Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Similar Datasets

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.

2023-03-23 | E-MTAB-11788 | biostudies-arrayexpress

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

2017-03-24 | GSE96955 | GEO

Genomic mapping of cAMP receptor protein binding in relation to transcriptional start sites in Mycobacterium tuberculosis

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.

2014-06-24 | E-MTAB-2390 | 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

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

Time course of the mRNA expression after phage ϕYS40 infection in crp deletion mutant of Thermus thermophilus HB8.

Project description:We observed the expression profile of the total mRNA in crp (TTHA1437) deletion mutant strain of Thermus thermophilus HB8 during infection of bacteriophage ϕYS40. Keywords: time course, bacteriophage, infection, CRP, cAMP receptor protein, deletion mutant

2009-11-03 | GSE16955 | GEO

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

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

| PRJNA610318 | ENA

Escherichia coli 042

Project description:Enteroaggregative Escherichia coli

| PRJNA340 | ENA