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Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells.

Clark KJ, Carlson DF, Leaver MJ, Foster LK, Fahrenkrug SC - Nucleic Acids Res. (2009)

Bottom Line: We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells.Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active.The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Science, University of Minnesota, St Paul, MN 55108, USA.

ABSTRACT
The Tc1/mariner family of DNA transposons is widespread across fungal, plant and animal kingdoms, and thought to contribute to the evolution of their host genomes. To date, an active Tc1 transposon has not been identified within the native genome of a vertebrate. We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells. In transposition assays, we found that the Passport transposon system improved stable cellular transgenesis by 40-fold, has an apparent preference for insertion into genes, and is subject to overproduction inhibition like other Tc1 elements. Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active. The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements.

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Phylogeny of Passport-like transposons and their hosts. (A) Neighbor-joining plot of multiply aligned transposase consensus amino acid sequences. Sequences were aligned with ClustalW, and plotted with NJplot. Numbers represent the percentage frequencies with which the tree topology was returned after 1000 iterations. The tree is rooted to Tc1 from C. elegans. Transposon designation is prefixed by host species identifier; om, rainbow trout; ol, medaka; ga, stickleback; tr, pufferfish; ss, Atlantic salmon; ce, C. elegans; rt, Rana temporaria (frog); xt, Xenopus tropicalis. Passport, Frog Prince and Sleeping Beauty were isolated from Pleuronectes platessa, Rana sylvestris, and a variety of salmonid species, respectively. (B) Phylogeny of host species adapted from Nelson (50). The colored dots assist in pairing the transposons shown in A with the species from B.
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Figure 4: Phylogeny of Passport-like transposons and their hosts. (A) Neighbor-joining plot of multiply aligned transposase consensus amino acid sequences. Sequences were aligned with ClustalW, and plotted with NJplot. Numbers represent the percentage frequencies with which the tree topology was returned after 1000 iterations. The tree is rooted to Tc1 from C. elegans. Transposon designation is prefixed by host species identifier; om, rainbow trout; ol, medaka; ga, stickleback; tr, pufferfish; ss, Atlantic salmon; ce, C. elegans; rt, Rana temporaria (frog); xt, Xenopus tropicalis. Passport, Frog Prince and Sleeping Beauty were isolated from Pleuronectes platessa, Rana sylvestris, and a variety of salmonid species, respectively. (B) Phylogeny of host species adapted from Nelson (50). The colored dots assist in pairing the transposons shown in A with the species from B.

Mentions: The availability of sequenced genomes provides an opportunity to compare and categorize all transposons within a species and derive consensus sequences with a minimum of experimental bias. While Passport elements were originally isolated from plaice, nearly identical elements have been identified in other flatfish, including flounder and turbot (99% and 98% DNA identity). A recent search of ENSEMBL revealed the presence of additional related transposases with high nucleotide identity (>80%) to Passport in the genomes and EST collections of Xenopus tropicalis, and pufferfish (Takafugu rubripes), stickleback (Gasterostreus aculeatus), medaka (Oryzis latipes), Atlantic salmon (Salmo salmar) and rainbow trout (Oncorhynchus mykiss). Passport-like transposons were absent from all other ENSEMBL genomes, including those of the zebrafish (Danio rerio), despite the wide range and high copy number of other Tc1-like elements in this species. Comparison of the encoded transposase amino acid sequences show that relatives of Passport form a distinct family of Tc1-like transposons that is further divided into two subfamilies, including Eagle/Glan and Barb/SSTN/RTTN (Figure 4). The salmonids (salmon and rainbow trout) contain members of both subfamilies, whilst X. tropicalis, pufferfish, stickleback and medaka contain only the Eagle/Glan subfamily. The structure of Passport is somewhat intermediate between that of Eagle/Glan and Barb/SSTN/RTTN, in that its ITRs bear a strong resemblance to Barb/SSTN/RTTN (Figure 5A) whereas its transposase-coding region seems to bear more resemblance to the Eagle/Glan subfamily. Intriguingly, alignment of the DNA-binding domains of the transposases demonstrates a distinction between Eagle/Glan and Passport/Barb/SSTN/RTTN (Figure 5B), a difference that may be functionally connected to the ITRs of these elements.Figure 4.


Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells.

Clark KJ, Carlson DF, Leaver MJ, Foster LK, Fahrenkrug SC - Nucleic Acids Res. (2009)

Phylogeny of Passport-like transposons and their hosts. (A) Neighbor-joining plot of multiply aligned transposase consensus amino acid sequences. Sequences were aligned with ClustalW, and plotted with NJplot. Numbers represent the percentage frequencies with which the tree topology was returned after 1000 iterations. The tree is rooted to Tc1 from C. elegans. Transposon designation is prefixed by host species identifier; om, rainbow trout; ol, medaka; ga, stickleback; tr, pufferfish; ss, Atlantic salmon; ce, C. elegans; rt, Rana temporaria (frog); xt, Xenopus tropicalis. Passport, Frog Prince and Sleeping Beauty were isolated from Pleuronectes platessa, Rana sylvestris, and a variety of salmonid species, respectively. (B) Phylogeny of host species adapted from Nelson (50). The colored dots assist in pairing the transposons shown in A with the species from B.
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Related In: Results  -  Collection

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Figure 4: Phylogeny of Passport-like transposons and their hosts. (A) Neighbor-joining plot of multiply aligned transposase consensus amino acid sequences. Sequences were aligned with ClustalW, and plotted with NJplot. Numbers represent the percentage frequencies with which the tree topology was returned after 1000 iterations. The tree is rooted to Tc1 from C. elegans. Transposon designation is prefixed by host species identifier; om, rainbow trout; ol, medaka; ga, stickleback; tr, pufferfish; ss, Atlantic salmon; ce, C. elegans; rt, Rana temporaria (frog); xt, Xenopus tropicalis. Passport, Frog Prince and Sleeping Beauty were isolated from Pleuronectes platessa, Rana sylvestris, and a variety of salmonid species, respectively. (B) Phylogeny of host species adapted from Nelson (50). The colored dots assist in pairing the transposons shown in A with the species from B.
Mentions: The availability of sequenced genomes provides an opportunity to compare and categorize all transposons within a species and derive consensus sequences with a minimum of experimental bias. While Passport elements were originally isolated from plaice, nearly identical elements have been identified in other flatfish, including flounder and turbot (99% and 98% DNA identity). A recent search of ENSEMBL revealed the presence of additional related transposases with high nucleotide identity (>80%) to Passport in the genomes and EST collections of Xenopus tropicalis, and pufferfish (Takafugu rubripes), stickleback (Gasterostreus aculeatus), medaka (Oryzis latipes), Atlantic salmon (Salmo salmar) and rainbow trout (Oncorhynchus mykiss). Passport-like transposons were absent from all other ENSEMBL genomes, including those of the zebrafish (Danio rerio), despite the wide range and high copy number of other Tc1-like elements in this species. Comparison of the encoded transposase amino acid sequences show that relatives of Passport form a distinct family of Tc1-like transposons that is further divided into two subfamilies, including Eagle/Glan and Barb/SSTN/RTTN (Figure 4). The salmonids (salmon and rainbow trout) contain members of both subfamilies, whilst X. tropicalis, pufferfish, stickleback and medaka contain only the Eagle/Glan subfamily. The structure of Passport is somewhat intermediate between that of Eagle/Glan and Barb/SSTN/RTTN, in that its ITRs bear a strong resemblance to Barb/SSTN/RTTN (Figure 5A) whereas its transposase-coding region seems to bear more resemblance to the Eagle/Glan subfamily. Intriguingly, alignment of the DNA-binding domains of the transposases demonstrates a distinction between Eagle/Glan and Passport/Barb/SSTN/RTTN (Figure 5B), a difference that may be functionally connected to the ITRs of these elements.Figure 4.

Bottom Line: We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells.Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active.The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Science, University of Minnesota, St Paul, MN 55108, USA.

ABSTRACT
The Tc1/mariner family of DNA transposons is widespread across fungal, plant and animal kingdoms, and thought to contribute to the evolution of their host genomes. To date, an active Tc1 transposon has not been identified within the native genome of a vertebrate. We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells. In transposition assays, we found that the Passport transposon system improved stable cellular transgenesis by 40-fold, has an apparent preference for insertion into genes, and is subject to overproduction inhibition like other Tc1 elements. Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active. The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements.

Show MeSH
Related in: MedlinePlus