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Bétermier M, Klobutcher LA, Orias E. Programmed chromosome fragmentation in ciliated protozoa: multiple means to chromosome ends. Microbiol Mol Biol Rev 2023; 87:e0018422. [PMID: 38009915 PMCID: PMC10732028 DOI: 10.1128/mmbr.00184-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
SUMMARYCiliated protozoa undergo large-scale developmental rearrangement of their somatic genomes when forming a new transcriptionally active macronucleus during conjugation. This process includes the fragmentation of chromosomes derived from the germline, coupled with the efficient healing of the broken ends by de novo telomere addition. Here, we review what is known of developmental chromosome fragmentation in ciliates that have been well-studied at the molecular level (Tetrahymena, Paramecium, Euplotes, Stylonychia, and Oxytricha). These organisms differ substantially in the fidelity and precision of their fragmentation systems, as well as in the presence or absence of well-defined sequence elements that direct excision, suggesting that chromosome fragmentation systems have evolved multiple times and/or have been significantly altered during ciliate evolution. We propose a two-stage model for the evolution of the current ciliate systems, with both stages involving repetitive or transposable elements in the genome. The ancestral form of chromosome fragmentation is proposed to have been derived from the ciliate small RNA/chromatin modification process that removes transposons and other repetitive elements from the macronuclear genome during development. The evolution of this ancestral system is suggested to have potentiated its replacement in some ciliate lineages by subsequent fragmentation systems derived from mobile genetic elements.
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Affiliation(s)
- Mireille Bétermier
- Department of Genome Biology, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Lawrence A. Klobutcher
- Department of Molecular Biology and Biophysics, UCONN Health (University of Connecticut), Farmington, Connecticut, USA
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
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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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Lindblad KA, Pathmanathan JS, Moreira S, Bracht JR, Sebra RP, Hutton ER, Landweber LF. Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms. BMC Genomics 2019; 20:1037. [PMID: 31888453 PMCID: PMC6937825 DOI: 10.1186/s12864-019-6189-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even "third generation" sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly. RESULTS We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall. CONCLUSIONS This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.
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Affiliation(s)
- Kelsi A. Lindblad
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA
| | - Jananan S. Pathmanathan
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
| | - Sandrine Moreira
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
| | - John R. Bracht
- Department of Biology, American University, 4400 Massachusetts Avenue, NW, Washington, DC 20016 USA
| | - Robert P. Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Elizabeth R. Hutton
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA
- Watson School of Biological Sciences, One Bungtown Road, Cold Spring Harbor,, NY 11724 USA
| | - Laura F. Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032 USA
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Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell 2015; 158:1187-1198. [PMID: 25171416 DOI: 10.1016/j.cell.2014.07.034] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 05/18/2014] [Accepted: 07/03/2014] [Indexed: 10/24/2022]
Abstract
Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.
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Affiliation(s)
- Xiao Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - John R Bracht
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Aaron David Goldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Egor Dolzhenko
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL 33620, USA
| | - Derek M Clay
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Estienne C Swart
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - David H Perlman
- Collaborative Proteomics and Mass Spectrometry Center, Molecular Biology Department and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Thomas G Doak
- Department of Biology, University of Indiana, Bloomington, IN 47405, USA
| | - Andrew Stuart
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Robert P Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura F Landweber
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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5
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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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McFarland CP, Chang WJ, Kuo S, Landweber LF. Conserved linkage of two genes on the same macronuclear chromosome in spirotrichous ciliates. Chromosoma 2006; 115:129-38. [PMID: 16520956 DOI: 10.1007/s00412-005-0040-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 10/04/2005] [Accepted: 10/05/2005] [Indexed: 11/30/2022]
Abstract
Macronuclear chromosomes of spirotrichous ciliates are mainly "nanochromosomes" containing only a single gene. We identified a two-gene chromosome in the spirotrich Sterkiella histriomuscorum (formerly Oxytricha trifallax) which, unlike other characterized two-gene molecules, contains reading frames oriented tail to tail. These are homologs of ribosomal protein L29 (RPL29) and cyclophilin. We found that both genes are transcribed, with their polyadenylation sites on opposite strands separated by only 135 bp. Furthermore, both genes in S. histriomuscorum are present only on one macronuclear chromosome and do not occur alone or linked to other genes. The corresponding micronuclear locus is fragmented into three nonscrambled gene segments (MDSs), separated by two noncoding segments (IESs). We also found that these two genes are linked on a macronuclear chromosome, similarly arranged tail to tail, in the three spirotrichs Stylonychia lemnae, Uroleptus sp., and Holosticha sp.. In addition, single-gene macronuclear chromosomes containing only the RPL29 gene were detected in the earlier diverged Holosticha and Uroleptus. These observations suggest a possible evolutionary trend towards loss of chromosomal breakage between these two genes. This study is the first to examine gene linkage in the macronucleus of several spirotrichs and may provide insight into the evolution of multi-gene macronuclear chromosomes and chromosomal fragmentation in spirotrichs.
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Affiliation(s)
- Craig P McFarland
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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7
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Ardell DH, Lozupone CA, Landweber LF. Polymorphism, Recombination and Alternative Unscrambling in the DNA Polymerase α Gene of the Ciliate Stylonychia lemnae (Alveolata; class Spirotrichea). Genetics 2003; 165:1761-77. [PMID: 14704164 PMCID: PMC1462920 DOI: 10.1093/genetics/165.4.1761] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
DNA polymerase α is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D.
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Affiliation(s)
- David H Ardell
- Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, SE-752 36 Uppsala, Sweden.
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Williams KR, Doak TG, Herrick G. Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites. BMC Genet 2002; 3:16. [PMID: 12199911 PMCID: PMC128808 DOI: 10.1186/1471-2156-3-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2002] [Accepted: 08/28/2002] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Ciliates employ massive chromatid breakage and de novo telomere formation during generation of the somatic macronucleus. Positions flanking the 81-MAC locus are reproducibly cut. But those flanking the Common Region are proposed to often escape cutting, generating three nested macronuclear chromosomes, two retaining "arms" still appended to the Common Region. Arm-distal positions must differ (in cis) from the Common Region flanks. RESULTS The Common-Region-flanking positions also differ from the arm-distal positions in that they are "multi-TAS" regions: anchored PCR shows heterogeneous patterns of telomere addition sites, but arm-distal sites do not. The multi-TAS patterns are reproducible, but are sensitive to the sequence of the allele being processed. Thus, random degradation following chromatid cutting does not create this heterogeneity; these telomere addition sites also must be dictated by cis-acting sequences. CONCLUSIONS Most ciliates show such micro-heterogeneity in the precise positions of telomere addition sites. Telomerase is believed to be tightly associated with, and act in concert with, the chromatid-cutting nuclease: heterogeneity must be the result of intervening erosion activity. Our "weak-sites" hypothesis explains the correlation between alternative chromatid cutting at the Common Region boundaries and their multi-TAS character: when the chromatid-breakage machine encounters either a weak binding site or a weak cut site at these regions, then telomerase dissociates prematurely, leaving the new end subject to erosion by an exonuclease, which pauses at cis-acting sequences; telomerase eventually heals these resected termini. Finally, we observe TAS positioning influenced by trans-allelic interactions, reminiscent of transvection.
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Affiliation(s)
- Kevin R Williams
- Department of Pathology, University of Utah School of Medicine, Salt Lake City UT 84132-2501, USA
| | - Thomas G Doak
- Department of Pathology, University of Utah School of Medicine, Salt Lake City UT 84132-2501, USA
| | - Glenn Herrick
- Department of Pathology, University of Utah School of Medicine, Salt Lake City UT 84132-2501, USA
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9
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Abstract
A comparative study of macronuclear DNA molecules from the following Paramecium species: the P. aurelia complex, P. caudatum, P. bursaria, P. putrinum and P. multimicronucleatum was performed using pulsed-field gel electrophoresis. The electrophoretic pattern was constant and unique for each species, and is referred to herein as its electrokaryotype. Large differences were observed between Paramecium species according to the range and major size of macronuclear DNA fragments, while different strains of the same species, even belonging to different syngens, were characterized by the same electrokaryotype. In this respect sibling species from the P. aurelia complex are as similar as syngens in other Paramecium species, but are unlike conventional species. The principles and value of electrokaryotype analysis for application to ciliates are discussed.
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Affiliation(s)
- Maria S Rautian
- Biological Institute of St. Petersburg State University, Stary Peterhof, Russia.
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10
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Seegmiller A, Williams KR, Herrick G. Two two-gene macronuclear chromosomes of the hypotrichous ciliates Oxytricha fallax and O. trifallax generated by alternative processing of the 81 locus. DEVELOPMENTAL GENETICS 2000; 20:348-57. [PMID: 9254909 DOI: 10.1002/(sici)1520-6408(1997)20:4<348::aid-dvg6>3.0.co;2-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We describe the first know macronuclear chromosomes that carry more than one gene in hypotrichous ciliated protozoa. These 4.9- and 2.8-kbp chromosomes each consist almost exclusively of two protein-coding genes, which are conserved and transcribed. The two chromosomes share a common region that consists of a gene that is a member of the family of mitochondrial solute carrier genes (CR-MSC; [Williams and Herrick (1991): Nucleic Acids Res 19:4717-4724]. Each chromosome also carries another gene appended to its common region: The 4.9-kbp chromosome also carries a gene that encodes a protein that is rich in glutamine and charged amino acids and bears regions of heptad repeats characteristic of coiled-coils. Its function is unknown. The second gene of the 2.8 kbp chromosome is a mitochondrial solute carrier gene (LA-MSC); thus, the 2.8-kbp chromosomes consists of two mitochondrial solute carrier paralogs. Phylogenetic analysis indicates that the two genes were duplicated before ciliates diverged from the main eukaryotic lineage and were subsequently juxtaposed. The CR- and LA-MSC genes are each interrupted by three introns. The introns are not in homologous positions, suggesting that they may have originated from multiple group II intron transpositions. These chromosomes and their genes are encoded in the Oxytricha germline by the 81 locus. This locus is alternatively processed to generate a nested set of three macronuclear chromosomes, the 4.9- and 2.8-kbp chromosomes and a third (1.6 kbp) which consists almost exclusively of the shared common gene, CR-MSC. Such alternative processing is common in macronuclear development of O. fallax [Cartinhour and Herrick (1984): Mol Cell Biol 4:931-938]. Possible functions for alternative processing are considered; e.g., it may serve to physically link genes to allow co-regulation or co-replication by a common cis-acting sequence.
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Affiliation(s)
- A Seegmiller
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City 84132, USA
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11
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Bernhard D. Several highly divergent histone H3 genes are present in the hypotrichous ciliate Stylonychia lemnae. FEMS Microbiol Lett 1999; 175:45-50. [PMID: 10361708 DOI: 10.1111/j.1574-6968.1999.tb13600.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In the protozoan Stylonychia lemnae 10 different histone H3 genes were discovered by polymerase chain reaction (PCR) amplification and sequence analysis. One of them is interrupted by a short intron sequence. These genes code for nine divergent histone H3 proteins. The genetic distances between some of these variants are very high. Most of the substitutions, as well as insertions/deletions, were found in the amino-terminal region. One variant shows an extremely elongated and altered N-terminus, which did not allow an unambiguous alignment with other histone H3 variants in this region. Hybridization experiments using the different H3 genes as probes indicate that even more histone H3 variants must exist in this species.
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Affiliation(s)
- D Bernhard
- Universität Leipzig, Institut für Zoologie, Spezielle Zoologie, Germany.
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12
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Klobutcher LA, Gygax SE, Podoloff JD, Vermeesch JR, Price CM, Tebeau CM, Jahn CL. Conserved DNA sequences adjacent to chromosome fragmentation and telomere addition sites in Euplotes crassus. Nucleic Acids Res 1998; 26:4230-40. [PMID: 9722644 PMCID: PMC147820 DOI: 10.1093/nar/26.18.4230] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the formation of a new macronucleus in the ciliate Euplotes crassus, micronuclear chromosomes are reproducibly broken at approximately 10 000 sites. This chromosome fragmentation process is tightly coupled with de novo telomere synthesis by the telomerase ribonucleoprotein complex, generating short linear macronuclear DNA molecules. In this study, the sequences of 58 macronuclear DNA termini and eight regions of the micronuclear genome containing chromosome fragmentation/telomere addition sites were determined. Through a statistically based analysis of these data, along with previously published sequences, we have defined a 10 bp conserved sequence element (E-Cbs, 5'-HATTGAAaHH-3', H = A, C or T) near chromosome fragmentation sites. The E-Cbs typically resides within the DNA destined to form a macronuclear DNA molecule, but can also reside within flanking micronuclear DNA that is eliminated during macronuclear development. The location of the E-Cbs in macronuclear-destined versus flanking micronuclear DNA leads us to propose a model of chromosome fragmentation that involves a 6 bp staggered cut in the chromosome. The identification of adjacent macronuclear-destined sequences that overlap by 6 bp provides support for the model. Finally, our data provide evidence that telomerase is able to differentiate between newly generated ends that contain partial telomeric repeats and those that do not in vivo.
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Affiliation(s)
- L A Klobutcher
- Department of Biochemistry, University of Connecticut Health Center, Farmington, CT 06030, USA.
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13
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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14
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Seegmiller A, Williams KR, Herrick G. Two two-gene macronuclear chromosomes of the hypotrichous ciliatesOxytricha fallax andO. trifallax generated by alternative processing of the 81 locus. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/(sici)1520-6408(1997)20:4%3c348::aid-dvg6%3e3.0.co;2-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Coyne RS, Chalker DL, Yao MC. Genome downsizing during ciliate development: nuclear division of labor through chromosome restructuring. Annu Rev Genet 1996; 30:557-78. [PMID: 8982465 DOI: 10.1146/annurev.genet.30.1.557] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The ciliated protozoa divide the labor of germline and somatic genetic functions between two distinct nuclei. The development of the somatic (macro-) nucleus from the germinal (micro-) nucleus occurs during sexual reproduction and involves large-scale, genetic reorganization including site-specific chromosome breakage and DNA deletion. This intriguing process has been extensively studied in Tetrahymena thermophila. Characterization of cis-acting sequences, putative protein factors, and possible reaction intermediates has begun to shed light on the underlying mechanisms of genome rearrangement. This article summarizes the current understanding of this phenomenon and discusses its origin and biological function. We postulate that ciliate nuclear restructuring serves to segregate the two essential functions of chromosomes: the transmission and expression of genetic information.
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Affiliation(s)
- R S Coyne
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA
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16
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Coyne RS, Yao MC. Evolutionary conservation of sequences directing chromosome breakage and rDNA palindrome formation in tetrahymenine ciliates. Genetics 1996; 144:1479-87. [PMID: 8978037 PMCID: PMC1207701 DOI: 10.1093/genetics/144.4.1479] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Extensive, programmed chromosome breakage occurs during formation of the somatic macronucleus of ciliated protozoa. The cis-acting signal directing breakage has been most rigorously defined in Tetrahymena thermophila, where it consists of a 15-bp DNA sequence known as Cbs, for chromosome breakage sequence. We have identified sequences identical or nearly identical to the T. thermophila Cbs at sites of breakage flanking the germline micronuclear rDNA locus of six additional species of Tetrahymena as well as members of two related genera. Other general features of the breakage site are also conserved, but surprisingly, the orientation and number of copies of Cbs are not always conserved, suggesting the occurrence of germline rearrangement events over evolutionary time. At one end of the T. thermophila micronuclear rDNA locus, a pair of short inverted repeats adjacent to Cbs directs the formation of a giant palindromic molecule. We have examined the corresponding sequences from two other Tetrahymena species. We find the sequence to be partially conserved, as previously implied from analysis of macronuclear rDNA, but of variable length and organization.
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Affiliation(s)
- R S Coyne
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA.
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17
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Miceli C, Ballarini P, Di Giuseppe G, Valbonesi A, Luporini P. Identification of the tubulin gene family and sequence determination of one beta-tubulin gene in a cold-poikilotherm protozoan, the antarctic ciliate Euplotes focardii. J Eukaryot Microbiol 1994; 41:420-7. [PMID: 8087111 DOI: 10.1111/j.1550-7408.1994.tb06100.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Four different tubulin genes were identified in the somatic nucleus (macronucleus) of Euplotes focardii, a strictly cold-adapted, Antarctic ciliate: one of 1,800 bp for alpha-tubulin and three of 2,150, 1,900, and 1,600 bp, respectively, for beta-tubulin. Preliminarily analysed for restriction fragment length polymorphisms, these genes showed remarkable differences in organisation from tubulin genes of other ciliates which live in temperate areas and were analysed in parallel with E. focardii. The complete coding sequence of the 1,600 bp beta-tubulin gene was then determined and shown to contain unique structural features of potential importance for E. focardii microtubule organization and activity. Of eight unique substitutions detected, seven were concentrated in the large amino terminal domain of the molecule that directly interacts with the carboxy terminal region of alpha-tubulin for heterodimer formation. Sequence analysis of the cloned gene revealed, in addition, a potential new exception in the use of the genetic code by ciliates. A TAG codon was aligned in correspondence with Trp-21 which is strictly conserved in every tubulin sequence so far determined.
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Affiliation(s)
- C Miceli
- Dipartimento di Biologia Molecolare, Cellulare ed Animale Università di Camerino, Italy
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18
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Abstract
Ciliates contain two types of nuclei: a micronucleus and a macronucleus. The micronucleus serves as the germ line nucleus but does not express its genes. The macronucleus provides the nuclear RNA for vegetative growth. Mating cells exchange haploid micronuclei, and a new macronucleus develops from a new diploid micronucleus. The old macronucleus is destroyed. This conversion consists of amplification, elimination, fragmentation, and splicing of DNA sequences on a massive scale. Fragmentation produces subchromosomal molecules in Tetrahymena and Paramecium cells and much smaller, gene-sized molecules in hypotrichous ciliates to which telomere sequences are added. These molecules are then amplified, some to higher copy numbers than others. rDNA is differentially amplified to thousands of copies per macronucleus. Eliminated sequences include transposonlike elements and sequences called internal eliminated sequences that interrupt gene coding regions in the micronuclear genome. Some, perhaps all, of these are excised as circular molecules and destroyed. In at least some hypotrichs, segments of some micronuclear genes are scrambled in a nonfunctional order and are recorded during macronuclear development. Vegetatively growing ciliates appear to possess a mechanism for adjusting copy numbers of individual genes, which corrects gene imbalances resulting from random distribution of DNA molecules during amitosis of the macronucleus. Other distinctive features of ciliate DNA include an altered use of the conventional stop codons.
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Affiliation(s)
- D M Prescott
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309-0347
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19
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Morin GB. Recognition of a chromosome truncation site associated with alpha-thalassaemia by human telomerase. Nature 1991; 353:454-6. [PMID: 1896089 DOI: 10.1038/353454a0] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Telomeres define the ends of chromosomes; they consist of short tandemly repeated DNA sequences loosely conserved in eukaryotes (G1-8(T/A)1-4). Telomerase is a ribonucleoprotein which, in vitro, recognizes a single-stranded G-rich telomere primer and adds multiple telomeric repeats to its 3' end by using a template in the RNA moiety. In conjunction with other components, telomerase may balance the loss of telomeric repeats due to DNA replication. Another role of telomerase may be the de novo formation of telomeres. In eukaryotes like Tetrahymena, this process is an integral part of the formation of macronuclear chromosomes. In other eukaryotes this process stabilizes broken chromosomes. A case of human alpha-thalassaemia is caused by a truncation of chromosome 16 that has been healed by the addition of telomeric repeats (TTAGGG)n. Using an in vitro assay, I show here that human telomerase correctly recognizes the chromosome 16 breakpoint sequence and adds (TTAGGG)n repeats. The DNA sequence requirements are minimal and seem to define two modes of DNA recognition by telomerase.
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Affiliation(s)
- G B Morin
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06510
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20
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Jahn CL. The nuclear genomes of hypotrichous ciliates: maintaining the maximum and the minimum of information. THE JOURNAL OF PROTOZOOLOGY 1991; 38:252-8. [PMID: 1652639 DOI: 10.1111/j.1550-7408.1991.tb04438.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- C L Jahn
- Department of Biological Sciences, University of Illinois, Chicago 60680
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21
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Abstract
Site-specific chromosome breakage occurs in many ciliated protozoa during nuclear differentiation. We have determined the cis-acting sequence that controls this process in Tetrahymena thermophila. The Tetrahymena ribosomal RNA gene is bounded by two breakage sites. Injection of this gene into developing macronuclei leads to breakage at these sites. Deletion analysis has localized the sequences essential for breakage to a 28 bp region that includes a 15 bp sequence (Cbs) known to be present in other breakage sites. Insertions of Cbs allow breakage to occur at new sites, which is accompanied by elimination of surrounding DNAs and formation of telomeric sequences, as it is at natural sites. Thus, Cbs is the necessary and sufficient sequence signal for chromosome breakage in Tetrahymena.
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Affiliation(s)
- M C Yao
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104
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22
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NG STEPHENF. DEVELOPMENTAL HETEROCHRONY IN CILIATED PROTOZOA: OVERLAP OF ASEXUAL AND SEXUAL CYCLES DURING CONJUGATION. Biol Rev Camb Philos Soc 1990. [DOI: 10.1111/j.1469-185x.1990.tb01131.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Wefes I, Lipps HJ. The two macronuclear histone H4 genes of the hypotrichous ciliate Stylonychia lemnae. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1990; 1:25-32. [PMID: 2132956 DOI: 10.3109/10425179009041344] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Macronuclear DNA of hypotrichous ciliates is organized in short gene-sized molecules, each containing all regulatory sequences for autonomous replication and expression. In these organisms the histone genes are not clustered but dispersed on different molecules of various sizes. Two histone H4 genes containing fragments, one of 1.7 kb and one of 2.8 kb, were found in the macronucleus of Stylonychia lemnae. Restriction and sequence data reveal that the two genes-sized pieces are derived from different micronuclear precursors. Both histone H4 genes code for the same protein of 103 aminoacids but differ greatly in their 5'-and 3'-regions.
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Affiliation(s)
- I Wefes
- Medizinisch-Naturwissenschaftliches-Forschungszentrum, Universität Tuebingen, FRG
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24
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Micronuclear genome organization in Euplotes crassus: a transposonlike element is removed during macronuclear development. Mol Cell Biol 1989. [PMID: 2550802 DOI: 10.1128/mcb.9.9.3793] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After mating, hypotrichous ciliated protozoa transform a set of their micronuclear chromosomes into thousands of short, linear DNA molecules that form the macronuclear genome. To examine micronuclear genome organization in the hypotrich Euplotes crassus, we have analyzed two cloned segments of micronuclear DNA as well as the macronuclear DNA molecules that are derived from them. E. crassus was found to display a number of features characteristic of other hypotrich genomes, including (i) clustering and close spacing of the precursors of macronuclear DNA molecules, (ii) the frequent occurrence of internal eliminated sequences within macronuclear precursors, (iii) overlapping macronuclear precursors, (iv) lack of telomeric repeats at the ends of macronuclear precursors, and (v) alternative processing of the micronuclear chromosome to yield multiple macronuclear DNA molecules. In addition, a moderately repetitive, transposonlike element that interrupts the precursors of two macronuclear DNA molecules has been identified and characterized. This transposonlike element, designated Tec1, is shown to be reproducibly removed from one of the macronuclear precursors during independent episodes of macronuclear development.
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25
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Baird SE, Fino GM, Tausta SL, Klobutcher LA. Micronuclear genome organization in Euplotes crassus: a transposonlike element is removed during macronuclear development. Mol Cell Biol 1989; 9:3793-807. [PMID: 2550802 PMCID: PMC362441 DOI: 10.1128/mcb.9.9.3793-3807.1989] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
After mating, hypotrichous ciliated protozoa transform a set of their micronuclear chromosomes into thousands of short, linear DNA molecules that form the macronuclear genome. To examine micronuclear genome organization in the hypotrich Euplotes crassus, we have analyzed two cloned segments of micronuclear DNA as well as the macronuclear DNA molecules that are derived from them. E. crassus was found to display a number of features characteristic of other hypotrich genomes, including (i) clustering and close spacing of the precursors of macronuclear DNA molecules, (ii) the frequent occurrence of internal eliminated sequences within macronuclear precursors, (iii) overlapping macronuclear precursors, (iv) lack of telomeric repeats at the ends of macronuclear precursors, and (v) alternative processing of the micronuclear chromosome to yield multiple macronuclear DNA molecules. In addition, a moderately repetitive, transposonlike element that interrupts the precursors of two macronuclear DNA molecules has been identified and characterized. This transposonlike element, designated Tec1, is shown to be reproducibly removed from one of the macronuclear precursors during independent episodes of macronuclear development.
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Affiliation(s)
- S E Baird
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06032
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26
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Baird SE, Klobutcher LA. Characterization of chromosome fragmentation in two protozoans and identification of a candidate fragmentation sequence in Euplotes crassus. Genes Dev 1989; 3:585-97. [PMID: 2744456 DOI: 10.1101/gad.3.5.585] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Following the sexual cycle, hypotrichous ciliated protozoans fragment a set of their micronuclear chromosomes to generate the thousands of short, linear DNA molecules present in the transcriptionally active macronucleus. We have used a hybrid selection procedure to examine macronuclear DNA molecules for subtelomeric length heterogeneity to determine whether chromosome fragmentation occurs at unique or multiple sites. The results suggest that multiple, but closely spaced, chromosome fragmentation sites are used by Oxytricha nova. In contrast, Euplotes crassus uses unique chromosome fragmentation sites in a reproducible manner to generate the ends of macronuclear DNA molecules. Additional studies compared DNA sequences in the vicinity of chromosome fragmentation sites in an attempt to define cis-acting sequences that direct the fragmentation process. A conserved sequence was found near chromosome fragmentation sites in E. crassus. The location of the conserved sequence suggests that chromosome fragmentation involves staggered cuts of the micronuclear DNA molecules.
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Affiliation(s)
- S E Baird
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06032
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27
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Abstract
In hypotrichous ciliated protozoa, genes are transcribed in the macronucleus where the genome consists of 'gene-sized' linear DNA molecules. We have isolated clones of actin, tubulin and H4 histone macronuclear genes from Oxytricha nova, Stylonychia lemnae and Euplotes crassus in an effort to determine if they possess molecules of similar size for a given coding function, and also to determine the size range of non-coding DNA present on these molecules. Our results indicate that while the length of their non-coding DNA can vary slightly, both between different hypotrichs and within the gene family of a single organism, actin and tubulin macronuclear molecules are similarly sized. The sizes observed for these molecules support the hypothesis that each macronuclear molecule encodes a single gene. However, the H4 histone macronuclear molecules show a much wider size range and generally are much longer than necessary to encode the H4 histone. We therefore sequenced a 1700-bp H4 histone macronuclear molecule from O. nova to determine if it might possibly encode additional gene products. Sequence data reveals the presence of nine open reading frames (ORFs) greater than 100 bp in length; however, Northern hybridization analysis of the products of this DNA molecule reveals only a single transcript.
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Affiliation(s)
- D S Harper
- Department of Biological Sciences, University of Illinois, Chicago 60680
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28
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Baird SE, Klobutcher LA. Genetic characterization and use of a restriction fragment length variant in the hypotrichous ciliate Euplotes crassus. THE JOURNAL OF PROTOZOOLOGY 1988; 35:459-65. [PMID: 2904496 DOI: 10.1111/j.1550-7408.1988.tb04130.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two forms of a macronuclear DNA molecule differing in the presence or absence of a restriction endonuclease recognition site have been detected in the hypotrichous ciliate Euplotes crassus. Through a series of genetic crosses the two forms were shown to be allelic, being derived from a single micronuclear genetic locus. This restriction fragment length variant (RFLV) was used as a genetic marker to determine that the migratory and stationary pronuclei generated during mating can be genetically non-identical. In addition, the RFLV was used to investigate the efficiency of processing of the alternate alleles during macronuclear development and their subsequent transmission during vegetative growth. Little or no bias in the processing and/or amplification of the two alleles was observed during macronuclear development. During vegetative growth, however, changes in the relative amounts of the two alleles were observed.
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Affiliation(s)
- S E Baird
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06032
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29
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Jahn CL, Nilles LA, Krikau MF. Organization of the Euplotes crassus micronuclear genome. THE JOURNAL OF PROTOZOOLOGY 1988; 35:590-601. [PMID: 2974078 DOI: 10.1111/j.1550-7408.1988.tb04157.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Euplotes crassus, like other hypotrichous ciliated protozoa, eliminates most of its micronuclear chromosomal DNA in the process of forming the small linear DNA molecules that comprise the macronuclear genome. By characterizing randomly selected lambda phage clones of E. crassus micronuclear DNA, we have determined the distribution of repetitive and unique sequences and the arrangement of macronuclear genes relative to eliminated DNA. This allows us to compare the E. crassus micronuclear genome organization to that of another distantly related hypotrichous ciliate, Oxytricha nova. The clones from E. crassus segregate into three prevalent classes: those containing primarily eliminated repetitive DNA (Class I); those containing macronuclear genes in addition to repetitive sequences (Class II); and those containing only eliminated unique sequence DNA (Class III). All of the repetitive sequences in these clones belong to the same highly abundant repetitive element family. Our results demonstrate that the sequence organization of the E. crassus and O. nova micronuclear genomes is related in that the macronuclear genes are clustered together in the micronuclear genome and the eliminated unique sequences occur in long stretches that are uninterrupted by repetitive sequences. In both organisms a single repetitive element family comprises the majority of the eliminated interspersed middle repetitive DNA and appears to be preferentially associated with the macronuclear sequence clusters. The similarities in the sequence organization in these two organisms suggest that clustering of macronuclear genes plays a role in the chromosome fragmentation process.
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Affiliation(s)
- C L Jahn
- Department of Biological Sciences, University of Illinois, Chicago 60680
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