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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

Hundreds of genes differentially expressed between strains including potential AP2 regulators.A) Using edgeR, we identify genes that are differentially expressed between strains (FDR <10%), generating three gene lists for tachyzoite condition and three for the bradyzoite condition. We generated Venn diagrams showing the overlap between the lists in the tachyzoite condition and bradyzoite condition. We also compared tachyzoite and bradyzoite gene lists to each other. Venn diagrams shows comparison of genes that appear in both the tachyzoite and the bradyzoite lists and therefore are “stage independent”. AP2 containing genes appearing on more than one list (any intersection) are indicated. The complete set of genes that are differentially expressed are listed in Table S2 and RPKM values for all replicates are listed in Table S1. B) Heat map of genes differentially expressed following CTG bradyzoite differentiation in all six conditions. Red indicates up regulation compared to that gene's expression level under other conditions, whereas green indicates down regulation. Conditions (columns) are clustered based on similarity of expression levels. The five AP2 genes that are differentially expressed are indicated on the right. Heat map was generated using the 'heatmap.2' function in the 'gplots' package for R. Hierarchical clustering of both the rows (genes) and columns (conditions) computed by the 'hclust' function in the R 'stats' package. Based on mean of replicate RPKM values.
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pone-0111297-g002: Hundreds of genes differentially expressed between strains including potential AP2 regulators.A) Using edgeR, we identify genes that are differentially expressed between strains (FDR <10%), generating three gene lists for tachyzoite condition and three for the bradyzoite condition. We generated Venn diagrams showing the overlap between the lists in the tachyzoite condition and bradyzoite condition. We also compared tachyzoite and bradyzoite gene lists to each other. Venn diagrams shows comparison of genes that appear in both the tachyzoite and the bradyzoite lists and therefore are “stage independent”. AP2 containing genes appearing on more than one list (any intersection) are indicated. The complete set of genes that are differentially expressed are listed in Table S2 and RPKM values for all replicates are listed in Table S1. B) Heat map of genes differentially expressed following CTG bradyzoite differentiation in all six conditions. Red indicates up regulation compared to that gene's expression level under other conditions, whereas green indicates down regulation. Conditions (columns) are clustered based on similarity of expression levels. The five AP2 genes that are differentially expressed are indicated on the right. Heat map was generated using the 'heatmap.2' function in the 'gplots' package for R. Hierarchical clustering of both the rows (genes) and columns (conditions) computed by the 'hclust' function in the R 'stats' package. Based on mean of replicate RPKM values.

Mentions: Globally, we see a much greater difference between the transcriptomes of different strains than we do between stressed and unstressed parasites of the same strain (Figures 1B and 1C). To identify which genes are expressed differently between strains, we used edgeR. We compared each strain against the other two under both tachyzoite (unstressed) and bradyzoite (stressed) conditions (FDR 10%). This created six lists of differentially expressed genes that are differentially expressed between strains in either tachyzoites or bradyzoites as well those genes that were differentially expressed in both stages (Figure 2A). The number in the center of the diagram represents the number of genes differentially expressed between all three strains. A full gene list is in Table S2. Genes in the outer intersections differed in only one strain and those not falling into any intersection are cases where the expression level is different between two strains, but the strain's expression level was not significantly different. It is important to note that the number differentially expressed genes between any two strains is always equal to or larger than number of genes affected by differentiation.


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)

Hundreds of genes differentially expressed between strains including potential AP2 regulators.A) Using edgeR, we identify genes that are differentially expressed between strains (FDR <10%), generating three gene lists for tachyzoite condition and three for the bradyzoite condition. We generated Venn diagrams showing the overlap between the lists in the tachyzoite condition and bradyzoite condition. We also compared tachyzoite and bradyzoite gene lists to each other. Venn diagrams shows comparison of genes that appear in both the tachyzoite and the bradyzoite lists and therefore are “stage independent”. AP2 containing genes appearing on more than one list (any intersection) are indicated. The complete set of genes that are differentially expressed are listed in Table S2 and RPKM values for all replicates are listed in Table S1. B) Heat map of genes differentially expressed following CTG bradyzoite differentiation in all six conditions. Red indicates up regulation compared to that gene's expression level under other conditions, whereas green indicates down regulation. Conditions (columns) are clustered based on similarity of expression levels. The five AP2 genes that are differentially expressed are indicated on the right. Heat map was generated using the 'heatmap.2' function in the 'gplots' package for R. Hierarchical clustering of both the rows (genes) and columns (conditions) computed by the 'hclust' function in the R 'stats' package. Based on mean of replicate RPKM values.
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Related In: Results  -  Collection

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pone-0111297-g002: Hundreds of genes differentially expressed between strains including potential AP2 regulators.A) Using edgeR, we identify genes that are differentially expressed between strains (FDR <10%), generating three gene lists for tachyzoite condition and three for the bradyzoite condition. We generated Venn diagrams showing the overlap between the lists in the tachyzoite condition and bradyzoite condition. We also compared tachyzoite and bradyzoite gene lists to each other. Venn diagrams shows comparison of genes that appear in both the tachyzoite and the bradyzoite lists and therefore are “stage independent”. AP2 containing genes appearing on more than one list (any intersection) are indicated. The complete set of genes that are differentially expressed are listed in Table S2 and RPKM values for all replicates are listed in Table S1. B) Heat map of genes differentially expressed following CTG bradyzoite differentiation in all six conditions. Red indicates up regulation compared to that gene's expression level under other conditions, whereas green indicates down regulation. Conditions (columns) are clustered based on similarity of expression levels. The five AP2 genes that are differentially expressed are indicated on the right. Heat map was generated using the 'heatmap.2' function in the 'gplots' package for R. Hierarchical clustering of both the rows (genes) and columns (conditions) computed by the 'hclust' function in the R 'stats' package. Based on mean of replicate RPKM values.
Mentions: Globally, we see a much greater difference between the transcriptomes of different strains than we do between stressed and unstressed parasites of the same strain (Figures 1B and 1C). To identify which genes are expressed differently between strains, we used edgeR. We compared each strain against the other two under both tachyzoite (unstressed) and bradyzoite (stressed) conditions (FDR 10%). This created six lists of differentially expressed genes that are differentially expressed between strains in either tachyzoites or bradyzoites as well those genes that were differentially expressed in both stages (Figure 2A). The number in the center of the diagram represents the number of genes differentially expressed between all three strains. A full gene list is in Table S2. Genes in the outer intersections differed in only one strain and those not falling into any intersection are cases where the expression level is different between two strains, but the strain's expression level was not significantly different. It is important to note that the number differentially expressed genes between any two strains is always equal to or larger than number of genes affected by differentiation.

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