Structural and functional analysis of a new retrotransposon class in Drosophila species

Several copies of the Penelope transposable element, previously described in Drosophila virilis, have been studied in different D. virilis strains and D. melanogaster strains transformed with P-based constructs bearing a full-size Penelope copy. Most Penelope copies in both species have large terminal inverted repeats (TIRs) and deletions of various sizes at the 5′ ends of their ORFs. Junctions between TIRs and ORFs usually have microhomologies of various lengths, which allowed a hypothesis explaining the emergence of these complex structures at the molecular level to be put forward. Most Penelope copies have a 34 bp long direct repeat at the ORF ends. Full-size and truncated Penelope copies are usually surrounded by target site duplications of various lengths.     

Conserved subfamilies of the Drosophila HeT-A telomere-specific retrotransposon.

HeT-A, a major component of Drosophila telomeres, is the first retrotransposon proposed to have a vital cellular function. Unlike most retrotransposons, more than half of its genome is noncoding. The 3'' end contains > 2.5 kb of noncoding sequence. Copies of HeT-A differ by insertions or deletions and multiple nucleotide changes, which initially led us to conclude that HeT-A noncoding sequences are very fluid. However, we can now report, on the basis of new sequences and further analyses, that most of these differences are due to the existence of a small number of conserved sequence subfamilies, not to extensive sequence change during each transposition event. The high level of sequence conservation within subfamilies suggests that they arise from a small number of replicatively active elements. All HeT-A subfamilies show preservation of two intriguing features. First, segments of extremely A-rich sequence form a distinctive pattern within the 3'' noncoding region. Second, there is a strong strand bias of nucleotide composition: The DNA strand running 5'' to 3'' toward the middle of the chromosome is unusually rich in adenine and unusually poor in guanine. Although not faced with the constraints of coding sequences, the HeT-A 3'' noncoding sequence appears to be under other evolutionary constraints, possibly reflecting its roles in the telomeres.     

Aurora,a non-mobile retrotransposon in Drosophila melanogaster heterochromatin

A novel retrotransposon, aurora, containing 324 by long terminal repeats (LTRs) was detected in Drosophila melanogaster as a 5 kb insertion in the heterochromatic Stellate gene. This insertion causes a 5 bp duplication of the integration site. Southern analysis and in situ hybridization data show that all detectable copies of aurora are immobilized in the D. melanogaster heterochromatin. However, mobile copies of aurora were revealed in the cuchromatin of D. simulans. The element was also found in various species of the melanogaster subgroup and in the D. virilis genome.     

The 412 retrotransposon and the development of gonadal mesoderm in Drosophila.

We have shown that the expression of the 412 retrotransposon provides a useful early marker for the development of the gonadal mesoderm in Drosophila embryos. 412 is initially expressed in a set of parasegmentally repeated stripes from parasegments (PS) 2-14 in the mesoderm at the extended germ band stage. During germ band retraction the bulk of 412 expression declines except in dorsolateral clusters of cells in PS10, 11 and 12, where high levels of 412 expression remain. These mesodermal cell clusters are associated with germ cells and subsequently they coalesce, rounding up to form the gonads. The gonadal mesoderm thus appears to originate specifically from three abdominal parasegments, PS10, 11 and 12. We show that the maintenance of high levels of 412 expression in gonadal mesoderm is not induced by contact with germ cells, but rather depends on genetic control by the homeotic genes abdominal-A and Abdominal-B.     

Heavy heat shock induced retrotransposon transposition in Drosophila

The phenomenon of transposition induction by heavy heat shock (HHS) was studied. Males of a Drosophila isogenic line with a mutation in the major gene radius incompletus (ri) were treated by HHS (37 degrees C for 1 h followed by 4 degrees C for 1 h, with the cycle repeated three times) and crossed to untreated females of the same line. The males were crossed 5 d after heat shock, and also 9 d after HHS. Many transpositions were seen in the F1 larvae by in situ hybridization. The rate of induced transposition was at least 2 orders of magnitude greater than that of the control sample, and was estimated to be 0.11 events per transposable element copy per sperm. Two 'hot' subdivisions for transpositions, induced probably during the post-meiotic stage of spermiogenesis, were found: 43B and 97DE. Three-quarters of all transpositions were localized in these positions. In other sites the rates of induced transpositions were (1.3-3.2) x 10(-2) events per occupied segment per sperm, 1 order of magnitude greater than those of the control.     

Mobilization of retrotransposon copia in the Drosophila melanogaster genome]

Considerable heterogeneity of retrotransposon copia sites of location on polytene chromosomes was revealed in one of the substocks of the inbred Drosophila melanogaster stock. Heterogeneity of copia sites of location was found in no other substocks analyzed. The heterogeneity was shown to be caused by copia insertions in new sites. The frequency of insertions is about 12% per haploid genome per generation. The retrotransposon excisions and somatic transpositions were not observed. The location of retrotransposons mdg1, mdg2, mdg3, mdg4, 297 and H.M.S. Beagle appeared to be stable in all the stocks analyzed. Thus, a model system allowing to study mechanisms of retrotransposon copia transpositions in D. melanogaster tissues as well as phenotypic effects of copia mobilization is described.     

Evolutionary pattern of the gtwin retrotransposon in the Drosophila melanogaster subgroup

The gtwin retrotransposon was recently discovered in the Drosophila melanogaster genome and it is evolutionarily closer to gypsy endogenous retrovirus. This study has identified gtwin homologous sequences in the genome of D. simulans, D. sechellia, D. erecta and D. yakuba by performing homology searches against the public genome database of Drosophila species. The phylogenetic analyses of the gtwin env gene sequences of these species have shown some incongruities with the host species phylogeny, suggesting some horizontal transfer events for this retroelement. Moreover, we reported the existence of DNA sequences putatively encoding full-length Env proteins in the genomes of Drosophila species other than D. melanogaster. The results suggest that the gtwin element may be an infectious retrovirus able to invade the genome of new species, supporting the gtwin evolutionary picture shown in this work.