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ChIP-seq of the multiple antibiotic resistance repressor (MarR) protein of Enterotoxigenic Escherichia coli strain H10407

ABSTRACT: ChIP-seq of the multiple antibiotic resistance repressor (MarR) protein of Enterotoxigenic Escherichia coli strain H10407

PROVIDER: PRJEB20037 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1886176.fastq.gz	Fastqsanger.gz
	ERR1886177.fastq.gz	Fastqsanger.gz
	ERR1886178.fastq.gz	Fastqsanger.gz
	ERR1886179.fastq.gz	Fastqsanger.gz

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ChIP-seq of the multiple antibiotic resistance repressor (MarR) protein of Enterotoxigenic Escherichia coli strain H10407

Project description:The experiment contains ChIP-seq data for Enterotoxigenic Escherichia coli strain H10407 transformed with plasmids pAMNF (encoding an N-terminal MarR-3xFLAG fusion) or pAMNM (encoding an N-terminal MarR-8xmyc fusion). The cells was cultured at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using an anti-FLAG antibody (i.e. the strain encoding the MarR-8xmyc fusion was used as a control). Libraries were prepared using DNA remaining after immunoprecipitation.

2017-12-01 | E-MTAB-5591 | biostudies-arrayexpress

ChIP-seq of the multiple antibiotic resistance activator (MarA) protein and RNA polymerase sigma70 subunit of Enterotoxigenic Escherichia coli strain H10407

Project description:The experiment contains ChIP-seq data for Enterotoxigenic Escherichia coli strain H10407 transformed with plasmid pRGM9818. The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using antibodies against MarA, MarR or the RNA polymerase sigma 70 subunit. Libraries were prepared using DNA remaining after immunoprecipitation. Note that the MarR immunoprecipitations were not successful but the data served as a useful control for non-specifically immunoprecipitated DNA sequences.

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Project description:Streptococcus pneumoniae D39 AdcR (adhesion competence repressor) is the first metal-sensing member of the MarR (multiple antibiotic resistance repressor) family to be characterized. Expression profiling of a âadcR strain grown in liquid culture under microaerobic conditions revealed that transcript amounts for 13 genes were up-regulated relative to the wild-type strain, among them adcR, adcCBA, encoding a high affinity ABC uptake system for zinc, and genes encoding cell-surface zinc-binding pneumococcal histidine triad (pht) and adcII (lmb, laminin binding) proteins. Down-regulated transcripts included those encoding two putative zinc-containing alcohol dehydrogenases. Bacterial strains were grown exponentially in rich (BHI) media at 37C and an atmosphere of 5% CO2 to OD620~0.2, and were processed as described in the related Sample records. Samples were collected from three independent biological replicates and included one dye swap. Data were normalized using the Lowess (block) method without background subtraction. Changes in relative transcript amounts of positive or negative 2-fold with Bayesian P value of <0.001 were considered significant, and were included as supplementary material for the accompanying manuscript (The metalloregulatory site in Streptococcus pneumoniae AdcR, a zinc-activated MarR-family repressor; Reyes-Caballero, H. et al, manuscript in preparation).

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ChIP-seq of the multiple antibiotic resistance activator (MarA) protein and RNA polymerase sigma70 subunit of Enterotoxigenic Escherichia coli strain H10407

Project description:ChIP-seq of the multiple antibiotic resistance activator (MarA) protein and RNA polymerase sigma70 subunit of Enterotoxigenic Escherichia coli strain H10407

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Project description:Illumina TruSeq stranded mRNA RNA-seq including Illumina ribezeo rRNA depletion of Mycobacterium smegmatis wild type and deletion mutant of the redox-sensing MarR-type repressor HypS in three bilogical replicates prior and after 30 min after exposure to 500 µM NaOCl stress revealed that hypS is autoregulated and represses transcription of the co-transcribed hypO gene which encodes a multidrug efflux pump. DNA binding activity of HypS to the 8-5-8 bp inverted repeat sequence upstream of the hypSO operon was inhibited under NaOCl stress. HypS was identified as a novel redox-sensitive repressor that contributes to mycobacterial resistance towards HOCl stress and antibiotics.

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MarR type regulator PA3458 is involved in osmoadaptation control in Pseudomonas aeruginosa (RNA-seq)

Project description:Pseudomonas aeruginosa is a common bacterium, but also a facultative human pathogen, especially fatal for immunocompromised patients. It is dangerous due to its high adaptability and intrinsic antibiotic resistance mechanisms making treatment of P. aeruginosa infections particularly difficult. Sophisticated, complex, multilevel regulatory systems engaging huge repertoire of transcriptional regulators (TRs) are the main factors that direct cellular processes to keep cellular homeostasis and adapt to changeable conditions. The PA3458 gene encodes a putative MarR-type TR. Most representatives of MarR family are described as repressors involved in response to various environmental signals and control of different processes e.g. adhesion, virulence, antibiotic resistance. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3458 showed changes in mRNA level of 133 genes, among them 100 was down-regulated, pointing out the role of PA3458 as a repressor. ChIP-seq analysis identified multiple PA3458 binding sites in P. aeruginosa genome suggesting its role as a global regulator. The preferred sequence motif recognised by PA3458 was identified. Many genes involved in stress response are under control of PA3458. The PA3459-PA3461 operon, divergent to PA3458 gene is regulated by PA3458. It encodes: asparagine synthase, GNAT-family acetyltransferase and glutamyl aminopeptidase, respectively engaged in the production of potent osmoprotectant an N-acetylglutaminylglutamine amide (NAGGN). Overall, the PA3458 is engaged in osmoadaptation control in P. aeruginosa.

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MarR type regulator PA3458 is involved in osmoadaptation control in Pseudomonas aeruginosa (ChIP-seq)

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