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Effect of BFD2 (TGME49_311100) knockout on T. gondii gene expression during BFD1 induction

ABSTRACT: Effect of BFD2 (TGME49_311100) knockout on T. gondii gene expression during BFD1 induction

PROVIDER: PRJNA928724 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23254427_1.fastq.gz	Fastqsanger.gz
	SRR23254427_2.fastq.gz	Fastqsanger.gz
	SRR23254428_1.fastq.gz	Fastqsanger.gz
	SRR23254428_2.fastq.gz	Fastqsanger.gz
	SRR23254429_1.fastq.gz	Fastqsanger.gz

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Effect of BFD2 (TGME49_311100) knockout on T. gondii gene expression during BFD1 induction

Project description:The acute-to-chronic stage transition in Toxoplasma gondii involes a global restructuring of the parasite transcriptome. Prior work identified a single transcription factor (BFD1) that is both necessary and sufficient to establish the chronic-stage program, making it the master regulator of this process. Recently, we found that parasites lacking a CCCH-type zinc finger RNA-binding protein (BFD2) are also unable to produce chronic forms. To understand how BFD2 aids in establishing the BFD1 transcriptional program, we knocked out BFD2 in a BFD1-conditional expression strain, wherein BFD1 is induced by treatment with the small molecule Shield-1.

2023-03-31 | GSE223877 | GEO

Effects of BFD1 (TGME49_200385) and BFD2 (TGME49_311100) deletion on gene expression in Toxoplasma gondii during infection in neurons

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In vitro analysis of pH responsiveness of T. gondii and H. hammondi sporozoites, and of T. gondii tachyzoites lacking either the BFD1 or the ROCY1 gene.

Project description:There are two experiments included in this particular GEO accession: For the first, freshly excysted sporozoites of T. gondii VEG or H. hammondi Amer1 were put into culture for 2 days, and then either allowed to continue growth in control (pH 7.2, 5% C02, 10% FCS) or high pH, bradyzoite-inducing (pH 8.2, low C02, 1% FCS) conditions for 3 days and then harvested for RNAseq analysis. In the second, T. gondii strain VEG was genetically manipulated to ablate either the ROCY1 gene (TGVEG_311100) or the BFD1 gene (TGME49_200385) and then compared to Wild Type VEG in a bradyzoite induction assay. Specifically, each parasite line was grown for 2 days in control conditions (same as above) or bradyzoite induction conditions (same as above) and then harvested for RNAseq. Data were mapped to the parasite genomes transcript abundance was normalized and calculated using DESeq2.

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Project description:WT (ME49∆KU80), ∆BFD1, or ∆BFD1/DD-BFD1-Ty parasites were treated with the stabilizing ligand Shield-1 (all three) or vehicle alone (WT and ∆BFD1/DD-BFD1-Ty) to identify genes differentially regulated by overexpression of BFD1.

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Effect of depleting BFD1-regulated gene-expression factors (TGME49_253790, TGME49_208020, TGME49_224630, TGME49_306620, TGME49_311100) on the Toxoplasma transcriptome during alkaline stress

Project description:The transcription factor BFD1 is the master regulator of the Toxoplasma chronic-stage differentiation program, which is induced under alkaline stress. Prior work indicated that BFD1 transcriptionally activates five other putative RNA- and DNA-binding proteins during differentiation, suggesting potential secondary roles in shaping the Toxoplasma chronic-stage transcriptome. To describe the distinct genetic cohorts controlled by these factors, we generated individual knockdown strains for each candidate using the auxin inducible degron system (TIR1/AID) and examined the transcriptomic effects of their depletion under alkaline stress.

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