Retroelements containing introns in diverse invertebrate taxa

Arkhipova, Irina R.; Pyatkov, Konstantin; Meselson, Matthew; Evgen’ev, Michael B.

doi:10.1038/ng1074

Cited by 114 publications

(129 citation statements)

References 13 publications

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“…28 (47). It may be that the distinct compartmentalization of TEs into telomeric versus gene-rich regions results from regional insertion preferences, from selective advantage of heterochromatin-forming sequences in such nongenic regions as telomeres and centromeres (48,49), or selection against TE insertions in gene-rich regions.…”

Section: Discussionmentioning

confidence: 99%

Diverse DNA transposons in rotifers of the class Bdelloidea

Arkhipova

Meselson

2005

Proc. Natl. Acad. Sci. U.S.A.

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We surveyed the diversity, structural organization, and patterns of evolution of DNA transposons in rotifers of the class Bdelloidea, a group of basal triploblast animals that appears to have evolved for millions of years without sexual reproduction. Representatives of five superfamilies were identified: ITm (IS630͞Tc͞mariner), hAT, piggyBac, helitron, and foldback. Except for mariners, no fully intact copies were found. Mariners, both intact and decayed, are present in high copy number, and those described here may be grouped in several closely related lineages. Comparisons across lineages show strong evidence of purifying selection, whereas there is little or no evidence of such selection within lineages. This pattern could have resulted from repeated horizontal transfers from an exogenous source, followed by limited intragenomic proliferation, or, less plausibly, from within-host formation of new lineages under host-or element-based selection for function, in either case followed by eventual inactivation and decay. Unexpectedly, the flanking sequences surrounding the majority of mariners are very similar, indicating either insertion specificity or proliferation as part of larger DNA segments. Members of all superfamilies are present near chromosome ends, associated with the apparently domesticated retroelement Athena, in large clusters composed of diverse DNA transposons, often inserted into each other, whereas the examined gene-rich regions are nearly transposon-free.foldback ͉ hAT ͉ helitron ͉ mariner ͉ piggyBac

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Section: Discussionmentioning

confidence: 99%

Diverse DNA transposons in rotifers of the class Bdelloidea

Arkhipova

Meselson

2005

Proc. Natl. Acad. Sci. U.S.A.

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“…The GIY-YIG domain of PLEs is of special interest in this respect because of its potential to participate in a DNA-dependent transposition pathway similar to that used by group I and occasionally group II introns (10,11). The ability of PLEs to retain introns during transposition, their peculiar structural organization, and the unusual sequence of their RT domain indicate that the members of this clade are clearly different from both LTR and non-LTR retrotransposons and constitute a third, probably very ancient, class of eukaryotic retroelement (8). The mechanism by which PLEs transpose is unknown, and from the amino acid sequence of the highly divergent RT it is not clear whether it can function as a RT, given the ability of PLEs to retain introns.…”

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confidence: 99%

“…Our recent investigation of PLEs in D. virilis and bdelloid rotifers revealed that the majority of PLE genomic copies in these species contain spliceosomal introns (8). The GIY-YIG domain of PLEs is of special interest in this respect because of its potential to participate in a DNA-dependent transposition pathway similar to that used by group I and occasionally group II introns (10,11).…”

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“…Elements from several different families, both transposons and retrotransposons, transpose in the progeny of such a cross, with Penelope apparently playing a key role in mobilizing the others (4). PLEs have been reported in genomes of crustaceans, echinoderms, fish, amphibians, f latworms, roundworms, and rotifers (5)(6)(7)(8). Phylogenetic analysis indicates that the reverse transcriptases (RTs) of Penelope and other PLEs do not belong to any of the characterized major RT lineages, being closer to telomerase RTs (TERTs) than to any other RT (8).…”

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confidence: 99%

“…PLEs have been reported in genomes of crustaceans, echinoderms, fish, amphibians, f latworms, roundworms, and rotifers (5)(6)(7)(8). Phylogenetic analysis indicates that the reverse transcriptases (RTs) of Penelope and other PLEs do not belong to any of the characterized major RT lineages, being closer to telomerase RTs (TERTs) than to any other RT (8). The C-terminal domain of the Penelope polyprotein is predicted to encode an endonuclease (EN) of the Uri family that could function as an integrase.…”

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Reverse transcriptase and endonuclease activities encoded by Penelope -like retroelements

Pyatkov

Arkhipova

Malkova

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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Penelope-like elements are a class of retroelement that have now been identified in >50 species belonging to at least 10 animal phyla. The Penelope element isolated from Drosophila virilis is the only transpositionally active representative of this class isolated so far. The single ORF of Penelope and its relatives contains regions homologous to a reverse transcriptase of atypical structure and to the GIY-YIG, or Uri, an endonuclease (EN) domain not previously found in retroelements. We have expressed the single ORF of Penelope in a baculovirus expression system and have shown that it encodes a polyprotein with reverse transcriptase activity that requires divalent cations (Mn 2؉ and Mg 2؉ ). We have also expressed and purified the EN domain in Escherichia coli and have demonstrated that it has EN activity in vitro. Mutations in the conserved residues of the EN catalytic module abolish its nicking activity, whereas the DNA-binding properties of the mutant proteins remain unaffected. Only one strand of the target sequence is cleaved, and there is a certain degree of cleavage specificity. We propose that the Penelope EN cleaves the target DNA during transposition, generating a primer for reverse transcription. Our results show that an active Uri EN has been adopted by a retrotransposon.GIY-YIG endonuclease ͉ retrotransposons ͉ Drosophila virilis ͉ Uri domain

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Telomerase, Retrotransposons, and Evolution

Arkhipova

2012

Telomerases

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Retroelements containing introns in diverse invertebrate taxa

Cited by 114 publications

References 13 publications

Diverse DNA transposons in rotifers of the class Bdelloidea

Diverse DNA transposons in rotifers of the class Bdelloidea

Reverse transcriptase and endonuclease activities encoded by Penelope -like retroelements

Telomerase, Retrotransposons, and Evolution

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