PA14-PA2444 vs. PA14-WT biofilm cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa PA14 Pseudomonas aeruginosa
PROVIDER: GSE29879 | GEO | 2013/06/08
SECONDARY ACCESSION(S): PRJNA140729
REPOSITORIES: GEO
Similar Datasets
Project description:Pseudomonas aeruginosa causes many biofilm infections, and the rugose small-colony variants (RSCVs) of this bacterium are important for infection. We found here that mutation in glyA2 (PA2444), which encodes a serine hydroxymethyltransferase, leads to the RSCV phenotype. The phenotype is related to increased c-di-GMP concentrations and depends on an active Wsp chemosensory system, including a diguanylate cyclase WspR. By characterizing the PA2444 enzyme both in vivo and in vitro, we determined the physiological function of PA2444 and related the enzyme to S-adenosylmethionine concentrations and the methylation of a membrane bound methyl-accepting chemotaxis protein WspA. A transcriptome analysis revealed the possible relationship between PA2444 and the redox state of the cells. Hence, we provide a mechanism for how an enzyme of central metabolism controls the community behavior of the bacterium. The P. aeruginosa genome array (Affymetrix, P/N 510596) was used to investigate differential gene expression in biofilm cells between PA14 and the PA2444 mutant. Biofilm cells were harvested from 10 g of glass wool after incubation for 7 h in LB with shaking at 250 rpm, 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. 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 when the expression ratio was higher than the standard deviation for the whole microarrays (1.8 for PA14 wild-type and PA2444).
2013-06-08 | E-GEOD-29879 | biostudies-arrayexpress
Project description:The Pseudomonas aeruginosa Wsp pathway undergoes positive evolutionary selection during chronic infection
| PRJNA491911 | ENA
Project description:Pseudomonas aeruginosa is a ubiquitous gram-negative bacterium capable of forming biofilms on living and non-living surfaces, frequently leading to undesirable consequences. We found that lauroyl arginate ethyl (LAE), a synthetic non-oxidizing biocide, inhibited biofilm formation by P. aeruginosa at sub-growth inhibitory concentrations in both static and flow conditions. To identify the genes targeted by LAE, a global transcriptome analysis was conducted using a gene chip microarray.
2017-06-29 | GSE96844 | GEO
Project description:Pseudomonas aeruginosa is a gram-negative, pathogenic, bacterium that produces biofilms containing phenotypically distinct subpopulations (Dodson et al., 2022). It was discovered that rugose small colony variants (RSCVs) were isolated with the biofilm subpopulations. RSCVs are hyper-biofilm producing bacterial mutants with increased antibiotic tolerance and are often found in chronic infections. When separating and characterizing the three biofilm cell subpopulations from a single P. aeruginosa PA14 biofilm, we discovered three novel RSCVs (denoted RSCV_1, RSCV_2, and RSCV_3). These RSCVs differed from stationary wild type (WT) PA14, the PA14 biofilm subpopulations, and between the RSCVs themselves. The observed phenotypic changes in the RSCVs included differences in cellular morphology, exopolysaccharide production, biosynthesis of virulence factors, biofilm formation, and antibiotic tolerance. Different molecules were ionized on the cell membranes of RSCVs and stationary phase WT PA14 using matrix assisted laser desorption ionization (MALDI) mass spectrometry. RNA sequencing analysis of stationary phase cells identified a high number of transcripts that were differentially expressed between the RSCVs and WT PA14 as well as between RSCV_1 and RSCV_3. The levels of the intracellular signaling molecule bis-(3′, 5′)-cyclic-dimeric-guanosine monophosphate (cyclic-di-GMP) were higher in all of the RSCVs compared to WT PA14 and significantly lower in RSCV_3 as compared to both RSCV_1 and RSCV_2. Whole-genome DNA sequencing analysis revealed single-nucleotide deletions and single-nucleotide polymorphisms (SNPs) among the RSCVs and between the RSCVs to WT PA14. The detected differences in the RSCVs have significant implications for biofilm production, antibiotic tolerance, and virulence.
2025-10-21 | GSE293895 | GEO
Project description:Polyamines are essential for various cell functions and are produced in most cells, as well as being taken up from extracellular sources. Polyamines, especially spermine, in blood cells increase when polyamines are supplied from the digestive tract. Altered polyamine metabolism has an impact on substrate concentrations and enzyme activities involved in gene methylation, and may affect gene expression. Therefore, we investigated the effect of decreased polyamine synthesis and extracellular spermine supply on substrate concentrations and enzyme activities involved in gene methylation and on changes of methylation in promoter regions using methylation arrays. In Jurkat cells and human mammary epithelial cells, changes in polyamine concentrations differed after polyamine synthesis inhibition. However, S-adenosylmethionine decarboxylase activity and the decarboxylated S-adenosylmethionine to S-adenosyl-L-methionine ratio were decreased by spermine addition in both cells. After inhibiting polyamine synthesis in Jurkat cells by D,L-alpha-difluoromethylornithine, the protein levels of DNA methyltransferase (DNMT) 1, 3A and 3B were not changed, but the activity of the three enzymes markedly decreased. The protein levels of these enzymes were not changed by addition of spermine; however, DNMT 3B was markedly activated and DNMT 3A was also activated. DNMT 1 was not activated. Effects on methylation of promoter regions included significant changes for tumor suppressor genes in response to altered polyamine metabolism. However, no significant changes in methylation status were found on genes of which methylation status and their related protein levels were affected by spermine. When considering these results, there are many genes for which polyamines have an impact on expression via methylation of promoter regions.
2018-03-15 | GSE111807 | GEO
Project description:Transcriptional responses to wildfire smoke, an increasingly important cause of human morbidity, are poorly understood. Here, using a combination of precision nuclear run-on sequencing (PRO-seq) and the assay for transposase-accessible chromatin using sequencing (ATAC-seq), we identify rapid and dynamic changes in transcription and chromatin structure in Beas-2B airway epithelial cells after exposure to wood smoke particles (WSP). By comparing 30 and 120 minutes of WSP exposure, we defined three distinct temporal patterns of transcriptional induction and chromatin responses to WSP. Whereas transcription of canonical targets of the aryl hydrocarbon receptor (AHR), such as CYP1A1 and AHRR, was robustly increased after 30 minutes of WSP exposure, transcription of these genes and associated enhancers returned to near baseline at 120 minutes. ChIP-qPCR assays and AHR knockdown confirmed a role for AHR in regulating these transcriptional responses, and we applied bioinformatics approaches to identify novel AHR-regulated pathways and targets including the DNA methyltransferase, DNMT3L, and its interacting factor, SPOCD1. Our analysis also defined a role for NFkB as a primary transcriptional effector of WSP-induced changes in gene expression. The kinetics of AHR- and NFkB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining the NFkB response. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFkB signaling in controlling pro-inflammatory gene expression.
2021-02-24 | GSE167370 | GEO
Project description:Transcriptional responses to wildfire smoke, an increasingly important cause of human morbidity, are poorly understood. Here, using a combination of precision nuclear run-on sequencing (PRO-seq) and the assay for transposase-accessible chromatin using sequencing (ATAC-seq), we identify rapid and dynamic changes in transcription and chromatin structure in Beas-2B airway epithelial cells after exposure to wood smoke particles (WSP). By comparing 30 and 120 minutes of WSP exposure, we defined three distinct temporal patterns of transcriptional induction and chromatin responses to WSP. Whereas transcription of canonical targets of the aryl hydrocarbon receptor (AHR), such as CYP1A1 and AHRR, was robustly increased after 30 minutes of WSP exposure, transcription of these genes and associated enhancers returned to near baseline at 120 minutes. ChIP-qPCR assays and AHR knockdown confirmed a role for AHR in regulating these transcriptional responses, and we applied bioinformatics approaches to identify novel AHR-regulated pathways and targets including the DNA methyltransferase, DNMT3L, and its interacting factor, SPOCD1. Our analysis also defined a role for NFkB as a primary transcriptional effector of WSP-induced changes in gene expression. The kinetics of AHR- and NFkB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining the NFkB response. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFkB signaling in controlling pro-inflammatory gene expression.
2021-02-24 | GSE167371 | GEO
Project description:Alcoholism is a relapsing disorder associated with excessive consumption after periods of abstinence. Neuroadaptations in brain structure, plasticity and gene expression occur with chronic intoxication but are poorly characterized. Here we report identification of pathways altered during abstinence in prefrontal cortex, a brain region associated with cognitive dysfunction and damage in alcoholics. To determine the influence of genetic differences, an animal model was employed with widely divergent responses to alcohol withdrawal, the Withdrawal Seizure-Resistant (WSR) and Withdrawal Seizure-Prone (WSP) lines. Mice were chronically exposed to highly intoxicating concentrations of ethanol and withdrawn, then left abstinent for 21 days. Transcriptional profiling by microarray analyses identified a total of 562 genes as significantly altered during abstinence. Hierarchical cluster analysis revealed that the transcriptional response correlated with genotype/withdrawal phenotype rather than sex. Gene Ontology category overrepresentation analysis identified thyroid hormone metabolism, glutathione metabolism, axon guidance and DNA damage response as targeted classes of genes in low response WSR mice, with acetylation and histone deacetylase complex as highly dimorphic between WSR and WSP mice. Confirmation studies in WSR mice revealed both increased neurotoxicity by histopathologic examination and elevated triidothyronine (T3) levels. Most importantly, relapse drinking was reduced by inhibition of thyroid hormone synthesis in dependent WSR mice compared to controls. These findings provide in vivo physiological and behavioral validation of the pathways identified. Combined, these results indicate a fundamentally distinct neuroadaptive response during abstinence in mice genetically selected for divergent withdrawal severity. Identification of pathways altered in abstinence may aid development of novel therapeutics for targeted treatment of relapse in abstinent alcoholics. A total of 32 microarrays were run with 4 biological replicates per treatment, line, and sex. Selection replicates (i.e. WSP-1 and WSP-2) for each treatment, line, and sex were collapsed to improve statistical power (n=4) and to facilitate in the identification of phenotype related effects and exclude selection artifacts. For comparisons, EtOH regulation was determined by comparing 4 arrays from (for example) Male WSR EtOH treated versus 4 arrays from Male WSR Air treated arrays.
2011-01-05 | E-GEOD-23165 | biostudies-arrayexpress
Project description:Analysis of the biosynthetic enzyme, ClbH, that incorporates S-adenosylmethionine into the backbone of the growing colibactin natural product.
2017-01-24 | MSV000080499 | MassIVE