Escherichia coli K-12
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ABSTRACT:
PROVIDER: PRJNA319968 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3481040_1.fastq.gz | Fastqsanger.gz | |||
| SRR3481040_2.fastq.gz | Fastqsanger.gz | |||
| SRR3481041_1.fastq.gz | Fastqsanger.gz | |||
| SRR3481041_2.fastq.gz | Fastqsanger.gz | |||
| SRR3481042_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Benzoate-Evolved Strains of Escherichia coli K-12 Obtained by Experimental Evolution
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Project description:Experimental Evolution of Escherichia coli K-12 under Acid Stress
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Project description:Laboratory Experimental Evolution of Escherichia coli K-12 under Aromatic Acid Stress
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Project description:Iron and Acid Adapted Strains of Halobacterium sp. NRC-1 obtained by Experimental Evolution
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Project description:In Escherichia coli, pH-dependent gene expression varies with oxygen level. Anaerobic pH-dependent expression ratios were analyzed and compared to the published analysis of aerated cultures (Maurer et al, 2005). E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Gene expression profiles were obtained by cDNA hybridization to Affymetrix arrays. pH-dependent expression was seen for 1,394 genes, of which 1,002 show no pH dependence under aeration. Four intergenic regions containing regulatory sRNAs were up-regulated by acid anaerobically (ryeA, csrB, gadY, rybC) and one sRNA (ryhA) by acid with aeration. Acid and anaerobiosis co-regulated the gad regulon; drug transporters (mdtEF, mdtL); catabolism of sugar derivatives whose fermentation minimized acid production; and all hydrogenases (hya, hyb, hyc, hyf, hyp). The hydrogenases however were up-regulated at high pH under aeration (observed by real-time PCR). Acid with anaerobiosis down-regulated penicillin-binding proteins (dacACD, mreBC) and ribosome biosynthesis. Ribosome down-regulation may be caused by restriction of anaerobic metabolism at low pH. A core group of 236 genes showed similar pH response with or without aeration. Core genes up-regulated by acid included fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), the “constitutive” Na+/H+ antiporter (nhaB), and over thirty unidentified proteins. Core genes at high pH included maltodextrin transport (lamB, malEFGKMPQT), ATP synthase, and DNA repair (recA and mutL). Overall, pH and anaerobiosis co-regulated metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm. Keywords: Steady State
2006-10-01 | GSE4556 | GEO
Project description:C. glutamicum strains adapted to higher growth temperatures were obtained through an adaptive laboratory evolution experiment. To elucidate molecular basis for thermotolerance acquired by the evolved strains, we examined transcriptional responses of the evolved and parental strains to thermal stress using microarray technology.
2015-01-06 | GSE64654 | GEO
Project description:Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Cultures were grown with aeration to an optical density at 600 nm of 0.3 in potassium-modified Luria-Bertani medium buffered at pH 5.0, 7.0, and 8.7. For each of the three pH conditions, cDNA from RNA of five independent cultures was hybridized to Affymetrix E. coli arrays. Analysis of variance with a significance level of 0.001 resulted in 98% power to detect genes showing a twofold difference in expression. Normalized expression indices were calculated for each gene and intergenic region (IG). Differential expression among the three pH classes was observed for 763 genes and 353 IGs. Hierarchical clustering yielded six well-defined clusters of pH profiles, designated Acid High (highest expression at pH 5.0), Acid Low (lowest expression at pH 5.0), Base High (highest at pH 8.7), Base Low (lowest at pH 8.7), Neutral High (highest at pH 7.0, lower in acid or base), and Neutral Low (lowest at pH 7.0, higher at both pH extremes). Flagellar and chemotaxis genes were repressed at pH 8.7 (Base Low cluster), where the cell's transmembrane proton potential is diminished by the maintenance of an inverted pH gradient. High pH also repressed the proton pumps cytochrome o (cyo) and NADH dehydrogenases I and II. By contrast, the proton-importing ATP synthase F1Fo and the microaerophilic cytochrome d (cyd), which minimizes proton export, were induced at pH 8.7. These observations are consistent with a model in which high pH represses synthesis of flagella, which expend proton motive force, while stepping up electron transport and ATPase components that keep protons inside the cell. Acid-induced genes, on the other hand, were coinduced by conditions associated with increased metabolic rate, such as oxidative stress. All six pH-dependent clusters included envelope and periplasmic proteins, which directly experience external pH. Overall, this study showed that (i) low pH accelerates acid consumption and proton export, while coinducing oxidative stress and heat shock regulons; (ii) high pH accelerates proton import, while repressing the energy-expensive flagellar and chemotaxis regulons; and (iii) pH differentially regulates a large number of periplasmic and envelope proteins. Keywords: Steady State
2006-03-23 | GSE4511 | GEO
Project description:The foodborne pathogen Escherichia coli O157:H7 is commonly exposed to organic acid in processed and preserved foods, allowing adaptation and the development of tolerance to pH levels otherwise lethal. Since little is known about the molecular basis of adaptation of E. coli to organic acids, we studied K-12 MG1655 and O157:H7 Sakai during exposure to acetic-, lactic-, and hydrochloric acid at pH 5.5. The conditions required to maximimally induce the ATR of the pathotypes to all acidulants was experimentally determined. This involved incubation at pH 5.5 for 3 h (K-12) and for 2 h (O157:H7), and generated acid adapted cultures more resistant to acid challenge at pH 3.5 than bacteria that had been grown at neutral pH prior to acid-shock. To determine the transcriptomic response of K-12 and O157:H7 to each of the three acids, RNA was extracted from samples of cultures at the time of incubation corresponding to maximal induction of the ATR and from the corresponding overnight culture to serve as a control. The Affy package of the Bioconductor software was used to process raw CEL files using the robust multiarray average algorithm (RMA) for normalization, background correction, and expression value calculation. Expression levels obtained from four independent biological replicates of every condition were compared using the Limma package of the Bioconductor software. Elements with expression levels ? twofold higher or lower than the reference at a statistical significance (P-value adjustment with Benjamini and Hochberg with an adjusted P value ? 0.01, Average Expression (A value) ? 2, Log-odds (B value) ? 0) were selected. This is the first transcriptomic study to demonstrate and characterise the stationary phase acidulant and pathotype specific ATR of E. coli. A core set of genes were also found to be universally expressed by both pathotypes regardless of acidulant type.
2010-10-08 | E-TABM-912 | biostudies-arrayexpress
Project description:Experimental evolution is a powerful approach to study how ecological forces shape microbial genotypes and phenotypes, but to date strains were predominantly adapted to conditions specific to laboratory environments. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in the dairy environment and it is generally believed, that dairy strains originate from the plant niche. Here we investigated the adaptive process from the plant to the dairy niche and show that during the experimental evolution of a L. lactis plant isolate in milk, several mutations are selected that affect amino acid metabolism and transport. Three independently evolved strains were characterized by whole genome re-sequencing, revealing 4 to 28 mutational changes in the individual strains. Two of the adapted strains showed clearly increased acidification rates and yields in milk, and contained three identical point mutations. Transcriptome profiling and extensive phenotyping of the wild-type plant isolate compared to the evolved mutants, and a "natural" dairy isolate confirmed that major physiological changes associated with improved performance in the dairy environment relate to nitrogen metabolism. The deletion of a putative transposable element led to a significant decrease of the mutation rate in two of the adapted strains. These results specify the adaptation of a L. lactis strain isolated from mung bean sprouts to growth in milk and they demonstrate that niche-specific adaptations found in environmental microbes can be reproduced by experimental evolution. Multiple loop design with 12 samples and 16 dual label arrays. Each sample is hybrdized at least on two different arrays and with both dyes.
2010-06-24 | E-GEOD-20373 | biostudies-arrayexpress