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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional profiling of the developmental gene whiB deletion mutant of Streptomyces venezuelae ATCC 10712 at 7 time points from 8 to 20 hours of growth

ABSTRACT: 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 essential for the process of developmentally controlled cell division that leads to sporulation. The aim of this transcription profiling experiment was to measure genome wide transcript levels in the wild type and the whiB deletion mutant at 7 time points from 8 to 20 hours during the growth cycle of Streptomyces venezuelae.

ORGANISM(S): Streptomyces venezuelae

SUBMITTER: Mark Buttner

PROVIDER: E-MTAB-10631 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis Shows that WhiB Is a Transcription Factor That Cocontrols Its Regulon with WhiA To Initiate Developmental Cell Division in Streptomyces.

Bush Matthew J MJ Chandra Govind G Bibb Maureen J MJ Findlay Kim C KC Buttner Mark J MJ

mBio 20160419 2

<h4>Unlabelled</h4>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 essential for the process of developmentally controlled cell division that leads to sporulation. The biochemical function of Wbl proteins has been controversial; here, we set out to d ...[more]

PMID: 27094333

Similar Datasets

Transcriptional profiling of the developmental gene whiA deletion mutant of Streptomyces venezuelae ATCC 10712 at 7 time points from 8 to 20 hours of growth.

Project description:WhiA is an unusual transcriptional regulator found in Streptomyces species related to eukaryotic homing endonucleases. It plays a central role in sporulation in these bacteria. The aim of this transcription profiling experiment was to measure genome wide transcript levels in the wild type and the whiA deletion mutant at 7 time points from 8 to 20 hours during the growth cycle of Streptomyces venezuelae.

2020-12-11 | E-MTAB-9728 | biostudies-arrayexpress

Transcriptional profiling of the developmental gene whiG deletion mutant of Streptomyces venezuelae ATCC 10712 at 7 time points from 8 to 20 hours of growth.

Project description:WhiG is a sigma factor found in Streptomyces species. It has a central role in sporulation in these bacteria. Although mutants in whiG are able to form aerial mycelia, these fail to differentiate into spores. The aim of this transcription profiling experiment was to measure genome wide transcript levels in the wild type and the whiG deletion mutant at 7 time points from 8 to 20 hours during the growth cycle of Streptomyces venezuelae.

2019-07-12 | E-MTAB-8114 | biostudies-arrayexpress

ChIP-Seq to determine the binding sites of the transcription factor WhiB in the genome of Streptomyces venezuelae

Project description: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 unambiguously if WhiB functions as a transcription factor in Streptomyces venezuelae and also to determine its regulon.

2021-06-25 | E-MTAB-10648 | biostudies-arrayexpress

Mutation of the cysteine residues that coordinate the WhiB [4Fe-4S] cluster prevents in vivo DNA binding by both WhiB and WhiA

Project description: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. ChIP-Seq using anti-FLAG anitbodies was performed in the following: 1. A whiB deletion strain expressing the FLAG-tagged serine version of WhiB (WhiBFLAG-Ser). 2. A whiB and whiA deletion strain expressing the FLAG-tagged serine version of WhiB (delAB_WhiBFLAG-Ser). 3. A whiB and whiA deletion strain expressing the serine version of WhiB and FLAG-tagged whiA (delAB_WhiAFLAG_WhiBcomp-Ser).

2021-08-16 | E-MTAB-10818 | biostudies-arrayexpress

WhiA and WhiB of Streptomyces venezuelae depend on each other for binding DNA

Project description: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 deletion background to show that the two proteins do indeed fail to bind DNA in the absence of one another.

2021-07-01 | E-MTAB-10673 | biostudies-arrayexpress

ChIP-Seq of the Streptomyces venezuelae regulator BldD and its D116A mutant.

Project description:The dimerization and binding of DNA by BldD is affected by its interaction with cyclic di-GMP. The D116A mutant of BldD is partially impaired in its biding of cyclic di-GMP. ChIP-Seq was carried out to determine the difference in the degree of DNA binding by the wild type and D116A mutated BldD in Streptomyces venezuelae.

2017-11-01 | E-MTAB-5328 | biostudies-arrayexpress

Determine whether Streptomyces venezuelae protein SepH (vnz_27360) binds DNA and where

Project description:SepH was identified having a potential role in sporulation following ChIP-seq analysis that showed the sepH gene is under the control of the WhiA and WhiB transcription factors (Bush et al., 2013; Bush et al., 2016). Since SepH has a helix-turn-helix motif, this ChIP-Seq experiment was carried out to determine whether SepH specifically binds DNA and if so, where.

2020-09-30 | E-MTAB-9064 | biostudies-arrayexpress

Differential gene expression analysis by RNA-Seq for the bldC deletion strain and the wild type of Streptomyces venezuelae strain NRRL B-65442 after 10 and 14 hours of culture

Project description:The BldC gene is required for the formation of aerial hyphae in Streptomyces venezuelae. It is a 68 amino acid DNA-binding protein related to the MerR family of transcription factors. BldC deletion strains are bald because they initiate sporulation prematurely, omitting the formation of aerial hyphae altogether. This RNA-Seq experiment was carried out to determine and quantify effect of BldC on the expression of all genes in the S. venezuelae genome after 10 and 14 hours of culture.

2019-01-14 | E-MTAB-7457 | biostudies-arrayexpress

Transcriptional 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.

Project description: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 sigE deletion strain of S. coelicolor. Samples were taken 0, 30, 60 and 90 minutes after addition of vancomycin and subjected to transcriptional profiling using Affymetrix arrays. Note – equivalent data for wild type Streptomyces coelicolor M600 is submitted as part of E-MEXP-3032. The data for both M600 (E-MEXP-3032) and J2130 (this submission) were generated at the same time employing the same protocols.

2019-04-24 | E-MTAB-7814 | biostudies-arrayexpress

Identification by ChIP-Seq of the binding sites of the sigma factor WhiG in the genome of Streptomyces venezuelae

Project description:The WhiG sigma factor gene is required for spore formation is Streptomyces venezuelae. It is similar to the FliA sigma factor of E. coli. WhiG deletion strains are able to make aerial hyphae but are defective in the spore maturation. This ChIP-Seq experiment was carried out to determine all the binding sites WhiG binds to in the genome of Streptomyces venezuelae. Anti-WhiG polyclonal antibodies were used for ChIP-Seq of the wild type (WT) strain after 34 hours of growth in shaken cultures. A WhiG deletion strain was made and anti-WhiG antibodies were used for ChIP-Seq in the deletion strain after 34 hours of growth in shaken cultures. This was used as the negative control and ChIP-Seq peak positions in this were disregarded in the WT.

2019-08-01 | E-MTAB-8160 | biostudies-arrayexpress

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