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MBE Advance Access published online on November 2, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj046
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted October 19, 2005

Research Article

The Trypanosoma Cruzi L1Tc and NARTc Non-LTR Retrotransposons Show Relative Site-Specificity for Insertion

Frédéric Bringaud 1*, Daniella C. Bartholomeu 2, Gaëlle Blandin 2, Arthur Delcher 2, Théo Baltz 1, Najib M. A. El-Sayed 3, and Elodie Ghedin 3

1 Laboratoire de Génomique Fonctionnelle des Trypanosomatides, Université Victor Segalen Bordeaux 2, UMR-5162 CNRS, 146 rue Léo Saignat, 33076 Bordeaux cedex, FRANCE
2 The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD, 10850, USA
3 The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD, 10850, USA; George Washington University, Dept. of Microbiology and Tropical Medicine, Washington, DC, USA

* To whom correspondence should be addressed.
Frédéric Bringaud, E-mail: bringaud{at}u-bordeaux2.fr


  Abstract

The trypanosomatid protozoan Trypanosoma cruzi contains long autonomous (L1Tc) and short non-autonomous (NARTc) non-LTR retrotransposons. NARTc (0.25 kb) probably derived from L1Tc (4.9 kb) by 3'-deletion. It has been proposed that their apparent random distribution in the genome is related to the L1Tc-encoded apurinic/apyrimidinic endonuclease activity, which repairs modified residues. To address this question we used the T. cruzi (CL Brener strain) genome data to analyze the distribution of all the L1Tc/NARTc elements present in contigs larger than 10 kilobases. This dataset, which represents 0.91x sequence coverage of the haploid nuclear genome (~55 Mb), contains 419 elements, including 112 full-length L1Tc elements (14 of which are potentially functional) and 84 full-length NARTc. Approximately half of the full-length elements are flanked by a target site duplication, most of them (87%) are 12 bp long. Statistical analyses of sequences flanking the full-length elements show the same highly conserved pattern upstream of both the L1Tc and NARTc retrotransposons. The two most conserved residues are a guanine and an adenine, which flank the site where first-strand cleavage is performed by the element-encoded endonuclease activity. This analysis clearly indicates that the L1Tc and NARTc elements display relative site-specificity for insertion, which suggests that the apurinic/apyrimidinic endonuclease activity is not responsible for first-strand cleavage of the target site.

Keywords: apurinic/apyrimidinic-endonuclease; L1Tc; NARTc; non-LTR retrotransposon; retroposon; site-specificity; Trypanosoma cruzi.
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