Escherichia coli BW25113
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA387063 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5585690_1.fastq.gz | Fastqsanger.gz | |||
| SRR5585690_2.fastq.gz | Fastqsanger.gz | |||
| SRR5585691_1.fastq.gz | Fastqsanger.gz | |||
| SRR5585691_2.fastq.gz | Fastqsanger.gz | |||
| SRR5585692_1.fastq.gz | Fastqsanger.gz |
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Project description:Escherichia coli BW25113 is the parent strain of the Keio collection comprising nearly 4,000 single-gene deletion mutants. We report the complete 4,631,469-bp genome sequence of this strain and the key variations from the type strain E. coli MG1655.
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Project description:The Escherichia coli strain Nissle 1917 (EcN) is used as a probiotic for the treatment of certain gastrointestinal diseases in several European and non-European countries. In vitro studies showed EcN to efficiently inhibit the production of Shiga toxin (Stx) by Stx producing E. coli (STEC) such as Enterohemorrhagic E. coli (EHEC). The occurrence of the latest EHEC serotype (O104:H4) responsible for the great outbreak in 2011 in Germany was due to the infection of an enteroaggregative E. coli by a Stx 2-encoding lambdoid phage turning this E. coli into a lysogenic and subsequently into a Stx producing strain. Since EHEC infected persons are not recommended to be treated with antibiotics, EcN might be an alternative medication. However, because a harmless E. coli strain might be converted into a Stx-producer after becoming host to a stx encoding prophage, we tested EcN for stx-phage genome integration. Our experiments revealed the resistance of EcN towards not only stx-phages but also against the lambda phage. This resistance was not based on the lack of or by mutated phage receptors. Rather the expression of certain genes (superinfection exclusion B (sieB) and a phage repressor (pr) gene) of a defective prophage of EcN was involved in the complete resistance of EcN to infection by the stx- and lambda phage. Obviously, EcN cannot be turned into a Stx producer. Furthermore, we observed EcN to inactivate phages and thereby to protect E. coli K-12 strains against infection by stx- as well as lambda-phages. Inactivation of lambda-phages was due to binding of lambda-phages to LamB of EcN whereas inactivation of stx-phages was caused by a thermostable protein of EcN. These properties together with its ability to inhibit Stx production make EcN a good candidate for the prevention of illness caused by EHEC and probably for the treatment of already infected people.
2018-06-14 | GSE109932 | GEO
Project description:High resolution view of bacteriophage lambda gene expression by ribosome profiling
| PRJNA205933 | ENA
Project description:Bacteriophage lambda is one of the most extensively studied organisms, and has been a primary model for understanding basic modes of genetic regulation. Here we examine the progress of lambda gene expression during phage development by ribosome profiling, and thereby provide a very high resolution view of lambda gene expression. The known genes are expressed in a predictable fashion, authenticating the analysis. But many previously unappreciated potential open reading frames become apparent in the expression analysis, revealing an unexpected complexity in the pattern of lambda gene function.
2013-07-01 | GSE47509 | GEO
Project description:The dual roles of capsular extracellular polymeric substances (EPS) in the photocatalytic inactivation of bacteria were demonstrated in a TiO2-UVA system, by comparing wild-type Escherichia coli strain BW25113 and isogenic mutants with upregulated and downregulated production of capsular EPS. In a partition system in which direct contact between bacterial cells and TiO2 particles was inhibited, an increase in the amount of EPS was associated with increased bacterial resistance to photocatalytic inactivation. In contrast, when bacterial cells were in direct contact with TiO2 particles, an increase in the amount of capsular EPS decreased cell viability during photocatalytic treatment. Taken together, these results suggest that although capsular EPS can protect bacterial cells by consuming photogenerated reactive species, it also facilitates photocatalytic inactivation of bacteria by promoting the adhesion of TiO2 particles to the cell surface. Fluorescence microscopy and scanning electron microscopy analyses further confirmed that high capsular EPS density led to more TiO2 particles attaching to cells and forming bacterium-TiO2 aggregates. Calculations of interaction energy, represented by extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) potential, suggested that the presence of capsular EPS enhances the attachment of TiO2 particles to bacterial cells via acid-base interactions. Consideration of these mechanisms is critical for understanding bacterium-nanoparticle interactions and the photocatalytic inactivation of bacteria.
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Project description:Glycerol is an attractive feedstock for biofuels since it accumulates as a byproduct during biodiesel operations; hence, it is interesting to consider converting glycerol to hydrogen using the formate hydrogen lyase system of Escherichia coli which converts pyruvate to hydrogen. Starting with Escherichia coli BW25113 frdC that lacks fumarate reductase to eliminate the negative effect of accumulated hydrogen on glycerol fermentation and by using both adaptive evolution and chemical mutagenesis combined with a selection method based on increased growth on glycerol, we obtained an improved strain, HW2, that produces 20-fold more hydrogen in glycerol medium (0.68 mmol/L/h) compared to that of frdC mutant. HW2 also grows 5-fold faster (0.25 1/h) than BW25113 frdC on glycerol, so it achieves a reasonable growth rate. Corroborating the increase in hydrogen production, glycerol dehydrogenase activity in HW2 increased 4-fold compared to BW25113 frdC. In addition, a whole-transcriptome study revealed that several pathways that would decrease hydrogen yields were repressed in HW2 (fbp, focA, and gatYZ) while a beneficial pathway, eno which encodes enolase was induced.
2010-10-31 | GSE18972 | GEO
Project description:Escherichia coli base editing raw sequence reads
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Project description:RNA-seq of E. coli BW25113 YgaV mutant.
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Project description:Escherichia coli BW25113 Raw sequence reads
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Project description:Experimental evolution of trmD-deficient E. coli
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