Plant retrotransposon from Lilium henryi is related to Ty3 of yeast and the gypsy group of Drosophila.

Abstract

The lily retrotransposon del 146 is 9345 base pairs (bp) long. It has long terminal repeats (LTRs) of 2406 bp (left) and 2415 bp (right), which differ in sequence by 1.4%. Sequences similar to those involved in priming DNA synthesis in retroviruses occur in the internal region. Near the left LTR is a sequence complementary to 18 residues at the 3' end of methionine initiator tRNA of three plant species, and a run of 12 purines occurs close to the right LTR. One internal reading frame of del 1-46 has relatively few stop codons. The 1462-codon product from this frame has motifs, in N to C terminus order, corresponding to those identified with RNA binding, protease, reverse transcriptase, RNase H, and integrase functions in retroviruses and certain other retrotransposons. Amino acid sequence comparisons of three conserved poi regions show delto be closely related to the Ty3 retrotransposon of yeast (37-40% identity). del is also related to the gypsy group of Drosophila (17.6, 297, gypsy/mdg4, and 412), showing closer identity with their reverse transcriptase (32-38%) and RNase H (36-45%) domains than with their integrase domain (21-26%). It is proposed that a gypsy group ancestor exchanged the integrase region with a more distantly related element since its divergence from a del/Ty3 common ancestor. The occurrence of related retrotransposons in three different kingdoms (plants, animals, and fungi) strongly implies their horizontal transmission in recent evolutionary time.The genome size of eukaryotes varies over an enormous range between species. Among flowering plants, for example, Lilium sp. have haploid genomes of =35 million kilobase pairs (kbp) (1), 500 times that ofArabidopsis thaliana, a plant at the other end of the scale (2). The DNA of very large genomes includes many families of repeated sequences whose individual members are interspersed with each other and with single copy sequences (3). The multiple copy number and scattered distribution of dispersed repeats together imply that they are derived from mobile elements.With the aim of defining the categories of dispersed repeat involved in the architecture of very large genomes, we have been characterizing the most abundant large element present in the genome of Lilium henryi (4,5 (10), and integrase activity has been demonstrated in vitro (11).By estimating the level of amino acid sequence identity in conserved pol domains, ancestral relationships have been deduced between retrotransposons including Tyl (12) and the recently described Ty3 of yeast (13), and the Drosophila elements copia (14, 15) and the gypsy group, which includes 17.6 (16), 297 (17), gypsy (18) [first recorded as mdg4 (19)], and 412 (20). These comparisons have been extended to include retroviruses and other retroid elements with coding potential for reverse transcriptase (21-23).We now report on the sequence of one del repeat from L. henryi and deduce its relationship to previously characterized retroid elements. METHODSThe 9.35 kbp of del in clone 1-46, a 15-kbp fragment of ge...

Involvement of Ethylene in Stress-Induced Expression of the TLC1.1 Retrotransposon from Lycopersicon chilense Dun.

“…Two classes of retrotransposons have been identified: the long terminal repeat (LTR) retrotransposons (flanked by LTRs) and the non-LTR retrotransposons. Regarding their sequence homology and gene organization, two major groups of LTR retroelements, the Ty1/copia and the Ty3/gypsy, have been distinguished (Grandbastien, 1992); representatives of both groups have been found in higher plants Smyth et al, 1989;Flavell et al, 1992;Voytas et al, 1992).…”

Do Plants Have a One-Way Ticket to Genomic Obesity?

“…Recent studies have indicated that the majority of this reiterated DNA is composed of retroelements, severa1 classes of mobile DNA that transpose through an RNA intermediate (Smyth et al, 1989;Moore et al, 1991;Pearce et al, 1996;SanMiguel et al, 1996;Suoniemi et al, 1996). In maize, a particular class of retroelements with long-terminal repeats (LTRs), the retrovirus-like retrotransposons, is most abundant.…”

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“…The internal domain contains a single 3927-bp open reading frame (QRF), and the predicted 1309 amino acid sequence includes both the gag and pol regions. A single ORF including both the gag and pol genes is unusual but is known in the Tf elements (5), in copia and its close relatives (19), and in micropia (26 4 (4,9,15). A short region of the presumptive protease gene is shown in Fig.…”

“…Immediately interior to the 5' LTR is a putative tR14A primer binding site for (-)-strand synthesis that begins with the, sequence TGG. Sea urchin nuclear tRNAs have not been characterized; however, starting with the TGG sequence, SURL1-3 (Tg) shares 11 of 12 bases with the methionine tRNA primer binding site of both RL elements Tal-3 ofArabidopsis (10) and del of lily (9). Tyl (3) and Ty3 (4) of yeast are also both inferred to be primed with methionine tRNA.…”

“…RL elements are known in a wide variety of organisms, including yeast (3)(4)(5), dipterans (6), lepidopterans (7), gymnosperms (8), angiosperms (9)(10)(11), and vertebrates, where they are recognized as retroviruses or endogenous retroviruses and sometimes as retrotransposons (12). RL elements are apparently widely distributed among echinoids.…”