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

Cappable-seq of Sinorhizobium meliloti ECF/anti-σ-free free strains overexpressing heterologous ecf genes compared to an empty vector control strain

ABSTRACT: Bacterial σ factors are dissociable subunits of the core RNA polymerase and important for promoter recognition and transcription initiation. Extracytoplasmic function (ECF) σ factors (σs) represent the most minimalistic and diverse group of alternative σs within the σ70 protein family. It has been shown that heterologous ECF σs hold great potential as context independent regulators in a variety of bacterial species and we implemented a core set of 12 heterologous ECF σs and their cognate promoters in Sinorhizobium meliloti. To analyze if heterologous ECF σs affect transcription from the host genome, we overexpressed the ecf02_2817 gene encoding σE from E. coli and the ecf11_0987 gene from Vibrio parahaemolyticus from ~20 copy number plasmid in RFF625c, a S. meliloti Rm1021 strain deleted for all native ECF/anti-σ genes (Lang et al. 2018, DOI: 10.1128/mSphereDirect.00454-18) . We employed Cappable-Seq to globally determine transcription start sites (TSS) in theses strains and compared it to the TSS profile of an empty vector control strain.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Sinorhizobium meliloti

SUBMITTER: Doreen Meier

PROVIDER: E-MTAB-12127 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNAseq of S. meliloti Rm1021 all ecf/anti-σ deletion mutants overexpressing heterologous ecf genes compared to an empty vector control strain

Project description:Bacterial σ factors are dissociable subunits of the core RNA polymerase and important for promoter recognition and transcription initiation. Extracytoplasmic function (ECF) σ factors (σs) represent the most minimalistic and diverse group of alternative σs within the σ70 protein family. It has been shown that heterologous ECF σs hold great potential as context independent regulators in a variety of bacterial species and we implemented a core set of 12 heterologous ECF σs and their cognate promoters in Sinorhizobium meliloti. To analyze if heterologous ECF σs affect transcription from the host genome, we overexpressed the ecf02_2817 gene encoding σE from E. coli and the ecf11_0987 gene from Vibrio parahaemolyticus from ~20 copy number plasmid in RFF625c, a S. meliloti Rm1021 strain deleted for all native ECF/anti-σ genes (Lang et al. 2018, DOI: 10.1128/mSphereDirect.00454-18) .We compared the RNAseq gene expression profile of these strains to an empty vector control strain.

2023-01-26 | E-MTAB-12126 | biostudies-arrayexpress

Overexpression of Sinorhizobium meliloti ECF sigma factors.

Project description:We characterized transcriptomes for strains overexpressing each of the Sinorhizobium meliloti ECF sigma factors the via a plasmid-borne, melibiose-inducible promoter plasmid (PmelA; pCAP11: Pinedo et al. 2008 J Bacteriol 190:2947-2956) compared to control strains carrying the empty vector.

2018-09-05 | GSE116665 | GEO

Overexpression of Sinorhizobium meliloti ECF sigma factors.

Project description:Overexpression of Sinorhizobium meliloti ECF sigma factors.

| PRJNA479836 | ENA

Regulation of Energy Metabolism by the Extracytoplasmic Function (ECF) σ factors of Arcobacter butzleri

Project description:The extracytoplasmic function (ECF) σ factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. The emerging pathogen Arcobacter butzleri possesses seven putative pairs of σ/anti-σ factors belonging to the ECF family. Here, we report the identification of the genes regulated by five out of the seven A. butzleri ECF σ factors. Three of the ECF σ factors play an apparent role in transport, energy generation and the maintainance of redox balance. Several genes like the nap, sox and tct genes are regulated by more than one ECF σ factor indicating that the A. butzleri ECF σ factors form a network of overlapping regulons. In contrast to other eubacteria, these A. butzleri ECF regulons appear to primarily regulate responses to changing environments in order to meet metabolic needs instead of an obvious role in stress adaptation.

2011-12-31 | GSE34089 | GEO

Most Sinorhizobium meliloti ECF-sigma factors perform accessory functions

Project description:Most Sinorhizobium meliloti ECF-sigma factors perform accessory functions

| PRJNA479859 | ENA

RNAseq of S. meliloti Rm1021 all ecf/anti-σ deletion mutants overexpressing heterologous ecf genes compared to an empty vector control strain

Project description:RNAseq of S. meliloti Rm1021 all ecf/anti-σ deletion mutants overexpressing heterologous ecf genes compared to an empty vector control strain

| PRJEB55576 | ENA

Cappable-seq of Sinorhizobium meliloti ECF/anti-σ-free free strains overexpressing heterologous ecf genes compared to an empty vector control strain

Project description:Cappable-seq of Sinorhizobium meliloti ECF/anti-σ-free free strains overexpressing heterologous ecf genes compared to an empty vector control strain

| PRJEB55577 | ENA

Identification of RpoE2 target genes in Sinorhizobium meliloti

Project description:Sinorhizobium meliloti lives as a soil saprophyte, and engages in a nitrogen fixing symbiosis with plant roots. To succeed in such diverse environments, the bacteria must continually adjust gene expression. Transcriptional plasticity in eubacteria is often mediated by alternative sigma factors interacting with core RNA polymerase. The S. meliloti genome encodes 14 of these alternative sigmas, including 11 extracytoplasmic function (ECF) sigmas. We used custom Affymetrix Symbiosis Chips to characterize the global transcriptional response of S. meliloti overexpressing the ECF sigma factor, RpoE2. Our work identifies over 200 genes whose expression is dependent on RpoE2.

2013-07-22 | GSE40391 | GEO

A novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa

Project description:Next to the two-component and quorum sensing systems, cell-surface signaling (CSS) has been recently identified as an important regulatory system in Pseudomonas aeruginosa. CSS senses signals from outside the cell and transmits them into the cytoplasm. It consists of a TonB-dependent outer membrane receptor, a cytoplasmic membrane-localized sigma factor regulator (or anti-sigma factor), and an extracytoplasmic function (ECF) sigma factor. Upon perception of the extracellular signal by the receptor the ECF sigma factor is activated and promotes the transcription of a specific set of gene(s). Although most P. aeruginosa ECF sigma factors are involved in the regulation of iron uptake, we have identified a novel ECF sigma factor (PA0675) involved in the regulation of virulence. By microarray analysis of cells overexpressing PA0675 from the pMUM3 plasmid we have identified the genes regulated by this sigma factor.

2009-04-21 | GSE15697 | GEO

Expression profiling analyses of ECF sigma factor PG1660 mutant of Porphyromonas gingivalis W83

Project description:To study the expression profile of ECF sigma factor PG1660 mutant under anaerobic conditions and hydrogen peroxide stress conditions compared to the wild-type W83 by using DNA-microarray. The role of ECF sigma factor PG1660 involved in oxidative stress was published Yuetan Dou, Devon Osbourne, Rachelle McKenzie, Hansel M Fletcher. (2010) Involvement of extracytoplasmic function sigma factors in virulence regulation in Porphyromonas gingivalis W83. FEMS Microbiology Letter, 312(1):24-32.

2017-09-14 | GSE103838 | 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