Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The genome-scale DNA-binding profile of BarR

ABSTRACT: The Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp-like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a -alanine aminotransferase gene, which is involved in -alanine degradation. In contrast to classical Lrp-like transcription factors, BarR is not responsive to any of the -amino acids but interacts specifically with -alanine. Besides the juxtaposed -alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although -alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome-wide perspective.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Sulfolobus acidocaldarius DSM 639

SUBMITTER: kun wang

PROVIDER: E-MTAB-4615 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The genome-scale DNA-binding of FadR transcription factor in Sulfolobus acidocaldarius

Project description:This is ChIPseq result of FadR, which is the only TetR family regulator presented in Sulfolobus acidocaldarius. The aim of the study is to gain insights into the function of TetR regulator by analyzing its whole genome binding sites.

2017-12-30 | E-MTAB-6328 | biostudies-arrayexpress

Transcription profiling of hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius to UV irradiation

Project description:Analysis of transcriptional response to UV irradiation in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius.

2007-11-21 | E-MEXP-1252 | biostudies-arrayexpress

The genome-scale DNA-binding of FadR transcription factor in Sulfolobus acidocaldarius

Project description:This is ChIPseq result of FadR (Saci_1107), which is the only TetR family regulator presented in Sulfolobus acidocaldarius. The aim of the study is to gain insights into the function of TetR regulator by analyzing its whole genome binding sites.

2017-12-14 | GSE108039 | GEO

Transcriptome analysis of Sulfolobus acidocaldarius DSM 639 under sugar-free and sugar-rich conditions

Project description:Sulfolobus acidocaldarius is an obligate aerobe that grows in hot and acidic environments. S. acidocaldarius have been reported to grow on a variety of organic compounds as carbon and energy sources. However, little is known about systemic elucidation of carbon utilization for biomass formation and energy metabolism in S. acidocaldarius. In this analysis, the effect of glucose on genome-wide transcriptional profiling in S. acidocaldarius DSM 639 was investigated by RNA-Seq technology.

2020-11-15 | GSE107083 | GEO

Genome-wide interaction map of YtrA transcription factor in S. Acidocaldarius

Project description:We report the characterization of GntR-like regulator in the Archaeon Sulfolobus acidocaldarius by looking at the genome wide interaction map of the protein in vivo

2019-09-26 | GSE129461 | GEO

MPLEx_Sulfolobus_acidocaldarius

Project description:Datasets of Sulfolobus acidocaldarius samples used to test the MPLEx method.

2015-12-03 | MSV000079410 | MassIVE

Cellular stress response of Sulfolobus acidocaldarius to nutrient limitation

Project description:This study provides novel insights into archaeal stress response. The effect of nutrient limitation on the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius was monitored over time on transcriptomic, proteomic and metabolic level. To our knowledge, this linkage of transcriptome, proteome, metabolome analysis makes this study a pioneer study to elucidate cellular stress response triggered by nutrient limitation. We further connect previously identified pH and salt stress responsive genes (1) with genes regulated in starvation and suggest that they constitute the core of stress responsive genes active under multiple stress sources.

2018-12-21 | GSE113716 | GEO

Next generation sequencing to identify differentially expressed genes in the YtrASa overexpression strain

Project description:We report the regulon of a GntR-like regulator from the archaeon Sulfolobus acidocaldarius by looking at differentially expressed genes comparing a YtrASa overexpression strain with its isogenic wild ype

2019-09-26 | GSE129463 | GEO

Transcription profiling of synchronized Sulfolobus acidocaldarius populations as they progress through the cell cycle

Project description:Exponentially growing Sulfolobus acidocaldarius were treated with NaAc to generate replication runout and arrest in G2 phase. The cells were then resuspended in fresh acetate-free media which generates a synchronous population. Samples for investigation of gene expression change were taken during the synchronised populations progress through the cell cycle.

2007-12-08 | E-MEXP-936 | biostudies-arrayexpress

High throughput analysis of binding of E. coli Lrp mutants

Project description:Feast-Famine Response Proteins are a widely conserved class of global regulators in prokaryotes, the most highly studied of which is the E. coli leucine-responsive regulatory protein (Lrp). Lrp senses environmental nutrition status and subsequently regulates up to one-third of the genes in E. coli, either directly or indirectly. Lrp exists predominantly as octamers and hexadecamers (16mers), where leucine is believed to shift the equilibrium towards the octameric state. In this study, we analyzed the effects of three oligomerization state mutants of Lrp in terms of their ability to bind to DNA and regulate gene expression in response to exogenous leucine. We find that oligomerization beyond dimers is required for Lrp’s regulatory activity, and that contrary to prior speculation, exogenous leucine modulates Lrp activity at its target promoters exclusively by inhibiting Lrp binding to DNA. We also find evidence that Lrp binding bridges DNA over length scales of multiple kilobases, revealing a new range of mechanisms for Lrp-mediated transcriptional regulation.

2023-01-31 | GSE198120 | GEO

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