Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq based transcriptional profiling of petroleum sludge-derived Pseudomonas aeruginosa ZS1 strain in response to alteration of growth conditions

ABSTRACT: We show that ZS1 in the medium supplemented with YE (YE-medium) produces more cell biomass but less rhamnolipid than it does in Glc-medium. To elucidate the transcriptional regulation of genes that are involved in biosynthesis of rhamnolipids and its precursors, RNA-seq-based transcriptional profiling of ZS1 cells in response to reciprocal change of YEand Glc-media is performed. Based on the assembly of ZS1 transcriptome using the reference PAO1 genome, we show that genes involved in energy metabolic pathways in ZS1 strain are highly transcribed in YE medium but not in Glc-medium, in agreement with their cell mass production. Similarly, transcription of quorum sensing systems genes lasI-lasR, rhlI-rhlR, and pqsH-mvfR are downregulated in Glc-medium. On the other hand, we show that two of the three enzymes RhlB and RhlC essential for rhamnolipid biosynthesis are transcriptionally upregulated, independent of quorum sensing signals. Notably, three of the four enzymes involved in dTDP-L-rhamnose, a precursor for the rhamnolipid biosynthesis, are downregulated in Glc except for RmlD that catalyzes the last reaction in the pathway. Together, our results indicate that increased rhamnolipid production in ZS1 cells is independent of quorum sensing signals. We propose that quorum sensing-independent rhamnolipid production in ZS1 Glc-culture is achieved by transcriptional re-programming of the minimum number of genes involved in rhamnolipid biosynthesis.

ORGANISM(S): Pseudomonas aeruginosa

PROVIDER: GSE107343 | GEO | 2023/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of the Pseudomonas aeruginosa regulon controlled by the sensor kinase KinB and sigma factor RpoN

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

Pseudomonas virulence factor controls expression of virulence genes in Pseudomonas entomophila

Project description:Quorum sensing is a communication strategy that bacteria use to collectively alter gene expression in response to cell density. Pathogens use quorum sensing systems to control activities vital to infection, such as the production of virulence factors and biofilm formation. The Pseudomonas virulence factor (pvf) gene cluster encodes a quorum sensing system (Pvf) that is present in over 500 strains of proteobacteria, including strains that infect a variety of plant and human hosts. We have shown that the Pvf quorum sensing system regulates the production of secreted proteins and small molecules in the insect pathogen Pseudomonas entomophila L48. Here, we identified genes that are likely regulated by Pvf using the model strain P. entomophila L48 which does not contain other known quorum sensing systems. Pvf regulated genes were identified through comparing the transcriptomes of wildtype P. entomophila and a pvf deletion mutant (ΔpvfA-D). We found that deletion of pvfA-D affected the expression of approximately 300 genes involved in virulence, the type VI secretion system, siderophore transport, and branched chain amino acid biosynthesis. Additionally, we identified seven putative biosynthetic gene clusters whose expression are reduced in ΔpvfA-D. Our results indicate that Pvf controls multiple virulence mechanisms in P. entomophila L48. Characterizing genes regulated by Pvf will aid understanding of host-pathogen interactions and development of anti-virulence strategies against P. entomophila and other pvf-containing strains.

2023-03-19 | GSE216056 | GEO

Expression profile for early stationary phase E. coli W3110 expression profile

Project description:Quorum signal uptake is an indispensable part of quorum sensing regulations. The coperative regulation of uptake repressor and kinase precisely signale the cells for quorum sensing uptake and terminate the quorum sensing signal production. We use the DNA microarray to detail the E. coli quorum sensing uptake reuglations and related gene regulations. Keywords: specific growth

2007-11-02 | GSE9203 | GEO

Protoanemonin: A new natural quorum sensing inhibitor that selectively activates iron starvation response

Project description:Many Gram-negative bacteria employ cell-to-cell communication mediated by N-acyl homoserine lactones (quorum sensing) to control expression of a wide range of genes including, but not limited to, genes encoding virulence factors. Outside the laboratory, the bacteria live in complex communities where signals may be perceived across species. We here present a newly found natural quorum sensing inhibitor, produced by the pseudomonads Pseudomonas sp. B13 and Pseudomonas reinekei MT1 as a blind end in the biodegradation of organochloride xenobiotics, which inhibits quorum sensing in P.M-bM-^@M-^Caeruginosa in naturally occurring concentrations. This catabolite, 4-methylenebut-2-en-4-olide, also known as protoanemonin, has been reported to possess antibacterial properties, but seems to have dual functions. Using transcriptomics and proteomics, we found that protoanemonin significantly reduced expression of genes and secretion of proteins known to be under control of quorum sensing in P.M-bM-^@M-^Caeruginosa. Moreover, we found activation of genes and gene products involved in iron starvation response. It is thus likely that inhibition of quorum sensing, as the production of antibiotics, is a phenomenon found in complex bacterial communities. Strain P. aeruginosa MPAO1 was cultivated under defined ABT medium. The orginal culture was divided in the early exponential phase into two parts. One was treated with 125M-NM-<M Protoanemonin and the other served as a control. The experiment was performed in duplicates.

2012-06-12 | E-GEOD-27674 | biostudies-arrayexpress

Transcription profiling of E. coli W3110 in early stationary phase

2008-06-17 | E-GEOD-9203 | biostudies-arrayexpress

Aflatoxin formation and gene expression in response to carbon source media shift in Aspergillus parasiticus

Project description:Aflatoxins are toxic and carcinogenic polyketide metabolites produced by fungal species, including Aspergillus flavus and A. parasiticus. The biosynthesis of aflatoxins is modulated by many environmental factors, including the availability of a carbon source. The gene expression profile of A. parasiticus was evaluated during a shift from a medium with low concentration of simple sugars, Yeast Extract (YE), to a similar medium with sucrose, Yeast Extract Sucrose (YES). Total RNA and aflatoxins (B1, B2, G1, and G2) were quantified from fungal mycelia harvested pre- and post-shifting. When compared to YE media, YES caused temporary reduction of the aflatoxin levels detected at 3 hours post-shifting and they remained low well past 12 hours post-shift. Aflatoxin levels did not exceed the levels in YE until 24 hrs post shift, at which time point a 10-fold increase was observed over YE. Microarray analysis comparing the RNA samples from the 48 hr YE culture to the YES samples identified a total of 2120 genes that were expressed across all experiments, including most of the aflatoxin biosynthesis genes. One-way Analysis of Variance (ANOVA) identified 56 genes that were expressed with significant variation across all time points. Three genes responsible for converting norsolorinic acid to averantin were identified among these significantly expressed genes. The potential role of these genes involvement in the regulation of aflatoxin biosynthesis is discussed. Keywords: time course, media shift, Aspergillus, aflatoxin

2007-10-01 | GSE8038 | GEO

Analysis of the Pseudomonas aeruginosa regulon controlled by the sensor kinase KinB and sigma factor RpoN

2012-03-01 | GSE35248 | GEO

Transcriptional analysis of quorum sensing deficient in Yersinia pestis CO92 at 37M-BM-0C

Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum-sensing synthase genes are knocked out. Two strains, M-bM-^HM-^Fpgm (pigmentation-negative) mutant R88 as treatment and quorum sensing null strain R115 with mutations (M-bM-^HM-^Fpgm, M-bM-^HM-^FypeIR, M-bM-^HM-^FyspIR, and M-bM-^HM-^FluxS) as control, are used in this analysis. Six independent RNA samples from R115 cultures were paired with six independent RNA samples from R88 cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

2013-09-05 | E-GEOD-21911 | biostudies-arrayexpress

Protoanemonin: A new natural quorum sensing inhibitor that selectively activates iron starvation response

Project description:Many Gram-negative bacteria employ cell-to-cell communication mediated by N-acyl homoserine lactones (quorum sensing) to control expression of a wide range of genes including, but not limited to, genes encoding virulence factors. Outside the laboratory, the bacteria live in complex communities where signals may be perceived across species. We here present a newly found natural quorum sensing inhibitor, produced by the pseudomonads Pseudomonas sp. B13 and Pseudomonas reinekei MT1 as a blind end in the biodegradation of organochloride xenobiotics, which inhibits quorum sensing in P. aeruginosa in naturally occurring concentrations. This catabolite, 4-methylenebut-2-en-4-olide, also known as protoanemonin, has been reported to possess antibacterial properties, but seems to have dual functions. Using transcriptomics and proteomics, we found that protoanemonin significantly reduced expression of genes and secretion of proteins known to be under control of quorum sensing in P. aeruginosa. Moreover, we found activation of genes and gene products involved in iron starvation response. It is thus likely that inhibition of quorum sensing, as the production of antibiotics, is a phenomenon found in complex bacterial communities.

2012-06-13 | GSE27674 | GEO

JHI Pa MC mutants

Project description:Plant cell wall degrading enzymes (PCWDEs) are key virulence determinants in the pathogenesis of the potato pathogen, Pectobacterium atrosepticum. In this study, we report the impact on virulence of a transposon insertion mutation in the metJ gene that codes for the repressor of the methionine biosynthesis regulon. In a mutant strain defective for the small regulatory RNA rsmB, PCWDEs are not produced and virulence in potato tubers is almost totally abolished. However, when the metJ gene is disrupted in this background, the rsmB- phenotype is suppressed and virulence and PCWDE production are restored. Additionally, when metJ is disrupted, production of the quorum sensing signal, N-(3-oxohexanoyl)-homoserine lactone, is induced precociously. The metJ mutant strains showed pleiotropic transcriptional impacts affecting approximately a quarter of the genome. Genes involved in methionine biosynthesis were most highly up-regulated, but many virulence-associated transcripts were also upregulated. This is the first report of the impact of the MetJ repressor on virulence in bacteria.

2012-11-02 | E-MTAB-1167 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data