Expression data from Pseudomonas aeruginosa ∆sbrR and ∆sbrIR mutants versus wild type
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ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa PAO1 Pseudomonas aeruginosa
PROVIDER: GSE74917 | GEO | 2015/12/23
SECONDARY ACCESSION(S): PRJNA301901
REPOSITORIES: GEO
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Project description:SbrI and SbrR are an extracytoplasmic function sigma factor and its cognate anti-sigma factor, respectively. To identify the SbrIR regulon, we measured gene expression in wild type PAO1 , PAO1 âsbrR, and PAO1 âsbrIR mutants using microarrays. WT PAO1 pPSV38 (empty vector), PAO1 âsbrR pPSV38, PAO1 âsbrR pSbrR, and PAO1 âsbrIR pPSV38 were grown to mid-log. RNA was extracted and reverse transcribed into cDNA. The cDNA was biotinylated and hybridized to Pseudomonas aeruginosa Affymetrix microarrays.
2015-12-23 | E-GEOD-74917 | biostudies-arrayexpress
Project description:Alginate overproduction by P. aeruginosa, also known as mucoidy is associated with chronic endobronchial infections in cystic fibrosis (CF). Alginate biosynthesis in this bacterium is initiated by the extracytoplasmic function sigma factor (σ22, AlgU/T). In the wild type (wt) nonmucoid strains, such as PAO1, AlgU is sequestered by the anti-sigma factor MucA that inhibits alginate production. However, the degradation of MucA by activated intramembrane proteases AlgW and/or MucP can lead to the conversion from nonmucoid strains to mucoid. Previously we reported that the absence of the sensor kinase KinB in PAO1 causes the initiation of AlgW-dependent proteolysis of MucA resulting in alginate overproduction. In the kinB mutant this activation requires alternate sigma factor RpoN (σ54). To determine the RpoN-dependent KinB regulon, microarray and proteomic analyses were performed on a mucoid kinB mutant and an isogenic nonmucoid kinB rpoN double mutant. In the kinB mutant, RpoN controlled the expression of approximately 20% of the genome. Besides alginate biosynthesis and regulator genes such as AlgW, KinB, in concert with RpoN, also control a large number of genes including: those involved in carbohydrate metabolism, quorum sensing, iron regulation, rhamnolipid production, and motility. In an acute pneumonia murine infection model, mice exhibited better survival when challenged with the kinB mutant than wt PAO1. Together, these data strongly suggest that KinB controls virulence factors important for acute pneumonia and conversion to mucoidy.
2012-03-01 | GSE35248 | GEO
Project description:Alginate overproduction by P. aeruginosa, also known as mucoidy is associated with chronic endobronchial infections in cystic fibrosis (CF). Alginate biosynthesis in this bacterium is initiated by the extracytoplasmic function sigma factor (σ22, AlgU/T). In the wild type (wt) nonmucoid strains, such as PAO1, AlgU is sequestered by the anti-sigma factor MucA that inhibits alginate production. However, the degradation of MucA by activated intramembrane proteases AlgW and/or MucP can lead to the conversion from nonmucoid strains to mucoid. Previously we reported that the absence of the sensor kinase KinB in PAO1 causes the initiation of AlgW-dependent proteolysis of MucA resulting in alginate overproduction. In the kinB mutant this activation requires alternate sigma factor RpoN (σ54). To determine the RpoN-dependent KinB regulon, microarray and proteomic analyses were performed on a mucoid kinB mutant and an isogenic nonmucoid kinB rpoN double mutant. In the kinB mutant, RpoN controlled the expression of approximately 20% of the genome. Besides alginate biosynthesis and regulator genes such as AlgW, KinB, in concert with RpoN, also control a large number of genes including: those involved in carbohydrate metabolism, quorum sensing, iron regulation, rhamnolipid production, and motility. In an acute pneumonia murine infection model, mice exhibited better survival when challenged with the kinB mutant than wt PAO1. Together, these data strongly suggest that KinB controls virulence factors important for acute pneumonia and conversion to mucoidy. 6 Samples total. Three with kinB mutant and three kinB wild type.
2012-03-01 | E-GEOD-35248 | biostudies-arrayexpress
Project description:Bacterial gene expression is controlled by modifying the promoter affinity of the RNA polymerase (RNAP). This control occurs through the substitution of the RNAP σ subunit and by the interaction with transcription factors. The pathogen Pseudomonas aeruginosa contains several σ factors, including σVreI. This protein belongs to the extracytoplasmic function group of the σ70 family. Expression and activity of σECFs are tightly regulated and only occur in response to specific signals. σVreI is encoded within the vreAIR gene cluster. The expression of this cluster occurs in response to inorganic phosphate (Pi) limitation. σVreI activity is modulated by VreR anti-sigma factor, which keeps σVreI inactive. In response to a still unidentified host signal, VreR is proteolytically degraded and σVreI released and activated. σVreI interacts then with the RNAP and targets expression of the σVreI regulon, which includes virulence genes that increase P. aeruginosa pathogenicity. In this work, we compared the transcriptome of the P. aeruginosa PAO1 wild-type strain with that of the ΔvreR mutant upon bacterial growth in Pi starvation. Forty-six transcripts were more abundant in the ΔvreR mutant than in the PAO1 wild-type strain, and nine were less abundant, including the vreR transcript.
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Project description:A novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa
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Project description:Next to the two-component and quorum sensing systems, cell-surface signaling (CSS) has been recently identified as an important regulatory system in Pseudomonas aeruginosa. CSS senses signals from outside the cell and transmits them into the cytoplasm. It consists of a TonB-dependent outer membrane receptor, a cytoplasmic membrane-localized sigma factor regulator (or anti-sigma factor), and an extracytoplasmic function (ECF) sigma factor. Upon perception of the extracellular signal by the receptor the ECF sigma factor is activated and promotes the transcription of a specific set of gene(s). Although most P. aeruginosa ECF sigma factors are involved in the regulation of iron uptake, we have identified a novel ECF sigma factor (PA0675) involved in the regulation of virulence. By microarray analysis of cells overexpressing PA0675 from the pMUM3 plasmid we have identified the genes regulated by this sigma factor.
2009-04-21 | GSE15697 | GEO
Project description:Cell-surface signaling is a sophisticated regulatory mechanism used by gram-negative bacteria to sense signals from outside the cell and transmit them into the cytoplasm. This regulatory system consists of an outer membrane-localized TonB-dependent receptor (TonB-dependent transducer), a cytoplasmic membrane-localized anti-sigma factor and an extracytoplasmic function (ECF) sigma factor. By microarray analysis we have identified the regulons of four novel P. aeruginosa signaling systems. For that, the ECF sigmas PA0149, PA2050, PA2093 and PA4896 have been overexpressed in P. aeruginosa and their target gene candidates have been identified using DNA microarray. Keywords: Overexpression of ECF sigma factors
2007-11-24 | GSE9657 | GEO
Project description:As production of virulence factors by Pseudomonas aeruginosa is influenced by the host environment, we examined the effect of 10% adult bovine serum (ABS) on the global transcription with P. aeruginoas PAO1 at different phases of growth. At early exponential phase (4 h), serum significantly enhanced expression of 138 genes, most of which are repressed by iron and carry binding sequences for the ferric uptake regulator or the Fur-regulated extracytoplasmic function sigma factor PvdS. The expression of another 40 genes was reduced at 4h. However, the expression of only a few genes was significantly altered (reduced) at the early stationary phase of growth (8 h). Transcriptional fusion analyses confirmed serum enhances the expression of toxA, regA, and their regulatory genes regA and pvdS, yet does not interfere with the repression of these genes by iron. The P. aeruginosa strain PAO1 was grown in the iron-limited medium TSB-DC with or without 10% (v/v) ABS. The presence of 10% ABS reduced PAO1 growth, but despite this reduction, the cultures reached early exponential phase at 4 h and early stationary phase at 8 h in both media. Accordingly, we determined the PAO1 transcriptome in both media at these two specific time points. To standardize the comprison, we adjusted the cultures to the same optical density at 600 nm (biomass) by diluting with fresh TSB-DC PAO1 grown in TSB-DC to the same OD as PAO1 grown in TSB-DC/ABS. We obtained the transcriptome profile of 5,552 genes representing the complete P. aeruginosa PAO1 genome.
2012-07-08 | E-GEOD-30698 | biostudies-arrayexpress
Project description:Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including ChIP-seq of 11 polyhistidine-tag sigma factors was performed to define the primary regulon of each sigma factor.
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Project description:As production of virulence factors by Pseudomonas aeruginosa is influenced by the host environment, we examined the effect of 10% adult bovine serum (ABS) on the global transcription with P. aeruginoas PAO1 at different phases of growth. At early exponential phase (4 h), serum significantly enhanced expression of 138 genes, most of which are repressed by iron and carry binding sequences for the ferric uptake regulator or the Fur-regulated extracytoplasmic function sigma factor PvdS. The expression of another 40 genes was reduced at 4h. However, the expression of only a few genes was significantly altered (reduced) at the early stationary phase of growth (8 h). Transcriptional fusion analyses confirmed serum enhances the expression of toxA, regA, and their regulatory genes regA and pvdS, yet does not interfere with the repression of these genes by iron.
2012-07-09 | GSE30698 | GEO