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DspoT suppressor mutations in E. coli

ABSTRACT: DspoT suppressor mutations in E. coli BW25113

PROVIDER: PRJEB6520 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR532261_1.fastq.gz	Fastqsanger.gz
	ERR532261_2.fastq.gz	Fastqsanger.gz
	ERR532262_1.fastq.gz	Fastqsanger.gz
	ERR532262_2.fastq.gz	Fastqsanger.gz
	ERR532263_1.fastq.gz	Fastqsanger.gz

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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

2010-01-20 | GSE14064 | GEO

Rapid accumulation of motility-activating mutations in resting liquid culture of Escherichia coli

Project description:Expression and use of motility genes is a potentially beneficial but costly process in bacteria. Interestingly, many isolate strains of Escherichia coli possess motility genes but have lost the ability to activate them in conditions in which motile cells are advantageous, raising the question of how they respond to these situations. Through transcriptome profiling of strains in the E. coli single-gene knockout Keio collection, we noticed drastic upregulation of motility genes in many of the deletion strains as compared to its typically non-motile parent strain (BW25113). This switch to a motile phenotype is not a direct consequence of the genes deleted, but is instead due to a variety of secondary mutations that increase the synthesis of the major motility regulator, FlhDC. We found that a phenotypic switch to motility at a population level can be induced in non-motile E. coli strains by incubation in non-shaking liquid medium overnight but not in shaking media. Individual isolates after the overnight incubation acquired distinct mutations upstream of the flhDC operon, including different insertion sequence (IS) elements and, to a lesser extent, point mutations. The rapid sweep in the non-shaking population shows that non-motile strains without existing regulatory mechanisms can quickly adapt to a motile lifestyle by quickly acquired genetic changes.

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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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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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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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Escherichia coli transcriptome reorganization caused by nutritional changes

Project description:Escherichia coli K-12 BW25113 were cultured in the LB and M63 media. Exponetially growing populations were collected for RNAseq. The culture medium-induced transcriptional changes were analyzed.

2020-08-31 | GSE136101 | GEO

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.

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Project description:Transcripitonal profiling of Escherichia coli K-12 BW25113 comparing cells with isooctane treatment at time point of 0, 10, 30 and 60 min with two biological replicates

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Impact of heavy atmospheric pollution on the transcriptome of Escherichia coli BW25113 and the adapted E. coli strain T56-1

Project description:Expression profile of E. coli BW25113 grown under standard laboratory atmosphere with a fine particulate matter (PM2.5) concentration of 17 mg m-3, under urban polluted atmosphere with a PM2.5 of 230 mg m-3 or under diesel exhaust atmosphere with a PM2.5 of 613 mg m-3. Expression profile of the diesel exhaust atmosphere-adapted E. coli strain T56-1 grown under diesel exhaust atmosphere.

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