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Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli [ChIP-exo]

ABSTRACT: Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli [ChIP-exo]

PROVIDER: PRJNA490633 | ENA |

REPOSITORIES: ENA

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Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli [ChIP-exo]

Project description:Carbon metabolism in diverse bacteria is primarily governed by two key transcription factors, CRP and Cra. Although numerous studies have investigated their regulatory mechanisms under glucose conditions, the understanding of their role in controlling central metabolism across different carbon sources, such as galactose, remains limited, with scarce in vivo binding information available. In this study, we focused on the Cra binding profile of Escherichia coli grown on galactose, an unfavorable carbon source. While genome-wide Cra binding sites on galactose closely resemble that on glucose, however, further examination of transcriptomic and flux simulation data suggests a complex regulatory mechanism by which Cra modulates central carbon metabolism on galactose. Additionally, conservation analysis across a wide range of bacterial taxa revealed that Cra and its regulons are more broadly conserved compared to CRP and its regulons, indicating a potential role for Cra in the early evolution of bacterial central carbon metabolism.

2025-08-11 | GSE119894 | GEO

Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli [RNA-seq]

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Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli

Project description:Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli

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Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli [RNA-seq]

Project description:Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli [RNA-seq]

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Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]

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

Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [ChIP-seq]

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Expansion of the Cra regulatory network and conservation of transcriptional regulation in carbon metabolism of Escherichia coli

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-08-11 | GSE232785 | GEO

Effect of Cra and carbon sources on global transcription

Project description:The Gram-negative bacterium Vibrio cholerae adapts to changes in environment by selectively producing the necessary machinery to uptake and metabolize available carbohydrates. The import of the six-carbon sugar fructose by the fructose-specific phosphoenolpyruvate (PEP) phosphotransferase system (PTS) is of particular interest because of its putative connection to biofilms, which have been shown to promote host colonization and cholera pathogenesis. This study focused on the transcriptional response to glucose and fructose, and the role of the Cra protein in this regulatory process.

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Effect of deletion of cra on E. coli biofilm formation

Project description:Transcriptional analysis of biofilm wild-type and cra mutant E. coli cells was carried out to determine the effect of cra on biofilm formation.

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Effect of deletion of cra on E. coli biofilm formation

Project description:Transcriptional analysis of biofilm wild-type and cra mutant E. coli cells was carried out to determine the effect of cra on biofilm formation. Samples were prepared in duplicates, with one of the replicates being dye swapped.

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