Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families
© Arkhipova et al.; licensee BioMed Central Ltd. 2013
Received: 3 December 2012
Accepted: 16 August 2013
Published: 27 August 2013
Penelope-like elements (PLEs) are an enigmatic group of retroelements sharing a common ancestor with telomerase reverse transcriptases. In our previous studies, we identified endonuclease-deficient PLEs that are associated with telomeres in bdelloid rotifers, small freshwater invertebrates best known for their long-term asexuality and high foreign DNA content. Completion of the high-quality draft genome sequence of the bdelloid rotifer Adineta vaga provides us with the opportunity to examine its genomic transposable element (TE) content, as well as TE impact on genome function and evolution.
We performed an exhaustive search of the A. vaga genome assembly, aimed at identification of canonical PLEs combining both the reverse transcriptase (RT) and the GIY-YIG endonuclease (EN) domains. We find that the RT/EN-containing Penelope families co-exist in the A. vaga genome with the EN-deficient RT-containing Athena retroelements. Canonical PLEs are present at very low copy numbers, often as a single-copy, and there is no evidence that they might preferentially co-mobilize EN-deficient PLEs. We also find that Penelope elements can participate in expansion of A. vaga multigene families via trans-action of their enzymatic machinery, as evidenced by identification of intron-containing host genes framed by the Penelope terminal repeats and characteristic target-site duplications generated upon insertion. In addition, we find that Penelope open reading frames (ORFs) in several families have incorporated long stretches of coding sequence several hundred amino acids (aa) in length that are highly enriched in asparagine residues, a phenomenon not observed in other retrotransposons.
Our results show that, despite their low abundance and low transcriptional activity in the A. vaga genome, endonuclease-containing Penelope elements can participate in expansion of host multigene families. We conclude that the terminal repeats represent the cis-acting sequences required for mobilization of the intervening region in trans by the Penelope-encoded enzymatic activities. We also hypothesize that the unusual capture of long N-rich segments by the Penelope ORF occurs as a consequence of peculiarities of its replication mechanism. These findings emphasize the unconventional nature of Penelope retrotransposons, which, in contrast to all other retrotransposon types, are capable of dispersing intron-containing genes, thereby questioning the validity of traditional estimates of gene retrocopies in PLE-containing eukaryotic genomes.
KeywordsRetrotransposon Reverse transcriptase GIY-YIG endonuclease
Penelope-like elements (PLEs) represent an ancient class of eukaryotic retroelements that shares a common ancestor with telomerase reverse transcriptases [1, 2]. They can be found in protists, fungi, animals and plants, although their representation in these taxa can be very sporadic. The first Penelope element was identified in Drosophila virilis, where it was shown to participate in hybrid dysgenesis [3, 4]. Its structural and functional properties are those of a typical retrotransposon, consisting of a single open reading frame (ORF). This ORF encodes a reverse transcriptase (RT) domain responsible for RNA-templated DNA synthesis, and an endonuclease (EN) domain responsible for integration of a reverse-transcribed cDNA copy into new chromosomal locations, generating short target site duplications (TSD) upon insertion. The EN domain associated with PLEs belongs to endonucleases of the GIY-YIG superfamily, which were originally identified in group I mobile introns from bacteria and organelles [5–8]. The Penelope EN domain was overexpressed in E. coli and shown to possess DNA cleavage activity, while the baculovirus-expressed RT was capable of RNA-dependent DNA synthesis in vitro.
In addition to EN-containing PLEs, there is a distinct PLE subclass which lacks the EN domain altogether . Such EN-deficient PLEs are apparently able to prime DNA synthesis from the 3′ ends of the exposed chromosome termini, either at deprotected telomeres or at sites of double-strand DNA breakage, thereby obviating the need for endonuclease activity. Accordingly, their transposition is largely confined to chromosome ends, where it is followed by the addition of telomeric repeats to the truncated 5′ end of the element. Such EN-deficient PLEs are found in selected animal, fungal, protist and plant species, but their distribution is highly sporadic.
Rotifers of the class Bdelloidea, in which EN-deficient PLEs were discovered, are microscopic freshwater invertebrates that reproduce asexually, can survive frequent rounds of desiccation and rehydration, and contain significant amounts of horizontally transferred genes in their genomes [11–13]. The high-quality draft genome sequence of the first representative of the phylum Rotifera, the bdelloid Adineta vaga, was recently completed . Only about 3% of its genomic DNA is represented by transposable elements (TEs), and while the diversity of families is high, each family contains very few members, indicating that incoming TEs do not proliferate efficiently in the A. vaga genome. While PLEs make up almost one-third of all A. vaga retroelements (a total of 24 families, occupying approximately 0.74 Mb of the 218-Mb assembly), the majority of the A. vaga PLEs are represented by EN-deficient Athena retroelements . Here we report that the A. vaga genome also contains a small number of “canonical” Penelope elements with the GIY-YIG endonuclease domain, which, however, exhibit several highly unusual features.
Identification and phylogenetic analysis of A. vaga Penelope families
The evolutionary history of Penelope retrotransposons in the sequenced A. vaga isolate reveals that all copies are arranged in two major branches, consisting of Pen1-2_Av and Pen3-6_Av elements, respectively. High support values for the majority of nodes are indicative of relatively few insertion events that gave rise to extant copies. Overall, 6 out of 37 ORFs presented in Figure 1 appear intact (boxed), although intactness is not associated with a higher degree of proliferation in the genome. The majority of copies contain defects in their ORFs, such as frameshifts, in-frame stop codons, indels or truncations.
Structural organization of Penelope families
For Pen2_Av, the only intact and potentially active ORF (838 aa) is present on scaffold 878 (Figure 2b). This element consists of two copies, one full-length and one 5′-truncated, which are arranged in a partial tandem and inserted into a single-copy non-LTR retrotransposon. Such partial tandems can be transpositionally active, as was demonstrated by the successful introduction of a similarly structured Penelope copy from D. virilis into D. melanogaster. Since the structure of another non-LTR retrotransposon closely related to the Pen2 target (76% identity) was already known, it was possible to determine that the Pen2 insertion in this case did not cause a TSD, but instead formed its 5′ junction via microhomology-mediated annealing, as was described for long interspersed elements (LINEs) . Its 193-bp pLTR contains an 18-bp palindrome at the 5′ end. This copy may also have given rise to another insertion on scaffold 304 organized in a way identical to Pen2a, that is, flanked by inverted pLTRs with a 10-bp TSD (Figure 2c). This incomplete derivative contains an internal microhomology-mediated deletion and an in-frame stop codon. A related Pen2 subfamily consists of two 5′-truncated members, with the longest one containing an in-frame stop codon and flanked by inverted 212-bp pLTRs, but no TSD.
Pen1_Av elements exhibit a similar overall structure to Pen2_Av, except that, in most cases, pLTRs are present in direct orientation only. Unexpectedly, the 3′-terminal pLTR in Pen1 is separated from the rest of the element by a long unique spacer varying between 0.9 and 1.5 kb in length (Figure 2e, f). Apparently, the spacer is formed via capture of host DNA, as copies that are 90% identical in sequence exhibit no detectable nucleotide sequence similarity between spacers. This family contains the largest number of apparently intact copies: three out of four members code for an 830-aa ORF preserving all of the functionally conserved characteristic RT and EN motifs.
Asparagine-rich insertions in Penelope coding sequences
An early-branching lineage of Pen2a, represented by two copies in the assembly, contains a lengthy 1.5-kb insertion (N1) into its coding region between the RT and EN domains (Figures 1 and 2d). The inserted fragment is exceptionally rich in asparagine (N) residues (approximately 30%), but nevertheless it does not interrupt the ORF on scaffold 942, resulting in a 1,309-aa coding sequence. Part of the N-rich insert (304 bp) is also found upstream of the 5′ pLTR in inverted orientation (Figure 2d).
Analogous structural variations were observed in Pen3 and Pen4 families, albeit in a different relative position - between the core RT and the thumb domain (Figure 2g-i). Due to the tendency to form long tandem/inverted repeat structures, none of these elements could be initially assembled in its entirety, with the exception of one copy on scaffold 607 containing an in-frame stop codon (Figure 2g). Two Pen3 copies were located on detached contigs containing permuted overlapping 5′- and 3′-terminal parts of the element, in inverted orientation. In these cases, the original structure was inferred by reconstituting the entire ORF from its overlapping N- and C-terminal halves, so that it would be similar in structure to the copy shown in Figure 2g. However, such structures cannot be dismissed as assembly artifacts, because small RNA profiles (see below) switch polarity between the two halves. All Pen3 and Pen4 elements carry an insertion of different N-rich segments (N2 to N4) into an ancestral copy resembling a single-copy intact Pen3a, which has no such insertions (Figure 1, Figure 2i). There were at least three independent occurrences of long N-rich insertions into the same relative position of Pen3/Pen4, with the length of inserted segments varying between 460 and 554 aa, all of them having an asparagine content of 25 to 30%. Overall, it appears that N-rich insertions tend to arise in ORF regions that were initially enriched in short (AAY)n motifs.
Transcription and RNA-mediated silencing
We sought to determine the possible origin of the N-rich segments inserted into Penelope ORF. While the 1.5-kb segments in Pen2a could not be found elsewhere in the assembly without being connected to Penelope ORF, a 1-kb region of homology 85% identical to the N-rich segment from Pen3 was found near a Pen3 solo pLTR on scaffold 412, and, moreover, it was highly transcribed on its own, but yielded a very poor antisense small RNA signal (Figure 3a, f). In contrast, transcription from most individual Penelope families was more than an order of magnitude lower, and was comparable in intensity to weakly transcribed A. vaga genes, such as Dicer endonuclease homologs  (Figure 3a). Families without full-length copies, such as Pen3b and Pen4, yielded very low transcript levels close to background, while Pen5 yielded higher transcript levels and low antisense small RNA coverage (Figure 3e). Overall, most Penelope families exhibit relatively low RNA-seq coverage and high steady-state levels of endogenous small RNA coverage predominantly in antisense orientation, indicating efficient operation of RNA-mediated silencing mechanisms directed against their activity (Figure 3).
Role of Penelope in host gene expansion
To verify that the pLTR-NRPS combination indeed originated as a result of transposition, rather than a recombinational event bringing together two pLTRs with the same adjacent 8-bp sequence by chance, we searched the assembly for the putative “empty site”. Indeed, we found that scaffold 385 has an allelic partner, scaffold 561, containing the same genes (glucose-6-phosphate isomerase and retinoic acid receptor RXR-alpha) with an overall nucleotide sequence divergence of 2% (Figure 4). As expected, the 8-bp TSD is present on scaffold 561 only once, providing direct evidence that it was indeed duplicated upon insertion of the entire pLTR-NRPS structure.
Phylogenetic placement of A. vaga Penelope families
Completion of the high-quality draft genome sequence of a bdelloid rotifer, Adineta vaga, provides us with an opportunity to investigate the entire TE complement in a long-term asexual species, and to obtain a comprehensive picture of genome-wide TE distribution and evolutionary history. This study is focused on PLEs, an enigmatic class of retroelements which include EN-containing retrotransposons from numerous animal genomes, as well as telomere-associated EN-deficient retroelements from rotifers, fungi, protists and plants [10, 16, 20]. While we observe co-existence, within the genome of the same species, between the conventional Penelope retrotransposons with the GIY-YIG EN domain and the EN-deficient PLEs, as was recently reported in the kuruma shrimp , there is no indication of cross-mobilization of EN-deficient Athena elements by the Penelope-encoded EN. For each A. vaga Penelope family, its mobility in the genome apparently relies on the presence of element-specific terminal structures required for retrotransposition, termed pLTRs, which do not exhibit any association with Athena elements. It should be noted that fungal genomes contain only EN-deficient PLEs and no EN-containing ones, again indicating that the maintenance of the former does not depend on the latter.
The present analysis of Penelope retrotransposons in A. vaga, while illustrating their overall similarity to Penelope elements in other species, including the extreme structural variability, also highlights their peculiar features that may contribute to the evolutionary plasticity of the bdelloid genome characterized by high levels of gene conversion, by relatively low but highly diversified TE content, and by the presence of numerous genes of foreign origin and substantial lineage-specific expansions of various multigene families . Expansions involve gene families, including NRPS and other foreign genes, as well as 7-transmembrane receptors and proteins containing repeated motifs, such as LRR, TPR, PPR, Kelch, NHL, FG-GAP and so on. Paradoxically, many gene families are amplified to a much higher copy number than TE families. These multigene families are likely involved in processes that involve diversification of gene function, such as host defense and immunity, production of secondary metabolites, chemosensory perception, extracellular signaling and cell-cell communication.
We find that A. vaga Penelope elements can mobilize host genes surrounded by terminal pLTR structures and, therefore, can contribute to observed lineage-specific expansions of certain gene families, shedding light on some of the mechanisms that multiply host genes to copy numbers higher than most TEs. While other TE classes also have the potential to contribute to amplification of gene families, which could then be followed by their diversification, Penelope elements have a distinct advantage over other retrotransposons in this respect, as their retrotransposition mechanism apparently allows intron retention . Our analysis reveals no strong evidence that any intact A. vaga Penelope ORFs were exapted as domesticated genes, as none of them are present on two collinear allelic chromosome segments. Those Penelope fragments that we do find in collinear pairs are badly damaged, and their function, if any, would not involve Penelope-encoded products. The most likely agents involved in gene amplification are the Penelope families with the capacity to incorporate relatively long stretches of host DNA between pLTRs, such as Pen1_Av and Pen3a_Av. Four out of six apparently intact Penelope ORFs belong to these families. While the propensity of A. vaga for DNA deletion could rapidly erase one or both pLTRs from the genome, making it difficult to detect additional cases of pLTR-mediated gene amplification, the example described here leaves little doubt that such events can indeed contribute to lineage-specific expansion of multigene families.
Even though the overall TE content in A. vaga is quite low by metazoan standards, the particularly low Penelope copy number in comparison to other retrotransposons is striking. While some TEs could remain undetected in a de novo assembly consisting of over 30,000 scaffolds with N50 of 260 kb , there is little reason to believe that most Penelope copies would be preferentially undetectable. Two circularly permuted copies located on isolated contigs with little or no flanking sequences may represent active elements which could not be properly assembled due to the fusion of several identical copies into a single contig. Although studies of PLE distribution along the chromosome length will have to await chromosome-sized scaffolds, the majority of Penelope copies are present on relatively small scaffolds (Additional file 1: Table S1), and inspection of their genomic environment shows that they are largely compartmentalized in TE-rich regions, which may represent non-essential genomic islands consisting of various TEs, genes of foreign origin and members of diverse multigene families.
Like all other TEs in the genome, Penelopes are subject to the generalized host defense responses, such as RNA-mediated silencing. Indeed, we find that most of the A. vaga Penelope copies give rise to small RNAs with preferential antisense polarity. The Penelope element in Drosophila was previously shown to elicit small RNA response after invasion [22, 23]. We also observed that many Penelope copies were disabled by microhomology-mediated deletions, a mechanism of TE inactivation that is applicable to most other TEs and likely operates during DNA repair following frequent cycles of desiccation and rehydration [14, 24]. However, Penelope elements constitute only about 2% of A. vaga TEs, and only 4% of its retroelements. Thus, additional family-specific mechanisms should be invoked to explain their much lower relative abundance in comparison with other TEs. Most likely, their low proliferation capacity may be associated with peculiarities of their replication mechanism in this species.
A previously undescribed phenomenon is the appearance of very long inserts in the coding regions of Pen2-Pen5 elements, which do not necessarily disrupt ORF integrity and are highly enriched in asparagine residues. It appears that copies with such inserts would still be capable of retrotransposition, although their ORFs would be increased in size from the usual 800 to 900 to 1,300 to 1,500 aa, and the domain structure perturbed. For Pen2a, the inserted segment could serve as a long linker between the RT and EN domains, while in Pen3 to 4 such a linker would connect the core RT with its thumb domain. Analogous inserts have not been previously observed in other TEs, and it is reasonable to suggest that they arise as a consequence of the complicated molecular gymnastics that PLEs perform during their replication. In particular, the existence of an autonomous highly transcribed N-rich segment in the vicinity of Pen3a pLTR indicates that it could have been captured in trans and internalized. We also noticed that in the candidate precursor elements, such as Pen2 and Pen3a, regions roughly corresponding to the linker insertion sites in Pen2a and Pen3 to 4 contain several short stretches of asparagine residues. In addition, a secondary insertion of Pen2a into Pen3 on scaffold 671 also occurred into the N-rich segment, indicating that this sequence may serve as an attractive target for Penelope insertions. Since Penelope elements were previously reported to favor simple AT-rich sequences as preferred targets , we propose that such inserts may arise as a result of spurious self-priming by read-through transcripts containing the adjacent flanks enriched in simple trinucleotide repeats, followed by template jumps. In such cases, the short internal stretches of the N-rich coding sequence (AAT)n or (AAC)n could help in keeping the reading frame of the inserted segment properly aligned, and a chimeric ORF could persist in the genome if it codes for an uninterrupted polypeptide.
The propensity of Penelope elements for self-priming may be inferred from the abundance of inverted-repeat structures containing palindromes at the inverted junction, as shown in Figure 2. Consistent occurrence of such palindromes is best interpreted in terms of self-priming, which, however, would have to occur on an antisense template (if a sense template is used, self-priming at the 3′ end would result in a tail-to-tail inverted repeat arrangement, as opposed to the most frequently observed head-to-head). Moreover, utilization of an antisense template is highly compatible with intron retention, since introns would not be recognized in an antisense orientation by the splicing machinery. The presence of oppositely oriented promoter motifs in pLTRs also argues in favor of bidirectional PLE transcription. However, we cannot currently exclude the possibility of utilization of an unspliced sense transcript as a template, and further experiments will be required to discriminate between these possibilities. Direct demonstration of antisense promoter activity in Penelope elements and full elucidation of its replication cycle constitutes a promising subject for future studies.
Penelope elements occupy a special place among TE superfamilies because of their variable structure representing a flexible arrangement of direct and/or inverted repeats. This structure exhibits a high degree of conservation among all animals harboring EN-containing PLEs, while the protist and fungal genomes contain only EN-deficient PLEs, which do not share this structural organization. Our analysis reveals co-existence of two distinct PLE types within the genome of the same host species with no evidence of cross-mobilization between families, indicating that the element-encoded enzymatic activities and its cis-acting sequences are co-adapted. The EN-containing PLEs were shown to participate in expansion of intron-containing multigene families in the host. We also describe a new phenomenon of insertion of long N-rich segments into the coding sequence, not previously observed in other retroelements, and hypothesize that it may occur as a consequence of the atypical replication mechanism. Taking all of the observed structural features into consideration, we hypothesize that EN-containing PLEs use a self-priming mechanism of replication, which would result in intron retention if it utilizes an antisense template. However, further experiments are required to discriminate between possible alternative models.
Initial PLE identification in A. vaga was done in the course of genome analysis as described in , with relatively low recovery from REPET and ReAS pipelines due to the low copy number, which hampers identification of numerous single-copy elements. Additional BLAST searches were performed using the conserved GIY-YIG and RT domains as queries, and after identification and boundary adjustment of full-length copies, these were used as queries to identify shorter fragments using BLAT . Multiple sequence alignment was done with MUSCLE . A. vaga Penelope sequences were aligned as amino acids in MEGA v.5.10  and untranslated back into nucleotides. Maximum likelihood analysis of nucleotide sequences was performed with RAxML . For comparison with PLEs from other species, the initial datasets from  and  were supplemented with PLEs characterized in the present study, and neighbor-joining and minimum evolution analyses of protein-coding sequences were performed in MEGA (Poisson model, gamma distributed rates among sites, 1,000 bootstrap replications). RNA-seq counts were determined with the aid of a custom Ruby script available upon request. DNA and RNA sequencing data were generated by the A. vaga sequencing consortium, and all of the scaffold numbers and coordinates correspond to the assembly in . Validation of selected sequences and closure of gaps in genomic DNA was done by PCR using custom oligonucleotide primers available upon request. Detailed procedures for small RNA isolation and analysis will be published elsewhere (Rodriguez and Arkhipova, in preparation). Briefly, HiTrap Q (GE Healthcare Life Sciences, Pittsburgh, PA, USA) column chromatography eluates corresponding to protein-bound fractions from A. vaga lysates were collected to extract endogenous small RNAs as described in . This protocol results in preferential extraction of small RNAs bound to Argonaute/Piwi proteins, and over 80% of the obtained reads correspond to the piRNA-like category 25 to 32 nt in length with a strong 5′-uridine bias. A small RNA library was processed for sequencing on the Illumina HiSeq platform. After initial filtering, small RNAs were mapped using Bowtie  to the individual A. vaga Penelope sequences. Coverage plots along each element were produced with custom C and R scripts.
Non-ribosomal peptide synthetase
Open reading frame
Polymerase chain reaction
Target site duplication.
We are thankful to D. Mark Welch for providing access to the draft genome sequences of B. manjavacas and B. calyciflorus, to D. Mozzherin for help with the RNA-seq script, to N. Lau and G. Chirn for sharing their coverage plot scripts, and to anonymous reviewers for constructive comments. This research was supported by grants MCB-0821956 and MCB-1121334 from the U.S. National Science Foundation to I.A.
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