Cloning and characterization of Paramecium mitochondrial DNA replication initiation regions

Genome plasticity in Paramecium bursaria revealed by population genomics

Background

Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae.

Results

We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways.

Conclusions

We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments.

Supplementary information

The online version contains supplementary material available at 10.1186/s12915-020-00912-2.

Structural and functional analysis of the origin of replication of mitochondrial DNA from Paramecium aurelia : I. Inverted complements form the terminal loop

Initiation of replication of the linear mitochondrial DNA from Paramecium occurs at a unique cross-linked terminus of the monomer molecule. Dimer length molecules, containing head-to-head monomers, are replicative intermediates. Previous studies have been with cloned dimer initiation region fragments but here we have isolated and sequenced isomeric forms of restriction fragments located at the initiation end of the monomer. The sequence isomers are inverted complements of each other in the region identified as the single-stranded DNA terminal loop. The unusual electrophoretic behaviour of these terminal restriction fragments supports the sequence data result that the loop is single stranded. These structural features are discussed in regard to mechanisms for the processing of dimer to monomer molecules.

Paramecium mitochondrial DNA sequences and RNA transcripts for cytochrome oxidase subunit I, URF1, and three ORFs adjacent to the replication origin

A 2-kb region adjacent to the replication origin (ori) and a 3-kb region located between the small and large ribosomal RNAs of Paramecium mitochondrial (mt) DNA have been sequenced and the locations of their transcripts determined. The ori segment contains four transcripts, some of which are overlapping, which encode a known protein and two other open reading frames. The other segment encodes, on separate transcripts, the cytochrome c oxidase subunit one gene (COI) and the URF1 gene (ND1) common to most mt genomes. All these genes have the same orientation and do not contain introns. The COI gene is the most divergent of those known and has an internal 108 amino acid 'insert' not found in COI genes from other organisms. With these data it is possible to define a probable Paramecium mt genetic code. With the exception that TGA codes for tryptophan and the use of different start codons, Paramecium mtDNA appears to follow the universal code. GTA possibly can be used as a start codon.

Identification of Paramecium mitochondrial proteins using antibodies raised against fused mitochondrial gene products

Paramecium aurelia mitochondrial (mt) DNA fragments carrying the coding regions for two proteins, P1 (in the region adjacent to the origin of replication) and COII (subunit II of cytochrome oxidase), were used to study mt gene expression. The sequence for the portion of mtDNA containing P1 has already been described [Pritchard et al., Gene 44 (1986) 243-253]. The complete nucleotide sequence of the portion containing the COII gene is presented here. An 18.5-kDa protein was produced in maxicells when a fragment containing a major portion of the sequence coding for P1 was used. This fragment and a fragment carrying the COII gene were cloned into the expression vector pTRPLE', and antibodies were raised against the resulting fusion proteins in an Escherichia coli lysate. Western blots of Paramecium mt extracts identified two proteins, one 21 kDa (COII) and the other 23.5 kDa (P1). The size of the P1 protein is in agreement with the size of the open reading frame in that region of mitochondrial DNA. Based on extensive amino acid homology to the Paramecium gene and limited homology to COII genes from other organisms, the COII gene in another ciliate, Tetrahymena pyriformis, was identified just upstream of the small subunit rDNA in previously published sequences (Schnare et al., 1986). The size of the COII gene and the homology with the COII gene from Tetrahymena suggest that ATC, ATT, GTG and GTC could be used as translational initiators in Paramecium mitochondria.

Molecular cloning of the terminal hairpin of vaccinia virus DNA as an imperfect palindrome in an Escherichia coli plasmid

The genome of vaccinia virus is a linear duplex molecule of approximately 185 kb with hairpins at each end that link the complementary strands. The hairpins, which exist in two forms that are inverted and complementary in sequence, were isolated as XbaI restriction fragments and converted to a linear intermolecular duplex structure by denaturation and reannealing. The latter was then stably cloned as a 142-bp imperfect palindrome in an Escherichia coli plasmid. The insert was excised from the plasmid and the palindrome was extended on both sides by ligating it to the adjacent vaccinia virus DNA segment. The resulting fragment was cloned as a 278-bp imperfect palindrome. Restriction endonuclease analysis and DNA sequencing indicated the absence of any deletions or rearrangements. After excision from the plasmid, the palindrome was converted by heating and rapid cooling to the original two hairpin forms. In this manner, large quantities of vaccinia virus telomeres may be obtained for physical and biochemical studies.

Inter-species sequence diversity in the replication initiation region of Paramecium mitochondrial DNA

Mitochondrial DNA from Paramecium aurelia is a linear molecule. Replication is initiated at a unique cross-linked molecular terminus. During replication dimer length molecules, consisting of two head-to-head monomers, are generated. We have cloned the head-to-head dimer initiation region from five different species and several stocks (or races) within species and determined its DNA sequence. For all species, this dimer initiation region consists of a central non-palindromic sequence containing almost exclusively A and T, arranged in an array of direct tandem repeats. In an intra-species comparison, the sequences of the repeat units are relatively homogeneous; inter-species comparisons, however, show diversity except for a conserved "Goldberg-Hogness box", T-A-T-A-A-A-T-A. The size of a repeat unit and the number of repeats within a molecule can vary over a wide range, even in an intra-species comparison. Because of these wide inter-species variations observed, it is likely that the function of this region imposes few constraints on the sequence other than its high A + T content and possibly a Goldberg-Hogness box. The array of direct tandem repeats may have arisen from unequal recombination or crossover within this region. Adjacent to the non-palindromic region is a transcribed sequence which is highly conserved for all species and presumably represents a gene coding region.

The terminal organization of macronuclear DNA in Oxytricha fallax

The macronucleus of the hypotrichous ciliate Oxytricha fallax is transcriptionally active and contains linear achromosomal DNA molecules that function as single-gene units. The terminal organization of macronuclear DNA was analyzed by chemical sequencing and S1 mapping. The terminal sequence of total macronuclear DNA was determined for molecules labeled at the 5' or 3' ends. Results indicate that the 5' sequence C4A4C4A4C4 and the 3' sequence G4T4G4T4G4T4G4T4G4 occur at both ends of all DNA molecules in the macronucleus. The discrepancy in the length of the common terminal sequence between the 5' and 3' ends was clarified by a limited S1 digestion experiment, which indicated the existence of a 16 nucleotide long single-stranded tail at the 3' ends.

Organization and closing of mitochondrial deoxyribonucleic acid from Paramecium tetraaurelia and Paramecium primaurelia

Previously we showed that the mitochondrial deoxyribonucleic acid (DNA) from Paramecium aurelia consists of a linear genome and that replication of this genome is initiated at one terminus and proceeds unidirectionally to the other terminus. Analyses of mitochondria from four closely related species (1, 4, 5, and 7) indicated that the species 1, 5, and 7 DNAs are essentially completely homologous but that the species 4 mitochondrial DNA is only 40 to 50% homologous with that from species 1. The major regions of homology are those containing the genes for ribosomal ribonucleic acid (RNA). To understand the replication and organization of the linear mitochondrial genome better, we compared species 1 (Paramecium primaurelia) and 4 (Paramecium tetraaurelia) DNAs with regard to restriction fragment mapping and homology between initiation regions; we also identified the sites of the genes for ribosomal RNA. In general, the structures of the species 1 and 4 mitochondrial genomes were quite similar. Each ribosomal RNA gene was present in one copy per genome, with the large ribosomal RNA gene located near the terminal region of replication and the small ribosomal RNA gene located more centrally. These two genes were separated by about 10 kilobases in the species 1 genome and by about 12 kilobases in the species 4 genome. In contrast to our previous findings, by using nonstringent hybridization conditions we detected homology between the species 1 and 4 DNA fragments containing the initiation regions. We constructed recombinant DNA clones for many fragments, especially those containing the initiation region and the ribosomal RNA genes. We also constructed restriction enzyme maps for six enzymes for both P. primaurelia and P. tetraaurelia.

Replication of linear mitochondrial DNA from Paramecium: sequence and structure of the initiation-end crosslink

Replication of the 14-micrometer linear Paramecium mitochondrial DNA is initiated by a crosslinking of the duplex strands at the initiation end of the molecule. As a consequence of the crosslink, a head-to-head dimer molecule, or palindrome, is a replicative intermediate. The central region of the dimer molecules of two species was cloned and sequenced, In the distal regions, the sequence is palindromic as expected; however, in the central region, there is a nonpalindromic sequence that is rich in A + T and contains direct tandem repeats. It is proposed that the nonpalindromic sequence constitutes the crosslink. Implications for the replication scheme are discussed. The model is unlike any other for a linear DNA.

Organization and closing of mitochondrial deoxyribonucleic acid from Paramecium tetraaurelia and Paramecium primaurelia

Previously we showed that the mitochondrial deoxyribonucleic acid (DNA) from Paramecium aurelia consists of a linear genome and that replication of this genome is initiated at one terminus and proceeds unidirectionally to the other terminus. Analyses of mitochondria from four closely related species (1, 4, 5, and 7) indicated that the species 1, 5, and 7 DNAs are essentially completely homologous but that the species 4 mitochondrial DNA is only 40 to 50% homologous with that from species 1. The major regions of homology are those containing the genes for ribosomal ribonucleic acid (RNA). To understand the replication and organization of the linear mitochondrial genome better, we compared species 1 (Paramecium primaurelia) and 4 (Paramecium tetraaurelia) DNAs with regard to restriction fragment mapping and homology between initiation regions; we also identified the sites of the genes for ribosomal RNA. In general, the structures of the species 1 and 4 mitochondrial genomes were quite similar. Each ribosomal RNA gene was present in one copy per genome, with the large ribosomal RNA gene located near the terminal region of replication and the small ribosomal RNA gene located more centrally. These two genes were separated by about 10 kilobases in the species 1 genome and by about 12 kilobases in the species 4 genome. In contrast to our previous findings, by using nonstringent hybridization conditions we detected homology between the species 1 and 4 DNA fragments containing the initiation regions. We constructed recombinant DNA clones for many fragments, especially those containing the initiation region and the ribosomal RNA genes. We also constructed restriction enzyme maps for six enzymes for both P. primaurelia and P. tetraaurelia.

Evolutionary divergence of mitochondrial DNA from Paramecium aurelia

Mitochondrial (mt) DNA from four sibling species within the Paramecium aurelia complex, including stocks of different geographic origin and mutants, were analyzed using four 6-bp recognition site and one 4-bp recognition site endonucleases and the sequence divergence was estimated using Upholt's (1977) statistical procedure. All four species were readily distinguishable regardless of the restriction endonuclease employed. With intraspecies comparisons, no differences were observed which could be accounted for on the basis of geographic origin. Except for species 4, each stock (and mutant) gave a species-specific fragment pattern. For species 4, while the patterns were distinct from the other species, two species-specific type of patterns were found, designated A and B. The sequence divergence between these was estimated to be between 1 and 2 percent. With interspecies comparisons, the sequence divergence ranged from 3.9 to 10.3% with the greatest divergence being between species 1 and 4, and the least between species 1 and 5. The similarity between species 1 and 5 is in accord with other criteria for interspecies comparisons. The degree of sequence divergence measured here in Paramecium mt DNA is well within the range reported for rodents and primates. All four species mt DNA were cleaved to many DNA fragments by DPN II, an enzyme which recognizes non-methylated sites, and not by DPNI, the methyl-site specific counterpart of DPN II, suggesting that mt DNA from Paramecium aurelia is not appreciably methylated, if at all.