Tetrahymena micronuclear genome mapping. a high-resolution meiotic map of chromosome 1l

Tetrahymena as a Unicellular Model Eukaryote: Genetic and Genomic Tools

Tetrahymena thermophila is a ciliate model organism whose study has led to important discoveries and insights into both conserved and divergent biological processes. In this review, we describe the tools for the use of Tetrahymena as a model eukaryote, including an overview of its life cycle, orientation to its evolutionary roots, and methodological approaches to forward and reverse genetics. Recent genomic tools have expanded Tetrahymena's utility as a genetic model system. With the unique advantages that Tetrahymena provide, we argue that it will continue to be a model organism of choice.

Selecting one of several mating types through gene segment joining and deletion in Tetrahymena thermophila

In Tetrahymena, a multi-sexed single-celled organism, the sex of the progeny is randomly determined by site-specific recombination events that assemble one complete gene pair and delete all others.

The unicellular eukaryote Tetrahymena thermophila has seven mating types. Cells can mate only when they recognize cells of a different mating type as non-self. As a ciliate, Tetrahymena separates its germline and soma into two nuclei. During growth the somatic nucleus is responsible for all gene transcription while the germline nucleus remains silent. During mating, a new somatic nucleus is differentiated from a germline nucleus and mating type is decided by a stochastic process. We report here that the somatic mating type locus contains a pair of genes arranged head-to-head. Each gene encodes a mating type-specific segment and a transmembrane domain that is shared by all mating types. Somatic gene knockouts showed both genes are required for efficient non-self recognition and successful mating, as assessed by pair formation and progeny production. The germline mating type locus consists of a tandem array of incomplete gene pairs representing each potential mating type. During mating, a complete new gene pair is assembled at the somatic mating type locus; the incomplete genes of one gene pair are completed by joining to gene segments at each end of germline array. All other germline gene pairs are deleted in the process. These programmed DNA rearrangements make this a fascinating system of mating type determination.

Tetrahymena thermophila is a single-celled organism with seven sexes. After two cells of different sexes mate, the progeny cells can be of any one of the seven sexes. In this article we show how this sex decision is made. Every cell has two genomes, each contained within a separate nucleus. The germline genome is analogous to that in our ovaries or testes, containing all the genetic information for the sexual progeny; the somatic or working genome controls the operation of the cell (including its sex). We show that the germline genome contains a tandem array of similarly organized but incomplete gene pairs, one for each sex. Sex is chosen after fertilization when a new somatic genome is generated by rearrangement of a copy of the germline genome. One complete sex gene pair is assembled when the cell joins DNA segments at opposite ends of the array to each end of one incomplete gene pair; this gene pair is thus completed and becomes fully functional, while the remaining sex gene pairs are excised and lost. The process involves programmed, site-specific genome rearrangements, and the physically independent rearrangements that occur at opposite ends of the selected gene pair happen with high reliability and precision.

Genome-wide characterization of Tetrahymena thermophila chromosome breakage sites. II. Physical and genetic mapping

The chromosomes of the macronuclear (expressed) genome of Tetrahymena thermophila are generated by developmental fragmentation of the five micronuclear (germline) chromosomes. This fragmentation is site specific, directed by a conserved chromosome breakage sequence (Cbs element). An accompanying article in this issue reports the development of a successful scheme for the genome-wide cloning and identification of functional chromosome breakage sites. This article reports the physical and genetic characterization of 30 functional chromosome breakage junctions. Unique sequence tags and physical sizes were obtained for the pair of macronuclear chromosomes generated by fragmentation at each Cbs. Cbs-associated polymorphisms were used to genetically map 11 junctions to micronuclear linkage groups and macronuclear coassortment groups. Two pairs of junctions showed statistically significant similarity of the sequences flanking the Cbs, suggestive of relatively recent duplications of entire Cbs junctions during Tetrahymena genome evolution. Two macronuclear chromosomes that lose at least one end in an age-related manner were also identified. The whole-genome shotgun sequencing of the Tetrahymena macronucleus has recently been completed at The Institute for Genome Research (TIGR). By providing unique sequence from natural ends of macronuclear chromosomes, Cbs junctions will provide useful sequence tags for relating macro- and micronuclear genetic, physical, and whole-genome sequence maps.

Organization and pairing of meiotic chromosomes in the ciliate Tetrahymena thermophila

During meiotic prophase in the ciliate Tetrahymena thermophila micronuclei dramatically elongate and form thread-like crescents. The arrangement of the chromosomes within the crescent as well as the timing of chromosome pairing and recombination with respect to the elongation process have been subjects of ongoing debate. Here, we addressed these issues by means of fluorescence in situ hybridization, labeling of individual chromosomes by BrdU (BrdU-painting) and by immunostaining of the recombination protein, Rad51. BrdU-painting indicated that chromosomes are arranged as parallel bundles within the crescent, and telomere-directed fluorescent in situ hybridization (FISH) revealed that most if not all telomeres are assembled near one end of the developing crescent. Prior to full crescent formation, Rad51 localizes to chromatin as numerous foci. Locus-specific FISH demonstrated that close pairing of homologues only occurs in the full crescent. Meiotic DNA double-strand break formation and the initiation of recombination thus seem to precede close pairing. A synaptonemal complex was not detected. We conclude that the chromosomes adopt a polarized arrangement within the crescent, probably resembling the classical bouquet arrangement. Furthermore, we propose that the elongated shape of meiotic micronuclei promotes the parallel arrangement of chromosomes and supports the juxtaposition of homologous regions in the absence of a synaptonemal complex. Several pieces of evidence indicate the presence of one to four chiasmata per bivalent, which would call for crossover interference to explain regular bivalent formation in spite of this low mean number. Tetrahymena might, therefore, pose a case of interference in the absence of a synaptonemal complex.

Analysis of expressed sequence tags (ESTs) in the ciliated protozoan Tetrahymena thermophila

To assess the utility of expressed sequence tag (EST) sequencing as a method of gene discovery in the ciliated protozoan Tetrahymena thermophila, we have sequenced either the 5' or 3' ends of 157 clones chosen at random from two cDNA libraries constructed from the mRNA of vegetatively growing cultures. Of 116 total non-redundant clones, 8.6% represented genes previously cloned in Tetrahymena. Fifty-two percent had significant identity to genes from other organisms represented in GenBank, of which 92% matched human proteins. Intriguing matches include an opioid-regulated protein, a glutamate-binding protein for an NMDA-receptor, and a stem-cell maintenance protein. Eleven-percent of the non-Tetrahymena specific matches were to genes present in humans and other mammals but not found in other model unicellular eukaryotes, including the completely sequenced Saccharomyces cerevisiae. Our data reinforce the fact that Tetrahymena is an excellent unicellular model system for studying many aspects of animal biology and is poised to become an important model system for genome-scale gene discovery and functional analysis.

Functional genomics: the coming of age for Tetrahymena thermophila

Over the past decade, researchers have manipulated the unique biology of Tetrahymena thermophila to generate a premier experimental organism for functional genomic analysis. A diverse array of DNA transformation methods have spearheaded in vivo strategies for discovering and dissecting universal eukaryotic processes, such as telomere addition and chromatin remodeling. Compartmentalization of this protist's genome into two functionally distinct nuclei - the silent 'germline' micronucleus and the transcriptionally active macronucleus - provides a powerful means for controlling the expression of transgenes. Heterokaryons that silently harbor homozygous recessive mutations (including lethal ones) in the germline have been exploited. The coupling of forward and reverse genetic approaches with genomics-based methods for gene discovery presents a bright future for research in this rising model eukaryote.

An antisense approach to phenotype-based gene cloning in Tetrahymena

We report a pioneering approach using Tetrahymena thermophila that permits rapid identification of genes based on their null or hypomorphic phenotypes. This technique involves cell transformation with a library of plasmids that encode 26S ribosomal subunits containing short insertions. The insertions correspond to antisense sequences for a large number of genes. The majority of cells each acquires a single antisense sequence, which silences a single genomic locus. Because the insertion site within the ribosomal sequence is known, the silenced gene is easily amplified. We demonstrate that this approach can be used to identify genes required for dense core granule exocytosis.

Tetrahymena micronuclear genome mapping. a high-resolution meiotic map of chromosome 1l

The ciliate Tetrahymena thermophila is a useful model organism that combines diverse experimental advantages with powerful capabilities for genetic manipulation. The genetics of Tetrahymena are especially rich among eukaryotic cells, because it possesses two distinct but related nuclear genomes within one cytoplasm, contained separately in the micronucleus (MIC) and the macronucleus (MAC). In an effort to advance fulfillment of Tetrahymena's potential as a genetic system, we are mapping both genomes and investigating the correspondence between them. With the latter goal especially in mind, we report here a high-resolution meiotic linkage map of the left arm of chromosome 1, one of Tetrahymena's five chromosomes. The map consists of 40 markers, with an average spacing of 2.3 cM in the Haldane function and a total length of 88.6 cM. This study represents the first mapping of any large region of the Tetrahymena genome that has been done at this level of detail. Results of a parallel mapping effort in the macronucleus, and the correspondence between the two genomes, can be found in this issue as a companion to this article.

Tetrahymena macronuclear genome mapping: colinearity Of macronuclear coassortment groups and the micronuclear map on chromosome 1l

The genetics of the ciliate Tetrahymena thermophila are richer than for most other eukaryotic cells, because Tetrahymena possesses two genomes: a germline (micronuclear) genome that follows a Mendelian model of genetic transmission and a somatic (macronuclear) genome, derived from the micronuclear genome by fragmentation, which follows a different genetic transmission model called phenotypic assortment. While genetic markers in the micronucleus fall into classical linkage groups under meiotic recombination and segregation, the same markers in the macronucleus fall into coassortment groups (CAGs) under phenotypic assortment by the random distribution of MAC chromosome pieces. We set out to determine whether genomic mapping in the macronucleus by genetic means is feasible. To investigate the relationship between the micronuclear map and coassortment groups, we systematically placed into CAGs all of the markers lying on chromosome 1L that are also found in the macronucleus. Sixteen CAGs were identified, 7 of which contain at least two loci. We have concluded that CAGs represent a fundamental genetic feature of the MAC. The MIC and MAC maps on 1L are colinear; that is, CAGs consist exclusively of markers that map to a continuous segment in a given region of the micronuclear map, with no intervening markers from other CAGs. These findings provide a solid foundation for exploiting the MAC chromosome pieces to build a physical map of the Tetrahymena genome.