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Escherichia coli str. K-12 substr. MG1655

ABSTRACT: Sigma38 binding sites in E. Coli

PROVIDER: PRJNA301623 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2932490.fastq.gz	Fastqsanger.gz
	SRR2932491.fastq.gz	Fastqsanger.gz
	SRR2932492.fastq.gz	Fastqsanger.gz
	SRR2932493.fastq.gz	Fastqsanger.gz
	SRR2932494.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA.

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RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

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YAMAT-seq of mature tRNA pools in the bacterium Escherichia coli str. K-12 substr. MG1655 and derivatives

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Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli

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Systematic identification and characterization of uncharacterized transcription factors in Escherichia coli K-12 MG1655

Project description:Bacteria regulate gene expression to adapt to changing environments through transcriptional regulatory networks (TRNs). Although extensively studied, TRNs are not fully characterized since we do not know the identity of all the transcriptional regulators that comprise a TRN. Here, we experimentally evaluate 40 uncharacterized proteins in the model organisms Escherichia coli K-12 MG1655, which were previously predicted to be transcription factors (TFs). First, we used myc-tagging and a multiplexed ChIP-exo assay to characterize genome-wide binding sites for the 40 candidate TFs. Then, we compared those binding sites with those of RNA polymerase and sigma factors to increase the confidence in the measured DNA-binding events. Finally, we used these data to infer potential functional annotation for 13 candidate TFs. As a result, we characterized 570 new binding sites for 34 of 40 candidate TFs. Taken together, the study; 1) expands the number of confirmed TFs from 249 to 278, that is close to the estimated total of about 280 TFs in E. coli K-12 MG1655, 2) it provides a roadmap for functional characterization of the 34 discovered TFs, and 3) it enables the elucidation of the first comprehensive TRN.

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