Escherichia coli K-12
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1138934 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Synthetic bacterial promoter library: spacer element variants
| PRJNA1049606 | ENA
Project description:Synthetic bacterial promoter library: -35 element and -10 element variants
| PRJNA1049603 | ENA
Project description:Substrains in Escherichia coli K-12 MG1655 can possess various swimming motility, which is mostly resulted from different expression levels of flhDC. Here, we studied the swimming motility of two MG1655 substrains, CY562 and CY570. Our results showed that CY562 had no insertion at the promoter region of flhDC and possessed no swimming motility. In contrast, CY570 had an IS-element insertion at the promoter region of flhDC and showed a hyper-motile phenotype. Transcriptomic data suggest that expression of flhDC and the other known flagella genes was much lower in CY562 than that in CY570. Moreover, CY562 possessed higher expression levels for genes involved in stress response, especially acid-stress response, than CY570. Consistently, CY562 showed a higher survival rate under acid stress than CY570. Our data indicate that there are mechanisms conversely regulating motility and stress response in E. coli.
2021-11-15 | GSE165438 | GEO
Project description:A synthetic oligo library and sequencing approach reveals an insulation mechanism encoded within bacterial σ54 promoters
| PRJNA407221 | ENA
Project description:E. coli butanol-responsive promoter library
| PRJNA787372 | ENA
Project description:We designed and assayed synthetic regulatory elements varying c-amp response element number, affinity, distance to the promoter, spacing between multiple CREs, and surrounding sequence content. Using 5 massively-parallel reporter assays, we measured the expression of 17,406 unique sequences when placed upstream of a minimal promoter using next-generation sequencing of barcodes associated with synthesized elements. We then determine how the varied c-amp response element architectures influence expression when these variants are assayed in an episomal and genomic context across a range of forskolin concentrations, an inducer of c-amp response element activity. Included here are all sequences designed and analyzed in the assay. Assay results from certain library designs were not insightful and not included in the main text but are additionally included here in the barcode-mapping and MPRA sequencing datasets.
2019-09-25 | GSE137922 | GEO
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:E. coli arabinose- & rhamnose-responsive promoter library
| PRJNA1124361 | ENA
Project description:Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of amines to the corresponding aldehydes by amine oxidases. The biological roles of ECAO have been less addressed. Therefore we have constructed a gene deletion Escherichia coli K-12 strain, E. coli tynA-, and used the microarray technique to address its function by comparing the total RNA gene expression to the one of the wt. Our results suggest that tynA is a reserve gene for stringent environmental conditions and its gene product ECAO a growth advantage compared to other bacteria due to H2O2 production.
2015-09-30 | GSE65385 | GEO
Project description:This study was designed to construct and quantitatively characterize a synthetic promoter library in Escherichia coli. Promoter variants were assembled into the low-to-medium copy plasmid pSEVA221 to generate the p221-Plib library, in which each promoter was associated with a barcode sequence. The library was introduced into E. coli DH5α, and pooled transformants were cultured under selective conditions. Promoter activities were determined by sequencing barcode abundances from both RNA-derived cDNA and plasmid DNA libraries. The normalized RNA/DNA ratio was used as a quantitative measure of promoter activity, correcting for differences in sequencing depth, plasmid abundance, and clone representation. This dataset provides promoter activity profiles that can facilitate promoter selection and optimization for synthetic biology and metabolic engineering applications.
2026-02-16 | GSE318900 | GEO