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

Recurrent emergence of structural variants of LTR retrotransposon CsRn1 evolving novel expression strategy and their selective expansion in a carcinogenic liver fluke, Clonorchis sinensis

Autonomous retrotransposons, in which replication and transcription are coupled, encode the essential gag and pol genes as a fusion or separate overlapping form(s) that are expressed in single transcripts regulated by a common upstream promoter. The element-specific expression strategies have driven development of relevant translational recoding mechanisms including ribosomal frameshifting to satisfy the protein stoichiometry critical for the assembly of infectious virus-like particles. Retrotransposons with different recoding strategies exhibit a mosaic distribution pattern across the diverse families of reverse transcribing elements, even though their respective distributions are substantially skewed towards certain family groups. However, only a few investigations to date have focused on the emergence of retrotransposons evolving novel expression strategy and causal genetic drivers of the structural variants. In this study, the bulk of genomic and transcribed sequences of a Ty3/gypsy-like CsRn1 retrotransposon in Clonorchis sinensis were analyzed for the comprehensive examination of its expression strategy. Our results demonstrated that structural variants with single open reading frame (ORF) have recurrently emerged from precedential CsRn1 copies encoding overlapping gag-pol ORFs by a single-nucleotide insertion in an upstream region of gag stop codon. In the parasite genome, some of the newly evolved variants appeared to undergo proliferative burst as active master lineages together with their ancestral copies. The genetic event was similarly observed in Opisthorchis viverrini, the closest neighbor of C. sinensis, whereas the resulting structural variants might have failed to overcome purifying selection and comprised minor remnant copies in the Opisthorchis genome.

Amplification of the 1731 LTR retrotransposon in Drosophila melanogaster cultured cells: Origin of neocopies and impact on the genome

Transposable elements (TEs), represent a large fraction of the eukaryotic genome. In Drosophila melanogaster, about 20% of the genome corresponds to such middle repetitive DNA dispersed sequences. A fraction of TEs is composed of elements showing a retrovirus-like structure, the LTR-retrotransposons, the first TEs to be described in the Drosophila genome. Interestingly, in D. melanogaster embryonic immortal cell culture genomes the copy number of these LTR-retrotransposons was revealed to be higher than the copy number in the Drosophila genome, presumably as the result of transposition of some copies to new genomic locations [Potter, S.S., Brorein Jr., W.J., Dunsmuir, P., Rubin, G.M., 1979. Transposition of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila. Cell 17, 415-427; Junakovic, N., Di Franco, C., Best-Belpomme, M., Echalier, G., 1988. On the transposition of copia-like nomadic elements in cultured Drosophila cells. Chromosoma 97, 212-218]. This suggests that so many transpositions modified the genome organisation and consequently the expression of targeted genes. To understand what has directed the transposition of TEs in Drosophila cell culture genomes, a search to identify the newly transposed copies was undertaken using 1731, a LTR-retrotransposon. A comparison between 1731 full-length elements found in the fly sequenced genome (y(1); cn(1)bw(1), sp(1) stock) and 1731 full-length elements amplified by PCR in the two cell line was done. The resulting data provide evidence that all 1731 neocopies were derived from a single copy slightly active in the Drosophila genome and subsequently strongly activated in cultured cells; and that this active copy is related to a newly evolved genomic variant (Kalmykova, A.I., et al., 2004. Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes. Mol. Biol. Evol. 21, 2281-2289). Moreover, neocopies are shown to be inserted in different sets of genes in the two cell lines suggesting they might be involved in the biological and physiological differences observed between Kc and S2 cell lines.

Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons

The Drosophila non-long terminal repeat (non-LTR) retrotransposons TART and HeT-A specifically retrotranspose to chromosome ends to maintain Drosophila telomeric DNA. Relatively little is known, though, about the regulation of their expression and their retrotransposition to telomeres. We have used rapid amplification of cDNA ends (RACE) to identify multiple transcription initiation and polyadenylation sites for sense and antisense transcripts of three subfamilies of TART elements in Drosophila melanogaster. These results are consistent with the production of an array of TART transcripts. In contrast to other Drosophila non-LTR elements, a major initiation site for sense transcripts was mapped near the 3′ end of the TART 5′-untranslated region (5′-UTR), rather than at the start of the 5′-UTR. A sequence overlapping this sense start site contains a good match to an initiator consensus for the transcription start sites of Drosophila LTR retrotransposons. Interestingly, analysis of 5′ RACE products for antisense transcripts and the GenBank EST database revealed that TART antisense transcripts contain multiple introns. Our results highlight differences between transcription of TART and of other Drosophila non-LTR elements and they provide a foundation for testing the relationship between exceptional aspects of TART transcription and TART's specialized role at telomeres.

Developmental expression analysis of the 1731 retrotransposon reveals an enhancement of Gag-Pol frameshifting in males of Drosophila melanogaster

Extensive analyses of Drosophila melanogaster retrotransposon transcriptions in cultured cells or during development have been reported, but little is known about their translation during the development of the fly. Analysis of the translational products of the 1731 Drosophila melanogaster retrotransposon in Kc Drosophila cultured cells has been reported, showing the existence of primary products (Gag and Pol) and of processed polypeptides of various sizes. Study of 1731 retrotransposon expression at both levels of transcription and translation during the development of Drosophila melanogaster, is presented. 1731 transcripts were detected by in situ hybridization and 1731 proteins were detected by immunostaining and immunoblotting in embryos and in adult gonads. 1731 transcripts and proteins were detected in the mesoderm and central nervous system during embryonic development, in nurse cells and follicle cells in adult ovaries and in primary spermatocytes in adult testes. Moreover, Western blot analysis of the 1731 proteins with anti-Gag or anti-Pol antibodies in gonads revealed that the 1731 mRNA could be translated differentially according to the expressing tissue: essentially, ovarian translation and/or processing of 1731 products is different from that operating in testes, where the Gag-Pol fusion polyprotein is the most prominent product. Our results indicate that expression of the 1731 mobile element is regulated not only at the transcriptional level but also at the translational level, and that this regulation is different in the two sexes.

UVB irradiation upregulation of the Drosophila 1731 retrotransposon LTR requires the same short sequence of U3 region in a human epithelial cell line as in Drosophila cells

Phylogenetic analysis of the retrotransposon and retrovirus suggests an evolutionary relationship between them and indicates that transactivation of the long terminal repeat (LTR)-containing retroelements could be ubiquitous. Using constructs expressing a reporter gene under the control of the entire or deleted LTR of 1731, which is a retrotransposable element of Drosophila melanogaster, we were able to show that the UVB-irradiation activation of the 1731-LTR requires the same short sequence of U3 region in a human epithelial cell line as in Schneider's Drosophila cell line (S2). This sequence is similar to the binding sequence of the members of the nuclear factor-kappa B (NF-kappa B)/rel family. In addition, human colonic carcinoma cells (HT29), in response to UVB-irradiation, produce some extracellular factor(s) that activates the 1731-LTR in nonirradiated cells.

An eye imaginal disc-specific transcriptional enhancer in the long terminal repeat of the tom retrotransposon is responsible for eye morphology mutations of Drosophila ananassae

Optic morphology (Om) mutations of Drosophila ananassae are semidominant, neomorphic and nonpleiotropic, map to at least 22 loci scattered throughout the genome, and are associated with the insertion of the tom retrotransposon. Molecular and genetic analyses have revealed that eye morphology defects of Om mutants are caused by the ectopic or excessive expression of Om genes in the eye imaginal discs of third instar larvae. It is therefore assumed that the tom element carries tissue-specific gene regulatory sequences which enhance expression of the Om genes. In the present study, we examined whether or not the long terminal repeats (LTR) of the tom element contain such an eye imaginal disc-specific enhancer, using D. melanogaster transformants containing a lacZ gene ligated to the tom LTR. Analyses of lacZ gene expression in the eye imaginal discs of third instar larvae of 18 independently established transformant lines showed that the tom LTR was capable of enhancing lacZ expression in all the transformant lines, but the degree of enhancement varied between lines. In addition, the effect of the tom LTR lacZ gene evidently changed when the tom LTR construct was relocated to different chromosomal positions. On the basis of these findings, it is hypothesized that ectopic and excessive expression of the Om genes in the eye imaginal discs is induced by an eye imaginal disc-specific enhancer present in the tom LTR, the effect of which may be subject to chromosomal position effects.

Characterization and cloning of p11, a transrepressor of Drosophila melanogaster retrotransposon 1731

The NssBF element has been characterized as a 26 nt sequence in the long terminal repeat of Drosophila melanogaster retrotransposon 1731. This sequence has been shown to be implicated in transcriptional repression of the 1731 promoter. We here report the cloning of a cDNA encoding a nuclear DNA binding protein named p11 that binds specifically to the NssBF element. P11 is a 98 amino acid polypeptide. It exhibits similarities with the mouse p9 single-stranded DNA binding protein, raising the possibility of a very general family of protein factors. Co-transfection experiments in human U937 cells showed repression of the 1731 promoter by overexpression of p11.

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.

The microinjected Drosophila melanogaster 1731 retrotransposon is activated after the midblastula stage of the amphibian Pleurodeles waltl development

The entire 1731 retrotransposon of Drosophila melanogaster, tagged with the E. coli lac Z gene inserted in its gag sequence, was injected into oocytes and fertilized eggs of the urodele amphibian Pleurodeles waltl. Expression of the reporter gene indicated that the 1731 promoter (its 5'LTR) is active in the embryos and not in the oocytes. It appeared that this element is regulated as amphibian genes are at the beginning of the development, i.e. that expression was detected after the mid blastula stage and maintained up to four or five days after injection. Another construction associating the modified 1731 promoter with the CAT gene is also expressed in Pleurodeles embryos during the same period of development. This indicated that the 1731 promoter issued from a Drosophila species is activated as promoting sequences of amphibian zygotic genes are, suggesting that in the case of horizontal transfer, 1731 can be expressed into vertebrate organisms.

Expression of a Bombyx cytoplasmic actin gene in cultured Drosophila cells: influence of 20-hydroxyecdysone and interference with expression of endogenous cytoplasmic actin genes

The expression of the Bombyx cytoplasmic actin A3 gene and its response to 20-hydroxyecdysone are studied after transfection in hormone responsive Drosophila cells and are compared to the expression of homologous resident genes. The host cells accumulate correct transcripts of the Bombyx gene in a gene dosage dependent way. The relative amount of endogenous cytoplasmic actin mRNAs is decreased in transfected cells, whether the transgene is integrated into the genome or not. When 20-hydroxyecdysone is added to the culture medium, the accumulation of the foreign mRNA is decreased whereas those of endogenous cytoplasmic actin transcripts are increased. These results are discussed in terms of competition for transcription and regulatory factors.

Analysis of the DNA topoisomerase-II-mediated cleavage of the long terminal repeat of Drosophila 1731 retrotransposon

The interaction of DNA topoisomerase II with the long terminal repeat (LTR) of the Drosophila melanogaster 1731 retrotransposon was studied. The covalent binding of topoisomerase II to the LTR was strongly stimulated by different inhibitors of the enzyme 4'-demethylepipodophyllotoxin-9-(4,6-O-2-ethylidene-beta-D-glucopy ranoside (VP-16), 4'-(9-acridinylamino)methanesulfon-m-anisidine) (m-AMSA) and an ellipticine derivative. Enzyme-mediated DNA cleavage could be observed in the absence of inhibitors and was stimulated in their presence. Cleavage occurred predominantly at sites located within or at the boundary of alternating purine/pyrimidine tracts in agreement with previous observations [Spitzner, J. R., Chung, I. K. & Muller, M. T. (1990) Eukaryotic topoisomerase II preferentially cleaves alternating purine-pyrimidine repeats, Nucleic Acids Res. 18, 1-11]. In addition, all of the cleavage sites observed in the absence of inhibitor were located in the U3 region of the LTR. The site specificity of drug-induced cleavage was studied and the conformity of the cleavage sites with previously established consensus sequences was examined. Our results suggest that DNA topoisomerase II, through its ability to alter the degree of DNA supercoiling, might be involved in the control of different functions of the LTR.

Translation and fates of the gag protein of 1731, a Drosophila melanogaster retrotransposon

An entire copy of 1731, a Drosophila melanogaster retrotransposon, was tagged by fusing in frame its putative gag gene with the reporter LacZ sequence. The high transfection efficiency of Drosophila virilis cells added to the absence of 1731 in their genome allowed, by combining histochemical staining and immunological detections, the demonstration of the translation of the 1731 gag gene. The gag protein is gathered in virus-like particles. Its occurrence in nuclei is consistent with a nuclear localization signal. The expression of the sense construction was inhibited by cotransfections with its antisense homologue.

Promoter activity of the 1731 Drosophila retrotransposon in a human monocytic cell line

The resemblance between retrotransposons and retroviruses suggests an evolutionary relationship and indicates that they may share common transcription factors. We have analyzed the behaviour of the Drosophila 1731 retrotransposon promoter in the human monocytic U937 cell line. We show that the long terminal repeat (LTR) of 1731 promotes CAT (chloramphenicol acetyl transferase) activity in these cells, in which it is enhanced by phorbol esters. Using gel mobility assays, we detected a human nuclear protein that binds in the U3 region of the LTR in a sequence-specific manner. Its precise target was determined by a DNase I footprinting experiment.

Activation of tobacco retrotransposons during tissue culture

Sequences of at least three new families of retrotransposons (Tto1-Tto3) were amplified by PCR from cDNA prepared from protoplasts of an established tobacco cell line, based on the fact that certain amino acids are highly conserved in the reverse transcriptases encoded by retrotransposons. Structural analysis indicates that Tto1 is 5.5 kb long and has features typical of retrotransposons. Transcription of Tto1 starting in the long terminal repeat was active only in cultured cells. Protoplast formation enhanced the transcription. The copy number of Tto1 increased 10-fold in established cell lines; it also increased in plants regenerated from tissue cultures and in transgenic plants. These results indicate that Tto1 is activated during tissue culture. This is the first demonstration of activation of a plant retrotransposon by tissue culture. The copy number of Tto2 and a previously isolated transposon, Tnt1, also increased in established cell lines, indicating that these two retrotransposons may also be activated by tissue culture. These three retrotransposons are cryptic in normally propagated plants: no difference in the copy number was observed between individuals of the same cultivars or even between different cultivars.

Characterization of the reverse transcriptase of 1731, a Drosophila melanogaster retrotransposon

The nucleotide sequence of 1731, a retrotransposon cloned from the genome of Drosophila melanogaster, reveals a structural similarity with the proviral form of the retroviruses including a pol-like gene containing a putative reverse-transcriptase(RT)-coding sequence. Diverse parts of that sequence were subcloned and expressed in Escherichia coli. It has been demonstrated that the expression of the RT-like sequence, when translated, gives rise to peptides displaying enzyme activity characteristic of a true RT enzyme. In addition, rabbit antisera directed against such recombinant proteins allowed us to detect an immunoreactive protein of around 110 kDa, which was only present in D. melanogaster cell lines, but not in cells derived from Drosophila virilis or Drosophila hydei, whose genomes do not bear the 1731 element. This protein is expected to correspond to a non-processed pol-gene translated product and cosediments with virus-like particles exhibiting RT activity.

A nuclear single-stranded-DNA binding factor interacts with the long terminal repeats of the 1731 Drosophila retrotransposon

Using gel mobility assays, we have detected two proteins that bind in the U3 region of the 1731 retrotransposon long terminal repeats (between positions -110 and -73) in nuclear extracts from Drosophila melanogaster cultured cells. The first one binds double-stranded DNA, whereas the other binds the mRNA-like strand in a sequence-specific manner. We report here the characterization of the latter protein, named NssBF for nuclear single-stranded-DNA binding factor. Gel filtration shows an apparent molecular mass of 95 kDa for NssBF. The points of contact between NssBF and its single-stranded DNA target were determined. This protein binds neither the complementary strand nor the corresponding RNA sequence. A possible role of NssBF in transcription is discussed.

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.

A short 5' region of the long terminal repeat is required for regulation by hormone and heat shock of Drosophila retrotransposon 1731

1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or deleted Long Terminal Repeats (LTRs) of 1731, we were able to show that a short (28 bp) sequence located in the U3 region of these LTRs was required for 1) the increase in promoter strength, 2) negative regulation by 20-OH and, 3) positive regulation by heat shock.

Specific expression of the tobacco Tnt1 retrotransposon in protoplasts

The Tnt1 transposable element of tobacco belongs to the retrotransposon family and shares the structural features of viral retroelements including two long terminal repeats (LTRs) which are known to contain promoter regions. We show that two Tnt1 RNAs of 5.2 and 6.5 kb can be found. The 5.2 kb RNA matches with the size of the Tnt1 elements so far isolated (5.3 kb), whilst the evidence suggests that the 6.5 kb RNA could be a chimaeric RNA initiated in a gene in which Tnt1 has inserted. The Tnt1 5.2 kb RNA starts in the LTR, and the LTR can promote the expression of a translational LTR-beta-glucuronidase (GUS) fusion at a high level in transient expression assays. The Tnt1 5.2 kb RNA and the LTR-GUS fusion of transgenic tobacco plants are specifically expressed in leaf-derived protoplasts whereas they are not expressed in leaf tissue. The 5.2 kb RNA is also transcribed at low levels in roots. This RNA is induced after 2 h of maceration in the protoplast isolation medium, and its level declines rapidly after protoplast isolation. The induction requires only the presence of cell wall hydrolases, and is independent of wounding and plasmolysis. The induction of Tnt1 expression is not mediated by typical oligosaccharide elicitors released from the cell wall known to mediate defense gene responses. Tnt1 transcription features provide a first example of tissue culture-induced mutagenesis in plants and a molecular basis for some of the somaclonal variation events.