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Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide phosphodiesterase (CNPase) in Escherichia coli K12 BW25113 (E. coli)

ABSTRACT: Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide phosphodiesterase (CNPase) in Escherichia coli K12 BW25113 (E. coli)

PROVIDER: PRJNA755275 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15476755_1.fastq.gz	Fastqsanger.gz
	SRR15476755_2.fastq.gz	Fastqsanger.gz
	SRR15476757_1.fastq.gz	Fastqsanger.gz
	SRR15476757_2.fastq.gz	Fastqsanger.gz
	SRR15476759_1.fastq.gz	Fastqsanger.gz

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Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide phosphodiesterase (CNPase) in Escherichia coli K12 BW25113 (E. coli)

Project description:The impact of 2',3'-cyclic nucleotide phosphodiesterase (CNPase) on global gene expression in E. coli was investigated by heterologous expression of mammalian CNPase in a strain containing a deletion of the 'rna' gene. 'rna' encodes an endoribonuclease capable of hydrolyzing RNA into 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) such that deletion of 'rna' drastically reduces 2',3'-cNMPs levels to undetectable levels. Expression of CNPase in this strain allowed any effects of CNPase unrelated to 2',3'-cNMPs to be observed.

2021-11-09 | GSE182184 | GEO

E. coli BW25113 ompA mutant vs wild type biofilm and E. coli BW25113 ompA/pCA24N_ompA vs ompA/pCA24N suspension cells

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Transcription profiling of E. coli K12 Bw25113/pCA24N-hha with 2 mM IPTG vs BW25113/pCA24N with 2 mM IPTG

Project description:gene expression profiles by overexpressing Hha from pCA24N-hha using 2 mM IPTG induction in BW25113 wild type suspension cells in LB medium at 37C relative to BW25113 carrying the empty vector plasmid in the same test conditions. Experiment Overall Design: Strains: E. coli K12 BW25113/pCA24N, BW25113/pCA24N-hha Experiment Overall Design: Growth conditions: grow culture in LB medium at 37C to OD600 0.1 and add 2 mM IPTG to induce, and grow to OD600 0.5 to collect cells. RNA was extraction, and gene expression profiles were evaluated.

2008-10-20 | E-GEOD-10116 | biostudies-arrayexpress

E. coli BW25113 frdC vs. E. coli BW25113 HW2

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.

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E. coli BW25113 azide treated vs untreated cells

Project description:Transcriptional profiling of mid-log phase (OD600 ~ 0.8) E. coli BW25113 cells grown treated with 2 mM NaN3 for 10 minutes

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Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide monophosphates in Escherichia coli

Project description:The impact of 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) on global gene expression in E. coli was investigated by heterologous expression of a 2',3'-cyclic nucleotide phosphodiesterase (CNPase), which reduces intracellular 2',3'-cNMP levels.

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E. coli BW25113 ompA mutant vs wild type biofilm and E. coli BW25113 ompA/pCA24N_ompA vs ompA/pCA24N suspension cells

Project description:This Series involves two studies: 1) The gene expression of E. coli K-12 BW25113 ompA mutant strain vs. wild type strain glasswool biofilm cells and E. coli K-12 BW25113 ompA mutant vs. wild type polystyrene biofilm cells. 2) The gene expression of E. coli BW25113 ompA/pCA24N_ompA vs. ompA/pCA24N suspension cells. Strains: E. coli K-12 BW25113 wild type, ompA mutant Medium: LB Cell type: Biofilm cells grown on glasswool and polystyrene surfaces Time: 15 h Temperature: 37C Strains: BW25113 ompA/pCA24N_ompA and ompA/pCA24N Medium: LB Time: 7 h Temperature: 37C Cell type: suspension cells, induced by 0.1 mM IPTG

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Project description:E. coli K-12 BW25113 persister cells generated via rifampicin pre-treatment relative to BW25113 wild-type stationary phase gene expression. Persister cells were generated following exposure to ampicillin 20 ug/mL.

2016-11-20 | GSE34177 | GEO

Control of gene expression by PdeL, a transcription regulator and c-di-GMP phosphodiesterase in Escherichia coli K12

Project description:PdeL is a transcription regulator and c-di-GMP specific phosphodiesterase in Escherichia coli. To address the transcription regulator function of PdeL we analyzed the transcriptomes of four E. coli K12 strains during the exponential growth phase by RNA-sequencing. These four strains included (1) wild-type E. coli K12 strain BW30270 carrying an empty vector control plasmid, (2) an isogenic pdeL deletion mutant carrying the control plasmid, as well as the pdeL mutant that was complemented with (3) a plasmid carrying pdeL under control of the IPTG-inducible tac promoter or (4) a plasmid encoding a fusion protein of the PdeL’s DNA-binding domain and the C-terminal dimerization domain of phage Lambda cI repressor (PdeL-DBD_cI-C). Expression of plasmid-encoded pdeL and pdeL-DBD_cI-C, respectively, was induced by addition of IPTG for 15 minutes prior to RNA isolation. Analyses of the RNA-seq data revealed that plasmid-provided PdeL (and PdeL-DBD_cI-C) repress transcription of class II flagellar genes and presumably regulate the transcription of additional loci, while only little differences were observed between the transcriptomes of wild-type strain BW30270 and its isogenic pdeL mutant.

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Expression Profiling of E. coli K-12 BW25113 in Minimal Media with Different Carbon Sources

Project description:mRNA sequencing was performed on E. coli K-12 BW25113 grown on Glucose, Pyruvate, Fumarate, and Acetate.

2017-02-14 | GSE59759 | GEO