Molecular study of the retrovirus-like transposable element 412, a 20-OH ecdysone responsive repetitive sequence in Drosophila cultured cells

A brief history of the status of transposable elements: from junk DNA to major players in evolution

The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as "transposable elements" in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work.

New regulatory regions of Drosophila 412 retrotransposable element generated by recombination

There are no doubts that transposable elements (TEs) have greatly influenced genomes evolution. They have, however, evolved in different ways throughout mammals, plants, and invertebrates. In mammals they have been shown to be widely present but with low transposition activity; in plants they are responsible for large increases in genome size. In Drosophila, despite their low amount, transposition seems to be higher. Therefore, to understand how these elements have evolved in different genomes and how host genomes have proposed to go around them, are major questions on genome evolution. We analyzed sequences of the retrotransposable elements 412 in natural populations of the Drosophila simulans and D. melanogaster species that greatly differ in their amount of TEs. We identified new subfamilies of this element that were the result of mutation or insertion-deletion process, but also of interfamily recombinations. These new elements were well conserved in the D. simulans natural populations. The new regulatory regions produced by recombination could give rise to new elements able to overcome host control of transposition and, thus, become potential genome invaders.

A temperature cline in copy number for 412 but not roo/B104 retrotransposons in populations of Drosophila simulans

The copy number of the retrotransposable element 412 of Drosophila simulans from populations collected worldwide shows a negative correlation with minimum temperature. No association was detected for the roo/B104 element. The possibility that selective pressures might regulate the 412 copy number in these natural populations is supported by detection of selection against the detrimental effects of 412 insertions (estimated by the proportion of insertions on the X chromosome in comparison with the autosomes) but not roo/B104. These data reveal different spatial patterns for two element families, and strongly suggest that some factors in the environment, such as temperature, may interfere with the control of retrotransposition, thus affecting important aspects of genomic evolution.

Burdock, a novel retrotransposon in Drosophila melanogaster, integrates into the coding region of the cut locus

The burdock element is known to be the 2.6-kb insertion into the same region of the cut locus in 12 independently obtained ct-lethal mutants. Here we have determined the complete sequences of this insertion and of the hot spot region. It was found that the burdock is a short retrotransposon with long terminal repeats and a single open reading frame (ORF). The polypeptide encoded by the burdock ORF contains two adjacent regions homologous to the gag and pol polyproteins of the gypsy mobile element. The burdock insertion interrupts the short ORF of the cut locus. The target site sequence of the burdock insertions is similar to the Drosophila topoisomerase II cleavage site.

Spatially regulated expression of retrovirus-like transposons during Drosophila melanogaster embryogenesis

Over twenty distinct families of long terminal direct repeat (LTR)-containing retrotransposons have been identified in Drosophila melanogaster. While there have been extensive analyses of retrotransposon transcription in cultured cells, there have been few studies of the spatial expression of retrotransposons during normal development. Here we report a detailed analysis of the spatial expression patterns of fifteen families of retrotransposons during Drosophila melanogaster embryogenesis (17.6, 297, 412, 1731, 3S18, blood, copia, gypsy, HMS Beagle, Kermit/flea, mdg1, mdg3, opus, roo/B104 and springer). In each case, analyses were carried out in from two to four wild-type strains. Since the chromosomal insertion sites of any particular family of retrotransposons vary widely among wild-type strains, a spatial expression pattern that is conserved among strains is likely to have been generated through interaction of host transcription factors with cis-regulatory elements resident in the retrotransposons themselves. All fifteen families of retrotransposons showed conserved patterns of spatially and temporally regulated expression during embryogenesis. These results suggest that all families of retrotransposons carry cis-acting elements that control their spatial and temporal expression patterns. Thus, transposition of a retrotransposon into or near a particular host gene-possibly followed by an excision event leaving behind the retrotransposon's cis-regulatory sequences-might impose novel developmental control on such a host gene. Such a mechanism would serve to confer evolutionarily significant alterations in the spatio-temporal control of gene expression.

Ingrowth by photoreceptor axons induces transcription of a retrotransposon in the developing Drosophila brain

The development of the lamina, the first optic ganglion of the fly visual system, depends on inductive cues from the innervating photoreceptor axons. lacZ expression from a P-element insertion, A72, occurs in the anlage of the lamina coincident with axon ingrowth from the eye imaginal disc. In eyeless mutants lacking photoreceptor axons, lacZ expression did not occur. The P-element was found to have inserted within the 3′ long terminal repeat (LTR) of a ‘17.6′ type retrotransposon. The expression pattern of 17.6 transcripts in the brain in wild-type and eyeless mutants paralleled the expression of the lacZ reporter. Analysis of 17.6 cis-regulatory sequences indicates that the lamina-specific expression is due to the combined action of an enhancer element in the LTR and a repressor element within the internal body of the retrotransposon. The regulation of the 17.6 retrotransposon provides a model for the study of innervation-dependent gene expression in postsynaptic cells during neurogenesis.

In Drosophila Kc cells 20-OHE induction of the 60C beta3 tubulin gene expression is a primary transcriptional event

In Drosophila Kc cells, the 60C beta3 tubulin transcription unit, whose expression is induced by 20-hydroxyecdysone (20-OHE), has the same structure as in Drosophila. This gene is characterized by an unusual 5' intron of regulating importance, by an alternatively spliced second intron and by a long 3' transcribed but untranslated region. This gene codes for two beta3 tubulin isoforms with one amino acid difference. We have established that beta3 tubulin gene expression is transcriptionally regulated by the steroid hormone in a time and hormonal concentration-dependent fashion, without requirement of protein synthesis. This implies that this transcriptional induction is a primary event and that this gene is probably a direct target for the 20-OHE receptor.

Control of transcription of Drosophila retrotransposons

Studies of transcriptional control sequences responsible for regulated and basal-level RNA synthesis from promoters of Drosophila melanogaster retrotransposons reveal novel aspects of gene regulation and lead to identification of trans-acting factors that can be involved in RNA polymerase II transcription not only of retrotransposons, but of many other cellular genes. Comparisons between promoters of retrotransposons and some other Drosophila genes demonstrate that there is a greater variety in basal promoter structure than previously thought and that many promoters may contain essential sequences downstream from the RNA start site.

Mutation mapping of the 2B5 ecdysone locus in Drosophila melanogaster reveals a long-distance controlling element

Mutations at the Broad-Complex, a key gene triggering metamorphosis in Drosophila melanogaster, were mapped at the DNA level. The Broad-Complex includes two mutually complementing allelic classes, br and l(1)2Bc, both of which can associate to insertions at the same intron. Alterations spreading over 50 kilobases upstream from the transcription unit also disrupt br but not l(1)2Bc function.

Functional analysis of the long terminal repeats of Drosophila 1731 retrotransposon: promoter function and steroid regulation

1731 is a Drosophila retrotransposon whose transcripts decrease in Drosophila cells after treatment by the steroid hormone 20-hydroxyecdysone (20-OH). Several constructions have been made where the bacterial chloramphenicol acetyltransferase (CAT) gene is put under the control of either the 5' or the 3' long terminal repeats (LTRs) of 1731. CAT activity assays in transfected Drosophila cells show that either the 5' or the 3'LTR constitutes a unidirectional promoter. Analysis of partially deleted LTR suggests the presence of so-called silencer and activator regions in these LTRs. Moreover, the first 260 bp of the LTR are sufficient to provoke 20-OH inhibition whereas the first 58 bp are necessary for hormonal responsiveness. These 58 bp contain sequences showing similarities with the targets of trans-acting factors such as Octal-c and NFkB.

20-OH-ecdysone regulates 60 C beta tubulin gene expression in Kc cells and during Drosophila development

Cultured Kc cells of Drosophila melanogaster are sensitive to the insect moulting hormone, 20-hydroxy-ecdysone (20-OH-E). Morphological changes of Kc-treated cells were observed and electron microscopic analysis of pseudopodia shows a large increase in the number of microtubules, all arranged in the same orientation. The 60 C beta tubulin gene which is expressed only in 20-OH-E-treated cells encodes a 2.6-kb mRNA which is essentially cytoplasmic and polyadenylated. The corresponding premessenger is 7 kb in length and is absent in untreated cells. Two peaks of expression of the 60 C beta tubulin gene are observed during Drosophila development: at midembryogenesis (stage 8-13 h) and at the late third instar larvae-early pupae stage. By use of the Ecdysone 1 mutant, 60 C beta tubulin gene expression was demonstrated to be regulated in part by 20-OH-E during Drosophila development. Through these two complementary biological models of study, the mode and role of beta tubulin gene regulation are discussed.

Extrachromosomal circular DNAs in Drosophila melanogaster: comparison between embryos and Kc0% cells

We established the size distribution of extrachromosomal covalently closed circular DNA molecules from embryos of various Drosophila melanogaster strains and from Kc0% tissue culture cells. In embryos, more than 80% of the circular DNA molecules are smaller than 2.5 kb and all the distributions show a peak of molecules of between 200 and 400 bp. The Kc0% cell distribution differs mainly from that of embryos in that 48% of the molecules have a size between 4 and 8 kb. Correlating with this, circular molecules homologous to copia, 412 and 297 were detected only in Kc0% cells. The three tandemly repeated families containing the 5S genes, the histone genes and the 240 bp repeat of the ribosomal DNA intergenic spacer, which had previously been identified in circular DNAs from embryos, were also found in cultured cells. A fourth tandemly repeated family corresponding to the 1.688 g/cm3 satellite DNA was detected, both in embryos and Kc0% cells. It consists of circular multimeric molecules containing multiple copies of the 359 bp repeated unit. No circular DNA molecules homologous to the actin genes, the type I ribosomal DNA insertion, or the F and I transposable elements were found in embryos or Kc0% cells. Thus it appears that the extrachromosomal circular DNA molecules from embryos and from tissue culture cells differ mainly in the presence of circular copies of the copia-like transposable elements.

The beta heterochromatic sequences flanking the I elements are themselves defective transposable elements

Phylogenetic studies suggest that mobile element families are unstable components of the Drosophila genome. Two examples of immobilization of a transposable element family are presented here: as judged by their constant genomic organization among unrelated strains, the F and I element families have been respectively immobilized for a long time in D. simulans and in the reactive D. melanogaster strains (these are the laboratory strains which escaped the recent I invasion of D. melanogaster natural populations). All the elements of these defective families are located in the beta heterochromatic portion of the genome. Moreover, most if not all of the beta heterochromatic sequences into which the defective I elements are embedded are themselves non-mobile members of various nomadic families such as mdg 4, 297, 1731, F and Doc. These results are discussed with special emphasis on the possible nomadic origin of beta heterochromatin components and on the mechanisms of evolutionary turnover of the transposable element families.

Mutation mapping of the 2B5 ecdysone locus in Drosophila melanogaster reveals a long-distance controlling element

Mutations at the Broad-Complex, a key gene triggering metamorphosis in Drosophila melanogaster, were mapped at the DNA level. The Broad-Complex includes two mutually complementing allelic classes, br and l(1)2Bc, both of which can associate to insertions at the same intron. Alterations spreading over 50 kilobases upstream from the transcription unit also disrupt br but not l(1)2Bc function.

Micropia: a retrotransposon of Drosophila combining structural features of DNA viruses, retroviruses and non-viral transposable elements

The retrotransposon micropia was first described from Y-chromosomal fertility genes of Drosophila hydei. Screening a Drosophila melanogaster genomic library yielded several clones representing micropia elements in D. melanogaster. The DNA sequences of two elements from D. hydei (micropia-DhMiF2 and micropia-DhMiF8) and two elements from D. melanogaster (micropia-Dm2 and micropia-Dm11) permitted a detailed analysis of the spatial organization of micropia constituents. Micropia represents the typical gene organization represented by "core"-protein domains followed by a protease, reverse transcriptase, RNase and integrase domain. New features of the micropia family compared with other retrotransposons are: (1) a region of similarity to class I major histocompatibility complex antigens of mammals; (2) only one main open reading frame of about 4000 bases length; (3) a non-protein-coding region of about 500 base-pairs length between the 3' end of the open reading frame and the 5' start of the 3' long terminal repeat. This region includes 32 base-pair tandem repeats; (4) within the long terminal repeats, 82 base-pair tandem repeats with four potential ecdysteroid receptor binding sites. Because micropia combines many evolutionary features of different viruses, non-viral transposable elements, chromosomal genes and repetitive sequence organizations, this retrotransposon may be seen as a "minigenome" reflecting evolutionary principles of the construction of genomic components.