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

ABSTRACT: 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

ORGANISM(S): Escherichia coli K-12 Escherichia coli

PROVIDER: GSE96955 | GEO | 2017/03/24

SECONDARY ACCESSION(S): PRJNA380212

REPOSITORIES: GEO

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Role of CRP K100 positive charge on Escherichia coli global transcriptome

Project description:We hypothesized that the positive charge of CRP K100 is important for transcription of Class II CRP-dependent genes. These data show mutations that affect K100 charge status result in genome-wide changes in transcription of both CRP-dependent and -independent genes.

2017-04-06 | GSE97406 | GEO

Histone citrullination in estrogen receptor signaling and breast cancer [PRO-seq]

Project description:PAD2, one of a family of PAD enzymes that convert positively charged arginine residues on target proteins to neutrally charged citrulline, has been shown to play a role in estrogen signaling through interactions with histone H3R26. The objectives of this project are to define the role of PAD2 in estrogen receptor alpha signaling, tumor progression, and tamoxifen resistance.

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Histone citrullination in estrogen receptor signaling and breast cancer [ChIP-seq]

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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

A member of the cAMP receptor protein family of transcription regulators in M. tuberculosis is required for virulence

Project description:Deletion of gene Rv3676 in Mycobacterium tuberculosis coding for a transcription factor belonging to the cAMP receptor protein (CRP) family caused growth defects in laboratory medium, in bone marrow-derived macrophages and in a mouse model of tuberculosis. Transcript profiling of M. tuberculosis grown in vitro identified 16 genes with significantly altered expression in the mutant compared with the wild type. Analysis of the DNA sequences upstream of the corresponding open reading frames revealed that 12 possessed sequences related to a consensus CRP binding site that could represent the sites of action of Rv3676. These included rpfA, lprQ, whiB1 and ahpC among genes with enhanced expression in the wild type, and Rv3616c-Rv3613c, Rv0188 and lipQ among genes exhibiting enhanced expression in the mutant. The activity of an rpfA::lacZ promoter fusion was lowered in the Rv3676 mutant and by mutation of the predicted Rv3676 binding site. Moreover, the product of Rv3676 (isolated as a TrxA fusion protein) interacted specifically with the rpfA promoter, and binding was inhibited by mutation of the Rv3676 site. Although Rv3676 retains four of the six amino acid residues that bind cAMP in Escherichia coli CRP addition of cAMP did not enhance Rv3676 binding at the rpfA promoter in vitro. In summary, it has been shown that Rv3676 is a direct regulator of rpfA expression, and because rpfA codes for a resuscitation promoting factor this may implicate Rv3676 in reactivation of dormant M. tuberculosis infections. Keywords: strain or line design, genetic modification design, and comparative genome hybridization design

2007-08-21 | GSE8830 | GEO

Gene transcriptional levels with or without acid treatment in Salmonella Typhimurium 14028s

Project description:Acetylation of lysine residues is conserved across organisms and plays important roles in various cellular functions. Maintaining intracellular pH homeostasis is crucial for the survival of enteric bacteria in acidic gastric tract. However, it remains unkown whether bacteria can utilize reversible protein acetylation system to adapt to acidic environment. Here we demonstrate that the protein acetylation/deacetylation is critical for Salmonella Typhimurium to survive in acidic environment. We first used RNA-seq to analyze the transcriptome patterns under acid stress, and found that the transcriptional levels of genes involved in NAD+/NADH metabolism were significantly changed, leading to the increase of intracellular NAD+/NADH ratio. Moreover, acid stress down-regulated the transcriptional level of pat (encoding an acetyltranseferase) and genes encoding adenylate cyclase and cAMP-regulatory protein (CRP) which regulates pat positively. Acid signal also affects TCA cycle to promote the consumption of Ac-CoA, which reduced the donor of acetylation. Lowered acetylation level is not only bacterial’s response to acid stress, but also positively regulates the survival rate of S. Typhimurium. The deletion mutant of pat had more stable intracellular pH, which paralleled with higher survival rate after acid treatment compared with the wild type strain and deletion mutant of cobB. Our data suggest that bacteria can down-regulate protein acetylation level to prevent intracellular pH further falling in acid stress, and this work may provide a new perspective to understand the bacterial acid resistance mechanism. To use RNA-seq to analyze the transcriptome patterns under acid stress

2015-04-16 | E-GEOD-67925 | biostudies-arrayexpress

Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa

Project description:Transcriptional profiles of Escherichia coli MG1655 in mixed culture with Pseudomonas aeruginosa PAO1 showed a number of E. coli genes to be upregulated including purA-F and other genes associated with purine synthesis. In contrast, genes associated with pyrimidine synthesis were unaffected. Competition experiments in both planktonic and biofilm cultures, using three purine synthesis mutants, purD, purH, and purT showed little difference in E. coli survival from the parent strain. As purines are components of the cell signals, cAMP and c-di-GMP, we conducted competition experiments with E. coli mutants lacking adenylate cyclase (cyaA), cAMP phosphodiesterase (cpdA), and the catabolite receptor protein (crp), as well as ydeH, an uncharacterized gene that has been associated with c-di-GMP synthesis. Survival of the cyaA and crp mutants during co-culture were significantly less than the parent strain. Supplementation of the media with 1mM cAMP could restore survival of the cyaA mutant but not the crp mutant. In contrast, survival of the cpdA mutant was similar to the parent strain. Survival of the ydeH mutant was moderately less than the parent, suggesting that cAMP has more impact on E. coli mixed culture growth than c-di-GMP. Addition of 1 mM indole restored the survival of both the cyaA and crp mutations. Mutants in genes for tryptophan synthesis (trpE) and indole production (tnaA) showed a loss of competition and recovery through indole supplementation, comparable to the cyaA and crp mutants. Overall, these results suggest indole and cAMP as major contributing factors to E. coli growth in mixed culture.

2011-11-09 | GSE26931 | GEO

Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine

2011-11-29 | GSE26932 | GEO

C-terminomics E. coli - C-terminal charge-reversal derivatization and parallel use of multiple proteases facilitates identification of protein C-termini by C-terminomics

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2016-03-11 | PXD003342 | Pride

PADI4 ChIP-chip from MCF-7 cells

Project description:Peptidylarginine deiminase IV (PADI4) catalyzes the conversion of positively charged arginine and methylarginine residues to neutrally charged citrulline residues on histone tails. This activity has been linked to the repression of gene transcription on a limited number of genes. To broaden our knowledge of the regulatory potential of PADI4, we utilized chromatin immunoprecipitation coupled with promoter tiling array (ChIP-chip) to more comprehensively investigate the range of PADI4 target genes across the genome in MCF-7 cells. Results showed that PADI4 is enriched in the gene promoter regions near the transcription start sites (TSSs) and, surprisingly, this pattern of binding is primarily associated with actively transcribed genes. Computational analysis found Elk-1, a member of the ETS oncogene family, to be highly enriched around PADI4 binding sites and coimmunoprecipitation analysis then confirmed that Elk-1 physically associates with PADI4. The expression of two well characterized Elk-1 target genes, c-fos and egr-1, was then found to be inhibited following treatment of MCF-7 cells with a PADI4 specific inhibitor. The inhibitor also significantly reduced levels of acetylation at H4 lysine 5 at these promoters suggesting that the activating function of PADI4 at these target genes is mediated, in part, by interplay between histone citrullination and HAT-mediated acetylation. These findings greatly expand our knowledge of the role of PADI4 in gene regulation by defining a new role for PADI4 catalyzed histone citrullination in mediating gene transactivation. Two PADI4 ChIP-chip biological replicates from MCF-7 human breast cancer cells are included.

2011-03-31 | E-GEOD-18755 | biostudies-arrayexpress

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