Original Paper

Molecular Genetics and Genomics

, Volume 265, Issue 2, pp 375-385

First online:

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

  • H. AbeAffiliated withDepartment of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan
  • , F. OhbayashiAffiliated withGraduate School of Agriculture and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
  • , T. SugasakiAffiliated withDepartment of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan
  • , M. KaneharaAffiliated withDepartment of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan
  • , T. TeradaAffiliated withDepartment of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan
  • , T. ShimadaAffiliated withGraduate School of Agriculture and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
  • , S. KawaiAffiliated withDepartment of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan
  • , K. MitaAffiliated withGenome Research Group, National Institute of Radiological Sciences, Anagawa, Inage-ku, Chiba 236-8555, Japan
  • , Y. KanamoriAffiliated withDrosophila Genetic Resource Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
    • , M.-T. YamamotoAffiliated withDrosophila Genetic Resource Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
    • , T. OshikiAffiliated withDepartment of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan

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Abstract.

To characterize the structural features common to Pao-like retrotransposons, we analyzed two lambda phage clones which contain the Pao-like elements from the silkworm species Bombyx mori and B. mandarina, and copies of Pao itself and ninja of Drosophila simulans, amplified by PCR. We previously identified two randomly amplified polymorphic DNAs (RAPDs), W-Kamikaze and W-Yamato, from B. mori and B. mandarina, which are part of two novel Pao-like retrotransposons, Kamikaze and Yamato, respectively. Complete characterization of these and other elements of this group reported here shows that Pao-like elements have common features that distinguish them from the other groups of LTR-retrotransposons. While the elements of the Ty1-copia group encode 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 motif in the integrase domain of the retrotransposon polyprotein seems to be conserved in Pao-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 the Pao-like elements are members of neither the Ty1-copia nor the gypsy-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, and Pao-like groups.

Retrotransposon Pao Bombyx mori Bombyx mandarina