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GenomicsSvenBldMWhiIChIPSeq
To determine the influence of BldM and WhiI on the binding of each other to their respective binding sites in the genome of Streptomyces venezuelae, ChIP-Seq experiments were carried out using polyclonal antibodies against the wild type proteins as well as anti-FLAG antibodies against FLAG-tagged pr...
ORGANISM(S): Streptomyces venezuelae 
2015-05-19 | E-MTAB-2698 | biostudies-arrayexpress
GenomicsRole of Fnr1 and Fnr3 in transcriptional regulation under oxygen limitation in Herbaspirillum seropedicae
To determine the direct promoter targets of Fnr proteins, we correlated transcriptional changes observed in single fnr1 and fnr3 mutants (E-MTAB-5741) with ChIP-Seq analysis, taking advantage of C-terminally 3xFlag fnr alleles engineered into the H. seropedicae genome. ChIP-seq data were obtained fr...
ORGANISM(S): Herbaspirillum seropedicae 
2018-02-26 | E-MTAB-6395 | biostudies-arrayexpress
TranscriptomicsMutation of the cysteine residues that coordinate the WhiB [4Fe-4S] cluster prevents in vivo DNA binding by both WhiB and WhiA
The purpose of this experiment was to show that the iron-sulphur cluster ([4Fe-4S]) of whiB is essential for the DNA binding by WhiB and WhiA. The \\"serine version of whiB\\" mentioned below is a whiB in which the 4 cysteine residues which coordinate the [4Fe-4S] cluster were mutated to serines. Ch...
ORGANISM(S): Streptomyces venezuelae 
2021-08-16 | E-MTAB-10818 | biostudies-arrayexpress
TranscriptomicsTranscriptional profiling of the developmental gene whiB deletion mutant of Streptomyces venezuelae ATCC 10712 at 7 time points from 8 to 20 hours of growth
WhiB is the founding member of a family of proteins (the WhiB-like [Wbl] family) that carry a [4Fe-4S] iron-sulfur cluster and play key roles in diverse aspects of the biology of actinomycetes, including pathogenesis, antibiotic resistance, and the control of development. In Streptomyces, WhiB is es...
ORGANISM(S): Streptomyces venezuelae 
2021-06-30 | E-MTAB-10631 | biostudies-arrayexpress
TranscriptomicsWhiA and WhiB of Streptomyces venezuelae depend on each other for binding DNA
WhiB regulon, as determined by ChIP-Seq turned out to be identical to the WhiA regulon leading to the speculation that the two proteins might be required to work together to bind DNA. In this experiment WhiA ChIP-Seq was done in a whiB deletion background and, WhiB ChIP-Seq was done in a whiA deleti...
ORGANISM(S): Streptomyces venezuelae 
2021-07-01 | E-MTAB-10673 | biostudies-arrayexpress
TranscriptomicsChIP-Seq to determine the binding sites of the transcription factor WhiB in the genome of Streptomyces venezuelae
WhiB is the founding member of a family of proteins (the WhiB-like [Wbl] family) that carry a [4Fe-4S] iron-sulfur cluster. It is essential for the process of developmentally controlled cell division leading to sporulation in Streptomyces species. This ChIP-Sea was carried out to determine unambiguo...
ORGANISM(S): Streptomyces venezuelae 
2021-06-25 | E-MTAB-10648 | biostudies-arrayexpress
GenomicsGenes required for aerial growth, cell division, and chromosome segregation are targets of WhiA before sporulation in Streptomyces venezuelae.
WhiA is a highly unusual transcriptional regulator related to a family of eukaryotic homing endonucleases. WhiA is required for sporulation in the filamentous bacterium Streptomyces, but WhiA homologues of unknown function are also found throughout the Gram-positive bacteria. To better understand th...
ORGANISM(S): Streptomyces venezuelae 
2016-05-20 | E-MTAB-4673 | biostudies-arrayexpress
GenomicsIdentification by ChIP-Seq of the binding sites of the extracytoplasmic function (ECF) sigma factor SigE in the genome of Streptomyces coelicolor A3(2) M600.
SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. This ChIP-Seq experiment was carried out to determine the binding sites of SigE under conditions of cell envelope stress induced by 10 ug / ml vancomycin for 30...
ORGANISM(S): Streptomyces coelicolor A3(2) 
2019-04-24 | E-MTAB-7827 | biostudies-arrayexpress
GenomicsRole of RccR in the transcriptional control of primary carbon metabolism in Pseudomonas
To characterise the RccR regulon, we performed a ChIP-seq assay using a polyclonal RccR antiserum on SBW25 WT/rccR strains grown in minimal pyruvate and glycerol media. We were able to identify 8 RccR binding sites from this experiment including one in the rccR promoter region itself. The peaks iden...
ORGANISM(S): Pseudomonas fluorescens 
2017-08-24 | E-MTAB-5745 | biostudies-arrayexpress
TranscriptomicsTranscriptional profiling of the sigma factor sigE deletion mutant of Streptomyces coelicolor (J2130) at 0, 30, 60 and 90 minutes after treatment with sub-lethal concentration of vancomycin.
SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. To determine the regulon of SigE under conditions of cell envelope stress, 10 ug / ml vancomycin was used to induce cell envelope stress in the wild type and a s...
ORGANISM(S): Streptomyces coelicolor A3(2) 
2019-04-24 | E-MTAB-7814 | biostudies-arrayexpress
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