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Transcriptional profile of Salmonella enterica serovar Typhimurium 4/74 wild-type and mutants using strand-specific RNA-seq

ABSTRACT: New tools for studying bacterial transcripts at the single nucleotide level offer an unparalleled opportunity to understand the bacterial transcriptome. For the model pathogen Salmonella enterica serovar Typhimurium, it is necessary to identify the regulatory inputs for all RNA transcripts, including small RNAs (sRNAs) and coding genes. Here, we use RNA-seq to define the transcriptomes of mutants lacking 18 global regulatory systems that, among other functions, modulate the expression of the SPI1 and SPI2 Type Three secretion systems in S. Typhimurium strain 4/74. We directly compared the roles of the major regulators of transcription, and reported the effects of the regulatory mutations on expression of sRNAs. We also use this method to describe the impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

PROVIDER: GSE79314 | GEO | 2016/08/09

SECONDARY ACCESSION(S): PRJNA315446

REPOSITORIES: GEO

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Transcriptional profile of Salmonella enterica serovar Typhimurium 4/74 wild-type and mutants using strand-specific RNA-seq

Project description:New tools for studying bacterial transcripts at the single nucleotide level offer an unparalleled opportunity to understand the bacterial transcriptome. For the model pathogen Salmonella enterica serovar Typhimurium, it is necessary to identify the regulatory inputs for all RNA transcripts, including small RNAs (sRNAs) and coding genes. Here, we use RNA-seq to define the transcriptomes of mutants lacking 18 global regulatory systems that, among other functions, modulate the expression of the SPI1 and SPI2 Type Three secretion systems in S. Typhimurium strain 4/74. We directly compared the roles of the major regulators of transcription, and reported the effects of the regulatory mutations on expression of sRNAs. We also use this method to describe the impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts. Transcriptome analysis of S. Typhimurium 4/74 using RNA isolated wild-type and mutants grown under infection-relevant conditions.

2016-08-09 | E-GEOD-79314 | biostudies-arrayexpress

Salmonella enterica serovar Typhimurium 4/74 transcriptomics using strand-specific RNA-seq

Project description:Bacterial transcription networks typically consist of hundreds of transcription factors and thousands of promoters. However, current attempts to map bacterial promoters have failed to report the true complexity of bacterial transcription. The differential RNA-seq (dRNA-seq) approaches only identified a subset of promoters because they involved few growth conditions. Here, we present a simplified approach for global promoter identification in bacteria, based upon the analysis of RNA-seq data from multiple environmental conditions. RNA was extracted from Salmonella enterica serovar Typhimurium (S. Typhimurium) grown in 22 different environmental conditions, which were devised to reflect the pathogenic lifestyle of S. Typhimurium. Individual RNA samples were combined into two pools for sequencing. In just two runs of strand-specific RNA-seq and dRNA-seq of the pooled sample we identified 3701 promoters (Pool sample). In further experiments, we found that individual in vitro conditions stimulate the expression of about 60% of the S. Typhimurium genome, whereas the suite of 22 conditions induced expression of 87% of S. Typhimurium genes. We discovered environmental conditions that induce many genes within Salmonella pathogenicity islands and identified 78 new sRNAs. In S. Typhimurium there is now experimental evidence for 280 sRNAs, and we classified them in terms of location and Hfq-binding.

2013-12-18 | GSE49829 | GEO

Salmonella enterica serovar Typhimurium 4/74 transcriptomics using strand-specific RNA-seq

2013-12-18 | E-GEOD-49829 | biostudies-arrayexpress

The nucleoid-associated protein HU controls three regulons that coordinate virulence and general physiology in Salmonella enterica serovar Typhimurium

Project description:The regulon of genes controlled by the HU nucleoid-associated proteins was examined in Salmonella enterica serovar Typhimurium (S. Typhimurium). DNA microarrays were used to detect the effect on the bacterial transcriptome of knockout mutations in the hupA, the hupB and in both the hupA and hupB genes. Distinct but overlapping patterns of gene expression were detected in the transcriptome at each time point for each of the three mutants, pointing to the existence of not one but three regulons of genes controlled by the HU proteins. Mutations in the hup genes altered the expression of regulatory and structural genes in both the SPI1 and the SPI2 pathogenicity islands. The hupA hupB double mutant was found to be defective in invasion of CACO2 and CHO epithelial cell lines and in its ability to survive in J774A.1 macrophage-like cells. The double mutant also had defective swarming activity and had a competitive fitness disadvantage compared to the wild type. In contrast, inactivation of just the hupB gene resulted in increased fitness and correlated with the up-regulation of members of the RpoS regulon in exponential phase cultures. Elimination of both the hupA and hupB genes resulted in strong down-regulation of the genes coding for the integration host factor, IHF, at all three time points.

2011-03-22 | GSE22860 | GEO

The nucleoid-associated protein HU controls three regulons that coordinate virulence and general physiology in Salmonella enterica serovar Typhimurium

2011-03-22 | E-GEOD-22860 | biostudies-arrayexpress

Using TraDIS to perform genetic interaction screens for S Typhimurium sRNAs in cell models of infection

Project description:Salmonella Typhimurium is a major human pathogen, and additionally serves as a model system for the study of both intracellular pathogens and bacterial small non-coding RNAs (sRNAs). Over the last decade, it has become increasingly clear that sRNAs play central roles in the regulation of a number of cellular processes, including quorum sensing, metabolism, and various stress responses. However, the contribution of sRNAs to virulence remains largely unexplored. Recent and preliminary RNA-seq and TraDIS data from our lab and others suggests that a number ofsRNAs are induced during infection of both epithelial and immune cells, and furthermore that their deletion leads to measurable replication phenotypes in whole animal model systems. However, these experiments leave the mechanisms underlying these phenotypes largely unexplained.We have used the TraDIS method to perform genetic interaction screens for S. Typhimurium sRNAs in cell models of infection, which will provide direct insight in to the processes affected by sRNA regulation during infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2016-06-14 | E-ERAD-464 | biostudies-arrayexpress

Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica

Project description:Salmonella enterica serovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis, S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract. S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derived Salmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered by S. Typhimurium within the cytosol, and the bacterial genes required for cytosolic colonization, remain unknown. Here we have exploited the parallel colonization strategies of S. Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes/sRNAs with cytosol-specific or vacuole-specific expression signatures. Using these genes/sRNAs as environmental biosensors, we defined that Salmonella is exposed to iron and manganese deprivation and oxidative stress in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimal S. Typhimurium replication in the cytosol, as well as entC, fepB, soxS and sitA-mntH. Virulence genes that are typically associated with extracellular bacteria, namely Salmonella pathogenicity island 1 (SPI1) and SPI4, had a cytosolic-specific expression profile. Our study reveals that the cytosolic and vacuolar S. Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. Therefore, this archetypical vacuole-adapted pathogen requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol.

2021-06-30 | GSE179103 | GEO

Effect of cortisol on S. Typhimurium parental strain and an isogenic scsA mutant

Project description:S. Typhimurium 112910a parental strain and an isogenic ΔscsA strain were grown to stationary phase in SPI2 inducing minimal medium (MM5.8 - Erikkson et al., 2006 Inf & Imm., 74:1243) with or without supplementation with 1µM cortisol

2014-02-28 | GSE55430 | GEO

Intra-macrophage transcriptome of Salmonella enterica serovar Typhimurium 4/74 using strand-specific RNA-seq

Project description:Bacterial transcription is controlled by many transcription factors and promoters. Currently many promoters are mapped only in in vitro conditions. We use an intra-macrophage model to map the promoters and their expression in vivo. InSPI2 is an in vitro growth condition mimicking intra-macrophage condition. We also characterize the transcriptome of Salmonella during growth in an in vitro intra-macrophage growth condition.

2015-07-30 | GSE59945 | GEO

Transcriptome analysis of Salmonella enterica serovar Typhimurium growth in physiological murine bile

Project description:Infection with Salmonella enterica serovar Typhi in humans causes the systemic, life-threatening disease typhoid fever. In the laboratory, typhoid fever can be modeled through the inoculation of susceptible mice with Salmonella enterica serovar Typhimurium. The ensuing disease is characterized by systemic dissemination and colonization of many organs, including the liver, spleen and gallbladder. Using this murine model, we previously characterized the interactions between Salmonella Typhimurium and host cells in the gallbladder and showed that this pathogen can successfully invade gallbladder epithelial cells and proliferate. Additionally, we showed that Salmonella Typhimurium can use bile phospholipids to grow at high rates. These abilities are likely important for quick colonization of the gallbladder during typhoid fever and further pathogen dissemination through fecal shedding. To further characterize the interactions between Salmonella and the gallbladder environment we compared the transcriptome of Salmonella cultures grown in LB or physiological murine bile. Our data showed that many genes involved in bacterial central metabolism are affected by bile, with the citric acid cycle being repressed and alternative respiratory systems being activated. Additionally, our study revealed a new aspect of Salmonella interactions with bile through the identification of phoP as a bile-responsive gene. Repression of phoP expression does not involve PhoPQ sensing of a bile component. Due to its critical role in Salmonella virulence, further studies in this area will likely reveal aspects of the interaction between Salmonella and bile that are relevant to disease.

2011-11-10 | GSE33604 | GEO

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