Escherichia coli KO11FL
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ABSTRACT:
PROVIDER: PRJNA33875 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This strain will be used for comparative genome analysis
| PRJNA34111 | ENA
Project description:This strain will be used for comparative genome analysis
| PRJNA34113 | ENA
Project description:A genome reduced E. coli strain MDS42ΔgalK::Ptet-gfp-kan were applied for the comparative transcriptome analysis. Genome-wide transcriptional changes under high osmotic prresure, high temperature condition and starvation were evaluated.
2013-11-04 | GSE49296 | GEO
Project description:This strain will be used for comparative genome analysis
| PRJDA32513 | ENA
Project description:This strain will be used for comparative genome analysis
| PRJDA32511 | ENA
Project description:Background: Based on 32 Escherichia coli and Shigella genome sequences, we have developed an E. coli pan-genome microarray. Publicly available genomes were annotated in a consistent manor to define all currently known genes potentially present in the species. The chip design was evaluated by hybridization of DNA from two sequenced E. coli strains, K-12 MG1655 (a commensal) and O157:H7 EDL933 (an enterotoxigenic E. coli). A dual channel and single channel analysis approach was compared for the comparative genomic hybridization experiments. Moreover, the microarray was used to characterize four unsequenced probiotic E. coli strains, currently marketed for beneficial effects on the human gut flora. Results: Based on the genomes included in this study, we were able to group together 2,041 genes that were present in all 32 genomes. Furthermore, we predict that the size of the E. coli core genome will approach ~1,560 essential genes, considerably less than previous estimates. Although any individual E. coli genome contains between 4,000 and 5,000 genes, we identified more than twice as many (11,872) distinct gene groups in the total gene pool (“pan-genome”) examined for microarray design. Benchmarking of the design based on sequenced control strain samples demonstrated a high sensitivity and relatively low false positive rate. Moreover, the array was highly sufficient to investigate the gene content of apathogenic isolates, despite the strong bias towards pathogenic E. coli strains that have been sequenced so far. Our analysis of four probiotic E. coli strains demonstrate that they share a gene pool very similar to the E. coli K-12 strains but also show significant similarity with enteropathogenic strains. Nonetheless, virulence genes were largely absent. Strain-specific genes found in probiotic E. coli but absent in E. coli K12 were most frequently phage-related genes, transposases and other genes related to mobile DNA, and metabolic enzymes or factors that may offer colonization fitness, which together with their asymptomatic nature may explain their nature. Conclusion: This high-density microarray provides an excellent tool for characterizing either DNA content or gene expression from unknown E. coli strains. Keywords: Comparative genomic hybridizations
2008-01-22 | GSE8595 | GEO
Project description:Archer2011 - Genome-scale metabolic model of
Escherichia coli (iCA1273)
This model is described in the article:
The genome sequence of E.
coli W (ATCC 9637): comparative genome analysis and an improved
genome-scale reconstruction of E. coli.
Archer CT, Kim JF, Jeong H, Park JH,
Vickers CE, Lee SY, Nielsen LK.
BMC Genomics 2011; 12: 9
Abstract:
BACKGROUND: Escherichia coli is a model prokaryote, an
important pathogen, and a key organism for industrial
biotechnology. E. coli W (ATCC 9637), one of four strains
designated as safe for laboratory purposes, has not been
sequenced. E. coli W is a fast-growing strain and is the only
safe strain that can utilize sucrose as a carbon source.
Lifecycle analysis has demonstrated that sucrose from sugarcane
is a preferred carbon source for industrial bioprocesses.
RESULTS: We have sequenced and annotated the genome of E. coli
W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two
plasmids, pRK1 (102,536 bp) and pRK2 (5,360 bp), are also
present. W has unique features relative to other sequenced
laboratory strains (K-12, B and Crooks): it has a larger genome
and belongs to phylogroup B1 rather than A. W also grows on a
much broader range of carbon sources than does K-12. A
genome-scale reconstruction was developed and validated in
order to interrogate metabolic properties. CONCLUSIONS: The
genome of W is more similar to commensal and pathogenic B1
strains than phylogroup A strains, and therefore has greater
utility for comparative analyses with these strains. W should
therefore be the strain of choice, or 'type strain' for group
B1 comparative analyses. The genome annotation and tools
created here are expected to allow further utilization and
development of E. coli W as an industrial organism for
sucrose-based bioprocesses. Refinements in our E. coli
metabolic reconstruction allow it to more accurately define E.
coli metabolism relative to previous models.
This model is hosted on
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MODEL1507180010.
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2015-07-30 | MODEL1507180010 | BioModels
Project description:Mapping the occupancy of FNR, HNS, and IHF throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anerobic growth conditions. We also mapped the binding of the ß subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a ∆fnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The ∆hns/∆stpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure
2013-06-20 | GSE41186 | GEO
Project description:This strain is being sequenced for comparative genome analysis.
| PRJDA19053 | ENA
Project description:We describe the design and evaluate the use of a high density oligonuclotide microarray covering seven sequenced E. coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labelled genomic DNA to query the microarrays and subsequently analyse common virulence genes and phage elements, and perform whole genome comparisons, we observed that O175:H16 D1 is a K-12 like strain and confirmed that its phi3538 phage element originated from the E. coli 3538 strain with which it shares a substantial proportion of phage elements. Moreover, a number of genes involved in DNA transfer and recombination was identified in both new strains providing a likely explanation for their capability to transfer phi3538 between them. Analyses of control samples demonstrated that results using our custom designed microarray were representative of the true biology, e.g. by confirming the presence of all known chromosomal phage elements as well as 98.8 and 97.7 percent of queried chromosomal genes for the two control strains. Finally, we demonstrate that use of spatial information, in terms of the physical chromosomal locations of probes, improves the analysis. Keywords: Genomic DNA hybridizations
2006-08-29 | GSE4690 | GEO