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RNA-seq analysis of the effect of overexpression of DsrA at 42°C on the transcriptome of E. coli wild-type and ∆dps strains

ABSTRACT: RNA-seq analysis of the effect of overexpression of DsrA at 42°C on the transcriptome of E. coli wild-type and ∆dps strains

PROVIDER: PRJNA882051 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21627107_1.fastq.gz	Fastqsanger.gz
	SRR21627107_2.fastq.gz	Fastqsanger.gz
	SRR21627108_1.fastq.gz	Fastqsanger.gz
	SRR21627108_2.fastq.gz	Fastqsanger.gz
	SRR21627109_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of the effect of overexpression of DsrA at 42°C on the transcriptome of E. coli wild-type and ∆dps strains

Project description:The bacteria were cultured in ABTG-CAA medium at 42°C until OD450=0.15-0.2. Cells were harvested for total RNA extraction and subsequent RNA-seq. Differential expression of various conditions was analyzed.

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Project description:Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. Ferroxidase activity of Dps is rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. Using the ChIP-seq data presented here, we found a non-random distribution of Dps binding sites in the bacterial chromosome of exponentially growing cells and showed their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. The transcription activity of several Dps-targeted genes evaluated by qRT-PCR, showed dependence on the presence of Dps. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA or, vice versa, competing with inhibitors to activate transcription.

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