Two novel Pao-like retrotransposons (Kamikaze and Yamato) from the silkworm species Bombyx mori and B-mandarina: common structural features of Pao-like elements

To characterize the structural features common to Pao-like retrotransposons , we analyzed two lambda phage clones which contain the Pao-like elements f rom the silkworm species Bombyx mori and B. mandarina, and copies of Pao it self and ninja of Drosophila simulans, amplified by PCR. We previously iden tified two randomly amplified polymorphic DNAs (RAPDs), W-Kamikaze and W-Ya mato, from B. mori and B. mandarina, which are part of two novel Pao-like r etrotransposons, Kamikaze and Yamato, respectively. Complete characterizati on of these and other elements of this group reported here shows that Pao-l ike elements have common features that distinguish them from the other grou ps of LTR-retrotransposons. While the elements of the Ty1-copia group encod e only one cysteine and histidine (Cys) motif in their gag-like region, the Pao-like elements specify three Cys motifs. The highly conserved D(35)E mo tif in the integrase domain of the retrotransposon polyprotein seems to be conserved in Pao-like elements, but the number of amino acid residues betwe en D and E varies and is greater than 35. A comparison of the deduced amino acid sequences of the reverse transcriptase domain revealed that the Pao-l ike elements are members of neither the Ty1-cepia nor the gypsy-Ty3 groups. Therefore, we confirmed that the long-terminal-repeat (LTR) retrotransposo ns should be divided into three major groups (or families), namely the Ty1- copia, gypsy-Ty3, and Pao-like groups.