Macronuclear DNA organization and transcription in Paramecium primaurelia

Paramecium Genetics, Genomics, and Evolution

The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.

An indexed genomic library for Paramecium complementation cloning

Recent pioneering work opened the way for cloning genes in Paramecium by functional complementation of mutants. We present here the construction and pilot utilization of a new indexed library of Paramecium macronuclear DNA. The library is made of 61,440 clones containing inserts mostly between 6 and 12 kilobases. It has already allowed the complementation cloning of four new genes, and this library has proven to be very useful for rapid hybridization cloning.

A high degree of macronuclear chromosome polymorphism is generated by variable DNA rearrangements in Paramecium primaurelia during macronuclear differentiation

DNA rearrangements in Paramecium lead to the formation of macronuclear chromosomes, the sizes of which range from 50 and 800 kb (1 kb is 10(3) base-pairs). This process does not appear to be a simple size reduction of the micronuclear chromosomes by specific and reproducible DNA sequence elimination and chromosomal breakage followed by chromosomal amplification. On the contrary, this process generates a variety of different, but sequence-related, macronuclear chromosomes from a unique set of micronuclear chromosomes. This paper describes an attempt to understand the nature of the diversity of the macronuclear chromosomes and the mechanisms of their production. The structure of three macronuclear chromosomes, 480, 250 and 230 kb in size, have been determined utilizing chromosome-jumping and YAC-cloning techniques. The two smallest chromosomes correspond roughly to the two halves of the longest chromosome. The main contribution to the diversity arises from the chromosomal ends and is due to variable positions of the telomere addition sites and/or to variable rearrangements of DNA sequences. The 480 kb chromosome contains a region of variable length, which is likely to be due to a variable deletion, located at the position of telomerization seen in the two small chromosomes. A model of chromosomal breakage is proposed to rationalize this result where micronuclear DNA is first amplified, broken and degraded to various extent from the newly formed ends, which subsequently are either telomerized or religated. Potential implications of these processes for gene expression is discussed. Known phenotypes that have a macronuclear determinism could be explained by this type of process.

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.

Developmental expression of macronuclear specific antigen in Paramecium caudatum

We obtained a monoclonal antibody (MA-1) specific for macronuclei of the ciliate Paramecium caudatum and P. dubosqui. Immunoblotting showed that the antigen was a polypeptide of 50 kilodalton (kDa). During the process of nuclear differentiation in P. caudatum, the MA-1 antigens appeared in the macronuclear anlagen immediately after four out of eight post zygotic nuclei differentiated morphologically into the macronuclear anlagen. Afterwards, the antigens could be detected in the macronucleus through the cell cycle, and disappeared when the macronucleus began to degenerate in exconjugant cells. These results suggest that the antigens may play a role in the differentiation and function of the macronucleus.

Telomeric site position heterogeneity in macronuclear DNA of Paramecium primaurelia

In Paramecium primaurelia, the macronuclear gene encoding the G surface protein is located near a telomere. In this study, multiple copies of this telomere have been isolated and the subtelomeric and telomeric regions of some of them have been sequenced. The telomeric sequences consist of tandem repeats of the hexanucleotides C4A2 or C3A3. We show that the location where these repeats are added, which we call the telomeric site, is variable within a 0.6-0.8-kb region. These results are discussed in relation with the formation of macronuclear DNA.

Isolation and translation of mRNA coding for the variant surface antigens of Paramecium

In the poly(A)+RNA isolated from the ciliate Paramecium primaurelia is found a discrete and abundant mRNA species of high molecular weight (corresponding to about 9,000 nucleotides). This mRNA species has size and abundance characteristics that identify it tentatively as the message coding for the variant cell-surface antigens. After microinjection of the high molecular weight mRNA into amphibian oocytes, polypeptides are synthesized that are immunoprecipitated specifically with antibodies directed against the homologous Paramecium antigen. On collecting the culture medium of oocytes microinjected with Paramecium mRNA, newly-synthesized complete antigen molecules (Mr approximately 300,000) can be recovered by immunoprecipitation.

Common terminal repeats of the macronuclear DNA are absent from the micronuclear DNA in hypotrichous ciliate, Stylonychia pustulata

Comparison of nucleotide sequences of a macronuclear DNA and its micronuclear counterpart of a hypotrichous ciliate, Stylonychia pustulata, demonstrates that common terminal repeats (C4A4) of the macronuclear DNA are not present at the corresponding region in the micronuclear genome. The results indicate that the common terminal C4A4 repeat is added or translocated during or after the rearrangement of the micronuclear DNA to the macronuclear DNA.

The effect of temperature change on gene expression in Paramecium primaurelia

When paramecia grown at 24 degrees C are transferred rapidly to 32 degrees C, DNA and protein synthesis continue uninterrupted but at higher rates. Electron microscopic observations indicate that more of the macronuclear chromatin is transcribed at the elevated temperature. This interpretation is supported by hybridization experiments which show that the percentage of the macronuclear genome transcribed into poly(A)+RNA is 24 degrees C and 35% at 32 degrees C. Kinetic analysis of cDNA-poly(A)+RNA hybridizations reveals three abundance classes of poly(A)+RNA and indicates that the number of genes expressing low abundance sequences is about 9000 at 24 degrees C and 13000 at 32 degrees C. The intermediately abundant and highly abundant classes are represented by 100-200 and 1-3 different kinds of RNA sequence, respectively. Cross hybridization shows that changes occur throughout the distribution of abundance classes of poly(A)+RNA with increase in temperature.

Genome size and DNA complexity of Plasmodium falciparum

Plasmodium falciparum DNA was prepared from cells cultured in vitro in human erythrocytes. The P. falciparum DNA was mixed with a tritium-labeled Escherichia coli DNA standard, and the kinetics of reassociation were measured using hydroxyapatite chromatography. It was found that the P. falciparum genome size is equal to 3.8 . 10(8) nucleotide pairs, and that a repetitive component is present which contains about 10% of the DNA. The average repetition frequency in this component is 95 copies of each sequence.

Macronuclear chromatin organization in Paramecium primaurelia

Chromatin organization and transcriptional activity in the macronucleus of the ciliate Paramecium primaurelia have been studied by electron microscopic examination of spread chromatin preparations. Under spreading conditions which inhibit the activity of endogenous nucleases and proteases, various morphologically distinct types of chromatin are seen: (1) Largely condensed chromatin in the form of 30-40 nm supranucleosomal globules which aggregate to form knobbly 40-60 nm fibres and unravel into 12 nm nucleosomal filaments; (2) In rapidly growing cells, extended chromatin arranged groups of 4-8 adjacent nucleofilaments, each bearing numerous and very densely packed lateral fibrils. These fibrils are 20 nm thick, have a smooth outline and extend to lengths of up to 3 micron. Such transcripts are grouped in units along the chromatin axis and are apparently organized in register in adjacent filaments; (3) In starved cells, extended nucleofilaments bearing only occasional RNP fibrils. These various morphological characteristics are discussed in terms of macronuclear transcriptional activity and the polyploid nature of macronuclei.

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.

RNA and macronuclear transcription in the ciliate Stylonychia mytilus

Nuclear and cytoplasmic RNA of Stylonychia mytilus were analyzed on denaturing polyacrylamide gels. The molecular weight of rRNA precursor molecules is within a range of 2.1 x 10(6) daltons. A comparison between the electrophoretic pattern of nuclear non-ribosomal RNA and cytoplasmic mRNA indicates that a considerable amount of nuclear RNA sequences is of higher molecular weight than cytoplasmic RNA sequences. The molecular weight distribution of cytoplasmic RNA supports the assumption that also in Stylonychia an average sized mRNA molecule contains 1,200-1,500 nucleotides according to a molecular weight of 4 x 10(5) to 5 x 10(5) daltons. The size of the polyadenylic acid fragment of poly-A+ RNA molecules is about 120 nucleotides. The total mass of cytoplasmic RNA is around 7.5/10(10)g/cell, corresponding to 1.2 x 10(7) average sized mRNA molecules per cell. RNA excess hybridization experiments show that 60% of the DNA sequences are transcribed into nuclear RNA and that the cytoplasmic mRNA sequences are homologous to about 40% of macronuclear DNA sequences. There is no indication of different frequency classes within the mRNA. The number of different mRNA species in a Stylonychia cell is 1.2-1.5 x 10(4). On the average each of them is present about 1,000 times in every cell.