A novel initiation complex for reverse transcription of an active LTR retrotransposon in sweetpotato [Ipomoea batatas]

Tahara, M.. Faculty of Agriculture; Yamashita, H.

A novel initiation complex for reverse transcription of an active LTR retrotransposon in sweetpotato [Ipomoea batatas]

2007

Tahara, M.(Okayama Univ. (Japan). Faculty of Agriculture) | Yamashita, H.

Sequence analysis of Rtsp-1, an active LTR retrotransposon in the sweetpotato genome, revealed a possible novel Rtsp-1 RNA/tRNAsup (Met) complex for initiation of reverse transcription and the first DNA strand transfer. The Rtsp-1 RNA has a primer binding site (PBS) that is partly complementary to the 3' end of tRNAsup(Met), and possesses an additional sequence complementary to the 5' end of tRNAsup(Met) downstream of the PBS. These additional base-pairings might stabilize the Rtsp-1 RNA/primer complex. In the free form, the 5' LTR of Rtsp-1 appears to form a stemloop structure apparently preventing the initiation of reverse transcription. While the stem-forming site adjacent to the PBS is complementary to the tRNAsup(Met), the other stem-forming site on the LTR complements a region just upstream of the 3' LTR. Additionally, another region at the 3' end of the Rtsp-1 RNA shows sequence complementarity to the tRNAsup(Met). As the 3' end of Rtsp-1 approaches the tRNAsup(Met) bound to the PBS, the stem-forming strands dissociate and basepair with their complementary regions in the tRNAsup(Met) and the 3' end of Rtsp-1, respectively. Consequently, the LTR loop opens, allowing reverse transcription to initiate. After the initial reverse transcription stops at the 5' end of the Rtsp-1 RNA, the synthesized minus strand DNA needs to be transferred to the 3' end of the RNA to synthesize internal sequences. The Rtsp-1 RNA/ tRNAsup(Met) complex may have evolved to facilitate this DNA transfer. Similar RNA/tRNA initiation complexes have been reported from reverse transcription in retroviruses and yeast retrotransposons (Ty1 and Ty3).

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