1
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Zhang L, Cervantes MD, Pan S, Lindsley J, Dabney A, Kapler GM. Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles. Mol Biol Cell 2023; 34:rs1. [PMID: 36475712 PMCID: PMC9930529 DOI: 10.1091/mbc.e22-08-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During vegetative growth, the "cell cycles" of the diploid micronucleus and polyploid macronucleus are offset. Micronuclear S phase initiates just before cytokinesis and is completed in daughter cells before onset of macronuclear DNA replication. Mitotic micronuclear division occurs mid-cell cycle, while macronuclear amitosis is coupled to cell division. Here we report the first RNA-seq cell cycle analysis of a binucleated ciliated protozoan. RNA was isolated across 1.5 vegetative cell cycles, starting with a macronuclear G1 population synchronized by centrifugal elutriation. Using MetaCycle, 3244 of the 26,000+ predicted genes were shown to be cell cycle regulated. Proteins present in both nuclei exhibit a single mRNA peak that always precedes their macronuclear function. Nucleus-limited genes, including nucleoporins and importins, are expressed before their respective nucleus-specific role. Cyclin D and A/B gene family members exhibit different expression patterns that suggest nucleus-restricted roles. Periodically expressed genes cluster into seven cyclic patterns. Four clusters have known PANTHER gene ontology terms associated with G1/S and G2/M phase. We propose that these clusters encode known and novel factors that coordinate micro- and macronuclear-specific events such as mitosis, amitosis, DNA replication, and cell division.
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Affiliation(s)
- L. Zhang
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - M. D. Cervantes
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - S. Pan
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - J. Lindsley
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - A. Dabney
- Department of Statistics, Texas A&M University, College Station, TX 77843,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
| | - G. M. Kapler
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
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2
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Zhou Y, Fu L, Mochizuki K, Xiong J, Miao W, Wang G. Absolute quantification of chromosome copy numbers in the polyploid macronucleus of Tetrahymena thermophila at the single-cell level. J Eukaryot Microbiol 2022; 69:e12907. [PMID: 35313044 DOI: 10.1111/jeu.12907] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amitosis is widespread among eukaryotes, but the underlying mechanisms are poorly understood. The polyploid macronucleus (MAC) of unicellular ciliates divides by amitosis, making ciliates a potentially valuable model system to study this process. However, a method to accurately quantify the copy number of MAC chromosomes has not yet been established. Here we used droplet digital PCR (ddPCR) to quantify the absolute copy number of the MAC chromosomes in Tetrahymena thermophila. We first confirmed that ddPCR is a sensitive and reproducible method to determine accurate chromosome copy numbers at the single-cell level. We then used ddPCR to determine the copy number of different MAC chromosomes by analyzing individual T. thermophila cells in the G1 and the amitotic (AM) phases. The average copy number of MAC chromosomes was 90.9 at G1 phase, approximately half the number at AM phase (189.8). The copy number of each MAC chromosome varied among individual cells in G1 phase and correlated with cell size, suggesting that amitosis accompanied by unequal cytokinesis causes copy number variability. Furthermore, the fact that MAC chromosome copy number is less variable among AM-phase cells suggests that the copy number is standardized by regulating DNA replication. We also demonstrated that copy numbers differ among different MAC chromosomes and that interchromosomal variations in copy number are consistent across individual cells. Our findings demonstrate that ddPCR can be used to model amitosis in T. thermophila and possibly in other ciliates.
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Affiliation(s)
- Yuanyuan Zhou
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Fu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of Montpellier, Montpellier, 34090, France
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,CAS Center for Excellence in Animal Evolution and Genetics, Kunming, 650223, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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3
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Plum K, Tarkington J, Zufall RA. Experimental Evolution in Tetrahymena. Microorganisms 2022; 10:microorganisms10020414. [PMID: 35208869 PMCID: PMC8877770 DOI: 10.3390/microorganisms10020414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 02/06/2023] Open
Abstract
Experimental evolution has provided novel insight into a wide array of biological processes. Species in the genus Tetrahymena are proving to be a highly useful system for studying a range of questions using experimental evolution. Their unusual genomic architecture, diversity of life history traits, importance as both predator and prey, and amenability to laboratory culture allow them to be studied in a variety of contexts. In this paper, we review what we are learning from experimental evolution with Tetrahymena about mutation, adaptation, and eco-evolutionary dynamics. We predict that future experimental evolution studies using Tetrahyemena will continue to shed new light on these processes.
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Affiliation(s)
- Karissa Plum
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA;
| | - Jason Tarkington
- Department of Genetics, Stanford University, Stanford, CA 94305, USA;
| | - Rebecca A. Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA;
- Correspondence:
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4
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Cayuela H, Jacob S, Schtickzelle N, Verdonck R, Philippe H, Laporte M, Huet M, Bernatchez L, Legrand D. Transgenerational plasticity of dispersal‐related traits in a ciliate: genotype‐dependency and fitness consequences. OIKOS 2022. [DOI: 10.1111/oik.08846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hugo Cayuela
- Dépt de Biologie, Inst. de Biologie Intégrative et des Systèmes (IBIS), Univ. Laval, Pavillon Charles‐Eugène‐Marchand Québec QC Canada
- Dept of Ecology and Evolution, Univ. of Lausanne Lausanne Switzerland
| | - Staffan Jacob
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Nicolas Schtickzelle
- Univ. Catholique de Louvain, Earth and Life Inst., Biodiversity Research Centre Louvain‐la‐Neuve Belgium
| | - Rik Verdonck
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Hervé Philippe
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
- Dépt de Biochimie, Centre Robert‐Cedergren, Univ. de Montréal Montréal QC Canada
| | - Martin Laporte
- Ministère des Forêts, de la Faune et des Parc (MFFP) du Québec Québec QC Canada
| | - Michèle Huet
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
| | - Louis Bernatchez
- Dépt de Biologie, Inst. de Biologie Intégrative et des Systèmes (IBIS), Univ. Laval, Pavillon Charles‐Eugène‐Marchand Québec QC Canada
| | - Delphine Legrand
- Theoretical and Experimental Ecology Station (UAR 2029), National Centre for Scientific Research (CNRS), Paul Sabatier Univ. (UPS) Moulis France
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5
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Tarkington J, Zufall RA. Temperature affects the repeatability of evolution in the microbial eukaryote Tetrahymena thermophila. Ecol Evol 2021; 11:13139-13152. [PMID: 34646458 PMCID: PMC8495795 DOI: 10.1002/ece3.8036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 11/09/2022] Open
Abstract
Evolutionary biologists have long sought to understand what factors affect the repeatability of adaptive outcomes. To better understand the role of temperature in determining the repeatability of adaptive trajectories, we evolved populations of different genotypes of the ciliate Tetrahymena thermophila at low and high temperatures and followed changes in growth rate over 6,500 generations. As expected, growth rate increased with a decelerating rate for all populations; however, there were differences in the patterns of evolution at the two temperatures. The growth rates of the different genotypes tended to converge as evolution proceeded at both temperatures, but this convergence was quicker and more pronounced at the higher temperature. Additionally, over the first 4,000 generations we found greater repeatability of evolution, in terms of change in growth rate, among replicates of the same genotype at the higher temperature. Finally, we found limited evidence of trade-offs in fitness between temperatures, and an asymmetry in the correlated responses, whereby evolution in a high temperature increases growth rate at the lower temperature significantly more than the reverse. These results demonstrate the importance of temperature in determining the repeatability of evolutionary trajectories for the eukaryotic microbe Tetrahymena thermophila and may provide clues to how temperature affects evolution more generally.
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Affiliation(s)
- Jason Tarkington
- Department of Biology and BiochemistryUniversity of HoustonHoustonTXUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Rebecca A. Zufall
- Department of Biology and BiochemistryUniversity of HoustonHoustonTXUSA
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6
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Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing. Microorganisms 2021; 9:microorganisms9091979. [PMID: 34576874 PMCID: PMC8467633 DOI: 10.3390/microorganisms9091979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
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.
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7
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Phenotypic plasticity through disposable genetic adaptation in ciliates. Trends Microbiol 2021; 30:120-130. [PMID: 34275698 DOI: 10.1016/j.tim.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/28/2022]
Abstract
Ciliates have an extraordinary genetic system in which each cell harbors two distinct kinds of nucleus, a transcriptionally active somatic nucleus and a quiescent germline nucleus. The latter undergoes classical, heritable genetic adaptation, while adaptation of the somatic nucleus is only short-term and thus disposable. The ecological and evolutionary relevance of this nuclear dimorphism have never been well formalized, which is surprising given the long history of using ciliates such as Tetrahymena and Paramecium as model organisms. We present a novel, alternative explanation for ciliate nuclear dimorphism which, we argue, should be considered an instrument of phenotypic plasticity by somatic selection on the level of the ciliate clone, as if it were a diffuse multicellular organism. This viewpoint helps to put some enigmatic aspects of ciliate biology into perspective and presents the diversity of ciliates as a large natural experiment that we can exploit to study phenotypic plasticity and organismality.
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Case Study of the Response of N 6-Methyladenine DNA Modification to Environmental Stressors in the Unicellular Eukaryote Tetrahymena thermophila. mSphere 2021; 6:e0120820. [PMID: 34047647 PMCID: PMC8265677 DOI: 10.1128/msphere.01208-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Rediscovered as a potential epigenetic mark, N6-methyladenine DNA modification (6mA) was recently reported to be sensitive to environmental stressors in several multicellular eukaryotes. As 6mA distribution and function differ significantly in multicellular and unicellular organisms, whether and how 6mA in unicellular eukaryotes responds to environmental stress remains elusive. Here, we characterized the dynamic changes of 6mA under starvation in the unicellular model organism Tetrahymena thermophila. Single-molecule, real-time (SMRT) sequencing reveals that DNA 6mA levels in starved cells are significantly reduced, especially symmetric 6mA, compared to those in vegetatively growing cells. Despite a global 6mA reduction, the fraction of asymmetric 6mA with a high methylation level was increased, which might be the driving force for stronger nucleosome positioning in starved cells. Starvation affects expression of many metabolism-related genes, the expression level change of which is associated with the amount of 6mA change, thereby linking 6mA with global transcription and starvation adaptation. The reduction of symmetric 6mA and the increase of asymmetric 6mA coincide with the downregulation of AMT1 and upregulation of AMT2 and AMT5, which are supposedly the MT-A70 methyltransferases required for symmetric and asymmetric 6mA, respectively. These results demonstrated that a regulated 6mA response to environmental cues is evolutionarily conserved in eukaryotes. IMPORTANCE Increasing evidence indicated that 6mA could respond to environmental stressors in multicellular eukaryotes. As 6mA distribution and function differ significantly in multicellular and unicellular organisms, whether and how 6mA in unicellular eukaryotes responds to environmental stress remains elusive. In the present work, we characterized the dynamic changes of 6mA under starvation in the unicellular model organism Tetrahymena thermophila. Our results provide insights into how Tetrahymena fine-tunes its 6mA level and composition upon starvation, suggesting that a regulated 6mA response to environmental cues is evolutionarily conserved in eukaryotes.
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9
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Çalıseki M, Üstüntanır Dede AF, Arslanyolu M. Characterization and use of Tetrahymena thermophila artificial chromosome 2 (TtAC2) constructed by biomimetic of macronuclear rDNA minichromosome. Microbiol Res 2021; 248:126764. [PMID: 33887535 DOI: 10.1016/j.micres.2021.126764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 11/26/2022]
Abstract
Efficient expression vectors for unicellular ciliate eukaryotic Tetrahymena thermophila are still needed in recombinant biology and biotechnology applications. Previously, the construction of the T. thermophila Macronuclear Artificial Chromosome 1 (TtAC1) vector revealed additional needs for structural improvements such as better in vivo stability and maintenance as a recombinant protein expression platform. In this study, we designed an efficiently maintained artificial chromosome by biomimetic of the native macronuclear rDNA minichromosome. TtAC2 was constructed by sequential cloning of subtelomeric 3'NTS region (1.8 kb), an antibiotic resistance gene cassette (2 kb neo4), a gene expression cassette (2 kb TtsfGFP), rDNA coding regions plus a dominant C3 origin sequence (10.3 kb), and telomeres (2.4 kb) in a pUC19 backbone plasmid (2.6 kb). The 21 kb TtAC2 was characterized using fluorescence microscopy, qPCR, western blot and Southern blot after its transformation to vegetative T. thermophila CU428.2 strain, which has a recessive B origin allele. All experimental data show that circular or linear forms of novel TtAC2 were maintained as free replicons in T. thermophila macronucleus with or without antibiotic treatment. Notably, TtAC2 carrying strains expressed a TtsfGFP marker protein, demonstrating the efficacy and functionality of the protein expression platform. We show that TtAC2 is functionally maintained for more than two months, and can be efficiently used in recombinant DNA, and protein production applications.
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Affiliation(s)
- Mehmet Çalıseki
- Department of Advanced Technologies, Graduate School of Sciences, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey.
| | - Ayça Fulya Üstüntanır Dede
- Department of Biology, Institute of Graduate Programs, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey.
| | - Muhittin Arslanyolu
- Department of Biology, Faculty of Sciences, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey.
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10
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Wang G, Fu L, Xiong J, Mochizuki K, Fu Y, Miao W. Identification and Characterization of Base-Substitution Mutations in the Macronuclear Genome of the Ciliate Tetrahymena thermophila. Genome Biol Evol 2021; 13:evaa232. [PMID: 33146387 PMCID: PMC7788487 DOI: 10.1093/gbe/evaa232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Polyploidy can provide adaptive advantages and drive evolution. Amitotic division of the polyploid macronucleus (MAC) in ciliates acts as a nonsexual genetic mechanism to enhance adaptation to stress conditions and thus provides a unique model to investigate the evolutionary role of polyploidy. Mutation is the primary source of the variation responsible for evolution and adaptation; however, to date, de novo mutations that occur in ciliate MAC genomes during these processes have not been characterized and their biological impacts are undefined. Here, we carried out long-term evolution experiments to directly explore de novo MAC mutations and their molecular features in the model ciliate, Tetrahymena thermophila. A simple but effective method was established to detect base-substitution mutations in evolving populations whereas filtering out most of the false positive base-substitutions caused by repetitive sequences and the programmed genome rearrangements. The detected mutations were rigorously validated using the MassARRAY system. Validated mutations showed a strong G/C→A/T bias, consistent with observations in other species. Moreover, a progressive increase in growth rate of the evolving populations suggested that some of these mutations might be responsible for cell fitness. The established mutation identification and validation methods will be an invaluable resource to make ciliates an important model system to study the role of polyploidy in evolution.
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Affiliation(s)
- Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lu Fu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of Montpellier, France
| | - Yunxin Fu
- Department of Biostatistics and Data Science and Human Genetics Center, School of Public Health, The University of Texas Health Science Center
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming, China
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11
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Bacteria-Derived Hemolysis-Related Genes Widely Exist in Scuticociliates. Microorganisms 2020; 8:microorganisms8111838. [PMID: 33266460 PMCID: PMC7709021 DOI: 10.3390/microorganisms8111838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 11/30/2022] Open
Abstract
Scuticociliatosis is an invasive external or systemic infection caused by ciliated protozoa, mainly those within the subclass Scuticociliatia (scuticociliates). Many scuticociliates are fish pathogens, including Miamiensis avidus, Philasterides dicentrarchi, Pseudocohnilembus persalinus, and Uronema marinum. Our previous study showed that hemolysis-related genes derived from bacteria through horizontal gene transfer (HGT) may contribute to virulence in P. persalinus. Hemorrhagic lesions are a common feature of scuticociliatosis, but it is not known whether other scuticociliates also have bacteria-derived hemolysis-related genes. In this study, we constructed a high-quality macronuclear genome of another typical pathogenic scuticociliate, U. marinum. A total of 105 HGT genes were identified in this species, of which 35 were homologs of hemolysis-related genes (including hemolysin-like genes) that had previously been identified in P. persalinus. Sequencing of an additional five species from four scuticociliate families showed that bacteria-derived hemolysis-related genes (especially hemolysin-like genes) are widely distributed in scuticociliates. Based on these findings, we suggest that hemolysin-like genes may have originated before the divergence of scuticociliates.
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12
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Rzeszutek I, Maurer-Alcalá XX, Nowacki M. Programmed genome rearrangements in ciliates. Cell Mol Life Sci 2020; 77:4615-4629. [PMID: 32462406 PMCID: PMC7599177 DOI: 10.1007/s00018-020-03555-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022]
Abstract
Ciliates are a highly divergent group of unicellular eukaryotes with separate somatic and germline genomes found in distinct dimorphic nuclei. This characteristic feature is tightly linked to extremely laborious developmentally regulated genome rearrangements in the development of a new somatic genome/nuclei following sex. The transformation from germline to soma genome involves massive DNA elimination mediated by non-coding RNAs, chromosome fragmentation, as well as DNA amplification. In this review, we discuss the similarities and differences in the genome reorganization processes of the model ciliates Paramecium and Tetrahymena (class Oligohymenophorea), and the distantly related Euplotes, Stylonychia, and Oxytricha (class Spirotrichea).
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Affiliation(s)
- Iwona Rzeszutek
- Institute of Biology and Biotechnology, Department of Biotechnology, University of Rzeszow, Pigonia 1, 35-310, Rzeszow, Poland.
| | - Xyrus X Maurer-Alcalá
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012, Bern, Switzerland
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012, Bern, Switzerland.
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13
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The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1534-1542. [PMID: 32297047 DOI: 10.1007/s11427-020-1689-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/26/2020] [Indexed: 01/03/2023]
Abstract
The ciliate Tetrahymena thermophila has been a powerful model system for molecular and cellular biology. However, some investigations have been limited due to the incomplete closure and sequencing of the macronuclear genome assembly, which for many years has been stalled at 1,158 scaffolds, with large sections of unknown sequences (available in Tetrahymena Genome Database, TGD, http://ciliate.org/ ). Here we completed the first chromosome-level Tetrahymena macronuclear genome assembly, with approximately 300× long Single Molecule, Real-Time reads of the wild-type SB210 cells-the reference strain for the initial macronuclear genome sequencing project. All 181 chromosomes were capped with two telomeres and gaps were entirely closed. The completed genome shows significant improvements over the current assembly (TGD 2014) in both chromosome structure and sequence integrity. The majority of previously identified gene models shown in TGD were retained, with the addition of 36 new genes and 883 genes with modified gene models. The new genome and annotation were incorporated into TGD. This new genome allows for pursuit in some underexplored areas that were far more challenging previously; two of them, genome scrambling and chromosomal copy number, were investigated in this study. We expect that the completed macronuclear genome will facilitate many studies in Tetrahymena biology, as well as multiple lines of research in other eukaryotes.
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14
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Agatha S, Utz LRP, Zufall RA, Warren A. Symposium on Ciliates in Memory of Denis Lynn. Eur J Protistol 2020; 78:125694. [PMID: 33500175 DOI: 10.1016/j.ejop.2020.125694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
Denis Lynn (1947-2018) was an outstanding protistologist, applying multiple techniques and data sources and thus pioneering an integrative approach in order to investigate ciliate biology. For example, he recognized the importance of the ultrastructure for inferring ciliate phylogeny, based on which he developed his widely accepted classification scheme for the phylum Ciliophora. In this paper, recent findings regarding the evolution and systematics of both peritrichs and the mainly marine planktonic oligotrichean spirotrichs are discussed and compared with the concepts and hypotheses formulated by Denis Lynn. Additionally, the state of knowledge concerning the diversity of ciliates in bromeliad phytotelmata and amitosis in ciliates is reviewed.
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Affiliation(s)
- Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria.
| | - Laura R P Utz
- School of Health and Life Sciences, PUCRS, Porto Alegre, Brazil
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK.
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15
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Yan Y, Maurer-Alcalá XX, Knight R, Kosakovsky Pond SL, Katz LA. Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates. mBio 2019; 10:e02524-19. [PMID: 31874915 PMCID: PMC6935857 DOI: 10.1128/mbio.02524-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022] Open
Abstract
Ciliates, a eukaryotic clade that is over 1 billion years old, are defined by division of genome function between transcriptionally inactive germline micronuclei and functional somatic macronuclei. To date, most analyses of gene family evolution have been limited to cultivable model lineages (e.g., Tetrahymena, Paramecium, Oxytricha, and Stylonychia). Here, we focus on the uncultivable Karyorelictea and its understudied sister class Heterotrichea, which represent two extremes in genome architecture. Somatic macronuclei within the Karyorelictea are described as nearly diploid, while the Heterotrichea have hyperpolyploid somatic genomes. Previous analyses indicate that genome architecture impacts ciliate gene family evolution as the most diverse and largest gene families are found in lineages with extensively processed somatic genomes (i.e., possessing thousands of gene-sized chromosomes). To further assess ciliate gene family evolution, we analyzed 43 single-cell transcriptomes from 33 ciliate species representing 10 classes. Focusing on conserved eukaryotic genes, we use estimates of transcript diversity as a proxy for the number of paralogs in gene families among four focal clades: Karyorelictea, Heterotrichea, extensive fragmenters (with gene-size somatic chromosomes), and non-extensive fragmenters (with more traditional somatic chromosomes), the latter two within the subphylum Intramacronucleata. Our results show that (i) the Karyorelictea have the lowest average transcript diversity, while Heterotrichea are highest among the four groups; (ii) proteins in Karyorelictea are under the highest functional constraints, and the patterns of selection in ciliates may reflect genome architecture; and (iii) stop codon reassignments vary among members of the Heterotrichea and Spirotrichea but are conserved in other classes.IMPORTANCE To further our understanding of genome evolution in eukaryotes, we assess the relationship between patterns of molecular evolution within gene families and variable genome structures found among ciliates. We combine single-cell transcriptomics with bioinformatic tools, focusing on understudied and uncultivable lineages selected from across the ciliate tree of life. Our analyses show that genome architecture correlates with patterns of protein evolution as lineages with more canonical somatic genomes, such as the class Karyorelictea, have more conserved patterns of molecular evolution compared to other classes. This study showcases the power of single-cell transcriptomics for investigating genome architecture and evolution in uncultivable microbial lineages and provides transcriptomic resources for further research on genome evolution.
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Affiliation(s)
- Ying Yan
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA
| | - Xyrus X Maurer-Alcalá
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Rob Knight
- University of California San Diego, Department of Pediatrics, San Diego, California, USA
- University of California San Diego, Department of Computer Science and Engineering, San Diego, California, USA
- University of California San Diego, Center for Microbiome Innovation, San Diego, California, USA
| | - Sergei L Kosakovsky Pond
- Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, Pennsylvania, USA
| | - Laura A Katz
- Smith College, Department of Biological Sciences, Northampton, Massachusetts, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
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16
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Andersen KL, Nielsen H. Knock-Down of a Novel snoRNA in Tetrahymena Reveals a Dual Role in 5.8S rRNA Processing and Generation of a 26S rRNA Fragment. Biomolecules 2018; 8:E128. [PMID: 30380771 PMCID: PMC6315972 DOI: 10.3390/biom8040128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/30/2022] Open
Abstract
In eukaryotes, 18S, 5.8S, and 28S rRNAs are transcribed as precursor molecules that undergo extensive modification and nucleolytic processing to form the mature rRNA species. Central in the process are the small nucleolar RNAs (snoRNAs). The majority of snoRNAs guide site specific chemical modifications but a few are involved in defining pre-rRNA cleavages. Here, we describe an unusual snoRNA (TtnuCD32) belonging to the box C/D subgroup from the ciliate Tetrahymena thermophila. We show that TtnuCD32 is unlikely to function as a modification guide snoRNA and that it is critical for cell viability. Cell lines with genetic knock-down of TtnuCD32 were impaired in growth and displayed two novel and apparently unrelated phenotypes. The most prominent phenotype is the accumulation of processing intermediates of 5.8S rRNA. The second phenotype is the decrease in abundance of a ~100 nt 26S rRNA fragment of unknown function. Sequence analysis demonstrated that TtnuCD32 share features with the essential snoRNA U14 but an alternative candidate (TtnuCD25) was more closely related to other U14 sequences. This, together with the fact that the observed rRNA processing phenotypes were not similar to what has been observed in U14 depleted cells, suggests that TtnuCD32 is a U14 homolog that has gained novel functions.
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MESH Headings
- Base Sequence
- Cell Survival
- Conserved Sequence
- Gene Expression Regulation
- Gene Knockdown Techniques
- Genome
- Methylation
- Nucleic Acid Conformation
- Protozoan Proteins/chemistry
- Protozoan Proteins/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- Tetrahymena/genetics
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Kasper L Andersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200N Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
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17
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Kaczanowski A, Kiersnowska M. Formation and degradation of large extrusion bodies in Tetrahymena thermophila: The role of intramacronuclear microtubules in chromatin segregation. Eur J Protistol 2018; 66:177-188. [DOI: 10.1016/j.ejop.2018.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 11/17/2022]
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18
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Maurer-Alcalá XX, Yan Y, Pilling OA, Knight R, Katz LA. Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics. Genome Biol Evol 2018; 10:1927-1939. [PMID: 29945193 PMCID: PMC6101598 DOI: 10.1093/gbe/evy133] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 12/30/2022] Open
Abstract
The emergence of robust single-cell 'omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a > 1 Gy old clade). Analysis of the data resulting from these single-cell 'omics approaches show: 1) the description of the ciliates in the class Karyorelictea as "primitive" is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani's (1890) observation of giant chromosomes in this lineage; and 3) gene scrambling exists in the underexplored Postciliodesmatophora (the classes Heterotrichea and Karyorelictea, abbreviated here as the Po-clade), one of two major clades of ciliates. Together these data highlight the complex evolutionary patterns underlying germline genome architectures in ciliates and provide a basis for further exploration of principles of genome evolution in diverse microbial lineages.
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Affiliation(s)
- Xyrus X Maurer-Alcalá
- Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst.,Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Olivia A Pilling
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego.,Department of Computer Science and Engineering, University of California San Diego, San Diego.,Center for Microbiome Innovation, University of California San Diego, San Diego
| | - Laura A Katz
- Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst.,Department of Biological Sciences, Smith College, Northampton, Massachusetts
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Wang Y, Wang Y, Sheng Y, Huang J, Chen X, AL-Rasheid KA, Gao S. A comparative study of genome organization and epigenetic mechanisms in model ciliates, with an emphasis on Tetrahymena , Paramecium and Oxytricha. Eur J Protistol 2017; 61:376-387. [DOI: 10.1016/j.ejop.2017.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 06/20/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
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20
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Whole Genome Sequencing Identifies a Novel Factor Required for Secretory Granule Maturation in Tetrahymena thermophila. G3-GENES GENOMES GENETICS 2016; 6:2505-16. [PMID: 27317773 PMCID: PMC4978903 DOI: 10.1534/g3.116.028878] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Unbiased genetic approaches have a unique ability to identify novel genes associated with specific biological pathways. Thanks to next generation sequencing, forward genetic strategies can be expanded to a wider range of model organisms. The formation of secretory granules, called mucocysts, in the ciliate Tetrahymena thermophila relies, in part, on ancestral lysosomal sorting machinery, but is also likely to involve novel factors. In prior work, multiple strains with defects in mucocyst biogenesis were generated by nitrosoguanidine mutagenesis, and characterized using genetic and cell biological approaches, but the genetic lesions themselves were unknown. Here, we show that analyzing one such mutant by whole genome sequencing reveals a novel factor in mucocyst formation. Strain UC620 has both morphological and biochemical defects in mucocyst maturation-a process analogous to dense core granule maturation in animals. Illumina sequencing of a pool of UC620 F2 clones identified a missense mutation in a novel gene called MMA1 (Mucocyst maturation). The defects in UC620 were rescued by expression of a wild-type copy of MMA1, and disrupting MMA1 in an otherwise wild-type strain phenocopies UC620. The product of MMA1, characterized as a CFP-tagged copy, encodes a large soluble cytosolic protein. A small fraction of Mma1p-CFP is pelletable, which may reflect association with endosomes. The gene has no identifiable homologs except in other Tetrahymena species, and therefore represents an evolutionarily recent innovation that is required for granule maturation.
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Dimond KL, Zufall RA. Hidden genetic variation in the germline genome of Tetrahymena thermophila. J Evol Biol 2016; 29:1284-92. [PMID: 26998689 DOI: 10.1111/jeb.12868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/29/2016] [Accepted: 03/13/2016] [Indexed: 11/28/2022]
Abstract
Genome architecture varies greatly among eukaryotes. This diversity may profoundly affect the origin and maintenance of genetic variation within a population. Ciliates are microbial eukaryotes with unusual genome features, such as the separation of germline and somatic genomes within a single cell and amitotic division. These features have previously been proposed to increase the rate of molecular evolution in these species. Here, we assessed the fitness effects of genetic variation in the two genomes of natural isolates of the ciliate Tetrahymena thermophila. We find more extensive genetic variation in fitness in the transcriptionally silent germline genome than in the expressed somatic genome. Surprisingly, this variation is not primarily deleterious, but has both beneficial and deleterious effects. We conclude that Tetrahymena genome architecture allows for the maintenance of genetic variation that would otherwise be eliminated by selection. We consider the effect of selection on the two genomes and the impacts of reproductive strategies and the mechanism of sex determination on the structure of this variation.
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Affiliation(s)
- K L Dimond
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - R A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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22
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Doerder FP. Abandoning sex: multiple origins of asexuality in the ciliate Tetrahymena. BMC Evol Biol 2014; 14:112. [PMID: 24885485 PMCID: PMC4045964 DOI: 10.1186/1471-2148-14-112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/14/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND By segregating somatic and germinal functions into large, compound macronuclei and small diploid micronuclei, respectively, ciliates can explore sexuality in ways other eukaryotes cannot. Sex, for instance, is not for reproduction but for nuclear replacement in the two cells temporarily joined in conjugation. With equal contributions from both conjugants, there is no cost of sex which theory predicts should favor asexuality. Yet ciliate asexuality is rare. The exceptional Tetrahymena has abandoned sex through loss of the micronucleus; its amicronucleates are abundant in nature where they reproduce by binary fission but never form conjugating pairs. A possible reason for their abundance is that the Tetrahymena macronucleus does not accumulate mutations as proposed by Muller's ratchet. As such, Tetrahymena amicronucleates have the potential to be very old. This study used cytochrome oxidase-1 barcodes to determine the phylogenetic origin and relative age of amicronucleates isolated from nature. RESULTS Amicronucleates constituted 25% of Tetrahymena-like wild isolates. Of the 244 amicronucleates examined for cox1 barcodes, 237 belonged to Tetrahymena, seven to other genera. Sixty percent originated from 12 named species or barcoded strains, including the model Tetrahymena thermophila, while the remaining 40% represent 19 putative new species, eight of which have micronucleate counterparts and 11 of which are known only as amicronucleates. In some instances, cox1 haplotypes were shared among micronucleate and amicronucleates collected from the same source. Phylogenetic analysis showed that most amicronucleates belong to the "borealis" clade in which mating type is determined by gene rearrangement. Some amicronucleate species were clustered on the SSU phylogenetic tree and had longer branch lengths, indicating more ancient origin. CONCLUSIONS Naturally occurring Tetrahymena amicronucleates have multiple origins, arising from numerous species. Likely many more new species remain to be discovered. Shared haplotypes indicate that some are of contemporary origin, while phylogeny indicates that others may be millions of years old. The apparent success of amicronucleate Tetrahymena may be because macronuclear assortment and recombination allow them to avoid Muller's ratchet, incorporate beneficial mutations, and evolve independently of sex. The inability of amicronucleates to mate may be the result of error(s) in mating type gene rearrangement.
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Affiliation(s)
- F Paul Doerder
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA.
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23
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Morgens DW, Stutz TC, Cavalcanti ARO. Novel Population Genetics in Ciliates due to Life Cycle and Nuclear Dimorphism. Mol Biol Evol 2014; 31:2084-93. [PMID: 24784136 DOI: 10.1093/molbev/msu150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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24
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Long HA, Paixão T, Azevedo RBR, Zufall RA. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics 2013; 195:527-40. [PMID: 23934880 PMCID: PMC3781978 DOI: 10.1534/genetics.113.153536] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/19/2013] [Indexed: 11/18/2022] Open
Abstract
Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U=0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s=11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h=0.26; 95% CI: -0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.
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Affiliation(s)
- Hong-An Long
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Tiago Paixão
- The Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ricardo B. R. Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001
| | - Rebecca A. Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001
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25
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Spring KJ, Pham S, Zufall RA. Chromosome copy number variation and control in the ciliate Chilodonella uncinata. PLoS One 2013; 8:e56413. [PMID: 23437129 PMCID: PMC3577910 DOI: 10.1371/journal.pone.0056413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/09/2013] [Indexed: 12/02/2022] Open
Abstract
Copy number variations are widespread in eukaryotes. The unusual genome architecture of ciliates, in particular, with its process of amitosis in macronuclear division, provides a valuable model in which to study copy number variation. The current model of amitosis envisions stochastic distribution of macronuclear chromosomes during asexual reproduction. This suggests that amitosis is likely to result in high levels of copy number variation in ciliates, as dividing daughter cells can have variable copy numbers of chromosomes if chromosomal distribution during amitosis is a stochastic process. We examined chromosomal distribution during amitosis in Chilodonella uncinata, a ciliate with gene-size macronuclear chromosomes. We quantified 4 chromosomes in evolving populations of C. uncinata and modeled the amitotic distribution process. We found that macronuclear chromosomes differ in copy number from one another but that copy number does not change as expected under a stochastic process. The chromosome carrying SSU increased in copy number, which is consistent with selection to increase abundance; however, two other studied chromosomes displayed much lower than expected among-line variance. Our models suggest that balancing selection is sufficient to explain the observed maintenance of chromosome copy during asexual reproduction.
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Affiliation(s)
- Kevin J Spring
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.
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26
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Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 2013; 11:e1001473. [PMID: 23382650 PMCID: PMC3558436 DOI: 10.1371/journal.pbio.1001473] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 12/12/2012] [Indexed: 01/03/2023] Open
Abstract
With more chromosomes than any other sequenced genome, the macronuclear genome of Oxytricha trifallax has a unique and complex architecture, including alternative fragmentation and predominantly single-gene chromosomes. The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ∼3.2 kb) and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease. The macronuclear genome of the ciliate Oxytricha trifallax, contained in its somatic nucleus, has a unique genome architecture. Unlike its diploid germline genome, which is transcriptionally inactive during normal cellular growth, the macronuclear genome is fragmented into at least 16,000 tiny (∼3.2 kb mean length) chromosomes, most of which encode single actively transcribed genes and are differentially amplified to a few thousand copies each. The smallest chromosome is just 469 bp, while the largest is 66 kb and encodes a single enormous protein. We found considerable variation in the genome, including frequent alternative fragmentation patterns, generating chromosome isoforms with shared sequence. We also found limited variation in chromosome amplification levels, though insufficient to explain mRNA transcript level variation. Another remarkable feature of Oxytricha's macronuclear genome is its inordinate fondness for telomeres. In conjunction with its possession of tens of millions of chromosome-ending telomeres per macronucleus, we show that Oxytricha has evolved multiple putative telomere-binding proteins. In addition, we identified two new domesticated transposase-like protein classes that we propose may participate in the process of genome rearrangement. The macronuclear genome now provides a crucial resource for ongoing studies of genome rearrangement processes that use Oxytricha as an experimental or comparative model.
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Affiliation(s)
- Estienne C. Swart
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - John R. Bracht
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Vincent Magrini
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Xiao Chen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Yi Zhou
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jaspreet S. Khurana
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Aaron D. Goldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mariusz Nowacki
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Klaas Schotanus
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Seolkyoung Jung
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Robert S. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Amy Ly
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sean McGrath
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kevin Haub
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jessica L. Wiggins
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Donna Storton
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - John C. Matese
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Lance Parsons
- Bioinformatics Group, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Wei-Jen Chang
- Department of Biology, Hamilton College, Clinton, New York, United States of America
| | - Michael S. Bowen
- Biology Department, Bradley University, Peoria, Illinois, United States of America
| | - Nicholas A. Stover
- Biology Department, Bradley University, Peoria, Illinois, United States of America
| | - Thomas A. Jones
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Sean R. Eddy
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Glenn A. Herrick
- Biology Department, University of Utah, Salt Lake City, Utah, United States of America
| | - Thomas G. Doak
- Department of Biology, University of Indiana, Bloomington, Indiana, United States of America
| | - Richard K. Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Elaine R. Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Laura F. Landweber
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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27
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Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax. Gene 2012; 505:75-80. [DOI: 10.1016/j.gene.2012.05.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 03/25/2012] [Accepted: 05/21/2012] [Indexed: 01/17/2023]
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Coyne RS, Lhuillier-Akakpo M, Duharcourt S. RNA-guided DNA rearrangements in ciliates: is the best genome defence a good offence? Biol Cell 2012; 104:309-25. [PMID: 22352444 DOI: 10.1111/boc.201100057] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/15/2012] [Indexed: 12/13/2022]
Abstract
Genomes, like crazy patchwork quilts, are stitched together over evolutionary time from diverse elements, including some unwelcome invaders. To deal with parasitic mobile elements, most eukaryotes employ a genome self-defensive manoeuvre to recognise and silence such elements by homology-dependent interactions with RNA-protein complexes that alter chromatin. Ciliated protozoa employ more 'offensive' tactics by actually unstitching and reassembling their somatic genomes at every sexual generation to eliminate transposons and their remnants, using as patterns the maternal genomes that were rearranged in the previous cycle. Genetic and genomic studies of the distant relatives Paramecium and Tetrahymena have begun to reveal how such events are carried out with remarkable precision. Whole genome, non-coding transcripts from the maternal genome are compared with transcripts from the zygotic genome that are processed through an RNA interference (RNAi)-related process. Sequences found only in the latter are targeted for elimination by the resulting short 'scanRNAs' in many thousand DNA splicing reactions initiated by a domesticated transposase. The involvement of widely conserved mechanisms and protein factors clearly shows the relatedness of these phenomena to RNAi-mediated heterochromatic gene silencing. Such malleability of the genome on a generational time scale also has profound evolutionary implications, possibly including the epigenetic inheritance of acquired adaptive traits.
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Cassidy-Hanley DM. Tetrahymena in the laboratory: strain resources, methods for culture, maintenance, and storage. Methods Cell Biol 2012; 109:237-76. [PMID: 22444147 PMCID: PMC3608402 DOI: 10.1016/b978-0-12-385967-9.00008-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
The ciliated protozoan Tetrahymena thermophila has been an important model system for biological research for many years. During that time, a variety of useful strains, including highly inbred stocks, a collection of diverse mutant strains, and wild cultivars from a variety of geographical locations have been identified. In addition, thanks to the efforts of many different laboratories, optimal conditions for growth, maintenance, and storage of Tetrahymena have been worked out. To facilitate the efficient use of Tetrahymena, especially by those new to the system, this chapter presents a brief description of many available Tetrahymena strains and lists possible resources for obtaining viable cultures of T. thermophila and other Tetrahymena species. Descriptions of commonly used media, methods for cell culture and maintenance, and protocols for short- and long-term storage are also presented.
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Affiliation(s)
- Donna M Cassidy-Hanley
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Abstract
Within the past decade, genomic studies have emerged as essential and highly productive tools to explore the biology of Tetrahymena thermophila. The current major resources, which have been extensively mined by the research community, are the annotated macronuclear genome assembly, transcriptomic data and the databases that house this information. Efforts in progress will soon improve these data sources and expand their scope, including providing annotated micronuclear and comparative genomic sequences. Future studies of Tetrahymena cell and molecular biology, development, physiology, evolution and ecology will benefit greatly from these resources and the advanced genomic technologies they enable.
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Abstract
The genus Tetrahymena is defined on the basis of a four-part oral structure composed of an undulating membrane and three membranelles. It is a monophyletic genus with 41 named species and numerous unnamed species, many of which are morphologically indistinguishable. Nuclear small subunit rRNA and mitochondrial cytochrome c oxidase subunit 1 sequences indicate two major clades, a "borealis" clade of less closely related species and an "australis" clade of more closely related species that correlate to differences in mating-type determination and frequency of amicronucleates. Members of both clades show convergence for histophagy (primarily facultative), macrostome transformation, and (rare) cyst formation. Life cycle parameters of species are presented and problematic species discussed.
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Affiliation(s)
- Denis H Lynn
- Department of Zoology, University of British Columbia, 6270 University Blvd., Vancouver, BC, Canada V6T 1Z4
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Motl JA, Chalker DL. Zygotic expression of the double-stranded RNA binding motif protein Drb2p is required for DNA elimination in the ciliate Tetrahymena thermophila. EUKARYOTIC CELL 2011; 10:1648-59. [PMID: 22021239 PMCID: PMC3232721 DOI: 10.1128/ec.05216-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/13/2011] [Indexed: 11/20/2022]
Abstract
Double-stranded RNA binding motif (DSRM)-containing proteins play many roles in the regulation of gene transcription and translation, including some with tandem DSRMs that act in small RNA biogenesis. We report the characterization of the genes for double-stranded RNA binding proteins 1 and 2 (DRB1 and DRB2), two genes encoding nuclear proteins with tandem DSRMs in the ciliate Tetrahymena thermophila. Both proteins are expressed throughout growth and development but exhibit distinct peaks of expression, suggesting different biological roles. In support of this, we show that expression of DRB2 is essential for vegetative growth while DRB1 expression is not. During conjugation, Drb1p and Drb2p localize to distinct nuclear foci. Cells lacking all DRB1 copies are able to produce viable progeny, although at a reduced rate relative to wild-type cells. In contrast, cells lacking germ line DRB2 copies, which thus cannot express Drb2p zygotically, fail to produce progeny, arresting late into conjugation. This arrest phenotype is accompanied by a failure to organize the essential DNA rearrangement protein Pdd1p into DNA elimination bodies and execute DNA elimination and chromosome breakage. These results implicate zygotically expressed Drb2p in the maturation of these nuclear structures, which are necessary for reorganization of the somatic genome.
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Affiliation(s)
- Jason A. Motl
- Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Dr., St. Louis, Missouri 63130-4899
| | - Douglas L. Chalker
- Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Dr., St. Louis, Missouri 63130-4899
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Andersen KL, Nielsen H. Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila. Nucleic Acids Res 2011; 40:1267-81. [PMID: 21967850 PMCID: PMC3273799 DOI: 10.1093/nar/gkr792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during vegetative growth or sexual reorganization. In order to get an overview of medium-sized (40-500 nt) RNAs expressed from the Tetrahymena genome, we created a size-fractionated cDNA library from macronuclear RNA and analyzed 80 RNAs, most of which were previously unknown. The most abundant class was small nucleolar RNAs (snoRNAs), many of which are formed by an unusual maturation pathway. The modifications guided by the snoRNAs were analyzed bioinformatically and experimentally and many Tetrahymena-specific modifications were found, including several in an essential, but not conserved domain of ribosomal RNA. Of particular interest, we detected two methylations in the 5'-end of U6 small nuclear RNA (snRNA) that has an unusual structure in Tetrahymena. Further, we found a candidate for the first U8 outside metazoans, and an unusual U14 candidate. In addition, a number of candidates for new non-coding RNAs were characterized by expression analysis at different growth conditions.
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Affiliation(s)
- Kasper L Andersen
- Department of Cellular and Molecular Medicine and Center for Non-coding RNA in Technology and Health, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, DK-2200N, Denmark
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Orias E, Cervantes MD, Hamilton EP. Tetrahymena thermophila, a unicellular eukaryote with separate germline and somatic genomes. Res Microbiol 2011; 162:578-86. [PMID: 21624459 DOI: 10.1016/j.resmic.2011.05.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 04/14/2011] [Indexed: 12/11/2022]
Abstract
Tetrahymena thermophila is a ciliate--a unicellular eukaryote. Remarkably, every cell maintains differentiated germline and somatic genomes: one silent, the other expressed. Moreover, the two genomes undergo diverse processes, some as extreme as life and death, simultaneously in the same cytoplasm. Conserved eukaryotic mechanisms have been modified in ciliates to selectively deal with the two genomes. We describe research in several areas of Tetrahymena biology, including meiosis, amitosis, genetic assortment, selective nuclear pore transport, somatic RNAi-guided heterochromatin formation, DNA excision and programmed nuclear death by autophagy, which has enriched and broadened knowledge of those mechanisms.
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Affiliation(s)
- Eduardo Orias
- Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106, USA.
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Brito PH, Guilherme E, Soares H, Gordo I. Mutation accumulation in Tetrahymena. BMC Evol Biol 2010; 10:354. [PMID: 21078144 PMCID: PMC2998532 DOI: 10.1186/1471-2148-10-354] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 11/15/2010] [Indexed: 12/01/2022] Open
Abstract
Background The rate and fitness effects of mutations are key in understanding the evolution of every species. Traditionally, these parameters are estimated in mutation accumulation experiments where replicate lines are propagated in conditions that allow mutations to randomly accumulate without the purging effect of natural selection. These experiments have been performed with many model organisms but we still lack empirical estimates of the rate and effects of mutation in the protists. Results We performed a mutation accumulation (MA) experiment in Tetrahymena thermophila, a species that can reproduce sexually and asexually in nature, and measured both the mean decline and variance increase in fitness of 20 lines. The results obtained with T. thermophila were compared with T. pyriformis that is an obligate asexual species. We show that MA lines of T. thermophila go to extinction at a rate of 1.25 clonal extinctions per bottleneck. In contrast, populations of T. pyriformis show a much higher resistance to extinction. Variation in gene copy number is likely to be a key factor in explaining these results, and indeed we show that T. pyriformis has a higher mean copy number per cell than T. thermophila. From fitness measurements during the MA experiment, we infer a rate of mutation to copy number variation of 0.0333 per haploid MAC genome of T. thermophila and a mean effect against copy number variation of 0.16. A strong effect of population size in the rate of fitness decline was also found, consistent with the increased power of natural selection. Conclusions The rate of clonal extinction measured for T. thermophila is characteristic of a mutational degradation and suggests that this species must undergo sexual reproduction to avoid the deleterious effects detected in the laboratory experiments. We also suggest that an increase in chromosomal copy number associated with the phenotypic assortment of amitotic divisions can provide an alternative mechanism to escape the deleterious effect of random chromosomal copy number variation in species like T. pyriformis that lack the resetting mechanism of sexual reproduction. Our results are relevant to the understanding of cell line longevity and senescence in ciliates.
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Dave D, Wloga D, Gaertig J. Manipulating ciliary protein-encoding genes in Tetrahymena thermophila. Methods Cell Biol 2009; 93:1-20. [PMID: 20409809 DOI: 10.1016/s0091-679x(08)93001-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Tetrahymena thermophila has emerged as an excellent protist model for studies on cilia that are based on reverse genetic approaches. In Tetrahymena, genes can be routinely disrupted by the DNA homologous recombination. We present established protocols for the manipulation of genes in either the germline micronucleus or the somatic macronucleus. A detailed protocol is provided for the construction of heterokaryon strains that carry a gene disruption only in the micronucleus. Heterokaryon strain can be propagated like wild-type cells, and ciliary phenotypes can be expressed on demand by mating. We describe methods that can be used for disruption of multiple genes. We include protocols for the generation and maintenance of Tetrahymena cells that either lack cilia or have paralyzed cilia.
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Affiliation(s)
- Drashti Dave
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, USA
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Plattner H, Sehring IM, Schilde C, Ladenburger E. Chapter 5 Pharmacology of Ciliated Protozoa—Drug (In)Sensitivity and Experimental Drug (Ab)Use. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 273:163-218. [DOI: 10.1016/s1937-6448(08)01805-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 2007; 4:e286. [PMID: 16933976 PMCID: PMC1557398 DOI: 10.1371/journal.pbio.0040286] [Citation(s) in RCA: 549] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 06/23/2006] [Indexed: 01/05/2023] Open
Abstract
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
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Affiliation(s)
- Jonathan A Eisen
- The Institute for Genomic Research, Rockville, Maryland, United States of America.
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Hamilton EP, Williamson S, Dunn S, Merriam V, Lin C, Vong L, Russell-Colantonio J, Orias E. The highly conserved family of Tetrahymena thermophila chromosome breakage elements contains an invariant 10-base-pair core. EUKARYOTIC CELL 2006; 5:771-80. [PMID: 16607024 PMCID: PMC1459666 DOI: 10.1128/ec.5.4.771-780.2006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As a typical ciliate, Tetrahymena thermophila is a unicellular eukaryote that exhibits nuclear dimorphism: each cell contains a diploid, germ line micronucleus (MICN) and a polyploid, somatic macronucleus (MACN). During conjugation, when a new MACN differentiates from a mitotic descendant of the diploid fertilization nucleus, the five MICN chromosomes are site-specifically fragmented into 250 to 300 MACN chromosomes. The classic chromosome breakage sequence (CBS) is a 15-bp element (TAAACCAACCTCTTT) reported to be necessary and sufficient for chromosome breakage. To determine whether a CBS is present at every site of chromosome fragmentation and to assess the range of sequence variation tolerated, 31 CBSs were isolated without preconception as to the sequence of the chromosome breakage element. Additional CBS-related sequences were identified in the whole-genome sequence by their similarities to the classic CBS. Forty CBS elements behaved as authentic chromosome breakage sites. The CBS nucleotide sequence is more diverse than previously thought: nearly half of the CBS elements identified by unbiased methods have a variant of the classic CBS. Only an internal 10-bp core is completely conserved, but the entire 15-bp chromosome breakage sequence shows significant sequence conservation. Our results suggest that any one member of the CBS family provides a necessary and sufficient cis element for chromosome breakage. No chromosome breakage element totally unrelated to the classic CBS element was found; such elements, if they exist at all, must be rare.
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Affiliation(s)
- Eileen P Hamilton
- Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106, USA.
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Cervantes MD, Coyne RS, Xi X, Yao MC. The condensin complex is essential for amitotic segregation of bulk chromosomes, but not nucleoli, in the ciliate Tetrahymena thermophila. Mol Cell Biol 2006; 26:4690-700. [PMID: 16738332 PMCID: PMC1489118 DOI: 10.1128/mcb.02315-05] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The macronucleus of the binucleate ciliate Tetrahymena thermophila contains fragmented and amplified chromosomes that do not have centromeres, eliminating the possibility of mitotic nuclear division. Instead, the macronucleus divides by amitosis with random segregation of these chromosomes without detectable chromatin condensation. This amitotic division provides a special opportunity for studying the roles of mitotic proteins in segregating acentric chromatin. The Smc4 protein is a core component of the condensin complex that plays a role in chromatin condensation and has also been associated with nucleolar segregation, DNA repair, and maintenance of the chromatin scaffold. Mutants of Tetrahymena SMC4 have remarkable characteristics during amitosis. They do not form microtubules inside the macronucleus as normal cells do, and there is little or no bulk DNA segregation during cell division. Nevertheless, segregation of nucleoli to daughter cells still occurs, indicating the independence of this process and bulk DNA segregation in ciliate amitosis.
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Affiliation(s)
- Marcella D Cervantes
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, Orias E. Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome. Genomics 2006; 88:443-51. [PMID: 16782302 PMCID: PMC3169840 DOI: 10.1016/j.ygeno.2006.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 05/05/2006] [Accepted: 05/06/2006] [Indexed: 10/24/2022]
Abstract
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.
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Affiliation(s)
- Eileen P Hamilton
- Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106, USA.
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Bowman GR, Elde NC, Morgan G, Winey M, Turkewitz AP. Core formation and the acquisition of fusion competence are linked during secretory granule maturation in Tetrahymena. Traffic 2005; 6:303-23. [PMID: 15752136 PMCID: PMC4708285 DOI: 10.1111/j.1600-0854.2005.00273.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The formation of dense core secretory granules is a multistage process beginning in the trans Golgi network and continuing during a period of granule maturation. Direct interactions between proteins in the membrane and those in the forming dense core may be important for sorting during this process, as well as for organizing membrane proteins in mature granules. We have isolated two mutants in dense core granule formation in the ciliate Tetrahymena thermophila, an organism in which this pathway is genetically accessible. The mutants lie in two distinct genes but have similar phenotypes, marked by accumulation of a set of granule cargo markers in intracellular vesicles resembling immature secretory granules. Sorting to these vesicles appears specific, since they do not contain detectable levels of an extraneous secretory marker. The mutants were initially identified on the basis of aberrant proprotein processing, but also showed defects in the docking of the immature granules. These defects, in core assembly and docking, were similarly conditional with respect to growth conditions, and therefore are likely to be tightly linked. In starved cells, the processing defect was less severe, and the immature granules could dock but still did not undergo stimulated exocytosis. We identified a lumenal protein that localizes to the docking-competent end of wildtype granules, but which is delocalized in the mutants. Our results suggest that dense cores have functionally distinct domains that may be important for organizing membrane proteins involved in docking and fusion.
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Affiliation(s)
- Grant R Bowman
- Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
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Hamilton E, Bruns P, Lin C, Merriam V, Orias E, Vong L, Cassidy-Hanley D. Genome-wide characterization of tetrahymena thermophila chromosome breakage sites. I. Cloning and identification of functional sites. Genetics 2005; 170:1611-21. [PMID: 15956677 PMCID: PMC1449750 DOI: 10.1534/genetics.104.031401] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2004] [Accepted: 05/10/2005] [Indexed: 11/18/2022] Open
Abstract
The chromosomes of the macronuclear (expressed) genome of Tetrahymena thermophila are generated by developmental fragmentation of the five micronuclear (germline) chromosomes. This fragmentation is site specific and directed by a conserved 15-bp chromosome breakage sequence (Cbs element). This article reports the construction of a library enriched for chromosome breakage junctions and the development of a successful scheme for the genome-wide isolation and characterization of functional Cbs junctions. Twenty-three new Cbs junctions were characterized and each was assigned to a specific micronuclear chromosome or chromosome arm. Two distinct previously unreported variant chromosome breakage sequences were found, each in two or more functional Cbs elements. Analysis of natural Cbs junctions confirmed that microheterogeneity in the macronuclear telomere addition site is associated with chromosome fragmentation. The physical and genetic characterization of these functional chromosome breakage junctions is reported in the accompanying article in this issue. The whole-genome shotgun sequencing and auto-assembly phase of the Tetrahymena Genome Initiative has recently been completed at The Institute for Genome Research (TIGR). By providing unique sequence from the natural ends of macronuclear chromosomes, Cbs junctions characterized in the work reported here will serve as useful sequence tags for relating macro- and micronuclear genetic, physical, and sequence maps.
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Affiliation(s)
- Eileen Hamilton
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA.
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Smith JJ, Cole ES, Romero DP. Transcriptional control of RAD51 expression in the ciliate Tetrahymena thermophila. Nucleic Acids Res 2004; 32:4313-21. [PMID: 15304567 PMCID: PMC514391 DOI: 10.1093/nar/gkh771] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Revised: 07/27/2004] [Accepted: 07/27/2004] [Indexed: 11/15/2022] Open
Abstract
The expression of Rad51p, a DNA repair protein that mediates homologous recombination, is induced by DNA damage and during both meiosis and exconjugant development in the ciliate Tetrahymena thermophila. To completely investigate the transcriptional regulation of Tetrahymena RAD51 expression, reporter genes consisting of the RAD51 5' non-translated sequence (5' NTS) positioned upstream of either the firefly luciferase or green fluorescent protein coding sequences have been targeted for recombination at the macronuclear btu1-1 (K350M) locus of T. thermophila strain CU522. Expression from RAD51-luciferase reporter constructs has been directly quantified from transformant whole cell lysates. Luciferase is induced to maximum levels in transformants harboring the full-length RAD51-luciferase reporter gene following exposure to DNA damaging UV irradiation. A series of truncations, deletions, insertions, substitutions and inversions of the RAD51 5' NTS have led to the identification of three distinct transcriptional promoter elements. The first of these sequence elements is required for basal levels of transcription. The second modulates expression in the absence of DNA damage, whereas the third ensures increased RAD51 transcription in response to DNA damage and during meiosis. Tetrahymena RAD51 is tightly regulated through these transcriptional elements to produce the appropriate expression during conjugation, and in response to DNA damage.
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Affiliation(s)
- Joshua J Smith
- Department of Pharmacology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
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Fujiu K, Numata O. Identification and molecular cloning of Tetrahymena 138-kDa protein, a transcription elongation factor homologue that interacts with microtubules in vitro. Biochem Biophys Res Commun 2004; 315:196-203. [PMID: 15013445 DOI: 10.1016/j.bbrc.2004.01.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2003] [Indexed: 11/18/2022]
Abstract
Macronucleus of Tetrahymena divides amitotically, although in a microtubule-dependent fashion. Besides the localization study and pharmacological study of macronuclear microtubules, mechanism of the macronuclear division is poorly understood. A biochemical search for microtubule-associated protein was attempted from the isolated macronucleus. Improvement on macronucleus isolation method and microtubule coprecipitation assay led to the cloning of p138, a new homologue of transcription elongation factor FACT (facilitates chromatin transcription) 140kDa subunit. DNase treatment test of macronuclear extract and the sequence of p138 suggested that p138 is associated with chromosome in the macronucleus. The release tests of p138 from microtubules indicated that p138 is released from microtubules in the presence of ATP but not in the presence of AMP-PNP. Together, the results suggest a novel function of FACT homologue, that p138 interacts with both microtubules and chromosome.
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Affiliation(s)
- Kenta Fujiu
- Institute of Biological Sciences, The University of Tsukuba, 1-1-1 Tennoudai, Tsukuba-shi, Ibaraki-ken 305-8572, Japan
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47
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Bowman GR, Turkewitz AP. Analysis of a mutant exhibiting conditional sorting to dense core secretory granules in Tetrahymena thermophila. Genetics 2001; 159:1605-16. [PMID: 11779800 PMCID: PMC1461923 DOI: 10.1093/genetics/159.4.1605] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The formation of dense core granules (DCGs) requires both the sorting of granule contents from other secretory proteins and a postsorting maturation process. The Tetrahymena thermophila strain SB281 fails to synthesize DCGs, and previous analysis suggested that the defect lay at or near the sorting step. Because this strain represents one of the very few mutants in this pathway, we have undertaken a more complete study of the phenotype. Genetic epistasis analysis places the defect upstream of those in two other characterized Tetrahymena mutants. Using immunofluorescent detection of granule content proteins, as well as GFP tagging, we describe a novel cytoplasmic compartment to which granule contents can be sorted in growing SB281 cells. Cell fusion experiments indicate that this compartment is not a biosynthetic intermediate in DCG synthesis. Sorting in SB281 is strongly conditional with respect to growth. When cells are starved, the storage compartment is degraded and de novo synthesized granule proteins are rapidly secreted. The mutation in SB281 therefore appears to affect DCG synthesis at the level of both sorting and maturation.
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Affiliation(s)
- G R Bowman
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
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48
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Angus SP, Edelmann RE, Pennock DG. Targeted gene knockout of inner arm 1 in Tetrahymena thermophila. Eur J Cell Biol 2001; 80:486-97. [PMID: 11499791 DOI: 10.1078/0171-9335-00178] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cilia and flagella contain at least eight different types of dynein arms. It is not entirely clear how the different types of arms are organized along the axoneme. In addition, the role each different type of dynein plays in ciliary or flagellar motility is not known. To initiate studies of dynein organization and function in cilia, we have introduced a mutation into one dynein heavy chain gene (DYH6) in Tetrahymena themophila by targeted gene knockout. We have generated mutant cells that lack wild-type copies of the DYH6 gene. We have shown that the DYH6 gene encodes one heavy chain (HC2) of Tetrahymena 18S dynein and that 18S dynein occupies the I1 position in the ciliary axoneme. We have also shown that Tetrahymena I1 is required for normal motility, normal feeding and normal doubling rate.
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Affiliation(s)
- S P Angus
- Department of Zoology, Miami University, Oxford, OH 45056, USA
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49
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Nilsson JR. On macronuclear “subnuclei”, or genome segregation, and “amitosis” in amicronucleate Tetrahymena pyriformis GL. A study utilizing the effect of vanadate on nuclear division. Eur J Protistol 2000. [DOI: 10.1016/s0932-4739(00)80048-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Doerder FP. Sequence and expression of the SerJ immobilization antigen gene of Tetrahymena thermophila regulated by dominant epistasis. Gene 2000; 257:319-26. [PMID: 11080598 DOI: 10.1016/s0378-1119(00)00380-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In ciliates, variable surface protein genes encoding the immobilization antigen (-ag) are expressed under different environmental conditions, including temperature and salt stress. These i-ags are GPI-linked and coat the entire external surface of the cell, including the cilia. In Tetrahymena thermophila-ag in natural isolates is the result of dominant epistasis masking the expression of the H i-ag ordinarily expressed at 20-36 degrees C. This report describes the expression and sequence of the Ser-ag. J is present on the cell surface up to 38 degrees C; above 38 degrees C SerSeranked by an A-rich 5' UTR and a 3' UTR containing putative mRNA destabilization motifs. The encoded J polypeptide consists of 438 amino acids and is rich in alanine, cysteine, serine and threonine. The N- and resemble signal peptide and GPI-anchor addition sites, respectively. The majority of the molecule consists of four imperfect repeats with 10 periodic cysteines per repeat in the pattern CX(6)CX(2)CX(21)CX(4)CX(13-15)CX(2)CX(18)CX(3)CX(11)CX(9-10). Although H i-ags encoded by paralogous SerH genes have 3.5 imperfect repeats with eight periodic cysteines per repeat, J nevertheless resembles H with respect to amino acid composition, codon usage, N- and C-termini, the arrangement of the cysteine periods, and regulation by mRNA stability. However, despite these similarities and epistasis, the evolutionary relationship between SerH and SerJ is unclear.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Animals
- Antigens, Protozoan
- Antigens, Surface/chemistry
- Antigens, Surface/genetics
- Base Sequence
- Blotting, Northern
- Cysteine/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- Epistasis, Genetic
- Gene Expression Regulation
- Molecular Sequence Data
- Protozoan Proteins
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Repetitive Sequences, Amino Acid/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Temperature
- Tetrahymena thermophila/genetics
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Affiliation(s)
- F P Doerder
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA.
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