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Distinct strains of Toxoplasma gondii feature divergent transcriptomes regardless of developmental stage.

Croken MM, Ma Y, Markillie LM, Taylor RC, Orr G, Weiss LM, Kim K - PLoS ONE (2014)

Bottom Line: These functions are likely associated with cell-cycle arrest.Using GSEA, we identified that ribosomal proteins were expressed at significantly higher levels in the CTG strain than in either the RH or PLK strains.This association holds true regardless of life cycle stage.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America.

ABSTRACT
Using high through-put RNA sequencing, we assayed the transcriptomes of three different strains of Toxoplasma gondii representing three common genotypes under both in vitro tachyzoite and in vitro bradyzoite-inducing alkaline stress culture conditions. Strikingly, the differences in transcriptional profiles between the strains, RH, PLK, and CTG, is much greater than differences between tachyzoites and alkaline stressed in vitro bradyzoites. With an FDR of 10%, we identified 241 genes differentially expressed between CTG tachyzoites and in vitro bradyzoites, including 5 putative AP2 transcription factors. We also observed a close association between cell cycle regulated genes and differentiation. By Gene Set Enrichment Analysis (GSEA), there are a number of KEGG pathways associated with the in vitro bradyzoite transcriptomes of PLK and CTG, including pyrimidine metabolism and DNA replication. These functions are likely associated with cell-cycle arrest. When comparing mRNA levels between strains, we identified 1,526 genes that were differentially expressed regardless of culture-condition as well as 846 differentially expressed only in bradyzoites and 542 differentially expressed only in tachyzoites between at least two strains. Using GSEA, we identified that ribosomal proteins were expressed at significantly higher levels in the CTG strain than in either the RH or PLK strains. This association holds true regardless of life cycle stage.

No MeSH data available.


Related in: MedlinePlus

GSEA detects bradyzoite-induced genes in PLK and CTG, but not RH parasites.(A) A schematic of strain virulence of the strains used as a function of ability to differentiate into bradyzoites. (B) GSEA enrichment plot for RH parasites under differentiation conditions compared to compound1 induced genes. Position of black bars indicate ranking of compound 1 genes relative to all other genes. Green line represents strength of enrichment under bradyzoite conditions (right) or tachyzoite conditions (left). (C) Enrichment plot for PLK parasites under differentiation conditions compared to compound 1 induced genes. (D) Enrichment plot for CTG parasites under differentiation conditions compared to compound 1 induced genes.
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pone-0111297-g003: GSEA detects bradyzoite-induced genes in PLK and CTG, but not RH parasites.(A) A schematic of strain virulence of the strains used as a function of ability to differentiate into bradyzoites. (B) GSEA enrichment plot for RH parasites under differentiation conditions compared to compound1 induced genes. Position of black bars indicate ranking of compound 1 genes relative to all other genes. Green line represents strength of enrichment under bradyzoite conditions (right) or tachyzoite conditions (left). (C) Enrichment plot for PLK parasites under differentiation conditions compared to compound 1 induced genes. (D) Enrichment plot for CTG parasites under differentiation conditions compared to compound 1 induced genes.

Mentions: Using GSEA, we compared the expression data to a set of genes shown to be differentially expressed after Compound 1 induced differentiation [22]. As Figure 3 shows, we are able to characterize both CTG and PLK, but not RH, as strongly enriched for bradyzoite genes. CTG has quantifiably more enrichment with a normalized enrichment score (NES) of 2.5 (p = 0.000) than PLK with an NES of 1.7 (p = 0.001). This is consistent with a continuum of differentiation competence with the type I lineage very resistant to bradyzoite development, type III differentiating readily, and type II parasites falling somewhere in the middle. Interestingly, the enrichment plot for RH (fig. 3B) is actually shaped like those of PLK, CTG (figs. 3C & 3D), even though the enrichment in RH is not statistically significant. This is consistent with data from other groups that indicates that RH is able to induce many of the stress-associated genes linked with bradyzoite differentiation, but is not able to complete the developmental transition.


Distinct strains of Toxoplasma gondii feature divergent transcriptomes regardless of developmental stage.

Croken MM, Ma Y, Markillie LM, Taylor RC, Orr G, Weiss LM, Kim K - PLoS ONE (2014)

GSEA detects bradyzoite-induced genes in PLK and CTG, but not RH parasites.(A) A schematic of strain virulence of the strains used as a function of ability to differentiate into bradyzoites. (B) GSEA enrichment plot for RH parasites under differentiation conditions compared to compound1 induced genes. Position of black bars indicate ranking of compound 1 genes relative to all other genes. Green line represents strength of enrichment under bradyzoite conditions (right) or tachyzoite conditions (left). (C) Enrichment plot for PLK parasites under differentiation conditions compared to compound 1 induced genes. (D) Enrichment plot for CTG parasites under differentiation conditions compared to compound 1 induced genes.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4230917&req=5

pone-0111297-g003: GSEA detects bradyzoite-induced genes in PLK and CTG, but not RH parasites.(A) A schematic of strain virulence of the strains used as a function of ability to differentiate into bradyzoites. (B) GSEA enrichment plot for RH parasites under differentiation conditions compared to compound1 induced genes. Position of black bars indicate ranking of compound 1 genes relative to all other genes. Green line represents strength of enrichment under bradyzoite conditions (right) or tachyzoite conditions (left). (C) Enrichment plot for PLK parasites under differentiation conditions compared to compound 1 induced genes. (D) Enrichment plot for CTG parasites under differentiation conditions compared to compound 1 induced genes.
Mentions: Using GSEA, we compared the expression data to a set of genes shown to be differentially expressed after Compound 1 induced differentiation [22]. As Figure 3 shows, we are able to characterize both CTG and PLK, but not RH, as strongly enriched for bradyzoite genes. CTG has quantifiably more enrichment with a normalized enrichment score (NES) of 2.5 (p = 0.000) than PLK with an NES of 1.7 (p = 0.001). This is consistent with a continuum of differentiation competence with the type I lineage very resistant to bradyzoite development, type III differentiating readily, and type II parasites falling somewhere in the middle. Interestingly, the enrichment plot for RH (fig. 3B) is actually shaped like those of PLK, CTG (figs. 3C & 3D), even though the enrichment in RH is not statistically significant. This is consistent with data from other groups that indicates that RH is able to induce many of the stress-associated genes linked with bradyzoite differentiation, but is not able to complete the developmental transition.

Bottom Line: These functions are likely associated with cell-cycle arrest.Using GSEA, we identified that ribosomal proteins were expressed at significantly higher levels in the CTG strain than in either the RH or PLK strains.This association holds true regardless of life cycle stage.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America.

ABSTRACT
Using high through-put RNA sequencing, we assayed the transcriptomes of three different strains of Toxoplasma gondii representing three common genotypes under both in vitro tachyzoite and in vitro bradyzoite-inducing alkaline stress culture conditions. Strikingly, the differences in transcriptional profiles between the strains, RH, PLK, and CTG, is much greater than differences between tachyzoites and alkaline stressed in vitro bradyzoites. With an FDR of 10%, we identified 241 genes differentially expressed between CTG tachyzoites and in vitro bradyzoites, including 5 putative AP2 transcription factors. We also observed a close association between cell cycle regulated genes and differentiation. By Gene Set Enrichment Analysis (GSEA), there are a number of KEGG pathways associated with the in vitro bradyzoite transcriptomes of PLK and CTG, including pyrimidine metabolism and DNA replication. These functions are likely associated with cell-cycle arrest. When comparing mRNA levels between strains, we identified 1,526 genes that were differentially expressed regardless of culture-condition as well as 846 differentially expressed only in bradyzoites and 542 differentially expressed only in tachyzoites between at least two strains. Using GSEA, we identified that ribosomal proteins were expressed at significantly higher levels in the CTG strain than in either the RH or PLK strains. This association holds true regardless of life cycle stage.

No MeSH data available.


Related in: MedlinePlus