&lt;i&gt;Penelope&lt;/i&gt;-like elements – a new class of retroelements: distribution, function and possible evolutionary significance

Evgen’ev, Michael B.; Arkhipova, Irina R.

doi:10.1159/000084984

Cited by 73 publications

(75 citation statements)

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“…Discovered in 1970 in the Rous Sarcoma and murine leukemia viruses (1,2), RT has since been studied for its central role in the replication of many eukaryotic genetic elements including retroviruses (e.g., HIV-1), pararetroviruses, hepadnaviruses, long terminal repeat (LTR), and non-LTR retroelements, Penelope-like elements, and telomerase (3,4,5,6,7,8,9,10). Over the years, the accumulated studies of RT have painted a picture in which the enzyme functions primarily as the replicative enzyme of selfish DNAs (viruses, retrotransposons), while occasionally becoming domesticated to perform useful cellular functions.…”

Section: Introductionmentioning

confidence: 99%

An Unexplored Diversity of Reverse Transcriptases in Bacteria

Zimmerly

2015

Microbiol Spectr

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Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.

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Section: Introductionmentioning

confidence: 99%

An Unexplored Diversity of Reverse Transcriptases in Bacteria

Zimmerly

2015

Microbiol Spectr

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“…Penelope does not belong to conventional long interspersed nuclear element or long terminal repeat (LTR) retroelement classes, but instead represents an active member of a little-studied element family termed, ''Penelope-like elements'' (PLEs) (Evgen'ev and Arkhipova 2005). These are distinguished by the presence of a GIY-YIG endonuclease domain and the ability to retain introns despite moving via an RNA intermediate.…”

Section: Introductionmentioning

confidence: 99%

Small RNA-based silencing strategies for transposons in the process of invading Drosophila species

Rozhkov¹,

Aravin²,

Zelentsova³

et al. 2010

RNA

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Colonization of a host by an active transposon can increase mutation rates or cause sterility, a phenotype termed hybrid dysgenesis. As an example, intercrosses of certain Drosophila virilis strains can produce dysgenic progeny. The Penelope element is present only in a subset of laboratory strains and has been implicated as a causative agent of the dysgenic phenotype. We have also introduced Penelope into Drosophila melanogaster, which are otherwise naive to the element. We have taken advantage of these natural and experimentally induced colonization processes to probe the evolution of small RNA pathways in response to transposon challenge. In both species, Penelope was predominantly targeted by endo-small-interfering RNAs (siRNAs) rather than by piwi-interacting RNAs (piRNAs). Although we do observe correlations between Penelope transcription and dysgenesis, we could not correlate differences in maternally deposited Penelope piRNAs with the sterility of progeny. Instead, we found that strains that produced dysgenic progeny differed in their production of piRNAs from clusters in subtelomeric regions, possibly indicating that changes in the overall piRNA repertoire underlie dysgenesis. Considered together, our data reveal unexpected plasticity in small RNA pathways in germ cells, both in the character of their responses to invading transposons and in the piRNA clusters that define their ability to respond to mobile elements.

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“…Penelope-like elements (PLEs) are a widespread but not very extensively studied class of eukaryotic TEs characterized by a single ORF coding for RT and an unusual GIY-YIG EN domain also found in bacterial group I introns, and by the presence of spliceosomal introns in several members (4,6). They occupy a special place in retroelement phylogeny by sharing a common ancestor with TERTs (4).…”

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confidence: 99%

Telomere-associated endonuclease-deficient Penelope -like retroelements in diverse eukaryotes

Gladyshev

Arkhipova

2007

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

123

132

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The evolutionary origin of telomerases, enzymes that maintain the ends of linear chromosomes in most eukaryotes, is a subject of debate. Penelope-like elements (PLEs) are a recently described class of eukaryotic retroelements characterized by a GIY-YIG endonuclease domain and by a reverse transcriptase domain with similarity to telomerases and group II introns. Here we report that a subset of PLEs found in bdelloid rotifers, basidiomycete fungi, stramenopiles, and plants, representing four different eukaryotic kingdoms, lack the endonuclease domain and are located at telomeres. The 5 truncated ends of these elements are telomereoriented and typically capped by species-specific telomeric repeats. Most of them also carry several shorter stretches of telomeric repeats at or near their 3 ends, which could facilitate utilization of the telomeric G-rich 3 overhangs to prime reverse transcription. Many of these telomere-associated PLEs occupy a basal phylogenetic position close to the point of divergence from the telomerase-PLE common ancestor and may descend from the missing link between early eukaryotic retroelements and present-day telomerases.reverse transcriptase ͉ telomerase ͉ transposable elements G enomic DNA in many eukaryotes is composed, to a large extent, of transposable elements (TEs), especially retrotransposons, which multiply via an RNA intermediate copied into DNA by reverse transcriptase (RT) and inserted into new sites by an endonuclease (EN)/integrase. Although RT creates new copies, DNA cleavage is essential for TE proliferation, i.e., insertion into previously unoccupied sites. Integrases of retrovirus-like (LTR) retrotransposons insert dsDNA into chromosomes, whereas EN of non-LTR retrotransposons generate the 3ЈOH-end that primes cDNA synthesis directly onto the chromosome (target-primed reverse transcription). The only known eukaryotic RT-containing genes lacking EN domains are telomerase RTs (TERTs), which are not TEs but specialized ribonucleoprotein enzymes maintaining telomeres by repeated copying of a short segment of an unlinked template RNA, primed by the 3ЈOH end of a linear chromosome (see refs. 1-5 for review).Penelope-like elements (PLEs) are a widespread but not very extensively studied class of eukaryotic TEs characterized by a single ORF coding for RT and an unusual GIY-YIG EN domain also found in bacterial group I introns, and by the presence of spliceosomal introns in several members (4, 6). They occupy a special place in retroelement phylogeny by sharing a common ancestor with TERTs (4). PLEs insert relatively randomly throughout the genome, preferring AT-rich targets (6). Indeed, the element-encoded EN, in which the conserved residues are essential for transposition, exhibits some sequence preferences but no pronounced sequence specificity (7).Rotifers of the class Bdelloidea, a large taxon of multicellular freshwater invertebrates considered to be anciently asexual (8,9), contain a distinct group of PLEs, called Athena (4), carrying spliceosomal introns within highly conserve...

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<i>Penelope</i>-like elements – a new class of retroelements: distribution, function and possible evolutionary significance

Cited by 73 publications

References 93 publications

An Unexplored Diversity of Reverse Transcriptases in Bacteria

An Unexplored Diversity of Reverse Transcriptases in Bacteria

Small RNA-based silencing strategies for transposons in the process of invading Drosophila species

Telomere-associated endonuclease-deficient Penelope -like retroelements in diverse eukaryotes

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