Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

Abstract

BackgroundThe model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression.Methodology/Principal FindingsA genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation.Conclusions/SignificanceOf the ∼27,000 predicted open reading frames, transcripts homologous to only ∼5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5× corrected background and 95 genes are expressed at >250× corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

Toxicogenomic investigation of Tetrahymena thermophila exposed to dichlorodiphenyltrichloroethane (DDT), tributyltin (TBT), and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)

“…Details regarding the chip design and microarray operation are available elsewhere [20]. Raw data were deposited in the Gene Expression Omnibus Database under data set accession numbers GSE26515 including three samples: GSM651904 for TCDD, GSM651903 for DDT, GSM651902 for DMSO and GSM651901 for TBT.…”

“…Recently, differentially expressed genes in T. thermophila exposed to DDT or TBT have been detected using genome-wide screening conducted by suppression subtractive hybridization [18,19]. Moreover, completion of the macronuclear sequencing project [16] and establishment of the first genome-wide microarray platform in T. thermophila [20] with the Tetrahymena Gene Expression Database (TGED, http://tged.ihb.ac.cn) [21] offers extensive resources for further functional genomic studies, including toxigenomics. Thus, there is an opportunity to make use of this unicellular model to study the toxicological mechanism of environmental hormones at the genomic level.…”

Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in Tetrahymena thermophila

“…1C). 28,29 CDC2, CDK1 and CDC28 were expressed under growth, starvation and conjugation conditions; in contrast, CDK3 was specifically expressed during conjugation, with maximal expression at 2 h after we had triggered the meiotic program by mixing cells. RNA-Seq data on CDK3 expression was consistent with the microarray data, confirming that maximal expression occurs at 2 h post mixing the cells (Fig.…”

Characterization of copper resistant ciliates: Potential candidates for consortia of organisms used in bioremediation of wastewater

“…thermophila is well-established as a model eukaryote, elaborating typical eukaryotic components (for example, microtubules, membrane systems) into a highly organized cell whose structural and functional complexity is comparable to or exceeds that of human and other metazoan cells (Gorovsky, 1973;Brownell et al, 1996;Orias, 2000;Mochizuki et al, 2002;Yao and Chao, 2005;Miao et al, 2009). It has been acknowledged as an efficient test organism for the detection of pollutant in aquatic ecosystems (Cronin et al, 1991).…”