Journal Article

<i>ATLN</i> Elements, LINEs from <i>Arabidopsis thaliana</i>: Identification and Characterization

Kenichi Noma, Hisako Ohtsubo and Eiichi Ohtsubo

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 7, issue 5, pages 291-303
Published in print January 2000 | ISSN: 1340-2838
Published online January 2000 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/7.5.291

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Non-LTR retrotransposons (LINEs) are ubiquitous elements in the plant kingdom. Two hundred and nineteen LINE homologues (named ATLN) were identified in the A. thaliana genome, about 90% of which have been sequenced by a computer-aided homology search. Of these, the structures of 62 were analyzedin detail. Most, including those truncated for the 5′ regions, were flanked by direct repeats of a sequence of 7–21 bp long, the target site sequence duplicated upon retrotransposition of each member. Thirty ATLN members had two consecutive open reading frames, corresponding to orf1 and orf2 essential for retrotransposition. The phylogenetic tree constructed from the amino acid sequences of the endonuclease domains of the Orf2 proteins showed that the ATLN members were grouped in two families (I and II) and that the members of each family could be further divided into several subfamilies. The members of each subfamily had several unique structural features in common in the intergenic region between orf1 and orf2 as well as in the downstream regions of orf2. Interestingly, orf2 in almost all the ATLN members is located in the −1 frame relative to orf1, indicative of the existence of such translational control mechanisms as translational coupling or frame shifting to produce an amount of Orf2 protein appropriate to that of Orf1. Moreover, the most proximal sequences in the 5′ untranslated regions were non-homologous, even in members with the highest homology, unlike the LINEs in animals. The non-homologous sequences in the 5′ untranslated regions might be acquired at or after transcription during retrotransposition of the ATLN elements.

Keywords: Arabidopsis thaliana; non-LTR retrotransposon (LINE); target site duplication; translational control

Journal Article.  0 words. 

Subjects: Genetics and Genomics

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