Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant
Ontology highlight
ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa
SUBMITTER: Akihiro Ueda
PROVIDER: E-GEOD-13871 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To investigate the impact of adenosine on gene expression of wild-type PA14. To investigate the impact of adenosine on gene expression of wild-type PA14, cells were harvested after incubating for 7 h in LB medium and LB with 10 mM adenosine medium, and RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) using a bead beater (Biospec, Bartlesville, OK ) with RNAlater buffer (Applied Biosystems, Foster City, CA) to stabilize the RNA.
2012-05-22 | E-GEOD-29665 | biostudies-arrayexpress
Project description:It has been proposed that the gastro-intestinal tract environment containing high levels of neuroendocrine hormones is important for gut-derived P. aeruginosa infections. In this study, we report that the hormone norepinephrine increases P. aeruginosa PA14 growth, virulence factor production, invasion of HCT-8 epithelial cells, and swimming motility in a concentration-dependent manner. Transcriptome analysis of P. aeruginosa exposed to 500 µM, but not 50 µM, norepinephrine for 7 h showed that genes involved in the regulation of the virulence determinants pyocyanin, elastase, and Pseudomonas quinolone signal (PQS, 2-heptyl-3-hydroxy-4-quinolone) were up-regulated. The production of rhamnolipids, which are also important in P. aeruginosa infections, was significantly decreased on semi-solid surfaces, but not in planktonic cultures, upon exposure to norepinephrine. Swarming motility, a phenotype that is directly influenced by rhamnolipids, was also decreased upon 500 µM norepinephrine exposure. The increase in the transcriptional activation of lasR, but not that of rhlR, suggest that the effects of norepinephrine are mediated primarily through the las quorum sensing pathway. Together, our data strongly suggests that norepinephrine can play an important role in gut-derived infections by increasing the pathogenicity of P. aeruginosa PA14. For growth rate measurements, a single colony of PA14 was grown overnight in Luria Bertini (LB) broth, and re-inoculated in serum-RPMI medium in the presence of 50 µM and 500 µM NE to an initial turbidity of ~ 0.05 at 600 nm. The turbidity of the cultures at 600 nm was monitored every hour and growth rate of the exponentially growing cultures was calculated. Growth curves were obtained in triplicate using three independent cultures, and the statistical significance of specific growth rate was determined using the unpaired Student’s t-test. Total RNA isolation and microarray analysis PA14 was grown overnight in LB to turbidity at 600 nm of ~5.0 and diluted in 100 mL of serum-RPMI medium to an initial turbidity at 600 nm of 0.05. Different concentrations of NE (50 µM or 500 µM) were added and the cultures grown for 7 hours till late exponential phase (turbidity at 600 nm of ~0.5, 1.1 and 1.5 with 0 µM, 50 µM and 500 µM NE, respectively). Cell pellets were prepared and RNA was isolated as described previously (Ren et al. 2004a). The P. aeruginosa Genome Array (Affymetrix, P/N 510596) containing 5,500 of the 5,570 open reading frames of P. aeruginosa PA01, was used to analyze changes in the PA14 transcriptome. cDNA synthesis, fragmentation and hybridizations were as described previously (Gonzalez Barrios et al. 2006). Hybridization was performed for 16 h at 50°C, and the total cell intensity was scaled to an average value of 500. The probe array images were inspected for any image artifact. Background values, noise values and scaling factors of all the arrays were examined and were comparable. The intensities of polyadenosine RNA control were used to monitor the labelling process. For each binary microarray comparison of differential genes expression, if the gene with the larger transcription rate did not have a consistent transcription rate based on the 13 probe pairs (P-value less than 0.05), these genes were discarded. A gene was considered differentially expressed when the P-value for comparing two chips was lower than 0.05 (to assure that the change in gene expression was statistically significant and that false positives arise less than 5%), and the expression ratio (between cells treated with NE and control) was greater than 4.0 for the 50 µM NE array and 2.0 for 500 µM NE array (based on the standard deviation of fold-change values) (Ren et al. 2004b). Gene functions and locus tag numbers were obtained from the Pseudomonas Genome Database (http://www.pseudomonas.com/download.jsp).
2009-08-27 | E-GEOD-13326 | biostudies-arrayexpress
Project description:We used DNA microarrays to investigate the impact of indole and 7-hdroxyindole on P. aeruginosa PAO1.For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures of P. aeruginosa PAO1 diluted that were 1:100. For P. aeruginosa with 7-hydroxyindole and indole, 500 uM 7-hydroxyindole in 250 uL DMF, 1000 uM indole in 250 uL DMF, or 250 uL DMF alone were added to cells grown in LB. The cells were shaken at 250 rpm and at 37oC for 7 h to form biofilms on the glass wool, and RNA was isolated from the biofilm cells. Keywords: comparison with E. coli signal indole on P. aeruginosa PAO1 For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures of P. aeruginosa PAO1 diluted that were 1:100. For P. aeruginosa with 7-hydroxyindole and indole, 500 uM 7-hydroxyindole in 250 uL DMF, 1000 uM indole in 250 uL DMF, or 250 uL DMF alone were added to cells grown in LB. The cells were shaken at 250 rpm and at 37oC for 7 h to form biofilms on the glass wool, and RNA was isolated from the biofilm cells.
2010-10-23 | E-GEOD-10065 | biostudies-arrayexpress
Project description:Wild type (2.4.1) strain, dark conditions, controlled oxtgen concentration in the growth medium (achieved by constant sparging with a gas mixture containing 1% CO2, variable - indicated for every sample - concentration O2 and balance N2). Keywords: dose response Cells were harvested at OD 0.16-0.18 after rapid addition of rifampicin, spun down and frozen for subsequent RNA isolation. RNA was isolated using bead beater and RNeasy kit. Traces of DNA were removed by DNAse I treatment until level non-detectable by 33-36 cycles of real-time PCR. Further sample preparaton -according Affymetrix protocols. Data processing: MAS 5.0 values are deposited here (for compatability with other submitted samples), values used in the publications are obtained with RMA and may be recreated using the supplied CEL files.
2010-06-11 | E-GEOD-7004 | biostudies-arrayexpress
Project description:Microorganisms form biofilms containing differentiated cell populations. To determine factors driving differentiation, we study protein distributions in bacterial biofilms using shotgun proteomics. Notably, zinc- and manganese-depleted portions of the biofilm repress the production of anti-staphylococcal molecules. Exposure to calprotectin (a host protein known to sequester metal ions at infectious foci) recapitulates responses occurring within metal-deplete portions of the biofilm and promotes interaction between P. aeruginosa and Staphylococcus aureus. Consistent with these results, the presence of calprotectin promotes co-colonization of the murine lung, and polymicrobial communities are found to co-exist in calprotectin-enriched airspaces of a cystic fibrosis lung explant. These findings, which demonstrate that metal fluctuations are a driving force of microbial community structure, have clinical implications because of the frequent occurrence of P. aeruginosa and S. aureus co-infections.
2016-06-22 | PXD004081 | Pride
Project description:Comparison of wild-type (2.4.1) and CT01 (contains an omega Spr/Smr insertion in RSP4157) gene expression; growth condition is (3% O2 + 96%N2 + 1%CO2) semi-aerobic growth in the dark. Manuscript in preparation. The below normalized data was generated using GeneSpring software with the following settings: A data: Data Transformation: set all values less than 0.01 to 0.01 Per Chip: normalize to 50th percentile, and then Per Gene: normalize to median B data: Data Transformation: set all values less than 0.01 to 0.01 Per Chip: normalize to 50th percentile Values from independent replicates were averaged Keywords = Rhodobacter sphaeroides Keywords = photosynthesis Keywords = semi-aerobic Keywords = purple bacteria Keywords: other
2010-06-10 | E-GEOD-2146 | biostudies-arrayexpress
Project description:To understand how an inhibition of the mitochondrial ATP synthase affects transcriptional programming and to identify potential candidates of the signaling machinery involved in ATP synthase deficiency responses, we used oligomycin on seedling liquid cultures. Seedlings were harvested at time points 0, 1 and 4 h after the start of oligomycin and control (EtOH) treatments. Already 1 h after addition of oligomycin a total of 102 genes were more than threefold up-regulated and 14 genes were repressed, with most of them showing persistent changes. After 4 h, 580 additional genes were more than threefold up-regulated, and 152 genes were repressed by oligomycin. Several genes for alternative NAD(P)H dehydrogenases and alternative oxidases (AOX1a, AOX1d and NDA1) were up-regulated early, and additional homologs (NDA2, NDB2, NDB4 and AOX1b) followed 4 h after the start of treatment. Several genes for subunits of complex I, complex IV and the ATP synthase were induced whereas hardly any genes encoding enzymes of glycolysis and the TCA cycle changed. Additionally, four of five hallmark genes for oxidative stress were increased by oligomycin. These genes are At2g21640 (UPOX), At1g19020, At1g05340 and At1g57630 and code for proteins of unknown function. Among oxidative stress proteins with known functions, several H2O2-responsive Glutathione-S-transferases and BCS1 (CYTOCHROME BC1 SYNTHESIS) were strongly up-regulated already after 1 h. BCS1 is induced by salicylic acid and independent of other reactive oxygen signaling (ROS) pathways, such as H2O2. The results indicate that several different ROS and defense signaling pathways were induced simultaneously by oligomycin. This is further corroborated by induction of several transcription factors of the WRKY and NAC families, which have been previously implicated in coordinating cellular defense signaling. Three replicates for each treatment including oligomycin and control (EtOH) samples.
2012-06-27 | E-GEOD-38965 | biostudies-arrayexpress
Project description:Comparison of wild-type (2.4.1) R. sphaeroides gene expression in 30% O2 aerobic respiration vs. photosynthesis 10W/m2 light, to identify candidate photosynthesis genes. RNA preparation: pellet cells from exponential phase cultures using 5% phenol in ethanol stop solution; lysozyme + SDS to lyse; phenol/chloroform extraction + DNase treatment + RNeasy kit clean up. Manuscript in preparation. The below normalized data was generated using GeneSpring software with the following settings: A data: Data Transformation: set all values less than 0.01 to 0.01 Per Chip: normalize to 50th percentile, and then Per Gene: normalize to median B data: Data Transformation: set all values less than 0.01 to 0.01 Per Chip: normalize to 50th percentile Values from independent replicates were averaged Keywords = Rhodobacter sphaeroides Keywords = photosynthesis Keywords = purple bacteria Keywords: other
2010-06-10 | E-GEOD-2145 | biostudies-arrayexpress
Project description:Vibrio parahaemolyticus scr genes modulate expression of gene sets pertinent to swarming and biofilm formation. They do so by affecting the level of the second messenger c-di-GMP. Here we explore the extent of this regulation by comparing the transcriptomes of a scrABC mutant and its wild-type parental strain. The scope of transcriptional effects modulated by c-di-GMP includes ~100 genes that are positively and negatively regulated. An elevated cellular level of c-di-GMP represses the surface sensing regulon including the genes encoding the lateral flagellar and type three secretion systems while inducing expression of genes encoding cell surface molecules and capsular polysaccharide. Expression of a few transcriptional regulators was also affected, and here we describe the role of one, CpsQ. CpsQ is one of four V. parahaemolyticus homologs in the CsgD/VpsT family of regulators, members of which have been implicated in c-di-GMP signaling. Mutations in cpsQ, like defects in another previously identified capsule regulator, cpsR, suppress the sticky phenotype of scr mutants. By using a combination of mutant and reporter analyses in Vibrio and E. coli, CpsQ is shown to be the direct positive regulator of cpsA transcription and its cpsA-activating ability is found to be responsive to the cellular level of c-di-GMP. Unexpectedly, we find that a low level of this nucleotide diminishes the stability of CpsQ. The molecular interplay in this signaling circuit is further defined by demonstrating that CpsQ is epistatic to CpsS, a negative regulator of capsule. CpsR activates cpsQ, and CpsQ can also regulate its own transcription. Wildtype Vibrio parahaemolyticus (LM5674) and scrABC mutant (LM6567) were grown on rich mediim agar plates and gene expression profiles were compared.
2011-12-31 | E-GEOD-30508 | biostudies-arrayexpress
Project description:This series contains two subsets of samples not being directly compared. The two subsets are: GSE2145: 30% O2 vs PS 10W/m2 GSE2146: CT01 vs wild-type at 3% O2 Below results represent the K-means (K=4) clustering analysis using GeneSpring software. The list contains genes/ORFs contained in each of the 4 clusters. Keywords: other
2005-04-01 | E-GEOD-2150 | biostudies-arrayexpress