Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage
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 identify 241 genes differentially expressed between CTG tachyzoites and in vitro bradyzoites, including 5 putative AP2 transcription factors. We also observe 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 identify 1,526 genes that are 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 identify ribosomal proteins as being expressed at significantly higher levels in the CTG strain than in either the RH or PLK strains. This association holds truemore »
- Authors:
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1188915
- Report Number(s):
- PNNL-SA-104591
Journal ID: ISSN 1932-6203; 40070; KP1704020
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 11; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Toxoplasma gondii; transcriptomes; RNA; sequencing; genotypes; in vitro; Environmental Molecular Sciences Laboratory
Citation Formats
Croken, Matthew, Ma, Yan Fen, Markillie, Lye Meng, Taylor, Ronald C., Orr, Galya, Weiss, Louis M., and Kim, Kami. Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage. United States: N. p., 2014.
Web. doi:10.1371/journal.pone.0111297.
Croken, Matthew, Ma, Yan Fen, Markillie, Lye Meng, Taylor, Ronald C., Orr, Galya, Weiss, Louis M., & Kim, Kami. Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage. United States. https://doi.org/10.1371/journal.pone.0111297
Croken, Matthew, Ma, Yan Fen, Markillie, Lye Meng, Taylor, Ronald C., Orr, Galya, Weiss, Louis M., and Kim, Kami. Thu .
"Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage". United States. https://doi.org/10.1371/journal.pone.0111297. https://www.osti.gov/servlets/purl/1188915.
@article{osti_1188915,
title = {Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage},
author = {Croken, Matthew and Ma, Yan Fen and Markillie, Lye Meng and Taylor, Ronald C. and Orr, Galya and Weiss, Louis M. and Kim, Kami},
abstractNote = {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 identify 241 genes differentially expressed between CTG tachyzoites and in vitro bradyzoites, including 5 putative AP2 transcription factors. We also observe 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 identify 1,526 genes that are 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 identify ribosomal proteins as being 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.},
doi = {10.1371/journal.pone.0111297},
journal = {PLoS ONE},
number = 11,
volume = 9,
place = {United States},
year = {Thu Nov 13 00:00:00 EST 2014},
month = {Thu Nov 13 00:00:00 EST 2014}
}
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ApiAP2 transcription factor restricts development of the Toxoplasma tissue cyst
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
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BEDTools: a flexible suite of utilities for comparing genomic features
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Genetic diversity of Toxoplasma gondii in animals and humans
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The transcription of bradyzoite genes in Toxoplasma gondii is controlled by autonomous promoter elements
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Transcription factor AP2-Sp and its target genes in malarial sporozoites
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The Toxoplasma nuclear factor TgAP2XI-4 controls bradyzoite gene expression and cyst formation: A novel Toxoplasma nuclear regulator
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The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment
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Coordinated Progression through Two Subtranscriptomes Underlies the Tachyzoite Cycle of Toxoplasma gondii
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T. gondii RP Promoters & Knockdown Reveal Molecular Pathways Associated with Proliferation and Cell-Cycle Arrest
journal, November 2010
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Genomic Data Reveal Toxoplasma gondii Differentiation Mutants Are Also Impaired with Respect to Switching into a Novel Extracellular Tachyzoite State
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Works referencing / citing this record:
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