Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [RNA-seq]

ABSTRACT: 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.

ORGANISM(S): Candida albicans

SUBMITTER: Denes Hnisz

PROVIDER: E-GEOD-38426 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [RNA-seq]

Project description:Transcriptome analysis of wild type and set3-deficient Candida albicans cells in yeast and hyphal morphological phases

2013-01-01 | GSE38426 | GEO

Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [ChIP-seq]

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.

2013-01-01 | E-GEOD-38425 | biostudies-arrayexpress

Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [ChIP-seq]

2013-01-01 | GSE38425 | GEO

Different protein cargo of whole cell lysates from yeast or hyphal Candida albicans cells

Project description:Whole cell lysates from yeast or hyphal Candida albicans cells were obtained and proteins were analysed by MS in order to have a global view of proteome differences between both fungal morphologies. This analysis constitute an interesting approach to decipher proteomic differences underlying morphological switch intimately related to Candida albicans virulence. A total of 811 different proteins were identified from hyphal whole cell lysates and 976 from yeast whole cell lysates. In terms of biological significance, we only took into consideration proteins that were identified in at least two biological replicates with at least two peptides and a q-value< 0.01.

2021-09-13 | PXD021504 | Pride

Time course gene expression profile of YPD medium grown Candida albicans mss11 mutant

Project description:Candida albicans is an important fungal pathogen in humans. Several virulence factors of C. albicans have been reported, including a morphological transition from yeast to filamentous forms (hyphae and pseudohyphae). Mss11 is a transcriptional activator required for hyphal formation. To reveal the potential target genes of Mss11, DNA microarray analysis was performed to compare wild type and mss11-deleted mutant.

2016-09-24 | GSE51168 | GEO

Arp2/3 complex mutants show a pronounced lack of hyphal specific gene expression in Candida albicans

Project description:Candida albicans is a diploid fungal pathogen lacking a defined complete sexual cycle, and thus has been refractory to standard forward genetic analysis. Instead, transcription profiling and reverse genetic strategies based on Saccharomyces cerevisiae have typically been used to link genes to functions. To overcome restrictions inherent in such indirect approaches, we have investigated a forward genetic mutagenesis strategy based on the UAU1 technology. We screened 4700 random insertion mutants for defects in hyphal development, and linked two new genes (ARP2 and VPS52) to hyphal growth. Deleting ARP2 abolished hyphal formation, generated round and swollen yeast phase cells, disrupted cortical actin patches and blocked virulence in mice. The mutants also showed a global lack of induction of hyphae-specific genes upon the yeast-to-hyphae switch. Surprisingly, both arp2Î/Î and arp2Î/Îarp3Î/Î mutants were still able to endocytose FM4-64 and Lucifer Yellow, although as shown by time-lapse movies internalization of FM4-64 was somewhat delayed in mutant cells. Thus the non-essential role of the Arp2/3 complex discovered by forward genetic screening in C. albicans showed that uptake of membrane components from the plasma membrane to vacuolar structures is not dependent on this actin nucleating machinery. By forward genetic screening, we have identified genes that are essential for hyphal formation. One of the hits is the Arp2/3 complex, which is essential for hyphal formation, but not for viability in Candida albicans. To gain insights into cellular processes affected by disrupting Arp2/3 complex functions, we performed transcriptional profiling under yeast growth conditions (YPD at 30Â°C for three hours) or hyphal induction (YPD + 10% FBS at 37Â°C for three hours) and compared transcriptional consequences of deleting ARP2 to MYO5 and SLA2 microarray data sets (Oberholzer et al., 2006).

2010-10-08 | E-GEOD-19565 | biostudies-arrayexpress

A Genome-wide Transcriptional Analysis of Morphology Determination in Candida albicans

Project description:Candida albicans, the most common cause of human fungal infections, undergoes a reversible morphological transition from yeast to pseudohyphal and hyphal filaments, which is required for virulence. For many years, the relationship between global gene expression patterns associated with determination of specific C. albicans morphologies has remained obscure. Using a strain that can be genetically manipulated to sequentially transition from yeast to pseudohyphae to hyphae in the absence of complex environmental cues and upstream signaling pathways, we demonstrate by whole-genome transcriptional profiling that genes associated with pseudohyphae represent a subset of those associated hyphae and are generally expressed at lower levels; interestingly, no genes appeared to be expressed exclusively in pseudohyphae. Our results also strongly suggest that in addition to dosage, extended duration of filament-specific gene expression is sufficient to drive the C. albicans yeast-pseudohyphal-hyphal transition. Finally, we describe the first transcriptional profile of the C. albicans reverse hyphal-pseudohyphal-yeast transition and demonstrate that this transition not only involves down-regulation of known hyphal-specific genes but also differential expression of additional genes which have not previously been associated with the forward transition, including many involved in protein synthesis. These findings provide new insight into genome-wide mechanisms important for determining fungal morphology and suggest that in addition to similarities, there are also fundamental differences in global gene expression as pathogenic filamentous fungi undergo forward and reverse morphological transitions.

2012-12-12 | GSE39677 | GEO

Conjugated linoleic acid inhibits hyphal growth in Candida albicans by modulating Ras1 cellular levels and down-regulating TEC1 expression

Project description:The polymorphic yeast Candida albicans exists in blastospore and filamentous forms. The switch from one morphological state to the other coincides with the expression of virulence factors, which makes the yeast-to-hypha transition an attractive target for the development of new antifungal agents. Because an untapped therapeutic potential resides in small molecules that hinder C. albicans filamentation, we characterized the inhibitory effect of conjugated linoleic acid (CLA) on hyphal growth and addressed its mechanism of action. CLA inhibited hyphal growth in a dose-dependent fashion, in both liquid- and solid-inducing media. The fatty acid blocked germ tube formation and impeded hyphal elongation. Global transcriptional profiling revealed that CLA downregulated the expression of hypha-specific genes and abrogated the induction of several morphogenesis regulators, including RAS1, TEC1 and UME6. CLA’s repressive effect on TEC1 expression was Ras1-dependent, but Efg1-independent. CLA treatment resulted in the delocalization of Ras1 and its degradation, resulting in the downregulation of the Ras1-cAMP-PKA signaling pathway. This study provides the biological and molecular explanations that underlie CLA’s ability to inhibit hyphal growth in C. albicans.

2011-03-10 | GSE25822 | GEO

Suppression of biofilm formation by Candida albicans and multispecies by nepodin of Rumex root via hyphal inhibition

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

Immunoproteomic analysis of antibody responses to extracellular proteins of Candida albicans in serum of candidemia patients revealed glycosylation effects on protein antigen recognition

Project description:During infection the yeast Candida albicans undergoes a yeast-to-hyphal transition and secretes numerous proteins required for the invasion and damage of host tissues and the modulation of the host immune responses. Still little is known about the interplay of Candida albicans secreted proteins and the host adaptive immune system. For the characterization of the extracellular proteins of C. albicans and their ability to trigger a serological response in candidemia patients we applied 2D gel electrophoresis and LC-MS/MS-based approaches. These analyses identified the secretion of 101 different proteins from C. albicans yeast cells and 410 proteins from hyphal cells. Morphology-dependent changes of the secretome were mostly associated with proteins involved in cell wall organization, general stress response and the interplay with host immune cells. Our immunoproteomics workflow for the identification of secreted C. albicans protein antigens revealed a core set of 20 immunodominant specific anti- C. albicans protein antibodies. However, some secreted protein antigens showed cross-reactivity with sera from control groups without Candida infection. Glycoprotein staining of C. albicans hyphal secretome demonstrated that some secreted proteins are strongly glycosylated. Enzymatic deglycosylation of secreted proteins uncovered a significant contribution of glycan epitopes to the recognition of the secreted aspartyl protease Sap6 by IgG antibodies from patient sera.

2022-03-03 | PXD003201 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data