Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome reorganization of gene-rewired Escherichia coli cells in response to histidine depletion

ABSTRACT: An assortment of genetically engineered Escherichia coli strains of the rewired gene regulation were used to study whether the cells could adapt to the environmental changes without the evolved gene regulatory machinaries. These E. coli strains had a synthetic gene circuit comprising a rewried gene that natively located within the His opeon. The cells growing under histidine supplied or depleted conditions were subjected to the macrioarray analysis. Multilevel analyses were performed to evaluate the global reorganization of gene expression in response to histidine depletion. A common pattern in transcriptome was observed in the adpative cells, indicating a survival strategy of "stochastic adaptation with regular transcriptome reorganization".

ORGANISM(S): Escherichia coli

PROVIDER: GSE55719 | GEO | 2015/01/12

SECONDARY ACCESSION(S): PRJNA240778

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome reorganization of gene-rewired Escherichia coli cells in response to histidine depletion

Project description:An assortment of genetically engineered Escherichia coli strains of the rewired gene regulation were used to study whether the cells could adapt to the environmental changes without the evolved gene regulatory machinaries. These E. coli strains had a synthetic gene circuit comprising a rewried gene that natively located within the His opeon. The cells growing under histidine supplied or depleted conditions were subjected to the macrioarray analysis. Multilevel analyses were performed to evaluate the global reorganization of gene expression in response to histidine depletion. A common pattern in transcriptome was observed in the adpative cells, indicating a survival strategy of "stochastic adaptation with regular transcriptome reorganization". The genetically engineered strains of rewired genes and the control strain of the native gene regulation were grown in the presence and absence of histidine, and the cells within the exponetially growing phase were collected for the microarray analysis. Temproal changes in response to histidine depletion were also investigated. Every 3 biological replications for each condition were performed. Total 90 array assays were reported here.

2015-01-12 | E-GEOD-55719 | biostudies-arrayexpress

Widespread protein histidine phosphorylation in bacteria

Project description:For decades, extreme difficulties in analyzing histidine phosphorylation have limited the study of phosphohistidine signaling. Here we report a method revealing widespread and abundant protein histidine phosphorylation in E. coli. Our new approach generated the largest E. coli phosphoproteome dataset to date, of which a remarkable high percentage (~10%) are phosphohistidine sites. This resource enables a major step forward towards a better understanding of the biological function of histidine phosphorylation.

2017-12-07 | PXD008369 | JPOST Repository

Expression of the genetically engineered E. coli in response to histidine starvation

Project description:Stochastic switching of a monostable circuit mediated the adaptation of the engineered OSU12-hisC Escherichia coli strain to histidine starvation. In this strain, the hisC gene was deleted from the His operon and placed under the control of a monostable foreign promoter. In response to histidine depletion, the OSU12-hisC population shifted to a higher HisC expression level, which are beneficial under starving conditions but are not favoured by the monostable circuit. Microarray analysis indicated that OSU12-hisC reorganised its transcriptome to reach the appropriate physiological state upon starvation. The study suggests that bacteria do not necessarily need to evolve signalling mechanisms to control gene expression appropriately, even for essential genes.

2011-03-29 | GSE28210 | GEO

RNA-seq of Clostridium acetobutylicum ATCC 55025, histidine kinase Cac3319 and Cac0437 inactivated strains.

Project description:The goal of this experiment is compare gene expression profiles between C. acetobutylicum ATCC 55025, histidine kinase cac3319 and cac0437 inactivated strains to determine the pleiotropic and distinctive functions of histidine kinases on cell differentiation and cellular metabolism. Samples for total RNA extraction were collected from fermentation broth at acidogenic phase (8 h) and solventogenic phase (16 h)

2019-05-01 | E-MTAB-7341 | biostudies-arrayexpress

WGS histidine overproducers

Project description:Whole genomes sequencing to determine mutations in histidine overproducers generated with a toxic histidine analog

| PRJEB45772 | ENA

Studying the effects of endogenous and exogenous histidine supplementation on Pichia pastoris cultured in YPA

Project description:A histidine prototrophic strain achieves A600 three-four fold higher than a histidine auxotroph when cultured in nutrient rich media YPA, which is abundant in amino acids. This retaded growth of histidine auxotroph in YPA can also be rescued by supplementing media with exogenous histidine. Here, we aim to study the transcriptomic changes associated with culturing of histidine auxotroph and prototroph in YPA and also the effects of histidine addition to the culture medium of histidine auxotroph.

2022-04-06 | GSE174633 | GEO

HUVEC Gene Regulation by Histidine-Rich Glycoprotein

Project description:HRG is a 75kDa heparin-binding protein non to extert gene regultaion changes on macropahges. To assess the effect of HRG on Enodothelial Cell gene regulation Human Umbilical Vein Endothelial Cells (HUVECs) were treated with Histidine-Rich Glycoprotein (HRG) 24 hour treatment with HRG. and examined for gene regulation changes versus untreated HUVECs after 6 and

2015-03-12 | GSE66768 | GEO

Escherichia coli

Project description:Transcriptome reorganization of gene-rewired Escherichia coli cells in response to histidine depletion

| PRJNA240778 | ENA

Histidine-dependent protein methylation is required for compartmentalization of CTP synthase

Project description:CTP synthase (CTPS) forms compartmentalized filaments in response to substrate availability and environmental nutrient status. However, the physiological role of filaments and mechanisms for filament assembly are not well understood. Here, we provide evidence that CTPS forms filaments in response to histidine influx during glutamine starvation. CTPS protein levels remained stable in the presence of histidine during nutrient deprivation, followed by rapid cell growth following nutrient replenishment. Tetramer conformation-based filament formation restricted CTPS enzyme activity duringnutrient deprivation. Furthermore, we demonstrated that filament formation controlled at two levels. Starvation stress/glutamine deficiency activates the GCN2/ATF4/MTHFD2 axis to accelerate the folate cycle in mitochondria for energy homeostasis. In addition, histidine promotes re-methylation of homocysteine by donating one-carbon to the cytosolic folate cycle. CTPS filament formation induced by histidine-mediated methylation maybe a strategy usedby cancer cells to maintain homeostasis and ensure a growth advantage in adverse environments.

2018-08-29 | GSE105251 | GEO

Regulation of sialidase production in clostridium perfringens by the orphan sensor histidine kinase ReeS

Project description:ReeS, previously named as CPE1512, was originally annotated as the only hybrid sensor histidine kinase/response regulator in Clostridium perfringens. Further evidence suggests that ReeS is more likely to function as an orphan sensor histidine kinase. A reeS deletion mutant was constructed and the transcriptome analysed using microarrays.

2013-08-31 | GSE36786 | GEO

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