Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Global gene expression differences between GT1, RH-ERP2009 and RH-JSR

ABSTRACT: Previous studies have shown that continuous in vitro passage can result in changes to the global gene expression profiles in mammalian cells. To examine the extent of gene expression differences between highly homologous type I strains, we took advantage of the T. gondii Affymetrix microarray containing probes to more than 8,000 genes. We compared the RH-JSR and GT1 strains, two isolates that share the small plaque phenotype, to the large plaque isolate RH-ERP2009. Following hybridization and normalization of data, we used two independent methods to generate lists of genes with expression differences that were statistically significant and 2-fold or greater in at least one sample. The 1-way ANOVA (P â¤ 0.05) identified 520 genes that were significantly differentially expressed between GT1, RH-ERP2009 and RH-JSR. Statistical Analysis of Microarray (SAM) (FDR = .05%) analysis identified 475 transcripts that were differentially expressed. Both lists were combined (610 genes) and used to perform pairwise fold comparisons between the three samples. This process identified 113 genes that were similarly expressed in GT1 and RH-JSR and differentially expressed in RH-ERP2009. Differentially expressed genes were located across all chromosomes and showed no pattern of clustering to one particular region of the genome. Interestingly, three out of 34 ABC transporters (ToxoDB) were significantly upregulated in RH-ERP2009 (hypergeometric distribution, P = 0.01) Three type I strains of Toxoplasma gondii, GT1, RH-ERP2009 and RH-JSR, were compared for global gene expression differences. Three biological replicates were obtained for each strain.

ORGANISM(S): Toxoplasma gondii

SUBMITTER: Michael Behnke

PROVIDER: E-GEOD-16115 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Phenotypic and gene expression changes among clonal type I strains of Toxoplasma gondii.

Khan Asis A Behnke Michael S MS Dunay Ildiko R IR White Michael W MW Sibley L David LD

Eukaryotic cell 20091002 12

Toxoplasma gondii has an unusual population structure consisting of three clonal lineages that predominate in North America and Europe. This simple pattern has encouraged the use of only a few laboratory isolates that are representative of each lineage. Principle among these is the type I RH strain, originally isolated from a child with encephalitis some 70 years ago. Comparison of different passages of the RH strain that have been propagated differently over the intervening time period revealed ...[more]

PMID: 19801420

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Project description:Toxoplasma gondii is a globally distributed obligate intracellular parasite which can cause zoonotic toxoplasmosis with great harms. The average death time of mice that infected with Toxoplasma gondii RH strain tachyzoites recovered from the liquid nitrogen was shortened after multiple generations. It has been reported that the parasite is in a state of static virulence during cryopreservation and the virulence of the protozoan parasite can be enhanced after continuous passages in hosts under laboratory conditions. However, no research has been conducted to elucidate its biological mechanism. Herein, we sequenced the T. gondii transcriptome using RNA-Seq technology and performed de novo assembly to investigated the virulence factors expression changes by comparing gene expression profiles between incipiently recovered and completely resuscitated tachyzoites. Transcriptome analysis identified 1,951 differentially expressed transcripts in infected liver, of which 1,752 were significantly downregulated and 199 upregulated. We identified many differentially expressed proteins and genes, including serine/threonine kinase, calnexin, myosin and microtubule-associated protein which have previously been reported to be either involved in cell adhesion, parasite gliding or participate in cell invasion. The great majority of the virulence factors including microneme proteins, rhoptry proteins and dense granule proteins were upregulated in fully recovered tachyzoites. The enhanced virulence of recovered Toxoplasma gondii RH strain from the liquid nitrogen is associated with the up-regulated expression of MICs, ROPs and GRAs. Our data will facilitate future genomic research and in-depth annotation of Toxoplasma gondii RH strain genomes. This study provides a profile of the candidate genes that are suspected to be involved with virulence enhancement of recovered Toxoplasma gondii RH strain tachyzoites. Many further studies should be carried out to confirm the function of the candidate genes. Moreover, the preliminary identification of genes and pathways exhibiting differential expression in complete resuscitation stage may further our general understanding of virulence enhancement in this parasite.

Dataset Information

Global gene expression differences between GT1, RH-ERP2009 and RH-JSR

Publications

Phenotypic and gene expression changes among clonal type I strains of Toxoplasma gondii.

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