Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA272158 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1751240.fastq.gz | Fastqsanger.gz | |||
| SRR1751250.fastq.gz | Fastqsanger.gz | |||
| SRR1751260.fastq.gz | Fastqsanger.gz | |||
| SRR1751270.fastq.gz | Fastqsanger.gz | |||
| SRR1751280.fastq.gz | Fastqsanger.gz |
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Project description:Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]
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Project description:Integrated analysis of molecular and systems level function of the Crp regulon
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Project description:The carbon metabolism in bacteria is regulated by two global TFs, CRP and Cra. While the regulon of CRP has been extensively studied, the complete definition of Cra has been missing. Thus, in vivo TF binding measurement with ChIP-exo and transcriptional expression measurement with RNA-seq for Cra was performed to define the Cra regulon.
2018-04-18 | GSE65642 | GEO
Project description:The carbon metabolism in bacteria is regulated by two global TFs, CRP and Cra. While the regulon of CRP has been extensively studied, the complete definition of Cra has been missing. Thus, in vivo TF binding measurement with ChIP-exo and transcriptional expression measurement with RNA-seq for Cra was performed to define the Cra regulon.
2018-04-18 | GSE65641 | GEO
Project description:A fundamental goal of biological research is to connect molecular events with macroscopic physiological phenomena. By incorporating a multi-scale approach that accounts for mechanistic properties of promoters and maps those findings to a genome-scale metabolic-regulatory network, the Escherichia coli Crp regulon is revealed, enabling systems analytics to be applied to delineate its governing role in regulating cellular carbon flow. Genome-wide promoter functions were characterized using ChIP-exo elucidating stable intermediates formed during transcription initiation and distinctions between transcriptional activators and repressors. Genome-wide analysis of Crp regulated genes showed a coordinate regulation of catabolism, anabolism, and energy-generating chemiosmotic processes. Examination of the functional state of the reconstructed regulon during growth on multiple substrates revealed a coherent quantitative adjustment of these overall metabolic processes based on substrate quality, revealing the detailed mechanistic basis for the phenomenologically observed homoeostatic response. Thus, a multi-scale relationship from individual molecular mechanisms to physiological properties is established.
2017-01-09 | GSE64848 | GEO
Project description:A fundamental goal of biological research is to connect molecular events with macroscopic physiological phenomena. By incorporating a multi-scale approach that accounts for mechanistic properties of promoters and maps those findings to a genome-scale metabolic-regulatory network, the Escherichia coli Crp regulon is revealed, enabling systems analytics to be applied to delineate its governing role in regulating cellular carbon flow. Genome-wide promoter functions were characterized using ChIP-exo elucidating stable intermediates formed during transcription initiation and distinctions between transcriptional activators and repressors. Genome-wide analysis of Crp regulated genes showed a coordinate regulation of catabolism, anabolism, and energy-generating chemiosmotic processes. Examination of the functional state of the reconstructed regulon during growth on multiple substrates revealed a coherent quantitative adjustment of these overall metabolic processes based on substrate quality, revealing the detailed mechanistic basis for the phenomenologically observed homoeostatic response. Thus, a multi-scale relationship from individual molecular mechanisms to physiological properties is established.
2017-01-09 | GSE64847 | GEO
Project description:We investigated the way global gene expression changed in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways with features varying in: carbon influx flow rate; entry points in the metabolic network; modes of transport. Quantitative coarse-grained expression-pattern analysis demonstrated that the gene expression trend following immediately the reduction of carbon influx flow rate was determined by its initial expression level. Subsequent fine-grained expression-pattern analysis demonstrated that the Crp regulator, associated to a change in growth rate, governed the response of most carbon influx-dependent genes. By contrast, the Cra, Mlc and Fur regulators governed the expression of genes responding to non-glycolytic substrates, glycolytic substrates or PTS (phosphotransferase system) transported sugars following an idiosyncratic way, with the function of each of these regulators being titrated by the metabolism of the corresponding substrates. This work also allowed us to expand the extent of the gene complement regulated by each regulator with additional genes (27 genes in the Crp regulon, 49 genes in the Cra regulon, 1 gene in the Mlc regulon and 2 genes in Fur regulon) and to elucidate the regulatory functions of each regulator comprehensively. Strikingly, Crp and Cra worked in concert to coordinate central carbon metabolism with amino acids biosynthesis. Together, these results demonstrated the power of physiology-based interperation of global data in revealing regulatory networks of bacteria.
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Project description:The control of cellular processes by direct electronic interface will facilitate the development of biosensors, synthetic biology, and nanobiotechnology by providing the means to pass information from synthetic to living elements of hybrid systems. To investigate the potential of manipulating cellular gene expression by means of electric current, Escherichia coli cultures were screened for electric current inducible genes using global gene expression profiling. Cells in stationary phase were subjected to a DC current density of 2.5 mA/cm2 for 2 min after which the cells were lysed and the total RNA extracted. Of the 4290 expressed genes in E. coli , 432 genes were found to be significantly differentially expressed at an effective alpha value of 5.8 X 10-6. Of these, 333 genes were induced and 99 repressed. Several genes were verified as differentially expressed by quantitative real-time RT-PCR. The set of differentially expressed genes were examined for the presence of regulatory factors, subsidiary regulon genes, and biological function, particularly redox functions. Transcripts for the regulatory proteins fnr, sspB, soxS, oxyR, creB and yeiL were found to be up-regulated, and crp was down regulated. While soxS and oxyR were up-regulated, the downstream genes controlled by these regulatory proteins were not differentially expressed, suggesting that the oxidative stress level of low-current electric exposure is small. Genes controlled by FNR and CRP, many of which have redox function, were found to be differentially expressed suggesting modulation by direct reduction that can only be partially explained as a response to the reducing environment created by the electrolytic generation of H2 at the cathode. Genes associated with phosphate metabolism and membrane proteins were also differentially expressed. Three biological replicates were exposed to electric current along with three biological replicate controls.
2010-06-25 | E-GEOD-5192 | biostudies-arrayexpress
Project description:The control of cellular processes by direct electronic interface will facilitate the development of biosensors, synthetic biology, and nanobiotechnology by providing the means to pass information from synthetic to living elements of hybrid systems. To investigate the potential of manipulating cellular gene expression by means of electric current, Escherichia coli cultures were screened for electric current inducible genes using global gene expression profiling. Cells in stationary phase were subjected to a DC current density of 2.5 mA/cm2 for 2 min after which the cells were lysed and the total RNA extracted. Of the 4290 expressed genes in E. coli , 432 genes were found to be significantly differentially expressed at an effective alpha value of 5.8 X 10-6. Of these, 333 genes were induced and 99 repressed. Several genes were verified as differentially expressed by quantitative real-time RT-PCR. The set of differentially expressed genes were examined for the presence of regulatory factors, subsidiary regulon genes, and biological function, particularly redox functions. Transcripts for the regulatory proteins fnr, sspB, soxS, oxyR, creB and yeiL were found to be up-regulated, and crp was down regulated. While soxS and oxyR were up-regulated, the downstream genes controlled by these regulatory proteins were not differentially expressed, suggesting that the oxidative stress level of low-current electric exposure is small. Genes controlled by FNR and CRP, many of which have redox function, were found to be differentially expressed suggesting modulation by direct reduction that can only be partially explained as a response to the reducing environment created by the electrolytic generation of H2 at the cathode. Genes associated with phosphate metabolism and membrane proteins were also differentially expressed. Keywords: electric current induced gene expression
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Project description:While global transcription factors (TFs) have been studied extensively in Escherichia coli model strains, conservation and diversity in TF regulation between strains is still unknown. Here we use a combination of ChIP-exo--to define ferric uptake regulator (Fur) binding sites--and differential gene expression--to define the Fur regulon in nine E. coli strains. We then define a pan-regulon consisting of 469 target genes that includes all Fur target genes in all nine strains. The pan-regulon is then divided into the core regulon (target genes found in all the strains, n=36), the accessory regulon (target found in two to eight strains, n=158) and the unique regulon (target genes found in one strain, n=275). Thus, there is a small set of Fur regulated genes common to all nine strains, but a large number of regulatory targets unique to a particular strain. Many of the unique regulatory targets are genes unique to that strain. This first-established pan-regulon reveals a common core of conserved regulatory targets and significant diversity in transcriptional regulation amongst E. coli strains, reflecting diverse niche specification and strain history.
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