Effect of enzyme IIANtr on gene expression in Escherichia coli
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli Escherichia coli str. K-12 substr. MG1655
PROVIDER: GSE24373 | GEO | 2010/09/28
SECONDARY ACCESSION(S): PRJNA132971
REPOSITORIES: GEO
Similar Datasets
Project description:Enzyme IIANtr (encoded by ptsN gene) is a component of the nitrogen phosphotransferase system (PTS). It has previously been shown that the dephosphorylated form of EIIANtr is required for the derepression of ilvBN encoding acetohydroxy acid synthase I (AHAS I) catalyzing the first step common to biosynthesis of branched-chain amino acids. Here we examine the effect of deletion of ptsN gene on global gene expression by microarray analysis. Most of the genes down-regulated in a ptsN mutant are controlled by sigma 70, while all the up-regulated genes are controlled by sigma S. As intracellular levels of sigma factors in the ptsN mutant were similar to those of the wild-type strain, this implied that the balance of sigma activities is modified by ptsN deletion. The E. coli K12 strain MG1655 and its isogenic ptsN mutant were used in all experiments. Overnight bacterial cultures were incubated in M9 minimal medium containing 0.5% glucose as carbon source. Cells from duplicate experiments were harvested in exponential growth phase when cultures reached an A600 of 0.4. RNA was extracted from each sample using a QIAGEN RNA extraction kit according to the manufacturer's instruction.
2010-09-28 | E-GEOD-24373 | biostudies-arrayexpress
Project description:Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of Listeria monocytogenes, and their significance for extra- and intracellular growth. Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in MM (minimal medium (Premaratne et al. 2001)) (supplemented with 10 mM Glucose). Listeria monocytogenes EGD-e possesses 86 pts genes encoding 29 complete and several incomplete PEP-dependent phosphotransferase systems (PTS) for the transport of carbohydrates and sugar alcohols. By a systematic deletion analysis we identified the major PTS involved in glucose, mannose and cellobiose transport, when L. monocytogenes grows in a defined minimal medium in the presence of either of these carbohydrates. Under these conditions two of the four PTSMan and at least one of the five PTSGlc function as glucose transporter with different affinities. Cellobiose is transported (with different efficiencies) mainly by two of the six PTSLac and by a PTSGlc that also transports glucose. One of the PTSMan and both PTSLac are regulated by LevR-homologous PRD containing transcriptional activators, detected with PRD deletion mutants. The growth rates of mutants that are lacking these PTS are drastically reduced compared to the wild-type strain upon growth in a defined medium with low concentrations of glucose and cellobiose, respectively. In contrast, replication of these PTS mutants within epithelial cells or macrophages is as efficient as that of the wild-type strain. Keywords: pts and prd deletion mutants A total of three independently isolated RNA samples from each condition were used for the analysis. PTS Samples: GSM458191-GSM458208 PRD Samples: GSM458209-GSM458214
2010-05-19 | E-GEOD-18363 | biostudies-arrayexpress
Project description:Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of Listeria monocytogenes, and their significance for extra- and intracellular growth. Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in MM (minimal medium (Premaratne et al. 2001)) (supplemented with 10 mM Glucose). Listeria monocytogenes EGD-e possesses 86 pts genes encoding 29 complete and several incomplete PEP-dependent phosphotransferase systems (PTS) for the transport of carbohydrates and sugar alcohols. By a systematic deletion analysis we identified the major PTS involved in glucose, mannose and cellobiose transport, when L. monocytogenes grows in a defined minimal medium in the presence of either of these carbohydrates. Under these conditions two of the four PTSMan and at least one of the five PTSGlc function as glucose transporter with different affinities. Cellobiose is transported (with different efficiencies) mainly by two of the six PTSLac and by a PTSGlc that also transports glucose. One of the PTSMan and both PTSLac are regulated by LevR-homologous PRD containing transcriptional activators, detected with PRD deletion mutants. The growth rates of mutants that are lacking these PTS are drastically reduced compared to the wild-type strain upon growth in a defined medium with low concentrations of glucose and cellobiose, respectively. In contrast, replication of these PTS mutants within epithelial cells or macrophages is as efficient as that of the wild-type strain. Keywords: pts and prd deletion mutants
2009-12-01 | GSE18363 | GEO
Project description:Analyses of the Wild type and the sigma 54 mutant strain NZ7306 with and without peroxide treatment: A Lactobacillus plantarum strain with a deletion in the alternative sigma factor 54 (?54) encoding gene rpoN, displayed a 100 fold higher sensitivity to peroxide as compared to its parental strain. This feature could be due to ?54-dependent regulation of genes involved in peroxide stress response. However, transcriptome analyses of the wild type and the mutant strain during peroxide exposure did not support such a role for ?54. Subsequent experiments revealed that the impaired expression of the mannose PTS operon in the rpoN mutant caused the observed increased peroxide sensitivity. Keywords: genetic modification
2008-05-08 | GSE11351 | GEO
Project description:Nishio2008 - Design of the phosphotransferase
system for enhanced glucose uptake in E. coli.
This model is described in the article:
Computer-aided rational
design of the phosphotransferase system for enhanced glucose
uptake in Escherichia coli.
Nishio Y, Usuda Y, Matsui K, Kurata
H.
Mol. Syst. Biol. 2008; 4: 160
Abstract:
The phosphotransferase system (PTS) is the sugar
transportation machinery that is widely distributed in
prokaryotes and is critical for enhanced production of useful
metabolites. To increase the glucose uptake rate, we propose a
rational strategy for designing the molecular architecture of
the Escherichia coli glucose PTS by using a computer-aided
design (CAD) system and verified the simulated results with
biological experiments. CAD supports construction of a
biochemical map, mathematical modeling, simulation, and system
analysis. Assuming that the PTS aims at controlling the glucose
uptake rate, the PTS was decomposed into hierarchical modules,
functional and flux modules, and the effect of changes in gene
expression on the glucose uptake rate was simulated to make a
rational strategy of how the gene regulatory network is
engineered. Such design and analysis predicted that the mlc
knockout mutant with ptsI gene overexpression would greatly
increase the specific glucose uptake rate. By using biological
experiments, we validated the prediction and the presented
strategy, thereby enhancing the specific glucose uptake
rate.
This model is hosted on
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and identified by:
BIOMD0000000571.
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2015-01-01 | BIOMD0000000571 | BioModels
Project description:Enterococcus faecalis is commonly isolated from different wound types. However, despite its prevalence, the pathogenic mechanisms of E. faecalis during wound infections remain poorly understood. We adopted an in vivo E. faecalis transposon sequencing and RNA sequencing approach to identify fitness determinants that are crucial for replication and persistence of E. faecalis during wound infections in a mouse model. We demonstrated that E. faecalis purine biosynthesis genes are important for replication as purine metabolites are low in wounds during the early phase of wound infections. Furthermore, we found that the E. faecalis MptABCD phosphotransferase system (PTS) involved in the uptake of galactose and mannose, is crucial for E. faecalis persistence in wounds, and that carbohydrate availability changes as the infection progresses. To understand how MptABCD PTS contributes to the reduced fitness observed during E. faecalis wound persistence, we performed an in vitro transcriptomic analysis using the galactose/mannose PTS gene deletion mutant (∆mptD). When mannose was the sole carbohydrate source, shikimate and purine biosynthesis genes in the ∆mptD mutant were downregulated compared to the isogenic wild-type strain, indicating that mannose transport is interconnected with shikimate and purine biosynthesis. Together, our results suggest that dynamic and temporal microenvironment changes at the wound site affects pathogenic requirements and mechanisms of E. faecalis during infections and raise the possibility of inhibiting purine biosynthesis and/or MptABCD PTS to control wound infections.
2023-11-06 | GSE206750 | GEO
Project description:Enterococcus faecalis is commonly isolated from different wound types. However, despite its prevalence, the pathogenic mechanisms of E. faecalis during wound infections remain poorly understood. We adopted an in vivo E. faecalis transposon sequencing and RNA sequencing approach to identify fitness determinants that are crucial for replication and persistence of E. faecalis during wound infections in a mouse model. We demonstrated that E. faecalis purine biosynthesis genes are important for replication as purine metabolites are low in wounds during the early phase of wound infections. Furthermore, we found that the E. faecalis MptABCD phosphotransferase system (PTS) involved in the uptake of galactose and mannose, is crucial for E. faecalis persistence in wounds, and that carbohydrate availability changes as the infection progresses. To understand how MptABCD PTS contributes to the reduced fitness observed during E. faecalis wound persistence, we performed an in vitro transcriptomic analysis using the galactose/mannose PTS gene deletion mutant (∆mptD). When mannose was the sole carbohydrate source, shikimate and purine biosynthesis genes in the ∆mptD mutant were downregulated compared to the isogenic wild-type strain, indicating that mannose transport is interconnected with shikimate and purine biosynthesis. Together, our results suggest that dynamic and temporal microenvironment changes at the wound site affects pathogenic requirements and mechanisms of E. faecalis during infections and raise the possibility of inhibiting purine biosynthesis and/or MptABCD PTS to control wound infections.
2023-11-06 | GSE206749 | GEO
Project description:Analyses of the Wild type and the sigma 54 mutant strain NZ7306 with and without peroxide treatment: A Lactobacillus plantarum strain with a deletion in the alternative sigma factor 54 (?54) encoding gene rpoN, displayed a 100 fold higher sensitivity to peroxide as compared to its parental strain. This feature could be due to ?54-dependent regulation of genes involved in peroxide stress response. However, transcriptome analyses of the wild type and the mutant strain during peroxide exposure did not support such a role for ?54. Subsequent experiments revealed that the impaired expression of the mannose PTS operon in the rpoN mutant caused the observed increased peroxide sensitivity. Keywords: genetic modification Two conditions were tested in the transcriptome comparison, the condition “peroxide stress exposure” and the condition “deletion of the rpoN-gene”. This resulted in 4 samples: “Wild type normal”, “rpoN-mutant normal”, “Wild type with peroxide”, and “rpoN-mutant with peroxide”. Samples were hybridised against a sample with only one variation, resulting in a total of 4 hybridisations (“Wild type vs Mutant”, “Wild type vs Wild type peroxide”, “Mutant vs Mutant peroxide”, and “Wild type peroxide vs Mutant peroxide”). The experiment was performed in duplicate (duplicates are designated A and B) and in order to discriminate the variation between the duplicates additional hybridisation were performed: “Wild type A vs Wild type B” and “Mutant with peroxide A vs Mutant with peroxide B”. This resulted in a total of 10 hybridisations (2 x 4 and 2).
2008-05-08 | E-GEOD-11351 | biostudies-arrayexpress
Project description:The presence of tagatose in Lactobacillus rhamnosus strain GG caused induction of a large number of genes associated with carbohydrate metabolism including the phosphotransferase system. In addition, these results indicate the tagatose enhanced the growth of Lactobacillus casei 01 and Lactobacillus rhamnosus strain GG and their probiotic activities by activating tagatose-associated PTS networks.
2013-09-19 | GSE41073 | GEO
Project description:To address and clarify the regulatory function of YfgL in K. pneumoniae, the transcriptome analyses of the yfgL mutant and the wild-type strain were compared. K. pneumoniae strain deleted for yfgL exhibited reduced adherence and invasion to host cells. A previous study has demonstrated that the YfgL lipoprotein is essential for type III secretion system expression of Salmonella enterica serovar Enteritidis. Several putative secretion systems, but not type III secretion system, were already identified of the genome of the NTUH-K2044. Transcription of type 1 fimbriae was more highly induced in the wild-type than in the yfgL mutant strain. In addition to the fim gene cluster, genes encoding some amino acid metabolism, peptidoglycan synthesis and putative phosphoenopyruvate:carbohydrate phosphotransferase system (PTS), including the tdc gene cluster, yraM and the kp0760-kp0763 (pts) gene cluster, were also up-regulated by YfgL. Among a total 2,848 cloned sequences covering 99.9% of the entire genome sequence of NTUH-K2044, the expression of 9 cloned sequences was up-regulated and 3 cloned sequences were down-regulated at a cut-off value of 2.
2016-05-25 | GSE69327 | GEO