Fur mutant A. salmonicida
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB17700 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1731882_1.fastq.gz | Fastqsanger.gz | |||
| ERR1731882_2.fastq.gz | Fastqsanger.gz | |||
| ERR1731883_1.fastq.gz | Fastqsanger.gz | |||
| ERR1731883_2.fastq.gz | Fastqsanger.gz | |||
| ERR1731884_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Global transcriptional profiling of Bacillus subtilis cells comparing fur mutant to mutants of the iron-sparing response: fur fsrA double mutant, fur fbpAB triple mutant, fur fbpC double mutant, and fur fbpABC quadruple mutant fur vs fur fsrA (fsrA), fur vs fur fbpAB (AB), fur vs fur fbpC (C), and fur vs fur fbpABC (ABC). Each experiemnt (fur vs mutant) was conducted three times using three independent total RNA preparations (2 independent experiement + 1 independent dye swap).
2011-02-19 | E-GEOD-27416 | biostudies-arrayexpress
Project description:Background Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Despite the identification of several virulence factors the pathogenesis is still poorly understood. We have used high-throughput proteomics to display the differences between in vitro secretome of A. salmonicida wild-type (wt, hypervirulent, JF5054) and T3SS-deficient (isogenic DeltaascV, extremely low-virulent, JF2747) strains in exponential (GP) and stationary (SP) phases of growth. Results Among the different experimental conditions we obtained semi-quantitative values for a total of 2136 A. salmonicida proteins. Proteins of specific A. salmonicida species were proportionally less detected than proteins common to the Aeromonas genus or those shared with other Aeromonas species, suggesting that in vitro growth did not induce the expression of these genes. Four detected proteins which are unidentified in the genome of reference strains of A. salmonicida were homologous to components of the conjugative T4SS of A. hydrophila pRA1 plasmid. Polypeptides of three proteins which are specific to the 01-B526 strain were also discovered. In supernatants (SNs), the number of detected proteins was higher in SP (326 for wt vs 329 for mutant) than in GP (275 for wt vs 263 for mutant). In pellets, the number of identified proteins (a total of 1536) was approximately the same between GP and SP. Numerous highly conserved cytoplasmic proteins were present in A. salmonicida SNs (mainly EF-Tu, EF-G, EF-P, EF-Ts, TypA, AlaS, ribosomal proteins, HtpG, DnaK, peptidyl-prolyl cis-trans isomerases, GAPDH, Enolase, FbaA, TpiA, Pgk, TktA, AckA, AcnB, Mdh, AhpC, Tpx, SodB and PNPase), and several evidences support the theory that their extracellular localization was not the result of cell lysis. According to the Cluster of Orthologous Groups classification, 29% of excreted proteins in A. salmonicida SNs were currently poorly characterized. Conclusions In this part of our work we elucidated the whole in vitro exoproteome of hypervirulent A. salmonicida subsp. salmonicida and showed the secretion of several highly conserved cytoplasmic proteins with putative moonlighting functions and roles in virulence. All together, our results offer new information about the pathogenesis of furunculosis and point out potential candidates for vaccine development.
2013-11-11 | PXD000429 | Pride
Project description:Wildtype G27 and it's Fur mutant derivative were exposed to pH 5.0 for the indicated length of time. Bacterial cells in the exponential phase of growth (denoted log) and stationary phase of growth were used. fur1 denotes a single fur mutant while fur2 denotes an additional fur mutant. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs
2006-02-03 | GSE4160 | GEO
Project description:Global tranascriptional profiling of Bacillus subtilis cells comparing fur mutant to mutants of the iron-sparing response: fur fsrA double mutant, fur fbpAB triple mutant, fur fbpC double mutant, and fur fbpABC quadruple mutant Abstract of associated manuscript: The Bacillus subtilis ferric uptake regulator (Fur) protein is the major sensor of cellular iron status. When iron is limiting for growth, derepression of the Fur regulon increases the cellular capacity for iron uptake and mobilizes an iron-sparing response mediated, in large part, by a small non-coding RNA named FsrA. FsrA functions together with three small, basic proteins (FbpABC) to repress many "low-priority" iron-containing enzymes. We have used transcriptome analyses to define the scope of the iron-sparing response and to define subsets of genes dependent on either FbpAB or FbpC for their repression. Enzymes of the tricarboxylic acid cycle, including both aconitase and succinate dehydrogenase, are major targets of FsrA-mediated repression and, as a consequence, flux through this pathway is significantly decreased under iron limitation. FsrA also mediates a physiologically significant repression of iron-sulfur containing enzymes required for ammonium assimilation (the GltAB glutamate synthase) and catabolism of lactic acid (LutABC). Repression of the lutABC operon requires both FsrA and FbpB which supports a model in which the Fbp proteins function to enable repression of subsets of the FsrA regulon.
2011-02-19 | GSE27416 | GEO
Project description:Wildtype G27 and it's Fur mutant derivative were exposed to pH 5.0 for the indicated length of time. Bacterial cells in the exponential phase of growth (denoted log) and stationary phase of growth were used. fur1 denotes a single fur mutant while fur2 denotes an additional fur mutant. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Computed
2006-02-02 | E-GEOD-4160 | biostudies-arrayexpress
Project description:Ferric uptake regulator (Fur) is the major regulator of iron acquisition in Escherichia coli and other bacteria. In the present study, the role of Fur in anaerobic S. enterica serovar Typhimurium was determined by transcriptome analysis, reporter assays, and enzymatic assays. In anaerobic ?fur, 298 genes were differentially expressed. In general, Fur repressed genes required for iron acquisition/storage, metabolism, electron transport, oxidative/nitrosative stress, and modulators of virulence. There were 73 genes whose expression required Fur, eleven of which contain a putative Fur box 5? of the gene. Transcription of sodA was >9-fold higher in ?fur but there was no corresponding increase in the activity of SodA. Anaerobic cultures of the fur mutant and the WT were used to inoculate two sets of three independent flasks each containing 150 ml of anoxic LB-MOPS-X. The three independent cultures were grown to an optical density at 600 nm (OD600) of 0.25 to 0.35, pooled, and treated with RNAlater (QIAGEN, Valencia, CA) to fix the cells and preserve the quality of the RNA. Total RNA was extracted with the RNeasy RNA extraction kit (QIAGEN), and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, CA). The absence of contaminating DNA and the quality of the RNA was confirmed by PCR amplification of known genes and by using agarose gel electrophoresis. Aliquots of the RNA samples were kept at –80°C for use in the microarray and quantitative real-time reverse transcription-PCR (qRT-PCR) studies. The SuperScript Indirect cDNA labeling system (Invitrogen) was used to synthesize the cDNA for the hybridizations. Each experiment consisted of two hybridizations, on two slides, and was carried out in Corning Hybridization Chambers at 42°C overnight. Dye swapping was performed to avoid dye-associated effects on cDNA synthesis. The slides were washed at increasing stringencies (2x SSC [1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 42°C; 0.1% SSC, 0.1% SDS, room temperature; 0.1% SSC, room temperature). Following hybridization, the microarrays were scanned for the Cy3 and Cy5 fluorescent signals with a ScanArray 4000 microarray scanner from GSI Lumonics (Watertown, MA). The intensity of every spot was codified as the sum of the intensities of all the pixels within a circle positioned over the spot itself and the background as the sum of the intensities of an identical number of pixels in the immediate surroundings of the circled spot. Cy3 and Cy5 values for each spot were normalized over the total intensity for each dye to account for differences in total intensity between the two scanned images. The consistency of the data obtained from the microarray analysis was evaluated by a pair-wise comparison, calculated with a two-tailed Student's t test and analyzed by the MEAN and TTEST procedures of SAS-STAT statistical software (SAS Institute, Cary, NC) . The signal intensity at each spot from the fur mutant and the WT were background subtracted, normalized, and used to calculate the ratio of gene expression between the two strains. All replicas were combined, and the median expression ratios and standard deviations were calculated for open reading frames (ORFs) showing 2.5-fold change.
2011-10-13 | E-GEOD-18441 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) was used to analyze gene expression in H. pylori strains expressing either WT Fur or a Fur variant (i.e. Fur-R88H). The goals of this study are to examine the role that WT Fur and Fur-R88H play in affecting salt-responsive gene expression in the 2 different strains. The H. pylori strains were grown in the presence of routine salt (0.5% added NaCl) or high salt (1.0% added NaCl).
2023-01-06 | GSE214216 | GEO
Project description:Ferric uptake regulator (Fur) is the major regulator of iron acquisition in Escherichia coli and other bacteria. In the present study, the role of Fur in anaerobic S. enterica serovar Typhimurium was determined by transcriptome analysis, reporter assays, and enzymatic assays. In anaerobic Δfur, 298 genes were differentially expressed. In general, Fur repressed genes required for iron acquisition/storage, metabolism, electron transport, oxidative/nitrosative stress, and modulators of virulence. There were 73 genes whose expression required Fur, eleven of which contain a putative Fur box 5‟ of the gene. Transcription of sodA was >9-fold higher in Δfur but there was no corresponding increase in the activity of SodA.
2011-10-14 | GSE18441 | GEO
Project description:FUR- mutant vs. WT
| PRJNA118243 | ENA
Project description:Investigation of whole genome gene expression level changes in a Clostridium difficile fur (ferric uptake regulator) mutant, compared to the wild type strain 630 erm. The fur mutant analyzed in this study is further described in Ho and Ellermeier (2015) J. Bacteriology
2015-05-27 | GSE69218 | GEO