Transcriptional profiling of Candida auris B8441 (CAU30) grown on different carbon and nitrogen sources
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ABSTRACT:
ORGANISM(S): Candidozyma auris
PROVIDER: GSE223318 | GEO | 2023/03/30
REPOSITORIES: GEO
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Project description:Goal of this study was to investigate the metabolic adaptation of C. albicans to different carbon sources (malic acid, α-ketoglutarate, proline) and nitrogen sources (dipeptides). As a control medium with glucose as carbon source and ammonium sulfate as nitrogen source was used. Transcriptional profiles were compared after 4 h incubation at 37°C.
2023-03-30 | GSE223317 | GEO
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2013-12-14 | GSE53303 | GEO
Project description:Aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae grown with six different nitrogen sources were subjected to transcriptome analysis. The use of chemostats enabled an analysis of nitrogen-source-dependent transcriptional regulation at a fixed specific growth rate. A selection of preferred (ammonium and asparagine) and non-preferred (leucine, phenylalanine, methionine and proline) nitrogen sources was investigated. For each nitrogen source, distinct sets of genes were induced or repressed relative to the other five nitrogen sources. A total number of 131 of such ‘signature transcripts’ were identified in this study. In addition to signature transcripts, genes were identified that showed a transcriptional co-response to two or more of the six nitrogen sources. For example, 33 genes were transcriptionally up-regulated in leucine-, phenylalanine- and methionine-grown cultures, which was partly attributed to the involvement of common enzymes in the dissimilation of these amino acids. In addition to specific transcriptional responses elicited by individual nitrogen sources, their impact on global regulatory mechanisms such as nitrogen catabolite repression (NCR) could be monitored. NCR-sensitive gene expression in the chemostat cultures showed that, ammonia and asparagine were ‘rich’ nitrogen sources. By this criterion, leucine, proline and methionine were ‘poor’ nitrogen sources and phenylalanine showed an ‘intermediate’ NCR response. Keywords: Response to growth on various nitrogen source transcriptome
2007-02-28 | GSE6405 | GEO
Project description:Transcriptome of A. fumigatus shifted from ammoniumtartrate to different nitrogen sources and incubated for a defined time was compared. After 16h preculture, the fungus was transferred into fresh medium containing ammonium tartrate, sodium nitrate, proline or bsa as nitrogen source. After 1h, fungus was reisolated, RNA was prepared from fungus, transcriptome was assessed and used for further analysis. Ammoniumtartrate, sodiumnitrate, BSA and proline as nitrogen sources, 2 biological replicates for each source. A. fumigatus liquid media shifts were performed according to ref. (Narendja et al.,2002) with minor modifications: 200 ml minimal medium base with 5 mM ammonium tartrate was inoculated with 10^8 conidia freshly harvested. A. fumigatus ATCC 46645 conidia were grown at 37°C and 150 rpm for 16 hours. This pre-culture was then harvested, washed liberally with sterile saline and divided into mycelial masses of equal size on a sterile surface. The portions were then added to 100 ml of minimal medium base without nitrogen source. When a defined carbon source was needed, 1% glucose was added. Flasks were incubated for 20 min at 37°C. Thereafter, one of the following sterile nitrogen sources was added: ammonium tartrate to a final concentration of 5 mM, Sodiumnitrate to a final concentration of 10 mM, 1 g proline suspended in 2 ml minimal medium base, or 0.5 g BSA (Albumin Fraktion V, Roth), suspended in 15 ml minimal medium base. The cultures were incubated for another 60 minutes, harvested by filtering through Miracloth, snap frozen in liquid nitrogen, and ground using a cooled mortar to obtain a fine powder.
2011-10-29 | E-GEOD-30384 | biostudies-arrayexpress
Project description:Transcriptome of A. fumigatus shifted from ammoniumtartrate to different nitrogen sources and incubated for a defined time was compared. After 16h preculture, the fungus was transferred into fresh medium containing ammonium tartrate, sodium nitrate, proline or bsa as nitrogen source. After 1h, fungus was reisolated, RNA was prepared from fungus, transcriptome was assessed and used for further analysis.
2011-10-30 | GSE30384 | GEO
Project description:Purpose: We explore gene expression changes when Neurospora crassa wild type responds to different carbon sources in Vogel's medium. Method: We obtained mRNA samples of Neurospora crassa WT in Vogel's minimal medium (VMM) with different carbon source and used RNA-seq technique to measure the trancriptome changes. Results: We identified many genes of transcription factors and enzymes that were up regulated or down regulated in response to the different carbon stimulation. Conclusion: Our data represents a systematic transcriptome profiling of filamentous fungi on different carbon source and identify COL-26 as a critical regulator in degradation of starch components.
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Project description:The pathogenic yeast Candida auris represents a global threat of the utmost clinical relevance. This emerging fungal species is remarkable in its resistance to commonly used antifungal and its persistence in the nosocomial settings. The innate immune system is one the first lines of defense preventing the dissemination of pathogens in the host. C. auris is susceptible to circulating phagocytes, namely neutrophils. However, some gaps of knowledge remain regarding the cellular and transcriptional responses towards other phagocytic lineages. In this work, we examined the interactions of this yeast with macrophages. We found that macrophages avidly phagocytose C. auris, however intracellular replication is not inhibited, indicating that C. auris is able to resist the killing mechanisms imposed by the phagocyte. Intracellular replication does not induce macrophage lysis, however. The transcriptional response of C. auris to macrophage phagocytosis is very similar to other members of the CUG clade (C. albicans, C. tropicalis, C. parapsilosis, C. lusitaniae), i.e., downregulation of transcription/translation and upregulation of alternative carbon metabolism pathways, transporters and induction of oxidative stress response and proteolysis. Gene family expansions are common in this yeast, and we found that many of these genes are induced in response to macrophage co-incubation. Among these, amino acid and oligopeptide transporters, as well as lipases and proteases are upregulated. Thus, C. auris shares key transcriptional signatures shared with other fungal pathogens and capitalizes on the expansion of gene families coding for potential virulence attributes that allow its survival, persistence, and evasion of the innate immune system.
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Project description:Carbon source is the basic nutrition and is essential for yeast growth. We grew the yeast cells (BY4741 strain) under different carbon sources including glucose with different concentration, galactose and raffinose. We generated bulk-cell RNA-seq data and investigated the dynamics of gene expression profiles under different growth conditions. We also generated single-cell RNA-seq data for yeast cells under 2% glucose, and explored the heterogeneity of gene expression within a cell population.
2019-05-24 | GSE131702 | GEO
Project description:Aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae grown with six different nitrogen sources were subjected to transcriptome analysis. The use of chemostats enabled an analysis of nitrogen-source-dependent transcriptional regulation at a fixed specific growth rate. A selection of preferred (ammonium and asparagine) and non-preferred (leucine, phenylalanine, methionine and proline) nitrogen sources was investigated. For each nitrogen source, distinct sets of genes were induced or repressed relative to the other five nitrogen sources. A total number of 131 of such M-bM-^@M-^Xsignature transcriptsM-bM-^@M-^Y were identified in this study. In addition to signature transcripts, genes were identified that showed a transcriptional co-response to two or more of the six nitrogen sources. For example, 33 genes were transcriptionally up-regulated in leucine-, phenylalanine- and methionine-grown cultures, which was partly attributed to the involvement of common enzymes in the dissimilation of these amino acids. In addition to specific transcriptional responses elicited by individual nitrogen sources, their impact on global regulatory mechanisms such as nitrogen catabolite repression (NCR) could be monitored. NCR-sensitive gene expression in the chemostat cultures showed that, ammonia and asparagine were M-bM-^@M-^XrichM-bM-^@M-^Y nitrogen sources. By this criterion, leucine, proline and methionine were M-bM-^@M-^XpoorM-bM-^@M-^Y nitrogen sources and phenylalanine showed an M-bM-^@M-^XintermediateM-bM-^@M-^Y NCR response. Keywords: Response to growth on various nitrogen source transcriptome Chemostat based transcriptomics study. Each growth condition was performed in triplicate.
2007-02-28 | E-GEOD-6405 | biostudies-arrayexpress
Project description:Filamentous cell growth is a vital property of fungal pathogens. The mechanisms of filamentation in the emerging multidrug-resistant fungal pathogen Candida auris are poorly understood. Here, we show that exposure of C. auris to glycerol triggers a rod-like filamentation-competent (RL-FC) phenotype, which forms elongated filamentous cells after a prolonged culture period. Whole-genome sequencing analysis reveals that all RL-FC isolates harbor a mutation in the C2H2 zinc finger transcription factor-encoding gene GFC1 (Gfc1 variants). Deletion of GFC1 leads to an RL-FC phenotype similar to that observed in Gfc1 variants. We further demonstrate that GFC1 mutation causes enhanced fatty acid β-oxidation metabolism and thereby promotes RL-FC/filamentous growth. This regulation is achieved through a Multiple Carbon source Utilizer (Mcu1)-dependent mechanism. Interestingly, both the evolved RL-FC isolates and the gfc1Δ mutant exhibit an enhanced ability to colonize the skin. Our results reveal that glycerol-mediated GFC1 mutations are beneficial during C. auris skin colonization and infection.
2024-06-12 | PXD047167 | Pride