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Escherichia coli glutathionylspermidine: Phylogeny and regulation of gene expression

ABSTRACT: Glutathionylspermdine synthetase/amidase (Gss) and the encoding gene (gss) have only been described in two widely separated species; namely Escherichia coli and several members of the Kinetoplastida phyla. In the present paper we have studied the species distribution more extensively. It is striking that all of the 75 Enterobacteria species that has been sequenced contain sequences with very high degree of homology to the E. coli Gss protein. Although homologous sequences are also present in various other bacteria, in contrast to Enterobacteria they are not present in all species of a given phyla. As previously reported homologous sequences were found in all five species of Kinetoplastids tested (including Trypansosma cruzi), but it is striking that comparable sequences are not found in a variety of invertebrate and vertebrate species, Archea and plants. Studies in E. coli show that the highest accumulation of glutathionylspermidine is found in stationary phase cultures where most of the intracellular spermidine is converted to glutathionylspermidine. However, even in log phase cells there is some formation of glutathionylspermidine, and isotope exchange experiments show that there is a rapid exchange between glutathionylspermidine and intracellular spermidine. We have not been able to define a specific physiologic function for glutathionylspermidine, but microarray studies comparing gss+ and -gss strains of E. coli show that a large number of genes are either upregulated or downregulated by the loss of the gss gene. Comparison of gss mutant of E. coli and wild type cells, with triplicate samples from each.

ORGANISM(S): Escherichia coli

SUBMITTER: WeiPing Chen

PROVIDER: E-GEOD-30679 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Escherichia coli glutathionylspermidine: Phylogeny and regulation of gene expression

Project description:Glutathionylspermdine synthetase/amidase (Gss) and the encoding gene (gss) have only been described in two widely separated species; namely Escherichia coli and several members of the Kinetoplastida phyla. In the present paper we have studied the species distribution more extensively. It is striking that all of the 75 Enterobacteria species that has been sequenced contain sequences with very high degree of homology to the E. coli Gss protein. Although homologous sequences are also present in various other bacteria, in contrast to Enterobacteria they are not present in all species of a given phyla. As previously reported homologous sequences were found in all five species of Kinetoplastids tested (including Trypansosma cruzi), but it is striking that comparable sequences are not found in a variety of invertebrate and vertebrate species, Archea and plants. Studies in E. coli show that the highest accumulation of glutathionylspermidine is found in stationary phase cultures where most of the intracellular spermidine is converted to glutathionylspermidine. However, even in log phase cells there is some formation of glutathionylspermidine, and isotope exchange experiments show that there is a rapid exchange between glutathionylspermidine and intracellular spermidine. We have not been able to define a specific physiologic function for glutathionylspermidine, but microarray studies comparing gss+ and -gss strains of E. coli show that a large number of genes are either upregulated or downregulated by the loss of the gss gene.

2012-07-12 | GSE30679 | GEO

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq]

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for those two species. With experimentally derived TSS datasets, we examined usage of multiple TSSs, length of 5' UTR (untranslated region), SD (Shine-Dalgarno) sequence motif, promoter sequence motif, and dinucleotide preference near TSS site. In addition, we used the TSS datasets to identify sRNAs (small RNAs) in E. coli and K. pneumoniae. Based on these analysis, we compared regulatory elements including promoter, 5' UTR and sRNAs between two species, and investigated similarities and differences of upstream regulatory regions. Moreover, sRNAs were also compared and analyzed in terms of their sequences and target sequences, presenting possible working mechanisms of K. pneumoniae sRNAs by transferring prior knowledge from E. coli sRNAs. Examination of transcription start sites by biological duplicates from E. coli and K. pneumoniae

2012-07-30 | E-GEOD-35821 | biostudies-arrayexpress

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq]

2012-07-30 | GSE35821 | GEO

Complex responses to hydrogen peroxide and hypochlorous acid by the probiotic bacterium Lactobacillus reuteri

Project description:Inflammatory diseases of the gut are associated with increased intestinal oxygen concentrations and high levels of inflammatory oxidants, including hydrogen peroxide (H2O2) and hypochlorous acid (HOCl), which are antimicrobial compounds produced by the innate immune system. This contributes to dysbiotic changes in the gut microbiome, including increased populations of pro-inflammatory enterobacteria (Escherichia coli and related species) and decreased levels of health-associated anaerobic Firmicutes and Bacteroidetes. The pathways for H2O2 and HOCl resistance in E. coli have been well-studied, but little is known about how commensal and probiotic bacteria respond to inflammatory oxidants. In this work, we have characterized the transcriptomic response of the anti-inflammatory, gut colonizing Gram-positive probiotic Lactobacillus reuteri to both H2O2 and HOCl. L. reuteri mounts distinct responses to each of these stressors, and both gene expression and survival were strongly affected by the presence or absence of oxygen. Oxidative stress response in L. reuteri required several factors not found in enterobacteria, including the small heat shock protein Lo18, polyphosphate kinase 2, and RsiR, an L. reuteri-specific regulator of anti-inflammatory mechanisms. These results raise the intriguing possibility of developing treatments for inflammatory gut diseases that could sensitize pro-inflammatory enterobacteria to killing by the immune system while sparing anti-inflammatory, health-associated species.

2019-08-15 | GSE127961 | GEO

The global transcriptomic profile in the spermidine-stressed E. coli

Project description:To achieve extreme spermidine stress we used DspeG E. coli strain. We identified the pathways that are altered under spermidine stress. Among many changes spermidine altered the iron-sulfur cluster metabolism and redox balance in the cells. Therefore, we have shown that superoxide quencher, NAC and ascorbate mitigates spermidine stress. Overall our data explains the importaance of tight spermidine homeostasisin the cell.

2021-09-01 | GSE154618 | GEO

The global transcriptomic profile in the spermidine-stressed E. coli

2022-03-01 | GSE186526 | GEO

DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines

Project description:DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA. These enzymes are widely conserved, sharing >91% amino acid identity between the closely related species Escherichia coli and Salmonella enterica serovar Typhimurium. Why, then, do E. coli and Salmonella exhibit different DNA supercoiling when experiencing the same conditions? We now report that this surprising difference reflects disparate activation of their DNA gyrases by the polyamine spermidine and its precursor putrescine. In vitro, Salmonella DNA gyrase activity was sensitive to changes in putrescine concentration within the physiological range, whereas activity of the E. coli enzyme was not. In vivo, putrescine activated the Salmonella DNA gyrase and spermidine the E. coli enzyme. High extracellular Mg2+ decreased DNA supercoiling exclusively in Salmonella by reducing the putrescine concentration. Our results establish the basis for the differences in global DNA supercoiling between E. coli and Salmonella, define a signal transduction pathway regulating DNA supercoiling, and identify potential targets for antibacterial agents.

2020-10-30 | GSE150757 | GEO

Monitoring Homology Search during DNA Double-Strand Break Repair in vivo

Project description:Homologous recombination (HR) is crucial for genetic exchange, accurate repair of DNA double-strand breaks and pivotal for genome integrity. HR uses homologous sequences for repair, but how homology search, the exploration of the genome for homologous DNA sequences, is conducted in the nucleus remains poorly understood. Here, we use time-resolved chromatin immunoprecipitations of repair proteins to monitor homology search in vivo. We found that homology search proceeds by a probing mechanism, which commences around the break and samples preferentially on the broken chromosome. However, elements thought to instruct chromosome loops mediate homology search shortcuts, and centromeres, which cluster within the nucleus, may facilitate homology search on other chromosomes. Our study thus revealed crucial parameters for homology search in vivo and emphasizes the importance of linear distance, chromosome architecture and proximity for recombination efficiency.

2013-03-21 | GSE44844 | GEO

Colibactin causes genomic instability and promotes Wnt independence in primary colon epithelial cells

Project description:Colorectal cancer is driven by a sequential cascade of mutations known as the adenoma-carcinoma sequence. Recent studies have revealed that specific bacterial species present in the colonic microbiota can induce mutations and contribute to this malignancy. Specifically, genotoxic colibactin-producing pks+ Escherichia coli strains can induce DNA double strand breaks (DSBs) and promote tumor development in mouse models of colorectal cancer. Here, we investigated the transformation potential of colibactin by using organoids and polarized monolayers derived from primary murine colon epithelial cells and reveal striking phenotypic changes upon short-term infection. This study demonstrates the direct pro-oncogenic potential of pks+ E. coli, as such transformations in vivo could facilitate colitis-associated colorectal carcinogenesis.

2020-12-03 | GSE140929 | GEO

Comparative genomic hybridization of Agrobacterium tumefaciens strains on tiling arrays covering the genome of strain C58

Project description:Comparative genomic hybridizations obtained with an original Agrobacterium tumefaciens strain C58 genome-based micro-array were used to detect the presence or absence of genes homologous to those of strain C58 in 25 agrobacterial strains. These strains included six other members of genomovar G8, one to three strains for each of the nine other A. tumefaciens genomovars and one for A. larrymoorei, a sister species of the A. tumefaciens complex. An original probabilistic method was used to segment C58 replicon sequences into regions, that are absent or present in tested strains, allowing us to detect the presence of homologues of C58 coding sequences (CDSs) in tested strains.

2011-09-08 | E-MTAB-558 | biostudies-arrayexpress

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