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Boscaro V, Kolisko M, Felletti M, Vannini C, Lynn DH, Keeling PJ. Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat Ecol Evol 2017; 1:1160-1167. [PMID: 29046583 DOI: 10.1038/s41559-017-0237-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 06/14/2017] [Indexed: 02/02/2023]
Abstract
Endosymbiosis plays an important role in ecology and evolution, but fundamental aspects of the origin of intracellular symbionts remain unclear. The extreme age of many symbiotic relationships, lack of data on free-living ancestors and uniqueness of each event hinder investigations. Here, we describe multiple strains of the bacterium Polynucleobacter that evolved independently and under similar conditions from closely related, free-living ancestors to become obligate endosymbionts of closely related ciliate hosts. As these genomes reduced in parallel from similar starting states, they provide unique glimpses into the mechanisms underlying genome reduction in symbionts. We found that gene loss is contingently lineage-specific, with no evidence for ordered streamlining. However, some genes in otherwise disrupted pathways are retained, possibly reflecting cryptic genetic network complexity. We also measured substitution rates between many endosymbiotic and free-living pairs for hundreds of genes, which showed that genetic drift, and not mutation pressure, is the main non-selective factor driving molecular evolution in endosymbionts.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Biology, University of Pisa, Pisa, 56126, Italy
| | - Martin Kolisko
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Prague, 370 05, Czech Republic
| | - Michele Felletti
- Department of Chemistry, University of Konstanz, Konstanz, 78464, Germany
| | - Claudia Vannini
- Department of Biology, University of Pisa, Pisa, 56126, Italy
| | - Denis H Lynn
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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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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Popenko VI, Potekhin AA, Karajan BP, Skarlato SO, Leonova OG. The Size of DNA Molecules and Chromatin Organization in the Macronucleus of the Ciliate Didinium nasutum
(Ciliophora). J Eukaryot Microbiol 2014; 62:260-4. [DOI: 10.1111/jeu.12161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 06/18/2014] [Accepted: 06/24/2014] [Indexed: 02/02/2023]
Affiliation(s)
- Vladimir I. Popenko
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow 119991 Russia
| | - Alexey A. Potekhin
- Faculty of Biology and Soil Science; St. Petersburg State University; St. Petersburg 199034 Russia
| | - Bella P. Karajan
- Institute of Cytology; Russian Academy of Sciences; St. Petersburg 194064 Russia
| | - Sergei O. Skarlato
- Institute of Cytology; Russian Academy of Sciences; St. Petersburg 194064 Russia
| | - Olga G. Leonova
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow 119991 Russia
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Forcob S, Bulic A, Jönsson F, Lipps HJ, Postberg J. Differential expression of histone H3 genes and selective association of the variant H3.7 with a specific sequence class in Stylonychia macronuclear development. Epigenetics Chromatin 2014; 7:4. [PMID: 24502432 PMCID: PMC3918171 DOI: 10.1186/1756-8935-7-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regulation of chromatin structure involves deposition of selective histone variants into nucleosome arrays. Numerous histone H3 variants become differentially expressed by individual nanochromosomes in the course of macronuclear differentiation in the spirotrichous ciliate Stylonychia lemnae. Their biological relevance remains to be elucidated. RESULTS We show that the differential assembly of H3 variants into chromatin is strongly correlated with the functional separation of chromatin structures in developing macronuclei during sexual reproduction in Stylonychia, thus probably determining the fate of specific sequences. Specific H3 variants approximately 15 kDa or 20 kDa in length are selectively targeted by post-translational modifications. We found that only the 15 kDa H3 variants including H3.3 and H3.5, accumulate in the early developing macronucleus, and these also occur in mature macronuclei. H3.7 is a 20 kDa variant that specifically becomes enriched in macronuclear anlagen during chromosome polytenization. H3.7, acetylated at lysine-32 (probably equivalent to lysine-36 of most H3 variants), is specifically associated with a sequence class that is retained in the mature macronucleus and therefore does not undergo developmental DNA elimination. H3.8 is another 20 kDa variant that is restricted to the micronucleus. H3.8 is selectively targeted by lysine methylation and by serine or threonine phosphorylation. Intriguingly, the expression and chromatin localization of the histone variant H3.3 was impaired during macronuclear differentiation after RNA interference knock-down of Piwi expression. CONCLUSIONS Differential deposition of H3 variants into chromatin strongly correlates with the functional distinction of genomic sequence classes on the chromatin level, thus helping to determine the fate of specific DNA sequences during sexual reproduction in Stylonychia. Consequently, H3 variants are selectively targeted by post-translational modifications, possibly as a result of deviations within the recognition motifs, which allow binding of effector proteins. We propose that differential assembly of histone variants into chromatin of various nuclear types could contribute to nuclear identity, for example, during differential development of either new micronuclei or a macronuclear anlage from mitosis products of the zygote nucleus (synkaryon). The observation that the Piwi-non-coding RNA (ncRNA) pathway influences the expression and deposition of H3.3 in macronuclear anlagen indicates for the first time that selective histone variant assembly into chromatin might possibly depend on ncRNA.
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Affiliation(s)
| | | | | | - Hans J Lipps
- Institute of Cell Biology, ZBAF, Centre for Biomedical Education and Research, Witten/Herdecke University, Witten, Germany.
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Fryd-Versavel G, Lemullois M, Aubusson-Fleury A. Maintaining cell polarity through vegetative cell pattern dedifferentiation: cytoskeleton and morphogenesis in the hypotrich ciliate Sterkiella histriomuscorum. Protist 2009; 161:222-36. [PMID: 20022806 DOI: 10.1016/j.protis.2009.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 10/06/2009] [Indexed: 11/17/2022]
Abstract
The morphological differentiation of ciliates is achieved through the development of a submembraneous cytoskeleton in which the cilia are anchored. In most hypotrich ciliates, this cytoskeleton is mainly constructed of microtubules. In these species, cells pass through vegetative cell pattern dedifferentiated stages during their biological cycle. In order to investigate the behaviour of the cytoskeleton during these stages, we analysed the reorganization of the cytoskeleton during the sexual cycle of Sterkiella histriomuscorum by microscopy. Sterkiella exconjugants transiently dedifferentiate to form zygocysts devoid of ciliature and infraciliature. Immunofluorescence images obtained with antibodies directed against pericentrosomal material and tubulin showed that the cells resorb their ciliature and basal bodies, but retain their submembraneous microtubular cytoskeleton during the whole process and that the body plan is maintained through vegetative cell pattern dedifferentiation: the cell polarity remains printed on the cell surface by the microtubular cytoskeleton which in turn could mark the sites of basal body assembly during zygocyst morphogenesis. The results are discussed in terms of mechanisms of cell patterning.
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Affiliation(s)
- Ghislaine Fryd-Versavel
- UMR8080 Développement, Morphogenèse et Evolution, Bat 444, Faculté d'Orsay, Université Paris XI, 91405 Orsay Cedex, France
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Ricard G, de Graaf RM, Dutilh BE, Duarte I, van Alen TA, van Hoek AH, Boxma B, van der Staay GWM, Moon-van der Staay SY, Chang WJ, Landweber LF, Hackstein JHP, Huynen MA. Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. BMC Genomics 2008; 9:587. [PMID: 19061489 PMCID: PMC2633312 DOI: 10.1186/1471-2164-9-587] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 12/05/2008] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus and a macronucleus. N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement. RESULTS We examined the structure of these gene-sized macronuclear chromosomes in N. ovalis. We determined the telomeres, subtelomeric regions, UTRs, coding regions and introns by sequencing a large set of macronuclear DNA sequences (4,242) and cDNAs (5,484) and comparing them with each other. The telomeres consist of repeats CCC(AAAACCCC)n, similar to those in spirotrichous ciliates such as Euplotes, Sterkiella (Oxytricha) and Stylonychia. Per sequenced chromosome we found evidence for either a single protein-coding gene, a single tRNA, or the complete ribosomal RNAs cluster. Hence the chromosomes appear to encode single transcripts. In the short subtelomeric regions we identified a few overrepresented motifs that could be involved in gene regulation, but there is no consensus polyadenylation site. The introns are short (21-29 nucleotides), and a significant fraction (1/3) of the tiny introns is conserved in the distantly related ciliate Paramecium tetraurelia. As has been observed in P. tetraurelia, the N. ovalis introns tend to contain in-frame stop codons or have a length that is not dividable by three. This pattern causes premature termination of mRNA translation in the event of intron retention, and potentially degradation of unspliced mRNAs by the nonsense-mediated mRNA decay pathway. CONCLUSION The combination of short leaders, tiny introns and single genes leads to very minimal macronuclear chromosomes. The smallest we identified contained only 150 nucleotides.
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Affiliation(s)
- Guénola Ricard
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Nijmegen, the Netherlands.
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Juranek SA, Lipps HJ. New Insights into the Macronuclear Development in Ciliates. INTERNATIONAL REVIEW OF CYTOLOGY 2007; 262:219-51. [PMID: 17631190 DOI: 10.1016/s0074-7696(07)62005-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During macronuclear differentiation in ciliated protozoa, most amazing "DNA gymnastics" takes place, which includes DNA excision, DNA elimination, DNA reorganization, and DNA-specific amplification. Although the morphological events occurring during macronuclear development are well described, a detailed knowledge of the molecular mechanisms and the regulation of this differentiation process is still missing. However, recently several models have been proposed for the molecular regulation of macronuclear differentiation, but these models have yet to be verified experimentally. The scope of this review is to summarize recent discoveries in different ciliate species and to compare and discuss the different models proposed. Results obtained in these studies are not only relevant for our understanding of nuclear differentiation in ciliates, but also for cellular differentiation in eukaryotic organisms in general as well as for other disciplines such as bioinformatics and computational biology.
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Affiliation(s)
- Stefan A Juranek
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York 10021, USA
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Katz LA, Lasek-Nesselquist E, Snoeyenbos-West OLO. Structure of the micronuclear alpha-tubulin gene in the phyllopharyngean ciliate Chilodonella uncinata: implications for the evolution of chromosomal processing. Gene 2004; 315:15-9. [PMID: 14557060 DOI: 10.1016/j.gene.2003.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ciliates are a group of microbial eukaryotes defined by the presence of dimorphic nuclei-each cell contains both a transcriptionally active macronucleus and a germline micronucleus. During the development of the macronucleus, germline chromosomes are rearranged through extensive fragmentation, removal of internally excised sequences (IESs) and DNA amplification. We have characterized three IESs in the gene that encodes alpha-tubulin in the phyllopharyngean ciliate Chilodonella uncinata. The IESs are located within the coding domain, range in size from 81 to 107 bp, and are flanked by direct repeats that vary in length from 6 to 8 bp. All three IESs are moderately AT-rich and each contains two copies of a conserved sequence motif. These data provide evidence for the existence of IESs in phyllopharyngean ciliates and suggest that IES processing in C. uncinata may rely on a novel cis-acting sequence. Comparisons of the IESs in C. uncinata with those of 'model' ciliates-Paramecium, Tetrahymena, Euplotes, Oxytricha and Stylonychia-reveal considerable variation in chromosomal processing among ciliates.
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Affiliation(s)
- Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA.
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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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