Nucleotide sequence characterization of a Drosophila retrotransposon, 412

Abstract

The nucleotide sequence of the internal region of a Drosophila retrotransposon. 412, was determined. The genome of 412 was found to consist of two long open-reading frames (ORFs 1 and 2), an unusually long putative leader region and long terminal repeats (LTRs). As with 17.6, 297 and gypsy, ORFs 1 and 2 slightly overlap each other and are out of phase by + 2 . ORF2 includes the nucleotide sequences coding for the putative protease, reverse transcriptase and integrase, and is similar in entire organization to the pol gene of Moloney murine leukaemia virus. In spite of the difference in insertion specificity, integrase, an enzyme presumably responsible for insertion, was found to be similar in amino acid sequence to the counterparts of 17.6, 297 and gypsy. There is no ORF in 412 which corresponds to retroviral env or ORF3s of 17.6 and 297. Analysis of 412 transcripts suggested that 412 LTR is composed of U3, R and U5. The gene for a potential primer tRNA for putative reverse transcription of 412 was also surveyed and the 3'-terminal 15 nucleotides of a putative arginine tRNA were found to be exactly complementary to the putative primer-binding site of 412.Drosophila copia-like elements or retrotransposons are formed from the largest group of transposable genetic elements in Drosophila melanogaster. They are intimately related in evolution to retroviral proviruses in vertebrates In our previous experiments the complete nucleotide sequences of three Drosophila retrotransposons 17.6 [15], 297 [16] and copia [17] were determined. 17.6 and 297 contained three open reading frames (ORFs) similar in size and location to retroviral gag, pol and env. The second ORFs of these two elements were further shown each to include the nucleotide sequence coding for a reverse-transcriptase-like enzyme and be, in all respects of their organization, very similar to the pol gene of Moloney murine leukaemia virus (Mo-MuLV) [15,16, 181. In contrast, the genome of copia contained a single long ORF [17, 191 including genes for the major capsid protein of copia-related virus-like particles and reverse-transcriptase-like enzyme much less similar to the reverse transcriptase of MoMuLV [17,19]. These results suggest the genome organization in Drosophila retrotransposons to be very much diversified.To confirm and determine the further implications of this notion, a determination was made of the complete nucleotide sequence of another Drosophila retrotransposon, 412, having terminal dinucleotides identical to those of copia and retrovirus proviruses but different from those of 17.6, 297 and gypsy [4, 15-17, 20, 211. The genome of 412 was found to contain two long ORFs (ORFs 1 and 2) and an unusually long putative leader region with two short ORFs. As with 17.6 [15], 297 [16] and gypsy (unpublished), ORFs 3 and 2 slightly overlap each other and are out of phase by t 2 . The entire structure of ORF2 is of the 17.6 type and the putative integrase encoded by a portion of ORF2 is similar in amino acid sequence to the counterparts of 17.6, 297 and gy...

Identification of novel random amplified polymorphic DNAs (RAPDs) on the W chromosome of the domesticated silkworm, Bombyx mori, and the wild silkworm, B. mandarina, and their retrotransposable elementrelated nucleotide sequences.

“…U43135); the sequence defined by nt 17-125 was 99% (108 of 109 nt) identical to nt 1621-1513 of the W-Kabuki RAPD. The second homology was found in the reverse transcriptase (RT)-like enzyme coding region of retrotransposon 412 of D. melanogaster (Yuki et al, 1986) (accession Nos. X04132, X03733) in which the sequence defined by nt 4757-4960 was 54% homologous to nt 2064-1861 of the W-Kabuki RAPD.…”

“…For example, aa 22-134, 22-148, and 29-124 exhibit aa identity (similarity) of 42% (58%) with aa 554-666 of the RNase H domain in the polyprotein of retrotransposon TED from Tricoplusia ni (accession No. B36329) (Friesen and Nissen, 1990), 37% (59%) with aa 579-705 of the pol polyprotein of retrotransposon 412 from D. melanogaster (Yuki et al, 1986), and 40% (61%) with aa 588-683 of CfT-1 isolated from the fungus Cladosporium fulvum (accession No. S23570), respectively (Fig.…”

Tissue-specificity of 412 retrotransposon expression in Drosophila simulans and D. melanogaster

“…Briefly, ovaries and testes from 5-day-old flies were dissected in 1× PBS, fixed with 4% paraformaldehyde, treated with proteinase K and simultaneously hybridized with an internal 1.8 kb 412 labelled fragment. The fragment was obtained by PCR amplification of region 4283-6088 according to the complete 412 sequence described by Yuki et al (1986), and was labelled with the digoxygenin DNA labelling kit (Boehringer Mannheim/Roche), according to the manufacturer's instructions. Ten males and 10 females were analysed for each population.…”

“…containing at its 3′ end a sequence homologous to region 4697-4716 (underlined) of the 412 element, and at its 5′ end, the 5′ oligonucleotide used for 412 amplification (position 4283-4308, Yuki et al (1986)). The 3′ oligonucleotide corresponded to the integrase region, position 6088-6063 (5′-TTCTATGACTTCTTTCTACTACTCC-3′) of the 412 sequence (Yuki et al, 1986).…”

“…The 3′ oligonucleotide corresponded to the integrase region, position 6088-6063 (5′-TTCTATGACTTCTTTCTACTACTCC-3′) of the 412 sequence (Yuki et al, 1986).…”