Ontology highlight
ABSTRACT:
PROVIDER: PRJNA808436 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18075300_1.fastq.gz | Fastqsanger.gz | |||
| SRR18075300_2.fastq.gz | Fastqsanger.gz | |||
| SRR18075301_1.fastq.gz | Fastqsanger.gz | |||
| SRR18075301_2.fastq.gz | Fastqsanger.gz | |||
| SRR18075302_1.fastq.gz | Fastqsanger.gz |
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Project description:To investigate whether salt-stress dependent activation of SigB is mitigated when cells are pre-loaded with the compatible solute glycine betaine, we analyzed salt induction of the SigB regulon in the presence of the precursor choline at a genome-wide level. The median expression value of SigB-regulated genes was 1.7-fold higher in cells that received choline immediately before salt stress compared to cells where choline was added 60 minutes prior to the salt stress.
2020-03-01 | GSE141882 | GEO
Project description:Pseudomonas aeruginosa displays tremendous metabolic diversity, controlled in part by the abundance of transcription regulators in the genome. We have been investigating P. aeruginosaM-bM-^@M-^Ys response to the host, particularly changes regulated by the host-derived quaternary amines choline and glycine betaine (GB). We previously identified GbdR as an AraC-family transcription factor that directly regulates choline acquisition from host phospholipids (via binding to plcH and pchP promoters), is required for catabolism of the choline metabolite GB, and is an activator that induces transcription in response to GB or dimethylglycine. Our goal was to characterize the GbdR regulon in P. aeruginosa using genetics and chemical biology in combination with transcriptomics and in vitro DNA-binding assays. Here we show that GbdR activation regulates transcription of 26 genes from 12 promoters; 11 of which have measureable binding to GbdR in vitro. The GbdR regulon includes the genes encoding GB, dimethylglycine, sarcosine, glycine, and serine catabolic enzymes, and the BetX and CbcXWV quaternary amine transport proteins. . Additionally, identification of two uncharacterized regulon members suggests roles for these proteins in response to choline metabolites. The conditions for inclusion in the gbdR regulon were: (i) called present in the array, (ii) changed more than 2.5-fold in signal in a statistically significant manner, (iii) altered in all three 'inducing' conditions (ethylcholine, choline+propargylcholine, and choline in the dgcA mutant), but (iv) not induced in the wild-type choline or diethylcholine treatments. Wild type and dgcA mutant cells were pre-grown in MOPS minimal media and then split and resuspended in MOPS pyruvate, MOPS pyruvate + choline, MOPS pyruvate + ethylcholine, MOPS pyruvate + diethylcholine, or MOPS pyruvate & choline + propargylcholine.
2013-10-23 | E-GEOD-49759 | biostudies-arrayexpress
Project description:Human fecal communities were dosed with either choline, carnitine, butyrobetaine, or glycine betaine to measure the microbial response to quaternary amine addition. Samples were digested with trypsin, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.
2021-03-04 | MSV000087004 | MassIVE
Project description:Enrichment culture DFE is capable of fermenting the toxic pollutant dichloromethane (DCM; CH2Cl2) into environmentally benign acetate. The dominant organism in the enrichment culture is a novel bacterium in the Peptococcaceae family, “Candidatus Formimonas warabiya” strain DCMF. This metaproteomic study analysed culture DFE during growth with four substrates – DCM, glycine betaine, choline, and methanol – all of which are primarily, if not solely, metabolised by strain DCMF.
2023-03-11 | PXD037334 | Pride
Project description:Alkaliphilic microorganisms are similar to mesophilic counterparts with exception to membrane proteins. Detection of membrane proteins is difficult due to hydrophobicity and low absolute abundance. Caldalkalibacillus thermarum TA2.A1 is of interest due to growth from pH 7.5 to pH 10. Combination of whole cell lysate proteomics and membrane extracts solubilized with either SDS or FOS-choline-12 detected 158 membrane proteins, including a complete electron transport chain. Additionally, transporters for osmolytes ectoine and glycine betaine were observed.
2023-07-11 | PXD042369 | Pride
Project description:Pseudomonas aeruginosa displays tremendous metabolic diversity, controlled in part by the abundance of transcription regulators in the genome. We have been investigating P. aeruginosa’s response to the host, particularly changes regulated by the host-derived quaternary amines choline and glycine betaine (GB). We previously identified GbdR as an AraC-family transcription factor that directly regulates choline acquisition from host phospholipids (via binding to plcH and pchP promoters), is required for catabolism of the choline metabolite GB, and is an activator that induces transcription in response to GB or dimethylglycine. Our goal was to characterize the GbdR regulon in P. aeruginosa using genetics and chemical biology in combination with transcriptomics and in vitro DNA-binding assays. Here we show that GbdR activation regulates transcription of 26 genes from 12 promoters; 11 of which have measureable binding to GbdR in vitro. The GbdR regulon includes the genes encoding GB, dimethylglycine, sarcosine, glycine, and serine catabolic enzymes, and the BetX and CbcXWV quaternary amine transport proteins. . Additionally, identification of two uncharacterized regulon members suggests roles for these proteins in response to choline metabolites. The conditions for inclusion in the gbdR regulon were: (i) called present in the array, (ii) changed more than 2.5-fold in signal in a statistically significant manner, (iii) altered in all three 'inducing' conditions (ethylcholine, choline+propargylcholine, and choline in the dgcA mutant), but (iv) not induced in the wild-type choline or diethylcholine treatments.
2013-10-23 | GSE49759 | GEO
Project description:Glycine betaine (GB) is a potent osmoprotectant for salt stressed Bacillus subtilis cells, which possess three high-affinity uptake systems for GB. OpuA is the dominant transporter for this compatible solute. Northern blot analysis, primer extension experiments and opuA-treA reporter gene fusion studies demonstrated that opuA expression is strongly induced at high osmolality from a single SigA-type promoter. Promoter mutations that improve the match of the opuA promoter to the consensus sequence substantially increase basal-level expression but reduce inducibility by high salinity. Expression of opuA is sensitively controlled by GB, which causes significant repression of opuA transcription at low and high salinity. GB influences the kinetics as well as the final level of high salinity induction of opuA in a concentration-dependent fashion. The repressing effect of GB on opuA transcription requires the intracellular presence of GB, regardless whether it is taken up via OpuA or other transporters or synthesized from choline. Genome-wide transcriptional profiling of salt-stressed B. subtilis cells demonstrated that the repressive effect of GB targets only a subset of high-salinity induced genes. This group of GB-responsive genes comprises in essence the full set of genes with demonstrated functions in either the uptake or synthesis of compatible solutes. Four different samples (untreated, GB, NaCl, and GB + NaCl treated) were analyzed and each sample was hybridized in triplicate.
2010-05-15 | E-GEOD-17435 | biostudies-arrayexpress
Project description:Burkholderia thailandensis is a soil-dwelling bacterium that shares many metabolic pathways with the ecologically similar, but evolutionarily distant, Pseudomonas aeruginosa. Among the diverse nutrients it can utilize is choline, which can be converted into the osmoprotectant glycine betaine and further catabolized as a source of carbon and nitrogen, similar to P. aeruginosa. Orthologs of genes in the choline catabolic pathway in these two bacteria showed distinct differences in gene arrangement as well as an additional orthologous transcriptional regulator in B. thailandensis. In this study, we showed that multiple glutamine amidotransferase1 (GATase1)-containing AraC-family transcription regulators (GATRs) are involved in regulation of the B. thailandensis choline catabolic pathway (gbdR1, gbdR2, souR). Using genetic analyses and sequencing the transcriptome in the presence and absence of choline, we identified the likely regulons of gbdR1 (BTH_II1869) and gbdR2 (BTH_II0968). We also identified a functional ortholog for P. aeruginosa souR, a GATR that regulates the metabolism of sarcosine to glycine. GbdR1 is absolutely required for expression of the choline catabolic locus, similar to P. aeruginosa GbdR, while GbdR2 is important to increase expression of the catabolic locus. Additionally, the B. thailandensis SouR ortholog (BTH_II0994) is required for catabolism of choline and its metabolites as carbon sources, whereas in P. aeruginosa, SouR function can by bypassed by GbdR. The strategy employed by B. thailandensis represents a distinct regulatory solution to control choline catabolism and thus provides both an evolutionary counterpoint and an experimental system to compare the acquisition and regulation of this pathway during environmental growth and infection.
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Project description:Betaine critically contributes to the control of hepatocellular hydration and provides protection of the liver from different kinds of stress. This study investigates to what extent hepatocellular hydration changes affect the expression levels of enzymes involved in the metabolism of betaine and related organic osmolytes by using qRT-PCR gene expression studies in rat hepatoma cells as well as metabolic and gene expression profiling in 5,10 - methylene tetrahydrofolate reductase (MTHFR) deficient primary hepatocytes. The results demonstrate a coordinated regulation of betaine degradation and synthesis under anisoosmotic conditions. Expression of betaine degrading enzymes is downregulated by hyperosmolarity and strongly induced by hypoosmolarity. In contrast, synthesis of glycerophosphocholine from phosphoethanolamine and conversion of choline to betaine are both induced by hyperosmolarity but decreased under hypoosmotic conditions. In addition we evaluated the flux of choline and its derivates in liver and plasma of methylene tetrahydrofolate reductase knockout (Mthfr-/-) mice by tandem mass spectrometry. Analyses of system-wide alterations of osmolyte metabolism with microarray studies revealed expression changes similar to those after hypoosmotic exposure in this betaine depletion model. In conclusion, regulation of betaine synthesis and degradation and concomitant changes in intracellular osmolyte concentrations contribute to long-term adaptation to anisoosmotic exposure of the liver. Expression of 280 genes were analyzed in wild type and mthr-/- mice (n=7) with spotted oligonucleotides.
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Project description:Global gene expression profiles of V. parahaemolyticus grown under 2% and 0.66% NaCl were compared to define the minimum low-salt stimulon. The ectABC-lysC operon for synthesis of the compatible solute ectoine, as well as three compatible-solute transport systems, namely ProU (glycine betaine), OpuD1 (glycine betaine) and Pot2 (spermidine), was up-regulated under 2% NaCl in relative to 0.66% NaCl. The 2% NaCl condition favored the inducible expression of OmpW, OmpN and OmpA2, while repressed the expression of OmpA1, OmpU and VP1008. These results indicated that, to master the hyperosmotic stress of saline environments, V. parahaemolyticus might not only accumulate osmoprotectants through uptake or endogenous synthesis of compatible solutes, but also remodel its profiles of outer membrane protein to restore its cell membrane. The above differentially regulated genes will provide novel candidates for the further investigation of the molecular mechanisms of osmoadaptation in V. parahaemolyticus.
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