Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nitrogen stress response and stringent response are coupled in Escherichia coli

ABSTRACT: Assimilation of nitrogen is an essential process in bacteria. The nitrogen regulation stress response is an adaptive mechanism used by nitrogen-starved Escherichia coli to scavenge for alternative nitrogen sources and requires the global transcriptional regulator NtrC.

INSTRUMENT(S): Agilent G2505C scanner

ORGANISM(S): Escherichia coli K-12

SUBMITTER: Daniel Brown

PROVIDER: E-MTAB-2612 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Nitrogen regulatory protein C couples nitrogen stress response and stringent response in nitrogen starved Escherichia coli.

Project description:We show that NtrC couples the Ntr stress response and stringent response in N starved E. coli, which appears to be a conserved adaptive strategy employed by many bacteria to manage conditions of nutritional adversity. N starved Escherichia coli initiate the nitrogen regulation (Ntr) stress response as an adaptive mechanism to scavenge for alternative N sources. The Ntr stress response requires the global transcriptional regulator nitrogen regulatory protein C (NtrC). We discovered that the transcription of relA, the key gene responsible for the synthesis of the major effector nucleotide alamorne of the bacterial stringent response, guanosine pentaphosphate (ppGpp), is positively regulated by NtrC in N starved E. coli. we addressed Ntr stress response-ppGpp alarmone links and mapped the genome-wide binding targets of NtrC in E. coli during N starvation using chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) to gain insight into the NtrC-dependent gene networks. To identify candidate genome regions that are preferentially associated with NtrC, we introduced an in-frame fusion encoding three repeats of the FLAG epitope to the 3-prime end of glnG in E. coli strain NCM3722, a prototrophic E. coli K-12 strain.

2014-05-01 | E-MTAB-2211 | 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

Whole-cell differential proteomics analysis of MG1655 Escherichia coli (Wild-type and mutants lacking the small regulatory RNA SdsR, OxyS or ZbiJ, or the RNA Chaperone Hfq) experiencing long-term nitrogen starvation in Gutnick minimal media.

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

Genome wide analysis of the GlnR regulon in Mycobacterium smegmatis

Project description:M. smegmatis wild type and glnR deletion strains grown in nitrogen limiting conditions (1 mM ammonium sulphate nitrogen source). Samples taken 1 hour after nitrogen depletion from the media for each strain.

2013-06-12 | E-MTAB-1456 | biostudies-arrayexpress

RNA-Seq of BW25113 Escherichia coli (wild-type and a mutant lacking yeaG) experiencing initial and sustained nitrogen starvation in Gutnick minimal media

Project description:RNA-seq was carried out to compare the transcriptomes of wild-type BW25133 E coli with a mutant lacking the conserved serine/threonine kinase, YeaG, with the aim of understanding how YeaG contributes to the transcriptional response to sustained nitrogen starvation, and identify pathways affected by YeaG. We also compare the wild-type transcriptome during nitrogen-replete, following nitrogen starvation, and under 24 h of sustained nitrogen starvation to identify pathways involved in the response to nitrogen run out, and also in adaptation to sustained nitrogen starvation.

2018-06-04 | E-MTAB-6481 | 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

Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress

Project description:The aim of this study was to extend our analysis to the obligate human pathogen M. tuberculosis, which has to deal with a more restricted set of environmental variables in terms of nitrogen sources, and to delineate the GlnR regulon, by peforming global analysis of GlnR-DNA interactions by Chromatin Immunoprecipitation and high-throughput sequencing (ChIP-seq) over nitrogen run-out.

2014-12-01 | E-MTAB-2492 | biostudies-arrayexpress

Transcription profiling of Herbaspirillum seropedicae SmR1 wild-type against its ntrC mutant under different nitrogen conditions

Project description:H. seropedicae wild-type or ntrC mutant were grown on three different nitrogen conditions: nitrogen limiting, ammonium shock and nitrate shock.

2024-07-02 | E-MTAB-8238 | biostudies-arrayexpress

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

RIL-seq analysis of MG1655 Escherichia coli experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA interaction by ligation and sequencing (RIL-seq) was carried out to compare the Hfq-RNA-RNA interactome of MG1655 E coli bacteria that grown in Gutnick minimal media. Wild-type and hfq::3xFLAG tagged K12 E.coli were grown in Gutnick minimal media with 3mM NH4Cl as the sole nitrogen source, and cell samples were taken during exponential growth (N+), ~20min following N-runout and induction of growth arrest (N-), 24hr following N-runout and induction of growth arrest (N-24) and 2hr following addition of NH4Cl to N-24 cells (N-24+2). All sampling was performed in triplicate for each strain and condition

2023-12-01 | E-MTAB-13403 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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