The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.

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Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

H3 phosphorylation has been correlated with mitosis temporally in mammalian cells and spatially in ciliated protozoa. In logarithmically growing Tetrahymena thermophila cells, for example, H3 phosphorylation can be detected in germline micronuclei that divide mitotically but not in somatic macronuclei that divide amitotically. Here, we demonstrate that micronuclear H3 phosphorylation occurs at a single site (Ser-10) in the amino-terminal domain of histone H3, the same site phosphorylated during mitosis in mammalian cells. Using an antibody specific for Ser-10 phosphorylated H3, we show that, in Tetrahymena, this modification is correlated with mitotic and meiotic divisions of micronuclei in a fashion that closely coincides with chromosome condensation. Our data suggest that H3 phosphorylation at Ser-10 is a highly conserved event among eukaryotes and is likely involved in both mitotic and meiotic chromosome condensation.

https://www.pnas.org/content/pnas/95/13/7480.full.pdf

Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena

Macro- and micronuclei were isolated from Tetrahymena pyriformis (Syngen 1, strain WH-6) and their DNAs compared by isopycnic centrifugation in neutral and alkaline CsCl, by analysis of thermal denaturation properties and by molecular hybridization. Unlike the situation observed in Stylonychia the buoyant densities and thermal denaturation patterns of Tetrahymena macro- and micronuclear DNAs were virtually identical—the only observable differences bordering on the limits of resolution of these techniques. DNA was isolated from the two nuclei which had been labelled with different radioactive isotopes (i.e.
14C-thymidine and 3H-thymidine), and the renaturation kinetics of mixtures of macro- and micronuclear DNA were examined using a single-strand specific deoxyribonuclease (S1). Renaturation kinetics obtained using varying ratios of macro- and micronuclear DNA suggested that 80–90% of the sequences present in micronuclei were present in similar amounts in macronuclei. However, careful analyses of the renaturation kinetics indicate that approximately 10–20% of the sequences found in micronuclei are probably absent in macronuclei, and that most of these sequences are probably moderately repetitive (100 copies per genome or less). These findings place severe constraint on possible models concerning the structure of the Tetrahymena macronucleus, and are very different from the situation observed in Stylonychia where it has been suggested that only a small percentage of the sequences in micronuclei are present in significant amounts in macronuclei. Nonetheless, these results along with those in Stylonychia can be taken as an indication that the loss or under-replication of some DNA sequences accompanies macronuclear differentiation in ciliates.

Comparison of the sequences of macro- and micronuclear DNA of Tetrahymena pyriformis

The process of pair formation by sexual strains of Tetrahymena pyriformis is an inducible pathway interrupting the cellular activities of vegetative growth. A specific series of events leading from vegetatively growing cells to mating pairs is described. The sequence is composed of two separate stages: initiation and co-stimulation. Initiation is the response to certain starvation conditions, is sensitive to tonicity, is independent of mating types, and takes about two hours at 30°C. Co-stimulation is a reaction between already initiated cells of different mating types, requires specific cell-cell interactions, takes about one hour at 30°C, and results in stimulated cells which are able to form pairs. An understanding of the sequence leading to the programmed developmental activities of conjugation makes possible efficient mating techniques and facilitates a search for genetic and physiological constituents of the entire pathway.

Pair formation in tetrahymena pyriformis, an inducible developmental system.

Abundant ∼28-nucleotide RNAs that are thought to direct histone H3 lysine 9 (H3K9) methylation and promote the elimination of nearly 15 Mbp of DNA from the developing somatic genome are generated during Tetrahymena thermophila conjugation. To identify the protein(s) that generates these small RNAs, we studied three Dicer-related genes encoded within the Tetrahymena genome, two that contain both RNase III and RNA helicase motifs, Dicer 1 (DCR1) and DCR2, and a third that lacks the helicase domain, Dicer-like 1 (DCL1). DCL1 is expressed upon the initiation of conjugation, and the protein localizes to meiotic micronuclei when bidirectional germ line transcription occurs and small RNAs begin to accumulate. Cells in which we disrupted the DCL1 gene (ΔDCL1) grew normally and initiated conjugation as wild-type cells but arrested near the end of development and eventually died, unable to resume vegetative growth. These ΔDCL1 cells failed to generate the abundant small RNAs but instead accumulated germ line-limited transcripts. Together, our findings demonstrate that these transcripts are the precursors of the small RNAs and that DCL1 performs RNA processing within the micronucleus. Postconjugation ΔDCL1 cells die without eliminating the germ line-limited DNA sequences from their newly formed somatic macronuclei, a result that shows that this Dicer-related gene is required for programmed DNA rearrangements. Surprisingly, ΔDCL1 cells were not deficient in overall H3K9 methylation, but this modification was not enriched on germ line-limited sequences as it is in wild-type cells, which clearly demonstrates that these small RNAs are essential for its targeting to specific loci.

Germ line transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila.

SUMMARY. Chromosome behavior of strains WH-6, and WH-14 mating types I and II respectively of variety 1, of T. pyriformis was studied during conjugation. Meiosis takes place during the first two prezygotic divisions. The chromosomes are at late pachytene-early diplotene during the maximum elongation of the crescent in prophase of the first micronuclear division. As the crescent shortens, five bivalent chromosomes are readily recognized. Five dyads go to each pole at the end of the first division. Following a brief interphase the second meiotic division results in four micronuclear products, each with five chromosomes. Three of these products disintegrate; the fourth undergoes mitosis resulting in two pronuclei each with five chromosomes. Following a reciprocal interchange of the migratory pronuclei between the two conjugants, the synkaryon of each is formed just anterior to the macronucleus. The diploid number of ten chromosomes has been counted at the first division of the synkaryon.

Meiosis and Nuclear Behavior in Tetrahymena pyriformis

Conjugating animals of the protozoan, Tetrahymena pryiformis, were affixed to cover slips by means of Nissenbaum's fluid, followed immediately by 1:3 acetic-alcohol for 18–24 hr. After fixation, the material was transferred through a descending alcohol series to water, then hydrolyzed in 1 N HCl, washed in water, followed by immersion in 45% acetic acid and subsequent mounting in aceto-carmine. Photomicrographs were made using a phase-contrast microscope and Microfile film. The schedule resulted in preparations with abundant material, adequate spacing of chromosomes in a single plane, and excellent differentiation of the chromosomes from the cytoplasm.

Charles Ray

Papers

Meiosis and Nuclear Behavior in Tetrahymena pyriformis

Preparation of chromosomes of Tetrahymena pyriformis for photomicrography.