Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor?

Horizontal transmission of functionally diverse transposons is a major source of new introns

Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.

Bioinformatic Annotation of Transposon DNA Processing Genes on the Long-Read Genome Assembly of Caenorhabditis elegans

Transposable elements (TEs) or transposons are thought to play roles in animal physiological processes, such as germline, early embryonic, and brain development, as well as aging. However, their roles have not been systematically investigated through experimental studies. In this study, we created a catalog of genes directly involved in replication, excision, or integration of transposon-coding DNA, which we refer to as transposon DNA processing genes (TDPGs). Specifically, to bridge the gap to experimental studies, we sought potentially functional TDPGs which maintain intact open reading frames and the amino acids at their catalytic cores on the latest long-read genome assembly of Caenorhabditis elegans, VC2010. Among 52 519 TE loci, we identified 145 potentially functional TDPGs encoded in long terminal repeat elements, long interspersed nuclear elements, terminal inverted repeat elements, Helitrons, and Mavericks/Polintons. Our TDPG catalog, which contains a feasible number of genes, allows for the experimental manipulation of TE mobility in vivo, regardless of whether the TEs are autonomous or non-autonomous, thereby potentially promoting the study of the physiological functions of TE mobility.

Annotation of transposable elements in the transcriptome of the Neotropical brown stink bug Euschistus heros and its chromosomal distribution

Transposable elements (TEs) are DNA sequences capable of moving within the genome. Their distribution is very dynamic among organisms, and despite advances, there are still gaps in the understanding of the diversity and evolution of TEs in many insect species. In the case of Euschistus heros, considered the main stink bug in the soybean crop in Brazil, little is known about the participation of these elements. Therefore, the objective of the current work was to identify the different groups of transposable elements present in the E. heros transcriptome, evidencing their chromosomal distribution. Through RNA-Seq and de novo assembly, 60,009 transcripts were obtained, which were annotated locally via Blastn against specific databases. Of the 367 transcripts identified as TEs, 202 belong to Class II, with emphasis on the TIR order. Among Class I elements or retrotransposons, most were characterized as LINE. Phylogenetic analyses were performed with the protein domains, evidencing differences between Tc1-mariner sequences, which may be related to possible horizontal transfer events. The transposable elements that stood out in the transcriptome were selected for fluorescent in situ hybridization. DNA transposon probes hAT, Helitron, and Tc1-mariner showed mostly scattered signals, with the presence of some blocks. Retrotransposon probes Copia, Gypsy, Jockey, and RTE showed a more pulverized hybridization pattern, with the presence of small interstitial and/or terminal blocks. Studies like this one, integrating functional genomics and molecular cytogenetic tools, are essential to expanding knowledge about transcriptionally active mobile elements, and their behavior in the chromosomes.

Clinical and Molecular Features of Anti-CENP-B Autoantibodies

Centromeric proteins are the foundation for assembling the kinetochore, a macromolecular complex that is essential for accurate chromosome segregation during mitosis. Anti-centromere antibodies (ACAs) are polyclonal autoantibodies targeting centromeric proteins (CENP-A, CENP-B, CENP-C), predominantly CENP-B, and are highly associated with rheumatologic disease (lcSSc/CREST syndrome). CENP-B autoantibodies have also been reported in cancer patients without symptoms of rheumatologic disease. The rise of oncoimmunotherapy stimulates inquiry into how and why anti-CENP-B autoantibodies are formed. In this review, we describe the clinical correlations between anti-CENP-B autoantibodies, rheumatologic disease, and cancer; the molecular features of CENP-B; possible explanations for autoantigenicity; and, finally, a possible mechanism for induction of autoantibody formation.

The IS630/Tc1/mariner transposons in three ctenophore genomes

Transposable elements (TEs) exert a significant effect on the structure and functioning of the genomes and also serve as a source of the new genes. The study of the TE diversity and evolution in different taxa is indispensable for the fundamental understanding of their roles in the genomes. IS630/Tc1/mariner (ITm) transposable elements represent the most prevalent and diverse group of DNA transposons. In this work, we studied the diversity, evolutionary dynamics and the phylogenetic relationships of the ITm transposons found in three ctenophore species: Mnemiopsis leidyi, Pleurobrachia bachei, Beroe ovata. We identified 29 ITm transposons, seven of which possess the terminal inverted repeats (TIRs) and an intact transposase, and, thus, are, presumably, active. Four other ITm transposons have the features of domesticated TEs. According to the results of the phylogenetic analysis, the ITm transposons of the ctenophores represent five groups - MLE/DD34D, TLE/DD34-38E, mosquito/DD37E, Visiror/DD41D and pogo/DDxD. Pogo/DDxD superfamily turnes out to be the most diverse and prevalent, since it accounts for more than 40% of the TEs identified. The data obtained in this research will fill the gap of knowledge of the diversity and evolution of the ITm transposons in the multicellular genomes and will lay the ground for the study of the TE effects on the evolution of the ctenophores.

Traveler, a New DD35E Family of Tc1/Mariner Transposons, Invaded Vertebrates Very Recently

The discovery of new members of the Tc1/mariner superfamily of transposons is expected based on the increasing availability of genome sequencing data. Here, we identified a new DD35E family termed Traveler (TR). Phylogenetic analyses of its DDE domain and full-length transposase showed that, although TR formed a monophyletic clade, it exhibited the highest sequence identity and closest phylogenetic relationship with DD34E/Tc1. This family displayed a very restricted taxonomic distribution in the animal kingdom and was only detected in ray-finned fish, anura, and squamata, including 91 vertebrate species. The structural organization of TRs was highly conserved across different classes of animals. Most intact TR transposons had a length of ∼1.5 kb (range 1,072-2,191 bp) and harbored a single open reading frame encoding a transposase of ∼340 aa (range 304-350 aa) flanked by two short-terminal inverted repeats (13-68 bp). Several conserved motifs, including two helix-turn-helix motifs, a GRPR motif, a nuclear localization sequence, and a DDE domain, were also identified in TR transposases. This study also demonstrated the presence of horizontal transfer events of TRs in vertebrates, whereas the average sequence identities and the evolutionary dynamics of TR elements across species and clusters strongly indicated that the TR family invaded the vertebrate lineage very recently and that some of these elements may be currently active, combining the intact TR copies in multiple lineages of vertebrates. These data will contribute to the understanding of the evolutionary history of Tc1/mariner transposons and that of their hosts.

GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals

Transposable elements represent the largest components of many eukaryotic genomes and different genomes harbor different combinations of elements. Here, we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla. Further searching for related sequences to the conserved DDE region uncovered the presence of this superfamily of elements in fish, coral, sea anemone, and other animal species. However, this element appears restricted to Bryophytes and Lycophytes in plants. This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100-150 bp terminal inverted repeats. Analysis of transposase sequences identified the DDE motif, a catalytic domain, which shows similarity to the integrase of Gypsy-like long terminal repeat retrotransposons, the most abundant component in plant genomes. A total of 77 intact and several hundred truncated copies of GingerRoot elements were identified in S. lepidophylla. Like Gypsy retrotransposons, GingerRoots show a lack of insertion preference near genes, which contrasts to the compact genome size of about 100 Mb. Nevertheless, a considerable portion of GingerRoot elements was found to carry gene fragments, suggesting the capacity of duplicating gene sequences is unlikely attributed to the proximity to genes. Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments, indicating they are preferentially retained in gene-poor regions. This study has identified a broadly dispersed, novel DNA transposon, and the first plant DNA transposon with an integrase-related transposase, suggesting the possibility of de novo formation of Gypsy-like elements in plants.

An Analysis of IS630/Tc1/mariner Transposons in the Genome of a Pacific Oyster, Crassostrea gigas

Transposable elements represent the DNA fragments capable of increasing their copy number and moving within the genome. Class II mobile elements represents the DNA transposons, which transpose via excision and the subsequent reinsertion at random genomic loci. The increase of their copy number occurs only when the transposition event is coupled with the replication. IS630/Tc1/mariner DNA transposon superfamily is one of the largest and widely distributed among the Class II elements. In this work, we provide a detailed analysis of IS630/Tc1/mariner DNA transposons from the Pacific oyster, Crassostrea gigas. IS630/Tc1/mariner transposons represented in the genome of the Pacific oyster belong to four families, Tc1 (DD34E), mariner (DD34D), pogo (DDxD), and rosa (DD41D). More than a half of IS630/Tc1/mariner elements from C. gigas belong to Tc1 family. Furthermore, Mariner-31_CGi element was shown to represent a new and previously unknown family with DD37E signature. We also discovered the full-size transcripts of eight elements from Tc1, mariner, and pogo families, three of which can, presumably, retain their transposition activity.

Ty3/Gypsy retrotransposons in the Pacific abalone Haliotis discus hannai: characterization and use for species identification in the genus Haliotis

Transposable elements are highly abundant elements that are present in all eukaryotic species. Here, we present a molecular description of abalone retrotransposon (Abret) elements. The genome of Haliotis discus hannai contains 130 Abret elements which were all Ty3/Gypsy retrotransposons. The Ty1/Copia elements were absent in the H. discus hannai genome. Most of the elements were not complete due to sequence truncation or coding region decay. However, three elements Abret-296, Abret-935, and Abret-3259 had most of the canonical features of LTR (long terminal repeat)-retrotransposons. There were several reading frame shifts in Abret-935 and Abret-3259 elements. Surprisingly, phylogenetic analysis indicated that all of the elements belonged to the Osvaldo lineage. The sequence divergence between LTRs revealed that the Abret elements were mostly active within 2 million years ago. Abret elements were used as molecular markers in SSAP analyses, which allowed clear distinction of different species in the genus Haliotis. The polymorphic markers were converted into SCAR markers for use in species identification by simple PCR in the Haliotis genus.

Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome

TC1/Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated "cut and paste" mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount of TC1/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1/Mariner (Bmmar) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of TC1/Mariner were grouped into five subgroups: Mariner, Tc1, maT, DD40D and DD41D/E. Of these five subgroups, maT rather than Mariner possessed most members of TC1/Mariner (51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that Bmmar15 (DD40D) formed a new basal subgroup of TC1/Mariner element in insects, which was referred to as bmori. Furthermore, we concluded that DD40D appeared to intermediate between mariner and Tc1. Finally, we estimated the insertion time for each copy of TC1/Mariner in the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed that Bmmar1, Bmmar6 and Bmmar9 had EST evidence and intact transposases. These implied that TC1/Mariner might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of TC1/Mariner in the insect genomes.

Characterization of autonomous families of Tc1/mariner transposons in neoteleost genomes

We report the comprehensive analysis of Tc1/mariner transposons in six species of neoteleost (cod, tetraodon, fugu, medaka, stickleback, and tilapia) for which draft sequences are available. In total, 33 Tc1/mariner families were identified in these neoteleost genomes, with 3-7 families in each species. Thirty of these are in full length and designed as autonomous families, and were classified into the DD34E (Tc1) and DD×D (pogo) groups. The DD34E (Tc1) group was further classified into five clusters (Passport-like, SB-like, Frog Prince-like, Minos-like, and Bari-like). Within the genomes of cod, tetraodon, fugu, and stickleback, the Tc1/mariner DNA transposons exhibit very low proliferation with <1% of genome. In contrast, medaka and tilapia display high accumulation of Tc1/mariner transposons with 2.91% and 5.09% of genome coverages, respectively. Divergence analysis revealed that most identified Tc1/mariner transposons have undergone one round of recent accumulation, followed by a decrease in activity. One family in stickleback (Tc1_6_Ga) exhibits a very recent and strong expansion, which suggests that this element is a very young invader and putatively active. The structural organization of these Tc1/mariner elements is also described. Generally, the Tc1/mariner transposons display a high diversity and varied abundance in the neoteleost genomes with current and recent activity.

Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian

A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans

Microsporidian genomes are the leading models to understand the streamlining in response to a pathogenic lifestyle; they are gene-poor and often possess small genomes. In this study, we show a feature of microsporidian genomes that contrasts this pattern of genome reduction. Specifically, genome investigations targeted at Anncaliia algerae, a human pathogen with a genome size of 23 Mb, revealed the presence of a hitherto undetected diversity in transposable elements (TEs). A total of 240 TE families per genome were identified, exceeding that found in many free-living fungi, and searches of microsporidian species revealed that these mobile elements represent a significant portion of their coding repertoire. Their phylogenetic analysis revealed that many cases of ancestry involve recent and bidirectional horizontal transfers with metazoans. The abundance and horizontal transfer origin of microsporidian TEs highlight a novel dimension of genome evolution in these intracellular pathogens, demonstrating that factors beyond reduction are at play in their diversification.

Chromosomal organization and evolutionary history of Mariner transposable elements in Scarabaeinae coleopterans

Background

With the aim to increase the knowledge on the evolution of coleopteran genomes, we investigated through cytogenetics and nucleotide sequence analysis Mariner transposons in three Scarabaeinae species (Coprophanaeus cyanescens, C. ensifer and Diabroctis mimas).

Results

The cytogenetic mapping revealed an accumulation of Mariner transposon in the pericentromeric repetitive regions characterized as rich in heterochromatin and C₀t-1 DNA fraction (DNA enriched with high and moderately repeated sequences). Nucleotide sequence analysis of Mariner revealed the presence of two major groups of Mariner copies in the three investigated coleoptera species.

Conclusions

The Mariner is accumulated in the centromeric area of the coleopteran chromosomes probably as a consequence of the absence of recombination in the heterochromatic regions. Our analysis detected high diversification of Mariner sequences during the evolutionary history of the group. Furthermore, comparisons between the coleopterans sequences with other insects and mammals, suggest that the horizontal transfer (HT) could have acted in the spreading of the Mariner in diverse non-related animal groups.

Tana1, a new putatively active Tc1-like transposable element in the genome of sturgeons

We report the discovery of a new putatively active Tc1-like transposable element (Tana1) in the genome of sturgeons, an ancient group of fish considered as living fossils. The complete sequence of Tana1 was first characterized in the 454-sequenced transcriptome of the Adriatic sturgeon (Acipenser naccarii) and then isolated from the genome of the same species and from 12 additional sturgeons including three genera of the Acipenseridae (Acipenser, Huso, Scaphirhynchus). The element has a total length of 1588bp and presents inverted repeats of 210bp, one of which partially overlapping the 3' region of the transposase gene. The spacing of the DDE motif within the catalytic domain in Tana1 is unique (DD38E) and indicates that Tana1 can be considered as the first representative of a new Tc1 subfamily. The integrity of the native form (with no premature termination codons within the transposase), the presence of all expected functional domains and its occurrence in the sturgeon transcriptome suggest a current or recent activity of Tana1. The presence of Tana1 in the genome of the 13 sturgeon species in our study points to an ancient origin of the element that existed before the split of the group 170 million years ago. The dissemination of Tana1 across sturgeon genomes could be interpreted by postulating vertical transmission from an ancestral Tana1 with a particularly slow evolutionary rate Horizontal transmission might have also played a role in the dissemination of Tana1 as evidenced by the presence of a complete copy in the genome of Atlantic salmon. Vertical and horizontal transmission are not mutually exclusive and may have concurred in shaping the evolution of Tana1.

Structural analysis of a 4414-bp element in Drosophila melanogaster

We cloned a 4414-bp element from a mutant of Drosophila melanogaster. Its insertion site was 18,929,626 bp. Analysis of the nucleotide and amino acid sequences demonstrated that the element is homologous to Pifo_I, first obtained from D. yabuka, which belongs to the gypsy/Ty3 subfamily. We also obtained a 3754-bp length element from a wild-type fly by PCR, with a pair of primers designed from the conserved region of the 4414-bp length element. The two elements included a pair of long terminal repeats and part of the GAG and ENV proteins, but the POL protein was completely lost. This element is found in the subgenus of D. melanogaster, but it is a degenerate type of Pifo_I and is not infective. Also, a 714-bp region structured in 5.0 tandem repeats of 143 bp each was found in the 5'UTR of the degenerate element; these could interact with transcription factor CF2. Phylogenetic analysis and alignment of amino acids indicated that the Pifo_I element was closer to the ZAM retrotransposon, which gave us some clues to their functional similarity. Based on these data, we propose that there is a relationship between the degenerate element and the mutant phenotype, which would provide a foundation for further research.

Normal and defective mariner-like elements in Rhynchosciara species (Sciaridae, Diptera)

Mariner-like elements are widely present in diverse organisms. These elements constitute a large fraction of the eukaryotic genome; they transpose by a "cut-and-paste" mechanism with their own transposase protein. We found two groups of mobile elements in the genus Rhynchosciara. PCR using primers designed from R. americana transposons (Ramar1 and Ramar2) were the starting point for this comparative study. Genomic DNA templates of four species: R. hollaenderi, R. millerii, R. baschanti, and Rhynchosciara sp were used and genomic sequences were amplified, sequenced and the molecular structures of the elements characterized as being putative mariner-like elements. The first group included the putative full-length elements. The second group was composed of defective mariner elements that contain a deletion overlapping most of the internal region of the transposase open reading frame. They were named Rmar1 (type 1) and Rmar2 (type 2), respectively. Many conserved amino acid blocks were identified, as well as a specific D,D(34)D signature motif that was defective in some elements. Based on predicted transposase sequences, these elements encode truncated proteins and are phylogenetically very close to mariner-like elements of the mauritiana subfamily. The inverted terminal repeat sequences that flanked the mariner-like elements are responsible for their mobility. These inverted terminal repeat sequences were identified by inverse PCR.

Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

Background

In eukaryotes, long terminal repeat (LTR) retrotransposons such as Copia, BEL and Gypsy integrate their DNA copies into the host genome using a particular type of DDE transposase called integrase (INT). The Gypsy INT-like transposase is also conserved in the Polinton/Maverick self-synthesizing DNA transposons and in the 'cut and paste' DNA transposons known as TDD-4 and TDD-5. Moreover, it is known that INT is similar to bacterial transposases that belong to the IS3, IS481, IS30 and IS630 families. It has been suggested that LTR retrotransposons evolved from a non-LTR retrotransposon fused with a DNA transposon in early eukaryotes. In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons.

Results

A new diverse eukaryotic superfamily of DNA transposons, named Ginger (for 'Gypsy INteGrasE Related') DNA transposons is defined and analyzed. Analogously to the IS3 and IS481 bacterial transposons, the Ginger termini resemble those of the Gypsy LTR retrotransposons. Currently, Ginger transposons can be divided into two distinct groups named Ginger1 and Ginger2/Tdd. Elements from the Ginger1 group are characterized by approximately 40 to 270 base pair (bp) terminal inverted repeats (TIRs), and are flanked by CCGG-specific or CCGT-specific target site duplication (TSD) sequences. The Ginger1-encoded transposases contain an approximate 400 amino acid N-terminal portion sharing high amino acid identity to the entire Gypsy-encoded integrases, including the YPYY motif, zinc finger, DDE domain, and, importantly, the GPY/F motif, a hallmark of Gypsy and endogenous retrovirus (ERV) integrases. Ginger1 transposases also contain additional C-terminal domains: ovarian tumor (OTU)-like protease domain or Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from the Gypsy integrases, apparently have evolved from the Ginger1 transposase genes. We also introduce a second Ginger group, designated Ginger2/Tdd, which includes the previously reported DNA transposon TDD-4.

Conclusions

The Ginger superfamily represents eukaryotic DNA transposons closely related to LTR retrotransposons. Ginger elements provide new insights into the evolution of transposable elements and certain transposable element (TE)-derived genes.

Lens epithelium-derived growth factor/p75 interacts with the transposase-derived DDE domain of PogZ

Lens epithelium-derived growth factor/p75 (LEDGF/p75) is a prominent cellular interaction partner of human immunodeficiency virus-1 (HIV-1) integrase, tethering the preintegration complex to the host chromosome. In light of the development of LEDGF/p75-integrase interaction inhibitors, it is essential to understand the cell biology of LEDGF/p75. We identified pogZ as new cellular interaction partner of LEDGF/p75. Analogous to lentiviral integrase, pogZ, a domesticated transposase, carries a DDE domain, the major determinant for LEDGF/p75 interaction. Using different in vitro and in vivo approaches, we corroborated the interaction between the C terminus of LEDGF/p75 and the DDE domain of pogZ, revealing an overlap in the binding of pogZ and HIV-1 integrase. Competition experiments showed that integrase is efficient in displacing pogZ from LEDGF/p75. Moreover, pogZ does not seem to play a role as a restriction factor of HIV. The finding that LEDGF/p75 is capable of interacting with a DDE domain protein that is not a lentiviral integrase points to a profound role of LEDGF/p75 in DDE domain protein function.

Two novel elements (CFG1 and PYG1) of Mag lineage of Ty3/Gypsy retrotransposons from Zhikong scallop (Chlamys farreri) and Japanese scallop (Patinopecten yessoensis)

Two novel elements (CFG1 and PYG1) of Mag lineage of Ty3/Gypsy retrotransposons were cloned from Zhikong scallop (Chlamys farreri) and Japanese scallop (Patinopecten yessoensis). The total length of the CFG1 element is 4826 bp, including 5'-LTR (192 bp), the entire ORF (4047 bp) and 3'-LTR (189 bp). The entire ORFs of both CFG1 and PYG1 elements are composed of 1348 aa and do not have any frameshifts. Their closest relative is Jule element from the poeciliid fish (Xiphophorus maculatus). On average, the diploid genome of C. farreri contains approximately 84 copies of CFG1 elements. We summarize the major features of CFG1, PYG1 and other elements of Mag lineage of the Ty3/Gypsy group. mRNA expression of CFG1 element in larvae increases gradually before the gastrulae stage and decreases gradually afterward, whereas in adductor such expression in adductor muscle and digestive gland are lower than those in other tissues. Overall, mRNA expression of CFG1 element in the early larvae is significantly higher than that in adult tissues. In muscle tissue, while the promoter and partial GAG domain of CFG1 element are unmethylated, the partial RT domain is highly methylated. These results suggest that CFG1 expression may be controlled by a post-transcriptional gene silencing mechanism that is associated with coding-region (RT domain) methylation.

Characterization of EamaT1, a member of maT family of transposable elements from the earthworm Eisenia andrei (Annelida, Oligochaeta)

The maT family is a unique clade within the Tc1-mariner superfamily, and their distribution is to date known as being limited to invertebrates. A novel transposon named EamaT1 is described from the genome of the earthworm Eisenia andrei. The full sized EamaT1 was obtained by degenerate and inverse PCR-based amplification. Sequence analysis of multiple copies of the EamaT1, which consisted of 0.9 and 1.4 kb elements, showed that the consensual EamaT1 with inverted terminal repeats (ITRs) of 69 bp was 1,422 bp long and flanked by a duplicated TA dinucleotide. The EamaT1 is present in approximately 120-250 copies per diploid genome but undergoes an inactivation process as a result of accumulating multiple mutations and is nonfunctional. The open reading frame (ORF) of the EamaT1 consensus encoding 356 amino acid sequences of transposase contained a DD37D signature and a conserved paired-like DNA binding motif for the transposition mechanism. The result of ITRs comparison confirmed their consensus terminal sequences (5'-CAGGGTG-3') and AT-rich region on the internal bases for ITRs-transposase interaction.

Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses

We previously identified a group of atypical mobile elements designated Mavericks from the nematodes Caenorhabditis elegans and C. briggsae and the zebrafish Danio rerio. Here we present the results of comprehensive database searches of the genome sequences available, which reveal that Mavericks are widespread in invertebrates and non-mammalian vertebrates but show a patchy distribution in non-animal species, being present in the fungi Glomus intraradices and Phakopsora pachyrhizi and in several single-celled eukaryotes such as the ciliate Tetrahymena thermophila, the stramenopile Phytophthora infestans and the trichomonad Trichomonas vaginalis, but not detectable in plants. This distribution, together with comparative and phylogenetic analyses of Maverick-encoded proteins, is suggestive of an ancient origin of these elements in eukaryotes followed by lineage-specific losses and/or recurrent episodes of horizontal transmission. In addition, we report that Maverick elements have amplified recently to high copy numbers in T. vaginalis where they now occupy as much as 30% of the genome. Sequence analysis confirms that most Mavericks encode a retroviral-like integrase, but lack other open reading frames typically found in retroelements. Nevertheless, the length and conservation of the target site duplication created upon Maverick insertion (5- or 6-bp) is consistent with a role of the integrase-like protein in the integration of a double-stranded DNA transposition intermediate. Mavericks also display long terminal-inverted repeats but do not contain ORFs similar to proteins encoded by DNA transposons. Instead, Mavericks encode a conserved set of 5 to 9 genes (in addition to the integrase) that are predicted to encode proteins with homology to replication and packaging proteins of some bacteriophages and diverse eukaryotic double-stranded DNA viruses, including a DNA polymerase B homolog and putative capsid proteins. Based on these and other structural similarities, we speculate that Mavericks represent an evolutionary missing link between seemingly disparate invasive DNA elements that include bacteriophages, adenoviruses and eukaryotic linear plasmids.

Molecular characterization and genomic distribution of Isis: a new retrotransposon of Drosophila buzzatii

A new transposable element, Isis, is identified as a LTR retrotransposon in Drosophila buzzatii. DNA sequence analysis shows that Isis contains three long ORFs similar to gag, pol and env genes of retroviruses. The ORF1 exhibits sequence homology to matrix, capsid and nucleocapsid gag proteins and ORF2 encodes a putative protease (PR), a reverse transcriptase (RT), an Rnase H (RH) and an integrase (IN) region. The analysis of a putative env product, encoded by the env ORF3, shows a degenerated protein containing several stop codons. The molecular study of the putative proteins coded by this new element shows striking similarities to both Ulysses and Osvaldo elements, two LTR retrotransposons, present in D. virilis and D. buzzatii, respectively. Comparisons of the predicted Isis RT to several known retrotransposons show strong phylogenetic relationships to gypsy-like elements, particulary to Ulysses retrotransposon. Studies of Isis chromosomal distribution show a strong hybridization signal in centromeric and pericentromeric regions, and a scattered distribution along all chromosomal arms. The existence of insertional polymorphisms between different strains and high molecular weight bands by Southern blot suggests the existence of full-sized copies that have been active recently. The presence of euchromatic insertion sites coincident between Isis and Osvaldo could indicate preferential insertion sites of Osvaldo element into Isis sequence or vice versa. Moreover, the presence of Isis in different species of the buzzatii complex indicates the ancient origin of this element.

The ancient Virus World and evolution of cells

Background

Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.

Results

Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms. On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool. In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution. We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene. Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle. The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes. Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.

Conclusion

The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes that went uninterrupted from the precellular stage of life's evolution to this day. This concept is tightly linked to two key conjectures on evolution of cells: existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes, and origin of the eukaryotic cell by archaeo-bacterial fusion. The virus world concept and these models of major transitions in the evolution of cells provide complementary pieces of an emerging coherent picture of life's history.

Reviewers

W. Ford Doolittle, J. Peter Gogarten, and Arcady Mushegian.

Transfer RNA gene-targeted integration: an adaptation of retrotransposable elements to survive in the compact Dictyostelium discoideum genome

Almost every organism carries along a multitude of molecular parasites known as transposable elements (TEs). TEs influence their host genomes in many ways by expanding genome size and complexity, rearranging genomic DNA, mutagenizing host genes, and altering transcription levels of nearby genes. The eukaryotic microorganism Dictyostelium discoideum is attractive for the study of fundamental biological phenomena such as intercellular communication, formation of multicellularity, cell differentiation, and morphogenesis. D. discoideum has a highly compacted, haploid genome with less than 1 kb of genomic DNA separating coding regions. Nevertheless, the D. discoideum genome is loaded with 10% of TEs that managed to settle and survive in this inhospitable environment. In depth analysis of D. discoideum genome project data has provided intriguing insights into the evolutionary challenges that mobile elements face when they invade compact genomes. Two different mechanisms are used by D. discoideum TEs to avoid disruption of host genes upon retrotransposition. Several TEs have invented the specific targeting of tRNA gene-flanking regions as a means to avoid integration into coding regions. These elements have been dispersed on all chromosomes, closely following the distribution of tRNA genes. By contrast, TEs that lack bona fide integration specificities show a strong bias to nested integration, thus forming large TE clusters at certain chromosomal loci that are hardly resolved by bioinformatics approaches. We summarize our current view of D. discoideum TEs and present new data from the analysis of the complete sequences of D. discoideum chromosomes 1 and 2, which comprise more than one third of the total genome.

DIRS-1 and the other tyrosine recombinase retrotransposons

DIRS-1 is a retroelement from the slime mold Dictyostelium discoideum. Until recently only two related retrotransposons had been described: PAT from the nematode Panagrellus redivivus and Prt1 from the zygomycete fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these three elements suggested that they were closely related to each other and more distantly related to the Ty3/gypsy Long Terminal Repeat (LTR) retroelements. They have several unusual structural features that distinguish them from typical LTR elements. For instance, they each encode a tyrosine recombinase (YR), but not a DDE-type integrase or an aspartic protease. Although the DIRS-1-related elements are bordered by terminal repeats these differ from typical LTRs in a number of ways. In DIRS-1, for example, the terminal repeats are inverted (complementary), non-identical in sequence, and the outer edges of the terminal sequences are repeated (adjacent to each other) in the internal region. PAT has so-called "split" direct repeats in which the unrelated terminal sequences appear as direct repeats adjacent to each other in the internal region. The only repetition displayed by Prt1 is the presence of short inverted terminal repeats, but the sequenced copy of this element is believed to be a truncated version of an element with a structure resembling DIRS-1. The unusual structure of the terminal repeats of the DIRS1-like elements appears to be related to their replication via free circular intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. In recognition of these important distinctions it is proposed that the retrotransposons that encode tyrosine recombinases be called the tyrosine recombinase (or YR) retrotransposons. Recently a large number of additional YR retrotransposons have been described, including elements from fungi (zygomycetes and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish and amphibia, while remnants of elements related to DIRS-1 occur in the human genome. The complete set of YR retrotransposons can be divided into two major groups, the DIRS elements and the Ngaro elements, the two groups forming distinct clades on phylogenetic trees based on alignments of RT/RH and recombinase sequences, and also having some structural distinctions. A third group of transposable elements, which we call Cryptons, also carry tyrosine recombinases. These elements do not encode a reverse transcriptase and so are believed to be DNA transposons not retrotransposons. They have been detected in several pathogenic fungi, including the basidiomycete Cryptococcus neoformans, and the ascomycetes Coccidioides posadasii and Histoplasma capsulatum. Sequence comparisons suggest that the Crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a Crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon.

The Caenorhabditis briggsae genome contains active CbmaT1 and Tcb1 transposons

The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and Tc transposons, with a distribution thus far limited to a few invertebrate species. We present evidence, based on searches of publicly available databases, that the nematode Caenorhabditis briggsae has several maT-like transposons, which we have designated as CbmaT elements, dispersed throughout its genome. We also describe two additional transposon sequences that probably share their evolutionary history with the CbmaT transposons. One resembles a fold back variant of a CbmaT element, with long (380-bp) inverted terminal repeats (ITRs) that show a high degree (71%) of identity to CbmaT1. The other, which shares only the 26-bp ITR sequences with one of the CbmaT variants, is present in eight nearly identical copies, but does not have a transposase gene and may therefore be cross mobilised by a CbmaT transposase. Using PCR-based mobility assays, we show that CbmaT1 transposons are capable of excising from the C. briggsae genome. CbmaT1 excised approximately 500 times less frequently than Tcb1 in the reference strain AF16, but both CbmaT1 and Tcb1 excised at extremely high frequencies in the HK105 strain. The HK105 strain also exhibited a high frequency of spontaneous induction of unc-22 mutants, suggesting that it may be a mutator strain of C. briggsae.

Medfly transposable elements: diversity, evolution, genomic impact and possible applications

The medfly genome has been shown to contain a rich assortment of transposable elements from the mariner, Tc1, hAT and gypsy/Ty3 families. These elements display different levels of diversity, abundance and distribution in the genome. The presence of actively transposing elements in the medfly genome is revealed by hybrid dysgenesis phenomena, insertion site polymorphisms and other genetic instabilities. The medfly has been a target of transformation studies involving the exogenous elements Minos, Hermes and piggyBac from three families. The presence of active endogenous homologous elements can have important implications for the stability of such transgenic lines. The potential applications of endogenous elements for medfly population analysis and control are discussed.

Cloning of shark RAG2 and characterization of the RAG1/RAG2 gene locus

The recombination-activating genes (RAG) encode a site-specific recombinase that is centrally responsible for the rearrangement of genomic V(D)J exons necessary to form functional immunoglobulin and T-cell receptor genes. To help elucidate the origins of the RAG genes, we have cloned the RAG2 gene from the sandbar shark (Carcharhinus plumbeus) and characterized the entire RAG1/RAG2 gene locus. The shark RAG2 protein consists of 520 amino acids, is approximately 50% identical with RAG2 proteins from other vertebrates, and contains the same three domains identified in mammalian RAG2. Residues critical for RAG2 function are conserved in the shark sequence. In common with other vertebrate species, the shark RAG2 coding region lacks introns and is closely linked in opposite orientation to the RAG1 gene. The intergenic region is 9.4 kb, which is considerably larger than of teleosts (2-3 kb) and is comparable to that of tetrapods. This length is partially explained by the presence of several SINE and LINE fragments. The ancestors of the sharks were apparently the first vertebrates in phylogeny to have RAG genes, and our results confirm that the RAG genes have been highly conserved during evolution both in terms of sequence and gene organization.

maT--a clade of transposons intermediate between mariner and Tc1

A group of transposons, named maT, with characteristics intermediate between mariner and Tc1 transposons, is described. Two defective genomic copies of MdmaT from the housefly Musca domestica, with 85% identity, were found flanking and imbedded in the MdalphaE7 esterase gene involved in organophosphate insecticide resistance. Two cDNA clones, with 99% identity to each other and 72%-89% identity to the genomic copies were also obtained, but both represented truncated versions of the putative open reading frame. A third incomplete genomic copy of MdmaT was also identified upstream of the putative M. domestica period gene. The MdmaT sequences showed high identity to the transposable element Bmmar1 from the silkworm moth, Bombyx mori, and to previously unidentified sequences in the genome of Caenorhabditis elegans. A total of 16 copies of full-length maT sequences were identified in the C. elegans genome, representing three variants of the transposon, with 34%-100% identity amongst them. Twelve of the copies, named CemaT1, were virtually identical, with eight of them encoding a putative full length, intact transposase. Secondary structure predictions and phylogenetic analyses confirm that maT elements belong to the mariner-Tc1 superfamily of transposons, but their intermediate sequence and predicted structural characteristics suggest that they belong to a unique clade, distinct from either mariner-like or Tc1-like elements.

A novel family of mobile genetic elements is limited to the germline genome in Tetrahymena thermophila

In the ciliated protozoan Tetrahymena thermophila, extensive DNA elimination is associated with differentiation of the somatic macronucleus from the germline micronucleus. This study describes the isolation and complete characterization of Tlr elements, a family of approximately 30 micronuclear DNA sequences that are efficiently eliminated from the developing macronucleus. The data indicate that Tlr elements are comprised of an approximately 22 kb internal region flanked by complex and variable termini. The Tlr internal region is highly conserved among family members and contains 15 open reading frames, some of which resemble genes encoded by transposons and viruses. The Tlr termini appear to be long inverted repeats consisting of (i) a variable region containing multiple direct repeats which differ in number and sequence from element to element and (ii) a conserved terminal 47 bp sequence. Taken together, these results suggest that Tlr elements comprise a novel family of mobile genetic elements that are confined to the Tetrahymena germline genome. Possible mechanisms of developmentally programmed Tlr elimination are discussed.

Phylogenetic analysis reveals stowaway-like elements may represent a fourth family of the IS630-Tc1-mariner superfamily

The genomes of plants, like virtually all other eukaryotic organisms, harbor a diverse array of mobile elements, or transposons. In terms of numbers, the predominant type of transposons in many plants is the miniature inverted-repeat transposable element (MITE). There are three archetypal MITEs, known as Tourist, Stowaway, and Emigrant, each of which can be defined by a specific terminal inverted-repeat (TIR) sequence signature. Although their presence was known for over a decade, only recently have open reading frames (ORFs) been identified that correspond to putative transposases for each of the archetypes. We have identified two Stowaway elements that encode a putative transposase and are similar to members of the previously characterized IS630-Tc1-mariner superfamily. In this report, we provide a high-resolution phylogenetic analysis of the evolutionary relationship between Stowaway, Emigrant, and members of the IS630-Tc1-mariner superfamily. We show that although Emigrant is closely related to the pogo-like family of elements, Stowaway may represent a novel family. Integration of our results with previously published data leads to the conclusion that the three main types of MITEs have different evolutionary histories despite similarity in structure.

Intra- and inter-specific diversity of Tc3-like transposons in nematodes and insects and implications for their evolution and transposition

Tc3 of Caenorhabditis elegans is one of the founding members of the Tc1 family which includes DNA transposons in vertebrates, insects, nematodes and fungi. It is one of the best characterized eukaryotic transposons in terms of structure and transposition mechanism. A Tc3-like transposon MsqTc3 has been recently described in a mosquito. Here we present the characterization of a number of Tc3-like transposons in C. elegans, Caenorhabditis briggsae, and Drosophila melanogaster, which has revealed high levels of inter- and intra-specific diversity and further suggests a broad distribution of the Tc3-like transposons. These newly defined transposons and the previously described Tc3 and MsqTc3 form a highly divergent yet distinct clade in the Tc1 family. The above phylogenetic analysis of the Tc3-like transposons and their high levels of intra-specific diversity underscore interesting questions of their evolutionary dynamics in their respective hosts. The majority of the Tc3-like transposons contain two putative binding sites for their transposases. The first is near the terminus and the second is approximately 164-184 bp from the first site. Comparative analysis suggests that the second binding site may have been maintained for an important function in vivo. There is a large amount of variation in the length (27-566 bp) and structure of the terminal inverted repeats (TIRs) of Tc3-like transposons. Long (318-566 bp) TIRs that extend significantly beyond the second binding site are only found in the first described Tc3 and its close relatives, whose transposases form a recently derived clade among the Tc3-like transposons. Thus, these unique TIRs may have evolved recently together with their corresponding transposases.

The DIRS1 group of retrotransposons

Only three retrotransposons of the DIRS1 group have previously been described: DIRS1 from the slime mold Dictyostelium discoideum, PAT from the nematode Panagrellus redivivus, and Prt1 from the zygomycetous fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these elements suggest that they are related to the long terminal repeat (LTR) retroelements, such as the Ty3/gypsy retrotransposons and the vertebrate retroviruses. The DIRS1-group elements, however, have several unusual structural features which distinguish them from typical LTR elements: (1) they lack the capacity to encode DDE-type integrases or aspartic proteases; (2) they have open reading frames (ORFs) of unknown function; (3) they integrate without creating duplications of their target sites; and (4) although they are bordered by terminal repeats, these sequences differ from typical LTRs in that they are either inverted repeats or "split" direct repeats. Because of the small number of DIRS1-like elements described, and the unusual structures of these elements, little is known about their evolution, distribution, and replication mechanisms. Here, we report the identification of several new DIRS1-like retrotransposons, including elements from nematodes, sea urchins, fish, and amphibia. We also present evidence for the existence of DIRS1-like sequences in the human genome. In addition, we show that the lack of DDE-type integrase genes from elements of the DIRS1 group is explained by the finding that the previously uncharacterized ORFs of these elements encode proteins related to the site-specific recombinase of bacteriophage lambda. The presence of lambda-recombinase-like genes in DIRS1 elements also accounts for the lack of target-site duplications for these elements and may be related to the unusual structures of their terminal repeats.

Expanding the diversity of the IS630-Tc1-mariner superfamily: discovery of a unique DD37E transposon and reclassification of the DD37D and DD39D transposons

A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

MsqTc3, a Tc3-like transposon in the yellow fever mosquito Aedes aegypti

A novel transposon, MsqTc3-Aa, has been discovered in the yellow fever mosquito, Aedes aegypti. Evidence of its past mobility is presented. There are approximately 100 copies of MsqTc3-Aa in A. aegypti, eight of which have been isolated and sequenced. All sequenced copies are more than 99% identical to their consensus, indicating recent mobilization. The MsqTc3-Aa consensus contains imperfect terminal inverted repeats (TIRs) and an open reading frame (ORF) interrupted by an intron. Sequence, structural and phylogenetic analysis showed that MsqTc3-Aa is a distant relative of Tc3, an active transposon in Caenorhabditis elegans. These results may provide useful information for the current effort to control mosquito-borne diseases using genetic approaches.

Tc8, a Tourist-like transposon in Caenorhabditis elegans

Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.

Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses

We have conducted a phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposons. Analysis of this simple yet highly conserved enzymatic domain from these disparate sources provides surprising insights into the evolution of eukaryotic retrotransposons. First, it indicates that the lineage of elements leading to vertebrate retroviruses acquired a new RNH domain either from non-LTR retrotransposons or from a eukaryotic host genome. The preexisting retroviral RNH domain degenerated to become the tether (connection) domain of the reverse transcriptase (RT)-RNH complex. Second, it indicates that all LTR retrotransposons arose in eukaryotes well after the origin of the non-LTR retrotransposons. Because of the younger age of the LTR retrotransposons, their complex structure, and the absence of any prokaryotic precursors, we propose that the LTR retrotransposons originated as a fusion between a DNA-mediated transposon and a non-LTR retrotransposon. The resulting two-step mechanism of LTR retrotransposition, in which RNA is reverse transcribed away from the chromosomal target site, rather than directly onto the target site, was probably an adaptation to the uncoupling of transcription and translation in eukaryotic cells.

Organization and distribution pattern of MGLR-3, a novel retrotransposon in the rice blast fungus Magnaporthe grisea

A specific telomere was deleted in spontaneous, gain-of-virulence mutants derived from a rice pathogen of Magnaporthe grisea. Three different types of transposons, including Pot2, Mg-SINE, and a novel, 6-kb-long LTR (long terminal repeat)-type retrotransposon designated MGLR-3, were identified on this chromosomal end. The 114-bp-long telomeric repeat is immediately followed by the 3' LTR of MGLR-3. A truncated copy of Pot2 immediately flanks the 5' LTR, suggesting that this telomere was generated by a transposition event of MGLR-3 into this Pot2 element, causing the breakage of a chromosome. The subsequent addition of a telomeric repeat to the 3' LTR of MGLR-3 most probably repaired the broken end of the chromosome. Mg-SINE is located 25 bp away from the truncated Pot2 element. MGLR-3 exhibited strong homology to various gypsy-class retrotransposons, including grh and MAGGY in M. grisea. MGLR-3 is ubiquitous regardless of the host of origin.

Tca5, a Ty5-like retrotransposon from Candida albicans

This report describes the identification and characterization of a retrotransposon, termed Tca5, from the pathogenic yeast Candida albicans. Tca5 has identical 685 bp LTRs flanking 4218 bp of internal sequence within which lies a single long ORF. Immediately internal to the left LTR is a primer binding site complementary to an internal portion of the initiator methionine tRNA and upstream of the right LTR is a polypurine tract. The ORF predicts a protein containing all the conserved motifs characteristic of Gag, protease, integrase, reverse transcriptase and RNaseH. Genomic Southern blots probed with Tca5 sequences show that it is a low copy number element and is present at different loci in different strains. This, together with the apparently intact structure of Tca5, suggests that it has transposed very recently. Potentially full-length Tca5 transcripts were detected in some strains raising the possibility that some copies of Tca5 may still be active. Phylogenetic analyses and other sequence comparisons suggest that Tca5 is most closely related to the Ty5 element of Saccharomyces cerevisiae and S. paradoxus. The nucleotide sequence of Tca5 has been submitted to GenBank under Accession No. AF093417.