Institution: NIH Library Sign In as Member / Individual

This Article Abstract Full Text Services Alert me to new issues of the journal Request Copyright Permission

Supporting Information

Files in this Data Supplement:

Fig. 5. Multiple sequence alignments of reverse transcriptase (RT) and endonuclease (EN) domains of Penelope-like elements (PLEs). RT motifs 3–7 and EN motifs A–E are indicated. The following PLE sequences are included in the alignments: Penelope, retrotransposon from Drosophila virilis (GI:1224056); Poseidon/Xena, retrotransposon from Fugu rubripes (GI:14285210); Neptune, retrotransposon from F. rubripes (GI:22425119); Cercyon, retrotransposon from Schistosoma mansoni (GI:28261408); ORFs from Danio rerio (GI:38453680 and GI:34996465), Ciona intestinalis (GI:26555599 and GI:26554523), Caenorhabditis briggsae (GI:22417579), Xenopus tropicalis (GI:48675390), Aedes aegypti (GI:30005240, GI:29943436, and GI:29910170), and Strongylocentrotus purpuratus (GI:8356985 and whole-genome shotgun trace files). PLE sequences from Schmidtea mediterranea and Caenorhabditis remanei were obtained from National Center for Biotechnology Information trace archives, and the assembled majority-rule consensus sequences are available from I.R.A. upon request. For comparison, the following amino acid sequences are also included: RTs of telomerases (TERT) from Giardia intestinalis (GI:29250227), Schisosaccharomyces pombe (GI:6226782), Encephalitozoon cuniculi (GI:19173151), and Rattus norvegicus (GI:34853341), of non-LTR retrotransposons CRE from Crithidia fasciculata (GI:102036) and jockey from D. melanogaster (GI:134083), and of LTR retrotransposons/retroviruses gypsy from D. melanogaster (GI:130583) and Moloney murine leukemia virus (Mo-MuLV; GI:13959690); Uri domain endonucleases from Chilo iridescent virus (CIV; GI:7461109), I-Tev1 from bacteriophage T4 (GI:6094464), and UvrC from Methanothermobacter thermautotrophicus (GI:2621507). Note the extended region of similarity between PLEs and TERT in motif 4. Alignments were constructed by using the clustal-based alignx program from the vectornti suite (InforMax, Bethesda) with amino acids colored as follows: yellow background, identical; green background, block of similar amino acids; blue letters, conservative; green letters, weakly similar amino acids. Consensus sequences (50%) are shown below each alignment.

Fig. 6. The 3D structure of the Penelope EN domain inferred from homology modeling. Homology modeling of the 3D structure of Penelope EN (residues 725–820) was done with swiss-pdbv (Swiss Institute of Bioinformatics, Basel) by using the I-TevI Protein Data Bank entry 1MK0 as a template. Optimization of the model was performed on the Swiss-Model automated comparative protein modeling server (http: expasy.org/swissmod/SWISS-MODEL.html) with what_if quality control option. A ribbon diagram of the Penelope EN (in color) is superimposed on the I-TevI template (in gray). Side chains are shown for highly conserved residues, including those subjected to mutagenesis (black), and for multiple lysines on the positively charged helix α1 (blue).