Browse
Submit Data
Databases
API
Help

Dataset Information

264 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AG3C glucose starvation time course

ABSTRACT: 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.

OTHER RELATED OMICS DATASETS IN: PRJNA279834

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Escherichia Coli

SUBMITTER: John Houser

LAB HEAD: Claus O. Wilke

PROVIDER: PXD002140 | Pride | 2015-08-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.

Houser John R JR Barnhart Craig C Boutz Daniel R DR Carroll Sean M SM Dasgupta Aurko A Michener Joshua K JK Needham Brittany D BD Papoulas Ophelia O Sridhara Viswanadham V Sydykova Dariya K DK Marx Christopher J CJ Trent M Stephen MS Barrick Jeffrey E JE Marcotte Edward M EM Wilke Claus O CO

PLoS computational biology 20150814 8

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 in stationary phase as a result of being starved for glucose, not on t ...[more]

PMID: 26275208

Similar Datasets

RNA-seq data of E. coli MG1655 WT and hfq knockout strains during short and long-term nitrogen starvation.

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

RNA-seq analysis of MG1655 Escherichia coli (Wild-type and mutant lacking the small regulatory RNA SdsR) experiencing long-term nitrogen starvation in Gutnick minimal media

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

RNA-seq analysis of MG1655 Escherichia coli (Wild-type and mutant lacking the RNA chaperone Hfq) experiencing long-term nitrogen starvation in Gutnick minimal media

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

Response and adaptation to growth with low glucose concentration

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

2006-04-26 | GSE4706 | GEO

RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)

Project description:In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like glucose or ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs. Previously, we characterized short- and long-term strategies of cells to adapt to glucose fluctuations. Here, we focused on fluctuating ammonia supply, while studying a continuously running two-compartment bioreactor system comprising a stirred tank reactor (STR) and a plug flow reactor (PFR). Genes were repeatedly switched on/off when E. coli returned to the STR. Moreover, E. coli revealed highly diverging long-term transcriptional responses in ammonia compared to glucose fluctuations. The identification of target genes may help to create robust cells and processes for large-scale application.

2017-03-27 | GSE90743 | GEO

RNA-seq of E18.5, C57BL6 mouse retinal cells treated with glucose starvation compared with untreated controls

Project description:The experiment was performed to investigate the effects of short-term glucose starvation on the transcriptome of embryonic retinal cells. Perinatal exposure to starvation is a risk factor for development of severe retinopathy in adult patients with diabetes. Underlying molecular mechanisms were investigated via this experimental design by looking into transcriptomic changes.

2022-06-26 | E-MTAB-10705 | biostudies-arrayexpress

Expression data from Caulobacter crescentus starved for carbon

Project description:Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of C. crescentus to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis. Glucose, the only carbon source in the minimal media M2G was removed from C. crescentus exponential phase cultures, and total RNA was extracted after 30 and 60 minutes of incubation. The controls are cells growing in complete media.

2011-04-20 | E-GEOD-25996 | biostudies-arrayexpress

Expression data from Caulobacter crescentus (syn. C. vibrioides) swarmer and stalked cells starved for carbon

Project description:Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of specific developmental stages of C. crescentus -swarmer and stalked cells- to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis. Glucose, the only carbon source in the minimal media M2G was removed from C. crescentus exponential phase cultures, and total RNA was extracted after 30 and 60 minutes of incubation. The controls are cells growing in complete media.

2011-04-20 | E-GEOD-25997 | biostudies-arrayexpress

Transcriptome profiles in E. coli under a prolonged starvation environment

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

Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data