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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ChIP-seq of C-terminal FLAG-tagged WhiA

ABSTRACT: ChIP-seq of Mycobacterium tuberculosis strain with a C-terminal FLAG-tagged WhiA allele compared to a strain carrying a FLAG attached to no protein (empty)

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Mycobacterium tuberculosis

SUBMITTER: Frances Marks

PROVIDER: E-MTAB-16185 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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ChIP-seq of N-terminal FLAG tagged WhiA

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Project description:In vitro DNA affinity purification sequencing of recombinant WhiA incubated with sheard genomic DNA.

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Project description:This experiment was performed to transriptioally profile bacteria with a whiA conditional knockdown using CRISPR interference (CRISPRi). A conditional knockdown strain was treated with 0 or 500 ng/mL anhydrotetracycline (ATC) for 4 days, which turns on the CRISPRi machinery. RNA extraction was performed using Zymo RNA miniprep kit. Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) using 150 ng of input RNA. Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected ay 250-450 bp in length using SparQ beads. Libraries were validated using Bioanalyzer high sensitivity DNA analysis.

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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).

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ChIP-seq of N-terminal FLAG tagged WhiA

Project description:ChIP-seq of N-terminal FLAG tagged WhiA

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ChIP-seq of C-terminal FLAG-tagged WhiA

Project description:ChIP-seq of C-terminal FLAG-tagged WhiA

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Mycoplasma gallisepticum WhiA knockdown and overexpression

Project description:Proteomes of Mycoplasma gallisepticum strains with overexpression and knockdown of WhiA transcription factor. The overexpression was introduced on a transposon vector carrying M. gallisepticum whiA gene with strong constitutive promoter and strong SD sequence. The knockdown was made by CRISPRi. dCas9 protein and sgRNA against whiA gene were introduced on a transposon vector.

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The conserved WhiA protein influences the fatty acid composition of the Bacillus subtilis cell membrane

Project description:The conserved WhiA protein family is present in most Gram-positive bacteria and plays a role in cell division. WhiA contains a DNA-binding motive and has been identified as a transcription factor in the actinomycetes. In Bacillus subtilis, a deletion of whiA influences cell division and chromosome segregation. However, WhiA does not seem to function as a transcription factor in this organism, and it is still unclear how WhiA influences these processes. The B. subtilis whiA gene is part of an operon and flanked by two metabolic genes, including yvcK required for growth under gluconeogenic conditions, and the gene encoding the catabolite repressor Crh. Therefore, B. subtilis WhiA might play a role in carbon metabolism which could indirectly affect cell division and chromosome maintenance. To study this, we followed a metabolomics approach and measured exo-metabolome flux during growth on different carbon sources, using nuclear magnetic resonance spectroscopy. The carbon utilization of wild type and whiA mutant cells was similar, however, the whiA mutant exhibited depleted pools of branched-chain fatty acid precursors and higher levels of acetate and 2-oxoglutarate. Transcriptome data could not link these effects to gene regulatory differences, but the reduction in branched-chain fatty acid precursors influenced the fatty acid composition of the cell membrane. In conclusion, WhiA does not participate in carbon catabolite regulation, but affects fatty acid composition of the membrane by an as yet unknown mechanism. We speculate that the effect on the membrane might be related to the pleiotropic phenotype of the B. subtilis whiA mutant.

2019-10-18 | GSE121479 | GEO

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