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Streptomyces griseus transcriptome analysis in delta sigD, encoding an ECF-sigma factor

ABSTRACT: To identify genes regulated by SigD, transcriptome profiles between wild type strain and sigD mutant with pI486-sigD, in which sigD level is low compared to wild type strain, were analyzed.

ORGANISM(S): Streptomyces griseus

PROVIDER: GSE27426 | GEO | 2011/02/23

SECONDARY ACCESSION(S): PRJNA137231

REPOSITORIES: GEO

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Streptomyces griseus transcriptome analysis in delta sigD, encoding an ECF-sigma factor

Project description:To identify genes regulated by SigD, transcriptome profiles between wild type strain and sigD mutant with pI486-sigD, in which sigD level is low compared to wild type strain, were analyzed. Analysis used wild type strain steady state RNA as control samples for comparison to the sigD mutant.

2011-02-23 | E-GEOD-27426 | biostudies-arrayexpress

Monitoring global differential gene expression in Corynebacterium glutamicum in response to sigma factor SigD disruption and overexpression

Project description:In this study, disruption and overexpression of sigD were performed in Corynebacterium glutamicum and analyzed by transcriptome sequencing (RNA-seq) to understand the SigD regulon in C. glutamicum. For the effect of sigD overexpression, the relative abundance of mRNA was compared in WT(pVWEx1-sigD) without IPTG or with 50 M of IPTG. For the effect of sigD disruption, the abundance was compared between the sigD disrupted mutant and the wild type strain.

2017-01-27 | E-MTAB-5411 | biostudies-arrayexpress

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

Comparison of the expression profiles of 630E strain and a sigD mutant after 6h of growth.

Project description:Transcriptionnal profiling of C. difficile 630E strain vs a sigD mutant after 6h of growth in BHI

2013-08-31 | GSE29275 | GEO

Comparison of the expression profiles of 630E strain and a sigD mutant after 6h of growth.

Project description:Transcriptionnal profiling of C. difficile 630E strain vs a sigD mutant after 6h of growth in BHI Two-conditions experiments, 630E strain 6h vs sigD mutant 6h, 4 biological replicates for each condition

2013-08-31 | E-GEOD-29275 | biostudies-arrayexpress

Streptomyces griseus

Project description:Streptomyces griseus transcriptome analysis in delta sigD, encoding an ECF-sigma factor

| PRJNA137231 | ENA

Roles of close homologues SigB and SigD in heat and bright light acclimation of the cyanobacterium Synechocystis sp. PCC 6803

Project description:Acclimation of cyanobacterium Synechocystis sp. PCC6803 to suboptimal conditions is largely dependent on adjustments of gene expression, which is highly controlled by the σ factor subunits of RNA polymerase (RNAP). The SigB and SigD σ factors are close homologues. Here we show that sigB and sigD genes are both induced in bright light and high temperature stresses. Comparison of transcriptomes of the control strain (CS), ΔsigB, ΔsigD, ΔsigBCE (SigD is an only functional group 2 σ factor), and ΔsigCDE (SigD is an only functional group 2 σ factor) strains in standard, bright light and high temperature conditions revealed that the SigB and SigD factors regulate different set of genes, and that SigB and SigD regulons are highly dependent on stress conditions. The SigB regulon is bigger than the SigD regulon at high temperature, whereas in bright light the SigD regulon is bigger the SigB regulon. Furthermore, our results show that favoring the SigB or SigD factor by deleting other group 2 σ factors do not lead to superior acclimation to bright light or high temperature conditions, indicating that all group 2 σ factors play roles in acclimation processes.

2022-01-19 | GSE192357 | GEO

The SCO4117 ECF Sigma Factor Pleiotropically Controls Secondary Metabolism and Morphogenesis in Streptomyces coelicolor.

Project description: Not available

| S-EPMC5826349 | biostudies-literature

An A-factor-dependent extracytoplasmic function sigma factor (sigma(AdsA)) that is essential for morphological development in Streptomyces griseus.

Project description: Not available

| S-EPMC94632 | biostudies-literature

Reactive oxygen species-inducible ECF σ factor involved in singlet-oxygen responsiveness of Bradyrhizobium japonicum

Project description:Expression data from B. japonicum strains 110spc4 (wild type), 0202 (Dbll1028), 9688 (Dblr3038-39) grown micro-oxically unstressed or stressed with 2 mM H2O2 for 10 min and strain 9692 (Dblr3039) grown micro-oxically

2012-08-24 | GSE39165 | GEO

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