Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1162486 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30712423_1.fastq.gz | Fastqsanger.gz | |||
| SRR30712423_2.fastq.gz | Fastqsanger.gz | |||
| SRR30712424_1.fastq.gz | Fastqsanger.gz | |||
| SRR30712424_2.fastq.gz | Fastqsanger.gz | |||
| SRR30712425_1.fastq.gz | Fastqsanger.gz |
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Project description:We have performed ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases respectively in Escherichia coli K12 MG1655. The dataset contains the genome wide binding patterns of Fis and CRP in the wildtype and the mutant strains
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Project description:To understand the influence of global transcription regulators Fis and CRP on global gene expression in different growth phases of E. coli.
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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.
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Project description:Crosstalk between global regulators CRP and FIS in E. coli.
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Project description:Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear.<br><br>Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA.
2010-09-01 | E-MTAB-332 | biostudies-arrayexpress
Project description:To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci.
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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 | GSE232784 | GEO
Project description:Integration host factor (IHF) is a widely distributed small heterodimeric protein member of the bacterial Nucleoid-Associated Proteins (NAPs), implicated in multiple DNA regulatory process. IHF recognizes a specific DNA sequence and induces a large bend of the nucleic acid. IHF function has been mainly linked with regulation of s54-dependent promoters, where IHF commonly recognizes a DNA sequence between the enhancer-binding region and the promoter, facilitating a close contact between the upstream bound activator and the promoter bound, RNA polymerase. In proteobacteria, the genes encoding IHF subunits (ihfA and ihfB) are found in a single copy. However, in some Deltaproteobacteria, like Geobacter sulfurreducens, those genes are duplicated. To date, the functionality of IHF reiterated encoding genes is unknown. In this work, we achieved the functional characterization of the ihfA-1, ihfA-2, ihfB-1, and ihfB-2 from G. sulfurreducens. Unlike the ΔihfA-2 or ΔihfB-1 strains, single gene deletion in ihfA-1 or ihfB-2, provokes an impairment in fumarate and Fe(III) citrate reduction. Accordingly, sqRT-PCR experiments showed that ihfA-1 and ihfB-2 were expressed at higher levels than ihfA-2 and ihfB-1. In addition, RNA-Seq analyzes of the ΔihfA-1 and ΔihfB-2 strains revealed a total of 89 and 122 differentially expressed genes, respectively. Futhermore, transcriptional changes in 25 genes were shared in both mutant strains. Among these genes, we confirmed the upregulation of the pilA-repressor, GSU1771, and downregulation of the triheme-cytochrome (pgcA) and the aconitate hydratase (acnA) genes by RT-qPCR. EMSA experiments also demonstrated the direct binding of IHF to the upstream promoter regions of GSU1771, pgcA and acnA. PilA changing in ΔihfA-1 and ΔihfB-2 strains was also verified by immunoblotting. Additionally, heme-staining of subcellular fractions in ΔihfA-1 and ΔihfB-2 strains revealed a remarkable deficit of c-type cytochromes. Overall, our data indicate that at least during fumarate and Fe(III) citrate reduction, the functional IHF regulator is likely assembled by the products of ihfA-1 and ihfB-2. Also, a role of IHF controlling expression of multiple genes (other than s54 dependent) affects G. sulfurreducens physiology and extracellular electron transfer.
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