Genomic distribution of transposable elements among individuals of an inbred Drosophila line

The stability of the elements of eleven transposon families (412, B 104, blood, 297, 1731, G, copia, mdg 4, hobo, jockey and I) has been compared by the Southern technique among individuals of a Drosophila line that has been subjected to 30 generations of sister sib matings. The 412, B104, blood, 297, 1731 and G elements appear stable. Heterochromatic copia and hobo elements and euchromatic I elements appear highly polymorphic. In addition, copia, mdg 4, jockey and I elements undergo an instability resulting in significant variations in relative intensity among autoradiographic bands. The extent of the polymorphisms detected strongly suggests de novo rearrangements of transposable elements.     

Mitomycin C induces genomic rearrangements involving transposable elements in Drosophila melanogaster

Summary Mitomycin C was injected into the abdomen of male flies of the y ² sc¹ w^aG strain of Drosophila melanogaster. They were mated with females bearing attached-X chromosomes, and the male offspring (F₁) were analysed for the appearance of mutations in the X chromosome. We observed y ¹ and sc ⁺ reversions induced either by excision of mdg4 (gypsy) with retention of one long terminal repeat (LTR) or by insertion of a foreign sequence into mdg4, partial reversion of the w ^aG mutation, w ^aGw ^aGd, and unstable f mutations. The overall mutation frequency was considerably higher than in control flies of the y ² sc¹ w^aG strain. Possible mechanisms of genomic rearrangements induced by Mitomycin C, in particular the role of homologous recombination, are discussed.     

The genomes of most animals have multiple members of the Tc1 family of transposable elements

A PCR assay was employed to detect sequences homologous to the transposase gene of the Tc1 family of transposable elements in a wide variety of animals. Amplification products of the appropriate size were obtained from most insects (92 of 108 examined; 85%), most other invertebrates (33 of 43; 77%), and many vertebrates (18 of 36; 50%). Sequencing a sample of cloned PCR products from eight insects, one hydra, and two frogs revealed that each had multiple distinct members of the family in their genomes. In the most extreme case, the horn fly Haematobia irritans yielded evidence of seventeen distinct types of Tc1 family elements. Most of the sequences obtained indicate that the elements are within the range of variation already known from fungi, nematodes, files, fish and frogs. Some, however, had novel length variants or divergent sequences, indicating that they represent new subfamilies of these transposons. These results indicate that this family of transposons is extremely common in animal genomes, with multiple representatives in most genomes.     

Population genetics of transposable DNA elements

This paper is an attempt to bring together the various, dispersed data published in the literature on insertion polymorphism of transposable elements from various kinds of populations (natural populations, laboratory strains, isofemale and inbred lines). Although the results deal mainly with Drosophila, data on other organisms have been incorporated when necessary to illustrate the discussion. The data pertinent to the regions of insertion, the rates of transposition and excision, the copy number regulation, and the degree of heterozygosity were analysed in order to be confronted with the speculations made with various theoretical models of population biology of transposable elements. The parameters of these models are very sensitive to the values of the transposable element characteristics estimated on populations, and according to the difficulties of these estimations (population not at equilibrium, particular mutations used to estimate the transposition and excision rates, trouble with the in situ technique used to localize the insertions, undesired mobilization of TEs in crosses, spontaneous genome resetting, environmental effects, etc.) it cannot be decided accurately which model better accounts for the population dynamics of these TEs. Tendencies, however, emerge in Drosophila: the copia element shows evidence for deficiency of insertions on the X chromosomes, a result consistent with selection against mutational effects of copia insertions; the P element repartition does not significantly deviate from the neutral assumption, in spite of a systematic copy number of insertions higher on the X than on the autosomes. Data on other elements support either the neutral model of TE containment, neither of the two models, or both. Prudence in conclusion should then be de rigueur when dealing with such kind of data. Finally the potential roles of TEs in population adaptation and evalution are discussed.     

Actin acetylation in Drosophila tissue culture cells

In a permanent cell line derived from Drosophila embryos, cytoplasmic actin is produced as an unstable precursor, which is subsequently converted to a stable form. This conversion results in a reduction in isoelectric point, with no apparent change in molecular weight. The conversion involves an enzymatic acetylation, and results in an insensitivity to aminopeptidase digestion, suggesting N-terminal blockage. Both the acetylated and unacetylated actins can participate in the assembly of F-actin, but with different efficiencies.This work was supported by a grant from the NIH (GM 22866).     

The distribution of the transposable elementBari-1 in theDrosophila melanogaster andDrosophila simulans genomes

The distribution of the transposable elementBari-1 inD. melanogaster andD. simulans was examined by Southern blot analysis and byin situ hybridization in a large number of strains of different geographical origins and established at different times.Bari-1 copies mostly homogeneous in size and physical map are detected in all strains tested. Both inD. melanogaster and inD. simulans a relatively high level of intraspecific insertion site polymorphism is detectable, suggesting that in both speciesBari-1 is or has been actively transposing. The main difference between the two sibling species is the presence of a large tadem array of the element in a well-defined heterochromatic location of theD. melanogaster genome, whereas such a cluster is absent inD. simulans. The presence ofBari-1 elements with apparently identical physical maps in allD. melanogaster andD. simulans strains examined suggests thatBari-1 is not a recent introduction in the genome of themelanogaster complex. Structural analysis reveals unusual features that distinguish it from other inverted repeat transposons, whereas many aspects are similar to the widely distributedTc1 element ofC. elegans.     

Molecular paleontology of transposable elements from Arabidopsis thaliana

We report results of a comprehensive computer-assisted analysis of new transposable elements (TEs) from Arabidopsis thaliana. Our analysis revealed several previously unknown pogo- and En/Spm-like families and two novel superfamilies of DNA transposons, Arnold and Harbinger. One of the En/Spm-like families (Atenspm) was found to be involved in generating satellite arrays in paracentromeric regions. Of the two superfamilies reported, Harbinger is distantly related to bacterial IS5-like insertion elements, and Arnold contains DNA transposons without terminal inverted repeats (TIRs), which were never reported in eukaryotes before. Furthermore, we report a large number of young and diverse copia-like autonomous and nonautonomous retroelements and discuss their potential evolutionary relationship with mammalian retroviruses. The A.thaliana genome harbors copia-like retroelements which encode a putative env-like protein reported previously in the SIRE-1 retrotransposon from soybean. Finally, we demonstrate a nonrandom chromosomal distribution of the most abundant A.thaliana TEs clustered in the first half of chromosome II, which includes the centromeric region. The families of TEs from A.thaliana are relatively young, extremely diverse and much smaller than those from mammalian genomes. We discuss the potential factors determining similarities and differences in the evolution of TEs in mammals and A. thaliana. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evolution of the transposable element mariner in the Drosophila melanogaster species group

The population biology and molecular evolution of the transposable element mariner has been studied in the eight species of the melanogaster subgroup of the Drosophila subgenus Sophophora. The element occurs in D. simulans, D. mauritiana, D. sechellia, D. teissieri, and D. yakuba, but is not found in D. melanogaster, D. erecta, or D. orena. Sequence comparisons suggest that the mariner element was present in the ancestor of the species subgroup and was lost in some of the lineages. Most species contain both active and inactive mariner elements. A deletion of most of the 3 end characterizes many elements in D. teissieri, but in other species the inactive elements differ from active ones only by simple nucleotide substitutions or small additions/deletions. Active mariner elements from all species are quite similar in nucleotide sequence, although there are some-species-specific differences. Many, but not all, of the inactive elements are also quite closely related. The genome of D. mauritiana contains 20–30 copies of mariner, that of D. simulans 0–10, and that of D. sechellia only two copies (at fixed positions in the genome). The mariner situation in D. sechellia may reflect a reduced effective population size owing to the restricted geographical range of this species and its ecological specialization to the fruit of Morinda citrifolia.     

Evolution of the transposable element Uhu in five species of Hawaiian Drosophila

The complete DNA sequence of three independent isolates of Uhu, a member of the Tc1-like class of transposable elements from D. heteroneura (Uhu-1, Uhu-3, and Uhu-4), has been determined. These isolates have between 95 and 96.4% nucleotide sequence identity indicating that Uhu is well conserved within this species. A comparison of the DNA sequences of Uhu and the D. melanogaster Hb1 transposable element shows that the nucleotide substitution rate for Uhu is comparable to the synonymous rate for the Adh gene in these species. Uhu has been identified in four other species of endemic Hawaiian Drosophila, D. silvestris, D. differens, D. planitibia and D. picticornis, and nine Uhu elements were isolated from genomic libraries of these four species. A 444 base pair region from within the coding region of the Uhu element, with well conserved ends, was amplified by the polymerase chain reaction and used for sequence comparison of elements from different species. The analysis of the sequence similarities between the elements within and between the species shows a grouping of the two pairs of most closely related species (D. heteroneura and D. silvestris, and D. differens and D. planitibia), but shows a much larger variation within the most recently diverged species (D. heteroneura and D. silvestris) than expected. There are extensive nucleotide substitutions and deletions in the Uhu elements from D. picticornis showing that they are degenerating and being lost in this species. These observations indicate that the Uhu element has been transmitted vertically and that transposition may have been activated at the time of formation of each species as it colonized the newly formed islands of the Hawaiian archipelago.     

Modification of Drosophila cell surfaces by concanavalin A

Summary The effect of Con A on the surface morphology of cultured cells of Drosophilia melanogaster growing on coverglasses was examined by scanning electron microscopy. With low lectin concentrations (5–10g/ml) surface filaments disappeared and the cells flattened and spread against the glass surface. Cytoplasmic fusion bridges were observed in areas where cells made contact. Concentrations of Con A ranging between 50–500 g/ml caused cell shrinkage and surface distortions without cell flattening and filament loss. These morphologic effects were not apparent if Con A binding sites were blocked by preincubation with -methyl-D-mannopyranoside before application to the cell cultures. However, once the Con A-mediated changes were in effect, the cells failed to show recovery when they were returned to growth medium and a majority of the cells on the coverglasses degenerated. Presumably the cells whose morphology appears unaffected by Con A treatment are the survivors that repopulate cultures returned to growth medium.Supported by Grants CA-12600 and CA 16619 awarded by the National Cancer Institute, DREW and in part by NIH Biomedical Sciences Grant No. RR-07050. CAA's participation in this project was supported by Training Grant No. 5T01-GM-71-17We wish to thank Dr. Imogene Schneider for providing the cell lines     

Evidence for interspecific transfer of the transposable element mariner betweenDrosophila andZaprionus

Summary The transposable element mariner occurs widely in themelanogaster species group ofDrosophila. However, in drosophilids outside of themelanogaster species group, sequences showing strong DNA hybridization with mariner are found only in the genusZaprionus. the mariner sequence obtained fromZaprionus tuberculatus is 97% identical with that fromDrosophila mauritiana, a member of themelanogaster species subgroup, whereas a mariner sequence isolated fromDrosophila tsacasi is only 92% identical with that fromD. mauritiana. BecauseD. tsacasi is much more closely related toD. mauritiana than isZaprionus, the presence of mariner inZaprionus may result from horizontal transfer. In order to confirm lack of a close phylogenetic relationship between the genusZaprionus and themelanogaster species group, we compared the alcohol dehydrogenase (Adh) sequences among these species. The results show that the coding region of Adh is only 82% identical betweenZ. tuberculatus andD. mauritiana, as compared with 90% identical betweenD. tsacasi andD. mauritiana. Furthermore, the mariner gene phylogeny obtained by maximum likelihood and maximum parsimony analyses is discordant with the species phylogeny estimated by using the Adh genes. The only inconsistency in the mariner gene phylogeny is in the placement of theZaprionus mariner sequence, which clusters with mariner fromDrosophila teissieri andDrosophila yakuba in themelanogaster species subgroup. These results strongly suggest horizontal transfer.     

Evidence for a host role in regulating the activity of transposable elements in Drosophila melanogaster: the case of the persistent instability of Bari 1 elements in Charolles stock

In most reports in which the activity of numerous Drosophila transposon families has been studied, only a subset of the families tested appears mobile. A comparison of these data shows that there are no transposons inherently more unstable than others and suggests that host factors regulate the activity of transposable elements. Consistent with this conclusion are the properties of Bari 1 elements, which are the only ones of the 14 families tested to be unstable in Charolles stock. Instability is persistent over 53 generations and appears to affect recurrent insertion sites. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus

Background

The mariner family of transposable elements is one of the most widespread in the Metazoa. It is subdivided into several subfamilies that do not mirror the phylogeny of these species, suggesting an ancient diversification. Previous hybridization and PCR studies allowed a partial survey of mariner diversity in the Metazoa. In this work, we used a comparative genomics approach to access the genus-wide diversity and evolution of mariner transposable elements in twenty Drosophila sequenced genomes.

Results

We identified 36 different mariner lineages belonging to six distinct subfamilies, including a subfamily not described previously. Wide variation in lineage abundance and copy number were observed among species and among mariner lineages, suggesting continuous turn-over. Most mariner lineages are inactive and contain a high proportion of damaged copies. We showed that, in addition to substitutions that rapidly inactivate copies, internal deletion is a major mechanism contributing to element decay and the generation of non-autonomous sublineages. Hence, 23% of copies correspond to several Miniature Inverted-repeat Transposable Elements (MITE) sublineages, the first ever described in Drosophila for mariner. In the most successful MITEs, internal deletion is often associated with internal rearrangement, which sheds light on the process of MITE origin. The estimation of the transposition rates over time revealed that all lineages followed a similar progression consisting of a rapid amplification burst followed by a rapid decrease in transposition. We detected some instances of multiple or ongoing transposition bursts. Different amplification times were observed for mariner lineages shared by different species, a finding best explained by either horizontal transmission or a reactivation process. Different lineages within one species have also amplified at different times, corresponding to successive invasions. Finally, we detected a preference for insertion into short TA-rich regions, which appears to be specific to some subfamilies.

Conclusions

This analysis is the first comprehensive survey of this family of transposable elements at a genus scale. It provides precise measures of the different evolutionary processes that were hypothesized previously for this family based on PCR data analysis. mariner lineages were observed at almost all “life cycle” stages: recent amplification, subsequent decay and potential (re)-invasion or invasion of genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-727) contains supplementary material, which is available to authorized users.     

I elements of Drosophila melanogaster generate specific chromosomal rearrangements during transposition

Summary We report a detailed molecular analysis of three chromosomal rearrangements, which have been produced during I-R hybrid dysgenesis in Drosophila melanogaster. They all disrupt the yellow gene. One of them is a deletion; the other two are inversions, which may be interpreted as the results of recombination events between I elements inserted at their break points. These events appear to occur at the time of transposition and involve integrating rather than resident I elements. They are produced by a mechanism very similar to homologous ectopic recombination.     

Genome and stresses: Reactions against aggressions,behavior of transposable elements

The action of stresses on the genome can be considered as responses of cells or organisms to external aggressions. Stress factors are of environmental origin (climatic or trophic) or of genomic nature (introduction of foreign genetic material, for example). In both cases, important perturbations can occur and modify hereditary potentialities, creating new combinations compatible with survival; such a situation may increase the variability of the genome, and allow evolutive processes to take place. The behavior of transposable elements under stress conditions is thus of particular interest, since these sequences are sources of mutations and therefore of genetic variability; they may play an important role in population adaptation. The survey of the available experimental results suggests that, although some examples of mutations and transposable elements movements induced by external factors are clearly described, environmental injuries or introduction of foreign material into a genome are not systematically followed by drastic genomic changes.     

Regulatory elements involved in the tissue-specific expression of the yellow gene of Drosophila

Summary We have assessed the DNA sequence requirements for the correct spatial pattern and phenotypic expression of y in the late embryo/larvae. The wild-type larval phenotype requires both the regions between-294 bp and-92 bp and a portion of the intron; the sequence element(s) located within the intron can act in a position independent manner to effect the wild-type larval phenotype. The larval expression pattern was examined by tissue experiments in situ and by staining germline transformants derived from various y/lacZ fusion constructs. The larval expression of y is restricted to the mouthparts, microsetae and anal plates. While the-495 bp to+194 bp region alone cannot effect a wild-type larval expression pattern, this region in conjunction with the intron appears to be sufficient to drive -gal expression in an essentially wild-type pattern. Our data further suggest that the-294 bp to-92 bp region contains elements which specify the larval pattern and that the element(s) in the intron normally act to enhance the level of expression necessary for the wild-type larval phenotype. We also present a phenotypic analysis of the adult cuticle structures of germline transformants derived from a variety of deletion and rearrangement constructs of the y gene. This analysis has revealed several new features associated with the regulation of y expression.     

Thehermit transposable element of the Australian sheep blowfly,Lucilia cuprina, belongs to thehAT family of transposable elements

We report the cloning ofhermit, a member of thehAT family of transposable elements from the genome of the Australian sheep blowfly,Lucilia cuprina. Hermit is 2716 bp long and is 49% homologous to the autonomoushobo element,HFL1, at the nucleic acid level.Hermit has 15 bp terminal inverted repeats that share 10 bp with the terminal inverted repeats ofHFL1. Conceptual translation reveals a 583 residue open reading frame (ORF) that is 64% similar and 42% identical to theHFL1 ORF. However, the sequence of thehermit element contains two frameshifts within the putative ORF, indication thathermit is an inactive element. Analysis ofL. cuprina strains from within and outside Australia suggested thathermit is present as a single copy in all the genomes analysed.     

Drosophila glial development is regulated by genes involved in the control of neuronal cell fate

The Drosophila proneural genes specify neuronal determination among cells within the ectoderm. Here we address the question of whether proneural genes also affect the specification of glia, the most abundant cell type in the nervous system. We provide evidence that the proneural gene daughterless is essential for the formation of two major classes of PNS glia. In contrast, the proneural genes in the achaete-scute complex have no detectable effect on the specification and differentiation of these PNS glia and certain CNS glia. We also show that, as with neuronal development, glial determination is restricted by the neurogenic genes neuralized, Delta, and the genes of the Enhancer of split complex. Finally, we demonstrate that prospero, a gene involved in neuronal differentiation, also affects glial development. These results demonstrate extensive overlap in the genetic control of glial and neuronal development.Abbreviations ß galactosidase - (ß-gal) Alkaline phosphatase - (AP) Central nervous system - (CNS) Peripheral nervous system - (PNS) Home domain binding sites - (HDS) Helix-loop-helix - (HLH) Peripheral glia - (PG) Exit glia - (EG) Dorsal roof glia - (DRG) Intersegmental glia - (ISG) Midline glia - (MG) chordotonal - (CH) Sensory mother cell     

Follicle cell development is partly independent of germ-line cell differentiation in Drosophila oogenesis

Summary The developmental potential of the cells of the somatic follicular epithelium (follicle cells) was studied in mutants in which the differentiation of the germ-line cells is blocked at different stages of oogenesis. In two mutants, sn ^36a and kelch, nurse cell regression does not occur, yet the follicle cells around the small oocyte continue their normal developmental program and produce an egg shell with micropylar cone and often deformed operculum and respiratory appendages. Neither the influx of nurse cell cytoplasm into the oocyte nor the few follicle cells covering the nurse cells are apparently required for the formation of the egg shell. In the tumor mutant benign gonial cell neoplasm (bgcn) the follicle cells can also differentiate to some extent although the germ-line cells remain morphologically undifferentiated. Vitelline membrane material was synthesized by the follicle cells in some bgcn chambers and in rare cases a columnar epithelium, which resembled morphologically that of wild-type stage-9 follicles, formed around the follicle's posterior end. The normal polarity of the follicular epithelium that is characteristic for mid-vitellogenic stages may, therefore, be established in the absence of morphologically differentiating germ-line cells. However, the tumorous germ-line cells do not constitute a homogeneous cell population since in about 30% of the analyzed follicles a cell cluster at or near the posterior pole can be identified by virtue of its high number of concanavalin A binding sites. This molecular marker reveals an anteroposterior polarity of the tumorous chambers. In follicles mutant for both bgcn and the polarity gene dicephalic the cluster of concanavalin A-stained germ-line cells shifts to more anterior positions in the follicle.     

Localization of ribosomal DNA insertion elements in polytene chromosomes of Drosophila simulans,Drosophila mauritiana and their interspecific hybrids

The locations of the ribosomal DNA (rDNA) insertion elements type I and type II along the polytene chromosomes of three Drosophila species of the melanogaster subgroup-D. simulans, D. mauritiana and D. melanogaster-have been compared. In situ hybridization has shown that the intragenomic distribution of type I as well as of type II insertions is different for these related species. In particular, we have revealed rDNA-free autosomal sites, containing type II element sequences within the D. simulans and D. mauritiana chromosomes. This finding confirms the ability of this type of insertion to transpose, as was demonstrated earlier for Bombyx mori. The appearance of the rDNA not associated with the nucleolar organizers, evident by additional nucleoli, occurred with species-specific frequency. At the same time, for all three species the pattern of such changes (an attachment of the nucleoti to varying sites of the chromosomes and the presence of ectopic contacts between them, a composition of the rDNA repeats in the nucleolar material not integrated at the nucleolar organizer) was similar. The number of additional nucleoti in the hybrid polytene nuclei corresponded to the value of the parental species exhibiting nucleolar replicative dominance.