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Identification of RpoE2 target genes in Sinorhizobium meliloti

ABSTRACT: 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.

ORGANISM(S): Medicago truncatula Sinorhizobium meliloti

PROVIDER: GSE40391 | GEO | 2013/07/22

SECONDARY ACCESSION(S): PRJNA173849

REPOSITORIES: GEO

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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. The gene expression profile of Sinorhizobium meliloti strain CL150 carrying the rpoE2 gene on a plasmid, where it was expressed from a melibiose-inducible promoter (the S. meliloti PmelA promoter), was compared to the gene expression profile of CL150 carrying the corresponding empty vector (pCAP11). CL150 is an Rm1021 strain that has been corrected for two point mutations: it is wild type for ecfR1 and pstC.

2013-07-22 | E-GEOD-40391 | biostudies-arrayexpress

Dual RpoH sigma factors in Sinorhizobium meliloti

Project description:Sinorhizobium meliloti can live as a soil saprophyte, and can engage 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 two putative RpoH (heat shock) sigmas. We used custom Affymetrix Symbiosis Chips to characterize the global transcriptional response of S. meliloti rpoH1, rpoH2 and rpoH1 rpoH2 mutants during heat shock and stationary phase growth. Under these conditions, expression of over 300 genes is dependent on rpoH1 and rpoH2.

2012-10-02 | GSE36186 | GEO

Dual RpoH sigma factors in Sinorhizobium meliloti

2012-10-02 | E-GEOD-36186 | biostudies-arrayexpress

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

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

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

Identifying the regulon of the Sinorhizobium meliloti JspA protease

Project description:Sinorhizobium meliloti establishes symbiotic relationship with compatible leguminous plants by inducing root nodule formation, colonizing such nodules, and fixing molecular nitrogen for the host in exchange for carbon compounds. This mutualistic process requires complex communication and tight regulation to allow yet constrain infection to specific tissues. Production of succinoglycan, or exopolysaccharide-I (EPS-I), enables S. meliloti to invade the root cortex via infection threads. A previous genetic screen identified jspA (SMc03872), encoding an extracytoplasmic protease, as a regulator of EPS-I production. To elucidate its molecular role, we performed transcriptome analyses of strains overexpressing wild-type or mutant alleles of jspA. We observed changes in gene expression suggesting that JspA contributes to symbiosis efficiency by modulating the critical ExoR-ExoS-ChvI signaling pathway.

2023-05-10 | GSE155833 | GEO

Overexpression of Sinorhizobium meliloti ECF sigma factors.

Project description:Overexpression of Sinorhizobium meliloti ECF sigma factors.

| PRJNA479836 | ENA

The temperature-regulation of Pseudomonas aeruginosa cmaX-cfrX-cmpX operon reveals an intriguing molecular network involving the sigma factors AlgU and SigX

Project description:Pseudomonas aeruginosa is a highly adaptable Gram-negative opportunistic pathogen, notablydue to its large number of transcription regulators. The extracytoplasmic sigma factor (ECF sigma AlgU, responsible for alginate biosynthesis, is also involved in responses to cell wall stress and heat shock via the RpoH alternative sigma factor. The SigX ECF sigma emerged as a major regulator involved in the envelope stress response via membrane remodelling, virulence and biofilm formation. However, their functional interactions to coordinate the envelope homeostasis in response to environmental variations remain to be determined. The regulation of the putative cmaX-cfrX-cmpX operon located directly upstream sigX was investigated by applying sudden temperature shifts from 37°C. We identified a SigX- and an AlgU- dependent promoter region upstream of cfrX and cmaX, respectively. We show that cmaX expression is increased upon heat shock through an AlgU-dependent but RpoH independent mechanism. In addition, the ECF sigma SigX is activated in response to valinomycin, an agent altering the membrane structure, and up-regulates cfrX-cmpX transcription in response to cold shock. Altogether, these data provide new insights into the regulation exerted by SigX and networks that are involved in maintaining envelope homeostasis.

2020-10-05 | PXD021299 | Pride

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