Hog Fuel Metagenomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA665309 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12718338_1.fastq.gz | Fastqsanger.gz | |||
| SRR12718338_2.fastq.gz | Fastqsanger.gz | |||
| SRR12718339_1.fastq.gz | Fastqsanger.gz | |||
| SRR12718339_2.fastq.gz | Fastqsanger.gz |
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Project description:The ability to sense and adapt to a hostile host environment is a crucial element for virulence of pathogenic fungi, including Cryptococcus neoformans. These cellular responses are evoked by diverse signaling cascades, including the stress-activated HOG pathway. Despite previous analysis of central components of the HOG pathway, its downstream signaling network is poorly characterized in C. neoformans. Here we performed comparative transcriptome analysis with HOG signaling mutants to explore stress-regulated genes and their correlation with the HOG pathway in C. neoformans. In this study we not only provide important insights into remodeling patterns of global gene expression for counteracting external stresses, but also elucidated novel characteristics of the HOG pathway in C. neoformans. First, inhibition of the HOG pathway increases expression of ergosterol biosynthesis genes and cellular ergosterol content, conferring a striking synergistic antifungal activity with amphotericin B and providing an excellent opportunity to develop a novel therapeutic method for treatment of cryptococcosis. Second, a number of cadmium-sensitive genes are differentially regulated by the HOG pathway, and their mutation causes resistance to cadmium. Finally, we have discovered novel stress-defense and HOG-dependent genes, which encodes a sodium/potassium efflux pump, protein kinase, multidrug transporter system, and elements of the ubiquitin-dependent system.
2009-06-27 | GSE16692 | GEO
Project description:Fuel ethanol is now considered a global energy commodity that is fully competitive with gasoline. We have determined genome copy number differences that are common to five industrially important fuel ethanol yeast strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane. The fuel strains used were CAT1, BG1, PE2, SA1, and VR1 (note that two independent isolates were analyzed, denoted by "-1" and "-2"). These array-CGH data were compared with array-CGH data from nine other non-fuel industrial yeasts: An ale brewing strain ("Sc-ale"), four wine strains (GSY2A, GSY3A, GSY10A, GSY11B), and 4 bakers' yeast strains (GSY149, GSY150, GSY154, GSY155). Our results reveal significant amplifications of the telomeric SNO and SNZ genes only in the fuel strains, whose protein products are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin). We show that these amplifications allow these yeasts to grow efficiently, especially at high sugar concentrations, regardless of the presence or absence of either of the two vitamins. Our results reveal important genetic adaptations that have been selected for in the industrial environment, which may be required for the efficient fermentation of biomass-derived sugars from other renewable feedstocks. A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Strain Name: fuel strains used for aCGH Strain_or_line_design
2010-06-25 | E-GEOD-13875 | biostudies-arrayexpress
Project description:In fungal species, differentiation to the filamentous/hyphal cell type is critical for entry into host cells and virulence. Comparative RNA sequencing was used to explore the pathways that regulate differentiation to the filamentous cell type in yeast. This approach uncovered a role for the stress-response MAPK pathway, HOG, during the increased metabolic respiration that induces filamentous growth. In this context, the AMPK Snf1p and ER stress kinase Ire1p regulated the HOG pathway. Cross-modulation between the HOG and filamentous growth (ERK-type) MAPK pathways optimized the differentiation response. The regulatory circuit described here may extend to behaviors in metazoans.
2014-09-26 | GSE61783 | GEO
Project description:Fuel ethanol is now considered a global energy commodity that is fully competitive with gasoline. We have determined genome copy number differences that are common to five industrially important fuel ethanol yeast strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane. The fuel strains used were CAT1, BG1, PE2, SA1, and VR1 (note that two independent isolates were analyzed, denoted by "-1" and "-2"). These array-CGH data were compared with array-CGH data from nine other non-fuel industrial yeasts: An ale brewing strain ("Sc-ale"), four wine strains (GSY2A, GSY3A, GSY10A, GSY11B), and 4 bakers' yeast strains (GSY149, GSY150, GSY154, GSY155). Our results reveal significant amplifications of the telomeric SNO and SNZ genes only in the fuel strains, whose protein products are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin). We show that these amplifications allow these yeasts to grow efficiently, especially at high sugar concentrations, regardless of the presence or absence of either of the two vitamins. Our results reveal important genetic adaptations that have been selected for in the industrial environment, which may be required for the efficient fermentation of biomass-derived sugars from other renewable feedstocks. A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Strain Name: fuel strains used for aCGH
2009-09-24 | GSE13875 | GEO
Project description:The ability to sense and adapt to a hostile host environment is a crucial element for virulence of pathogenic fungi, including Cryptococcus neoformans. These cellular responses are evoked by diverse signaling cascades, including the stress-activated HOG pathway. Despite previous analysis of central components of the HOG pathway, its downstream signaling network is poorly characterized in C. neoformans. Here we performed comparative transcriptome analysis with HOG signaling mutants to explore stress-regulated genes and their correlation with the HOG pathway in C. neoformans. In this study we not only provide important insights into remodeling patterns of global gene expression for counteracting external stresses, but also elucidated novel characteristics of the HOG pathway in C. neoformans. First, inhibition of the HOG pathway increases expression of ergosterol biosynthesis genes and cellular ergosterol content, conferring a striking synergistic antifungal activity with amphotericin B and providing an excellent opportunity to develop a novel therapeutic method for treatment of cryptococcosis. Second, a number of cadmium-sensitive genes are differentially regulated by the HOG pathway, and their mutation causes resistance to cadmium. Finally, we have discovered novel stress-defense and HOG-dependent genes, which encodes a sodium/potassium efflux pump, protein kinase, multidrug transporter system, and elements of the ubiquitin-dependent system. There is more than 95% genome homology between JEC21 (Cryptococcus neoformans var. neoformans serotype D) and H99 (Cryptococcus neoformans var. grubii serotype A). Therefore, 100 slides of JEC21 70-mer oligo arrays are used in this analysis. 3 biological replicate experiments are performed. Total RNAs are extracted under 3 conditions (1M NaCl, 20ug/ul Fludioxonil, 2.5mM Hydrogen peroxide) at 3 time points (0time, 30min, 60min) with 4 strains from H99 (wild type, hog1Î , ssk1Î , skn7Î). We use a mix of all the total RNAs from this experiment as the control RNA. We use Cy5 as the sample dye and Cy3 as the control dye. Several samples are dye swapped.
2010-05-17 | E-GEOD-16692 | biostudies-arrayexpress
Project description:In fungal species, differentiation to the filamentous/hyphal cell type is critical for entry into host cells and virulence. Comparative RNA sequencing was used to explore the pathways that regulate differentiation to the filamentous cell type in yeast. This approach uncovered a role for the stress-response MAPK pathway, HOG, during the increased metabolic respiration that induces filamentous growth. In this context, the AMPK Snf1p and ER stress kinase Ire1p regulated the HOG pathway. Cross-modulation between the HOG and filamentous growth (ERK-type) MAPK pathways optimized the differentiation response. The regulatory circuit described here may extend to behaviors in metazoans. Comparison of expression patterns of wild-type and mutant yeast cells grown in salt, tunicamycin or galactose by comparative RNA sequencing analysis.
2014-09-26 | E-GEOD-61783 | biostudies-arrayexpress
Project description:HOG cells were plated in 6-well plates (0.5 × 10^6 cells per well). 24 hours later, HOG-EV or HOG-R132H cells were treated for 24 hours with 10 nM BAY 2402234 or DMSO. Cells were then harvested for LC-MS analysis.
2022-07-14 | ST002231 | MetabolomicsWorkbench
Project description:Here we have stimulated human fetal microglia HMC3 cells and human oligodendroglioma HOG cells with LPS for 24 hours and subsequently with a combination of TNFα and IL-1β for 24 hours , and analyzed their transcriptome-wide response to compare the responsivity of the two cell lines to the pro-inflammatory stimuli.
2022-05-02 | GSE200354 | GEO