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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression profiling of the Staphylococcus aureus GraSR regulon

ABSTRACT: The GraS/GraR two-component system has been shown to control cationic antimicrobial peptide (CAMP) resistance in the major human pathogen Staphylococcus aureus. We identified a highly conserved ten base pair palindromic sequence (5’ ACAAATTTGT 3’) located upstream from GraR-regulated genes (mprF and the dltA and vraFG operons), which we show to be essential for transcriptional regulation by GraR and induction in response to colistin, a bacterial CAMP, suggesting it is the likely GraR binding site. Genome-based predictions and transcriptome analysis revealed several novel GraR target genes. Global expression changes between the wild type strain HG001 (a rsbU+ variant of strain NCTC 8325) and a DgraSR mutant, grown to mid-exponential phase in TSB with 50 µg/ml colistin, were examined. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

ORGANISM(S): Staphylococcus aureus

SUBMITTER: Ulrike Mäder

PROVIDER: E-GEOD-26016 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways.

Falord Mélanie M Mäder Ulrike U Hiron Aurélia A Débarbouillé Michel M Msadek Tarek T

PloS one 20110701 7

The GraS/GraR two-component system has been shown to control cationic antimicrobial peptide (CAMP) resistance in the major human pathogen Staphylococcus aureus. We demonstrated that graX, also involved in CAMP resistance and cotranscribed with graRS, encodes a regulatory cofactor of the GraSR signaling pathway, effectively constituting a three-component system. We identified a highly conserved ten base pair palindromic sequence (5' ACAAA TTTGT 3') located upstream from GraR-regulated genes (mprF ...[more]

PMID: 21765893

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Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions

Project description:We report the condition-dependent transcriptome of S. aureus HG001, a derivative of strain NCTC 8325, by strand-specific tiling array hybridizations. More than 40 experimental conditions were investigated ranging from optimal in vitro growth to interaction with host cells. Analyses included the systematic mapping of transcription units, annotation of non-coding RNAs, the classification of promoters according to their dependency on SigA and SigB, and the prediction of potentially new transcription factor target sites. Antisense RNAs being of particular interest because of the small number of alternative sigma factors used by S. aureus were found to be relatively rare, overlapping only 6% of the annotated coding genes. RNA samples prepared from S. aureus HG001 grown in shake flask or cell culture infection experiments were reverse transcribed, labeled and hybridized to tiling arrays. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

2016-03-08 | E-GEOD-70040 | biostudies-arrayexpress

Expression profiling of the Staphylococcus aureus GraSR regulon

Project description:The GraS/GraR two-component system has been shown to control cationic antimicrobial peptide (CAMP) resistance in the major human pathogen Staphylococcus aureus. We identified a highly conserved ten base pair palindromic sequence (5’ ACAAATTTGT 3’) located upstream from GraR-regulated genes (mprF and the dltA and vraFG operons), which we show to be essential for transcriptional regulation by GraR and induction in response to colistin, a bacterial CAMP, suggesting it is the likely GraR binding site. Genome-based predictions and transcriptome analysis revealed several novel GraR target genes.

2011-09-01 | GSE26016 | GEO

Tiling array hybridizations of genomic DNA from Staphylococcus aureus HG001.

Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (MÃ¤der, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different bilogical conditions. Genomic DNA was prepared from four independent cultures of S. aureus HG001 cells; after sonication, DNA was labeled with Cy3 and hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift. genomic DNA from wild type

2016-03-08 | E-GEOD-70042 | biostudies-arrayexpress

Transcriptome analysis of the WalKR regulon in Staphylococcus aureus

Project description:The WalKR regulon was studied by comparing genes expression in a strain producing a constitutively active WalR regulator (WalRc) versus the wild type strain carrying the empty expression vector. Hybridizations were performed with three independent biological replicates. Our data allowed to identify 165 genes differentially expressed in the walRc expressing strain with a P-value M-bM-^IM-$ 0.05 using Z-test and a threshold value of two-fold change in transcriptional levels. Among them, 108 genes are activated, and 57 genes are repressed. About 10% of these results were confirmed by quantitative real time PCR, revealing the high reliability of this overall study. Beyond the major effect of the WalKR system on genes expressing cell wall hydrolases, we have shown that it activates a large number of genes involved in virulence, and probably through its positive impact on the SaeRS two-component system, is a major activator of S. aureus virulence. Cells were grown in TSB rich medium added with 0.25 M-BM-5M CdCl2 to allow walRc expression until OD600nm of 1. Gene expression was compared between the HG001 wild type reference strain carrying the pCN51 empty vector (HG001/pCN51) and the HG001 strain carrying a pCN51 derivative with the walRc allele under the control of the Pcad inducible promoter (HG001/pSD3-12). Each condition was done in triplicate and the data were analyzed using the Arraystat software. Genes were considered as differentially expressed if their transcriptional level differed by at least two-fold with a Z-test P-value M-bM-^IM-$ 0.05 in at least two of the replicates.

2012-09-13 | E-GEOD-29337 | biostudies-arrayexpress

Transcription profiling of Pseduomonas aeruginosa PAO1 exposed to subinhibitory colistin

Project description:Colistin is an important cationic antimicrobial peptide (CAMP) in the fight against Pseudomonas aeruginosa infection within the cystic fibrosis (CF) lungs. The effects of sub-inhibitory colistin on gene expression in P. aeruginosa were investigated by transcriptome microarray and functional analysis. Analysis revealed an alteration in the expression of 60 genes in total from a variety of pathways. Genes associated with bacterial chronic colonisation and virulence such as response to osmotic stress, motility, and biofilm formation, as well as those associated with LPS modification and quorum sensing are the most highly represented. Most striking among these is the upregulation of the PQS biosynthesis operon including pqsH, pqsE, and the anthranilate biosynthetic genes phnAB. Early activation of this central component of the QS-network may represent a switch to a more robust population, with increased fitness in the competitive environment of the CF-lung. Experiment Overall Design: Three independent cultures of the P. aeruginosa strain PAO1 were exposed to 0.15 Âµg colistin mlâ1. The untreated and treated samples were grown from OD600 0.05 to 0.8 and subsequently total RNA was extracted using the Ambion RiboPureTm- Bacteria kit according to the manufacturerâs instructions.

2009-09-12 | E-GEOD-13252 | biostudies-arrayexpress

Aminocandin versus Aminocandin plus Colistin

Project description:We found that the antibiotic colistin acts synergistically with antifungals of the echinocandin class (e.g. aminocandin) on C. albicans cells. In order to elucidate the mode of action of colistin in fungi we performed microarray analysis of samples treated with only aminocandin (0.00125µg/ml) or treated with aminocandin (0.00125µg/ml) and colistin (5µg/ml). We compared: (A). untreated cells to cells treated with aminocandin only; (B). cells treated with aminocandin to cells treated with aminocandin and colistin (which is the focus of this experiment). By comparing those datasets it should be possible to identify genes differentially expressed in response to aminocandin and in response to both drugs. And subsequently to be able to interpret where in the cell colistin acts. (See related experiment in ArrayExpress: E-MEXP-3437 for comparison between untreated cells vs cells treated with aminocandin only.)

2012-03-03 | E-MEXP-3438 | biostudies-arrayexpress

Secretome of Acinetobacter baumannii KAB strains

Project description:We analyzed the extracellular proteome of colistin-resistant Korean Acinetobacter baumannii (KAB) strains to identify proteome profiles that can be used to characterize extensively drug-resistant KAB strains.

2020-05-27 | PXD015959 | Pride

Staphylococcus aureus HG001

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-08 | E-GEOD-70043 | biostudies-arrayexpress

Exoproteome profiling reveals the involvement of the foldase PrsA in the cell surface properties and pathogenesis of S. aureus

Project description:Staphylococcus aureus is a bacterial pathogen that produces and exports many virulence factors that cause human diseases. PrsA, a membrane-bound foldase that is found ubiquitously in Gram-positive bacteria, is required for the folding of exported proteins into a stable and active structure. However, the involvement of PrsA in post-translocational protein folding in S. aureus remains unclear. In this study, a PrsA-deficient mutant of S. aureus HG001 was constructed and prsA deletion was shown to enhance auto-aggregation and increase the ability of S. aureus HG001 to adhere to human lung epithelial cells. The lack of PrsA made the bacteria more sensitive to sonication-induced lysis. In a mouse infection model, mice that were infected with a prsA-knockout strain HG001ΔprsA had a higher survival rate than those infected with the wild-type strain. An iTRAQ-based quantitative exoproteome analysis was conducted to identify the proteins whose secretion was affected by PrsA. The exoproteomic analysis revealed that prsA deletion altered the amounts of several proteins that were related to the properties of the cell surface and virulence. These include proteins involved in cellular adhesion and cell wall synthesis such as extracellular adhesion protein (Eap), undecaprenyl-diphosphatase (UppP) and FmtA, and proteins involved in subverting host innate immunity such as immunoglobulin-binding proteins Spa and Sbi, chemotaxis inhibitory protein (CHIP) and staphylococcal complement inhibitor (SCIN). The results of this study suggested that PrsA is required for the post-translocational folding of many exported proteins and critically affects the cell surface properties and pathogenesis of S. aureus.

2018-01-24 | PXD008528 | Pride

Transcriptome analysis of a Staphylococcus aureus mutant defective in the transcription termination factor Rho.

Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (MÃ¤der, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different biological conditions. The data revealed a relatively low abundance of antisense RNAs in S. aureus, overlapping only 6% of the coding genes. Transcriptome analysis of the rho deletion mutant revealed a remarkable overall increase in antisense transcription in S. aureus. delta rho and wild type

2016-03-08 | E-GEOD-70041 | biostudies-arrayexpress

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