Recent advances in the genetics of Paramecium and Euplotes

Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters

Disentangling biodiversity and community assembly effects on ecosystem function has always been an important topic in ecological research. The development and application of a DNA metabarcoding method has fundamentally changed the way we describe prokaryotic communities and estimate biodiversity. Compared to prokaryotes (bacteria and archaea), the eukaryotic microbes (unicellular eukaryotes) also fulfill extremely important ecological functions in different ecosystems regarding their intermediate trophic positions. For instance, ciliated microbes (accounting for a substantial portion of the diversity of unicellular eukaryotes) perform pivotal roles in microbial loops and are essential components in different ecosystems, especially in water purification processes. Therefore, the community composition of ciliated species has been widely utilized as a proxy for water quality and biological assessment in urban river ecosystems and WWTPs (wastewater treatment plants). Unfortunately, investigating the dynamic changes and compositions in ciliate communities relies heavily on existing morpho-taxonomical descriptions, which is limited by traditional microscopic approaches. To deal with this dilemma, we discuss the DNA-based taxonomy of ciliates, the relative merits and challenges of deploying its application using DNA metabarcoding for surveys of ciliate community diversity in urban waterbodies, and provide suggestions for minimizing relevant sources of biases in its implementation. We expect that DNA metabarcoding could untangle relationships between community assembly and environmental changes affecting ciliate communities. These analyses and discussions could offer a replicable method in support of the application of evaluating communities of ciliated protozoa as indicators of urban freshwater ecosystems.

The transient Spt4-Spt5 complex as an upstream regulator of non-coding RNAs during development

The Spt4-Spt5 complex is conserved and essential RNA polymerase elongation factor. To investigate the role of the Spt4-Spt5 complex in non-coding transcription during development, we used the unicellular model Paramecium tetraurelia. In this organism harboring both germline and somatic nuclei, massive transcription of the entire germline genome takes place during meiosis. This phenomenon starts a series of events mediated by different classes of non-coding RNAs that control developmentally programmed DNA elimination. We focused our study on Spt4, a small zinc-finger protein encoded in P. tetraurelia by two genes expressed constitutively and two genes expressed during meiosis. SPT4 genes are not essential in vegetative growth, but they are indispensable for sexual reproduction, even though genes from both expression families show functional redundancy. Silencing of the SPT4 genes resulted in the absence of double-stranded ncRNAs and reduced levels of scnRNAs – 25 nt-long sRNAs produced from these double-stranded precursors in the germline nucleus. Moreover, we observed that the presence of a germline-specific Spt4-Spt5m complex is necessary for transfer of the scnRNA-binding PIWI protein between the germline and somatic nucleus. Our study establishes that Spt4, together with Spt5m, is essential for expression of the germline genome and necessary for developmental genome rearrangements.

Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing

Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis have been gleaned by assessing the rate of phenotypic assortment. Though powerful, this experimental approach relies on the availability of phenotypic markers. Leveraging Paramecium tetraurelia, a unicellular eukaryote with nuclear dualism and a highly polyploid somatic nucleus, we probe the limits of single-cell whole-genome sequencing to study the consequences of amitosis. To this end, we first evaluate the suitability of single-cell sequencing to study the AT-rich genome of P. tetraurelia, focusing on common sources of genome representation bias. We then asked: can alternative rearrangements of a given locus eventually assort after a number of amitotic divisions? To address this question, we track somatic assortment of developmentally acquired Internal Eliminated Sequences (IESs) up to 50 amitotic divisions post self-fertilization. To further strengthen our observations, we contrast empirical estimates of IES retention levels with in silico predictions obtained through mathematical modeling. In agreement with theoretical expectations, our empirical findings are consistent with a mild increase in variation of IES retention levels across successive amitotic divisions of the macronucleus. The modest levels of somatic assortment in P. tetraurelia suggest that IESs retention levels are largely sculpted at the time of macronuclear development, and remain fairly stable during vegetative growth. In forgoing the requirement for phenotypic assortment, our approach can be applied to a wide variety of amitotic species and could facilitate the identification of environmental and genetic factors affecting amitosis.

Evolutionary Plasticity of Mating-Type Determination Mechanisms in Paramecium aurelia Sibling Species

The Paramecium aurelia complex, a group of morphologically similar but sexually incompatible sibling species, is a unique example of the evolutionary plasticity of mating-type systems. Each species has two mating types, O (Odd) and E (Even). Although O and E types are homologous in all species, three different modes of determination and inheritance have been described: genetic determination by Mendelian alleles, stochastic developmental determination, and maternally inherited developmental determination. Previous work in three species of the latter kind has revealed the key roles of the E-specific transmembrane protein mtA and its highly specific transcription factor mtB: type O clones are produced by maternally inherited genome rearrangements that inactivate either mtA or mtB during development. Here we show, through transcriptome analyses in five additional species representing the three determination systems, that mtA expression specifies type E in all cases. We further show that the Mendelian system depends on functional and nonfunctional mtA alleles, and identify novel developmental rearrangements in mtA and mtB which now explain all cases of maternally inherited mating-type determination. Epistasis between these genes likely evolved from less specific interactions between paralogs in the P. aurelia common ancestor, after a whole-genome duplication, but the mtB gene was subsequently lost in three P. aurelia species which appear to have returned to an ancestral regulation mechanism. These results suggest a model accounting for evolutionary transitions between determination systems, and highlight the diversity of molecular solutions explored among sibling species to maintain an essential mating-type polymorphism in cell populations.

DNA deletion as a mechanism for developmentally programmed centromere loss

A hallmark of active centromeres is the presence of the histone H3 variant CenH3 in the centromeric chromatin, which ensures faithful genome distribution at each cell division. A functional centromere can be inactivated, but the molecular mechanisms underlying the process of centromere inactivation remain largely unknown. Here, we describe the loss of CenH3 protein as part of a developmental program leading to the formation of the somatic nucleus in the eukaryote Paramecium. We identify two proteins whose depletion prevents developmental loss of CenH3: the domesticated transposase Pgm involved in the formation of DNA double strand cleavages and the Polycomb-like lysine methyltransferase Ezl1 necessary for trimethylation of histone H3 on lysine 9 and lysine 27. Taken together, our data support a model in which developmentally programmed centromere loss is caused by the elimination of DNA sequences associated with CenH3.

Sex determination: ciliates' self-censorship

Differentiation involves the expression of certain latent cellular characteristics and the repression of others. A new study has revealed how Paramecium uses short RNAs to delete information from the somatic genome of one of its two sexes.

Genome-defence small RNAs exapted for epigenetic mating-type inheritance

In the ciliate Paramecium, transposable elements and their single-copy remnants are deleted during the development of somatic macronuclei from germline micronuclei, at each sexual generation. Deletions are targeted by scnRNAs, small RNAs produced from the germ line during meiosis that first scan the maternal macronuclear genome to identify missing sequences, and then allow the zygotic macronucleus to reproduce the same deletions. Here we show that this process accounts for the maternal inheritance of mating types in Paramecium tetraurelia, a long-standing problem in epigenetics. Mating type E depends on expression of the transmembrane protein mtA, and the default type O is determined during development by scnRNA-dependent excision of the mtA promoter. In the sibling species Paramecium septaurelia, mating type O is determined by coding-sequence deletions in a different gene, mtB, which is specifically required for mtA expression. These independently evolved mechanisms suggest frequent exaptation of the scnRNA pathway to regulate cellular genes and mediate transgenerational epigenetic inheritance of essential phenotypic polymorphisms.

Phenotypic conversion of mating type specificity induced by transplantation of macronucleoplasm in Paramecium caudatum

According to the classical genetic analysis inParamecium caudatumby Tsukii & Hiwatashi (1983), the E mating type of each syngen is expressed when the cell bears alleles specific for syngen at theMtlocus. The O mating type is expressed when cells are homozygous for the null allele,mt, at theMtlocus. In suchmt/mtcells the O syngen specificity is determined by alleles at two other loci calledMAandMB. Inthe study reported here, macronucleoplasmic transplantation technique was used to test the above hypothesis. When macronucleoplasm of type E3(mating type E of syngen 3) was injected into a macronucleus of type O12(mating type O of syngen 12), some recipients changed to type E of the donor syngen but some others changed to type E of the recipient syngen. Thus, syngen specificity of donor macronucleoplasm controlling type E was converted into that of the recipients, even though the latter has no gene that controls type E. When this transformant expressing type E of the recipiexnt syngen was re-injected back into E of the other syngen, the expression of the converted mating type in some way continued in the recipient. This suggests that syngen specificity of geneMtof the donor was changed to that of the recipients by intersyngenic transplantation of macronucleoplasm. We also obtained results suggesting that the gene dosage ratio ofMttomtorMttoMAandMBmay be important for syngen specific expression of type E.

New results on the genetics of mating types in Paramecium bursaria

1. The four mating-types I, II, III, IV known for P. bursaria, syngen 1 are determined by specific combinations of dominant and recessive alleles at two unlinked loci. Mating-type I is formed by cells with the genotypes AABB, AABb, AaBB and AaBb; type II is controlled by the genotypes aaBB and aaBb; the double recessive, aabb is type III, genotypes AAbb and Aabb bring about type IV.

2. Clones which are exceptions to these rules for mating-type determination occur in low frequency (2–3%) in one line of descent. All can be explained by assuming either a mutation of dominant gene B to its recessive allele b or to a loss of the B locus. The data suggest that in four clones, the macronuclear but not the micronuclear genotype is affected; in two clones both nuclei are aberrant.

3. The cytogenetic events of conjugation were verified by the use of the new genetic markers. No evidence for uniparental nuclear reorganization, autogamy, was found.

Mating types and mating-inducing factors (gamones) in the ciliate Euplotes patella syngen 2

Relationships between mating type genes and mating-inducing factors (gamones) were investigated in the ciliateEuplotes patellasyngen 2. Ten mating types were distinguished, and genetic data indicated that the ten mating types were determined by four codominant alleles in possible combinations of two of them. There were six heterozygous types (mt1/mt2,mt3/mt4, etc.) and four homozygous types (mt1/mt1,mt2/mt2, etc.). Conjugation-conditioned fluid (CCF) obtained from a mixture of cells of homozygous types could induce homotypic pair formation in cells of all mating types except for a particular type. Genetic data of cell-CCF combination experiments suggest that each mating type allele controls the production of a specific gamone which induces pair formation in cells which do not produce the same gamone. Gamones and their hypothetical receptors are discussed.

An analysis of the development of resistance to metachloridine in clones of Plasmodium gallinaceum

1. The development of resistance to metachloridine (3-metanilamido-5-chloropyrimidine) was studied in two clones of Plasmodium gallinaceum derived from single erythrocytic parasites and maintained by serial inoculation in young chicks. Resistance developed with equal facility and similarly in the two clones.

2. In thirteen strains of these clones an enhancement of resistance was obtained after three to five courses of treatment, each of seven doses of metachloridine over a period of 3½ days.

3. The effect of the size of the inoculum (2·5 × 107–109 parasites), and of the dose of drug upon the rate of development of resistance was studied. Although the number of courses of treatment required to produce an enhancement of resistance was not always related to the size of the inoculum, with the largest inoculum an enhancement of resistance was observed after the minimum number of courses of treatment (three), whereas with the smallest inoculum no enhancement of resistance was obtained. The rate of the development of resistance did not appear to be related to the size of the dose of drug.

4. In some strains the increase in resistance was sudden, whereas in others it was more gradual. Resistance was retained when parasites of a newly resistant strain were transmitted through Aëdes aegypti or maintained for 43 days in the absence of the drug.

5. A comparison of the development of resistance in populations of normal parasites, and of populations composed of mixtures of known numbers of resistant and normal parasites, indicated that the pattern of the development of resistance in normal populations could be explained by the selections of mutations of a frequency of less than 1 in 5 × 107, or probably less than 1 in 109 parasites.

Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome

Tetrahymena thermophila is the best studied of the ciliates, a diversified and successful lineage of eukaryotic protists. Mirroring the way in which many metazoans partition their germ line and soma into distinct cell types, ciliates separate germ line and soma into two distinct nuclei in a single cell. The diploid, transcriptionally silent micronucleus undergoes meiosis and fertilization during sexual reproduction and determines the genotype of the progeny; in contrast, the expressed macronucleus contains many copies of hundreds of small chromosomes, determines the cell's phenotype, and is inherited only through vegetative reproduction. Here we demonstrate the power of HAPPY physical mapping to aid the complete assembly of T. thermophila macronuclear chromosomes from shotgun sequence scaffolds. The finished genome, one of only two ciliate genomes shotgun sequenced, will shed valuable additional light upon the biology of this extraordinary, diverse, and, from a genomics standpoint, as yet largely unexplored evolutionary branch of eukaryotes.

Preferential cleavage of Paramecium DNA mediated by the C. elegans Tc1 transposase in vitro

In the ciliate Paramecium aurelia complex, thousands of internal eliminated sequences (IESs) are excised from the germline micronuclear DNA during macronuclear differentiation. Based on the resemblance of Paramecium IES end sequences to Tc1 transposon termini, it has been proposed that Paramecium IESs might have degenerately evolved from Tc1 family transposons, and still be removed by an enzyme homologous to a Tc1 transposase. In this study, we found that transposase preferentially cleaved (or nicked) 58 sites near the IESs in Paramecium DNA, at sequences consisting of TT or TCTA. Since one excision junction of the P. primaurelia W2 IES was included in such sites, this suggests that a Tc1-like transposase is involved in the IES excision process, although it is probably not a sole factor responsible for the precise cleavage. In addition, unmethylated substrate DNA appeared to decrease the cleavage specificity, suggesting an involvement of DNA methylation in the cleavage. Although these results do not directly address the transposon origin of Paramecium IESs, it is likely that the enzymatic machinery responsible for the initial cleavage is derived from a Tc1-like transposase. The mechanism necessary for precise excision is discussed, in relation to recent knowledge of IES excision obtained in Tetrahymena and Paramecium.

Non-Mendelian inheritance induced by gene amplification in the germ nucleus of Paramecium tetraurelia

A genetic investigation of strain d4-95, which carries a recessive mutant allele (pwB(95)) of pawn-B, one of the controlling elements of voltage-dependent calcium channels in Paramecium tetraurelia, revealed a non-Mendelian feature. Progeny of the cross between d4-95 and wild type often expressed a clonally stable mutant phenotype, even when they had a wild-type gene. The mutant phenotype was also expressed after self-fertilization of theoretical wild-type homozygotes recovered from the cross. Our molecular analysis demonstrated that the copy number of the mutant pwB gene in the micro- and macronucleus of d4-95 was much greater than that of the wild type. Most of the amplified, extra pwB gene copies in d4-95 were heritable independently from the original pwB locus. Repeated backcrossing of d4-95 with the wild type to dilute extra pwB genes in the strain produced segregants with a completely normal Mendelian trait in testcrosses. These results strongly suggest that a non-Mendelian inheritance of d4-95 was induced by gene amplification in the micronucleus.

Epigenetic mechanisms affecting macronuclear development in Paramecium and Tetrahymena

Epigenetic inheritance includes all non-Mendelian inheritance, in fact any inheritance that does not arise from base changes. Ciliates, particularly Paramecium and Tetrahymena, undergo epigenetic changes to their macronuclei when they are formed at nuclear reorganization. Once set, however, they are reproduced in a constant fashion, except for allelic segregations, during vegetative fissions in Tetrahymena and certain life cycle changes in both Paramecium and Tetrahymena. This review is meant to be inclusive, discussing all the known cases of epigenetic changes in macronuclei. They involve virtually all traits. We find that these macronuclear changes are subject to a variety of modifications in the way that they are implemented. They constitute a major feature of ciliate genetics, probably because the separation of generative and vegetative functions to micronuclei and macronuclei makes such changes possible.

Laboratory and evolutionary history of Tetrahymena thermophila

An account is given of the early efforts to domesticate tetrahymenas as laboratory instruments for genetics. The rationale for developing a new organismic technology was the comparative leverage provided by a eukaryotic microorganism at a large evolutionary distance from both prokaryotic microbes and multicellular organisms. The tetrahymenine ciliates were considered more favorable materials than paramecia because of their ability to grow on simple media, though in fact their simpler nutritional needs have never been fully exploited. The first task was to sort the large set of phenotypically similar but evolutionarily and molecularly diverse ciliates referred to at the time as T. pyriformis. Then a species amenable to genetic manipulation was identified and its culture and cytogenetics were brought under control. Fortunately, the very first breeding system investigated--that in the species now called T. thermophila--has proved to be suitable for a wide range of studies. A large factor in the program's success was its use of the foundation previously established by studies on paramecia. However, serious unforeseen difficulties were encountered on the way to "domestication." These included inbreeding deterioration associated with their outbreeding life-style and germinal deterioration (mutational erosion) in the unexpressed micronuclear genome after long maintenance in vegetative culture. Cryogenic preservation was an important means of escaping these organismic limitations, and somatic (macronuclear) assortment has proved a valuable supplement to meiotic recombination.

Embryological perspective of sexual somatic development in ciliated protozoa: implications on immortality, sexual reproduction and inheritance of acquired characters

This essay addresses somatic development during sexual reproduction of ciliated protozoa, which is interpreted as an embryological phenomenon resembling embryogenesis of multicellular organisms. The uniqueness of this somatic development, as distinct from asexual development, resides in its dependence on new information associated with the germ nucleus, and on its involvement of both maternal and postzygotic informational inputs. This understanding derives from experimental dissection of nuclear control of somatic development inParamecium, and in several hypotrichous ciliates. The embryological perspective enables us to reorganize our thinking on several historical issues of development and evolution: whether protozoa are immortal, and whether mortality only arose together with multicellularity; whether their sexual process can be regarded as reproduction, equivalent to sexual reproduction of multicellular organisms; whether the inheritance of acquired cortical variations of non- genic origins in ciliates constitutes a threat to neo-Darwinism. Conceptual predicaments on these issues have often stemmed from unwarranted parallelism drawn between asexual propagation of protozoa and sexual reproduction of multicellular organisms. The embryological reply to these questions is that ciliated protozoa are mortal, since during fertilization the maternal soma perishes by resorption, and is replaced by a new one which developsin situin the maternal soma. The consequence of their sexual process is the same as in sexually reproducing multicellular organisms, in that the post-fertilization protozoan is an ontogenetically new individual, equipped with a new soma unlike those generated during asexual propagation. On the basis of the characteristicin situdevelopment of the embryonic soma during sexual reproduction, two evolutionary perceptions are formulated. First, the extensiveness of resorption of the maternal soma, and release of development of the embryonic soma from cytotactic constraints imposed by the maternal soma, constitute major themes of phylogenetic evolution. Second, the evolutionary outcome of acquired cortical variations has to be evaluated in terms of the fidelity of perpetuation of such variations through sexual reproduction, and their potential of being assimilated into the genomic programme of embryonic development. The evolutionary predictions accordingly may turn out to be radically different from those based on the inheritance of such variations during asexual propagation alone.