1
|
Madani M, Ward L, Vierstraete A, De Boer SH, Moens M. The ribosomal intergenic spacer (IGS) in the potato and tobacco cyst nematodes, Globodera pallida, G. rostochiensis and G. tabacum. Mol Cell Probes 2019; 48:101441. [PMID: 31470078 DOI: 10.1016/j.mcp.2019.101441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 08/18/2019] [Accepted: 08/27/2019] [Indexed: 11/20/2022]
Abstract
The potato cyst nematodes Globodera pallida and G. rostochiensis (PCN), and tobacco cyst nematode (TCN), G. tabacum, are the most important parasitic nematodes of potato and tobacco worldwide. Ribosomal DNA provides useful molecular data for diagnostics, the study of polymorphisms and for evolutionary research in eukaryotic organisms including nematodes. Here we present data on the structure and organization of a rarely studied part of the intergenic spacer (IGS) region of the PCN and TCN genome of cyst nematodes. This region has shown potential for diagnostic purposes and population studies in other organisms including nematodes. In nematodes, the ribosomal RNA gene cluster comprises three genes: 5.8S, 18S and 28S rRNA, which are separated by spacer regions: the intergenic spacer (IGS), non-transcribed spacer (NTS), externally transcribed spacer (EST) and the internally transcribed spacer (ITS). The intergenic spacer (IGS) region consists of an external transcribed spacer (ETS) and a non-transcribed spacer (NTS) which is located between the 28S of one repeat and the 18S gene of the next repeat within the rRNA genes cluster. In this study, the first flanking portion of the IGS was amplified, cloned and sequenced from PCN and TCN. Primers were then designed to amplify the whole IGS sequence. PCR amplification of IGS from G. tabacum, G. pallida, and G. rostochiensis yielded respectively: a single amplicon of 3 kb, three amplicons sized 2.5, 2.6 and 2.9 kb, and two amplicons sized 2.8 and 2.9 kb. Results showed that Globodera spp. has more than one variant copy of the IGS, with both long and short repetitive DNA elements. An approximately 400 bp long region without any internal repetitive elements, were identified in a position between the two repetitive regions suggesting that there is a 5S gene in the IGS of these species.
Collapse
Affiliation(s)
- Mehrdad Madani
- Department of Soil Science, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada; Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown Laboratory, Charlottetown, PE, Canada.
| | - Len Ward
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown Laboratory, Charlottetown, PE, Canada
| | - Andy Vierstraete
- Biology Department, Gent University, K.L. Ledeganckstraat, 35, 9000, Gent, Belgium
| | - Solke H De Boer
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown Laboratory, Charlottetown, PE, Canada
| | - Maurice Moens
- Research Institute for Agriculture, Fisheries and Food (ILVO), 9280, Merelbeke, Belgium; Department of Plants and Crops, Ghent University, Coupure Links 653, Ghent, Belgium
| |
Collapse
|
2
|
Scavariello C, Luchetti A, Martoni F, Bonandin L, Mantovani B. Hybridogenesis and a potential case of R2 non-LTR retrotransposon horizontal transmission in Bacillus stick insects (Insecta Phasmida). Sci Rep 2017; 7:41946. [PMID: 28165062 PMCID: PMC5292737 DOI: 10.1038/srep41946] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/04/2017] [Indexed: 01/16/2023] Open
Abstract
Horizontal transfer (HT) is an event in which the genetic material is transferred from one species to another, even if distantly related, and it has been demonstrated as a possible essential part of the lifecycle of transposable elements (TEs). However, previous studies on the non-LTR R2 retrotransposon, a metazoan-wide distributed element, indicated its vertical transmission since the Radiata-Bilateria split. Here we present the first possible instances of R2 HT in stick insects of the genus Bacillus (Phasmida). Six R2 elements were characterized in the strictly bisexual subspecies B. grandii grandii, B. grandii benazzii and B. grandii maretimi and in the obligatory parthenogenetic taxon B. atticus. These elements were compared with those previously retrieved in the facultative parthenogenetic species B. rossius. Phylogenetic inconsistencies between element and host taxa, and age versus divergence analyses agree and support at least two HT events. These HT events can be explained by taking into consideration the complex Bacillus reproductive biology, which includes also hybridogenesis, gynogenesis and androgenesis. Through these non-canonical reproductive modes, R2 elements may have been transferred between Bacillus genomes. Our data suggest, therefore, a possible role of hybridization for TEs survival and the consequent reshaping of involved genomes.
Collapse
Affiliation(s)
- Claudia Scavariello
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Francesco Martoni
- Bio-Protection Research Centre, Lincoln University, Lincoln 7647, New Zealand
| | - Livia Bonandin
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| |
Collapse
|
3
|
Kojima KK, Seto Y, Fujiwara H. The Wide Distribution and Change of Target Specificity of R2 Non-LTR Retrotransposons in Animals. PLoS One 2016; 11:e0163496. [PMID: 27662593 PMCID: PMC5035012 DOI: 10.1371/journal.pone.0163496] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/09/2016] [Indexed: 12/23/2022] Open
Abstract
Transposons, or transposable elements, are the major components of genomes in most eukaryotes. Some groups of transposons have developed target specificity that limits the integration sites to a specific nonessential sequence or a genomic region to avoid gene disruption caused by insertion into an essential gene. R2 is one of the most intensively investigated groups of sequence-specific non-LTR retrotransposons and is inserted at a specific site inside of 28S ribosomal RNA (rRNA) genes. R2 is known to be distributed among at least six animal phyla even though its occurrence is reported to be patchy. Here, in order to obtain a more detailed picture of the distribution of R2, we surveyed R2 using both in silico screening and degenerate PCR, particularly focusing on actinopterygian fish. We found two families of the R2C lineage from vertebrates, although it has previously only been found in platyhelminthes. We also revealed the apparent movement of insertion sites of a lineage of actinopterygian R2, which was likely concurrent with the acquisition of a 28S rRNA-derived sequence in their 3' UTR. Outside of actinopterygian fish, we revealed the maintenance of a single R2 lineage in birds; the co-existence of four lineages of R2 in the leafcutter bee Megachile rotundata; the first examples of R2 in Ctenophora, Mollusca, and Hemichordata; and two families of R2 showing no target specificity. These findings indicate that R2 is relatively stable and universal, while differences in the distribution and maintenance of R2 lineages probably reflect characteristics of some combination of both R2 lineages and host organisms.
Collapse
Affiliation(s)
- Kenji K. Kojima
- Genetic Information Research Institute, Mountain View, CA, 94043, United States of America
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277–8562, Japan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
- * E-mail:
| | - Yosuke Seto
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277–8562, Japan
| | - Haruhiko Fujiwara
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277–8562, Japan
| |
Collapse
|
4
|
Abstract
R2 elements are sequence specific non-LTR retrotransposons that exclusively insert in the 28S rRNA genes of animals. R2s encode an endonuclease that cleaves the insertion site and a reverse transcriptase that uses the cleaved DNA to prime reverse transcription of the R2 transcript, a process termed target primed reverse transcription. Additional unusual properties of the reverse transcriptase as well as DNA and RNA binding domains of the R2 encoded protein have been characterized. R2 expression is through co-transcription with the 28S gene and self-cleavage by a ribozyme encoded at the R2 5' end. Studies in laboratory stocks and natural populations of Drosophila suggest that R2 expression is tied to the distribution of R2-inserted units within the rDNA locus. Most individuals have no R2 expression because only a small fraction of their rRNA genes need to be active, and a contiguous region of the locus free of R2 insertions can be selected for activation. However, if the R2-free region is not large enough to produce sufficient rRNA, flanking units - including those inserted with R2 - must be activated. Finally, R2 copies rapidly turnover within the rDNA locus, yet R2 has been vertically maintained in animal lineages for hundreds of millions of years. The key to this stability is R2's ability to remain dormant in rDNA units outside the transcribed regions for generations until the stochastic nature of the crossovers that drive the concerted evolution of the rDNA locus inevitably reshuffle the inserted and uninserted units, resulting in transcription of the R2-inserted units.
Collapse
|
5
|
Martoni F, Eickbush DG, Scavariello C, Luchetti A, Mantovani B. Dead element replicating: degenerate R2 element replication and rDNA genomic turnover in the Bacillus rossius stick insect (Insecta: Phasmida). PLoS One 2015; 10:e0121831. [PMID: 25799008 PMCID: PMC4370867 DOI: 10.1371/journal.pone.0121831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/04/2015] [Indexed: 11/18/2022] Open
Abstract
R2 is an extensively investigated non-LTR retrotransposon that specifically inserts into the 28S rRNA gene sequences of a wide range of metazoans, disrupting its functionality. During R2 integration, first strand synthesis can be incomplete so that 5’ end deleted copies are occasionally inserted. While active R2 copies repopulate the locus by retrotransposing, the non-functional truncated elements should frequently be eliminated by molecular drive processes leading to the concerted evolution of the rDNA array(s). Although, multiple R2 lineages have been discovered in the genome of many animals, the rDNA of the stick insect Bacillus rossius exhibits a peculiar situation: it harbors both a canonical, functional R2 element (R2Brfun) as well as a full-length but degenerate element (R2Brdeg). An intensive sequencing survey in the present study reveals that all truncated variants in stick insects are present in multiple copies suggesting they were duplicated by unequal recombination. Sequencing results also demonstrate that all R2Brdeg copies are full-length, i. e. they have no associated 5' end deletions, and functional assays indicate they have lost the active ribozyme necessary for R2 RNA maturation. Although it cannot be completely ruled out, it seems unlikely that the degenerate elements replicate via reverse transcription, exploiting the R2Brfun element enzymatic machinery, but rather via genomic amplification of inserted 28S by unequal recombination. That inactive copies (both R2Brdeg or 5'-truncated elements) are not eliminated in a short term in stick insects contrasts with findings for the Drosophila R2, suggesting a widely different management of rDNA loci and a lower efficiency of the molecular drive while achieving the concerted evolution.
Collapse
Affiliation(s)
- Francesco Martoni
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Danna G. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Claudia Scavariello
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- * E-mail:
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| |
Collapse
|
6
|
Elliott TA, Stage DE, Crease TJ, Eickbush TH. In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome. Mob DNA 2013; 4:20. [PMID: 24059783 PMCID: PMC3849761 DOI: 10.1186/1759-8753-4-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/29/2013] [Indexed: 11/16/2022] Open
Abstract
Background Only a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within the multigene rDNA. The only known rDNA-specific DNA transposon, Pokey (superfamily: piggyBac) is found in the freshwater microcrustacean, Daphnia pulex. Here, we present a genome-wide analysis of Pokey based on the recently completed whole genome sequencing project for D. pulex. Results Phylogenetic analysis of Pokey elements recovered from the genome sequence revealed the presence of four lineages corresponding to two divergent autonomous families and two related lineages of non-autonomous miniature inverted repeat transposable elements (MITEs). The MITEs are also found at the same 28S rRNA gene insertion site as the Pokey elements, and appear to have arisen as deletion derivatives of autonomous elements. Several copies of the full-length Pokey elements may be capable of producing an active transposase. Surprisingly, both families of Pokey possess a series of 200 bp repeats upstream of the transposase that is derived from the rDNA intergenic spacer (IGS). The IGS sequences within the Pokey elements appear to be evolving in concert with the rDNA units. Finally, analysis of the insertion sites of Pokey elements outside of rDNA showed a target preference for sites similar to the specific sequence that is targeted within rDNA. Conclusions Based on the target site preference of Pokey elements and the concerted evolution of a segment of the element with the rDNA unit, we propose an evolutionary path by which the ancestors of Pokey elements have invaded the rDNA niche. We discuss how specificity for the rDNA unit may have evolved and how this specificity has played a role in the long-term survival of these elements in the subgenus Daphnia.
Collapse
Affiliation(s)
- Tyler A Elliott
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Deborah E Stage
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.,Department of Biology, Butler County Community College, Butler, PA 16002, USA
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Thomas H Eickbush
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| |
Collapse
|
7
|
Eickbush DG, Burke WD, Eickbush TH. Evolution of the R2 retrotransposon ribozyme and its self-cleavage site. PLoS One 2013; 8:e66441. [PMID: 24066021 PMCID: PMC3774820 DOI: 10.1371/journal.pone.0066441] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/07/2013] [Indexed: 12/23/2022] Open
Abstract
R2 is a non-long terminal repeat retrotransposon that inserts site-specifically in the tandem 28S rRNA genes of many animals. Previously, R2 RNA from various species of Drosophila was shown to self-cleave from the 28S rRNA/R2 co-transcript by a hepatitis D virus (HDV)-like ribozyme encoded at its 5' end. RNA cleavage was at the precise 5' junction of the element with the 28S gene. Here we report that RNAs encompassing the 5' ends of R2 elements from throughout its species range fold into HDV-like ribozymes. In vitro assays of RNA self-cleavage conducted in many R2 lineages confirmed activity. For many R2s, RNA self-cleavage was not at the 5' end of the element but at 28S rRNA sequences up to 36 nucleotides upstream of the junction. The location of cleavage correlated well with the types of endogenous R2 5' junctions from different species. R2 5' junctions were uniform for most R2s in which RNA cleavage was upstream in the rRNA sequences. The 28S sequences remaining on the first DNA strand synthesized during retrotransposition are postulated to anneal to the target site and uniformly prime second strand DNA synthesis. In species where RNA cleavage occurred at the R2 5' end, the 5' junctions were variable. This junction variation is postulated to result from the priming of second strand DNA synthesis by chance microhomologies between the target site and the first DNA strand. Finally, features of R2 ribozyme evolution, especially changes in cleavage site and convergence on the same active site sequences, are discussed.
Collapse
Affiliation(s)
- Danna G. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - William D. Burke
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Thomas H. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
| |
Collapse
|
8
|
Non-LTR R2 element evolutionary patterns: phylogenetic incongruences, rapid radiation and the maintenance of multiple lineages. PLoS One 2013; 8:e57076. [PMID: 23451148 PMCID: PMC3581529 DOI: 10.1371/journal.pone.0057076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/17/2013] [Indexed: 01/02/2023] Open
Abstract
Retrotransposons of the R2 superclade specifically insert within the 28S ribosomal gene. They have been isolated from a variety of metazoan genomes and were found vertically inherited even if their phylogeny does not always agree with that of the host species. This was explained with the diversification/extinction of paralogous lineages, being proved the absence of horizontal transfer. We here analyze the widest available collection of R2 sequences, either newly isolated from recently sequenced genomes or drawn from public databases, in a phylogenetic framework. Results are congruent with previous analyses, but new important issues emerge. First, the N-terminal end of the R2-B clade protein, so far unknown, presents a new zinc fingers configuration. Second, the phylogenetic pattern is consistent with an ancient, rapid radiation of R2 lineages: being the estimated time of R2 origin (850–600 Million years ago) placed just before the metazoan Cambrian explosion, the wide element diversity and the incongruence with the host phylogeny could be attributable to the sudden expansion of available niches represented by host’s 28S ribosomal genes. Finally, we detect instances of coexisting multiple R2 lineages showing a non-random phylogenetic pattern, strongly similar to that of the “library” model known for tandem repeats: a collection of R2s were present in the ancestral genome and then differentially activated/repressed in the derived species. Models for activation/repression as well as mechanisms for sequence maintenance are also discussed within this framework.
Collapse
|
9
|
A population genetic model for the maintenance of R2 retrotransposons in rRNA gene loci. PLoS Genet 2013; 9:e1003179. [PMID: 23326244 PMCID: PMC3542110 DOI: 10.1371/journal.pgen.1003179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 11/02/2012] [Indexed: 01/03/2023] Open
Abstract
R2 retrotransposable elements exclusively insert into the tandemly repeated rRNA genes, the rDNA loci, of their animal hosts. R2 elements form stable long-term associations with their host, in which all individuals in a population contain many potentially active copies, but only a fraction of these individuals show active R2 retrotransposition. Previous studies have found that R2 RNA transcripts are processed from a 28S co-transcript and that the likelihood of R2-inserted units being transcribed is dependent upon their distribution within the rDNA locus. Here we analyze the rDNA locus and R2 elements from nearly 100 R2-active and R2-inactive individuals from natural populations of Drosophila simulans. Along with previous findings concerning the structure and expression of the rDNA loci, these data were incorporated into computer simulations to model the crossover events that give rise to the concerted evolution of the rRNA genes. The simulations that best reproduce the population data assume that only about 40 rDNA units out of the over 200 total units are actively transcribed and that these transcribed units are clustered in a single region of the locus. In the model, the host establishes this transcription domain at each generation in the region with the fewest R2 insertions. Only if the host cannot avoid R2 insertions within this 40-unit domain are R2 elements active in that generation. The simulations also require that most crossover events in the locus occur in the transcription domain in order to explain the empirical observation that R2 elements are seldom duplicated by crossover events. Thus the key to the long-term stability of R2 elements is the stochastic nature of the crossover events within the rDNA locus, and the inevitable expansions and contractions that introduce and remove R2-inserted units from the transcriptionally active domain. Selfish transposable elements survive in eukaryotic genomes despite the elaborate mechanisms developed by the hosts to limit their activity. One accessible system that simplifies the complex interactions between element and host involves the R2 elements, which exclusively insert in the tandemly arranged rRNA genes. R2 exhibits remarkable stability in animal lineages even though each insertion inactivates one rRNA gene. Here we determine the size of the rDNA locus and R2 number in natural isolates of Drosophila simulans. Combined with previous data concerning the expression and regulation of R2, we develop a detailed population genetic model for rRNA gene and R2 evolution that duplicates all properties of the rRNA loci in natural populations. Critical components of the model are that only a contiguous 40 unit array of rRNA gene units are needed for transcription, that R2 elements are active only when present in this transcription domain, and that most of the crossovers in the rDNA loci occur in this domain. These results suggest that the key to the long-term survival of R2 is the redistribution of rDNA units in the locus brought about by the crossovers that maintain sequence identity in all rDNA units.
Collapse
|
10
|
Swim MM, Kaeding KE, Ferree PM. Impact of a selfish B chromosome on chromatin dynamics and nuclear organization in Nasonia. J Cell Sci 2012; 125:5241-9. [PMID: 22899710 DOI: 10.1242/jcs.113423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
B chromosomes are centric chromosomal fragments present in thousands of eukaryotic genomes. Because most B chromosomes are non-essential, they can be lost without consequence. In order to persist, however, some B chromosomes can impose strong forms of intra-genomic conflict. An extreme case is the paternal sex ratio (PSR) B chromosome in the jewel wasp Nasonia vitripennis. Transmitted solely via the sperm, PSR 'imprints' the paternal chromatin so that it is destroyed during the first mitosis of the embryo. Owing to the haplo-diploid reproduction of N. vitripennis, PSR-induced loss of the paternal chromatin converts embryos that should become females into PSR-transmitting males. This conversion is key to the persistence of PSR, although the underlying mechanisms are largely unexplored. We assessed how PSR affects the paternal chromatin and then investigated how PSR is transmitted efficiently at the cellular level. We found that PSR does not affect progression of the paternal chromatin through the cell cycle but, instead, alters its normal Histone H3 phosphorylation and loading of the Condensin complex. PSR localizes to the outer periphery of the paternal nucleus, a position that we propose is crucial for it to escape from the defective paternal set. In sperm, PSR consistently localizes to the extreme anterior tip of the elongated nucleus, while the normal wasp chromosomes localize broadly across the nucleus. Thus, PSR may alter or bypass normal nuclear organizational processes to achieve its position. These findings provide new insights into how selfish genetic elements can impact chromatin-based processes for their survival.
Collapse
Affiliation(s)
- Megan M Swim
- W. M. Keck Science Department of Claremont McKenna, Pitzer and Scripps Colleges, 925 N. Mills Avenue, Claremont, CA 91711, USA
| | | | | |
Collapse
|
11
|
Luchetti A, Mingazzini V, Mantovani B. 28S junctions and chimeric elements of the rDNA targeting non-LTR retrotransposon R2 in crustacean living fossils (Branchiopoda, Notostraca). Genomics 2012; 100:51-6. [PMID: 22564473 DOI: 10.1016/j.ygeno.2012.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 04/17/2012] [Accepted: 04/23/2012] [Indexed: 11/29/2022]
Abstract
The 28S rRNA genes of several metazoans are interrupted by site-specific targeting non-LTR retrotransposons, such as R2. R2 elements have been deeply analyzed but aspects of their retrotransposition mechanism and the origin of the wide diversity observed are still debated. We characterized six new R2 lineages in four tadpole shrimp species (Notostraca), samples deriving from a parthenogenetic population of Triops cancriformis (R2Tc_it) and from bisexual Lepidurus populations of L. lubbocki (R2Ll), L. couesii (R2LcA, R2LcB, R2LcC) and L. arcticus (R2La). All elements fit the canonical R2 structure but R2Ll which turned out to be a chimera with an additional ORF originating from another R2. Consistently with data on LINEs, R2Ll could be the result of recombination due to reverse transcriptase template jump. The analysis of 28S/R2 5' end junctions further suggests aberrant homologous recombination, as observed in RNA viruses.
Collapse
Affiliation(s)
- Andrea Luchetti
- Dip. Biologia Evoluzionistica Sperimentale, Università di Bologna, via Selmi 3, 40126 Bologna, Italy.
| | | | | |
Collapse
|
12
|
Thompson BK, Christensen SM. Independently derived targeting of 28S rDNA by A- and D-clade R2 retrotransposons: Plasticity of integration mechanism. Mob Genet Elements 2011; 1:29-37. [PMID: 22016843 PMCID: PMC3190273 DOI: 10.4161/mge.1.1.16485] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 05/16/2011] [Accepted: 05/16/2011] [Indexed: 12/24/2022] Open
Abstract
Restriction-like endonuclease (RLE) bearing non-LTR retrotransposons are site-specific elements that integrate into the genome through a target primed reverse transcription mechanism (TPRT). R2 elements have been used as a model system for investigating non-LTR retrotransposon integration. We previously demonstrated that R2 retrotransposons require two subunits of the element-encoded multifunctional protein to integrate-one subunit bound upstream of the insertion site and one bound downstream. R2 elements have been phylogenetically categorized into four clades: R2-A, B, C and D, that diverged from a common ancestor more than 850 million years ago. All R2 elements target the same sequence within 28S rDNA. The amino-terminal domain of R2Bm, an R2-D clade element, contains a single zinc finger and a Myb motif that are responsible for binding R2 protein downstream of the insertion site. Target site recognition is of interest as it is the first step in the integration reaction and may help elucidate evolutionary history and integration mechanism. The amino-terminal domain of R2-A clade members contains three zinc fingers and a Myb motif. We show here that R2Lp, an R2-A clade member, uses its amino-terminal DNA binding motifs to bind upstream of the insertion site. Because the R2-A and R2-D clade elements recognize 28S rDNA differently, we conclude the A- and D-clades represent independent targeting events to the 28S site. Our results also indicate a certain plasticity of insertional mechanics exists between the two clades.
Collapse
Affiliation(s)
- Blaine K Thompson
- Department of Biology; University of Texas at Arlington; Arlington, TX USA
| | | |
Collapse
|
13
|
Brown S. The Nasonia genome sequence: finding gems in the jewel (wasp) box. INSECT MOLECULAR BIOLOGY 2010; 19 Suppl 1:v-vii. [PMID: 20167012 DOI: 10.1111/j.1365-2583.2009.00989.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|