The APSES Transcription factor Efg1 regulates a novel phenotype switch in Candida parapsilosis.
Ontology highlight
ABSTRACT:
ORGANISM(S): Candida parapsilosis
SUBMITTER: Geraldine Butler
PROVIDER: E-GEOD-41065 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:All but a few eukaryotes die without oxygen and respond dynamically to changes in the level of oxygen available to them. One ancient oxygen-requiring biochemical pathway in eukaryotes is the pathway for the biosynthesis of sterols, leading to cholesterol in animals and ergosterol in fungi. Mutations in this pathway are a frequent cause of azole drug resistance in pathogenic fungi. The regulatory mechanism for the sterol pathway is also widely conserved between animals and fungi and is centred on a transcription activator, SREBP, that forms part of a sterol-sensing complex. However, in one group of yeasts M-bM-^@M-^S the Saccharomycotina, which includes the major pathogen Candida albicans M-bM-^@M-^S control of the sterol pathway has been taken over by an unrelated regulatory protein, Upc2. We show here by analysis of the yeast Yarrowia lipolytica that the evolutionary switch from SREBP to Upc2 was a two-step process in which Upc2 appeared in an ancestor of Saccharomycotina, and SREBP subsequently degenerated and lost its sterol-regulatory function while retaining an ancient role in filamentation. RNA was isolated from Y. lipolytica wildtype (JMY2900) in normoxia (21% oxygen, 4 biological replicates), wildtype (JMY2900) in hypoxia (1% oxygen, 5 biological replicates), upc2 deletion (SMY2) in hypoxia (1% oxygen, 3 biological replicates), and from sre1 (SMY5, SMY8) deletion in hypoxia (1% oxygen, 2 biological replicates). Gene expression was determined using strand-specific RNA-seq.
2013-11-19 | E-GEOD-47433 | biostudies-arrayexpress
Project description:In Candida albicans the Efg1 transcription factor (a member of the APSES family) is an important regulator of hyphal growth, and of the white-to-opaque transition. In contrast, we show that the Efg1 ortholog in Candida parapsilosis is a major regulator of a different morphological switch at the colony level, from a concentric to smooth morphology. The rate of switching is at least 100-fold increased in an efg1 knockout relative to wild type. Deleting efg1 also reduces biofilm formation, and results in increased sensitivity to SDS, Congo red, caspofungin and calcofluor white in cells of both morphologies. Biofilm reduction is more dramatic in in vitro than in in vivo models. We use ChIP-seq to show that Efg1 binds to 502 promoter regions, including 70 potential transcription factors or regulatory proteins. Several of the transcription factors belong to networks that regulate biofilm development and white-opaque switching in C. albicans. Efg1 also binds to its own promoter. The binding site for C. parapsilosis Efg1 resembles that of orthologs in other fungi. Many Efg1 targets are probably also regulated by the Ndt80 transcription factor. We show that a paralog of Efg1 (Efh1) is restricted to Candida species. Efh1 does not regulate concentric-smooth phenotype switching, biofilm formation or stress response in C. parapsilosis. Our analysis supports the hypothesis that Efg1 has an ancient role as regulator of development in fungi, but we have identified a new role in C. parapsilosis as a regulator of colony switching that is distinct from the white-opaque switch in C. albicans. RNA was isolated from C. parapsilosis wild type (three biological replicates, concentric phenotype), and from efg1 deletion strains (three biological replicates from both concentric and smooth phenotype). Gene expression was determined using strand-specific RNA-seq.
2013-06-20 | E-GEOD-41064 | biostudies-arrayexpress
Project description:We used next generation sequencing (RNA-seq) to determine the transcriptional profile of C. parapsilosis growing in several conditions including different media, temperatures and oxygen concentrations. We have 37 Samples representing BMW and YPD media, 1% and 21% oxygen, 30 and 37 degree celsius temperature, and CLIB214 and CDupc5 strains.
2011-11-30 | E-GEOD-32714 | biostudies-arrayexpress
Project description:We use ChIP-seq to identify the targets of Efg1 in Candida parapsilosis. We show that Efg1 binds to 502 promoter regions, including 70 potential transcription factors or regulatory proteins. Several of the transcription factors belong to networks that regulate biofilm development and white-opaque switching in C. albicans. Efg1 also binds to its own promoter. The binding site for C. parapsilosis Efg1 resembles that of orthologs in other fungi. Many Efg1 targets are probably also regulated by the Ndt80 transcription factor. Efg1 in C. parapsilosis was tagged in situ using a myc epitope. Examination of Efg1-myc DNA binding sites by ChIP-seq. Three immunoprecipitated samples were sequenced and three input samples (pre-immunoprecipitation) were sequenced as controls.
2013-06-20 | E-GEOD-41063 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE32712: Transcriptional profile of Candida parapsilosis CLIB214 21% Oxygen (normoxia) versus at 1% oxygen (hypoxia). GSE32713: Transcriptional profile of Candida parapsilosis CLIB214 versus UPC2 delete, both at 1% oxygen (hypoxia) GSE32714: Transcriptional landscape of Candida parapsilosis Refer to individual Series
2011-11-30 | E-GEOD-32716 | biostudies-arrayexpress
Project description:In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density AffymetrixM-BM-. GeneChipM-BM-. Bovine Genome Array platform from the same PBL-extracted RNA Identify changes occuring at the transcriptome level of PBL in response to M. bovis
2014-08-18 | E-GEOD-60265 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE24073: Transcriptional profile of Candida albicans during Hypoxic conditions. GSE24074: Transcriptional profile of Candida albicans DAY286 culture without ketoconazole versus DAY286 culture with 0.04 μg/ml ketoconazole, both at 20% oxygen (normoxia). GSE24075: Transcriptional profile of Candida albicans DAY286 versus UPC2 delete, both at 1% oxygen (hypoxia). Refer to individual Series
2010-11-15 | E-GEOD-24076 | biostudies-arrayexpress
Project description:Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis in hypoxic condition. RNA was isolated from CLIB214 grown in YPD medium in normoxia or hypoxia at 30 degree Celsius for 3.5 h, and labeled with Cy3 or Cy5. Four independent biological replicates were compared. Isolates from normoxic condition were labeled with Cy3 and isolates from hypoxic condition were labeled with Cy5.
2011-11-30 | E-GEOD-32712 | biostudies-arrayexpress
Project description:Phenothiazines are antipsychotic drugs used in the treatment of schizophrenia, which have been shown to present antimicrobial activity (in vitro and in vivo) against a great variety of pathogenic microorganisms, including bacteria, parasites (protozoa and helmints) and fungi. In this study, we used competitive microarray hybridization to evaluate the effects of increasing concentrations of the piperidinic phenothiazine derivative thioridazine (TR) on the transcriptome of Paracoccidioides brasiliensis, the causative agent of paracoccidioidomycosis (PCM) - the most common systemic mycosis in Latin America. These analyses showed that the presence of TR affected expression of more than 1,800 genes from this fungus, including genes related to cellular processes such as cell wall metabolism and drug resistance. Microarray hybridizations were carried out with amplified RNA (aRNA), which was produced starting with total RNA extracted from cells treated with thioridazine (15, 20 or 25 M-BM-5M) for 168 hours. The aRNA synthesized from cells unexposed to TR was taken as reference. Each treatment was analyzed with two independent hybridizations (a pair of hybridizations, with dye-swaps within each pair). Since each biochip carried two replicas of the arrayed genes, a total of four intensity readings were generated for each element in the microarray.The data has been filtered, normalized and adjusted as described in the "data processing" box for each individual sample. Dye swap consistency checking has been performed between equivalent experimental pairs with the aid of the software TIGR MIDAS v2.19 and inconsistent spots have been flagged and excluded from further analyses. The values obtained from each dye swap pair have been averaged and consolidated into a single data file, generating a total of 8 hybridization files (four from each treatment concentration). These files have been loaded into the software TIGR Multi-Experiment Viewer, v.3.1 Experiments were then normalized and genes that displayed statistically significant modulation were identified by one-way ANOVA, considering p < 0.01 as a cutoff value. A list of statisticaly significant, modulated genes was created, showing the average log ratio for each one of these genes, within each time point.
2013-12-31 | E-GEOD-41881 | biostudies-arrayexpress
Project description:SMORE-seq (Simultaneous Mapping Of RNA Ends by sequencing) is developted to simultaneously identify the strongest TSS (Transcription Start Site) and PAS (Polyadenylation Site) SMORE-seq were performed in wild type Saccharomyces cerevisiae
2014-02-04 | E-GEOD-49026 | biostudies-arrayexpress