Tc8, a Tourist-like Transposon in Caenorhabditis elegans

Corresponding author: Thomas Bureau, Department of Biology, McGill University, 1205 Ave. Docteur Penfield, Montreal, QC H3A 1B1, Canada., thomas_bureau{at}maclan.mcgill.ca (E-mail)

Communicating editor: P. ANDERSON

	ABSTRACT

TOP ABSTRACT MATERIALS AND METHODS RESULTS AND DISCUSSION LITERATURE CITED

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.

TRANSPOSONS are mobile genetic elements found in most, if not all, prokaryotic and eukaryotic genomes. Typically, transposons are defined as either class I, members of which move via an RNA intermediate (e.g., retrotransposons), or class II, members of which move directly as DNA (e.g., Tc1/mariner, Ac/Ds, En/Spm; BERG and HOWE 1989 ). Miniature inverted-repeat transposable elements (MITEs) are transposons found in abundance among a wide variety of plant genomes. They are typically short (100–500 bp), with conserved terminal inverted repeats (TIRs), have a potential to form a stable DNA secondary structure (i.e., a hairpin structure), and generate a 2- or 3-bp target site duplication (TSD) upon integration. Based on their TSD size and sequence, MITEs can primarily be divided into Tourist-like (5'-TAA-3') and Stowaway-like (5'-TA-3') families of elements (BUREAU and WESSLER 1992 , BUREAU and WESSLER 1994B ). MITEs are usually found in intimate association with genes and occasionally contributing cis-regulatory sequences (BUREAU and WESSLER 1994A , BUREAU and WESSLER 1994B ). For these reasons, they are thought to play an important role in the evolution of plant genomes (WESSLER et al. 1995 ). Although ubiquitous in plants, there are only few reported MITEs from other eukaryotes such as fungi, insects, Caenorhabditis elegans, Xenopus, teleost fish, and humans (OOSUMI et al. 1995 ; UNSAL and MORGAN 1995 ; YEADON and CATCHESIDE 1995 ; BESANSKY et al. 1996 ; SMIT and RIGGS 1996 ; TU 1997 ; IZSVAK et al. 1999 ; FESCHOTTE and MOUCHES 2000 ). However, many of these MITEs are structurally similar to Tc1/mariner-like elements, though members with open reading frames (ORFs) are typically not available. The reason behind this difference in MITE abundance between plants and other organisms, and how this difference impacts host genome evolution, is not clear.

Since MITEs with coding capacity were previously unknown, the mechanism underlying their transposition remained elusive. Structurally, MITEs are reminiscent of nonautonomous deletion derivatives of class II transposons, presumably mobilized in trans by a transposase from a related autonomous element located elsewhere in the genome. Recently however, ORFs coding for putative Tourist transposases from Arabidopsis thaliana (Columbia) and Stowaway transposases from Arabidopsis and Oryza sativa (domesticated rice) have been found, clearly defining MITEs as class II transposons (LE et al. 2000 ; TURCOTTE et al. 2001 ).

Further analysis of the putative Arabidopsis Tourist transposases indicates that Tourist elements are more related to specific bacterial IS, a large and heterogeneous group of simple inverted-repeat transposons widespread among prokaryotes (MAHILLON and CHANDLER 1998 ; LE et al. 2000 ), than they are to Stowaway. Detailed analysis of the putative transposases encoded by Stowaway suggests that these elements are related to members of the Tc1/mariner transposons (LE et al. 2000 ; K. TURCOTTE and T. BUREAU, unpublished results), a widespread superfamily of elements with representatives in vertebrates, invertebrates, and fungi. Phylogenetic studies of transposases and integrases revealed that Tc1/mariner elements, members of diverse bacterial IS elements, retroviruses, and retrotransposons share conserved catalytic residues (DOAK et al. 1994 ), known as the DDE motif, suggesting a common ancestry and even more widespread distribution.

Traditionally, transposons were identified and analyzed through genetic and molecular studies. However, the availibility of sequence information and bioinformatic tools has now allowed for the identification and characterization of transposons through computer-assisted searches of sequence databases (BUREAU and WESSLER 1992 ; BUREAU and WESSLER 1994B ; BRITTEN 1995 ; OOSUMI et al. 1995 ; SURZYCKI and BELKNAP 1999 , SURZYCKI and BELKNAP 2000 ; LE et al. 2000 ). In C. elegans, molecular, genetic, and sequence database search tools have revealed the presence of diverse representatives of both classes of transposons. Among these, Tc1 is probably one of the best characterized eukaryotic class II transposon and has been effectively used as a mapping, mutagenesis, and gene-tagging tool (GREENWALD 1985 ; WILLIAMS et al. 1992 ; RUSHFORTH et al. 1993 ; PLASTERK and VAN LUENEN 1997 ). Tc1 transposition and regulation has been finely dissected at the molecular and biochemical levels (PLASTERK and VAN LUENEN 1997 ). Most Tc1 elements have a 54-bp TIR delimited by a 5'-TA-3' TSD. Autonomous Tc1 encodes a 343-amino-acid transposase, which is the only protein required for transposition (VOS et al. 1993 , VOS et al. 1996 ; PLASTERK and VAN LUENEN 1997 ). Tc1 copy number can vary from 10- to 15-fold depending on the C. elegans strain and element activity is cell-type dependent (EGILMEZ et al. 1995 ). In Bergerac, Tc1 excision is detected in both somatic and germline cells whereas it is restricted to somatic cells in Bristol N2 (EIDE and ANDERSON 1988 ; VOS et al. 1993 , VOS et al. 1996 ; EGILMEZ et al. 1995 ; PLASTERK and VAN LUENEN 1997 ). Recently, mut-7 was found to encode a RNaseD homolog in C. elegans and may be involved in the regulation of transposon activity by post-transcriptional gene silencing (KETTING et al. 1999 ).

Tc1, Tc2, Tc3, and Tc7 are members of the Tc1/mariner superfamily found in C. elegans (COLLINS et al. 1989 ; LEVITT and EMMONS 1989 ; DREYFUS and EMMONS 1991 ; REZSOHAZY et al. 1997 ). In addition, other types of transposons endogenous to C. elegans include long terminal repeat (LTR)-retrotransposons (BRITTEN 1995 ; BOWEN and MCDONALD 1999 ), non-LTR retrotransposons (or long interspersed nuclear elements; MALIK and EICKBUSH 1998 ) and hAT- (or Ac)-like elements (BIGOT et al. 1996 ). Elements designated as Tc4 and Tc5 were initially classified as foldback transposons (YUAN et al. 1991 ; COLLINS and ANDERSON 1994 ) but further analysis of their putative transposases revealed that they contain a DDE motif suggesting a distant relationship to the Tc1/mariner elements pogo, Tigger1, and Tigger2 (ROBERTSON 1996 ; SMIT and RIGGS 1996 ). Tc6 also has a foldback structure but its terminal sequences and TSDs are reminiscent of those of Tc1/mariner transposons (DREYFUS and EMMONS 1991 ). A number of MITEs have also been identified in C. elegans (OOSUMI et al. 1995 , OOSUMI et al. 1996 ; C. ELEGANS SEQUENCING CONSORTIUM 1998; SURZYCKI and BELKNAP 2000 ) but these were not found to be related to Tourist. To date, Tourist-like transposons appear to be confined to plant genomes.

In this article, we analyze two predicted ORFs in C. elegans that share amino acid similarity to the putative Arabidopsis Tourist and bacterial IS transposases. The same ORFs were also identified independently by sequence similarity to an Arabidopsis element called Harbinger but no further attempts were made to characterize these putative C. elegans elements (KAPITONOV and JURKA 1999 ). We determine that one of the C. elegans ORFs is part of a Tourist-like element that belongs to a large group of nematode transposons, referred to as Tc8. The majority of Tc8 members are short (150–400 bp), can potentially form DNA hairpins, and have TIRs and TSDs similar to other Tourist-like elements. The Tc8 transposase shares similarity to a number of plant, insect, and vertebrate EST sequences, indicating that the Tourist family of transposons are potentially active in other organisms. In addition, several eukaryotic genomic sequences were identified with similarity to the Arabidopsis Tourist and C. elegans Tc8 transposases. Together our data confirm the presence of Tourist-like transposons beyond the plant kingdom and suggest that Tourist-like elements share a common ancestry with specific bacterial IS and are widely distributed in the prokaryote and eukaryote genomes.

	MATERIALS AND METHODS

TOP ABSTRACT MATERIALS AND METHODS RESULTS AND DISCUSSION LITERATURE CITED

Transposon mining:
All sequence information and BLAST search tools (ALTSCHUL et al. 1990 , ALTSCHUL et al. 1997 ) were accessed through GenBank (http://www.ncbi.nlm.nih.gov/), the Genome Sequencing Center (http://www.genome.wustl.edu/gsc/index.shtml), or the Sanger Centre (http://www.sanger.ac.uk/Projects/C_elegans/). Tc8.1 was identified by using sequences corresponding to putative MITE transposases from Arabidopsis (LE et al. 2000 ) as queries in BLAST searches against the GenBank sequence database. Additional database searches were performed to identify other C. elegans elements related to Tc8.1 (BLAST score of >80).

Identification of related to empty sites:
Related to empty sites (RESites) are sequences highly similar or nearly identical to the sequences flanking an insertion (LE et al. 2000 ). However, RESites do not harbor the transposon sequence and the target site of insertion is not duplicated. RESites may correspond to orthologous or paralogous sequences, serve to delimit the ends of the elements, determine the TSDs, and suggest evidence of past mobility. The identification of RESites was performed as previously described (LE et al. 2000 ). In brief, RESites are identified using the region immediately flanking an insertion as queries in BLAST searches.

Data and phylogenetic analysis:
Further sequence analysis and alignments were performed using TRANSLATE, PILEUP, BESTFIT, and GAP as part of the University of Wisconsin Genetics Computing Group suite of programs (version 10.0) or additional BLAST search tools (BLASTP, BLASTX, TBLASTN, PSI-BLAST, and BLAST 2 sequences) provided at the National Center for Biotechnology Information (NCBI; ALTSCHUL et al. 1997 ; TATUSOVA and MADDEN 1999 ). For phylogenetic analysis, the sequences surrounding the DDE motif of the transposase of 14 transposable elements were manually aligned on the basis of previous reports (REZSOHAZY et al. 1993 ; CAPY et al. 1996 ). Phylogenetic relationships were inferred with maximum parsimony (multiple trees heuristic search with Tree Bisection Reconnection) and neighbor-joining methods from the PAUP program, version 4.0b4a (SWOFFORD 2000 ) from the amino acid sequence alignment shown in Fig 3. All amino acids and stop codons were equally weighted. Unrooted trees were displayed using the midpoint rooting method. Bootstrap analysis of the data set was done with 200 replicates.

View larger version (28K): In this window In a new window Download PPT slide   Figure 1. Tourist-like elements in the C. elegans genome. (A) Diagram of Tc8 members. The majority of the elements are 150 bp and share high sequence similarity. Additional longer members were found but were truncated. Dashes represent gaps and the hatched box indicates the region (300 amino acids) of the annotated ORF that is similar to the C-terminal domain of other transposases. Boxes above Tc8.1 with inverted arrowheads represent nested insertions. The TIR and TSD sequences of the nested Tourist-like element are degenerate. GenBank gi numbers and positions of elements on corresponding clones are indicated to the right and below, respectively. (B) A Tc8-like group of elements in the genome of C. briggsae. Nucleotide alignment of C. elegans Tc8 from gi 2746790, position 24108–24275 and C. briggsae Cb-Tc8 from gi 11095049, position 34282–34399.

View larger version (33K): In this window In a new window Download PPT slide   Figure 2. RESites corresponding to Tc8 element insertions. The identification of RESites suggests evidence of past mobility. Solid boxes with inverted arrowheads represent Tc8 insertions. GenBank gi numbers and position on clones are indicated. Target sites are underlined and TSDs are in boldface.

View larger version (52K): In this window In a new window Download PPT slide   Figure 3. Similarity between putative MITE and bacterial IS transposases. GenBank gi numbers for amino acid sequences used in the alignment are indicated in Table 1. Amino acid coordinates are indicated to the left. The conserved DDE residues are indicated below the alignment. The DX(G/A)(Y/F) and YREK motifs found in other IS families (CAPY et al. 1996 ) are boxed.

	RESULTS AND DISCUSSION

TOP ABSTRACT MATERIALS AND METHODS RESULTS AND DISCUSSION LITERATURE CITED

Computer-based searches using the amino acid sequence of the putative Tourist-like transposases from Arabidopsis MITE X (conceptual translation of gi 4454587, position 4650–5865) and MITE XI (gi 4585884) as queries revealed the presence of similar coding regions in several other plant, animal, and eubacterial ESTs and/or genomic sequences. For the most part, no other full-length plant Tourist-like element could be resolved and likely reflects the presence of truncated or degenerate elements. Many of the eubacterial sequences, however, correspond to previously described mobile elements. Although, as in the case of plants, the animal sequences typically did not lead to the identification of full-length elements, a 7568-bp element was mined from the genomic sequence of C. elegans. This element, designated as Tc8.1, is located on chromosome 2 (clone CELF14D2, gi 2746790), has large imperfect TIRs, a putative 3-bp TSD (5'-TAA-3'), and a predicted ORF coding for a hypothetical protein of 743 amino acids (gi 7499082). Overall, the presence of sequences with similarity to the Tourist-like element transposases in several eubacterial and eukaryotic genomes suggests a wide distribution.

Using the Tc8.1 nucleotide sequence as a query in computer-assisted database searches, we found 282 related sequences within the C. elegans genome. Of these sequences, 128 represent shorter versions of Tc8.1 complete with TIRs and a specific TSD sequence of 5'-TAA-3'. The remainder were truncated versions with only one discernable terminal end immediately flanked by the sequence 5'-TAA-3'. Together, Tc8.1 and the shorter intact and truncated elements compose the Tc8 group of transposons within C. elegans. Even though Tc8 elements are highly abundant in C. elegans, the total nucleotide contribution represents only 0.05% of the genome.

Strikingly, 63 members (49%) of the Tc8 group are exactly 150 bp in length and share >94% sequence similarity. Like plant Tourist-like members, these elements have the potential to form hairpin-like DNA secondary structures. Excluding Tc8.1, 6 members of the Tc8 group were >1 kb in size but did not possess any coding capacity (Fig 1A). For four of these larger elements, the increase in size is the result of nested insertions of other types of transposons or repetitive elements. Evidence of past mobility for some members of Tc8 was provided through the identification of RESites (Fig 2), which are sequences similar to the empty site of an insertion. Furthermore, BLASTN searches also revealed the presence of Tc8 within the genome of the related nematode C. briggsae (Fig 1B), which is thought to have diverged from C. elegans 10–40 million years ago (BUTLER et al. 1981 ; HESCHL and BAILLIE 1990 ; KENNEDY et al. 1993 ). To date, eight complete and three truncated Tc8 elements were identified from C. briggsae genomic clones deposited in GenBank. Tc8 transposons in C. briggsae vary from 95 to 368 bp in length and are not as well conserved as are the Tc8 elements in C. elegans (data not shown). A complete list of the C. elegans and C. briggsae transposons mined in this survey is available at http://www.tebureau.mcgill.ca/. A second predicted ORF (gi 7504556) was identified in the C. elegans genome and shared 46.5% amino acid sequence similarity to the Arabidopsis Tourist transposase. However, neither TIRs nor TSD could be identified. This putative element did not share nucleotide sequence similarity to Tc8 members and was not found to be repetitive in the C. elegans genome.

In contrast to the 150-bp elements that appear to be recent insertions, Tc8.1 seems to be an ancient insertion since it has accumulated at least four nested insertions and a corresponding RESite appears degenerate (Fig 2). Alternatively, Tc8.1 mobilization occurred after all or some of the nested insertion events. An unusual feature of the nested insertions within Tc8.1 is the presence of another shorter member of the Tc8 group at the same position in each of the TIRs. These elements are not identical (99.3% similarity with a single nucleotide substitution and an indel). Therefore, the nested elements could be independent insertions that occurred at exactly the same location in the TIRs. However, the level of divergence between the nested insertions is similar to the level of divergence between both TIRs (data not shown). Thus, we cannot distinguish between the possibility that they represent independent insertions or that the actual structure of Tc8.1 TIRs is the result of a rearrangement, localized duplication, conversion, or a combination of these events. The two other nested insertions within Tc8.1, are located at positions 26747–27109 and 29990–31095 (gi 2746790, Fig 1) and are repetitive in the C. elegans genome. The insertion at position 26747–27109 shares >85% nucleotide similarity with members of a group of putative inverted-repeat transposons previously identified as Cele1 (OOSUMI et al. 1995 ). However, it appears to be a truncated insertion as element boundaries or TSDs could not be clearly identified. The insertion located at position 29990–31095 is annotated in ACeDB as RepQ and, upon closer examination, displays structural characteristics of IS630/Tc1/mariner-like elements. It is not clear whether Tc8 or any of the other elements within Tc8.1 preferentially insert into mobile elements. Such a phenomenon has been suggested to reflect a mechanism to minimize deleterious insertion events in other organisms (VAURY et al. 1989 ; SANMIGUEL et al. 1996 ).

The short hairpin-like Tc8 elements are most likely deletion derivatives of larger elements. As in the case of other DNA-based transposons (i.e., class II), the mobilization and spread of deletion derivatives would be facilitated by transposase provided in trans by an autonomous element located elsewhere in the genome. The high copy number of very similar Tc8 elements may reflect recent activity. Tc8.1 could have been the source of transposase that mobilized the 150-bp elements. It is unlikely, however, that Tc8.1 is presently active because the putative transposase ORF is disrupted by the Cele1 insertion (Fig 1). Alternatively, a functional transposase may have been provided by a full-length Tc8 element that has been lost from the Bristol N2 strain. It is also possible that Tc8 elements, similar to the case of Tc7, which can be mobilized by a Tc1 transposase (REZSOHAZY et al. 1997 ), are currently being mobilized in trans by the Tc4 and/or Tc5 transposases as these transposons have structural characteristics similar to Tc8 (see below). An abundance in shorter deletion derivatives is also observed for Tourist-like elements in Arabidopsis and other plant genomes. The selective spread of shorter elements may be a mechanism inherent in the transposition process of these elements or may reflect an active host mechanism to minimize element contribution to genome size.

Upon closer examination, the transposases of Arabidopsis MITE X and XI elements share amino acid similarity to members of the bacterial IS4 and IS5 family of elements, suggesting a common evolutionary history (KAPITONOV and JURKA 1999 ; LE et al. 2000 ). Likewise, PSI-BLAST searches (ALTSCHUL et al. 1997 ) indicate that the Tc8.1 transposase also shares similarity to the same IS transposases. This similarity is restricted to the N-terminal region that contains the DDE motif found in many transposases and integrases and is known to be essential in the catalysis of DNA integration step of transposition (REZSOHAZY et al. 1993 ). Members of the IS4 and IS5 families have additional conserved residues proximal to the DDE motif, namely, the DX(G/A)(F/Y) and YX₂RX₃EX₆K, or YREK, motifs neighboring the last aspartic and glutamic acid residues (REZSOHAZY et al. 1993 ). These motifs are also present in the putative Tourist transposases (Fig 3). Although the YREK motif appears to be only partially conserved in the putative Tourist transposases from C. elegans and Arabidopsis, the invariant arginine and glutamic acid residues are conserved (Fig 3).

Phylogenetic analysis using the region corresponding to the conserved DDE motif shows that the Tc8 transposase clusters with the transposases from members of the IS5 element family (Fig 4). According to both maximum parsimony and neighbor-joining analyses, Tc8 is more closely related to the other eukaryotic elements, Arabidopsis MITE-X and -XI, than they are to bacterial IS elements. Moreover, the eukaryotic Tourist elements are more related to bacterial IS5 members that generate a 3-bp TSD (typically, 5'-TAA-3'). This suggests that the Arabidopsis and C. elegans Tourist-like elements have evolved from a common ancestral IS. We cannot rule out the possibility, however unlikely, that the results of our analysis reflect convergence of the Tourist and IS during evolution. With the identification of new Tourist transposases from other organisms, it will be interesting to test the hypothesis that eukaryotic Tourist emerged from a common ancestral IS5 member. Nevertheless, these results suggest that Tourist and bacterial IS5 elements form an IS5/Tourist superfamily.

View larger version (15K): In this window In a new window Download PPT slide   Figure 4. Evolutionary relationship between Tourist and bacterial IS5 elements. Phylogenetic analysis showing the relationship between the putative Tourist transposases from Arabidopsis (MITE-X and -XI) and from C. elegans to transposases from bacterial IS5 elements. GenBank gi numbers for amino acid sequences used in the alignment are indicated in Table 1. Parsimony and neighbor-joining (not shown) trees are all concordant with the placement of Tc8 transposases with representatives of the bacterial IS5 family. The unique and most parsimonious tree, based on the alignment in Fig 3, is shown (length = 335, CI = 0.818, RI = 0.564). Numbers at the base of nodes correspond to bootstrap values. Typical sizes of TSDs are indicated to the right.

The terminal nucleotides of the Tc8 TIRs not only are similar to plant Tourist-like TIRs but also are reminiscent of the TIRs of bacterial IS elements. The preference for insertion into the trinucleotide 5'-TAA-3' of Tc8, as confirmed by the RESite analysis, is also a feature of other Tourist and IS5 elements (Fig 2; Table 1). Curiously, the 3-bp TSDs and terminal sequences of Tc8 TIRs are also reminiscent of two other well-described active transposons endogenous to C. elegans, namely Tc4 and Tc5 (YUAN et al. 1991 ; COLLINS and ANDERSON 1994 ). Even though Tc4 and Tc5 putative transposases also contain the DDE motif (ROBERTSON 1996 ; SMIT and RIGGS 1996 ), no significant nucleotide or amino acid sequence similarity could be detected beyond the TSDs and terminal nucleotides. The TIRs and TSDs are important in transposase-mediated recognition of element termini and catalytic cleavage of the target sequence, respectively (VAN LUENEN et al. 1994 ; FISCHER et al. 1999 ). Consequently, sequence similarity between the TIRs and TSDs of different transposons suggests a common transposase specificity.

Although the identification of RESites provides evidence of past mobility, to date, no Tourist element has yet been unambiguously shown to be currently active. Even though we could not identify ESTs similar to the putative Tourist transposases from C. elegans or Arabidopsis, we did mine ESTs from other plant species, insects, and vertebrates (Table 2). Additional ESTs displayed high sequence similarity but only entries with similarities to the conserved motifs in the C-terminal end of the query (Fig 3) are shown in Table 2. These ESTs may correspond to the transposases of different Tourist element groups (Table 1). Alternatively, similarity to ESTs may not correspond to transposase expression but may simply represent the transcription of Tourist elements that have inserted into or near expressed genes. Unfortunately, genomic sequences corresponding to the EST clones were not found, but TBLASTN searches using Tc8 amino acid sequences did reveal the presence of similar sequences in these organisms and in C. briggsae (data not shown); discernable ends of these putative elements could be identified. Despite these, it would appear that Tourist elements are present and possibly active in these other genomes. The lack of corresponding ESTs does not necessarily indicate lack of Tc8 activity. Transposon activity in C. elegans is highly strain dependent. For example, copy number of Tc1 elements can be 10- to 15-fold lower in Bristol N2 than in Bergerac BO (EGILMEZ et al. 1995 ). In Bergerac, Tc1 excision activity is higher in somatic cells than in germline cells, indicating that element activity may be limited to specific tissues or developmental stages (EIDE and ANDERSON 1988 ). In some eukaryotes (e.g., higher plants), host-mediated regulation such as DNA methylation may play a role in silencing transposon activity (HIROCHIKA et al. 2000 ).

MITE insertions are often closely associated with normal plant genes (BUREAU and WESSLER 1992 , BUREAU and WESSLER 1994A , BUREAU and WESSLER 1994B ). This is in contrast to retrotransposons, which are frequently found as nested insertions within heterochromatic regions (VAURY et al. 1989 ; SANMIGUEL et al. 1996 ). Although a more detailed examination is required to determine if Tc8 are preferentially found associated with genes or contribute cis-regulatory sequences, there seems to be a negative correlation between Tc8 and gene distribution in C. elegans, where genes are clustered near the center of the chromosomes (Fig 5). However, this is not as obvious on the X chromosome where gene clustering is less pronounced (BARNES et al. 1995 ; C. ELEGANS SEQUENCING CONSORTIUM 1998). Interestingly, Tc8 abundance and distribution relative to genes is similar to what has been previously observed for Tc1 elements in C. elegans and Tourist-like elements in Arabidopsis, which has a genome of approximately the same size as C. elegans (KORSWAGEN et al. 1996 ; C. ELEGANS SEQUENCING CONSORTIUM 1998).

View larger version (23K): In this window In a new window Download PPT slide   Figure 5. Distribution of Tc8 elements in the C. elegans genome. Each line represents a Tc8 insertion. Location of Tc8.1 is indicated. Scale is indicated at the bottom. The first nucleotide position on the chromosome is located at the top.

Eukaryotic Tourist and bacterial IS elements appear to have emerged from a common ancestor. This is analogous to other eukaryotic elements, namely members of the Tc1/mariner superfamily, which are related to IS630 family of bacterial transposons (CAPY et al. 1996 ). Furthermore, many members of the Tc1/mariner have been shown to be transpositionally active. Although active mobilization of a Tourist still needs to be fully demonstrated, the identification of ESTs similar to Tourist putative transposases suggests that this family is not merely a collection of transposon relics. Thus, Tourist-like transposons are potentially active elements related to the widespread bacterial IS5 transposons and, together, members of the IS5/Tourist superfamily have successfully populated both prokaryotic and eukaryotic genomes.

	ACKNOWLEDGMENTS

We thank Julie Poupart, Dr. Rick Roy, and Dr. Joseph Dent for critical comments on our manuscript. We are grateful to Boris-Antoine Legault for providing computer-programming support. This work was funded by a National Science and Engineering Research Council of Canada grant to T.B. and a Formation de Chercheurs et l'Aide à la Recherche fellowship to K.T.

Manuscript received February 1, 2001; Accepted for publication April 26, 2001.

	LITERATURE CITED

TOP ABSTRACT MATERIALS AND METHODS RESULTS AND DISCUSSION LITERATURE CITED

ALTSCHUL, S. F., W. GISH, W. MILLER, E. W. MYERS, and D. J. LIPMAN, 1990  Basic local alignment search tool. J. Mol. Biol. 215:403-410[Medline].

ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHAFFER, J. ZHANG, and Z. ZHANG et al., 1997  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402[Abstract/Free Full Text].

BARNES, T. M., Y. KOHARA, A. COULSON, and S. HEKIMI, 1995  Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans.. Genetics 141:159-179[Abstract].

BERG, D. E., and M. M. HOWE, 1989 Mobile DNA. American Society for Microbiology, Washington, DC.

BESANSKY, N. J., O. MUKABAYIRE, J. A. BEDELL, and H. LUSZ, 1996  Pegasus, a small terminal inverted repeat transposable element found in the white gene of Anopheles gambiae.. Genetica 98:119-129[Medline].

BIGOT, Y., C. AUGE-GOUILLOU, and G. PERIQUET, 1996  Computer analyses reveal a hobo-like element in the nematode Caenorhabditis elegans, which presents a conserved transposase domain common with the Tc1-Mariner transposon family. Gene 174:265-271[Medline].

BOWEN, N. J. and J. F. MCDONALD, 1999  Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res. 9:924-935[Abstract/Free Full Text].

BRITTEN, R. J., 1995  Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans.. Proc. Natl. Acad. Sci. USA 92:599-601[Abstract/Free Full Text].

BUREAU, T. E. and S. R. WESSLER, 1992  Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4:1283-1294[Abstract/Free Full Text].

BUREAU, T. E. and S. R. WESSLER, 1994a  Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc. Natl. Acad. Sci. USA 91:1411-1415[Abstract/Free Full Text].

BUREAU, T. E. and S. R. WESSLER, 1994b  Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6:907-916[Abstract].

BUTLER, M. H., S. M. WALL, K. R. LUEHRSEN, G. E. FOX, and R. M. HECHT, 1981  Molecular relationships between closely related strains and species of nematodes. J. Mol. Evol. 18:18-23[Medline].

Genome sequence of the nematode C. elegans: a platform for investigating biology. (1998) Science 282:2012-2018[Abstract/Free Full Text].

CAPY, P., R. VITALIS, T. LANGIN, D. HIGUET, and C. BAZIN, 1996  Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor? J. Mol. Evol. 42:359-368[Medline].

COLLINS, J., E. FORBES, and P. ANDERSON, 1989  The Tc3 family of transposable genetic elements in Caenorhabditis elegans.. Genetics 121:47-55[Abstract/Free Full Text].

COLLINS, J. J. and P. ANDERSON, 1994  The Tc5 family of transposable elements in Caenorhabditis elegans.. Genetics 137:771-781[Abstract].

DOAK, T. G., F. P. DOERDER, C. L. JAHN, and G. HERRICK, 1994  A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif. Proc. Natl. Acad. Sci. USA 91:942-946[Abstract/Free Full Text].

DREYFUS, D. H. and S. W. EMMONS, 1991  A transposon-related palindromic repetitive sequence from C. elegans.. Nucleic Acids Res. 19:1871-1877[Abstract/Free Full Text].

EGILMEZ, N. K., R. H. EBERT, II, and R. J. SHMOOKLER REIS, 1995  Strain evolution in Caenorhabditis elegans: transposable elements as markers of interstrain evolutionary history. J. Mol. Evol. 40:372-381[Medline].

EIDE, D. and P. ANDERSON, 1988  Insertion and excision of Caenorhabditis elegans transposable element Tc1. Mol. Cell. Biol. 8:737-746[Abstract/Free Full Text].

FESCHOTTE, C. and C. MOUCHES, 2000  Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Mol. Biol. Evol. 17:730-737[Abstract/Free Full Text].

FISCHER, S. E., H. G. VAN LUENEN, and R. H. PLASTERK, 1999  Cis requirements for transposition of Tc1-like transposons in C. elegans.. Mol. Gen. Genet. 262:268-274[Medline].

GREENWALD, I., 1985  lin-12, a nematode homeotic gene, is homologous to a set of mammalian proteins that includes epidermal growth factor. Cell 43:583-590[Medline].

HESCHL, M. F. and D. L. BAILLIE, 1990  Functional elements and domains inferred from sequence comparisons of a heat shock gene in two nematodes. J. Mol. Evol. 31:3-9[Medline].

HIROCHIKA, H., H. OKAMOTO, and T. KAKUTANI, 2000  Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12:357-369[Abstract/Free Full Text].

IZSVAK, Z., Z. IVICS, N. SHIMODA, D. MOHN, and H. OKAMOTO et al., 1999  Short inverted-repeat transposable elements in teleost fish and implications for a mechanism of their amplification. J. Mol. Evol. 48:13-21[Medline].

KAPITONOV, V. V. and J. JURKA, 1999  Molecular paleontology of transposable elements from Arabidopsis thaliana.. Genetica 107:27-37[Medline].

KENNEDY, B. P., E. J. AAMODT, F. L. ALLEN, M. A. CHUNG, and M. F. HESCHL et al., 1993  The gut esterase gene (ges-1) from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.. J. Mol. Biol. 229:890-908[Medline].

KETTING, R. F., T. H. HAVERKAMP, H. G. VAN LUENEN, and R. H. PLASTERK, 1999  Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99:133-141[Medline].

KORSWAGEN, H. C., R. M. DURBIN, M. T. SMITS, and R. H. A. PLASTERK, 1996  Transposon Tc1-derived, sequence-tagged sites in Caenorhabditis elegans as marker for gene mapping. Proc. Natl. Acad. Sci. USA 93:14680-14685[Abstract/Free Full Text].

LE, Q. H., S. WRIGHT, Z. YU, and T. BUREAU, 2000  Transposon diversity in Arabidopsis thaliana.. Proc. Natl. Acad. Sci. USA 97:7376-7381[Abstract/Free Full Text].

LEVITT, A. and S. W. EMMONS, 1989  The Tc2 transposon in Caenorhabditis elegans.. Proc. Natl. Acad. Sci. USA 86:3232-3236[Abstract/Free Full Text].

MAHILLON, J. and M. CHANDLER, 1998  Insertion sequences. Microbiol. Mol. Biol. Rev. 62:725-774[Abstract/Free Full Text].

MALIK, H. S. and T. H. EICKBUSH, 1998  The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Mol. Biol. Evol. 15:1123-1134[Abstract].

OOSUMI, T., B. GARLICK, and W. R. BELKNAP, 1995  Identification and characterization of putative transposable DNA elements in solanaceous plants and Caenorhabditis elegans.. Proc. Natl. Acad. Sci. USA 92:8886-8890[Abstract/Free Full Text].

OOSUMI, T., B. GARLICK, and W. R. BELKNAP, 1996  Identification of putative nonautonomous transposable elements associated with several transposon families in Caenorhabditis elegans.. J. Mol. Evol. 43:11-18[Medline].

PLASTERK, R. H. A., and H. G. A. M. VAN LUENEN, 1997 Transposons, pp. 97–116 in C. elegans II, edited by D. L. RIDDLE, T. BLUMENTHAL, B. J. MEYER and J. R. PRIESS. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

REZSOHAZY, R., B. HALLET, J. DELCOUR, and J. MAHILLON, 1993  The IS4 family of insertion sequences: evidence for a conserved transposase motif. Mol. Microbiol. 9:1283-1295[Medline].

REZSOHAZY, R., H. G. VAN LUENEN, R. M. DURBIN, and R. H. PLASTERK, 1997  Tc7, a Tc1-hitch hiking transposon in Caenorhabditis elegans.. Nucleic Acids Res. 25:4048-4054[Abstract/Free Full Text].

ROBERTSON, H. M., 1996  Members of the pogo superfamily of DNA-mediated transposons in the human genome. Mol. Gen. Genet. 252:761-766[Medline].

RUSHFORTH, A. M., B. SAARI, and P. ANDERSON, 1993  Site-selected insertion of the transposon Tc1 into a Caenorhabditis elegans myosin light chain gene. Mol. Cell. Biol. 13:902-910[Abstract/Free Full Text].

SANMIGUEL, P., A. TIKHONOV, Y. K. JIN, N. MOTCHOULSKAIA, and D. ZAKHAROV et al., 1996  Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768[Abstract/Free Full Text].

SMIT, A. F. and A. D. RIGGS, 1996  Tiggers and DNA transposon fossils in the human genome. Proc. Natl. Acad. Sci. USA 93:1443-1448[Abstract/Free Full Text].

SURZYCKI, S. A. and W. R. BELKNAP, 1999  Characterization of repetitive DNA elements in Arabidopsis.. J. Mol. Evol. 48:684-691[Medline].

SURZYCKI, S. A. and W. R. BELKNAP, 2000  Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Proc. Natl. Acad. Sci. USA 97:245-249[Abstract/Free Full Text].

SWOFFORD, D. L., 2000 PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, MA.

TATUSOVA, T. A. and T. L. MADDEN, 1999  BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174:247-250[Medline].

TU, Z., 1997  Three novel families of miniature inverted-repeat transposable elements are associated with genes of the yellow fever mosquito, Aedes aegypti.. Proc. Natl. Acad. Sci. USA 94:7475-7480[Abstract/Free Full Text].

TURCOTTE, K., S. SRINIVASAN, and T. BUREAU, 2001  Survey of transposable elements from rice genomic sequences. Plant J. 25:1-13[Medline].

UNSAL, K. and G. T. MORGAN, 1995  A novel group of families of short interspersed repetitive elements (SINEs) in Xenopus: evidence of a specific target site for DNA-mediated transposition of inverted-repeat SINEs. J. Mol. Biol. 248:812-823[Medline].

VAN LUENEN, H. G., S. D. COLLOMS, and R. H. PLASTERK, 1994  The mechanism of transposition of Tc3 in C. elegans.. Cell 79:293-301[Medline].

VAURY, C., A. BUCHETON, and A. PELISSON, 1989  The beta heterochromatic sequences flanking the I elements are themselves defective transposable elements. Chromosoma 98:215-224[Medline].

VOS, J. C., H. G. VAN LUENEN, and R. H. PLASTERK, 1993  Characterization of the Caenorhabditis elegans Tc1 transposase in vivo and in vitro.. Genes Dev. 7:1244-1253[Abstract/Free Full Text].

VOS, J. C., I. DE BAERE, and R. H. PLASTERK, 1996  Transposase is the only nematode protein required for in vitro transposition of Tc1. Genes Dev. 10:755-761[Abstract/Free Full Text].

WESSLER, S. R., T. E. BUREAU, and S. E. WHITE, 1995  LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5:814-821[Medline].

WILLIAMS, B. D., B. SCHRANK, C. HUYNH, R. SHOWNKEEN, and R. H. WATERSTON, 1992  A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites. Genetics 131:609-624[Abstract].

YEADON, P. J. and D. E. CATCHESIDE, 1995  Guest: a 98 bp inverted repeat transposable element in Neurospora crassa.. Mol. Gen. Genet. 247:105-109[Medline].

YUAN, J. Y., M. FINNEY, N. TSUNG, and H. R. HORVITZ, 1991  Tc4, a Caenorhabditis elegans transposable element with an unusual fold-back structure. Proc. Natl. Acad. Sci. USA 88:3334-3338[Abstract/Free Full Text].

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