Margaret G. Kidwell

PERSPECTIVE: TRANSPOSABLE ELEMENTS, PARASITIC DNA, AND GENOME EVOLUTION

Abstract The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as “selfish DNA” and “junk DNA” may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions. Corresponding Editor: T. Markow.

Transposable elements and the evolution of genome size in eukaryotes

It is generally accepted that the wide variation in genome size observed among eukaryotic species is more closely correlated with the amount of repetitive DNA than with the number of coding genes. Major types of repetitive DNA include transposable elements, satellite DNAs, simple sequences and tandem repeats, but reliable estimates of the relative contributions of these various types to total genome size have been hard to obtain. With the advent of genome sequencing, such information is starting to become available, but no firm conclusions can yet be made from the limited data currently available. Here, the ways in which transposable elements contribute both directly and indirectly to genome size variation are explored. Limited evidence is provided to support the existence of an approximately linear relationship between total transposable element DNA and genome size. Copy numbers per family are low and globally constrained in small genomes, but vary widely in large genomes. Thus, the partial release of transposable element copy number constraints appears to be a major characteristic of large genomes.

Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis.

There is strong inferential evidence for recent horizontal gene transfer of the P (mobile) element to Drosophila melanogaster from a species of the Drosophila willistoni group. One potential vector of this transfer is a semiparasitic mite, Proctolaelaps regalis DeLeon, whose morphology, behavior, and co-occurrence with Drosophila are consistent with the properties necessary for such a vector. Southern blot hybridization, polymerase chain reaction (PCR) amplification, and DNA sequencing showed that samples of P. regalis associated with a P strain of D. melanogaster carried P element sequences. Similarly, Drosophila ribosomal DNA sequences were identified in P. regalis samples that had been associated with Drosophila cultures. These results have potentially important evolutionary implications, not only for understanding the mechanisms by which genes may be transferred between reproductively isolated species, but also for improved detection of some host-parasite and predator-prey relationships.

Horizontal transfer of P elements and other short inverted repeat transposons

Evidence for horizontal transfer of the P family of transposable elements in the genus Drosophila is reviewed and evaluated, along with observations consistent with the recent invasion of Drosophila melanogaster by these elements. Some other examples of horizontal transfer involving other groups of transposable elements having short inverted terminal repeats are also briefly described. The sequential mechanistic steps likely to be involved in a horizontal transfer event are explored, including the requirement for suitable interspecific vectors or carriers. Finally, the frequency and significance of horizontal transfer of transposable elements are briefly discussed within an evolutionary framework.

The Structure and Evolution of Penelope in the virilis Species Group of Drosophila: An Ancient Lineage of Retroelements

Abstract. The Penelope element is the key element responsible for mobilization of other transposable elements in the course of hybrid dysgenesis in Drosophila virilis. Penelope has an unusually complex, highly variable organization in all studied species of the virlis group. Thc BRIDGE1 element from the fish Fugu rubripes is homologous to Penelope, and database searches detected additional homologous sequences among Expressed Sequence Tags from the flatworm Schistosoma mansonii and the nematode Ancylostoma caninum. Phylogenetic analysis shows that the reverse transcriptase of the Penelope group does not belong to any of the characterized major retroelement lineages, but apparently represents a novel branch of non-LTR retroelements. Sequence profile analysis results in the prediction that the C-terminal domain of the Penelope polyprotein is an active endonuclease related to intron-encoded endonucleases and the bacterial repair endonuclease UvrC, which could function as an integrase. No retroelements containing a predicted endonuclease of this family have been described previously. Phylogenetic analysis of Penelope copies isolated from several species of the virilis group reveals two subfamilies of Penelope elements, one of which includes full-length copies whose nucleotide sequences are almost identical, whereas the other one consists of highly diverged defective copies. Phylogenetic analysis of Penelope suggests both vertical transmission of the element and probable horizontal transfers. These findings support the notion that Penelope invasions occurred repeatedly in the evolution of the virilis group.

Distribution and evolution of mobile elements in the virilis species group of Drosophila

Abstract.The distributions of Penelope and Ulysses, two transposable elements that can induce hybrid dysgenesis, were studied in several species groups of Drosophila. No significant hybridization to Penelope and Ulysses probes was detected by Southern blot analyses of species outside the virilis group. In contrast, both element families have had a long residence in all species of the virilis species group, as indicated by their strong presence in the heterochromatic chromocenter. Except for D. kanekoi, D. lummei, and some strains of D. virilis, species of the group carry full-sized, and at least potentially functional, copies of both element families. Consistent with the occurrence of recent transposition, Penelope and Ulysses elements are located at different chromosomal sites in different geographical strains of the same species. A total of 79 Penelope and 47 Ulysses euchromatic insertion sites were localized to chromosomal subsections in species of the virilis group. Highly significant deviations from independence of the distributions of Penelope and Ulysses and previously established inversion breakpoints were documented, suggesting that these transposable elements may have played an important role in genomic reorganization and evolution of the virilis species group, which is especially rich in karyotypic variation.

Differences in P element population dynamics between the sibling species Drosophila melanogaster and Drosophila simulans.

Patterns of P element establishment and evolution were compared in populations of D. melanogaster and D. simulans. For each species, mixed populations were initiated with M strain flies lacking P elements together with P strain flies having similar P element copy numbers and phenotypes. The mixed populations were subsequently maintained under similar environmental conditions. On the basis of gonadal sterility assays, P elements tended to be significantly more active in D. melanogaster than in D. simulans populations. This activity difference between the two species was positively associated with P element copy number, determined by restriction enzyme analysis, and transposition frequency, as determined by a transposition assay. Host factors are the most likely explanation for the observed species variation. Difficulty of establishment may be a factor determining the absence of P elements in natural populations of D. simulans.

Testing transposable elements as genetic drive mechanisms using Drosophila P element constructs as a model system

The use of transposable elements (TEs) as genetic drive mechanisms was explored using Drosophila melanogaster as a model system. Alternative strategies, employing autonomous and nonautonomous P element constructs were compared for their efficiency in driving the ry+ allele into populations homozygous for a ry- allele at the genomic rosy locus. Transformed flies were introduced at 1%, 5%, and 10% starting frequencies to establish a series of populations that were monitored over the course of 40 generations, using both phenotypic and molecular assays. The transposon-borne ry+ marker allele spread rapidly in almost all populations when introduced at 5% and 10% seed frequencies, but 1% introductions frequently failed to become established. A similar initial rapid increase in frequency of the ry+ transposon occurred in several control populations lacking a source of transposase. Constructs carrying ry+ markers also increased to moderate frequencies in the absence of selection on the marker. The results of Southern and in situ hybridization studies indicated a strong inverse relationship between the degree of conservation of construct integrity and transposition frequency. These finding have relevance to possible future applications of transposons as genetic drive mechanisms.

Invasion of Drosophila virilis by the Penelope transposable element

Abstract The Penelope family of transposable elements (TEs) is broadly distributed in most species of the virilis species group of Drosophila. This element plays a pivotal role in hybrid dysgenesis in Drosophila virilis, in which at least four additional TE families are also activated. Here we present evidence that the Penelope family of elements has recently invaded D. virilis. This evidence includes: (1) a patchy geographical distribution, (2) genomic locations mainly restricted to euchromatic chromosome arms in various geographical strains, and (3) a high level of nucleotide similarity among members of the family. Two samples from a Tashkent (Middle Asia) population of D. virilis provide further support for the invasion hypothesis. The 1968 Tashkent strain is free of Penelope sequences, but all individuals collected from a 1997 population carry at least five Penelope copies. Furthermore, a second TE, Ulysses, has amplified and spread in this population. These results provide evidence for the Penelope invasion of a D. virilis natural population and the mobilization of unrelated resident transposons following the invasion.

Distribution of Drosophila melanogaster transposable element sequences in species of the obscura group

Fifteen species belonging to the obscura group of the genus Drosophila were screened for sequences homologous to Drosophila melanogaster transposable elements (TEs) as an initial step in the examination of the possible occurrence of TEs at chromosomal inversion breakpoints. Blots of genomic DNAs from species of the obscura group were hybridized at three different stringencies with 14 probes representing the major families of TEs described in D. melanogaster. The probe DNAs included copia, gypsy, 412, 297, mdg1, mdg3, 3S18, F, G, I, jockey, P, hobo, and FB3. D. melanogaster TEs were not well represented in the species of the obscura group analyzed. The TEs that were observed generally exhibited heterogeneous distributions, with the exception of F, gypsy and 412 which were ubiquitous, and 297, G, Sancho 2, hobo and FB which were not detected.