Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-transposable element.

The recently described THAP domain motif characterizes a DNA-binding domain (DBD) that is widely conserved in human and in animals. It presents a similarity with the DBD of the P element transposase of D. melanogaster. We show here that the P Drosophila neogenes derived from P-transposable elements conserve the THAP domain. Moreover, secondary rearrangements by exon shuffling indicate the recurrent recruitment of this domain by the host genome. As P sequences and THAP genes are found together in many animal genomes, we discuss the possibility that the THAP proteins have acquired their domain as a result of recurrent molecular domestication of P-transposable elements.

P-Element repression in Drosophila melanogaster by a naturally occurring defective telomeric P copy.

In Drosophila melanogaster, hybrid dysgenesis occurs in progeny from crosses between females lacking P elements and males carrying P elements scattered throughout the genome. We have genetically isolated a naturally occurring P insertion at cytological location 1A, from a Tunisian population. The Nasr'Allah-P(1A) element [NA-P(1A)] has a deletion of the first 871 bp including the P promoter. It is flanked at the 3' end by telomeric associated sequences and at the 5' end by a HeT-A element sequence. The NA-P(1A) element strongly represses dysgenic sterility and P transposition. However, when testing P-promoter repression, NA-P(1A) was unable to repress a germinally expressed P-lacZ construct bearing no 5'-homology with it. Conversely, a second P-lacZ construct, in which the fusion with lacZ takes place in exon 3 of P, was successfully repressed by NA-P(1A). This suggests that NA-P(1A) repression involves a homology-dependent component.

A P element has induced intron formation in Drosophila.

We report evidence supporting the hypothesis that some introns could be originated from transposable elements. In the Drosophila montium species subgroup, we recently described a novel example of domestication by the host genome of a P transposable element. The element is a unique truncated P sequence transcribed into a polyadenylated RNA encoding a putative 66-kDa transposition repressor-like protein. Here, we analyze the genomic modifications associated with this transition of a transposable element into a stationary gene that is useful for the host. Study of the transcription modalities of this neogene reveals that the new transcriptional unit harbors a de novo synthesis of a new exon and a new intron upstream of the original P sequence initiation site. The new exon was constructed from the genomic flanking sequence of the P sequence, whereas the first half of the new intron is composed of genomic flanking sequence and the second half is composed of P sequence. This domestication event has involved the capture of a new promoter. An investigation of a large number of species belonging to the melanogaster species group revealed that this P element domestication is restricted to the species of the montium subgroup and that the new exon-intron structure is present in at least three other species. From sequence data, we hypothesize that cryptic acceptor and donor splicing sites present on the P element and flanking sequences have been under selective constraints which have led to the emergence of a new intron.

Molecular domestication--more than a sporadic episode in evolution.

Transposable elements are short but complex pieces of DNA or RNA containing a streamlined minimal-genome with the capacity for its selfish replication in a foreign genomic environment. Cis-regulatory sections within the elements orchestrate tempo and mode of TE expression. Proteins encoded by TEs mainly direct their own propagation within the genome by recruitment of host-encoded factors. On the other hand, TE-encoded proteins harbor a very attractive repertoire of functional abilities for a cell. These proteins mediate excision, replication and integration of defined DNA fragments. Furthermore, some of these proteins are able to manipulate important host factors by altering their original function. Thus, if the host genome succeeds in domesticating such TE-encoded proteins by taming their 'anarchistic behavior,' such an event can be considered as an important evolutionary innovation for its own benefit. In fact, the domestication of TE-derived cis-regulatory modules and protein coding sections took place repeatedly in the course of genome evolution. We will present prominent cases that impressively demonstrate the beneficial impact of TEs on host biology over evolutionary time. Furthermore, we will propose that molecular domestication might be considered as a resumption of the same evolutionary process that drove the transition from 'primitive genomes' to 'modern' ones at the early dawn of life, that is, the adaptive integration of a short piece of autonomous DNA into a complex regulatory network.

P element domestication: a stationary truncated P element may encode a 66-kDa repressor-like protein in the Drosophila montium species subgroup.

Functional P transposable elements can be separated into two distinct classes: mobile elements, which present the canonical structure, with transposase and repressor functions, and immobile P sequences truncated in 5' and 3' by loss of the terminal inverted repeats and exon 3, which retain only the repressor function. This second class was first described in some species of the Drosophila obscura group. Here, we describe a new truncated immobile P sequence cloned from one species of the Drosophila montium subgroup (D. tsacasi) that produces a polyadenylated RNA with a coding capacity for a 66-kDa "repressor-like" protein. The results from a number of different comparisons between P-homologous sequences concerning both coding and noncoding regions strongly suggest that the obscura and montium immobile P sequences as well as the T-type P subfamily derive from the same ancestral mobile P element family. Study of the flanking regions of these immobile P sequences shows that the two immobilizations were produced by two independent events. Our results provide evidence that the molecular domestication of a transposable element family may recur in a species lineage.

P element regulation and X-chromosome subtelomeric heterochromatin in Drosophila melanogaster.

In Drosophila melanogaster, crossing males carrying autonomous P elements with females devoid of P copies results in hybrid dysgenesis in the germline of progeny. The reciprocal cross produces non-dysgenic progeny due to a maternally inherited state non-permissive for P transposition. The capacity of a P copy to repress transposition depends on both its structure and its chromosomal location. Naturally occurring regulatory P elements inserted at the telomere of the X chromosome have been genetically isolated in a genomic context devoid of other P elements. One or two copies of autonomous P elements at this site (1A) are sufficient to elicit a strong P repression in the germline. These elements are flanked by Telomeric Associated Sequences, previously identified and described by Karpen and Spradling (1992) as having heterochromatic properties. The regulatory properties of P elements at 1A are strongly impaired by mutations affecting Su(var)205, which encodes Heterochromatin Protein 1, a non-histone heterochromatin protein. The regulatory properties of classical P strains are not sensitive to Su(var)205. Models based on chromatin structure or on nuclear localisation of the telomeres are discussed in order to explain both the strong regulatory properties of P elements at the X chromosome telomere and their sensitivity to Su(var)205.

The regulatory properties of autonomous subtelomeric P elements are sensitive to a Suppressor of variegation in Drosophila melanogaster.

Genetic recombination was used in Drosophila melanogaster to isolate P elements, inserted at the telomeres of X chromosomes (cytological site IA) from natural populations, in a genetic background devoid of other P elements. We show that complete maternally inherited P repression in the germline (P cytotype) can be elicited by only two autonomous P elements at 1A and that a single element at this site has partial regulatory properties. The analysis of the surrounding chromosomal regions of the P elements at 1A shows that in all cases these elements are flanked by Telomeric Associated Sequences, tandemly repetitive noncoding sequences that have properties of heterochromatin. In addition, we show that the regulatory properties of P elements at 1A can be inhibited by some of the mutant alleles of the Su(var)205 gene and by a deficiency of this gene. However, the regulatory properties of reference P strains (Harwich and Texas 007) are not impaired by Su(var)205 mutations. Su(var)205 encodes Heterochromatin Protein 1 (HP1). These results suggest that the HP1 dosage effect on the P element properties is site-dependent and could involve the structure of the chromatin.

A particular P-element insertion is correlated to the P-induced hybrid dysgenesis repression in Drosophila melanogaster.

Transposable P elements in Drosophila melanogaster cause hybrid dysgenesis if their mobility is not repressed. The ability to regulate the dysgenic activity of the P elements depends on several mechanisms, one of which hypothesized that a particular deleted P element (the KP element) results in a non-susceptibility which is biparentally transmitted. In this study totally non-susceptible lines, and susceptible lines containing exclusively KP elements (IINS2 line and IIS2 line) were isolated from a M' strain. We show that non-susceptibility is correlated with a particular insertion of one KP element located at the cytological site 47D1. The repression ability of the GD sterility is determined by a recessive chromosomal factor, and cannot be due to the KP-element number. Here the repression of the P mobility is associated with reduction of the P transcripts and the inhibition of P promoter activity.

EVOLUTIONARY STEPS AND TRANSPOSABLE ELEMENTS IN DROSOPHILA MELANOGASTER: THE MISSING RP TYPE OBTAINED BY GENETIC TRANSFORMATION.

The I-R and P-M hybrid dysgenesis systems in Drosophila melanogaster have been interpreted as due to recent invasions of the genome by the I and P mobile genetic elements. Temporal and geographical surveys have never shown individuals harboring P sequences but devoid of active I elements. We describe here the successful genetic transformation by autonomous P elements of embryos initially devoid of active I elements and any P sequences. The results demonstrate that P elements may invade the genome of Drosophila melanogaster in the absence of active I elements. Using gel blotting, in situ hybridization techniques, and genetic experiments, we have monitored the behavior of newly introduced P elements in several transformed lines over 30 generations. The switch of cytotype from M to P occurred very slowly and the number of P copies simultaneously increased to about 25. These RP lines possess the properties required to induce P-M hybrid dysgenesis but totally retain the R cellular state. Consequently, this new mobile element combination presents a strong reciprocal post-zygotic isolation with IM strains due to both P-M and I-R hybrid dysgenesis systems. This genomic incompatibility could be considered as a first step toward speciation in Drosophila populations.

Hybridization on squashed flies: a method to detect gene sequences in individual Drosophila.

Specific gene sequences can be detected by DNA hybridization to individual Drosophila squashed on cellulose or nylon filters. This "squash-blot" method permits the rapid survey of DNA polymorphism in large Drosophila population samples. It could also be useful for studying chromosome aberrations, departure from diploidy, and detection of pathogenic agents in vector insects.

P-element distribution in Eurasian populations of Drosophila melanogaster: A genetic and molecular analysis.

Genetic and molecular investigations were carried out with Eurasian Drosophila melanogaster populations on the P-M system of hybrid dysgenesis. In 27 strains sampled from France to Middle Asia, a clear gradient exists between Western Europe, in which most modern strains are of the Q type, and eastern areas, in which M-cytotype strains predominate. Molecular analysis on individual flies was performed with two complementary probes of the cloned 2.9-kilobase P element. The results provide evidence for a gradually decreasing frequency of P elements from west to east, but the presence of P-homologous sequences has been ascertained in all of the wild M-cytotype populations analyzed. Moreover, some active P elements with GD sterility potential were revealed in the majority of M-cytotype populations when tested with a highly sensitive reference line. The gradual change in distribution of the polymorphic P family in Eurasia is discussed in relation to the structure of the elements together with the theories of P-M evolution and is interpreted as the present invasion of Eurasian populations by these elements.

Cytotype polymorphism of the P-M system in two wild populations of Drosophila melanogaster.

In Drosophila melanogaster the interactions of the P-M system generate germ-line aberrations (e.g., sterility, mutations) found in certain interstrain hybrids. Two wild populations, from France and Tunisia, were examined in order to determine the distribution of the chromosomal P factor and the extrachromosomal cytotypes. No P factors active for potential GD sterility were found in these populations. But search for the M cytotype, which causes susceptibility to the P factors, and for the P cytotype, which causes resistance to the P factors, showed that both populations are polymorphic for the cytotypes. Such a polymorphism seems to be stable in the wild, at least over a 2-year period. Mutator activity (measured by generated mutations at the sn and ras loci) was found to be present. Some possible interactions between cytotype polymorphism, mutator activity, and the structure of Drosophila populations are discussed.