The hobo transposon and hobo-related elements are expressed as developmental genes in Drosophila

Interaction effect of mutations in the genes (piwi and aub) of the Argonaute family and hobo transposons on the integral survival parameters of Drosophila melanogaster

The Argonaute family genes (piwi and aub) involved in the production of small RNAs are responsible for the regulation of many cellular processes, including the suppression of genome instability, modulation of gene activity, and transposable elements. Dysfunction of these genes and the associated activation of transposable elements adversely affect reproductive development and quality of life. The role of transposons in contrast to retrotransposons and their interaction with genes of the Argonaute family in aging processes have not been studied. This study considers a scenario in which the piwi and aub genes in the presence of functional hobo transposons can modify the effects from the level of DNA damage to lifespan. The simultaneous presence of mutation (piwi or aub) and hobo (regardless of size) in the genome has practically no effect or (less often) leads to a decrease in the level of DNA damage in ovarian cells. A high level of sterility and low ovarian reserve were noted mainly with a combination of mutations and full-sized hobo elements. The combination of these two genetic factors negatively affects the fertility of young females and embryonic survival. Isolated cases of restoration of reproductive functions with age were noted but only in females that had low fertility in the early period of life. The presence of hobo transposons contributed to an increase in the lifespan of both mutant and non-mutant females. Dysfunction of the piwi and aub genes (without hobo) can reduce the lifespan of both sexes. Together, each mutation and hobo transposons act antagonistically/additively (in females) and synergistically/antagonistically (in males) to change the lifespan. In parameters of locus-specific instability, hobo activation was more pronounced in piwi gene dysfunction. The results obtained complement data on the study of new functions of Argonaute family genes and their interactions with transposable elements in the aging process.

Interpopulation variation of transposable elements of the hAT superfamily in Drosophila willistoni (Diptera: Drosophilidae): in-situ approach

Transposable elements are abundant and dynamic part of the genome, influencing organisms in different ways through their presence or mobilization, or by acting directly on pre- and post-transcriptional regulatory regions. We compared and evaluated the presence, structure, and copy number of three hAT superfamily transposons (hobo, BuT2, and mar) in five strains of Drosophila willistoni species. These D. willistoni strains are of different geographical origins, sampled across the north-south occurrence of this species. We used sequenced clones of the hAT elements in fluorescence in-situ hybridizations in the polytene chromosomes of three strains of D. willistoni. We also analyzed the structural characteristics and number of copies of these hAT elements in the 10 currently available sequenced genomes of the willistoni group. We found that hobo, BuT2, and mar were widely distributed in D. willistoni polytene chromosomes and sequenced genomes of the willistoni group, except for mar, which is restricted to the subgroup willistoni. Furthermore, the elements hobo, BuT2, and mar have different evolutionary histories. The transposon differences among D. willistoni strains, such as variation in the number, structure, and chromosomal distribution of hAT transposons, could reflect the genomic and chromosomal plasticity of D. willistoni species in adapting to highly variable environments.

Involvement of DNA Repair Genes and System of Radiation-Induced Activation of Transposons in Formation of Transgenerational Effects

The study of the genetic basis of the manifestation of radiation-induced effects and their transgenerational inheritance makes it possible to identify the mechanisms of adaptation and possible effective strategies for the survival of organisms in response to chronic radioactive stress. One persistent hypothesis is that the activation of certain genes involved in cellular defense is a specific response of the cell to irradiation. There is also data indicating the important role of transposable elements in the formation of radiosensitivity/radioresistance of biological systems. In this work, we studied the interaction of the systems of hobo transposon activity and DNA repair in the cell under conditions of chronic low-dose irradiation and its participation in the inheritance of radiation-induced transgenerational instability in Drosophila. Our results showed a significant increase of sterility and locus-specific mutability, a decrease of survival, fertility and genome stability (an increase the frequency of dominant lethal mutations and DNA damage) in non-irradiated F1/F2 offspring of irradiated parents with dysfunction of the mus304 gene which is responsible for excision and post-replicative recombination repair and repair of double-stranded DNA breaks. The combined action of dysfunction of the mus309 gene and transpositional activity of hobo elements also led to the transgenerational effects of irradiation but only in the F1 offspring. Dysfunction of the genes of other DNA repair systems (mus101 and mus210) showed no visible effects inherited from irradiated parents subjected to hobo transpositions. The mei-41 gene showed specificity in this type of interaction, which consists in its higher efficiency in sensing events induced by transpositional activity rather than irradiation.

"What You Need, Baby, I Got It": Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome's structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE-host interactions in any complex eukaryotic genome.

Effects of ionizing radiation at Drosophila melanogaster with differently active hobo transposons

Purpose: The role of transposable elements in formation of radiobiological effects is understudied and contradictory. The aim of this study was to investigate the response of Drosophila melanogaster to irradiation depending on the level of activity hobo transposons and the role of hobo transposons in formation of ionizing radiation late effects.Materials and methods: The individuals of Drosophila melanogaster with different level activity of hobo-elements were exposed to acute irradiation in doses of 1-100 Gy at early ontogenesis stages. The reaction of individuals to exposure was studied using the larvae survival rate, morphological parameters of reproduction system, DNA damage rate, and mutability of mini-white locus.Results: We found the pronounced linear deferred effects of irradiation for animals with a high activity level of full-size hobo copies. The radiosensitivity of individuals with a mean level of activity transposon was whether higher or did not differ from the radiosensitivity of animals with a low activity hobo.Conclusion: The obtained results suggest that full-size hobo-elements with a high activity level (less often with a mean activity level) are responsible for delayed deleterious irradiation effects.

Drosophila relics hobo and hobo-MITEs transposons as raw material for new regulatory networks

Hypermutable strains of Drosophila simulans have been studied for 20 years. Several mutants were isolated and characterized, some of which had phenotypes associated with alteration in development; for example, showing ectopic legs with eyes being expressed in place of antennae. The causal agent of this hypermutability is a non-autonomous hobo-related sequence (hoboVA). Around 100 mobilizable copies of this element are present in the D. simulans genome, and these are likely mobilized by the autonomous and canonical hobo element. We have shown that hoboVA has transcription factor binding sites for the developmental genes, hunchback and even-skipped, and that this transposon is expressed in embryos, following the patterns of these genes. We suggest that hobo and hobo-related elements can be material for the emergence of new regulatory networks.

Paternal Induction of Hybrid Dysgenesis in Drosophila melanogaster Is Weakly Correlated with Both P-Element and hobo Element Dosage

Transposable elements (TEs) are virtually ubiquitous components of genomes, yet they often impose significant fitness consequences on their hosts. In addition to producing specific deleterious mutations by insertional inactivation, TEs also impose general fitness costs by inducing DNA damage and participating in ectopic recombination. These latter fitness costs are often assumed to be dosage-dependent, with stronger effects occurring in the presence of higher TE copy numbers. We test this assumption in Drosophila melanogaster by considering the relationship between the copy number of two active DNA transposons, P-element and hobo element, and the incidence of hybrid dysgenesis, a sterility syndrome associated with transposon activity in the germline. By harnessing a subset of the Drosophila Genetic Reference Panel (DGRP), a group of fully-sequenced D. melanogaster strains, we describe quantitative and structural variation in P-elements and hobo elements among wild-derived genomes and associate these factors with hybrid dysgenesis. We find that the incidence of hybrid dysgenesis is associated with both P-element and hobo element copy number in a dosage-dependent manner. However, the relationship is weak for both TEs, suggesting that dosage alone explains only a small part of TE-associated fitness costs.

Somatizing the transposons action

The somatic mobilization of transposable elements is more common than previously thought. In this review we discuss how the intensity and the biologic consequences of somatic mobilization are dependent on the transposable elements landscapes of each genome, and on the "momentum" of each particular TE with respect to the mechanisms that control its transposition and the possibility to escape this control. Additionally, the biologic consequences of somatic mobilization vary among organisms that show an early separation between the germline and somatic cells and those organisms that do not exhibit this separation or that reproduce asexually. In the former, somatic transposition can be involved in phenotypic plasticity, detrimental conditions such as disease, or processes such as aging. For the organisms without separation between the germ and soma, somatic mobilization can be a source of genetic variability.

Reevaluating the infection status by the Wolbachia endosymbiont in Drosophila Neotropical species from the willistoni subgroup

Infections by the endosymbiotic bacterium Wolbachia developed a rapid global expansion within Old World Drosophila species, ultimately infecting also Neotropical species. In this sense, screenings are necessary to characterize new variants of Wolbachia or new hosts, and also in order to map the dynamics of already known infections. In this paper, we performed a double screening approach that combined Dot-blot and PCR techniques in order to reevaluate the infection status by Wolbachia in species from the willistoni subgroup of Drosophila. Genomic DNA from isofemale lines descendent from females collected in the Amazonian Rainforest (n=91) were submitted to Dot-blot, and were positive for Wolbachia, producing a gradient of hybridization signals, suggesting different infection levels, which was further confirmed through quantitative PCR. Samples with a strong signal in the Dot-blot easily amplified in the wsp-PCR, unlike most of the samples with a medium to weak signal. It was possible to molecularly characterize three Drosophila equinoxialis isofemale lines that were found to be infected in a low density by a wMel-like Wolbachia strain, which was also verified in a laboratory line of Drosophila paulistorum Amazonian. We also found Drosophila tropicalis to be infected with the wAu strain and a Drosophila paulistorum Andean-Brazilian semispecies laboratory line to be infected with a wAu-like Wolbachia. Moreover, we observed that all Drosophila willistoni samples tested with the VNTR-141 marker harbor the same Wolbachia variant, wWil, either in populations from the South or the North of Brazil. Horizontal transfer events involving species of Old World immigrants and Neotropical species of the willistoni subgroup are discussed.

Mar, a MITE family of hAT transposons in Drosophila

Background

Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements flanked by subterminal or terminal inverted repeats (TIRs) with no coding capacity. MITEs were originally recognized as important components of plant genomes, where they can attain extremely high copy numbers, and are also found in several animal genomes, including mosquitoes, fish and humans. So far, few MITEs have been described in Drosophila.

Results

Herein we describe the distribution and evolution of Mar, a MITE family of hAT transposons, in Drosophilidae species. In silico searches and PCR screening showed that Mar distribution is restricted to the willistoni subgroup of the Drosophila species, and a phylogenetic analysis of Mar indicates that this element may have originated prior to the diversification of these species. Most of the Mar copies in D. willistoni present conserved target site duplications and TIRs, indicating recent mobilization of these sequences. We also identified relic copies of potentially full-length Mar transposon in D. tropicalis and D. willistoni. The phylogenetic relationship among transposases from the putative full-length Mar and other hAT superfamily elements revealed that Mar is placed into the recently determined Buster group of hAT transposons.

Conclusion

On the basis of the obtained data, we can suggest that the origin of these Mar MITEs occurred before the subgroup willistoni speciation, which started about 5.7 Mya. The Mar relic transposase existence indicates that these MITEs originated by internal deletions and suggests that the full-length transposon was recently functional in D. willistoni, promoting Mar MITEs mobilization.

Ancestral polymorphism and recent invasion of transposable elements in Drosophila species

BACKGROUND

During the evolution of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements Bari and 412 in the sequenced genomes of the Drosophila melanogaster group and in the sibling species D. melanogaster and D. simulans using traditional phylogenetic and network approaches.

RESULTS

Maximum likelihood (ML) phylogenetic analyses revealed incongruences and unresolved relationships for both the Bari and 412 elements. The DNA transposon Bari within the D. ananassae genome is more closely related to the element of the melanogaster complex than to the sequence in D. erecta, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the Bari and host gene sequences explain the incongruence as an ancestral polymorphism that was inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving D. melanogaster, D. simulans and D. sechellia. A network approach was used to attempt to resolve these relationships. The resulting tree suggests recent transfers of both elements between D. melanogaster and D. simulans. The divergence values of the elements between these species support this conclusion.

CONCLUSIONS

We showed that ancestral polymorphism and recent invasion of genomes due to introgression or horizontal transfer between species occurred during the evolutionary history of the Bari and 412 elements in the melanogaster group. These invasions likely occurred in Africa during the Pleistocene, before the worldwide expansion of D. melanogaster and D. simulans.

Spatiotemporal transcription of the P element and the 412 retrotransposon during embryogenesis of Drosophila melanogaster and D. willistoni

Transposable elements (TEs) are mobile nucleotide sequences which, through changing position in host genomes, partake in important evolutionary processes. The expression patterns of two TEs, P element transposon and 412 retrotransposon, were investigated during Drosophila melanogaster and D. willistoni embryogenesis, by means of embryo hybridization using riboprobes. Spatiotemporal transcription patterns for both TEs were similar to those of developmental genes. Although the two species shared the same P element transcription pattern, this was not so with 412 retrotransposon. These findings suggest that the regulatory sequences involved in the initial development of Drosophila spp are located in the transposable element sequences, and differences, such as in this case of the 412 retrotransposon, lead to losses or changes in their transcription patterns.

DNA sequence requirements for hobo transposable element transposition in Drosophila melanogaster

We have conducted a structure and functional analysis of the hobo transposable element of Drosophila melanogaster. A minimum of 141 bp of the left (L) end and 65 bp of the right (R) end of the hobo were shown to contain sequences sufficient for transposition. Both ends of hobo contain multiple copies of the motifs GGGTG and GTGGC and we show that the frequency of hobo transposition increases as a function of the copy number of these motifs. The R end of hobo contains a unique 12 bp internal inverted repeat that is identical to the hobo terminal inverted repeats. We show that this internal inverted repeat suppresses transposition activity in a hobo element containing an intact L end and only 475 bp of the R end. In addition to establishing cis-sequences requirements for transposition, we analyzed trans-sequence effects of the hobo transposase. We show a hobo transposase lacking the first 49 amino acids catalyzed hobo transposition at a higher frequency than the full-length transposase suggesting that, similar to the related Ac transposase, residues at the amino end of the transposase reduce transposition. Finally, we compared target site sequences of hobo with those of the related Hermes element and found both transposons have strong preferences for the same insertion sites.