Arkhipova Irina R.

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Last Name
Arkhipova
First Name
Irina R.
ORCID
0000-0002-4805-1339

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End date: 2009 × Subject: Reverse transcriptase ×

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  • Article
    Distribution and phylogeny of Penelope-like elements in eukaryotes
    (Oxford University Press, 2006-10) Arkhipova, Irina R.
    Penelope-like elements (PLEs) are a relatively little studied class of eukaryotic retroelements, distinguished by the presence of the GIY-YIG endonuclease domain, the ability of some representatives to retain introns, and the similarity of PLE-encoded reverse transcriptases to telomerases. Although these retrotransposons are abundant in many animal genomes, the reverse transcriptase moiety can also be found in several protists, fungi, and plants, indicating its ancient origin. A comprehensive phylogenetic analysis of PLEs was conducted, based on extended sequence alignments and a considerably expanded data set. PLEs exhibit the pattern of evolution similar to that of non-LTR retrotransposons, which form deep-branching clades dating back to the Precambrian era. However, PLEs seem to have experienced a much higher degree of lineage losses than non-LTR retrotransposons. It is suggested that PLEs and non-LTR retrotransposons are included into a larger eTPRT (eukaryotic target-primed) group of retroelements, characterized by 5' truncation, variable target-site duplication, and the potential of the 3' end to participate in formation of non-autonomous derivatives.
  • Preprint
    Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes
    ( 2007-02-27) Gladyshev, Eugene A. ; Arkhipova, Irina R.
    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.
  • Preprint
    A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers
    ( 2006-09-12) Gladyshev, Eugene A. ; Meselson, Matthew ; Arkhipova, Irina R.
    Rotifers of class Bdelloidea, a group of aquatic invertebrates in which males and meiosis have never been documented, are also unusual in their lack of multicopy LINE-like and gypsy-like retrotransposons, groups inhabiting the genomes of nearly all other metazoans. Bdelloids do contain numerous DNA transposons, both intact and decayed, and domesticated Penelope-like retroelements Athena, concentrated at telomeric regions. Here we describe two LTR retrotransposons, each found at low copy number in a different bdelloid species, which define a clade different from previously known clades of LTR retrotransposons. Like bdelloid DNA transposons and Athena, these elements have been found preferentially in telomeric regions. Unlike bdelloid DNA transposons, many of which are decayed, the newly described elements, named Vesta and Juno, inhabiting the genomes of Philodina roseola and Adineta vaga, respectively, appear to be intact and to represent recent insertions, possibly from an exogenous source. We describe the retrovirus-like structure of the new elements, containing gag, pol, and env-like open reading frames, and discuss their possible origins, transmission, and behavior in bdelloid genomes.