Macronuclear Subunits of Tetrahymena thermophila Are Functionally Haploid

Absolute quantification of chromosome copy numbers in the polyploid macronucleus of Tetrahymena thermophila at the single-cell level

Amitosis is widespread among eukaryotes, but the underlying mechanisms are poorly understood. The polyploid macronucleus (MAC) of unicellular ciliates divides by amitosis, making ciliates a potentially valuable model system to study this process. However, a method to accurately quantify the copy number of MAC chromosomes has not yet been established. Here we used droplet digital PCR (ddPCR) to quantify the absolute copy number of the MAC chromosomes in Tetrahymena thermophila. We first confirmed that ddPCR is a sensitive and reproducible method to determine accurate chromosome copy numbers at the single-cell level. We then used ddPCR to determine the copy number of different MAC chromosomes by analyzing individual T. thermophila cells in the G1 and the amitotic (AM) phases. The average copy number of MAC chromosomes was 90.9 at G1 phase, approximately half the number at AM phase (189.8). The copy number of each MAC chromosome varied among individual cells in G1 phase and correlated with cell size, suggesting that amitosis accompanied by unequal cytokinesis causes copy number variability. Furthermore, the fact that MAC chromosome copy number is less variable among AM-phase cells suggests that the copy number is standardized by regulating DNA replication. We also demonstrated that copy numbers differ among different MAC chromosomes and that interchromosomal variations in copy number are consistent across individual cells. Our findings demonstrate that ddPCR can be used to model amitosis in T. thermophila and possibly in other ciliates.

Mutants of TETRAHYMENA THERMOPHILA with Temperature-Sensitive Food Vacuole Formation. I. Isolation and Genetic Characterization

Germ-line mutants have been isolated in Tetrahymena thermophila that have recessive, temperature-sensitive defects in phagocytosis. Nitrosoguanidine-mutagenized cells were induced to undergo cytogamy, and clones were isolated that were unable to form food vacuoles after two days of growth at 39 degrees . Most of the mutants belong to a single complementation group, designated vacA. They have defects in oral development-not in phagocytosis per se-that are undetectable under light microscopy. One fertile mutant, phenotypically indistinguishable from the vacA group, has its vac mutation(s) restricted to the macronucleus, and it is a heterokaryon for two other markers. This clone probably resulted from a failure of the two gametic nuclei to fuse after normal exchange. Two additional mutants were studied, but their sterility prevented a full genetic analysis. One of these clones has a rudimentary oral apparatus and defective contractile vacuole pores; both defects may be determined by the same mutation. The other clone has a structurally normal oral apparatus and may be defective in phagocytosis per se.-The induction and characterization of germ-line mutations that affect oral development open the way for the genetic dissection of the morphogenesis of a complex eukaryotic organelle, and make available additional useful mutants for the study of nutrition and transmembrane active transport.

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.

Regulation of macronuclear DNA content in Chilodonella steini (Trithigmostoma steini)

Our presented studies describe a correlation between the content of macronuclear DNA in mother cells and their progeny after one cycle of cell growth in Chilodonella steini. We have found that the cells with a high level of macronuclear DNA produce daughter cells with a low DNA level and vice versa, and that the compensation of differences in the content of macronuclear DNA in sister cells requires several cell cycles. This compensation does not depend on the full replication rounds (as in the case of Tetrabymena) nor on the "increment" phenomenon (as in the case of Paramecium). Furthermore, we have found that in Chilodonella the length of the cell cycle is inversely proportional to the initial content of macronuclear DNA, i.e., the higher the Gl level, the shorter the cell cycle.

Rate of phenotypic assortment in Tetrahymena thermophila

During vegetative, asexual reproduction in heterozygous Tetrahymena thermophila, the macronucleus divides amitotically to produce clonal lineages that express either one or the other allele but not both. Because such phenotypic assortment has been described for every locus studied, its mechanism has important implications concerning the development and structure of the macronucleus. The primary tools to study assortment are Rf, the rate at which subclones come to express a single allele stably, and the output ratio, the ratio of assortee classes. Because Rf is related to the number of assorting units, a constant Rf for all loci suggests that all genes are maintained at the same copy number. Output ratios reflect the input ratio of assorting units, with a 1:1 output ratio implying equal numbers of alleles at the end of macronuclear development. Because different outcomes would suggest a different macronuclear structure, it is crucial that these parameters be accurately measured. Although published Rf values are similar for all loci measured, there has been no commonly accepted form of presentation and analysis. Here we examine the experimental determination of Rf. First, we use computer simulation to describe how the variability inherent in the assortment process affects experimental determination of Rf. Second, we describe a simple method of plotting assortment data that permits the uniform calculation of Rf, and we describe how to measure Rf accurately in instances when it is possible to score only the recessive allele. Using this method to produce truly comparable Rfs for all published data, we find that most, if not all, loci assort at Rfs consistent with approximately 45 assorting units, as has been asserted.

Identification of a cDNA coding for the SerH3 surface protein of Tetrahymena thermophila

We have identified a Tetrahymena thermophila cDNA-containing plasmid (pC6) which hybridizes to a 1.47-kB RNA whose changes in cellular concentration parallel the changes in synthetic rate of a major cell surface protein. From a molecular and genetic analysis of strains expressing the gene (SerH3) encoding this protein, and of strains expressing immunologically distinct alleles of this gene, we conclude that pC6 encodes a portion of the SerH3 allele.

Nucleo-cytoplasmic interaction during macronuclear differentiation in ciliate protists: genetic basis for cytoplasmic control of SerH expression during macronuclear development in Tetrahymena thermophila

A novel class of mutations affecting the developmental expression of SerH cell surface antigen genes of Tetrahymena thermophila is described. Unlike previous categories of mutation, the four independently isolated mutations of this class act through the cytoplasm to affect SerH genes during macronuclear development. That is, macronuclei which develop under the influence of mutant cytoplasm do not subsequently express H, most likely because the developmental processing of SerH genes is affected. The cytoplasmic effect is specific for the SerH locus and is independent of which SerH allele is present. In place of H, hitherto unknown antigens are expressed. Expression of SerH can be rescued during development either by wild-type cytoplasm exchanged between conjugants or by the homozygous wild-type genotype. The mutations segregate independently of the SerH genes and identify one, possibly two, bistable genes. Possible models to explain these results are discussed.

Rearrangement of repeated DNA sequences during development of macronucleus in Tetrahymena thermophila

Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, the remaining three clones with repetitive sequences had apparently different organization in the two nuclear DNAs. All these repetitive sequences showed a smear on the blot in addition to a number of discrete bands when micronuclear DNA was digested with EcoR I. In macronuclear DNAs, these sequences invariably became one or two bands and the smear disappeared. We conclude that, when a macronucleus develops from a micronucleus, the non-repetitive sequences amplify by more than 20 times with relatively few rearrangement, whereas some selected portions of repeated and/or repeat-contiguous sequences are amplified with rather extensive reorganization.

Chromatin elimination and the genetic organisation of the macronucleus in Tetrahymena thermophila

In exponentially growing Tretrahymena thermophila the DNA content of the following structures was determined by cytophotometry: macronuclei of sister cells immediately after division; micronuclei; extranuclear chromatin in dividing cells and postdividers. Further, the development of macronuclear DNA amount in successive cell generations was determined. It was found that chromatin elimination is a frequent process reducing DNA content by about 4% per fission. This chromatin disappears within 20 min after division. The quantity of DNA extruded is highly variable and is different from the micronuclear DNA amount of multiples of it. The frequency of generations with two replication rounds as well as those without replication is estimated to be in the range of 2% each. These findings together with the qualitative difference between micro- and macronuclear DNAs suggest that the macronucleus of Tetrahymena is not entirely composed of complete genomes and that parts of the genetic material must be treated specifically for different sequences either during extrusion or during replication.

A possible skeletal substructure of the macronucleus of Tetrahymena

Upon removal of chromatin from isolated macronuclei of tetrahymena, residual structures are obtained, the organization of which faithfully reflects the distinctive architecture of the macronucleus. Macronuclei are isolated by a new procedure in which cells are lysed by immersion in citric acid and Triton X-100. This method is rapid and efficient and leaves the nuclear structures stripped of nuclear envelope and nucleoli. The remaining interconnected chromatin bodies are structurally differentiated into a dense outer shell and a fibrillar inner core. The fibrillar component is identified as chromatin because it is removed upon digestion with DNase and extraction with 2 M NaCl. The dense shell of the chromatin body is unaffected by the digestion procedure, which leaves a skeletal structure comprised of hollow spherical bodies. Analysis of the protein composition by SDS acrylamide gel electrophoresis before and after digestion with DNase and RNase and high-salt extraction shows that histones are diminished, whereas the nonhistone protein composition remains unchanged. It was found the DNase not only extracts chromatin but also protects the nonchromatin structure from the otherwise disruptive effects of high-salt extraction. The method used for isolating the nuclei also affects the structure remaining after the digestion procedure the citric acid/Triton X-100 method enhances the stability of the interconnected spherical bodies. The results indicate that the method for isolating nuclei and the procedure by which chromatin is extracted are both major factors contributing to the detection of a possible nonchromatin nuclear skeleton.

Variability in the timing and outcome of macronuclear assortment in Tetrahymena thermophila

New experimental designs have detected unexpectedly large variations in the time at which macronuclear assortment begins, and in the ratios of the stabilized products. Variation is detected between strains, and, within strains, between conjugating pairs. TheChxlocus gave results ranging from late assortment (40–60 fissions) to early assortment with skewed input, indicating the existence of some relation between the parameters of input ratio and time of determination.

The functional units of macronuclear assortment in Tetrahymena thermophila

Macronuclei assorting simultaneously forH, Chx, Mpr, andco, and containing only one or two copies of theHDallele produced several combinations of phenotypes at the other loci, instead of only one or two such combinations. It follows that macronuclear subnuclei, if they exist at all, must frequently exchange parts. Models involving somatic recombination, transient subnuclei, or progressive chromosome fragmentation are discussed as possible explanations.

Life cycle variation and regulation of macronuclear DNA content in Tetrahymena thermophila

The mean DNA content of G2 macronuclei varies during the life cycle of the ciliate Tetrahymena thermophila. Early in the life cycle the mean is about 130 C; later it is about 94 C. In hybrids between strains A and B the decrease from 130 C to 94 C usually began after 60 fissions after conjugation. In B X B clones the decrease was complete by 50 fissions. The data suggest that there may be a genetic difference between strains A and B with respect to the onset of the decrease in DNA content. The downward regulation of the mean DNA content appears to be related to the mechanism which removes the variance in macronuclear DNA content which is added to macronuclei by unequal macronuclear division. Unequal macronuclear division regularly occurs at all stages of the life cycle, with larger macronuclei tending to divide more unequally. In the absence of regulation, unequal macronuclear division would constantly add variance to G1 macronuclei and their range would continue to increase. Analysis of the variances of G1 and G2 macronuclei suggests that at all stages of the life cycle the added variance is removed by acting upon nuclei which become too small or too large. According to this model, macronuclei with smaller amounts of DNA are regulated upward by an extra macronuclear S phase, while larger amounts are regulated downward by chromatin extrusion and the skipping of macronuclear S. The mean DNA content appears to change during the life cycle because the thresholds at which macronuclei become too small or too large are readjusted. It is postulated that these thresholds are a function of gene dosage.