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A single master regulator controls asexual cell cycle division patterns in Toxoplasma gondii [ChIP-Seq]

ABSTRACT: ApiAP2 are a family of conserved transcription factors (TF) that play an important role in regulating gene expression in apicomplexan parasites. ApiAP2 proteins that may control the cell cycle dependent expression program are to be discovered. To better understand how these cell-cycle dependent gene expression profiles are established, we identified ApiAP2 proteins showing a cell cycle dependent expression. Using the Auxin-degradation system, we produced several inducible knock-down (iKD) mutant for these ApiAP2 proteins. Among them, a cell-cycle regulated ApiAP2 is expressed during the late S-phase of the tachyzoite cell-cycle. The iKD mutant parasites for this gene are unable to proliferate. In presence of Auxin, the mutant parasites do not produce daughter cells and are arrested in the early phase of budding. This indicates that this TF may specifically regulate the early steps of the daughter cell formation. Using RNA-Seq, we demonstrate that the level of expression of number of transcripts is affected by the knock-down of this potential TF.

ORGANISM(S): Toxoplasma gondii

PROVIDER: GSE150405 | GEO | 2020/10/29

REPOSITORIES: GEO

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A single master regulator controls asexual cell cycle division patterns in Toxoplasma gondii [RNA-Seq]

Project description:ApiAP2 are a family of conserved transcription factors (TF) that play an important role in regulating gene expression in apicomplexan parasites. ApiAP2 proteins that may control the cell cycle dependent expression program are to be discovered. To better understand how these cell-cycle dependent gene expression profiles are established, we identified ApiAP2 proteins showing a cell cycle dependent expression. Using the Auxin-degradation system, we produced several inducible knock-down (iKD) mutant for these ApiAP2 proteins. Among them, a cell-cycle regulated ApiAP2 is expressed during the late S-phase of the tachyzoite cell-cycle. The iKD mutant parasites for this gene are unable to proliferate. In presence of Auxin, the mutant parasites do not produce daughter cells and are arrested in the early phase of budding. This indicates that this TF may specifically regulate the early steps of the daughter cell formation. Using RNA-Seq, we demonstrate that the level of expression of number of transcripts is affected by the knock-down of this potential TF.

2020-10-29 | GSE150334 | GEO

Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii. [RNA-seq]

Project description:Toxoplasma gondii is a unicellular eukaryote belonging to the Apicomplexa phylum. It is an obligate intracellular parasite of critical importance to primarily infected pregnant women and immunosuppressed patient. ApiAP2 are a family of conserved transcription factors (TF) that play an important role in regulating gene expression in apicomplexan parasites. Previous studies had revealed the ability of one of these TFs, TgAP2XI-5, to bind to transcriptionally active promoters of genes expressed during the S/M phase such as rhoptry and micronemes genes. However, expression of TgAP2XI-5 is constitutive during the tachyzoite cell cycle. To better understand how its function is regulated, we identified proteins interacting with TgAP2XI-5 including a cell cycle regulated ApiAP2 TFs, TgAP2X-5. The purpose of the study is to determine the impact of the absence of a TF (TgAP2X-5) on the wide expression profile of a Toxoplasma gondii strain.

2018-05-30 | GSE106864 | GEO

Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii. [ChIP-chip]

Project description:Toxoplasma gondii is a unicellular eukaryote belonging to the Apicomplexa phylum. It is an obligate intracellular parasite of critical importance to primarily infected pregnant women and immunosuppressed patient. ApiAP2 are a family of conserved transcription factors (TF) that play an important role in regulating gene expression in apicomplexan parasites. Previous studies had revealed the ability of one of these TFs, TgAP2XI-5, to bind to transcriptionally active promoters of genes expressed during the S/M phase such as rhoptry and micronemes genes. However, expression of TgAP2XI-5 is constitutive during the tachyzoite cell cycle. To better understand how its function is regulated, we identified proteins interacting with TgAP2XI-5 including a cell cycle regulated ApiAP2 TFs, TgAP2X-5. The purpose of the study is to determine the impact of the absence of TgAP2X-5 on the binding of TgAP2XI-5 on its targets. Chromatin immunoprecipitation (ChIP) of TgAP2XI-5 together with chromatin in absence of TgAP2X-5 profiling by ChIP-on-chip analysis demonstrated that TgAP2X-5 co-acts with TgAP2XI-5 for its binding to DNA of certain promoter targets.

2018-05-30 | GSE109086 | GEO

Identification of antimalarial compounds that inhibit Apicomplexan AP2 transcription factor proteins in the human malaria parasite Plasmodium falciparum [ChIP-seq]

Project description:Plasmodium parasites are reliant on the Apicomplexan AP2 (ApiAP2) transcription factor family to regulate gene expression programs. AP2 DNA binding domains have no homologs in the human or mosquito host genomes, making them potential antimalarial drug targets. Using an in-silico screen to dock thousands of small molecules into the crystal structure of the AP2-EXP (Pf3D7_1466400) AP2 domain (PDB:3IGM), we identified compounds that interact with this domain. Four compounds were found to compete for DNA binding with AP2-EXP and at least one additional ApiAP2 protein. Our top ApiAP2 competitor compound perturbs the transcriptome of P. falciparum trophozoites and results in a decrease in abundance of log2 fold change > 2 for 50% (46/93) of AP2-EXP target genes. Additionally, two ApiAP2 competitor compounds have multi-stage anti-Plasmodium activity against blood and mosquito stage parasites. In summary, we describe a novel set of antimalarial compounds that are targeted against the ApiAP2 family of proteins. These compounds may be used for future chemical genetic interrogation of ApiAP2 proteins or serve as starting points for a new class of antimalarial therapeutics.

2022-07-15 | GSE208155 | GEO

A knockout screen of ApiAP2 genes reveals networks of interacting transcriptional regulators controlling the Plasmodium life cycle.

Project description:The family of apicomplexa-specific proteins with DNA binding AP2 domains (ApiAP2s) includes sequence-specific transcription factors that are key regulators of development in malaria parasites. However, functions for the majority of ApiAP2 genes remain unknown. Here, a systematic knockout screen in Plasmodium berghei identifies ten ApiAP2 genes essential for mosquito transmission, of which four are critical for the formation of infectious ookinetes and three for sporogony. We describe unexpected non-essential functions for AP2-O and AP2-SP proteins in blood stages and identify AP2-G2 as a universal repressor active in both, asexual and sexual stages. Comparative transcriptomics across mutants and developmental stages reveals clusters of co-regulated genes with shared cis elements in their promoters, whose expression can be controlled positively or negatively by different ApiAP2 gene deletions. We propose that stage-specific interactions between ApiAP2 proteins on partly overlapping sets of target genes generate the complex transcriptional network that controls the Plasmodium life cycle.

2017-02-08 | PXD005180 | Pride

The Class VIII myosin ATM1 is integral for root apical meristem function

Project description:Myosins are evolutionarily conserved motor proteins that interact with actin filaments to regulate organelle transport, cytoplasmic streaming and cell growth. Plant specific Class XI myosin proteins direct cell division and root organogenesis. However, the roles of Class VIII myosin proteins in plant growth and development are less understood. Here, we investigated the function of an auxin-regulated Class VIII myosin, Arabidopsis thaliana Myosin 1 (ATM1), using genetics and live cell microscopy. ATM1 is a plasmodesmata-localized protein that is enriched in actively dividing cells in the root apical meristem (RAM). Loss of ATM1 function results in impaired primary root growth due to decreased RAM size and reduced cell proliferation in a sugar dependent manner. Examination of stem cell marker line expression in atm1-1 indicated impaired division of the lateral root cap and columella cells and a diminished auxin response. Transcriptome analysis of atm1-1 linked these growth defects to dysregulation of cell cycle and auxin pathway genes. Complementation of ATM1 loss-of- function mutant restored root growth and cell cycle progression in the root meristem. Collectively, these results provide novel evidence that ATM1 functions to influence cell proliferation and differentiation in primary roots in response to auxin and sugar cues.

2023-06-08 | GSE200917 | GEO

Toxoplasma gondii arginine methyltransferase 1 (PRMT1) regulates parasite counting during tachyzoite cell division

2015-09-18 | GSE73177 | GEO

Heterochromatin protein 1 secures survival and transmission of malaria parasites

Project description:The malaria parasite Plasmodium falciparum relies on clonally variant gene expression in order to escape immune recognition and secure continuous proliferation during blood stage infection. Here, we studied the role of heterochromatin protein 1 (HP1), an evolutionary conserved regulator of heritable gene silencing, in the biology of P. falciparum blood stage parasites. We demonstrate that conditional PfHP1 depletion de-represses hundreds of heterochromatic virulence genes and disrupts the elusive mechanism underlying mutually exclusive expression and antigenic variation of PfEMP1. Intriguingly, we also discovered that the PfHP1-dependent regulation of an ApiAP2 transcription factor controls the switch from asexual parasite proliferation to sexual differentiation. This uncovers the first mechanistic insight into the unknown pathway triggering gametocyte conversion and establishes a new concept of HP1-dependent cell fate decision in unicellular eukaryotes. P. falciparum 3D7 parasites expressing endogenous PfHP1-GFP-DD were grown in presence of 4nM WR/625nM Shield-1 (3D7/HP1ON) or 4nM WR (3D7/HP1OFF). RNA extracted from these samples at eleven consecutive time points each was processed for microarray analysis.

2014-07-09 | E-GEOD-53176 | biostudies-arrayexpress

Toxoplasma gondii arginine methyltransferase 1 (PRMT1) regulates parasite counting during tachyzoite cell division

Project description:PRMT1 is thought to be responsible for the majority of PRMT activity in Toxoplasma gondii, but its exact function is unknown. We generated T. gondii mutants lacking PRMT1 (∆prmt1) by deletion of the PRMT1 gene. ∆prmt1 parasites exhibit morphological defects during cell division and grow slowly, and this phenotype reverses in the complemented strain ∆prmt::PRMT1mRFP. PRMT1 localizes primarily in the cytoplasm with enrichment at the centrosome, and the strain lacking PRMT1 is unable to segregate progeny accurately. Unlike wild-type and complemented parasites, ∆prmt1 parasites have abnormal daughter buds, perturbed centrosome stoichiometry, and loss of synchronous replication. Whole genome expression profiling demonstrated differences in expression of cell cycle regulated genes in ∆prmt1 relative to the complemented ∆prmt1::PRMT1mRFP and parental wild-type strains, but these changes did not correlate with a specific block in cell cycle. Although PRMT1’s primary biological function was previously proposed to be methylation of histones, our genetic studies suggest that the most critical function of PRMT1 is within the centrosome as a regulator of daughter cell counting to assure the proper replication of the parasite. RNA samples were isolated in triplicates from RH-hxgprt parent strain (W), PRMT1 knockout (K) strain and PRMT1 knockout strain complemented with RFP-tagged PRMT1 protein (C). Parasites were grown for 32h at 37C. Samples were hybridized to the Toxoplasma gondii Affymetrix microarray (ToxoGeneChip: http://ancillary.toxodb.org/docs/Array-Tutorial.html). Hybridization data was preprocessed with Robust Multi-array Average (RMA) and normalized using per chip and per gene median polishing and analyzed using the software package GeneSpring GX (Agilent Technologies).

2015-09-18 | E-GEOD-73177 | biostudies-arrayexpress

Coordinated Progression Through Two Subtranscriptomes Underlies the Tachyzoite Cycle of Toxoplasma gondii

Project description:We describe the cell cycle transcriptome of the Toxoplasma gondii that has emerged as a major genetic model for the study of Apicomplexa parasites. Two distinct transcriptional waves accompany the relatively simple binary replication of tachyzoite stage (endodyogeny) functionally separating conserved gene expression in the eukaryotic G1 phase from the lineage-specific expression that predominates in the parasite S phase and mitotic periods. This division of transcriptional focus closely mirrors the intimate relationship that has evolved between mitosis and building of the daughter parasites and invasion organelles. Promoter mechanisms appear to orchestrate the induction of gene expression in dividing tachyzoites with up to two dozen cell cycle AP2 factors likely acting within a transcriptional regulatory network to coordinate the parasite cell cycle transcriptome.

2010-08-27 | GSE19092 | GEO

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