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ABSTRACT: Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the Salmonella fis and dps genes

PROVIDER: PRJNA638833 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11996341.fastq.gz	Fastqsanger.gz
	SRR11996341_1.fastq.gz	Fastqsanger.gz
	SRR11996341_2.fastq.gz	Fastqsanger.gz
	SRR11996342.fastq.gz	Fastqsanger.gz
	SRR11996342_1.fastq.gz	Fastqsanger.gz

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Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the Salmonella fis and dps genes.

Project description:Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the Salmonella fis and dps genes.

| PRJNA638663 | ENA

Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the Salmonella fis and dps genes. [ChIP-Seq]

| PRJNA638745 | ENA

Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the Salmonella fis and dps genes. [RNA-Seq]

| PRJNA638747 | ENA

Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the Salmonella fis and dps genes. [RNA-Seq]

Project description:The Fis nucleoid-associated protein controls the expression of a large and diverse regulon of genes in Gram-negative bacteria. Fis production is normally maximal in bacteria during the early exponential phase of batch culture growth, becoming almost undetectable by the onset of stationary phase. We tested the effect of rewiring the Fis regulatory network in Salmonella by moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the Right macrodomain of the chromosome, creating the strain GX. In a parallel experiment, we tested the effect of placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within Ter, creating the strain OX. ChIP-seq was used to measure global Fis protein binding and gene expression patterns. Strain GX showed few changes when compared with the wild type, although we did detect increased Fis binding at Ter, accompanied by reduced binding at Ori. Strain OX displayed a more pronounced version of this distorted Fis protein-binding pattern together with numerous alterations in the expression of genes in the Fis regulon. OX, but not GX, had a reduced ability to infect cultured mammalian cells, had undergone a reduction in competitive fitness and had reduced motility compared to the wild type. These findings illustrate the inherent robustness of the Fis regulatory network to rewiring based on gene repositioning alone and emphasise the importance of fis expression signals in phenotypic determination.

2020-07-06 | GSE152227 | GEO

Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the Salmonella fis and dps genes. [ChIP-Seq]

2020-07-06 | GSE152225 | GEO

The consequences of reciprocally exchanging the genomic sites of Integration Host Factor (IHF) subunit production for subunit stoichiometry and bacterial physiology in Salmonella enterica serovar Typhimurium

Project description:Integration host factor (IHF) is a heterodimeric nucleoid-associated protein that plays roles in bacterial nucleoid architecture and genome-wide gene regulation. The ihfA and ihfB genes that encode the subunits are located 350 kilobase pairs apart, in the Right replichore of the Salmonella chromosome. IHF is composed of one IhfA and one IhfB subunit. Despite this 1:1 stoichiometry, mass spectrometry revealed that IhfB is produced in 2-fold excess over IhfA. Results from several studies suggest that a gene's location on the bacterial chromosome is an important factor in establishing the appropriate spatiotemporal expression pattern of that gene and its influence on physiology. We re-engineered Salmonella to exchange reciprocally the protein-coding regions of ihfA and ihfB, such that each relocated protein-encoding region was driven by the expression signals of the other's gene. Mass spectrometry showed that in this 'rewired' strain, IhfA is produced in excess over IhfB, correlating with enhanced stability of the hybrid ihfB-ihfA mRNA that was expressed from the ihfB promoter. Nevertheless, the rewired strain grew at a similar rate to the wild type, had identical cell morphology, and was similar in competitive fitness. However, it was less motile than the wild type, had growth-phase-specific reductions in SPI-1 and SPI-2 gene expression and was engulfed at a higher rate by RAW macrophage. Our data show that while exchanging the physical locations of its ihf genes and the rewiring of their regulatory circuitry are well tolerated in Salmonella, genes involved in the production of type 3 secretion systems exhibit dysregulation that accompanies altered phenotypes.

2021-11-02 | PXD027465 | Pride

RNA-Seq analysis among dps-disrupted mutants in Deinococcus geothermalis

Project description:Transcriptomic analysis was performed in Deinococcus geothermalis wild-type and three mutants including dgeo_0257, dgeo_0281, and double knockout (DK) mutants. dgeo_0281 is a major Dps-coding gene and dgeo_0257 is a novel Dps candidate. Thus, to detecte physiological functions of both Dps-encoded genes, each gene-disrupted mutant and DK mutant was constructed and performed RNA-Seq analysis. This result support better understanding for Dps roles in radiation resistant bacterium through up-regulated and down-regulated genes profile.

2025-04-30 | GSE284126 | GEO

Fis occupancy along the Salmonella enterica serovar Typhimurium SL1344 fis::3XFlag strain grown in different aeration regimes.

Project description:The regulatory role of the Fis protein in fis and in the transcription of several gene regions during mid-exponential and late-stationary phase, and during different growth aeration regimes, has been investigated. Studies were done during those two growth phases and in aerated and non-aerated (microaerobic) conditions, to measure Fis enrichment and binding peaks in strategic gene regions by genome-wide microarray analysis ChIP-chip. This research investigation points to central roles for SPI-1, SPI-2, DNA gyrase and topoisomerase I, the elements of the stringent response, and the regulatory function of Fis-binding patterns, in setting and re-setting the activity of the fis gene and other involved promoters as a function of the growth conditions and aeration regimes experienced by Salmonella.

2013-05-01 | GSE38661 | GEO

WT (Fis+) strain

Project description:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Keywords: time course

2007-08-15 | GSE7380 | GEO

Fis KO strain

2007-08-15 | GSE7379 | GEO