Two novelPao-like retrotransposons (KamikazeandYamato) from the silkworm speciesBombyx moriandB.mandarina: common structural features ofPao-like elements

To characterize the structural features common toPao-like retrotransposons, we analyzed two lambda phage clones which contain thePao-like elements from the silkworm speciesBombyx moriandB.mandarina, and copies ofPaoitself andninjaofDrosophila simulans, amplified by PCR. We previously identified two randomly amplified polymorphic DNAs (RAPDs), W-Kamikaze and W-Yamato, fromB.moriandB.mandarina, which are part of two novelPao-like retrotransposons,KamikazeandYamato, respectively. Complete characterization of these and other elements of this group reported here shows thatPao-like elements have common features that distinguish them from the other groups of LTR-retrotransposons. While the elements of the Ty1-copiagroup encode only one cysteine and histidine (Cys) motif in theirgag-like region, thePao-like elements specify three Cys motifs. The highly conserved D(35)E motif in the integrase domain of the retrotransposon polyprotein seems to be conserved inPao-like elements, but the number of amino acid residues between D and E varies and is greater than 35. A comparison of the deduced amino acid sequences of the reverse transcriptase domain revealed that thePao-like elements are members of neither the Ty1-copianor thegypsy-Ty3 groups. Therefore, we confirmed that the long-terminal-repeat (LTR) retrotransposons should be divided into three major groups (or families), namely the Ty1-copia,gypsy-Ty3, andPao-like groups.