Escherichia coli
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD002140
PROVIDER: PRJNA279834 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1945190_1.fastq.gz | Fastqsanger.gz | |||
| SRR1945190_2.fastq.gz | Fastqsanger.gz | |||
| SRR1945200_1.fastq.gz | Fastqsanger.gz | |||
| SRR1945200_2.fastq.gz | Fastqsanger.gz | |||
| SRR1945210_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 154 |
Similar Datasets
Project description:RNA-seq was carried out to compare the transcriptomes of wild-type MG1655 E coli with mutant lacking the prominent sRNA, SdsR, in bacteria that had been exposed to long-term (24hr) nitrogen starvation in Gutnick minimal media. The aim of this was to understand what the regulatory contribution of SdsR was to bacteria experiencing long-term nitrogen starvation.
2023-12-01 | E-MTAB-13402 | biostudies-arrayexpress
Project description:Proteomics was carried out to compare the proteomes of wild-type MG1655 E coli with mutants lacking either prominent sRNA, SdsR, OxyS or ZbiJ, or lacking the ubiquitous RNA chaperone proteins hfq, in bacteria that had been exposure to long-term (24hr) nitrogen starvation in Gutnick minimal media. The aim of this was to understand what the regulatory contribution of these three sRNA was to bacteria experiencing long-term nitrogen starvation.
2024-05-24 | PXD045656 | Pride
Project description:RNA-seq was carried out to compare the transcriptomes of wild-type MG1655 E coli with mutant lacking the prominent RNA chaperone, Hfq, in bacteria that had been exposed to short-term (20min, N-) and long-term (24hr, N-24) nitrogen starvation, and following replenishment of nitrogen to long-term starved bacteria (~2hrs, N-24+2) in Gutnick minimal media. The aim of this was to understand what the regulatory contribution of Hfq was to bacteria experiencing nitrogen starvation.
2023-12-01 | E-MTAB-13527 | biostudies-arrayexpress
Project description:Huarat2016 -Starvation-induced Ser/Thr
protein kinase ArnS (Saci_1181) (Model 14)
This model is described in the article:
ArnS, a kinase involved in
starvation-induced archaellum expression.
Haurat MF, Figueiredo AS, Hoffmann
L, Li L, Herr K, J Wilson A, Beeby M, Schaber J, Albers SV.
Mol. Microbiol. 2016 Oct; :
Abstract:
Organisms have evolved motility organelles that allow them
to move to favourable habitats. Cells integrate environmental
stimuli into intracellular signals to motility machineries to
direct this migration. Many motility organelles are complex
surface appendages that have evolved a tight, hierarchical
regulation of expression. In the crenearchaeon Sulfolobus
acidocaldarius, biosynthesis of the archaellum is regulated by
regulatory network proteins that control expression of
archaellum components in a phosphorylation-dependent manner. A
major trigger for archaellum expression is nutrient starvation,
but although some components are known, the regulatory cascade
triggered by starvation is poorly understood. In this work, the
starvation-induced Ser/Thr protein kinase ArnS (Saci_1181)
which is located proximally to the archaellum operon was
identified. Deletion of arnS results in reduced motility,
though the archaellum is properly assembled. Therefore, our
experimental and modelling results indicate that ArnS plays an
essential role in the precisely controlled expression of
archaellum components during starvation-induced motility in
Sulfolobus acidocaldarius. Furthermore they combined in vivo
experiments and mathematical models to describe for the first
time in archaea the dynamics of key regulators of archaellum
expression.
This model is hosted on
BioModels Database
and identified by:
MODEL1607210000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2016-12-05 | MODEL1607210000 | BioModels
Project description:RNA-seq data to compare the transcriptomes of wild-type and hfq mutant E. coli strain MG1655 experiencing nitrogen starvation for 20 min (N-) and 24 hours (N-24). To look at the RNA expression profile of E. coli during Nitrogen starvation and comparing how this changes in bacteria lacking Hfq at two specific timepoints; short-term Nitrogen starvation, N- (20min into starvation), and long-term Nitrogen starvation, N-24 (24hours into starvation).
2023-12-29 | E-MTAB-12794 | biostudies-arrayexpress
Project description:This data set consists of a long term glucose starvation time course of E. coli grown in minimal media for up to two weeks. Unlike previous studies of long term starvation,Our study focuses on the physiological response of E. Coli in stationary phase as a result of being starved for glucose, not on the genetic adaptation of E. coli to utilize alternative nutrients.
2015-08-24 | PXD002140 | Pride
Project description:Pi availability is a significant limiting factor for plant growth in both natural and agricultural systems. To cope with such limiting conditions, plants have adapted developmental and biochemical strategies to enhance Pi acquisition and to avoid starvation. A myriad of genes that are involved in the regulation and display of these strategies have been identified. However, the possible epigenetic components regulating the phosphate starvation responses have not been thoroughly investigated. DNA methylation is a major epigenetic mark involved in diverse biological processes and it may play a critical role in Pi starvation stress adaptation, also changes in DNA methylation can lead to a unique gene expression pattern in response to specific developmental and environmental conditions. Here in we demonstrate that non-CpG DNA methylation is required for proper expression of a number of Pi-limitation responsive genes in Arabidopsis thaliana and results in altered morphologic and physiologic phosphate starvation responses.Our data suggest that DNA methylation is involved in the modulation of Pi starvation responses via the transcriptional regulation of a set of phosphate-starvation responsive genes. Analysis of 8 different treatments, 2 different Organs (Root and Shoot), 2 different Phosphate treatments (High Pi, Low Pi), 2 different Times (Short Term, Long Term), 2 biological replicates for treatment
2015-12-31 | E-GEOD-72770 | biostudies-arrayexpress
Project description:The plant chloroplast thylakoid membrane must respond to environmental variations in light intensity to maximise the efficiency of photosynthesis and minimise photo-oxidative stress. Plants respond to changing light intensity in the short-term (seconds to minutes) through altered regulation of the structure and function of existing thylakoid components, whereas long-term acclimation (hours to days) involves changes in gene expression, protein synthesis and degradation, which modulate the composition of the thylakoid membrane. Here we have investigated the long-term changes in the thylakoid membrane composition in Arabidopsis thaliana plants acclimated to a controlled laboratory environment to those acclimated to the field using quantitative label-free proteomics in combination with biochemical and structural analyses.
2022-02-17 | PXD027391 | Pride
Project description:How microorganisms resist nutrient-deficiency is important for understanding the pervasive prosperity of microbes in severe nutrient conditions. In laboratory culture, E. coli can survive for a long period of time under starvation, denoted as long-term stationary phase (LSP). Although physiology of those viable cells is of great interest, their genome-wide response has not yet been fully understood. In this study, we employed high-density oligonucleotide array to investigate the transcriptional profile of the cells exposed with supernatant of LSP culture. We compared the expression profiles of LSP to those of exponentially and short-term stationary phase, and revealed that the cellular physiology in the LSP environment is primarily represented by up-regulation of transporter genes and down-regulation of biosynthesis genes, which is similar to those in the short-term stationary phase. Our analysis further detected the differentially expressed functional gene categories between short- and long-term stationary phase, in terms of increasing the expressions of some stress-response genes and repressing the translational genes expressions, suggesting more survival/maintenance weighted metabolism in LSP. We also found the population-density-susceptible expression profiles in the LSP condition, which is also informative to understand the survival mechanism in long-term starvation.
2020-04-24 | GSE149236 | GEO
Project description:How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E. coli to starvation, not on the genetic adaptation of E. coli to utilize alternative nutrients. In our analysis, we have taken advantage of the temporal correlations within and among RNA and protein abundances to identify systematic trends in gene regulation. Specifically, we have developed a general computational strategy for classifying expression-profile time courses into distinct categories in an unbiased manner. We have also developed, from dynamic models of gene expression, a framework to characterize protein degradation patterns based on the observed temporal relationships between mRNA and protein abundances. By comparing and contrasting our transcriptomic and proteomic data, we have identified several broad physiological trends in the E. coli starvation response. Strikingly, mRNAs are widely down-regulated in response to glucose starvation, presumably as a strategy for reducing new protein synthesis. By contrast, protein abundances display more varied responses. The abundances of many proteins involved in energy-intensive processes mirror the corresponding mRNA profiles while proteins involved in nutrient metabolism remain abundant even though their corresponding mRNAs are down-regulated. Time course of E. coli growth and starvation in glucose-limited minimal medium
2015-03-31 | E-GEOD-67402 | biostudies-arrayexpress