Role of Yap4 in Yeast Osmotic Stress Response
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE5070 | GEO | 2006/06/15
SECONDARY ACCESSION(S): PRJNA95507
REPOSITORIES: GEO
Similar Datasets
Project description:Mycoplasma genitalium is the causative agent of non-gonococcal, chlamydia-negative urethritis in men and has been linked to reproductive tract disease syndromes in women. As with other mycoplasmas, M. genitalium lacks many regulatory genes because of its streamlined genome and total dependence on a parasitic existence. Therefore, it is important to understand how gene regulation occurs in M. genitalium, particularly in response to environmental signals likely to be encountered in vivo. In this study, we developed an oligonucleotide-based microarray to investigate transcriptional changes in M. genitalium following osmotic shock. Using a physiologically relevant osmolarity condition (0.3 M sodium chloride), we identified 39 up-regulated and 72 down-regulated genes. Of the up-regulated genes, 21 were of unknown function and 15 encoded membrane-associated proteins. The majority of down-regulated genes encoded enzymes involved in energy metabolism and components of the protein translation process. These data provide insight into the in vivo response of M. genitalium to hyperosmolarity conditions and identify candidate genes that may contribute to mycoplasma survival in the urogenital tract. To examine the effects of hyperosmolarity on M. genitalium transcription, four 50 ml cultures of strain G37 in 75 cm2 tissue culture flasks (Corning) were grown to exponential phase, as determined by medium colour change and colony density. Then, NaCl was added to three flasks to achieve final concentrations of 0.1, 0.2 and 0.3 M. Parallel cultures of M. genitalium in the absence of NaCl served as controls. All cultures were incubated for 1 h at 37M-bM-^DM-^C prior to RNA extraction. Experiments were repeated six times, which produced six independent RNA sample pairs from NaCl-treated cultures and control cultures for each NaCl condition. Dye swap was performed on three of six RNA pairs to minimize effects caused by biased labelling efficiencies.
2010-11-15 | E-GEOD-22661 | biostudies-arrayexpress
Project description:Mycoplasma genitalium is the causative agent of non-gonococcal, chlamydia-negative urethritis in men and has been linked to reproductive tract disease syndromes in women. As with other mycoplasmas, M. genitalium lacks many regulatory genes because of its streamlined genome and total dependence on a parasitic existence. Therefore, it is important to understand how gene regulation occurs in M. genitalium, particularly in response to environmental signals likely to be encountered in vivo. In this study, we developed an oligonucleotide-based microarray to investigate transcriptional changes in M. genitalium following osmotic shock. Using a physiologically relevant osmolarity condition (0.3 M sodium chloride), we identified 39 up-regulated and 72 down-regulated genes. Of the up-regulated genes, 21 were of unknown function and 15 encoded membrane-associated proteins. The majority of down-regulated genes encoded enzymes involved in energy metabolism and components of the protein translation process. These data provide insight into the in vivo response of M. genitalium to hyperosmolarity conditions and identify candidate genes that may contribute to mycoplasma survival in the urogenital tract.
2010-11-15 | GSE22661 | GEO
Project description:Time course of the S. meliloti response to an osmotic upshift elicited by salt (300mM or 400mM) or sucrose (500mM or 700mM)
2006-08-17 | E-MEXP-785 | biostudies-arrayexpress
Project description:The genome of the osmophilic Aspergillus wentii, unlike that of the osmotolerant Aspergillus nidulans, contains only the gfdA but not the gfdB glycerol 3-phosphate dehydrogenase gene. Here, we studied transcriptomic changes of A. nidulans (reference strain and DgfdB gene deletion mutant) and A. wentii (reference strain and An-gfdB expressing mutant) elicited by high osmolarity. A. nidulans showed canonic hyperosmotic stress response characterized by upregulation of trehalose and glycerol metabolism genes (including gfdB) as well as genes of the high-osmolarity glycerol (HOG) map kinase pathway. Deletion of gfdB caused only negligible alterations in the transcriptome suggesting that the glycerol metabolism was flexible enough to compensate for the missing GfdB activity in this species. A. wentii responded differently to increased osmolarity than A. nidulans: E.g.; bulk upregulation of glycerol and trehalose metabolism genes as well as HOG pathway genes were not detected. Expression of An-gfdB in A. wentii did not abolish osmophilia, but it reduced growth and caused much bigger alterations in the transcriptome than the missing gfdB gene did in A. nidulans. Flexible glycerol metabolism and hence two differently regulated gfd genes may be more beneficial for osmotolerant (living under changing osmolarity) than for osmophilic (living under constantly high osmolarity) species.
2024-02-28 | GSE255841 | GEO
Project description:Daily rhythms in mammalian behaviour and physiology are generated by a multi-oscillator circadian system entrained through environmental cues (e.g. light and feeding). The presence of tissue niche-dependent physiological time cues has been proposed, allowing tissues the ability of circadian phase adjustment based on local signals. However, to date, such stimuli have remained elusive. Here we show that daily patterns of mechanical loading and associated osmotic challenge within physiological ranges reset circadian clock phase and amplitude in cartilage and intervertebral disc tissues in vivo and in tissue explant cultures. Hyperosmolarity (but not hypo-osmolarity) resets clocks in young and ageing skeletal tissues and induce genome-wide expression of rhythmic genes in cells. Mechanistically, RNAseq and biochemical analysis revealed the PLD2-mTORC2-AKT-GSK3β axis as a convergent pathway for both in vivo loading and hyperosmolarity-induced clock changes. These results reveal diurnal patterns of mechanical loading and consequent daily surges in osmolarity as a bona fide tissue niche-specific time cue to maintain skeletal circadian rhythms in sync.
2023-08-17 | E-MTAB-12877 | biostudies-arrayexpress
Project description:In this research we were interested in answering a question whether subjecting Y. lipolytica strain overproducing recombinant secretory protein (rs-Prot) to a specific, pre-optimized stress factor may enhance synthesis of the target macromolecule. Increased osmolarity (3 Osm/kg) was the primary stress factor studied here, implemented alone or in combination with decreased temperature (20C), known to promote synthesis of rs-Prots. The treatments were executed in batch bioreactor cultures, and the cellular reaction was studied in terms of the culture progression, gene expression and global proteomic profiles, to get insight into molecular bases underlying awaken reaction. First of all, we observed that hyperosmolarity executed by high sorbitol concentration does not enhance synthesis of the rs-Prot, but increases its transcription. Expectedly, hyperosmolarity induced synthesis of polyols, at the expense of citric acid and growth, which was severely limited. A number of stress-related genes were upregulated, including several HSPs, AKRs, as observed at transcriptomics and proteomics level. Interestingly, the accompanying concerted downregulation of central carbon metabolism, incl. glycolysis, TCA and fatty acid synthesis, highlighted redirection of carbon fluxes. Elevated abundance of HSPs and osmolytes did not outbalance severe limitation of protein synthesis, marked by orchestrated downregulation of translation (EF-gamma; a number of aa-tRNA synthetases), amino acids biosynthesis and ribosome biogenesis in response to hyperosmolarity. Altogether we ultimately settled that increased osmolarity is not beneficial for rs-Prot synthesis in Y. lipolytica, even though some elements of the response could assist this process. Insight into global changes in the yeast proteome under the treatments is provided.
2021-10-13 | MSV000088228 | MassIVE
Project description:Background The osmotic regulator OmpR in Escherichia coli regulates differentially the expression of major porin proteins OmpF and OmpC. In Yersinia enterocolitica and Y. pseudotuberculosis, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in Y. pestis are not yet fully understood. Results Y. pestis OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. The ompR mutation likely did not affect the virulence of Y. pestis strain 201 that was a human-avirulent enzootic strain. The microarray-based comparative transcriptome analysis disclosed a set of 224 genes whose expressions were affected by the ompR mutation, indicating the global regulatory role of OmpR in Y. pestis. Real-time RT-PCR or lacZ fusion reporter assay further validated 16 OmpR-dependent genes, for which OmpR consensus-like sequences were found within their upstream DNA regions. ompC, F, X, and R were up-regulated dramatically with the increase of medium osmolarity, which was mediated by OmpR occupying the target promoter regions in a tandem manner. Conclusion OmpR contributes to the resistance against phagocytosis or survival within macrophages, which is conserved in the pathogenic yersiniae. Y. pestis OmpR regulates ompC, F, X, and R directly through OmpR-promoter DNA association. There is an inducible expressions of the pore-forming proteins OmpF, C, and X at high osmolarity in Y. pestis, in contrast to the reciprocal regulation of them in E. coli. The main difference is that ompF expression is not repressed at high osmolarity in Y. pestis, which is likely due to the absence of a promoter-distal OmpR-binding site for ompF.
2011-10-24 | GSE26601 | GEO
Project description:The antifungal compound fludioxonil targets the fungal specific group III hybrid histidin kinaseTcsC of A. fumigatus, which in turn activate the High Osmolarity Glycerol (HOG) pathway and leads to drastic swelling of the fungal cells. We investigated the different responses of the AfS35 (wild type), the completely resistant mutant strain DtcsC and the partial resistant mutant strain Dskn7 to fludioxonil.
2023-11-16 | GSE224696 | GEO
Project description:mRNA amount (RA) and Transcription rate (TR) analysis of W303-1a (wt) and hog1 mutant yeast strains growing in exponential phase in YPD subjected to osmotic stress This SuperSeries is composed of the following subset Series: GSE13096: Transcription rate analysis of wild type strain subjected to osmotic stress GSE13097: mRNA amount analysis of wild type strain subjected to osmotic stress GSE13098: Transcription rate analysis of W303 hog1 mutant strain subjected to osmotic stress GSE13099: mRNA amount analysis of W303 hog1 mutant strain subjected to osmotic stress Refer to individual Series Transcriptomic and transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F11-F24). A single DNA genomic hybridization from the same labeling reaction was done on the same microarrays for normalization.
2010-06-19 | E-GEOD-13100 | biostudies-arrayexpress
Project description:In response to osmolarity, Salmonella enterica serotype Typhi (S. Typhi) regulates genes required for Vi capsular antigen expression oppositely to those required for motility and invasion. Previous studies suggest that osmoregulation of motility, invasion and capsule expression is mediated through the RcsC/RcsD/RcsB phosphorelay system. Here we performed gene expression profiling and functional studies to determine the role of TviA, an auxiliary protein of the RcsB response regulator, in controlling virulence gene expression in S. Typhi. TviA repressed expression of genes encoding flagella and the invasion associated type III secretion system (T3SS-1) through repression of the flagellar regulators flhDC and fliZ, resulting in reduced invasion and reduced expression of FliC. Both RcsB and TviA reduced expression of flhDC, but only TviA altered flhDC expression in response to osmolarity. These data suggest that the auxiliary TviA protein integrates a new regulatory input into the RcsB regulon of S. Typhi, thereby altering expression of genes encoding flagella, the Vi antigen and T3SS-1 in response to osmolarity. Gene expression profiles of the S. Typhi wild-type strain, a rcsB mutant, a (delta)tviB-vexE (tviBCDEvexABCDE) mutant, and a (delta)viaB (tviABCDEvexABCDE) mutant (lacking tviA expression) was compared. Strains were cultured in SOB broth (low salt), a condition known to induce expression of TviA and the RcsCB system. Total RNA was extracted from two independent cultures (biological replicates) of each strain. cDNA was differentially labeled with Alexa Fluor 555 and 648, respectively and competitively hybridized on S.Typhimurium arrays (PFGRC, version 4). The submitted samples are biological replicates of a competitive hybridization of cDNA from the wild-type strain (Ty2) and the rcsB mutant (SW237) (GSM395580, GSM395581) or the viaB mutant (STY2) and the tviB-vexE mutant (SW74) (GSM395582, GSM395583), respectively.
2010-05-18 | E-GEOD-15752 | biostudies-arrayexpress