Evolution of biofilm formation in Candida
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA674407 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13012200.fastq.gz | Fastqsanger.gz | |||
| SRR13012300.fastq.gz | Fastqsanger.gz | |||
| SRR13012201.fastq.gz | Fastqsanger.gz | |||
| SRR13012301.fastq.gz | Fastqsanger.gz | |||
| SRR13012202.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 91 |
Similar Datasets
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: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:The purpose of this experiment was to identify the genes bound by the biofilm master regulators (Bcr1, Brg1, Efg1, Ndt80, Rob1 and Tec2) in Candida albicans, C. dubliniensis, C. tropicalis and C. parapsilosis during biofilm formation. The regulators were tagged with a c-myc epitope and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain.
2021-04-14 | GSE161133 | GEO
Project description:The ability of the fungus Candida albicans to filament and form biofilms contributes to its burden as a leading cause of hospital-acquired infections. Biofilm development involves an interconnected transcriptional regulatory network (TRN) consisting of nine transcription factors (TFs) that bind both to their own regulatory regions and to those of the other network TFs. Here, we show that seven of the nine TFs in the C. albicans biofilm network contain prion-like domains (PrLDs) that have been linked to the ability to form phase-separated condensates. Construction of PrLD mutants in four biofilm TFs reveals that these domains are essential for filamentation and biofilm formation in C. albicans. Moreover, biofilm PrLDs promote the formation of phase-separated condensates in the nuclei of live cells, and PrLD mutations that abolish phase separation (such as the removal of aromatic residues) also prevent biofilm formation. Biofilm TF condensates can selectively recruit other TFs through PrLD-PrLD interactions and can co-recruit RNA polymerase II, implicating condensate formation in the assembly of active transcriptional complexes. Finally, we show that PrLD mutations that block the phase separation of biofilm TFs also prevent filamentation in an in vivo model of gastrointestinal colonization. Together, these studies associate transcriptional condensates with the regulation of filamentation and biofilm formation in C. albicans, and highlight how targeting of PrLD-PrLD interactions could prevent pathogenesis by this species.
2023-11-20 | GSE245897 | GEO
Project description:Biofilms are sessile microbial communities that are often resistant to conventional antimicrobial therapeutics and the host immune system. Candida albicans is an opportunistic pathogenic yeast and responsible for candidiasis. It readily colonizes host tissues and implant devices, and forms biofilms, which play an important role in pathogenesis and drug resistance. Its morphological transition from budding yeast to hyphal form and subsequent biofilm formation is regarded as the crucial factor for drug tolerance and virulence of Candida infections. In this study, nepodin (also called musizin) from Rumex japonicus root was investigated for antibiofilm, antihyphae, and antivirulence activities against fluconazole-resistant C. albicans strain. Nepodin at 2 µg/ml from Rumex plant effectively inhibited C. albicans biofilm formation by more than 90% but had no effect on planktonic cell growth. Also, Rumex root extract and nepodin inhibited hyphal growth and cell aggregation of C. albicans. Interestingly, nepodin also showed antibiofilm activity against Staphylococcus aureus or A. baumannii strains and two systems of dual biofilms of C. albicans and S. aureus or A. baumannii, respectively. Transcriptomic analysis using RNA-seq and qRT-PCR showed nepodin repressed the expressions of several hypha/biofilm related genes (ECE1, HWP1, and UME6) and overexpressed several transport genes (CDR4, CDR11, IFD6, and TPO2), which supported observed phenotypic changes.
2021-09-01 | GSE119822 | GEO
Project description:In this study we were interested in studying the role of SAGA subunits in various cellular processes- morphogenetic changes, growth, invasiveness, biofilm formation and to check the role of these subunits under various cellular and genotoxic conditions. In this work, we investigated conditional and null mutants of components of the SAGA complex modules; Ngg1 of the HAT module, Ubp8 of the Dub module, Tra1 of the recruitment module, Spt7 of the architecture module, and Spt8 of the TBP interaction unit to assess their role in processes such as filamentation, invasiveness, and biofilm formation. Spt7 and Spt8 deletion in Candida albicans resulted in ifilamentatation, invasiveness in YPD media at 30 degrees Celsius and also showed sensitivity to antifungal drugs. Wild type SN148 do not make any filaments in YPD at 30 degrees Celsius and didn't show antifungal sensitivity . The aim was to look for transcription profiling of SAGA mutants against wild type to find genes up and down regulated in the mutant especially those ones critical for filamentation, invasiveness and antifungal drug resistance.
2022-03-09 | GSE193907 | GEO
Project description:Present study represents the peptide mass data of proteins expressed during biofilm form growth of Candida albicans ATCC10231.
2023-01-06 | MSV000091018 | MassIVE
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.
2021-04-30 | GSE140427 | GEO
Project description:The planktonic versus biofilm gene expression arrays were performed in a/alpha cell types. Gene expression arrays were performed on planktonic vs biofilm cells grown in Spider medium at 37C. Normalized data is reported in matrix.
2011-07-08 | GSE30474 | GEO
Project description: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
2023-01-11 | E-MTAB-11384 | biostudies-arrayexpress