Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR221808_1.fastq.gz | Fastqsanger.gz | |||
| DRR221808_2.fastq.gz | Fastqsanger.gz | |||
| DRR221809_1.fastq.gz | Fastqsanger.gz | |||
| DRR221809_2.fastq.gz | Fastqsanger.gz | |||
| DRR221810_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional profiling of Salmonella enterica serovar Typhimurium SL1344 cells comparing wildtype with ΔfabR mutant. Salmonella strains were cultured under free-living TSB conditions (TSB 1/20, 200 rpm, 25 °C) for 6h (ca. 2 x 108 cells/ml).
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Project description:InvF ChIP-chip on Salmonella enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged InvF (IP samples) and wildtype strain (mock IP samples) Salmonella enterica serovar Typhimurium causes a range of diseases from self-limiting gastroenteritis to life-threatening systemic infections. Its complex infection process is initiated by the invasion of the intestinal epithelial monolayer by means of a type three secretion system. InvF is one of the key regulators governing the invasion of epithelial cells. By mapping the InvF regulon, i.e. locating its direct target genes, the gene network underlying invasion can be further examined, including identifying possible new effector-encoding genes. In order to map the InvF regulon, we performed chromatin immunoprecipitation combined with tiling microarray analysis (ChIP-chip) and compared expression of the identified target genes in an invF mutant and a wildtype strain. In addition, the promoter regions of these target genes were searched for the presence of an InvF recognition site. Finally, a query-driven biclustering method, combined with a microarray compendium containing publically available S. Typhimurium gene expression data, was applied as an in silico validation technique for functional relatedness between newly identified target genes and known invasion genes. As expected, under invasion inducing conditions, InvF activates the expression of invasion chaperone encoding sicA and the effector-encoding genes sopB, sopE, sopE2 and sopA by binding their promoter region. Newly identified InvF targets are steB, encoding a secreted effector, and STM1239. The presence of an InvF recognition site in the promoter regions of these target genes further supports this observation. In addition, the query-driven biclustering method revealed similarities in expression profiles between STM1239 and known InvF regulated invasion genes over a range of experimental conditions. In conclusion, we here deliver the first evidence for direct binding of InvF to the promoter regions of sopA and sopE2, and associate genes encoding a secreted effector (steB) and a putative novel effector (STM1239) with the Salmonella invasion regulator InvF.
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Project description:In enteric bacteria, DNA supercoiling is highly responsive to environmental conditions. Host specific features of environment serve as cues for the expression of genes required for colonization of host niches via changing supercoiling [1]. It has been shown that substitution at position 87 of GyrA of Salmonella enterica str. SL1344 influences global supercoiling and results in an altered transcriptome with increased expression of stress response pathways [2]. Aminocoumarin antibiotics, such as novobiocin, can be used to relax supercoiling and alter the expression of supercoiling-sensitive genes. Meanwhile, Salmonella enterica demonstrates a significant resistance to this antibiotic and relatively small variability of supercoiling in response to the growth phase, osmotic pressure, and novobiocin treatment. Here we present for the first time transcriptome data of Salmonella enterica subsp. Enterica serovar Typhimurium str. 14028S grown in the presence of novobiocin. These data will help identify genes involved in novobiocin resistance and adaptation processes associated with torsion perturbations in S. enterica. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP239815) and have been assigned BioProject accession PRJNA599397.
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Project description:We performed transcriptome abundance analysis of Salmonella Typhimurium strain SL1344 swap which has been genetically engineered to express the hns open-reading frame from the stpA promoter and the stpA open reading frame from the hns promoter. This strain is designated SL1344(swap). Transcript abundance was compared with that of wild-type SL1344. This comparison was performed to determine the effect of chromosome location of the expression of two related global regulators and how alterations to their expression patterns would impact on their regulons.
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Project description:We performed Chromatin Immunoprecipitation (ChIP) and microarray hybridization analysis of CspC binding in Salmonella Typhimurium strain SL1344 which has been genetically engineered to express a 3xFLAG tagged CspC protein.
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Project description:InvF ChIP-chip on Salmonella enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged InvF (IP samples) and wildtype strain (mock IP samples) Salmonella enterica serovar Typhimurium causes a range of diseases from self-limiting gastroenteritis to life-threatening systemic infections. Its complex infection process is initiated by the invasion of the intestinal epithelial monolayer by means of a type three secretion system. InvF is one of the key regulators governing the invasion of epithelial cells. By mapping the InvF regulon, i.e. locating its direct target genes, the gene network underlying invasion can be further examined, including identifying possible new effector-encoding genes. In order to map the InvF regulon, we performed chromatin immunoprecipitation combined with tiling microarray analysis (ChIP-chip) and compared expression of the identified target genes in an invF mutant and a wildtype strain. In addition, the promoter regions of these target genes were searched for the presence of an InvF recognition site. Finally, a query-driven biclustering method, combined with a microarray compendium containing publically available S. Typhimurium gene expression data, was applied as an in silico validation technique for functional relatedness between newly identified target genes and known invasion genes. As expected, under invasion inducing conditions, InvF activates the expression of invasion chaperone encoding sicA and the effector-encoding genes sopB, sopE, sopE2 and sopA by binding their promoter region. Newly identified InvF targets are steB, encoding a secreted effector, and STM1239. The presence of an InvF recognition site in the promoter regions of these target genes further supports this observation. In addition, the query-driven biclustering method revealed similarities in expression profiles between STM1239 and known InvF regulated invasion genes over a range of experimental conditions. In conclusion, we here deliver the first evidence for direct binding of InvF to the promoter regions of sopA and sopE2, and associate genes encoding a secreted effector (steB) and a putative novel effector (STM1239) with the Salmonella invasion regulator InvF. Three IP samples (from three biological replicates using anti-Myc antibody against Salmonella Typhimurium SL1344 strain encoding chromosomally 9Myc-tagged InvF) and three control mock IP samples (from three biological replicates using anti-Myc antibody against Salmonella Typhimurium SL1344 wildtype strain) were labeled with Cy5 and hybridized against a common genomic DNA reference, labeled with Cy3, on 6 S. Typhimurium LT2 whole genome tiling arrays
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