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Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [microarray II]

ABSTRACT: Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII grown under aerobic or anaerobic conditions to stationary phase.

ORGANISM(S): Yersinia pseudotuberculosis YPIII Yersinia pseudotuberculosis

PROVIDER: GSE56476 | GEO | 2014/12/05

SECONDARY ACCESSION(S): PRJNA243387

REPOSITORIES: GEO

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Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [microarray I]

Project description:Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII grown under aerobic or anaerobic conditions to exponential phase.

2014-12-05 | GSE56475 | GEO

Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [microarray II]

Project description:Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII grown under aerobic or anaerobic conditions to stationary phase. Y. pseudotuberculosis YPIII was grown at 25Â°C in LB medium supplemented with 10 g/l glucose and 0.2 M HEPES buffer under aeration or under anaerobic growth conditions (in a nitrogen atmosphere) on a rotary shaker. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

2014-12-05 | E-GEOD-56476 | biostudies-arrayexpress

Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [microarray I]

Project description:Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII grown under aerobic or anaerobic conditions to exponential phase. Y. pseudotuberculosis YPIII was grown at 25Â°C in LB medium supplemented with 10 g/l glucose and 0.2 M HEPES buffer under aeration or under anaerobic growth conditions (in a nitrogen atmosphere) on a rotary shaker. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

2014-12-05 | E-GEOD-56475 | biostudies-arrayexpress

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [rovA mutant]

2014-09-17 | GSE54546 | GEO

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [csrA mutant]

Project description:Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis csrA regulon was determined in Yersinia minimal minimum developed for the study. CsrA is a key regulator coordinating virulence and metabolism.

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The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [crp mutant]

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Yersinia pseudotuberculosis YPIII

Project description:Yersinia pseudotuberculosis YPIII Genome sequencing

| PRJNA239354 | ENA

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [rovA mutant]

Project description:Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis rovA regulon was determined in Yersinia minimal minimum developed for the study. RovA is a key regulator for Yersinia virulence. Y. pseudotuberculosis YPIII or the isogenic rovA mutant strain were cultivated at 25M-BM-0C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAMM-bM-^@M-^Ys F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM). The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

2014-09-17 | E-GEOD-54546 | biostudies-arrayexpress

Lead-seq: transcriptome-wide in vivo structure probing with lead

Project description:In vivo probing of the Yersinia pseudotuberculosis YPIII transcriptome at 25 °C and 37 °C

2019-11-20 | GSE140649 | GEO

Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [RNA-seq]

Project description:We recently found that Yersinia pseudotuberculosis can be used as a model of persistent bacterial infections. We performed in vivo RNA-seq of bacteria in small cecal tissue biopsies at early and persistent stages of infection to determine strategies associated with persistence. Comprehensive analysis of mixed RNA populations from infected tissues revealed that Y. pseudotuberculosis undergoes transcriptional reprogramming with drastic down-regulation of T3SS virulence genes during persistence when the pathogen resides within the cecum. At the persistent stage, the expression pattern in many respects resembles the pattern seen in vitro at 26oC, with for example up-regulation of flagellar genes and invA. These findings are expected to have impact on future rationales to identify suitable bacterial targets for new antibiotics. Other genes that are up-regulated during persistence are genes involved in anaerobiosis, chemotaxis, and protection against oxidative and acidic stress, which indicates the influence of different environmental cues. We found that the Crp/CsrA/RovA regulatory cascades influence the pattern of bacterial gene expression during persistence. Furthermore, arcA, fnr, frdA, and wrbA play critical roles in persistence. Our findings suggest a model for the life cycle of this enteropathogen with reprogramming from a virulent to an adapted phenotype capable of persisting and spreading by fecal shedding. Examination of Y. pseudotuberculosis expression in two mouse cecal tissue at early and at persistent infection. Also pure bacterial cultures two at 26C and two 37C. Additionally, the bacterial content of cecal tissue during infections and before infection were analyzed with read mapping on 16SMicrobial NCBI database with non-rRNA-depleted reads.

2014-12-05 | E-GEOD-55292 | biostudies-arrayexpress

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