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Lyu L, Zhang X, Gao Y, Zhang T, Fu J, Stover NA, Gao F. From germline genome to highly fragmented somatic genome: genome-wide DNA rearrangement during the sexual process in ciliated protists. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:31-49. [PMID: 38433968 PMCID: PMC10901763 DOI: 10.1007/s42995-023-00213-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/27/2023] [Indexed: 03/05/2024]
Abstract
Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements (PGR) play important roles in generating genomic diversity. However, genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR. To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements, we focus on ciliated protists (ciliates). Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes. PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome during development of the somatic genome. We report the partial germline genomes of two spirotrich ciliate species, namely Strombidium cf. sulcatum and Halteria grandinella, along with the most compact and highly fragmented somatic genome for S. cf. sulcatum. We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates. Our analyses reveal: (1) DNA sequence loss through evolution and during PGR in S. cf. sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date; (2) the compact, transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences; (3) long chromosome breakage site motifs are duplicated and retained in the somatic genome, revealing a complex model of chromosome fragmentation in spirotrichs; (4) gene scrambling and alternative processing are found throughout the core spirotrichs, offering unique opportunities to increase genetic diversity and regulation in this group. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00213-x.
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Affiliation(s)
- Liping Lyu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xue Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Yunyi Gao
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Tengteng Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Jinyu Fu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Naomi A. Stover
- Department of Biology, Bradley University, Peoria, IL 61625 USA
| | - Feng Gao
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
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2
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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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Jin D, Li C, Chen X, Byerly A, Stover NA, Zhang T, Shao C, Wang Y. Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:300-315. [PMID: 37637252 PMCID: PMC10449743 DOI: 10.1007/s42995-023-00175-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/12/2023] [Indexed: 08/29/2023]
Abstract
One of the most diverse clades of ciliated protozoa, the class Spirotrichea, displays a series of unique characters in terms of eukaryotic macronuclear (MAC) genome, including high fragmentation that produces nanochromosomes. However, the genomic diversity and evolution of nanochromosomes and gene families for spirotrich MAC genomes are poorly understood. In this study, we assemble the MAC genome of a representative euplotid (a new model organism in Spirotrichea) species, Euplotes aediculatus. Our results indicate that: (a) the MAC genome includes 35,465 contigs with a total length of 97.3 Mb and a contig N50 of 3.4 kb, and contains 13,145 complete nanochromosomes and 43,194 predicted genes, with the majority of these nanochromosomes containing tiny introns and harboring only one gene; (b) genomic comparisons between E. aediculatus and other reported spirotrichs indicate that average GC content and genome fragmentation levels exhibit interspecific variation, and chromosome breaking sites (CBSs) might be lost during evolution, resulting in the increase of multi-gene nanochromosome; (c) gene families associated with chitin metabolism and FoxO signaling pathway are expanded in E. aediculatus, suggesting their potential roles in environment adaptation and survival strategies of E. aediculatus; and (d) a programmed ribosomal frameshift (PRF) with a conservative motif 5'-AAATAR-3' tends to occur in longer genes with more exons, and PRF genes play an important role in many cellular regulation processes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00175-0.
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Affiliation(s)
- Didi Jin
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Chao Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Adam Byerly
- Department of Computer Science and Information Systems, Bradley University, Peoria, 61625 USA
| | - Naomi A. Stover
- Department of Biology, Bradley University, Peoria, 61625 USA
| | - Tengteng Zhang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Chen Shao
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
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4
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Kazmi SSUH, Xu H, Xuexi T. An approach to determining the nitrofurazone-induced toxic dynamics for ecotoxicity assessment using protozoan periphytons in marine ecosystems. MARINE POLLUTION BULLETIN 2022; 175:113329. [PMID: 35066415 DOI: 10.1016/j.marpolbul.2022.113329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
With several observable responses and sensitivity of protozoans to nitrofurazone (NFZ), the toxic effects of NFZ on protozoans can be an early warning signal of NFZ contamination in the aquatic environment. To evaluate the toxic dynamics induced by NFZ, protozoan samples were collected using microscopy glass slides and exposed to the five concentrations of NFZ: 0, 1, 2, 4, and 8 mg ml-1. Substantial differences in the species composition and toxic-dynamics patterns were observed among all concentrations. Briefly, periphytic euplotids and pleurostomatids were the most prevalent at each concentration level, while dysteriids were less dominant among all treatments. Multivariate analysis revealed significant (P < 0.05) differences in the taxonomic patterns of the test organisms among the five treatments. Furthermore, significant deviation of protozoan communities from the expected taxonomic breadth was observed to occur in a dose-dependent manner. Based on these findings, it is suggested that protozoan periphytons could be used as bioindicators to assess the ecotoxicity of NFZ in the marine environment.
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Affiliation(s)
| | - Henglong Xu
- Department of Microbial Ecology, Ocean University of China, Qingdao 266003, PR China.
| | - Tang Xuexi
- Department of Microbial Ecology, Ocean University of China, Qingdao 266003, PR China
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Feng Y, Neme R, Beh LY, Chen X, Braun J, Lu MW, Landweber LF. Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. eLife 2022; 11:82979. [PMID: 36421078 PMCID: PMC9797194 DOI: 10.7554/elife.82979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila, and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precisely programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi, Tetmemena sp., and the model ciliate O. trifallax. We sequenced, assembled, and annotated the germline and somatic genomes of E. woodruffi, which provides an outgroup, and the germline genome of Tetmemena sp. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha's: 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier diverged spirotrich, E. woodruffi, also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.
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Affiliation(s)
- Yi Feng
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Rafik Neme
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States,Department of Chemistry and Biology, Universidad del NorteBarranquillaColombia
| | - Leslie Y Beh
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Xiao Chen
- Pacific BiosciencesMenlo ParkUnited States
| | - Jasper Braun
- Department of Mathematics and Statistics, University of South FloridaTampaUnited States
| | - Michael W Lu
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Laura F Landweber
- Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia UniversityNew YorkUnited States
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6
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Vilas-Boas JA, Cardoso SJ, Senra MVX, Rico A, Dias RJP. Ciliates as model organisms for the ecotoxicological risk assessment of heavy metals: A meta-analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 199:110669. [PMID: 32450358 DOI: 10.1016/j.ecoenv.2020.110669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/14/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Ciliates are key components of aquatic ecosystems, significantly contributing to the decomposition of organic matter and energy transfer to higher trophic levels. They are considered good biological indicators of chemical pollution and relatively sensitive to heavy metal contamination. In this study, we performed a meta-analysis of the available toxicity data of heavy metals and ciliates to assess: (1) the sensitivity of freshwater ciliates to different heavy metals, (2) the relative sensitivity of ciliates in comparison to the standard test species used in ecotoxicological risk assessment, and (3) the difference in sensitivity across ciliate taxa. Our study shows that the tolerance of ciliates to heavy metals varies notably, which is partly influenced by differences in methodological conditions across studies. Ciliates are, in general, sensitive to Mercury > Cadmium > Copper > Zinc > Lead > Chromium. Also, this study shows that most ciliates are more tolerant to heavy metal pollution than the standard test species used in ecotoxicological risk assessments, i.e., Raphidocelis subcapitata, Daphnia magna, and Onchornyncus mykiss. Threshold concentrations derived from toxicity data for these species is expected to confer sufficient protection for the vast majority of ciliate species. Our data analysis also shows that the most commonly tested ciliate species, Paramecium caudatum and Tetrahymena thermophila, are not necessarily the most sensitive ones to heavy metal pollution. Finally, this study stresses the importance of developing standard toxicity test protocols for ciliates, which could lead to a better comprehension of the toxicological impact of heavy metals and other contaminants to ciliate species.
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Affiliation(s)
- Jéssica Andrade Vilas-Boas
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil.
| | - Simone Jaqueline Cardoso
- Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil; Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil
| | - Marcus Vinicius Xavier Senra
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil; Instituto de Recursos Naturais, Pós-graduação em Meio Ambiente e Recursos Hídricos, Universidade Federal de Itajubá, 36036-900, Itajubá, Minas Gerais, Brazil
| | - Andreu Rico
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Madrid, Spain
| | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil; Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil
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7
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Ricci F, Candelori A, Brandi A, Alimenti C, Luporini P, Vallesi A. The Sub-Chromosomic Macronuclear Pheromone Genes of the Ciliate Euplotes raikovi: Comparative Structural Analysis and Insights into the Mechanism of Expression. J Eukaryot Microbiol 2018; 66:376-384. [PMID: 30076754 DOI: 10.1111/jeu.12677] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/16/2018] [Accepted: 07/25/2018] [Indexed: 12/23/2022]
Abstract
In Euplotes raikovi, we have determined the full-length sequences of a family of macronuclear genes that are the transcriptionally active versions of codominant alleles inherited at the mating-type (mat) locus of the micronuclear genome, and encode cell type-distinctive signaling pheromones. These genes include a 225-231-bp coding region flanked by a conserved 544-bp 5'-leader region and a more variable 3'-trailer region. Two transcription initiation start sites and two polyadenylation sites associated with nonconventional signals cooperate with a splicing phenomenon of a 326-bp intron residing in the 5'-leader region in the generation of multiple transcripts from the same gene. In two of them, the synthesis of functional products depends on the reassignment to a sense codon, or readthrough of a strictly conserved leaky UAG stop codon. That this reassignment may take place is suggested by the position this codon occupies in the transcripts, close to the transcript extremity and far from the poly(A) tail. In such a case, one product is a 69-amino acid protein in search of function and the second product is a 126-amino acid protein that represents a membrane-bound pheromone isoform candidate to function as a cell type-specific binding site (receptor) of the soluble pheromones.
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Affiliation(s)
- Francesca Ricci
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Annalisa Candelori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Anna Brandi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Claudio Alimenti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Pierangelo Luporini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
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8
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Bondarenko VS, Gelfand MS. Evolution of the Exon-Intron Structure in Ciliate Genomes. PLoS One 2016; 11:e0161476. [PMID: 27603699 PMCID: PMC5014332 DOI: 10.1371/journal.pone.0161476] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/06/2016] [Indexed: 12/27/2022] Open
Abstract
A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus) possess only ultra-short introns, around 25 bp long. In Paramecium, ultra-short introns with length divisible by three (3n) are under strong evolutionary pressure and have a high frequency of in-frame stop codons, which, in the case of intron retention, cause premature termination of mRNA translation and consequent degradation of the mis-spliced mRNA by the nonsense-mediated decay mechanism. Here, we analyzed introns in five genera of Ciliates, Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. Introns can be classified into two length classes in Tetrahymena and Ichthyophthirius (with means 48 bp, 69 bp, and 55 bp, 64 bp, respectively), but, surprisingly, comprise three distinct length classes in Oxytricha and Stylonychia (with means 33–35 bp, 47–51 bp, and 78–80 bp). In most ranges of the intron lengths, 3n introns are underrepresented and have a high frequency of in-frame stop codons in all studied species. Introns of Paramecium, Tetrahymena, and Ichthyophthirius are preferentially located at the 5' and 3' ends of genes, whereas introns of Oxytricha and Stylonychia are strongly skewed towards the 5' end. Analysis of evolutionary conservation shows that, in each studied genome, a significant fraction of intron positions is conserved between the orthologs, but intron lengths are not correlated between the species. In summary, our study provides a detailed characterization of introns in several genera of Ciliates and highlights some of their distinctive properties, which, together, indicate that splicing spellchecking is a universal and evolutionarily conserved process in the biogenesis of short introns in various representatives of Ciliates.
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Affiliation(s)
- Vladyslav S. Bondarenko
- Institute of Molecular Biology and Genetics, NASU, Zabolotnogo Str. 150, Kyiv, 03680, Ukraine
- * E-mail:
| | - Mikhail S. Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127994, Russia
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
- Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Vorobievy Gory 1–73, Moscow GSP-1, 119234, Russia
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9
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Burns J, Kukushkin D, Chen X, Landweber LF, Saito M, Jonoska N. Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax. J Theor Biol 2016; 410:171-180. [PMID: 27593332 DOI: 10.1016/j.jtbi.2016.08.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/21/2016] [Accepted: 08/30/2016] [Indexed: 12/27/2022]
Abstract
Some genera of ciliates, such as Oxytricha and Stylonychia, undergo massive genome reorganization during development and provide model organisms to study DNA rearrangement. A common feature of these ciliates is the presence of two types of nuclei: a germline micronucleus and a transcriptionally-active somatic macronucleus containing over 16,000 gene sized "nano-chromosomes". During conjugation the old parental macronucleus disintegrates and a new macronucleus forms from a copy of the zygotic micronucleus. During this process, macronuclear chromosomes assemble through DNA processing events that delete 90-98% of the DNA content of the micronucleus. This includes the deletion of noncoding DNA segments that interrupt precursor DNA regions in the micronucleus, as well as transposons and other germline-limited DNA. Each macronuclear locus may be present in the micronucleus as several nonconsecutive, permuted, and/or inverted DNA segments. Here we investigate the genome-wide range of scrambled gene architectures that describe all precursor-product relationships in Oxytricha trifallax, the first completely sequenced scrambled genome. We find that five general, recurrent patterns in the sets of scrambled micronuclear precursor pieces can describe over 80% of Oxytricha's scrambled genes. These include instances of translocations and inversions, and other specific patterns characterized by alternating stretches of consecutive odd and even DNA segments. Moreover, we find that iterating patterns of alternating odd-even segments up to four times can describe over 96% of the scrambled precursor loci. Recurrence of these highly structured genetic architectures within scrambled genes presumably reflects recurrent evolutionary events that gave rise to over 3000 of scrambled loci in the germline genome.
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Affiliation(s)
- Jonathan Burns
- Department of Mathematics & Statistics, University of South Florida, Tampa, FL 33620.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Denys Kukushkin
- Department of Mathematics & Statistics, University of South Florida, Tampa, FL 33620
| | - Xiao Chen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Laura F Landweber
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Masahico Saito
- Department of Mathematics & Statistics, University of South Florida, Tampa, FL 33620
| | - Nataša Jonoska
- Department of Mathematics & Statistics, University of South Florida, Tampa, FL 33620
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10
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Pedrini B, Suter-Stahel T, Vallesi A, Alimenti C, Luporini P. Molecular Structures and Coding Genes of the Water-Borne Protein Pheromones of Euplotes petzi, an Early Diverging Polar Species of Euplotes. J Eukaryot Microbiol 2016; 64:164-172. [PMID: 27455370 DOI: 10.1111/jeu.12348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/27/2016] [Accepted: 07/19/2016] [Indexed: 12/01/2022]
Abstract
Euplotes is diversified into dozens of widely distributed species that produce structurally homologous families of water-borne protein pheromones governing self-/nonself-recognition phenomena. Structures of pheromones and pheromone coding genes have so far been studied from species lying in different positions of the Euplotes phylogenetic tree. We have now cloned the coding genes and determined the NMR molecular structure of four pheromones isolated from Euplotes petzi, a polar species which is phylogenetically distant from previously studied species and forms the deepest branching clade in the tree. The E. petzi pheromone genes have significantly shorter sequences than in other congeners, lack introns, and encode products of only 32 amino acids. Likewise, the three-dimensional structure of the E. petzi pheromones is markedly simpler than the three-helix up-down-up architecture previously determined in another polar species, Euplotes nobilii, and in a temperate-water species, Euplotes raikovi. Although sharing the same up-down-up architecture, it includes only two short α-helices that find their topological counterparts with the second and third helices of the E. raikovi and E. nobilii pheromones. The overall picture that emerges is that the evolution of Euplotes pheromones involves progressive increases in the gene sequence length and in the complexity of the three-dimensional molecular structure.
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Affiliation(s)
- Bill Pedrini
- Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Thea Suter-Stahel
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Vallesi
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC) 62032, Italy
| | - Claudio Alimenti
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC) 62032, Italy
| | - Pierangelo Luporini
- Laboratory of Eukaryotic Microbiology and Animal Biology, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC) 62032, Italy
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11
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Aeschlimann SH, Jönsson F, Postberg J, Stover NA, Petera RL, Lipps HJ, Nowacki M, Swart EC. The draft assembly of the radically organized Stylonychia lemnae macronuclear genome. Genome Biol Evol 2014; 6:1707-23. [PMID: 24951568 PMCID: PMC4122937 DOI: 10.1093/gbe/evu139] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: A small, germline micronucleus and a massive, vegetative macronucleus. The genome within Stylonychia’s macronucleus has a very unusual architecture, comprised variably and highly amplified “nanochromosomes,” each usually encoding a single gene with a minimal amount of surrounding noncoding DNA. As only a tiny fraction of the Stylonychia genes has been sequenced, and to promote research using this organism, we sequenced its macronuclear genome. We report the analysis of the 50.2-Mb draft S. lemnae macronuclear genome assembly, containing in excess of 16,000 complete nanochromosomes, assembled as less than 20,000 contigs. We found considerable conservation of fundamental genomic properties between S. lemnae and its close relative, Oxytricha trifallax, including nanochromosomal gene synteny, alternative fragmentation, and copy number. Protein domain searches in Stylonychia revealed two new telomere-binding protein homologs and the presence of linker histones. Among the diverse histone variants of S. lemnae and O. trifallax, we found divergent, coexpressed variants corresponding to four of the five core nucleosomal proteins (H1.2, H2A.6, H2B.4, and H3.7) suggesting that these ciliates may possess specialized nucleosomes involved in genome processing during nuclear differentiation. The assembly of the S. lemnae macronuclear genome demonstrates that largely complete, well-assembled highly fragmented genomes of similar size and complexity may be produced from one library and lane of Illumina HiSeq 2000 shotgun sequencing. The provision of the S. lemnae macronuclear genome sets the stage for future detailed experimental studies of chromatin-mediated, RNA-guided developmental genome rearrangements.
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Affiliation(s)
| | - Franziska Jönsson
- Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, Germany
| | - Jan Postberg
- Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, GermanyDepartment of Neonatology, HELIOS Children's Hospital, Witten/Herdecke University, Wuppertal, Germany
| | | | | | - Hans-Joachim Lipps
- Centre for Biological Research and Education (ZBAF), Institute of Cell Biology, Witten/Herdecke University, Wuppertal, Germany
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Abstract
Ciliates are an ancient and diverse group of microbial eukaryotes that have emerged as powerful models for RNA-mediated epigenetic inheritance. They possess extensive sets of both tiny and long noncoding RNAs that, together with a suite of proteins that includes transposases, orchestrate a broad cascade of genome rearrangements during somatic nuclear development. This Review emphasizes three important themes: the remarkable role of RNA in shaping genome structure, recent discoveries that unify many deeply diverged ciliate genetic systems, and a surprising evolutionary "sign change" in the role of small RNAs between major species groups.
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Dobri N, Oumarou EEN, Alimenti C, Ortenzi C, Luporini P, Vallesi A. Methionine sulfoxide reduction in ciliates: characterization of the ready-to-use methionine sulfoxide-R-reductase genes in Euplotes. Gene 2013. [PMID: 23206970 DOI: 10.1016/j.gene.2012.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genes encoding the enzyme methionine sulfoxide reductase type B, specific to the reduction of the oxidized methionine-R form, were characterized from the expressed (macronuclear) genome of two ecologically separate marine species of Euplotes, i.e. temperate water E. raikovi and polar water E. nobilii. Both species were found to contain a single msrB gene with a very simple structural organization encoding a protein of 127 (E. raikovi) or 126 (E. nobilii) amino acid residues that belongs to the group of zinc-containing enzymes. Both msrB genes are constitutively expressed, suggesting that the MsrB enzyme plays an essential role in repairing oxidative damages that appear to be primarily caused by physiological cell aging in E. raikovi and by interactions with an O(2) saturated environment in E. nobilii.
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Affiliation(s)
- Nicoleta Dobri
- Dipartimento di Scienze Ambientali e Naturali, University of Camerino, 62032 Camerino (MC), Italy
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