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Escherichia coli str. K-12 substr. MG1655

ABSTRACT: Programmable Drug Dosing allows the Manipulation, Suppression, and Reversal of Antibiotic Drug Resistance

PROVIDER: PRJNA348693 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4427240.fastq.gz	Fastqsanger.gz
	SRR4427241.fastq.gz	Fastqsanger.gz
	SRR4427242.fastq.gz	Fastqsanger.gz
	SRR4427243.fastq.gz	Fastqsanger.gz
	SRR4427244.fastq.gz	Fastqsanger.gz

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

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

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Escherichia coli strain: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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The PurR regulon in Escherichia coli K-12 MG1655.

Project description:The PurR transcription factor plays a critical role in transcriptional regulation of purine metabolism in enterobacteria. Here, we elucidate the role of PurR under exogenous adenine stimulation at the genome-scale using high-resolution chromatin immunoprecipitation (ChIP)-chip and gene expression data obtained under in vivo conditions. Analysis of microarray data revealed that adenine stimulation led to changes in transcript level of about 10% of Escherichia coli genes, including the purine biosynthesis pathway. The E. coli strain lacking the purR gene showed that a total of 56 genes are affected by the deletion. From the ChIP-chip analysis, we determined that over 73% of genes directly regulated by PurR were enriched in the biosynthesis, utilization and transport of purine and pyrimidine nucleotides, and 20% of them were functionally unknown. Compared to the functional diversity of the regulon of the other general transcription factors in E. coli, the functions and size of the PurR regulon are limited.

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Escherichia coli str. K-12 substr. MDS42

Project description:Acceleration and Suppression of Resistance Development by Antibiotic Combinations

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Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.

Project description:Transcriptional regulation enables cells to respond to environmental changes. Of the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified, but ChIP methods have been used to fully characterize only a few dozen. Identifying these remaining TFs is key to improving our knowledge of the E. coli transcriptional regulatory network (TRN). Here, we developed an integrated workflow for the computational prediction and comprehensive experimental validation of TFs using a suite of genome-wide experiments. We applied this workflow to (i) identify 16 candidate TFs from over a hundred uncharacterized genes; (ii) capture a total of 255 DNA binding peaks for ten candidate TFs resulting in six high-confidence binding motifs; (iii) reconstruct the regulons of these ten TFs by determining gene expression changes upon deletion of each TF and (iv) identify the regulatory roles of three TFs (YiaJ, YdcI, and YeiE) as regulators of l-ascorbate utilization, proton transfer and acetate metabolism, and iron homeostasis under iron-limited conditions, respectively. Together, these results demonstrate how this workflow can be used to discover, characterize, and elucidate regulatory functions of uncharacterized TFs in parallel.

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Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.

Project description:With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell, highly accurate genomes were determined for two closely related K-12 strains, MG1655 and W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13 sites with an insertion sequence element or defective prophage in only one strain and two sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with short indel and base disparities revealed that only eight sites are true differences. The other 243 discrepancies were due to errors in the original MG1655 sequence, including 79 frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense, and 17 silent changes within coding regions. Errors in the original MG1655 sequence (<1 per 13,000 bases) were mostly within portions sequenced with out-dated technology based on radioactive chemistry.

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2018-10-10 | PXD009279 | Pride

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