Escherichia coli K-12
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ABSTRACT:
PROVIDER: PRJNA1049606 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-l-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions. Keywords: Genetic modification
2007-11-14 | GSE9582 | GEO
Project description:Here we report the results of a study comparing the global transcriptional responses of Escherichia coli to two well-studied CAMPs, LL37 and colistin, and two ceragenins with related structures, CSA13 and CSA131. We found that E. coli responds similarly to both CAMPs and ceragenins by inducing a Cpx envelope stress response. However, whereas E. coli exposed to CAMPs increased expression of genes involved in colanic acid biosynthesis, bacteria exposed to ceragenins specifically modulated functions related to phosphate transport, indicating distinct mechanisms of action between these two classes of molecules. Overall, this study suggests that while some bacterial responses to ceragenins overlap with those induced by naturally-occurring CAMPs, these synthetic molecules target the bacterial envelope using a distinctive mode of action.
2020-10-26 | GSE160082 | GEO
Project description:It is now possible to discover the physiological function of LysR-family transcription factors (LLTF) in E. coli using ChIP-Exo (in vivo DNA-binding), growth phenotype, conserved gene clustering, and transcriptional analysis (RNA-seq deletion mutants). The LysR-family regulator phenotype microarray has been detected for YbdO, YbeF, YcaN, YiaU, and YgfI deletion mutants and for the isogenic E. coli BW25113 strain in minimal medium at carbon/nitrogen starvation or L-threonine supplement conditions. The LLTF YbdO and YgfI regulation is important for bacterial growth adaptation to low pH with citrate supplementation or glycerol as the carbon source, respectively. A systems analysis approach allows for the identification of the YneJ (putrescine utilization), YgfI, and YbdO transcription factor regulated genes in Escherichia coli. YgfI regulates DhaKLM, the phosphotransferase system involved in glycerol and dihydroxyacetone utilization. YbdO is a repressor for ybdMN and is likely involved in citrate lyase regulation. YneJ, re-named PtrR, directly controls the expression of the succinate-semialdehyde dehydrogenase Sad (YneI) and is important for bacterial growth in the presence of L-glutamate as a nitrogen source. The sad promoter is repressed by PtrR. PtrR is also a repressor of the fnrS gene, encoding a small regulatory RNA involved in the regulation of the sodB gene, as shown by RNA-seq data. A 15-bp palindromic PtrR-binding site was identified in the upstream regions of the sad / ptrR and fnrS genes and confirmed by ChIP-Exo and fluorescent polarization assays. The PtrR-dependent regulation of fnrS likely leads to a regulatory cascade induced by this small RNA.
2022-08-23 | GSE182695 | GEO