P-element-induced interallelic gene conversion of insertions and deletions in Drosophila melanogaster.

We studied the process by which whd, a P-element insertion allele of the Drosophila melanogaster white locus, is replaced by its homolog in the presence of transposase. These events are interpreted as the result of double-strand gap repair following excision of the P transposon in whd. We used a series of alleles derived from whd through P-element mobility as templates for this repair. One group of alleles, referred to collectively as whd-F, carried fragments of the P element that had lost some of the sequences needed in cis for mobility. The other group, whd-D, had lost all of the P insert and had some of the flanking DNA from white deleted. The average replacement frequencies were 43% for whd-F alleles and 7% for the whd-D alleles. Some of the former were converted at frequencies exceeding 50%. Our data suggest that the high conversion frequencies for the whd-F templates can be attributed at least in part to an elevated efficiency of repair of unexpanded gaps that is possibly caused by the closer match between whd-F sequences and the unexpanded gap endpoints. In addition, we found that the gene substitutions were almost exclusively in the direction of whd being replaced by the whd-F or whd-D allele rather than the reverse. The template alleles were usually unaltered in the process. This asymmetry implies that the conversion process is unidirectional and that the P fragments are not good substrates for P-element transposase. Our results help elucidate a highly efficient double-strand gap repair mechanism in D. melanogaster that can also be used for gene replacement procedures involving insertions and deletions. They also help explain the rapid spread of P elements in populations.     

A P Element Chimera Containing Captured Genomic Sequences Was Recovered at the Vestigial Locus in Drosophila following Targeted Transposition

A P element carrying the Dopa decarboxylase gene, P[Ddc], was targeted into vg21, a cryptic P element induced mutant allele of the vestigial (vg) locus. The resulting allele, vg28w, contained the expected P[Ddc] plus an additional 9.5 kb of DNA, captured from elsewhere on chromosome II. Reversion of the vg28w mutant allele demonstrated that the entire insert can excise but cannot reinsert at an appreciable frequency. We explain the targeted transposition as the repair of a double stranded gap, created by the excision of the P element at vg21, and suggest that the formation of chimeric elements may be an important component of P element dependent genomic instability.     

Origination of Ds elements from Ac elements in maize: evidence for rare repair synthesis at the site of Ac excision.

Although it has been known for some time that the maize transposon Ac can mutate to Ds by undergoing internal deletions, the mechanism by which these mutations arise has remained conjectural. To gain further insight into this mechanism in maize we have studied a series of Ds elements that originated de novo from Ac elements at known locations in the genome. We present evidence that new, internally deleted Ds elements can arise at the Ac donor site when Ac transposes to another site in the genome. However, internal deletions are rare relative to Ac excision footprints, the predominant products of Ac transposition. We have characterized the deletion junctions in five new Ds elements. Short direct repeats of variable length occur adjacent to the deletion junction in three of the five Ds derivatives. In the remaining two, extra sequences or filler DNA is inserted at the junction. The filler DNAs are identical to sequences found close to the junction in the Ac DNA, where they are flanked by the same sequences that flank the filler DNA in the deletion. These findings are explained most simply by a mechanism involving error-prone DNA replication as an occasional alternative to end-joining in the repair of Ac-generated double-strand breaks.     

Distribution and structure of cloned P elements from the Drosophila melanogaster P strain pi 2.

P transposable elements of Drosophila melanogaster cloned from the strong P strain pi 2 have been analysed. The structures and chromosomal locations of 26 of the 30-50 elements estimated to be present in pi 2 have been determined. At one location two elements are inserted 100 base pairs (bp) apart, and in a second location two elements are only separated by the 8 bp duplicated upon P-element insertion. In addition to 2.9 kilobase-pair (kbp) elements, elements with 14 different internal deletions from 1.3 to 2.3 kbp in size have been isolated. There are 7 copies of the 2.9 kbp element, 2 copies each of 5 internally deleted elements and a single copy of 9 internally deleted elements. One of the elements found twice is the KP element, which may play a role in the regulation of hybrid dysgenesis in strains which contain many copies of this element. Apart from internal deletions the elements are extremely homogeneous in DNA sequence, with only 2 single base polymorphisms detected twice each in over 16 kbp of P-element sequence. Although transpositions are infrequent in an inbred P cytotype strain such as pi 2, the distribution of these cloned elements indicates that when the genomic library was made, the strain was polymorphic with respect to element location. The distribution and structures of the element are discussed with respect to models for regulation of P-element transposition.     

Three-partner conversion induced by the P-element transposase in Drosophila melanogaster

Conversion of one P-derived transposon into another has already been shown to occur with a measurable frequency. However, the mechanism responsible for such replacements has remained controversial. We previously proposed a mechanism involving three partners. We assumed that after excision of the P-element inserted at the target site, the double-strand break was repaired using, first, the homologous P sequences on the sister chromatid, and second, a remote template, the donor P-derived transposon. However, two other mechanisms have been proposed. The first involves two partners only, the broken end and the remote template, while the second involves transposition of the donor into the target P-element, followed by a double recombination event. Here we describe the conversion of a defective P-element using as a remote template an enhancer-trap element that is itself unable to transpose because it lacks 21 bp at its 5' end. This result makes it possible to exclude the possibility that this conversion event occurred after transposition. The new allele was molecularly and genetically characterized. The occurrence of a polymorphism at position 33 of the P-element sequence and of an imperfect copy of the template on the 3' side of the converted transposon confirmed that the sister chromatid was absolutely necessary as a partner for repair. Our results show that targeting of a marked P-element is possible, even when this element is unable to transpose. This provides a means of improving recovery of conversion events by eliminating unwanted transpositions catalyzed by the P transposase.     

Three-partner conversion induced by the P-element transposase in <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Conversion of one P-derived transposon into another has already been shown to occur with a measurable frequency. However, the mechanism responsible for such replacements has remained controversial. We previously proposed a mechanism involving three partners. We assumed that after excision of the P-element inserted at the target site, the double-strand break was repaired using, first, the homologous P sequences on the sister chromatid, and second, a remote template, the donor P-derived transposon. However, two other mechanisms have been proposed. The first involves two partners only, the broken end and the remote template, while the second involves transposition of the donor into the target P-element, followed by a double recombination event. Here we describe the conversion of a defective P-element using as a remote template an enhancer-trap element that is itself unable to transpose because it lacks 21?bp at its 5′ end. This result makes it possible to exclude the possibility that this conversion event occurred after transposition. The new allele was molecularly and genetically characterized. The occurrence of a polymorphism at position 33 of the P-element sequence and of an imperfect copy of the template on the 3′ side of the converted transposon confirmed that the sister chromatid was absolutely necessary as a partner for repair. Our results show that targeting of a marked P-element is possible, even when this element is unable to transpose. This provides a means of improving recovery of conversion events by eliminating unwanted transpositions catalyzed by the P transposase.     

Evidence for multiple cycles of strand invasion during repair of double-strand gaps in Drosophila

DNA double-strand breaks (DSBs), a major source of genome instability, are often repaired through homologous recombination pathways. Models for these pathways have been proposed, but the precise mechanisms and the rules governing their use remain unclear. In Drosophila, the synthesis-dependent strand annealing (SDSA) model can explain most DSB repair. To investigate SDSA, we induced DSBs by excision of a P element from the male X chromosome, which produces a 14-kb gap relative to the sister chromatid. In wild-type males, repair synthesis tracts are usually long, resulting in frequent restoration of the P element. However, repair synthesis is often incomplete, resulting in internally deleted P elements. We examined the effects of mutations in spn-A, which encodes the Drosophila Rad51 ortholog. As expected, there is little or no repair synthesis in homozygous spn-A mutants after P excision. However, heterozygosity for spn-A mutations also resulted in dramatic reductions in the lengths of repair synthesis tracts. These findings support a model in which repair DNA synthesis is not highly processive. We discuss a model wherein repair of a double-strand gap requires multiple cycles of strand invasion, synthesis, and dissociation of the nascent strand. After dissociation, the nascent strand may anneal to a complementary single strand, reinvade a template to be extended by additional synthesis, or undergo end joining. This model can explain aborted SDSA repair events and the prevalence of internally deleted transposable elements in genomes.     

What is the impact of transposable elements on host genome variability?

The spread of a transposable element family through a wild population may be of astonishing rapidity. At least three families of transposable genetic elements have recently invaded Drosophila melanogaster worldwide, including the P element. The mechanism has been a process of effectively replicative transposition, and, for the P element, has occurred notwithstanding the sterility induced by unrestricted movement. This element's invasion into D. melanogaster has been accompanied by the development of heterogeneity between P sequences, most of which now have internal deletions. Increasing evidence suggests that some deleted elements can repress P transposition, thereby protecting the host from the harmful effects of complete elements. Such repressing elements may rise to high frequencies in populations as a result of selection at the level of the host. We here investigate selective sweeps invoked by the spread of P sequences in D. melanogaster populations. Numerous high-frequency sites have been identified on the X chromosome, which differ in frequency between populations, and which are associated with repression of P-element transposition. Unexpectedly, sequences adjacent to high-frequency P-element sites do not show reduced levels of genetic diversity, and DNA variability is in linkage equilibrium with the presence or absence of a P element at the adjacent selected site. This might be explained by multiple insertions or through a selection for recombination analogous to that seen in 'hitchhiking'.     

Chromosome interactions in P-M dysgenic male recombination of Drosophila melanogaster.

The frequency, distribution and structure of P elements on the second and third chromosomes of Texas 1, a wild-type inbred strain of Drosophila melanogaster, were investigated by in situ hybridization. These autosomes were isolated individually and used as P-element donors to study the frequency and distribution of male recombination events generated on recipient chromosomes which were originally devoid of P sequences. The P-element array of chromosome 2 was shown to generate higher male recombination frequencies on chromosome 3 than vice versa, despite having fewer P factors and fewer P elements in general. This is likely to be due to the presence and distribution of specific P-deletion derivatives, which vary in their ability to repress P mobility. The male recombination generated on recipient chromosomes is associated with the insertion of donated P sequences, but only in a small minority of cases could a novel P-element site be detected at, or near, the recombination breakpoint. The majority of such breakpoints appear to be associated either with unsuccessful P insertion, or with the action of P transposase attracted by P elements newly inserted elsewhere on the recipient chromosome. Recent evidence also suggests that a small proportion of the breakpoints may be associated with the action of P transposase alone. Male recombination breakpoints appear to be distributed effectively at random along the recipient autosomes, and their frequency of occurrence was shown to correlate with the physical length of DNA available between markers, as revealed by the polytene map distance.     

Selective constraints on P-element evolution.

P elements, like mariners, inhabit eukaryotic genomes and transpose via a DNA intermediate. Mutant and wild-type elements in the same genome should be transposed with equal probability by trans-acting transposase, and so no selection should counteract the accumulation of inactivating mutations in transposase genes. Thus, copies of mariner elements diverge within a host species under no selection (Robertson and Lampe 1995). It is unknown whether or not this pattern holds for P elements, which are unrelated to mariner elements but share the same life history. Publicly available P-element sequences were analyzed for evidence of conservative selection for the function of P-element-encoded proteins. Results were compared to predictions derived from several hypotheses that could explain selection, or the lack of it. P-element protein-coding sequences do evolve under conservative selection but apparently because of more than one selective force. Of the four exons in the P-element transposase, the first three (exons 0, 1, and 2) can be translated alone into a repressor of transposition, while the last (exon 3) is only expressed as part of the full-length transposase and probably serves a transposition-specific role. As full-length P-element copies diverge from each other within a host population, selection maintains exons 0-2 but apparently not exon 3. The selection acting on exons 0-2 may act at the host level for repression of transposition (since host level selection does act on orthologous truncated elements that contain only exons 0-2). Evidence of selection on exon 3 is only found in comparisons of more diverged elements from different species, suggesting that selection for transposition acts primarily at horizontal transfer events. Thus, horizontal transfer events may be the sole source of the selection that is crucial to the maintenance of autonomous P elements in the face of mutation (as suggested by Robertson and Lampe 1995). The predictions derived here suggest a strategy for collecting sequence data that could definitively answer these questions.     

High-frequency P element loss in Drosophila is homolog dependent

P transposable elements in Drosophila melanogaster can undergo precise loss at a rate exceeding 13% per generation. The process is similar to gene conversion in its requirement for a homolog that is wild type at the insertion site and in its reduced frequency when pairing between the homologs is inhibited. However, it differs from classical gene conversion by its high frequency, its requirement for P transposase, its unidirectionality, and its occurrence in somatic and premeiotic cells. Our results suggest a model of P element transposition in which jumps occur by a "cut-and-paste" mechanism but are followed by double-strand gap repair to restore the P element at the donor site. The results also suggest a technique for site-directed mutagenesis in Drosophila.     

Germline excision of the transposable element Tc1 in C. elegans.

We have examined eight germline revertants generated by the excision of Tc1 from a site within the unc-22 gene of Caenorhabditis elegans. A rich variety of rearrangements accompanied Tc1 excision at this site, including transposon 'footprints', deletions of sequences flanking the insertion site and direct nontandem duplications of flanking DNA. With only modest modification the double-strand gap repair model for transposition, recently proposed by Engles and coworkers (Cell 62: 515-525 1990), can explain even the most complex of these rearrangements. In light of this model rearrangements of the target site accompanying transposition/excision may not be the end result of imprecise excision of the element. Instead, these rearrangements may be the result of imprecise repair of the double-strand gap by the host replication and repair machinery. Sequences surrounding an insertion site influence the fidelity of gap repair by this machinery. This may lead to a number of possible resolutions of a double-strand gap as documented here for a Tc1 site in unc-22.     

P transposable element in Drosophila melanogaster: horizontal transfer]

The P transposable element family in Drosophila melanogaster is responsible for the syndrome of hybrid dysgenesis which includes chromosomal rearrangements, male recombination, high mutability and temperature sensitive agametic sterility (called gonadal dysgenesis sterility). P element activity is controlled by a complex regulation system, encoded by the elements themselves, which keeps their transposition rate low within the strain bearing P elements and limits copy number by genome. A second regulatory mechanism, which acts on the level of RNA processing, prevents P mobility to somatic cells. The oldest available strains, representing most major geographical regions of the world, exhibited no detectable hybridization to the P-element. In contrast, all recently collected natural populations that were tested carried P-element sequences. The available evidence is consistent with the hypothesis of a worldwide P-element invasion of D. melanogaster during the past 30 years. Timing and direction of the invasion are discussed. The lack of P-element in older strains of Drosophila melanogaster as well as in the species must closely related to Drosophila melanogaster, suggests that P entered the Drosophila melanogaster genome recently, probably by horizontal transfer from an other species. The analysis of P-element elsewhere in the genus Drosophila reveals that several more distantly related species carried transposable elements with sequences quite similar to P. The species with the best-matching P-element is D. willistoni. A P-element from this species was found to match all but one of the 2907 nucleotides of the Drosophila melanogaster P-element. The phylogenic distributions and the likely horizontal transfers of the two other Drosophila transposable elements are discussed.     

Novel events associated with phenotypic reversion of a P element mutant in Drosophila melanogaster.

Transposable P elements have been used extensively for Drosophila mutagenesis. While their mutagenic activity has long been recognized, the mechanisms by which P elements cause mutations are varied and not completely understood. We describe here an experiment to replace a P element at vestigial (vg) that caused a strong mutant phenotype (P[21-3]) with a P element (P[21]) known to produce a very weak phenotype when inserted at vg. In addition to testing the feasibility of P element replacements at vg, our investigation led to the production of 7 new vg alleles and 1 apparent second site suppressor. All the vg21-3 revertants that we recovered had a P element inserted into the first exon of vg at the same location and in the same orientation as the original element in vg21-3, providing a unique opportunity to study the mechanism of transposon mutagenesis. A majority of the revertants arose from a previously described event: internal deletion of P sequences, including the P promoter. In addition, 3 novel reversions of the vg21-3 wing phenotype were recovered. The wings of homozygous vg21r36 flies were normal. However, vg21r36 in combination with a deletion of the vg locus exhibited a strong mutant wing phenotype. This was surprising, because the P element insertion in vg21r36 was very similar to that found in the vg21 allele, which showed only slight nicking of the wings in combination with a deletion. In vg21r4, reversion was caused by a tandem insertion of P[21] and the original P[21-3] element present in vg21-3. Finally, the vg21r7 revertant had a P[21-3] insert at vg and 3 additional P elements elsewhere in the genome. We hypothesize that reversion in the 3 novel cases might be caused by P repressor produced by an element at vg or, in the case of vg21r7, elsewhere in the genome. This raises an interesting aspect of P element evolution. While P transposons produce mutations that might prove deleterious to their host, their success in invading the genome of D. melanogaster may be explained by their ability to silence those same mutations by a range of repressor-producing elements.     

P transposition in Drosophila provides a new tool for analyzing postreplication repair and double-strand break repair.

A genetic screen has been developed in Drosophila for identifying host-repair genes responsible for processing DNA lesions formed during mobilization of P transposable elements. Application of that approach to repair deficient mutants has revealed that the mei-41 and mus302 genes are necessary for recovery of P-bearing chromosomes undergoing transposition. Both of these genes are required for normal postreplication repair. Mutants deficient in excision repair, on the other hand, have no detected effect on the repair of transposition-induced lesions. These observations suggest that P element-induced lesions are repaired by a postreplication pathway of DNA repair. The data further support recent studies implicating double-strand DNA breaks as intermediates in P transposition, because the mei-41 gene has been genetically and cytologically associated with the repair of interrupted chromosomes. Analysis of this system has also revealed a striking stimulation of site-specific gene conversion and recombination by P transposition. This result strongly suggests that postreplication repair in this model eukaryote operates through a conversion/recombination mechanism. Our results also support a recently developed model for a conversion-like mechanism of P transposition (Engels et al., 1990). Involvement of the mei-41 and mus302 genes in the repair of P element-induced double-strand breaks and postreplication repair points to a commonality in the mechanisms of these processes.     

P element-mediated duplications of genomic regions in Drosophila melanogaster

Previously we have described highly unstable yellow mutations induced by chimeric elements that consist of genomic sequences originating from different regions of the X chromosome flanked by identical copies of an internally deleted 1.2 kb P element. To study further the origin and the mechanism of formation of chimeric mobile elements, we analyzed complex y-sc mutations, induced by inversions between P elements located in the neighboring yellow and scute loci. The breakpoints of the inversions are flanked by two P elements in head-to-head orientation on one side and by one P element on the other side. Such an arrangement of P elements leads to frequent duplication into the site between the two P element copies located in head-to-head orientation of the yellow sequences adjacent to the single P element. The duplicated yellow sequences either partly replace the sequence of one of the P elements or are inserted between the conserved head-to-head oriented P elements. In some cases two copies of the yellow sequence are duplicated between the P elements in inverted tail-to-tail orientation. The structure of the P elements at the place of duplication and of the P element- yellow junction suggests that the described duplications, which form chimeric mobile elements, are generated through the previously proposed synthesis-dependent strand annealing mechanism.     

Extra sequences found at P element excision sites in Drosophila melanogaster.

Summary. We have previously established a transgenic Drosophila line with a highly transposable P element insertion. Using this strain we analyzed transposition and excision of the P element at the molecular level. We examined sequences flanking the new insertion sites and those of the remnants after excision. Our results on mobilization of the P element demonstrate that target-site duplication at the original insertion site does not play a role in forward excision and transposition. After P element excision an 8 by target-site duplication and part of the 31 by terminal inverted repeat (5–18 bp) remained in all the strains examined. Moreover, in 11 out of 28 strains, extra sequences were found between the two remaining inverted repeats. The double-strand gap repair model does not explain the origin of these extra sequences. The mechanism creating them may be similar to the hairpin model proposed for the transposon Tam in Antirrhinum majus.