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ChIP-seq analysis of the cAMP binding protein (CRP) in Enteroaggregative Escherichia coli 042

ABSTRACT: ChIP-seq analysis of the cAMP binding protein (CRP) in Enteroaggregative Escherichia coli 042

PROVIDER: PRJEB84381 | ENA |

REPOSITORIES: ENA

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ChIP-seq analysis of the cAMP binding protein (CRP) in Enteroaggregative Escherichia coli 042

Project description:ChIP-seq experiments were carried out in Enteroaggregative Escherichia coli 042. Wildtype 042 cells were grown to mid-log phase in LB medium, before being crosslinked with 1% formaldehyde and sonicated to lyse cells and shear DNA. Immunocomplexes were established using anti-FLAG antibodies. The immunocomplexes were then washed before DNA was eluted and libraries prepared for sequencing.

2025-07-09 | E-MTAB-14748 | biostudies-arrayexpress

Transcriptomic study of single mutant hns and hns2 from enteroaggregative E. coli 042 by RNA-seq

Project description:Bacterial genomes encode in many instances more than one copy of genes coding for global modulators. The enteroaggregative E. coli strain 042 encodes, in addition to the hns and stpA genes, an additional hns-like gene, hns2. We have previously determined the patterns of the H-NS2 regulation in cells grown at 37ºC by using RNA-seq (see https://doi.org/10.1128/mSystems.00220-17). In this work, we used RNA-seq to compare the transcriptome of the wt strain and its hns and hns2 derivatives grown at 25ºC in LB medium.

2020-10-24 | GSE146396 | GEO

Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq

Project description:Bacterial genomes encode in many instances more than one copy of genes coding for global modulators. In the Enterobacteriaceae, cells express the global modulator H-NS and its paralogue StpA. The enteroaggregative E. coli strain 042 encodes, in addition to the hns and stpA genes, an additional hns gene. We used RNA-seq to compare the transcriptome of the wt strain and its hns, hns2 and double hns hns2 derivatives, as well as of an hha null mutant (hhahha2). It is well known that the Hha protein co-modulates gene expression with H-NS. The results obtained have shown that the main role of H-NS2 is to modulate a subset of H-NS modulated genes, those that also are targeted by Hha, which are mainly HGT genes. When compared with H-NS, H-NS2 also shows a differential expression level and a different regulatory pattern.

2018-02-15 | GSE105133 | GEO

ChIP-Seq of the Sinorhizobium meliloti CRP-like protein Clr in combination with either cAMP or cGMP under different growth conditions

Project description:In bacteria, Crp-Fnr superfamily transcription factors mediate 3',5'-cyclic adenosine monophosphate (cAMP) and 3',5'-cyclic guanosine monophosphate (cGMP) signaling. The CRP-like protein Clr of the soil-dwelling and plant-symbiotic α-proteobacterium Sinorhizobium meliloti was previously shown to activate target promoters in both its cAMP- and cGMP-bound states (Krol et al., Microbiology 62:1840–1856, 2016). In order to further characterize the overall regulon of Clr in S. meliloti Chromatin Immuno Precipitation DNA-Sequencing (ChIP-Seq) experiments were performed with C-terminally FLAG tagged Clr under four different growth conditions, namely growth in TY complex medium and MOPS minimal medium, each supplemented with either cAMP or cGMP. For each condition, the respective immunoprecipitated (IP) and non-immunoprecipitated (control) samples were analyzed and compared to locate genomic positions in which Clr-DNA binding occurs. In combining ChIP-Seq with Electrophoretic Mobility Shift Assays and promoter-probe assays we expanded the list of known Clr-regulated target promoters and showed that virtually all of these promoters containing a palindromic Clr binding site (CBS) motif are activated both by Clr•cAMP and Clr•cGMP.

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Lysine 100 acetylation effect of CRP (catabolite activator protein) in gene expression in Escherichia coli

Project description:cAMP receptor protein (CRP, also known as the catabolite activator protein [CAP]) is arguably the best-studied of the global transcription factors of E coli. CRP alone is responsible for regulating at least 283 operons. Upon binding cAMP, the CRP dimer binds DNA and directly interacts with RNA polymerase (RNAP). At Class II promoters, CRP binds near position -41,5 relative to the transcription start site and contacts the amino-terminal domain of the RNAP α subunit (RNAPα-NTD). This interaction requires AR2, a patch of primarily positively charged residues (H19, H21, E96, and K101) that interact with negatively charged residues on RNAPα-NTD. Acetylome analyses consistently detect lysine 100 (K100) of CRP as acetylated. Since K100 is adjacent to the positively charged AR2, we hypothesized that the K100 positive charge may also play a role in CRP function. We further hypothesized that acetylation of K100 would neutralize this positive charge, leading to a potential regulatory mechanism

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Project description:In this study we have used ChIPseq analysis to perform comprehensive mapping of the binding profile of the cAMP receptor protein (CRPMt) of M. tuberculosis combined with RNAseq studies to further investigate the transcriptional response following crp gene deletion and under alternative growth conditions.

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Escherichia coli CRP ChIP-seq

Project description:ChIP-seq was performed to map the association of FLAG-tagged CRP across the Escherichia coli MG1655 chromosome during exponential phase growth in LB alone or LB supplemented with cAMP or arabinose and IPTG. ChIP-seq was also performed to map the association of CRP across the Escherichia coli MG1655 chromosome using a CRP antibody during exponential phase growth in LB alone.

2025-10-01 | E-MTAB-15621 | biostudies-arrayexpress

Genomic binding for cAMP responsive transcription factors, CRP (Rv3676) and Cmr (Rv1675c) in TB complex mycobacteria

Project description:We identified the genome-wide binding sites of CRP/FNR family transcription factors CRP and Cmr in M. bovis BCG using ChIP-seq, and cross-referenced these binding sites to orthologous regions in M. tuberculosis. Selected binding sites for each transcription factor were further characterized for their importance to gene regulation.

2017-10-26 | GSE106135 | GEO

A mutation mimicking post-translational acetylation of CRP at Lysine 52 creates a multitude of novel binding sites that activate transcription

Project description:As a model in the field of bacterial transcription, the structure and function of the cAMP receptor protein (CRP), a global transcription factor, has been exhaustively studied. These studies have demonstrated three contacts between CRP and RNA polymerase, of which only two were thought to activate transcription in the wild-type protein. Here we provide evidence that post-transcriptional acetylation of V. cholerae CRP engages activating region 3 leading to the hundreds of novel CRP binding sites that activate transcription of genes involved in uptake and catabolism of specific carbon sources, virulence, and biofilm formation. This establishes CRP activating region 3 as a critical mediator of association both with DNA and RNA polymerase in WT CRP.

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Genomic binding for cAMP responsive transcription factors, CRP (Rv3676) and Cmr (Rv1675c) in TB complex mycobacteria

Project description:Genomic binding for cAMP responsive transcription factors, CRP (Rv3676) and Cmr (Rv1675c) in TB complex mycobacteria

| PRJNA415712 | ENA