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

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

PROVIDER: PRJEB55577 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10113285.fastq.gz	Fastqsanger.gz
	ERR10113286.fastq.gz	Fastqsanger.gz
	ERR10113287.fastq.gz	Fastqsanger.gz

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Cappable-seq of Sinorhizobium meliloti ECF/anti-σ-free free strains 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 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.

2023-01-26 | E-MTAB-12127 | biostudies-arrayexpress

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

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

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

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

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

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

2009-04-21 | E-GEOD-15697 | biostudies-arrayexpress

Overexpression of Sinorhizobium meliloti ECF sigma factors.

Project description:Overexpression of Sinorhizobium meliloti ECF sigma factors.

| PRJNA479836 | ENA

SCO4117 ECF sigma factor pleiotropically controls secondary metabolism and morphogenesis in Streptomyces coelicolor

Project description:Extracytoplasmic function (ECF) sigma factors are a major type of bacterial signal transducer whose biological functions remain poorly characterised in streptomycetes. In this work, we studied SCO4117, a conserved ECF sigma factor from the ECF52 family, a class of ECF sigma factors exclusive to Actinobacteria. We demonstrate that SCO4117 is a pleiotropic activator of secondary metabolism, germination, aerial mycelium differentiation and sporulation. The expression of genes encoding secondary metabolism pathways (deoxysugar synthases, actinorhodin biosynthetic genes), and genes involved in differentiation (bld, whi, rdl, chp, nepA, ssgB, scbR), was dramatically reduced (up to 300-fold) in a SCO4117 knockout strain. SCO4117 expression depends on its position in the chromosome, as the knockout mutant phenotype can only be fully complemented when the SCO4117 ORF is restored in the chromosome. A strain expressing a truncated version of SCO4117 harbouring only the ECF sigma factor domain, has an opposite phenotype to that observed in the knockout strain, consisting of overproduction of antibiotics (actinorhodin, CDA, cryptic antibiotics) and acceleration of differentiation (aerial mycelium differentiation and sporulation), suggesting a complex interaction between the SCO4117 domains that affects protein activity. Some genes from predicted secondary metabolite clusters (cryptic pathways) were up-regulated compared to the wild strain, indicating that this truncated version of the SCO4117 protein might be useful to activate cryptic pathways. Overall, in this work we demonstrate the pleiotropic effects on the regulation of secondary metabolism and differentiation of SCO4117, the first member of the ECF52 family to be characterised. SCO4117 is a conserved gene overexpressed during the substrate and aerial mycelium stages, showing complex regulation at the transcriptional and post-translational levels.

2018-03-07 | GSE107661 | GEO

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