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Open Biology Oct 2017Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between... (Review)
Review
Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between transposable elements (TEs) and host genomes. DNA elimination in removes approximately 12 000 internal eliminated sequences (IESs), which correspond to one-third of the genome, when the somatic macronucleus (MAC) differentiates from the germline micronucleus (MIC). More than half of the IESs, many of which show high similarity to TEs, are targeted for elimination in by the small RNA-mediated genome comparison of the MIC to the MAC. Other IESs are targeted for elimination in by the same small RNAs through repetitive sequences. Furthermore, the small RNA-heterochromatin feedback loop ensures robust DNA elimination. Here, we review an updated picture of the DNA elimination mechanism, discuss the physiological and evolutionary roles of DNA elimination, and outline the key questions that remain unanswered.
Topics: DNA, Protozoan; Evolution, Molecular; Gene Rearrangement; Genome, Protozoan; RNA, Small Untranslated; Tetrahymena
PubMed: 29021213
DOI: 10.1098/rsob.170172 -
Cells Jan 2022Histone modification and nucleosome assembly are mainly regulated by various histone-modifying enzymes and chaperones. The roles of histone-modification enzymes have...
Histone modification and nucleosome assembly are mainly regulated by various histone-modifying enzymes and chaperones. The roles of histone-modification enzymes have been well analyzed, but the molecular mechanism of histone chaperones in histone modification and nucleosome assembly is incompletely understood. We previously found that the histone chaperone Nrp1 is localized in the micronucleus (MIC) and the macronucleus (MAC) and involved in the chromatin stability and nuclear division of . In the present work, we found that truncated C-terminal mutant HA-Nrp1 abnormally localizes in the cytoplasm. The truncated-signal-peptide mutants HA-Nrp1 and HA-Nrp1 are localized in the MIC and MAC. Overexpression of Nrp1 inhibited cellular proliferation and disrupted micronuclear mitosis during the vegetative growth stage. During sexual development, Nrp1 overexpression led to abnormal bouquet structures and meiosis arrest. Furthermore, Histone H3 was not transported into the nucleus; instead, it formed an abnormal speckled cytoplastic distribution in the Nrp1 mutants. The acetylation level of H3K56 in the mutants also decreased, leading to significant changes in the transcription of the genome of the Nrp1 mutants. The histone chaperone Nrp1 regulates the H3 nuclear import and acetylation modification of H3K56 and affects chromatin stability and genome transcription in .
Topics: Acetylation; Chromatin; Histone Chaperones; Histones; Mutation; Nucleosomes; Tetrahymena thermophila
PubMed: 35159218
DOI: 10.3390/cells11030408 -
Current Biology : CB Jan 2021The replication band in the macronucleus of ciliated protozoa has fascinated microscopists since the 19 Century. It migrates through the nucleus, corresponding to a...
The replication band in the macronucleus of ciliated protozoa has fascinated microscopists since the 19 Century. It migrates through the nucleus, corresponding to a region of DNA replication and nascent chromatin assembly. A new study shows that calcium and actin filaments may participate in the formation and migration of the replication band.
Topics: Cell Nucleus; Chromatin Assembly and Disassembly; Ciliophora; DNA Replication
PubMed: 33434478
DOI: 10.1016/j.cub.2020.10.058 -
Methods in Molecular Biology (Clifton,... 2022Tetrahymena is a fascinating organism for studying the nuclear pore complex because it has two structurally and functionally distinct nuclei (macronucleus and...
Tetrahymena is a fascinating organism for studying the nuclear pore complex because it has two structurally and functionally distinct nuclei (macronucleus and micronucleus) within a cell, and there are two compositionally distinct nuclear pore complexes (NPCs) with different functions in each nucleus. Therefore, it is possible to link the function of a specific constituent protein with the nuclear function of the macronucleus and micronucleus. Additionally, these NPCs undergo dynamic changes in their structures and compositions during nuclear differentiation. Live CLEM imaging, a method of correlative light and electron microscopy (CLEM) combined with live cell imaging, is a powerful tool for visualizing these dynamic changes of specific molecules/structures of interest at high resolution. Here, we describe Live CLEM that can be applied to the study of the dynamic behavior of NPCs in Tetrahymena cells undergoing nuclear differentiation.
Topics: Electrons; Macronucleus; Microscopy, Electron; Nuclear Pore; Tetrahymena
PubMed: 35412257
DOI: 10.1007/978-1-0716-2337-4_30 -
Cells Dec 2023Histones and DNA associate to form the nucleosomes of eukaryotic chromatin. Chromatin assembly factor 1 (CAF-1) complex and histone regulatory protein A (HIRA) complex...
Histones and DNA associate to form the nucleosomes of eukaryotic chromatin. Chromatin assembly factor 1 (CAF-1) complex and histone regulatory protein A (HIRA) complex mediate replication-couple (RC) and replication-independent (RI) nucleosome assembly, respectively. CHAF1B and HIRA share a similar domain but play different roles in nucleosome assembly by binding to the different interactors. At present, there is limited understanding for the similarities and differences in their respective functions. contains transcriptionally active polyploid macronuclei (MAC) and transcriptionally silent diploid micronuclei (MIC). Here, the distribution patterns of Caf1b and Hir1 exhibited both similarities and distinctions. Both proteins localized to the MAC and MIC during growth, and to the MIC during conjugation. However, Hir1 exhibited additional signaling on parental MAC and new MAC during sexual reproduction and displayed a punctate signal on developing anlagen. Caf1b and Hir1 only co-localized in the MIC with Pcna1 during conjugation. Knockdown of impeded cellular growth and arrested sexual reproductive development. Loss of led to MIC chromosome defects and aborted sexual development. Co-interference of and led to a more severe phenotype. Moreover, knockdown led to the up-regulation of expression, while knockdown of also led to an increase in expression. Furthermore, Caf1b and Hir1 interacted with different interactors. These results showed that CAF-1 and Hir1 have independent and complementary functions for chromatin assembly in .
Topics: Nucleosomes; Tetrahymena thermophila; Chromatin Assembly and Disassembly; Chromatin; Histones
PubMed: 38132148
DOI: 10.3390/cells12242828 -
Microbiology and Molecular Biology... Dec 2023SUMMARYCiliated protozoa undergo large-scale developmental rearrangement of their somatic genomes when forming a new transcriptionally active macronucleus during... (Review)
Review
SUMMARYCiliated protozoa undergo large-scale developmental rearrangement of their somatic genomes when forming a new transcriptionally active macronucleus during conjugation. This process includes the fragmentation of chromosomes derived from the germline, coupled with the efficient healing of the broken ends by telomere addition. Here, we review what is known of developmental chromosome fragmentation in ciliates that have been well-studied at the molecular level (, , , , and ). These organisms differ substantially in the fidelity and precision of their fragmentation systems, as well as in the presence or absence of well-defined sequence elements that direct excision, suggesting that chromosome fragmentation systems have evolved multiple times and/or have been significantly altered during ciliate evolution. We propose a two-stage model for the evolution of the current ciliate systems, with both stages involving repetitive or transposable elements in the genome. The ancestral form of chromosome fragmentation is proposed to have been derived from the ciliate small RNA/chromatin modification process that removes transposons and other repetitive elements from the macronuclear genome during development. The evolution of this ancestral system is suggested to have potentiated its replacement in some ciliate lineages by subsequent fragmentation systems derived from mobile genetic elements.
Topics: Base Sequence; DNA, Protozoan; Chromosomes; DNA Transposable Elements
PubMed: 38009915
DOI: 10.1128/mmbr.00184-22 -
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 -
Genes Nov 2019In the ciliate somatic macronuclei differentiate from germline micronuclei during sexual reproduction, accompanied by developmental sequence reduction. Concomitantly,... (Review)
Review
In the ciliate somatic macronuclei differentiate from germline micronuclei during sexual reproduction, accompanied by developmental sequence reduction. Concomitantly, over 95% of micronuclear sequences adopt a heterochromatin structure characterized by the histone variant H3.4 and H3K27me3. RNAi-related genes and histone variants dominate the list of developmentally expressed genes. Simultaneously, 27nt-ncRNAs that match sequences retained in new macronuclei are synthesized and bound by PIWI1. Recently, we proposed a mechanistic model for 'RNA-induced DNA replication interference' (RIRI): during polytene chromosome formation PIWI1/27nt-RNA-complexes target macronucleus-destined sequences (MDS) by base-pairing and temporarily cause locally stalled replication. At polytene chromosomal segments with ongoing replication, H3.4K27me3-nucleosomes become selectively deposited, thus dictating the prospective heterochromatin structure of these areas. Consequently, these micronucleus-specific sequences become degraded, whereas 27nt-RNA-covered sites remain protected. However, the biogenesis of the 27nt-RNAs remains unclear. It was proposed earlier that in stichotrichous ciliates 27nt-RNA precursors could derive from telomere-primed bidirectional transcription of nanochromosomes and subsequent Dicer-like (DCL) activity. As a minimalistic explanation, we propose here that the 27nt-RNA precursor could rather be mRNA or pre-mRNA and that the transition of coding RNA from parental macronuclei to non-coding RNAs, which act in premature developing macronuclei, could involve RNA-dependent RNA polymerase (RDRP) activity creating dsRNA intermediates prior to a DCL-dependent pathway. Interestingly, by such mechanism the partition of a parental somatic genome and possibly also the specific nanochromosome copy numbers could be vertically transmitted to the differentiating nuclei of the offspring.
Topics: Ciliophora; DNA Replication; Gene Expression Regulation, Developmental; Genome, Protozoan; Histones; Micronucleus, Germline; Nucleosomes; RNA Interference; RNA Precursors; RNA, Messenger; RNA, Small Nuclear; Telomere
PubMed: 31752243
DOI: 10.3390/genes10110940 -
Theoretical Population Biology Jun 2022Cell division is a necessity of life which can be either mitotic or amitotic. While both are fundamental, amitosis is sometimes considered a relic of little importance...
Cell division is a necessity of life which can be either mitotic or amitotic. While both are fundamental, amitosis is sometimes considered a relic of little importance in biology. Nevertheless, eukaryotes often have polyploid cells, including cancer cells, which may divide amitotically. To understand how amitosis ensures the completion of cell division, we turn to the macronuclei of ciliates. The grand scheme governing the proliferation of the macronuclei of ciliate cells, which involves chromosomal replication and amitosis, is currently unknown, which is crucial for developing population genetics model of ciliate populations. Using a novel model that encompasses a wide range of mechanisms together with experimental data of the composition of mating types at different stages derived from a single karyonide of Tetrahymena thermophila, we show that the chromosomal replication of the macronucleus has a strong head-start effect, with only about five copies of chromosomes replicated at a time and persistent reuse of the chromosomes involved in the early replication. Furthermore the fission of a fully grown macronucleus is non-random with regard to chromosome composition, with a strong tendency to push chromosomes and their replications to the same daughter cell.
Topics: Cell Division; Chromosomes; Ciliophora; Macronucleus; Tetrahymena thermophila
PubMed: 35331774
DOI: 10.1016/j.tpb.2022.03.004 -
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