Genome amplification and gene expression in the ciliate macronucleus

Kinesin-14 is Important for Chromosome Segregation During Mitosis and Meiosis in the Ciliate Tetrahymena thermophila

Ciliates such as Tetrahymena thermophila have two distinct nuclei within one cell: the micronucleus that undergoes mitosis and meiosis and the macronucleus that undergoes amitosis, a type of nuclear division that does not involve a bipolar spindle, but still relies on intranuclear microtubules. Ciliates provide an opportunity for the discovery of factors that specifically contribute to chromosome segregation based on a bipolar spindle, by identification of factors that affect the micronuclear but not the macronuclear division. Kinesin-14 is a conserved minus-end directed microtubule motor that cross-links microtubules and contributes to the bipolar spindle sizing and organization. Here, we use homologous DNA recombination to knock out genes that encode kinesin-14 orthologues (KIN141, KIN142) in Tetrahymena. A loss of KIN141 led to severe defects in the chromosome segregation during both mitosis and meiosis but did not affect amitosis. A loss of KIN141 altered the shape of the meiotic spindle in a way consistent with the KIN141's contribution to the organization of the spindle poles. EGFP-tagged KIN141 preferentially accumulated at the spindle poles during the meiotic prophase and metaphase I. Thus, in ciliates, kinesin-14 is important for nuclear divisions that involve a bipolar spindle.

Dynamic Change of Cellular Localization of Microtubule-Organizing Center During Conjugation of Ciliate Tetrahymena thermophila

To obtain a comprehensive picture of microtubule dynamics during conjugation, the mode of sexual reproduction in ciliates, we combined indirect immunofluorescence and three-dimensional imaging using confocal laser-scanning microscope to visualize the cellular localization of DNA, microtubules, and γ-tubulin, the main component of the microtubule-organizing center in mating Tetrahymena cells. As the conjugational stages proceeded, the distribution of γ-tubulin changed drastically and microtubules showed dynamic appearance and disappearance during meiosis, nuclear selection, nuclear exchange, and the development of new macronuclei. This study highlights the involvement of cytoskeletal regulation in the modulation of germline nuclear motilities required for ciliate reproduction.

Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence

Paramecium has long been a model eukaryote. The sequence of the Paramecium tetraurelia genome reveals a history of three successive whole-genome duplications (WGDs), and the sequences of P. biaurelia and P. sexaurelia suggest that these WGDs are shared by all members of the aurelia species complex. Here, we present the genome sequence of P. caudatum, a species closely related to the P. aurelia species group. P. caudatum shares only the most ancient of the three WGDs with the aurelia complex. We found that P. caudatum maintains twice as many paralogs from this early event as the P. aurelia species, suggesting that post-WGD gene retention is influenced by subsequent WGDs and supporting the importance of selection for dosage in gene retention. The availability of P. caudatum as an outgroup allows an expanded analysis of the aurelia intermediate and recent WGD events. Both the Guanine+Cytosine (GC) content and the expression level of preduplication genes are significant predictors of duplicate retention. We find widespread asymmetrical evolution among aurelia paralogs, which is likely caused by gradual pseudogenization rather than by neofunctionalization. Finally, cases of divergent resolution of intermediate WGD duplicates between aurelia species implicate this process acts as an ongoing reinforcement mechanism of reproductive isolation long after a WGD event.

Macronuclear Subunits of Tetrahymena thermophila Are Functionally Haploid

In Tetrahymena thermophila the major argument for the existence of diploid subunits has been that some loci show a delay in the accumulation of stable subclones during macronuclear assortment. This delay is based on the assumption that throughout the life cycle there are 45 subunits. We find that for at least 50 fissions after conjugation there is sufficient DNA for 66 haploid subunits. These additional subunits early in the life cycle are sufficient to explain the observed accumulation of stable subclones in all instances. This removes the need to invoke diploidy to explain assortment, thus resolving the question of subunit ploidy in favor of haploidy.

Comparison of the evolutionary distances among syngens and sibling species of Paramecium

The morphospecies of the genus Paramecium have several mating type groups, so-called syngens, composed of cells of complementary mating types. The Paramecium aurelia complex is composed of 15 sibling species assigned to the species from the syngen. To increase our understanding of the evolutionary relationships among syngen and sibling species of the genus Paramecium, we investigated the gene sequences of cytosol-type hsp70 from 7 syngens of Paramecium caudatum and 15 sibling species of P. aurelia. Molecular phylogenetic trees indicated that the P. aurelia complex could be divided into four lineages and separated into each sibling species. However, we did not find any obvious genetic distance among syngens of P. caudatum, and they could only be separated into two closely related groups. These results indicated that the concept of syngens in P. caudatum differs quite markedly from that of the P. aurelia complex. In addition, we also discuss the relationships among these species and other species, Paramecium jenningsi and Paramecium multimicronucleatum, which were once classified as varieties of P. aurelia.

Developmentally excised sequences in micronuclear DNA of Paramecium

DNA processing occurs in ciliates at autogamy and conjugation when new macronuclei are formed from micronuclei and old macronuclei degrade. Processing of micronuclear DNA consists of removal of certain internal sequences, chromosomal fragmentation, addition of new telomeres, and amplification. Aside from a recent brief report, internal eliminated sequences have not been described in Paramecium. In this paper we characterize nine internal eliminated sequences found within and near the gene that codes for surface protein A in Paramecium tetraurelia. Of these nine, seven are located within the translated portion of the gene, and all include short, inverted terminal repeats. The characteristic sequence, TA, appears at the boundaries of all of the internal eliminated sequences.

Induction of specific macronuclear developmental mutations by microinjection of a cloned telomeric gene in Paramecium primaurelia

In Paramecium, the differentiation of a highly polyploid macronucleus from a diploid nucleus is accompanied by an extensive reorganization of the genome, involving reduction in chromosome size and formation of new telomeres at heterogeneous, but reproducible, positions. The results presented here, as well as work by others, indicate that telomere addition regions are not strictly determined by the micronuclear sequence, but are at least partially controlled by the old macronucleus. It is shown that microinjecting a high copy number of a plasmid containing the G surface antigen gene into the macronucleus of wild-type cells specifically modifies the processing of the G gene-bearing micronuclear chromosome at the following autogamy. Telomeric repeats are added upstream of the gene, rather than at their wild-type position 5 kb downstream of its 3' end, resulting in the deletion of the gene from the new macronucleus. This macronuclear mutation is unstable at the following autogamy, giving rise to many different telomere addition regions in different postautogamous clones. However, after several successive autogamies, cell lines can be obtained in which the telomeres reproducibly form in the same region. In crosses with wild-type cells, these macronuclear mutations show cytoplasmic inheritance; the micronuclei of the mutants are shown to be fully functional. The implications for the mechanism of choice of telomere addition sites are discussed.

Alternative processing of sequences during macronuclear development in Tetrahymena thermophila

DNA is eliminated during development of the somatic MACronucleus from the germinal MICronucleus in the ciliated protozoan, Tetrahymena thermophila. Facultatively persistent sequences are a class of sequences that persist in the MAC DNA of some cell lines but are eliminated from the MAC DNA of other cell lines. One cloned MAC fragment contains a persistent sequence as well as sequences normally retained in the MAC. When this cloned fragment was used to construct MAC restriction maps of this region in cell lines whose MAC DNAs do, or do not, contain the persistent sequence, extensive variation in the map flanking this region was observed. The different DNA rearrangements of this MIC segment are epigenetically determined during or soon after MAC development. Moreover, different rearrangements may occur among the 45 copies of this MIC segment as a MAC is formed, resulting in polymorphisms that are later resolved by phenotypic assortment.

Eliminated sequences with different copy numbers clustered in the micronuclear genome of Tetrahymena thermophila

As the ciliated protozoan Tetrahymena thermophila develops a new macronucleus (MAC) from products of its micronucleus (MIC), several repetitive sequences are eliminated from the MAC genome. Four MIC DNA clones containing repetitive sequences that are eliminated from the MAC were obtained. One clone contains a representative from each of three families of eliminated sequences. One, present in 200-300 copies in the MIC, is almost completely eliminated from the MAC. A second, present in approximately 50 copies in the MIC, is scattered throughout the genome, although up to half of the family members examined could be localized to chromosome 2. Approximately one tenth of the members of this less repetitive family persist in the MAC while the rest are eliminated. The third type of eliminated sequence has three to four members, all of which are eliminated from the MAC. Three of the members are located on three of the five MIC chromosomes, and one could not be mapped. This sequence is clustered with the other two families of sequences in at least three of the four sites. All three types of eliminated sequences are found in similar arrangements in the MIC of several different inbred strains of T. thermophila.

Repair of 8-methoxypsoralen induced DNA interstrand cross-links in Tetrahymena thermophila. The effect of inhibitors of macromolecular synthesis

The effect of several growth-inhibiting compounds on the repair of 8-methoxypsoralen-UVA-light-induced DNA interstrand cross-links has been studied in the protozoan Tetrahymena thermophila. The repair process was analyzed by the alkaline elution technique and could be divided into 3 phases: a protein-DNA complexing phase, a DNA-incision phase and finally a DNA-ligation phase. The incision was found to be completely inhibited by novobiocin (50 micrograms/ml), nalidixic acid (150 micrograms/ml), n-butyrate (15 mM) and cycloheximide (1 microgram/ml), while no effect was observed for cytosine-1-beta-D-arabinofuranoside (10 mM), puromycin (1 mM), hydroxyurea (5 mM) or 3-aminobenzamide (2.5 mM). None of the compounds showed any effect on the protein-DNA complexing step, and the ligation was partly inhibited only by nalidixic acid (150 micrograms/ml). The involvement of topoisomerases in the repair of psoralen-induced DNA interstrand cross-links is suggested.

Characterization of macronuclear DNA in five species of ciliates

Macronuclear DNA of four hypotrichous and one holotrichous ciliate species was characterized by biochemical techniques. The renaturation kinetics of the macronuclear DNAs of all five species were similar. Repetitive sequences occur only in an amount below 2%. Although the DNA content of the macronuclei of the species differs considerably, the kinetic complexity of the macronuclear DNA is rather uniform (around 3 x 10(10) daltons, i.e., 4-11 x the E. coli genome). Only in the macronuclei of the hypotrichous species the DNA exists as gene-sized fragments.

Macronuclear DNA organization and transcription in Paramecium primaurelia

Macronuclear DNA was isolated from Paramecium primaurelia, stock 168. Although the macronucleus is polyploid to the extent of 840C, in other respect the DNA appears to be simply organized, having neither satellite sequences nor substantial amounts of intermediately repetitive sequence. The sequence complexity of macronuclear DNA is quite low for a eukaryote cell, being approximately 19 times more complex than the genome of Escherichia coli. In addition, the GC content is low (25%) and the isolated DNA molecules have lengths mostly in the range 0.2-5 micrometer. In these various respects, the macronuclear DNA of Paramecium is similar to that of other ciliates. A clone of Paramecium cultured under controlled conditions contains polyadenylated RNA sequences which are homologous to 5-8% of the macronuclear DNA. Sequence complexity analysis indicates that the polyadenylated RNA contains two abundance classes of molecules, one present at low frequency and transcribed from approximately 10(4) genes, the other at 100 times greater concentration and transcribed from about 100 genes. The relevance of these results to the control of gene expression in Paramecium is discussed.

Genome structure of Tetrahymena pyriformis

Reassociation kinetics of DNA from the macronucleus of the ciliate, Tetrahymena pyriformis GL, has been studied. The genome size determined by the kinetic complexity of DNA was found to be 2.0 X 10(8) base pairs (or 1.2 X 10(11) daltons). About 90% of the macronuclear DNA fragments 200-300 nucleotides in length reassociate at a rate corresponding to single-copy nucleotide sequences, and 7-9% at a rate corresponding to moderate repetitive sequences; 3-4% of such DNA fragments reassociate at C0t practically equal to zero. To investigate the linear distribution of repetitive sequences, DNA fragments of high molecular weight were reassociated and reassociation products were treated with S1-nuclease. DNA double-stranded fragments were then fractionated by size. It has been established that in the Tetrahymena genome long regions containing more than 2000 nucleotides make up about half of the DNA repetitive sequences. Another half of the DNA repetitive sequences (short DNA regions about 200-300 nucleotides long) intersperse with single-copy sequences about 1,000 nucleotides long. Thus, no more than 15% of the Tetrahymena genome is patterned on the principle of interspersing single-copy and short repetitive sequences. Most of the so called "zero time binding" or "foldback" DNA seem to be represented by inverted self-complementary (palindromic) nucleotide sequences. The conclusion has been drawn from the analysis of this fraction isolated preparatively by chromatography. About 75% of the foldback DNA is resistant to S1-nuclease treatment. The S1-nuclease resistance is independent of the original DNA concentration. Heat denaturation and renaturation are reversible and show both hyper- and hypochromic effects. The majority of the inverted sequences are unique and about 20% are repeated tens of times. According to the equilibrium distribution in CsCl density gradients the average nucleotide content of the palindromic fraction does not differ significantly from that of total macronuclear DNA. It was shown that the largest part of this fraction of the Tetrahymena genome are not fragments of ribosomal genes.

Regulation of macronuclear DNA content in Paramecium tetraurelia

The macronucleus of Paramecium divides amitotically, and daughter macronuclei with different DNA contents are frequently produced. If no regulatory mechanism were present, the variance of macronuclear DNA content would increase continuously. Analysis of variance within cell lines shows that macronuclear DNA content is regulated so that a constant variance is maintained from one cell generation to the next. Variation in macronuclear DNA content is removed from the cell population by the regulatory mechanism at the same rate at which it is introduced through inequality of macronuclear division. Half of the variation in macronuclear DNA content introduced into the population at a particular fission by inequality of division is compensated for during the subsequent period of DNA synthesis. Half of the remaining variation is removed during each subsequent cell cycle. The amount of variation removed in one cell cycle is proportional to the postfission variation. The cell's power to regulate DNA content is substantially greater than that required to compensate for the small differences that arise during division of wild-type cells. For example, a constant variance was still maintained when the mean difference between sister cells was increased to ten times its normal level in a mutant strain. The observations are consistent with a replication model that assumes that each cell synthesizes an approximately constant amount of DNA which is independent of the initial DNA content of the macronucleus. It is suggested that the amount of DNA synthesized may be largely determined by the mass of the cell.

The structure of Tetrahymena pyriformis mitochondrial DNA. I. Strain differences and occurrence of inverted repetitions

We have analysed the structure of the mtDNAs of six amicronucleate Tetrahymena pyriformis strains, belonging to at least four phenosets, as defined by Borden et al. (Borden, D., Whitt, G.S. and Nanney, D.L. (1973) J. Protozool. 20, 693--700). 2. The mtDNAs of all strains are linear, but they differ in size, in their fragmentation by endonuclease EcoRI and in overall sequence; less than 20% sequence homology was found by DNA-DNA hybridization in all combinations tested, except for the mtDNAs from strains T and ST which are indistinguishable. 3. In spite of these marked sequence differences the mtDNAs of all strains share two structural peculiarities: ragged (gnawed) duplex ends and a duplication-inversion, which varies in length between 0.3 and 1.2 micrometer, depending on the strain. In four strains the duplication-inversion is terminal, allowing formation of single-stranded DNA circles with a duplex tail; in two strains it is subterminal. 4. The ragged ends and sub-terminal position of the duplication-inversion in some of the Tetrahymena mtDNAs do not fit any of the current models for the replication of linear mtDNAs.

Unequal distribution of DNA in the macronuclear division of the ciliate Euplotes eurystomus

During asexual fission in the ciliate Euplotes eurystomus, the macronucleus divides amitotically. The macronucleus was found to divide unequally, yielding sister pairs having a mean difference in DNA content of 11.6% DNA content was determined by the Feulgen reaction using a fluorescent Schiff's reagent, and measuring fluorescence by cytophotometry. Variability in macronuclear DNA content was also examined in randomly-paired non-sister cells, and found to be greater than in sister cells. This greater variability could be due to accumulation of differences over a number of divisions, or to interclonal differences in equality of division. Two categories of non-sister cells were examined: recently divided, and "parents" constructed by averaging the DNA contents of progeny. Both showed similar variability in quantity of macronuclear DNA. The fact that cells surviving to divide showed no less variability in amount of DNA than cells immediately after division suggests that extremes in amounts of DNA resulting from unequal division are not selected against.

Quantitative predictions of random segregation models of the ciliate macronucleus

Models of the macronucleus inParamecium tetraureliawhich assume known levels of ploidy and random segregation of subunits smaller than a haploid set at both fission and macronuclear regeneration (MR) are not consistent with the hypothesis that senescence is due to aneuploid imbalance. Either senescence has some other basis or there is a mechanism for regular distribution of subunits at MR. Random segregation models for fission and MR are consistent with most data on survival and heterozygote stability, but if the ploidy level is 860 they fail to account for the data of Nyberg (this volume). Since the ploidy level may be higher than 860, models of random segregation cannot be ruled out forParamecium. Models of the macronucleus in hypotrichs which assume randomly segregating chromosome fragments are consistent with data on survival and on stability of heterozygous genotypes at fission.

Macronuclear DNA in Stentor coeruleus: a first approach to its characterization

The macronuclei of Stentor coeruleus were isolated on a discontinuous sucrose gradient and their DNA was purified by conventional methods. The GC content was 32 mole%. The DNA banded as a single peak on analytical ultracentrifugation at 1·691 g/cm3. The molecular weight of the DNA was 5 × 106 to 4 × 107 daltons. Genome size determined by DNA–DNA reassociation kinetics was 6 × 1010 daltons. The macronuclear genome was mostly simple, about 85% being made of non-repetitive sequences.

Studies on the amount and location of the tRNA and 5-S rRNA genes in Tetrahymena pyriformis GL

The amount and location of tRNA and 5-S rRNA genes in the macronucleus of Tetrahymena pyriformis GL was investigated by DNA-RNA hybridization. Hybridization of 32P-labelled tRNA in excess of unlabelled rRNA (25-S + 17-S + 5-S) showed that at saturation 0.021% of the macronuclear DNA was complementary to tRNA. Hybridization of 32P-labelled 5-S rRNA in excess of unlabelled 25-S + 17-S rRNA and tRNA showed a saturation value of 0.017%. In contrast to the 25-S + 17-S rRNA genes, which are found in DNA of high bouyant density, tRNA and 5-S rRNA genes were distributed evenly throughout the main peak observed when bulk macronuclear DNA was fractionated by density centrifugation in CsCl gradients. Sucrose gradient analyses of total macronuclear DNA showed that tRNA and 5-S rRNA genes were found in DNA of all size classes but a significant enrichment in the slowly sedimenting DNA fraction was observed. Saturation hybridization of 5-S rRNA to purified rDNA showed that rDNA did not contain any 5-S rRNA genes.

Are macronuclear subunits in Paramecium functionally diploid?

The organization of the genetic material in the macronucleus of ciliates has been the subject of considerable controversy. Two of the four models of macronuclear structure predict assortment of the alternative phenotypes of heterozygotes during vegetative growth. Early studies of the phenotypic behaviour of heterozygotes after macronuclear regeneration (Sonneborn, 1947) had supported a diploid subunit model. The availability of quantitative predictions of the rate of assortment for the haploid and chromosomal models (Preer, this volume) and the existence of two alleles controlling a quantitative trait, copper tolerance, inParamecium tetraurelia, has provided an opportunity to test these models. The median tolerance limits to copper of unselected sublines were measured as a function of age. There was no increase in the variance among sublines, as the haploid and chromosomal models predict. Quantitative evaluation shows that subdiploid models with a kinetic complexity of 860 or less are not compatible with the results. This experiment was not sensitive enough, however, to exclude subdiploid models if the kinetic complexity is 2000 or greater. Selection on heterozygotes also failed to provide evidence in favour of assortment. All the results are consistent with and support the diploid subunit model of theParameciummacronucleus.

Studies on Macronuclear DNA from Paramecium aurelia

Macronuclear DNA was isolated from purified macronuclei of Paramecium aurelia and the size distribution was determined with regard to growth phase and method of extraction. DNA molecules as long as 105 microns and as short as 0.2 microns were observed. It was concluded that the method of extraction affected the observed length of DNA extracted and that macronuclear DNA isolated from cells in balanced growth was less susceptible to nuclease degradation than was DNA isolated from cells in stationary phase. Renaturation studies were performed on macronuclear DNA and a kinetic complexity of 22-times E. coli DNA was determined. This value was similar to those values reported for Tetrahymena and Stylonychia macronuclear DNA. Correcting for GC base content yielded a kinetic complexity for Paramecium macronuclear DNA of 11-times E. coli DNA which corresponded to 3 X 10(10) daltons. There would be about 1400 copies of a unit genome of this complexity within each newly replicated macronucleus. Density gradient analysis indicated that the genes coding for ribosomal RNA had a greater density in CsCl than the bulk DNA. Molecular hybridization studies indicated that the genes coding for 25 S RNA represented 0.14 percent of the total macronuclear DNA. Correcting for GC base content, this corresponded to 30-35 25 S RNA genes per unit genome. These results on Paramecium are discussed in relationship to other ciliate macronuclear DNA.