Crystal Structure of the Endonuclease Domain Encoded by the Telomere-specific Long Interspersed Nuclear Element, TRAS1

Abstract

The telomere-specific long interspersed nuclear element, TRAS1, encodes an endonuclease domain, TRAS1-EN, which specifically cleaves the telomeric repeat targets (TTAGG) n of insects and (TTAGGG) n of vertebrates. To elucidate the sequence-specific recognition properties of TRAS1-EN, we determined the crystal structure at 2.4-Å resolution. TRAS1-EN has a four-layered ␣/␤ sandwich structure; its topology is similar to apurinic/ apyrimidinic endonucleases, but the ␤-hairpin (␤ 10 -␤ 11 ) at the edge of the DNA-binding surface makes an extra loop that distinguishes TRAS1-EN from cellular apurinic/apyrimidinic endonucleases. A protein-DNA complex model suggests that the ␤ 10 -␤ 11 hairpin fits into the minor groove, enabling interaction with the telomeric repeats. Mutational studies of TRAS1-EN also indicated that the Asp-130 and ␤ 10 -␤ 11 hairpin structure are involved in specific recognition of telomeric repeats.Non-long terminal repeat retrotransposons, also known as long interspersed nuclear elements (LINEs), 1 are transposable elements that encode a reverse transcriptase and insert into genomic locations via RNA intermediates. The recent progress of the human genome project has revealed that one LINE, L1, integrates throughout chromosomes and occupies more than 20% of the genome (1). The integration of L1 may play a role in genetic diseases and cancers (2) and in gene evolution and genome reconstruction (3-5).The LINEs have been classified into two types according to the number of open reading frames (ORFs) (6). The first type of element has a single ORF and encodes an endonuclease domain near its C terminus; this type of endonuclease (also known as restriction enzyme-like endonuclease) is similar in some residual motifs to various prokaryotic restriction enzymes (7). The second type of element has two ORFs; ORF1 encodes a retroviral Gag-like protein whose function is still unclear, and ORF2 encodes a protein with an endonuclease domain at its N terminus and a reverse transcriptase domain in the center of the ORF. This class of endonuclease domain is made up of about 250 amino acid residues and shares sequence homology with apurinic/apyrimidinic endonucleases (APE), such as human APE1 and Escherichia coli exonuclease III.Most of the APE-like endonuclease-encoding retrotransposons do not insert in a sequence-specific manner into the host genome, like the human L1 elements that cleave AT-rich sequences with a low sequence specificity (8). However, several endonuclease-encoding LINE have very restricted integration targets within the genome (9). TRAS1 and R1Bm, found in Bombyx mori, are the typical sequence-specific elements, which insert between T and A of the (TTAGG) n telomeric repeat and a specific site in 28 S rDNA of B. mori, respectively (10, 11). Recent studies have shown that the endonuclease domain in the ORF2 of TRAS1 (12) and R1Bm (13) determines its own target sequence recognition and DNA cleavage activity.The amino acid identity between human APE1 and the endonuclease domain of TRAS1 (TRAS1-EN) is n...

Two families of non-LTR retrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni

“…In the APE domain, the distances between motifs V-VI and VII-VIII are shorter than the corresponding AP-pinches in AP endonucleases, and are similar to most other non-LTR elements, indicating that, like other LINEs, they should not be able to recognize apurinic/apyrimidinic DNA (Kajikawa et al, 2005). Secondary structure predictions for the EN domain of Syrinx and Daphne also correspond to that for other non-LTR retrotransposons (Kajikawa et al, 2005) and do not reveal an extra β-sheet implicated in sequence-specific interaction of TRAS1 EN with Bombyx mori telomeric DNA (Maita et al, 2004) (Fig. 2A).…”

Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus

“…4A). These six amino acid residues are superimposable on the corresponding conserved amino acid residues of enzymes in the DNase I-like folding superfamily (DNA repair exonuclease III from Escherichia coli (30), DNA repair endonuclease HAP1 from human (31), inositol polyphosphate-5-phosphatase of synaptojanin from Schizosaccharomyces pombe (32), the subunit B of cytolethal distending toxin from Haemophilus ducreyi (33), endonuclease of human Line-1 Orf2P (34) and endonuclease from the telomere-specific long interspersed nuclear element (35)). Almost all these residues are conserved in other bacterial and mammalian nSMases.…”

“…The amino acid residues of Bc-SMase are shown by the thick stick models. The amino acid residues from bovine DNase I (Protein Data Bank code 1DNK; blue) (12), DNA repair exonuclease III from E. coli (code 1AKO; red) (30), DNA repair endonuclease HAP1 from human (code 1BIX; orange) (31), inositol polyphosphate-5-phosphatase domain of synaptojanin from S. pombe (code 1I9Z; violet) (32), subunit B of cytolethal distending toxin from H. ducreyi (code 1SR4; pink) (33), endonuclease domain of human Line-1 Orf2P (code 1VYB; yellow) (34),and endonuclease domain from the telomere-specific long interspersed nuclear element (code 1WDU; cyan) (35) are shown as thin stick models.…”

Site-specific non-LTR retrotransposons

“…Crystal structures of APEs from some non-LTR elements have revealed folding patterns similar to those of AP endonucleases (34,59,92). However, the structures have an extra beta-hairpin at the DNA-binding surface, which is a common feature among APEs of non-LTR elements (34,59,92).…”

“…4). TRAS1, a predominant element in the TRAS family, is 7.8 kb in length and is inserted specifically into the site between the C and T of the CCTAA telomeric strand (58,59). A major element in the silkworm SART family, SART1 (SART1Bm), is 6.7 kb in length and is inserted specifically between the T and A of the TTAGG strand (60,61).…”