Ontology highlight
ABSTRACT:
PROVIDER: PRJNA530228 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8832571_1.fastq.gz | Fastqsanger.gz | |||
| SRR8832571_2.fastq.gz | Fastqsanger.gz | |||
| SRR8832572_1.fastq.gz | Fastqsanger.gz | |||
| SRR8832572_2.fastq.gz | Fastqsanger.gz | |||
| SRR8832573_1.fastq.gz | Fastqsanger.gz |
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Project description:Rapid accumulation of motility-activating mutations in resting liquid culture of Escherichia coli
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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.
2019-07-11 | GSE129161 | GEO
Project description:Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli
| PRJNA1081798 | ENA
Project description:Escherichia coli can survive for long periods in batch culture in the laboratory, where they experience a stressful and heterogenous environment. During this incubation, E. coli acquires mutations that are selected for in response to this environment, ultimately leading to evolved populations that are better adapted to these complex conditions, which can lead to a better understanding of evolutionary mechanisms. Mutations in regulatory genes often play a role in adapting to heterogenous environments. To identify such mutations, we examined transcriptional differences during log phase growth in unaged cells compared to those that had been aged for 10-days and regrown. We identified expression changes in genes involved in motility and chemotaxis after adaptation to long-term cultures. We hypothesized that aged populations would also have phenotypic changes in motility and that motility may play a role in survival and adaptation to long-term cultures. While aged populations did show an increase in motility, this increase was not essential for survival in long-term cultures. We identified putative mutations in the regulatory gene sspA, as well as other genes, that may contribute to the observed differences in motility. Taken together, these data provide an overall picture of the role of mutations in regulatory genes for adaptation, while underscoring that all changes that occur during evolution in stressful environments are not necessarily adaptive.
2022-05-27 | GSE188790 | GEO
Project description:Responses of Escherichia coli MG1655/pTrc99a(NOX+) grown at different growth rates in chemostat in M9 + salts NOX: NADH oxygenase converts NADH to NAD. Cells with NOX are able to recycle the excess NADH generated during rapid growth, leading to lesser accumulation of acetate Keywords: different growth rates in parallel
2006-03-08 | GSE4365 | GEO
Project description:Most of the proteomic studies done so far uses bacterial cells harvested from liquid culture media. However it is widely accepted that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media. As an attempt to complement previous studies, in this study we compare the proteome coverage of Escherichia coli K12 from a single colony on solid media with those at different growth phases in liquid culture; i.e. early log, mid log, early - and late stationary growth phases. A total of 2044 protein groups covering approximately 47% of the total proteome were identified across all studied conditions; 1650 number of proteins identified from single colonies and 1679 proteins from liquid cultured cells. Label-free quantitative analysis revealed that single colony proteome in a solid agar differs largely from that in liquid culture. The presence of the Suf-operon, involved in iron mobilisation and swarming motility were associated exclusively with single colony profiles. Whereas proteins involved in motility such as MotA, MotB, fliH, flip, fliD and fliJ were associated exclusively to cells grown in liquid culture. The data presented here provide a valuable resource for understanding the role of key proteins within microenvironments surrounding E.coli single colonies.
2021-09-09 | PXD019140 | Pride
Project description:Human Peptidoglycan Recognition Proteins (PGRPs) kill bacteria, likely by over-activating stress responses in bacteria. To gain insight into the mechanism of PGRP killing of Escherichia coli and bacterial defense against PGRP killing, gene expression in E. coli treated with a control protein (bovine serum albumin, BSA), human recombinant PGRP (PGLYRP4), gentamicin (aminoglycoside antibiotic), and CCCP (membrane potential decoupler) were compared. Each treatment induced unique and somewhat overlapping pattern of gene expression. PGRP highly increased expression of genes for oxidative and disulfide stress, detoxification and efflux of Cu, As, and Zn, repair of damaged proteins and DNA, methionine and histidine synthesis, energy generation, and Fe-S clusters repair. PGRP also caused marked decrease in the expression of genes for Fe uptake and motility. Gene expression microarray in E. coli exposed to a human bactericidal innate immunity protein, PGRP, showed induction of oxidative stress response and defense genes, with different expression pattern than E. coli exposed to an aminoglycoside antibiotic and a membrane potential decoupler. E. coli was treated with PGRP (human recombinant PGLYRP4), gentamicin, or CCCP (carbonyl cyanide 3-chlorophenylhydrazone). RNA was obtained from each culture and assayed for gene expression using whole genome Affymetrix E. coli Genome 2.0 Array. Each experiment was repeated 3 times.
2014-07-25 | E-GEOD-44211 | biostudies-arrayexpress
Project description:Purpose: To understand the dynamic transcriptional response of Escherichia coli cells to intracellular HMBPP accumulation. Methods: RNA-seq libraries were constructed for three samples, including (I) CAR005, which used as control; (II) IspG1, which strong over-expressed ispG in CAR005; (III) G4H14, which simultaneously over-expressed ispG and ispH in CAR005.For preparation of RNA samples, single colonies were inoculated into 15x100 mm tubes containing 4 ml LB, and grown at 30ºC and 250 rpm overnight. 100 μl seed culture was inoculated into a 100 ml flask containing 10 ml LB medium, and grown at 30ºC and 250 rpm. After 5 h, 1 ml culture was harvested by centrifugation, frozen in liquid nitrogen and sent to Beijing Genomics Institute (BGI, Shenzhen, China). The three 90-nt paired-end RNA-seq libraries were generated commercially at Beijing Genomics Institute by using the HiSeq™ 2000 platform. Sequencing data was handled essentially with Bowtie2, Tophat2, NOIseq. Expression levels are presented as Reads Per Kilobase of transcript per Million mapped reads (RPKM). Results: We assessed expression levels of a 5 hour culture of ispG1 and compared to the parent strain CAR005. Among the 4200 predicted genes in E. coli ATCC 8739, relative expression levels for 504 genes were found changed in strain ispG1, with 166 markedly up-regulated and 338 repressed. FunCat was used to analyze the biological processes represented by these genes and found categories related to “nucleotide/nucleoside/nucleobase metabolism” (P=7.76E-05), “ribosome biogenesis,” (P=1.06E-20), “translation,” (P=4.26E-12) and “nucleobase binding” (P=1.86E-06) were markedly enriched in the repressed genes set, suggested that HMBPP accumulation might exert deterious effect on cell growth and viability. As for G4H14, only 64 genes were found down-regulated in G4H14. Biological processes associated with macromolecular synthesis no longer markedly enriched, suggesting that cell growth and viability tended to be restored to control level after eliminating HMBPP accumulation. Conclusions: Transcriptome profiling exhibited additional evidence to the cytotoxicity of HMBPP, meanwhile, demonstrated that activating downstream IspH could contribute to attenuation of such deterious effects.
2017-09-06 | GSE84255 | GEO
Project description:The faecal indicator bacterium Escherichia coli K12 was used to study the cellular events that take place at the transcription level using the microarray technology during short-term (physiological) and long-term (genetic) adaptation to slow growth under limited nutrient supply. Short-term and long-term adaptation were assessed by comparing the mRNA levels isolated after 40 or 500 hours of glucose-limited continuous culture at a dilution rate of 0.3 h-1 with those from batch culture with glucose excess. Keywords: glucose-limited continuous culture, adaptation, microarray, high affinity transport systems, transcriptome, Escherichia coli
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Project description:Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures. Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol.
2013-12-30 | GSE24914 | GEO