The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants
© Roffler et al. 2015
Received: 24 September 2015
Accepted: 4 December 2015
Published: 17 December 2015
Helitrons are Class II transposons which are highly abundant in almost all eukaryotes. However, most Helitrons lack protein coding sequence. These non-autonomous elements are thought to hijack recombinase/helicase (RepHel) and possibly further enzymes from related, autonomous elements. Interestingly, many plant Helitrons contain an additional gene encoding a single-strand binding protein homologous to Replication Factor A (RPA), a highly conserved, single-copy gene found in all eukaryotes.
Here, we describe the analysis of DHH_Mothra, a high-copy non-autonomous Helitron in the genome of rice (Oryza sativa). Mothra has a low GC-content and consists of two distinct blocs of tandem repeats. Based on homology between their termini, we identified a putative mother element which encodes an RPA-like protein but has no RepHel gene. Additionally, we found a putative autonomous sister-family with strong homology to the Mothra mother element in the RPA protein and terminal sequences, which we propose provides the RepHel domain for the Mothra family. Furthermore, we phylogenetically analyzed the evolutionary history of RPA-like proteins. Interestingly, plant Helitron RPAs (PHRPAs) are only found in monocotyledonous and dicotyledonous plants and they form a monophyletic group which branched off before the eukaryotic “core” RPAs.
Our data show how erosion of autonomous Helitrons can lead to different “levels” of autonomy within Helitron families and can create highly successful subfamilies of non-autonomous elements. Most importantly, our phylogenetic analysis showed that the PHRPA gene was most likely acquired via horizontal gene transfer from an unknown eukaryotic donor at least 145–300 million years ago in the common ancestor of monocotyledonous and dicotyledonous plants. This might have led to the evolution of a separate branch of the Helitron superfamily in plants.
KeywordsTransposon Helitron RPA Rice Horizontal transfer
Helitrons are a superfamily of transposable elements (TEs) in eukaryotes which was discovered only relatively recently in Arabidopsis thaliana, Caenorhabditis elegans and Oryza sativa . They have since been found in many genomes of flowering plants [1, 2], mosses , fungi [4–6] but also many animals such as sea urchin , fish [8, 9] and bats . A recent in silico analysis using the program Helsearch  estimates the number of Helitrons in rice and sorghum to approximately 7000 and 5000, respectively, covering several megabases of their hosts' genomes. The most extensively studied genome regarding Helitrons is the one of maize, where approximately 2000 intact Helitrons and more than 20,000 Helitron fragments were found. Based on high homology between individual elements they are thought to still be very active . As for most DNA transposons, the majority of Helitron elements are non-autonomous and do not encode any proteins. These non-autonomous elements presumably depend for their transposition on enzymes encoded by “mother” or “master” elements elsewhere in the genome.
One reason why Helitrons remained undiscovered for a long time is their limited diagnostic features. They lack terminal inverted repeats (TIRs) and the only motifs common to all Helitrons are the dinucleotide TC at the 5' end as well as a CTRR motif at the 3' end. Additionally, almost all Helitrons have a G/C rich 15–20 bp hairpin motif approximately 10–12 bp upstream of the 3' end, which is thought to serve as a stop signal in the transposition process . Finally, Helitrons have a strong preference to insert between the bases A and T or sometimes between two Ts .
The transposition mechanism of Helitrons and the involved proteins differ from those of the well described DDE transposases. Autonomous Helitrons encode a RepHel protein of 1000–3000 amino acids (aa) length, which is thought to initiate the replication. The RepHel constitutes a replication initiation domain (RCR/Rep) followed by a helicase enzyme (Hel) of approximately 400 aa . Because of structural homology with the catalytic core of HUH endonucleases of a bacterial rolling-circle transposons , it was suggested that Helitrons use a rolling-circle mechanism involving a single-stranded DNA intermediate for transposition and replication [1, 12]. Li and Dooner , however, clearly showed excisions of Helitrons from 0.4 to 6 kb size in somatic Maize tissue. This challenges the current model and suggests an alternative mode of transposition involving excision and repair similar to TIR transposons. Indeed, it is possible that single stranded DNA transposition can result in the elimination of that copy from that locus when occurring during S phase of meiosis 1 .
Even though Helitrons are ascribed to the Class II (DNA) transposons, they remain unique due to their exclusive structural features and transposition mechanism and belong to a separate subclass within the DNA transposons . However, rolling-circle transposition mechanisms have been described for gemini viruses , plasmids and some bacterial transposons . Structural homology between their transposases suggests very ancient origin of Helitrons .
In plants, some Helitrons have been reported to also encode a distant homolog of the Replication Protein A (RPA), a protein ubiquitous in eukaryotes [19, 20]. RPA has several single-strand DNA binding sites and is involved in processes such as DNA replication and repair. RPA homologs have also been identified in Helitrons from zebrafish and sea anemone  and in Helentrons (a sub-type of Helitrons) in Drosophila melanogaster .
At least in maize, Helitrons seem to acquire close by gene fragments very frequently. Several studies showed an ongoing gene movement, gene shuffling and transcriptional read-troughts, which is attributed to Helitron activity [22, 23]. In the maize line B73, approximately 11,000 such chimeric transcripts have been found to be expressed which represents almost one quarter of all genes . Therefore, it is thought that Helitrons contributed substantially to the recent diversification observed in the maize genus. Moreover, frequent gene capturing mediated by Helitrons was also reported in the silk worm Bombyx mori  and in the bat Myotis lucifugus .
In this study we describe the analysis and origin of a high-copy Helitron family in rice, which we named DHH_Mothra. Non-autonomous Mothra elements are present in hundreds or even thousands of copies in multiple rice species, which merited an in-depth analysis of this TE family. We identified a putative mother element for the Mothra family that encodes an RPA homolog but no RepHel protein. We moreover identified a closely related Helitron family, which we propose to be the donor for the lacking RepHel enzyme of Mothras. According to our model, this introduces an additional level of autonomy. We furthermore investigated the evolutionary background of Helitron RPA acquisition in plants and suggest horizontal transfer most likely from a unicellular eukaryote into the common ancestor of mono- and dicotyledonous plants.
Mothra is a high-copy non-autonomous Helitron
In a previous study  we compared the two closely related rice species O. sativa, the Asian rice, with its relative O. glaberrima, the African rice, and investigated presence/absence polymorphisms of Class II transposons of the TIR subclass. While scanning polymorphic TE sites, we repeatedly encountered a sequence which was obviously of repetitive nature but we were unable to classify it at that time. Now, we found that it was in fact a non-autonomous TE of the Helitron order which we called Mothra.
Mothra contains tandem repeats and gene fragments
Mothra contains two distinct sequence blocs (Bloc A and B, Fig. 1a). Bloc A, which ranges approximately from position 80 to position 900 in the consensus sequence, consists of six direct repeats and shows a very low GC content of 20 %. Bloc B ranges from position 950 – 1860 and consists of six different, less conserved direct repeats and exhibits an average GC content of about 40 % (Fig. 1b). There is great variety in the number of the repeat units within the Blocs A and B among the individual copies. In some cases, the order of the blocs is even reversed. In other cases, additional sequence is present between or sometimes even within one of the two blocs.
By definition, non-autonomous elements do not encode any proteins. But interestingly, the Mothra consensus sequence contains a putative open reading frame (ORF) of 96 amino acids in reverse orientation in Bloc B. The predicted protein shows sequence homology to the APG6 domain (Pfam ID: pfam04111, e-value: 2,2e-03) which has been described to be involved in autophagy and vascular sorting pathways in yeast . Because of the repeat structure of Bloc B, this homology is partially repeated two more times downstream of this ORF. These additional copies, however, lack start codons and therefore do not constitute intact ORFs. We assume that this ORF is the result of gene fragment capture but probably has no function. The fact that this gene fragment is part of the Mothra consensus sequence indicates that the gene capture event occurred before the radiation of the Mothra family.
The putative Mothra mother element lacks a RepHel gene
Polymorphisms between O. sativa and O. glaberrima demonstrate recent activity of Mothra elements
The eight polymorphic elements correspond to 5,4 % of subset of 148 manually investigated polymorphisms. Considering that we identified a total of 856 insertion/deletion polymorphisms between the two species, we extrapolate that a total of approximately 46 Mothra elements have moved since the two species diverged about 600,000 years ago . However, this number is based on approximately 60 % of the genome which was aligned. Thus, the actual number of transposed elements might be even higher. Compared to the previously investigated TIR transposons , we conclude that Mothra has a level of activity similar to that of highly active DTT-Mariner elements.
Phylogenetic analysis of the Mothra RPA homolog family
Our results show that most major eukaryotic clades cluster in monophyletic groups. We observe a clear grouping into plants, animals, fungi and Oomycetes. The phylogeny within these clades is consistent with the established taxonomy of eukaryotes . For example plant RPAs first split into algae, mosses and later into monocots and dicots (Fig. 5). Because of the robustness of the tree and the great concordance with the taxonomy, these proteins most probably represent the intrinsic, eukaryotic “core” RPAs.
Most clades have exactly one RPA gene but there are exceptions. Interestingly, one of the two copies obtained from the Alveolata, Cryptosporidium, also clusters at the root of the plant branch. However, the other copy we find, as expected, in the clade of Alveolates, which are even more distant to the core RPA clade than the PHRPA family. Furthermore, we found two RPA paralogs in the genomes of Physcomitrella, a Moss, and the green alga Chlorella, to form a monophyletic group on the same level as the PHRPAs. It is possible that there are contaminations since these organisms are difficult to isolate and cultivate.
Most importantly, we find the PHRPAs to form a separate, monophyletic group outside the core RPA clade. Thus, we conclude that the PHRPA ancestor protein has evolved very early in the transition from prokaryotes to eukaryotes. Interestingly, we only find representatives of mono- and dicotyledonous plants in the PHRPA clade. Moreover, PHRPAs are more diverse than core RPAs. Indeed, PHRPA proteins are on average 21 % identical to each other, while core RPAs show an average of 39 % sequence identity (Additional file 1: Figure S1). Also the branch lengths of the PHRPA clade are noticeable long. This suggests diversification of new, independent gene subfamilies. The possible reasons why these proteins are only found in monocots and dicots which diverged approximately 145–300 million years ago (mya) [32, 33] are discussed below (see discussion). Moreover, our analysis reveals that the RPA proteins acquired by Helentrons seem to be of another, even more distant origin. These proteins form a separate group which branches off before the radiation of eukaryotes (Fig. 5).
Mothras might use the RepHel protein of closely related Helitrons
Above, we describe that the putative mother element of the non-autonomous Mothras encoded an PHRPA protein but not for a RepHel protein. This raises the question of how these elements would actually transpose. As it has been described for non-autonomous elements, that they recruit closely related transposases, we suspect that RepHel from a closely related Helitron family would be used by Mothra elements. Therefore, we scanned the O. sativa genome for homologs of the PHRPA protein and extracted 21 fragments including 20 kb up- and downstream of the protein. Out of these we identified nine sequences with sizes from 8064 to 15,513 bp that all contain a PHRPA homolog and an adjacent RepHel gene.
Overview of all identified copies of the putatively autonomous elements of the Mothra sister-family in O. sativa and O. glaberrima
Mothra sister-family copies
The goal of our study was to characterize the origin and evolution of the high-copy Helitron family Mothra in rice. Although Helitrons are found in nearly all eukaryotic genomes they are much less well understood than other TE superfamilies. Despite their considerable role in exon shuffling and gene movement in plants [22–24], only few studies are available that shed light on their transposition mechanism. Initially, it was proposed that Helitrons replicate via a rolling-circle mechanism . However, this was challenged by the discovery of Helitron excisions in somatic maize tissue . Our data also suggest that some of the presence/absence polymorphism in rice might represent Helitron excisions. While Li and Dooner  mainly found repair patterns introducing TA micro-satellites as “filler” DNA, our putative excision events were also associated with deletions of the flanking sequences. These footprints strongly resemble those of TIR transposon excisions [27, 29, 34, 35]. Thus, these combined findings suggest the existence of at least one alternative transposition pathway to the proposed rolling-circle mechanism.
Despite these open questions, the main findings of our study provided insight into the evolution of different levels of non-autonomous elements and, more importantly, of the Helitron superfamily in plants in general. Our main conclusions are discussed in the following.
Sequence composition of non-autonomous Mothras elements might play a role in transposition efficiency
Non-autonomous transposons can create hundreds or even thousands of copies in only few generations . Loss of protein coding sequences and thereby autonomy has happened in all major Class II TE superfamilies. It can be explained by the fact that hosts regulate TEs via epigenetic silencing. Thus, constant reshaping, shortening and the accumulation of “nonsense” sequences might be mechanisms to avoid RNA silencing . Alternatively, the presence of an active functional copy might release selection pressure on other copies, allowing for non-autonomous derivatives to emerge. Still, non-autonomous elements retain the ability to cross-mobilize related transposases. This type of trans-acting system has best been described in detail for the TIR transposons of the DTT-Mariner superfamily . Transient expression experiments in yeast showed that the affinity for the autonomous element was determined by the TIR region. The efficiency of transposition, however, was influenced dramatically, positively or negatively, by different compositions of internal sequences.
We suspect that the great success of Mothra elements might have to do with their unusual sequence composition (see Fig. 1). The Blocs A and B of the non-autonomous element are unique to Mothra elements and their high conservation within the Mothra family suggests functional importance. When we screened the genomes of O. sativa and O. glaberrima for Mothra related polymorphisms (see above), we found that the majority of the differences were variations in the number of repeat units. Most likely these were caused by repeat slippage or unequal crossing-over for which the repeat arrays of Blocs A and B served as templates. Thus, these repeat arrays may be a sources of plasticity and permanent turnover within non-autonomous Mothra elements.
The Mothra RPA homolog likely originated from horizontal transfer
In our phylogenetic analysis of RPA proteins we found clear monophyletic clustering of the “core” RPAs in all major eukaryotic groups which broadly reflects the separation of early eukaryotes into distinct lineages (see Fig. 5). Interestingly, the clade representing the RPA homologs from plant Helitrons (PHRPAs) branches off even before the separation of plants, animals, fungi and Oomycetes, indicating a very ancient origin of these proteins. It is the more surprising that this clade only includes proteins from monocotyledonous and dicotyledonous plants which only separated approximately 145–300 mya [32, 33]. Previous studies proposed that plant Helitrons hijacked and modified the eukaryotic core RPA gene which later became the plant Helitron RPA [1, 38]. However, the clear monophyletic origin of PHRPAs outside the core RPA clade challenges this model.
In Prokaryotes (bacteria and archaea), horizontal gene transfer is common and and it is believed to be a major mechanism for adaptation . It becomes more and more evident that horizontal transfer is also a common process in eukaryotes. For example the extremophilic red alga Galdieria sulphuraria exhibits a enormous metabolic flexibility which it acquired by various genes from different bacteria and archaea . Like genes, also TEs (if they are not the vector for gene transfer themselves) can be transfered between hosts. Often this involves intermediate vectors such as blood feeding insects or pathogens carrying bacteria or viruses to their new hosts. For example in 24 species of the insect order Lepidoptera two non-autonomous Helitrons were identified which were also found in the genomes of several double-stranded DNA polydnaviruses . In plants, up to two million horizontal TE transfers only of LTR-retrotransposons were suggested by a comparative analysis among flowering plants .
However, what makes the case of PHRPA special is that the proposed horizontal transfer resulted in a successful new type of TE whose widespread distribution in monocots and dicots suggests advantages over normal Helitrons lacking this gene. Indeed, Dong et al.  described how stepwise acquisition of gene fragments can produce elements of increasing complexity.
Interestingly, our analysis also suggests that RPA homologs in Drosophila, called Helentrons, might also have been acquired though horizontal transfer. But the phylogenetic analysis indicates that they are of an even more distant origin. Furthermore, highly divergent RPA homologs were also found in Helitrons of zebrafish and starlet sea anemone . However, here we were not able to identify any homology to PHRPAs, which is why they were not included in our phylogenetic analysis. Thus, it appears that Helitrons acquired single-strand binding proteins at least three times independently during evolution, suggesting convergent evolution.
A model for the evolution of semi-autonomous and non-autonomous plant Helitrons
Our data suggest that the numerous non-autonomous Mothra elements are mobilized by a single mother element. Surprisingly, this putative mother element encodes for PHRPA but not for a RepHel protein. We speculate that the mother element might itself be depending on a related and fully autonomous element. Indeed, we found one candidate Helitron family that shows strong homology with the RPA protein and the termini of the Mothra mother element. We referred to that Helitron family as the Mothra sister-family.
According to our model, the next step in Mothra evolution was the loss of the PHRPA gene, resulting in a completely non-autonomous element that relies both on the Mothra mother element and functional copies of the Mothra sister-family (Fig. 8). Finally, the non-autonomous Mothra element acquired the complex tandem repeat blocs which, we propose, improved its transposition efficiency. This proposed stepwise evolution ultimately led to the situation we find in modern rice species where all three types of elements (fully autonomous, semi-autonomous and non-autonomous) exist side-by-side. However, biochemical assays will be needed to confirm the functional relationship between the described elements.
Analysis of the Mothra family of Helitrons has provided unexpected insight in to the early evolution of plant Helitrons through the identification of a putative horizontal gene transfer that resulted in a successful sub-group of the Helitron superfamily. Furthermore, the great success of the non-autonomous Mothra elements suggests that combinations of different levels of transposition autonomy might be particularly efficient in Helitrons.
To generate the Mothra consensus sequence, we extracted and aligned 100 putative copies including 5 kb of flanking sequence which we used to manually determine the boundaries of the element. The identified termini matched the previously described canonical Helitron termini . To deduce the consensus sequences for the sub-types and finally the consensus sequence of the non-autonomous Mothra element, we used the multiple alignment software Clustal X , the graphical dot-matrix program Dotter from the SeqTools package (https://www.sanger.ac.uk/resources/software/seqtools/) and in-house Perl scripts which are available upon request. To annotate Mothra elements we used the Mothra consensus sequence in Blastn searches against the O. sativa Nipponbare cultivar genome (Version 5) provided by the International Rice Genome Sequencing Project (IRGSP) (plantbiology.msu.edu/pub/data/) . We included hits with a minimum length of 80 basepairs and at least 80 % identity. Because we found many fragments, we merged all hits that were found within 200 bps of flanking sequence to single hits.
To identify the Mothra mother element we used Blastn searches of the first 50 and the last 80 bps of the Mothra consensus sequence. We considered fragments where we found both ends in the same orientation and that were located within 25 kb from each other. We used the online NCBI platform (http://blast.ncbi.nlm.nih.gov/Blast.cgi) to perform Blastn and Blastx searches against the 323 putative sequences to identify the RPA gene. To identify the polymorphisms between O. sativa and O. glaberrima we used the whole genome alignment produced in a previous study .
The sequences for the phylogenetic tree were retrieved from the NCBI database (http://www.ncbi.nlm.nih.gov/). We used the sequences of the identified Mothra RPA and the core RPA of O. sativa as queries and searched each of the main eukaryotic groups, animal, fungi, plants, Alveolata, Amoebae, Rhizaria, Oomycetes and archaea separately. We aligned them using Clustal X  with the following parameters for multiple alignments: Gap opening penalty of 10 and Gap extension penalty of 0.1. The phylogenetic tree was generated using MrBayes 3.2.2 . We conducted two runs with 4 chains, each for 4 million generations, sampling every 500 generations. We used all the protein models available in MrBayes and used a reversible jump Monte Carlo Markov Chain (MCMC) . Heterogeneity of substitution rates among different sites was modeled with a gamma distribution. The first quartile of generations was discarded (burn-in) and convergence was evaluated with the average standard deviation of split frequencies (0.002). To illustrate and re-root the tree we used the program Figtree (http://tree.bio.ed.ac.uk/software/figtree/).
Sequences of Mothra elements were deposited in the TREP database (http://www.botinst.uzh.ch/research/genetics/thomasWicker/TREP.html). Sequence alignments that were used for phylogenetic analyses as well as in-house Perl scripts are available upon request.
Terminal inverted repeat
Replication protein A
Open reading frame
Plant helitron replication protein A
Million years ago
This study was supported by the Swiss National Foundation grant # 31003A_138505/1.
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