Localization of genes for ribosomal RNA in the nuclei of Oxytricha fallax

Synthesis of pre-rRNA and mRNA is directed to a chromatin-poor compartment in the macronucleus of the spirotrichous ciliate Stylonychia lemnae

In contrast to the chromosomal genome organization common to most eukaryotes, DNA in the macronucleus of spirotrichous ciliates like Stylonychia lemnae is organized into small gene-sized nanochromosomes. We intended to elucidate whether a spatial organization of nucleoli similar to other eukaryotes can be found in absence of typical chromosomes. Whereas micronuclei of Stylonychia exhibit homogenously stained heterochromatin and possess no nucleoli, macronuclear chromatin is compartmentalized and contains numerous putative nucleoli. Since the identity of these spherical structures has never been unequivocally demonstrated to date, we applied immunofluorescence techniques together with confocal laser scanning microscopy to identify nucleolar bodies in the macronucleus of Stylonychia and to analyse their spatial organization. We found that multiple spherical bodies, which fulfil nucleolar function, occupy a peripheral localization in mature macronuclei. Using fibrillarin/Nop1p as a nucleolar marker, we monitored the assembly of such nucleolar bodies during macronuclear differentiation. 3D-FISH experiments revealed that rRNA genes are mostly concentrated adjacent to but not inside of fibrillarin/Nop1p-containing bodies. We further showed that transcription sites for rRNA synthesis but also for mRNA synthesis occur predominantly at surfaces of nucleolar bodies and chromatin-poor spaces bordering condensed chromatin. Our data suggest that transcription of rRNA genes in the macronucleus of Stylonychia does not rely on a classical nucleolus-type organization. We assume that vectorial synthesis and processing of rRNA and mRNA is directed to a functional interchromatin compartment.

Spatiotemporal sites of DNA replication in macro- and micronuclei of the ciliate Paramecium caudatum

Spatiotemporal sites of DNA replication in macro- and micronuclei of the ciliated protozoan Paramecium caudatum were analyzed by confocal laser scanning microscopy following incorporation of the thymidine analogue BrdU and indirect immunofluorescence. In the macronucleus, replication sites were localized to numerous small domains and scattered throughout the nucleoplasm. This pattern persisted during all periods of the S phase. A single constant pattern with discrete replication foci was also observed in the micronucleus. No obvious differences were seen between the two kinds of nuclei. Pulse-chase-pulse double-labeling experiments with two thymidine analogues (CldU and IdU) revealed that dispersed sites of replication were activated at different times during the S phase and a replication site takes about 2h to complete replication in the macronucleus. When cells were labeled by BrUTP to examine transcriptional activity in the two kinds of nuclei, incorporation of BrUTP into the macronucleus occurred throughout the cell cycle, whereas there was no detectable RNA synthesis in the micronucleus. From these findings, we conclude that, despite large differences in structure and function of macro- and micronuclear genomes, both nuclei show a similar replication pattern with discrete subnuclear foci scattered throughout the nucleoplasm at all times during the S phase.

The DNA of ciliated protozoa

Ciliates contain two types of nuclei: a micronucleus and a macronucleus. The micronucleus serves as the germ line nucleus but does not express its genes. The macronucleus provides the nuclear RNA for vegetative growth. Mating cells exchange haploid micronuclei, and a new macronucleus develops from a new diploid micronucleus. The old macronucleus is destroyed. This conversion consists of amplification, elimination, fragmentation, and splicing of DNA sequences on a massive scale. Fragmentation produces subchromosomal molecules in Tetrahymena and Paramecium cells and much smaller, gene-sized molecules in hypotrichous ciliates to which telomere sequences are added. These molecules are then amplified, some to higher copy numbers than others. rDNA is differentially amplified to thousands of copies per macronucleus. Eliminated sequences include transposonlike elements and sequences called internal eliminated sequences that interrupt gene coding regions in the micronuclear genome. Some, perhaps all, of these are excised as circular molecules and destroyed. In at least some hypotrichs, segments of some micronuclear genes are scrambled in a nonfunctional order and are recorded during macronuclear development. Vegetatively growing ciliates appear to possess a mechanism for adjusting copy numbers of individual genes, which corrects gene imbalances resulting from random distribution of DNA molecules during amitosis of the macronucleus. Other distinctive features of ciliate DNA include an altered use of the conventional stop codons.

An endonuclease restriction analysis of the ribosomal RNA genes of Trypanosoma cruzi

The location of ribosomal RNA genes in total-nuclear-enriched DNA preparations of Trypanosoma cruzi was analyzed by using restriction endonucleases and the eight cytoplasmic ribosomal RNA species of this organism. Two contiguous SstI DNA fragments of about 9.88 and 1.7 kilobase pairs contained the three large-size ribosomal RNA species, 18 S, beta, and alpha, and three small-size ribosomal RNA species, s1, s2 and s3. The other two small-size ribosomal species, s4 and s5, were located outside the ribosomal RNA cistron and independently of each other. Spacers of a presumed large length, about 20 kilobase pairs or more, hampered the identification of putative adjacent ribosomal RNA cistrons.