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Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

ABSTRACT: Exposure of Salmonella enterica serovar Typhimurium to three humectants used in the food industry: NaCl, KCl and glycerol

PROVIDER: PRJNA286968 | ENA |

REPOSITORIES: ENA

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Exposure of Salmonella enterica serovar Typhimurium to three humectants used in the food industry: NaCl, KCl and glycerol

2015-06-15 | GSE69857 | GEO

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Project description:Salmonella Typhimurium was exposed to NaCl, KCl and glycerol (equilibrated to the same water activity) for 1, 6 and 24 h after which the expression profiles were examined using microarray. An non-exposed early stationary phase culture grown in LB medium was used as the control. Carried out using 3 biological replicates for each sample; each sample hybridised in a two-channel hybridization against Salmonella genomic DNA as the comparator/reference

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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.

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