derg11 mutant, defective in ergosterol biosynthesis, was highly sensitive to L. fermentum. In conclusion, our analysis indicates an unexpected direct function of ergosterol for C. glabrata proliferation in coculture with L. fermentum.
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Project description:This SuperSeries is composed of the following subset Series: GSE26611: [URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)-ScUre2 GSE26612: [URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)-CgUre2 GSE26613: [URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)-CaUre2 Refer to individual Series
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