Isolation and characterization of copia-type retrotransposons in Arabidopsis thaliana

We isolated two copia-type retrotransposons from Arabidopsis thaliana. We n amed these elements AtRE1 Arabidopsis thaliana Retro Element 1) and AtRE2. Nucleotide sequence analysis revealed that both elements have long terminal repeals (LTRs), and that their internal sequences include one large open r eading frame that could encode Gag protein, protease, integrase, reverse tr anscriptase, and RNaseH. The deduced amino acids sequences contain several domains that are conserved among a large family of retrotransposons. The pr imer binding site for first-strand DNA synthesis and the polypurine tract f or second-strand DN4 synthesis existed at corresponding positions. A 5 bp t arget site duplication (TSD) sequence was also found in the flanking region of LTRs. Southern hybridization and sequence determination of the flanking region demonstrated that ArREs exist at different loci in the two A. thali ana ecotypes Columbia and Landsberg erecta. Moreover, AtRE2 exists at two l oci in Landsberg erecta, in contrast to the existence of only one copy in C olumbia. These findings suggest that ArREs were recently transfected via so me mediators or that AtREs were transposed after differentiation of the two ecotypes. One cDNA clone derived from the transcripts of AtRE1 was isolate d, and the nucleotide sequence showed that this RNA was transcribed in the antisense direction. RT-PCR analysis revealed that AtRE1 was transcribed in both directions. This result suggests that the antisense RNA controls the expression of AtRE1 at the post-transcriptional level. (C) 2000 Elsevier Sc ience B.V. All rights reserved.