-
Cells Nov 2021Nuclear autophagy is an important selective autophagy process. The selective autophagy of sexual development micronuclei (MICs) and the programmed nuclear degradation of...
Nuclear autophagy is an important selective autophagy process. The selective autophagy of sexual development micronuclei (MICs) and the programmed nuclear degradation of parental macronucleus (paMAC) occur during sexual reproduction in . The molecular regulatory mechanism of nuclear selective autophagy is unclear. In this study, the autophagy-related protein Atg5 was identified from . Atg5 was localized in the cytoplasm in the early sexual-development stage and was localized in the paMAC in the late sexual-development stage. During this stage, the degradation of meiotic products of MIC was delayed in mutants. Furthermore, paMAC was abnormally enlarged and delayed or failed to degrade. The expression level and lipidation of Atg8.2 significantly decreased in the mutants. All these results indicated that Atg5 was involved in the regulation of the selective autophagy of paMAC by regulating Atg8.2 in
Topics: Acids; Autophagy; Autophagy-Related Protein 5; Gene Knockdown Techniques; Macronucleus; Meiosis; Models, Biological; Mutation; Protozoan Proteins; Reproduction; Tetrahymena thermophila
PubMed: 34831293
DOI: 10.3390/cells10113071 -
RNA Biology Aug 2016De novo addition of telomeric sequences can occur at broken chromosomes and must be well controlled, which is essential during programmed DNA reorganization processes....
De novo addition of telomeric sequences can occur at broken chromosomes and must be well controlled, which is essential during programmed DNA reorganization processes. In ciliated protozoa an extreme form of DNA-reorganization is observed during macronuclear differentiation after sexual reproduction leading to the elimination of specific parts of the germline genome. Regulating these processes involves small noncoding RNAs, but in addition DNA-reordering, excision and amplification require RNA templates deriving from the parental macronucleus. We show that these putative RNA templates can carry telomeric repeats. Microinjection of RNA templates carrying modified telomeres into the developing macronucleus leads to modified telomeres in vegetative cells, providing strong evidence, that de novo addition of telomeres depends on a telomere-containing transcript from the parental macronucleus.
Topics: Cell Nucleolus; Ciliophora; DNA Replication; Gene Amplification; Genetic Variation; Models, Biological; RNA; RNA, Double-Stranded; RNA, Untranslated; Telomere; Templates, Genetic
PubMed: 26786510
DOI: 10.1080/15476286.2015.1134414 -
G3 (Bethesda, Md.) Oct 2019The ciliate contains two nuclei: a germline micronucleus and a somatic macronucleus. These two nuclei diverge significantly in genomic structure. The micronucleus...
The ciliate contains two nuclei: a germline micronucleus and a somatic macronucleus. These two nuclei diverge significantly in genomic structure. The micronucleus contains approximately 100 chromosomes of megabase scale, while the macronucleus contains 16,000 gene-sized, high ploidy "nanochromosomes." During its sexual cycle, a copy of the zygotic germline micronucleus develops into a somatic macronucleus via DNA excision and rearrangement. The rearrangement process is guided by multiple RNA-based pathways that program the epigenetic inheritance of sequences in the parental macronucleus of the subsequent generation. Here, we show that the introduction of synthetic DNA molecules homologous to a complete native nanochromosome during the rearrangement process results in either loss or heavy copy number reduction of the targeted nanochromosome in the macronucleus of the subsequent generation. This phenomenon was tested on a variety of nanochromosomes with different micronuclear structures, with deletions resulting in all cases. Deletion of the targeted nanochromosome results in the loss of expression of the targeted genes, including gene knockout phenotypes that were phenocopied using alternative knockdown approaches. Further investigation of the chromosome deletion showed that, although the full length nanochromosome was lost, remnants of the targeted chromosome remain. We were also able to detect the presence of telomeres on these remnants. The chromosome deletions and remnants are epigenetically inherited when backcrossed to wild type strains, suggesting that an undiscovered mechanism programs DNA elimination and cytoplasmically transfers to both daughter cells during conjugation. Programmed deletion of targeted chromosomes provides a novel approach to investigate genome rearrangement and expands the available strategies for gene knockout in .
Topics: Chromosome Deletion; DNA Fragmentation; Epigenesis, Genetic; Gene Rearrangement; Genome, Protozoan; Genomics; High-Throughput Nucleotide Sequencing; Oxytricha
PubMed: 31506317
DOI: 10.1534/g3.118.200930 -
BMC Biology Nov 2020Ciliates 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...
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.
Topics: Genome, Protozoan; Macronucleus; Metagenomics; Paramecium
PubMed: 33250052
DOI: 10.1186/s12915-020-00912-2 -
Medecine Sciences : M/S Apr 2005Since the middle of the last century, Paramecium has appeared as an intriguing genetic model, displaying a variety of heritable characters which do not follow the Mendel... (Review)
Review
Since the middle of the last century, Paramecium has appeared as an intriguing genetic model, displaying a variety of heritable characters which do not follow the Mendel laws but are cytoplasmically inherited. The analysis of the hereditary mechanisms at play in this eukaryotic unicellular organism has provided new insight into epigenetics mechanisms. Interestingly, the revealing phenomena concern two pecularities of Paramecium, its highly elaborate surface structure (with thousands of ciliary basal bodies as cytoskeleton organizers), and its nuclear dualism (coexistence of a diploid "germline" micronucleus and a highly polyploid somatic macronucleus devoted to transcription, which contains a rearranged version of the germline genome). Analysis of variant cortical organization has led to the concept of structural inheritance, implying that assembly of new organelles and supramolecular protein complexes is guided by pre-existing organization. Analysis of other cytoplasmically inherited characters revealed that the developing macronucleus is epigenetically programmed by the maternal macronucleus through RNA-mediated, homology-dependent effects, suggesting the transcriptome should be recognized as a third actor in cellular inheritance, along with the "structurome" and the genome.
Topics: Animals; Cell Nucleus; Epigenesis, Genetic; Paramecium
PubMed: 15811302
DOI: 10.1051/medsci/2005214377 -
Nucleic Acids Research Jan 2016Ciliated protists exhibit nuclear dimorphism through the presence of somatic macronuclei (MAC) and germline micronuclei (MIC). In some ciliates, DNA from precursor...
Ciliated protists exhibit nuclear dimorphism through the presence of somatic macronuclei (MAC) and germline micronuclei (MIC). In some ciliates, DNA from precursor segments in the MIC genome rearranges to form transcriptionally active genes in the mature MAC genome, making these ciliates model organisms to study the process of somatic genome rearrangement. Similar broad scale, somatic rearrangement events occur in many eukaryotic cells and tumors. The
(http://oxytricha.princeton.edu/mds_ies_db) is a database of genome recombination and rearrangement annotations, and it provides tools for visualization and comparative analysis of precursor and product genomes. The database currently contains annotations for two completely sequenced ciliate genomes: Oxytricha trifallax and Tetrahymena thermophila. Topics: Databases, Nucleic Acid; Gene Rearrangement; Genome; Molecular Sequence Annotation; Oxytricha; Recombination, Genetic; Tetrahymena thermophila
PubMed: 26586804
DOI: 10.1093/nar/gkv1190 -
Genes To Cells : Devoted To Molecular &... Jul 2018Ciliated protozoa possess two morphologically and functionally distinct nuclei: a macronucleus (MAC) and a micronucleus (MIC). The MAC is transcriptionally active and...
Ciliated protozoa possess two morphologically and functionally distinct nuclei: a macronucleus (MAC) and a micronucleus (MIC). The MAC is transcriptionally active and functions in all cellular events. The MIC is transcriptionally inactive during cell growth, but functions in meiotic events to produce progeny nuclei. Thus, these two nuclei must be distinguished by the nuclear proteins required for their distinct functions during cellular events such as cell proliferation and meiosis. To understand the mechanism of the nuclear transport specific to either MAC or MIC, we identified specific nuclear localization signals (NLSs) in two MAC- and MIC-specific nuclear proteins, macronuclear histone H1 and micronuclear linker histone-like protein (Mlh1), respectively. By expressing GFP-fused fragments of these proteins in Tetrahymena thermophila cells, two distinct regions in macronuclear histone H1 protein were assigned as independent MAC-specific NLSs and two distinct regions in Mlh1 protein were assigned as independent MIC-specific NLSs. These NLSs contain several essential lysine residues responsible for the MAC- and MIC-specific nuclear transport, but neither contains any consensus sequence with known monopartite or bipartite NLSs in other model organisms. Our findings contribute to understanding how specific nuclear targeting is achieved to perform distinct nuclear functions in binucleated ciliates.
Topics: Active Transport, Cell Nucleus; Amino Acid Sequence; Animals; Cell Nucleus; Histones; Macronucleus; Micronucleus, Germline; Nuclear Localization Signals; Protein Domains; Protozoan Proteins; Tetrahymena thermophila
PubMed: 29882620
DOI: 10.1111/gtc.12602 -
Wiley Interdisciplinary Reviews. RNA 2010Extensive programmed rearrangement of DNA, including DNA elimination, chromosome fragmentation, and DNA unscrambling, takes place in the newly developed macronucleus... (Review)
Review
Extensive programmed rearrangement of DNA, including DNA elimination, chromosome fragmentation, and DNA unscrambling, takes place in the newly developed macronucleus during the sexual reproduction of ciliated protozoa. Recent studies have revealed that two distant classes of ciliates use distinct types of non-coding RNAs to regulate such DNA rearrangement events. DNA elimination in Tetrahymena is regulated by small non-coding RNAs that are produced and utilized in an RNA interference (RNAi)-related process. It has been proposed that the small RNAs produced from the micronuclear genome are used to identify eliminated DNA sequences by whole-genome comparison between the parental macronucleus and the micronucleus. In contrast, DNA unscrambling in Oxytricha is guided by long non-coding RNAs that are produced from the parental macronuclear genome. These long RNAs are proposed to act as templates for the direct unscrambling events that occur in the developing macronucleus. Both cases provide useful examples to study epigenetic chromatin regulation by non-coding RNAs.
Topics: Animals; Ciliophora; Gene Rearrangement; Genetic Variation; Humans; Models, Biological; RNA Interference; RNA, Small Interfering; RNA, Untranslated; Recombination, Genetic; Tetrahymena
PubMed: 21956937
DOI: 10.1002/wrna.34 -
Journal of Genetics Jun 2015
Review
Origin, structure and function of millions of chromosomes present in the macronucleus of unicellular eukaryotic ciliate, Oxytricha trifallax: a model organism for transgenerationally programmed genome rearrangements.
Topics: Chromosomes; Gene Rearrangement; Genome, Protozoan; Inheritance Patterns; Macronucleus; Models, Biological; Oxytricha
PubMed: 26174664
DOI: 10.1007/s12041-015-0504-2 -
Nucleic Acids Research Mar 1999Genes in the germline (micronuclear) genome of hypotrichous ciliates are interrupted by multiple, short, non-coding, AT-rich sequences called internal eliminated... (Review)
Review
Genes in the germline (micronuclear) genome of hypotrichous ciliates are interrupted by multiple, short, non-coding, AT-rich sequences called internal eliminated segments, or IESs. During conversion of a micronucleus to a somatic nucleus (macronucleus) after cell mating, all IESs are excised from the germline genes and the gene segments, called macronuclear-destined segments, or MDSs, are spliced. Excision of the approximately 150 000 IESs from a haploid germline genome in Oxytricha nova requires approximately 150 000 recombinant events. In three of 10 genes the MDSs are scrambled. During macronuclear development the MDSs are unscrambled, possibly by folding of the DNA to allow MDSs to ligate in the correct order. The nine MDSs in the actin I gene of O.nova are scrambled in the random order, 3-4-6-5-7-9-2-1-8, and MDS 2 is inverted. The 14 MDSs in the alphaTP gene of O.nova and Stylonychia mytilus are scrambled in the non-random order, 1-3-5-7-9-11-2-4-6-8-10-12-13-14. The 45 MDSs in the DNA pol alpha gene are non-randomly scrambled into an odd/even series, with an inversion of one-third of the gene. Additional IESs have been inserted into these three genes during evolution of Oxytricha trifallax, slightly modifying scrambling patterns. The non-random scrambled patterns in the alphaTP and DNA pol alpha genes are explained by multiple, simultaneous IES insertions. The randomly scrambled pattern in the actin I gene may arise from an initially non-randomly scrambled pattern by recombination among multiple IESs. Alternatively, IESs inserted sporadically (individually) in a non-scrambled configuration might subsequently recombine, converting a non-scrambled gene into a randomly scrambled one. IESs shift along a DNA molecule, most likely as a result of mutations at MDS/IES junctions. Shifting of IESs has the effect of 'transferring' nucleotides from one MDS to another, but does not change the overall sequence of nucleotides in the combined MDSs. In addition to shifting in position, IESs accumulate mutations at a high rate and increase and decrease in length within a species and during speciation. The phenomena of IESs and of MDS scrambling represent remarkable flexibility of the hypotrich genome, possibly reflecting a process of MDS shuffling that facilitates the evolution of genes.
Topics: Animals; Base Sequence; Cell Nucleus; Ciliophora; DNA Polymerase I; DNA, Protozoan; Evolution, Molecular; Genes, Protozoan
PubMed: 9973610
DOI: 10.1093/nar/27.5.1243