Two novel Pao -like retrotransposons ( Kamikaze and Yamato ) from the silkworm species Bombyx mori and B . mandarina : c
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O R I GI N A L P A P E R
H. Abe á F. Ohbayashi á T. Sugasaki á M. Kanehara T. Terada á T. Shimada á S. Kawai á K. Mita Y. Kanamori á M.-T. Yamamoto á T. Oshiki
Two novel Pao -like retrotransposons (Kamikaze and Yamato) from the silkworm species Bombyx mori and B. mandarina : common structural features of Pao -like elements Received: 29 August 2000 / Accepted: 4 December 2000 / Published online: 21 February 2001 Ó Springer-Verlag 2001
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, ampli®ed by PCR. We previously identi®ed two randomly ampli®ed polymorphic DNAs (RAPDs), W-Kamikaze and W-Yamato, from B. mori and B. mandarina, which are part of two novel Paolike retrotransposons, Kamikaze and Yamato, respectively. Complete characterization of these and other elements of this group reported here shows that Paolike 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 Communicated by D. Gubb H. Abe (&) á T. Sugasaki á M. Kanehara á T. Terada S. Kawai á T. Oshiki Department of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan E-mail: [email protected] Fax: +81-42-3608830 F. Ohbayashi á T. Shimada Graduate School of Agriculture and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan K. Mita Genome Research Group, National Institute of Radiological Sciences, Anagawa, Inage-ku, Chiba 236-8555, Japan Y. Kanamori á M.-T. Yamamoto Drosophila Genetic Resource Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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 con®rmed 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. Key words Retrotransposon á Pao á Bombyx mori á Bombyx mandarina
Introduction In general, retrotransposons are divided into two major classes: one class is the long terminal repeat (LTR) type, and the second class is the non-LTR type. LTR retrotransposons themselves have been divided into two major groups, namely the Ty1-copia and gypsy-Ty3 groups (or families). In retrotransposons of the Ty1copia group the integrase (Int) domain is located between the
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