Primary structure and functional organization of Drosophila 1731 retrotransposon

Abstract

We have determined the nucleotide sequence of the Drosophila retrotransposon 1731. 1731 is 4648 bp long and is flanked by 336 bp terminal repeats (LTRs) previously described as being reminiscent of provirus LTRs. The 1731 genome consists of two long open reading frames (ORFs 1 and 2) which slightly overlap each other. The ORF 1 and 2 present similarities with retroviral gag and pol genes respectively as shown by computer analysis. The pol gene exhibits several enzymatic activities in the following order: protease, endonuclease and reverse transcriptase. It is possible that 1731 also encompasses a ribonuclease H activity located between the endonuclease and reverse transcriptase domains. Moreover, comparison of the 1731 pol gene with the pol region of copia shows similarities extending over the protease, endonuclease and reverse transcriptase domains. We show that codon usage in the two retrotransposons is different. Finally, no ORF able to encode an env gene is detected in 1731.

copia-like retrotransposons are ubiquitous among plants.

“…2 Table 1, and sequences for previously characterized retrotransposons not referenced in Fig. 1 include 1731 of D. melanogaster (7) and TalO of A. thaliana (8). copia-like reverse transcriptases.…”

“…The structural organization ofthese elements and phylogenetic analyses based on the Tal reverse transcriptase clearly placed this family of elements among the copia-like retrotransposons (3). At the time of their discovery in Arabidopsis, characterized copia-like retrotransposons included Ty) and Ty2 of Saccharomyces cerevisiae (5) and two element families in D. melanogaster, copia and 1731 (6,7). More recently we have characterized two other copia-like retrotransposons in A. thaliana (Ta2 and Ta3) (8), and additional copia-like elements have been identified in tobacco (Tnt)) (9), potato (Tstl) (10), wheat (WIS-2) (11), and the slime mold Physarum polycephalum (Tp)) (12).…”

The Gag polypeptides of the Drosophila 1731 retrotransposon are associated to virus‐like particles and to nuclei

“…Analysis of the amino-acid sequence of 1731 ORF 1 revealed the presence of a nucleic acid binding domain and led us to consider it as a putative retroviral-like Gag protein [5] which is expected to be the main structural component of 1731 VLPs. Following insertion of the E. coli lacZ gene into the NruI site of 1731 (see fig.…”

“…Internal sequences homologous to retroviral gag and pol genes have been reported in all retrotransposons described so far. Such a canonical structure has been reported for the Drosophila melanogaster 1731 retrotransposon: the internal sequence should be the template for both the structural protein components of the virus-like particle (Gag proteins) and the enzymes involved in the replication of the genomic RNA, namely the protease, the integrase and the RNase H-reverse transcriptase (RT) (Pol proteins) [5]. In retrotransposons, such an internal order of the pol genes is a typical feature of the copia/Ty 1 group [2][3][4]6].…”

“…We hypothesised that such a sequence was brought by the p22 peptide, enabling its nuclear localization. This polypeptide is expected to derive from the C-terminal moiety of the 1731 Gag protein and to possess not only the NLS but also a nucleic acid binding site (nucleotide position: 1099-1147 in [5]). It is now well established that proteolytic control is involved in the mechanism of nuclear addressing of some transcription factors [34].…”