Reverse transcriptase and endonuclease activities encoded by
            <i>Penelope</i>
            -like retroelements

Pyatkov, Konstantin; Arkhipova, Irina R.; Malkova, Natalia; Finnegan, David J.; Evgen’ev, Michael B.

doi:10.1073/pnas.0406281101

Cited by 47 publications

(39 citation statements)

References 43 publications

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“…The NTR and MR of EndoII (Fig. 1) show little similarity to the catalytic domains of I-TevI and UvrC enzymes, or to other GIY-YIG endonucleases (10,11,19,23,30,35,37,42,45,46); I-TevI lacks sequences N-terminal to motif A. In I-TevI and UvrC the largely helical heterologous regions between motives B and C are believed to be structurally important, stabilizing the hydrophobic core of the domain (40,41).…”

Section: Residues In the Giy-yig Motives (I)mentioning

confidence: 99%

Amino Acid Residues in the GIY-YIG Endonuclease II of Phage T4 Affecting Sequence Recognition and Binding as Well as Catalysis

Lagerbäck

Carlson

2008

J Bacteriol

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Phage T4 endonuclease II (EndoII), a GIY-YIG endonuclease lacking a carboxy-terminal DNA-binding domain, was subjected to site-directed mutagenesis to investigate roles of individual amino acids in substrate recognition, binding, and catalysis. The structure of EndoII was modeled on that of UvrC. We found catalytic roles for residues in the putative catalytic surface (G49, R57, E118, and N130) similar to those described for I-TevI and UvrC; in addition, these residues were found to be important for substrate recognition and binding. The conserved glycine (G49) and arginine (R57) were essential for normal sequence recognition. Our results are in agreement with a role for these residues in forming the DNA-binding surface and exposing the substrate scissile bond at the active site. The conserved asparagine (N130) and an adjacent proline (P127) likely contribute to positioning the catalytic domain correctly. Enzymes in the EndoII subfamily of GIY-YIG endonucleases share a strongly conserved middle region (MR, residues 72 to 93, likely helical and possibly substituting for heterologous helices in I-TevI and UvrC) and a less strongly conserved N-terminal region (residues 12 to 24). Most of the conserved residues in these two regions appeared to contribute to binding strength without affecting the mode of substrate binding at the catalytic surface. EndoII K76, part of a conserved NUMOD3 DNA-binding motif of homing endonucleases found to overlap the MR, affected both sequence recognition and catalysis, suggesting a more direct involvement in positioning the substrate. Our data thus suggest roles for the MR and residues conserved in GIY-YIG enzymes in recognizing and binding the substrate.Endonuclease II (EndoII) of coliphage T4, encoded by gene denA, catalyzes the initial step in host DNA degradation. It causes irreversible host shutoff and also initiates a nucleotide scavenge pathway that provides precursors for phage DNA synthesis (8). T4 phage DNA is protected from EndoII by the substitution of 5-hydroxymethyl deoxycytosine for dC during T4 DNA synthesis (9, 43). EndoII shares the sequence elements defining the GIY-YIG family of proteins (13,20) that includes the repair endonuclease UvrC and many homing endonucleases, such as the intron-encoded T4 endonuclease ITevI (20) and I-BmoI (10), as well as some type II restriction endonucleases (2,19). Like the homing endonucleases in the GIY-YIG family, EndoII cleaves a long, asymmetric, and ambiguous DNA sequence (4-6, 21). However, in contrast to what has been found for I-TevI (24), EndoII cleaves the two strands independently of each other (7), and only a CG dinucleotide 2 bp away from the scissile bond is strongly conserved (5). Double-strand cleavage by EndoII is the result of concerted singlestrand nicks (7), but many positions are only nicked, not cleaved.In UvrC (44), as well as in the GIY-YIG homing endonucleases (10, 12), the conserved motifs and catalytic activity reside in the amino-terminal domain, but the primary binding energy is conferred by a carboxy-termin...

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Section: Residues In the Giy-yig Motives (I)mentioning

confidence: 99%

Amino Acid Residues in the GIY-YIG Endonuclease II of Phage T4 Affecting Sequence Recognition and Binding as Well as Catalysis

Lagerbäck

Carlson

2008

J Bacteriol

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“…Remarkably many of the elements retain introns, which is unexpected for an element that makes additional copies of itself by reverse transcription. Given the significant divergence of the RT domains, it was important that the ORF of the original Penelope element was expressed, purified and shown to exhibit authentic RT activity (Pyatkov et al, 2004). …”

Section: Penelope-like Retrotransposonsmentioning

confidence: 99%

The diversity of retrotransposons and the properties of their reverse transcriptases

2008

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A number of abundant mobile genetic elements called retrotransposons reverse transcribe RNA to generate DNA for insertion into eukaryotic genomes. Four major classes of retrotransposons are described here. First, the long-terminal-repeat (LTR) retrotransposons have similar structures and mechanisms to those of the vertebrate retroviruses. Genes that may enable these retrotransposons to leave a cell have been acquired by these elements in a number of animal and plant lineages. Second, the tyrosine recombinase retrotransposons are similar to the LTR retrotransposons except that they have substituted a recombinase for the integrase and recombine into the host chromosomes. Third, the non-LTR retrotransposons use a cleaved chromosomal target site generated by an encoded endonuclease to prime reverse transcription. Finally, the Penelope-like retrotransposons are not well understood but appear to also use cleaved DNA or the ends of chromosomes as primer for reverse transcription. Described in the second part of this review are the enzymatic properties of the reverse transcriptases (RTs) encoded by retrotransposons. The RTs of the LTR retrotransposons are highly divergent in sequence but have similar enzymatic activities to those of retroviruses. The RTs of the non-LTR retrotransposons have several unique properties reflecting their adaptation to a different mechanism of retrotransposition.

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“…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).…”

mentioning

confidence: 99%

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

Gladyshev

Arkhipova

2007

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

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127

133

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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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Reverse transcriptase and endonuclease activities encoded by Penelope -like retroelements

Cited by 47 publications

References 43 publications

Amino Acid Residues in the GIY-YIG Endonuclease II of Phage T4 Affecting Sequence Recognition and Binding as Well as Catalysis

Amino Acid Residues in the GIY-YIG Endonuclease II of Phage T4 Affecting Sequence Recognition and Binding as Well as Catalysis

The diversity of retrotransposons and the properties of their reverse transcriptases

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

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