A Novel Initiation Complex for Reverse Transcription of an Active LTR Retrotransposon in Seeetpotato

Sequence analysis of Rtsp-1, an active LTR retrotransposon in the sweetpotato genome,revealed a possible novel Rtsp-1 RNA/tRNAMet 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 tRNAMet, and possesses an additional sequence complementary to the 5’ end of tRNAMet 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 stemforming site adjacent to the PBS is complementary to the tRNAMet, 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 tRNAMet. As the 3’ end of Rtsp-1 approaches the tRNAMet bound to the PBS, the stem-forming strands dissociate and basepair with their complementary regions in the tRNAMet 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/tRNAMet 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).