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RNA-seq of pathogenic Escherichia coli strains CFT073 and EDL933 wild-type, rpoN mutant, and rpoN mutant + rpoN strains

ABSTRACT: RNA-seq of pathogenic Escherichia coli strains CFT073 and EDL933 wild-type, rpoN mutant, and rpoN mutant + rpoN strains

PROVIDER: PRJEB49945 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR7928540.fastq.gz	Fastqsanger.gz
	ERR7928531.fastq.gz	Fastqsanger.gz
	ERR7928541.fastq.gz	Fastqsanger.gz
	ERR7928532.fastq.gz	Fastqsanger.gz
	ERR7928542.fastq.gz	Fastqsanger.gz

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RNA-seq of pathogenic Escherichia coli strains CFT073 and EDL933 wild-type, rpoN mutant, and rpoN mutant + rpoN strains

Project description:Experiment conducted to investigate the genetic factors associated with variable and heterogeneous non-planktonic in a mutant lacking rpoN unique to CFT073 bacteria. The aim was to try to understand why RpoN suppresses this heterogeneity in the wild-type during colony growth, but also asses why this phenotype does not occur in other pathogenic strains by also sequencing transcripts from EHEC EDL933. The rpoN mutant strains was complemented with plasmid-borne rpoN containing its native promoter to ensure any differences in gene expression could solely be attributed to the absence of rpoN alone.

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Analysis of the Pseudomonas aeruginosa regulon controlled by the sensor kinase KinB and sigma factor RpoN

Project description:Alginate overproduction by P. aeruginosa, also known as mucoidy is associated with chronic endobronchial infections in cystic fibrosis (CF). Alginate biosynthesis in this bacterium is initiated by the extracytoplasmic function sigma factor (σ22, AlgU/T). In the wild type (wt) nonmucoid strains, such as PAO1, AlgU is sequestered by the anti-sigma factor MucA that inhibits alginate production. However, the degradation of MucA by activated intramembrane proteases AlgW and/or MucP can lead to the conversion from nonmucoid strains to mucoid. Previously we reported that the absence of the sensor kinase KinB in PAO1 causes the initiation of AlgW-dependent proteolysis of MucA resulting in alginate overproduction. In the kinB mutant this activation requires alternate sigma factor RpoN (σ54). To determine the RpoN-dependent KinB regulon, microarray and proteomic analyses were performed on a mucoid kinB mutant and an isogenic nonmucoid kinB rpoN double mutant. In the kinB mutant, RpoN controlled the expression of approximately 20% of the genome. Besides alginate biosynthesis and regulator genes such as AlgW, KinB, in concert with RpoN, also control a large number of genes including: those involved in carbohydrate metabolism, quorum sensing, iron regulation, rhamnolipid production, and motility. In an acute pneumonia murine infection model, mice exhibited better survival when challenged with the kinB mutant than wt PAO1. Together, these data strongly suggest that KinB controls virulence factors important for acute pneumonia and conversion to mucoidy.

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