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PubMed1995

Simple plaque hybridization method for the detection of differentially represented repetitive DNA.

A differential DNA hybridization method of detecting moderately repetitive strain-specific or species-specific DNA is described. Two Drosophila melanogaster strains, one with and one without transposable elements, were utilized as a model system to demonstrate the effectiveness of this procedure. A genomic library was constructed from flies of the pi 2 strain, which contains both P and hobo transposable elements. Duplicate plaque lifts of this library were probed with DNA from the same strain and with DNA from the Canton-S strain, which contains neither of these two families of transposable elements. Plaques that hybridized stronger to the genomic DNA that contained elements were noted, and then the filters were stripped and reprobed with P and hobo element DNA. Many of the differentially hybridizing plaques were shown to contain DNA homologous to one of the two known elements. This method should allow the isolation and cloning of any repetitive DNA present in one species or isolate, but absent or present in reduced copy number in another species or isolate. By analogy to the recent invasion of D. melanogaster by P elements, such differentially represented DNA is likely to represent recently invading transposable elements that are actively mobile.

Animals↗
PubMed1998

Molecular identification of the active ninja retrotransposon and the inactive aurora element in Drosophila simulans and D. melanogaster.

How transposable elements evolve is a key facet in understanding of spontaneous mutation and genomic rearrangements in various organisms. One of the best ways to approach this question is to study a newly evolved transposable element whose presence is restricted to a specific population or strain. The retrotransposons ninja and aurora may provide insights into the process of their evolution, because of their contrasting characteristics, even though they show high sequence identity. The ninja retrotransposon was found in a Drosophila simulans strain in high copy number and is potent in transposition. On the other hand, aurora elements are distributed widely among the species belonging to the Drosophila melanogaster species complex, but are immobile at least in D. melanogaster. In order to distinguish the two closely resembled retrotransposons by molecular means, we determined and compared DNA sequence of the elements, and identified characteristic internal deletions and nucleotide substitutions in 5'-long terminal repeats (LTR). Analyses of the structure of ninja homologs and LTR sequences amplified from both genomic and cloned DNA revealed that the actively transposable ninja elements were present only in D. simulans strains, but inactive aurora elements exist in both D. melanogaster and D. simulans.

Animals↗
PubMed1986

Transposable genetic element found in the 5'-flanking region of the fibroin H-chain gene in a genomic clone from the silkworm Bombyx mori.

A transposable genetic element was found in the 5'-flanking region of the fibroin H-chain gene in one of the genomic clones from the silkworm Bombyx mori. This element, named K-1.4, is about 1 X 4 X 10(3) base-pairs long, contains an open reading frame of only 225 base-pairs and has inverted repeats of 12 base-pairs at both ends. Duplication of three base-pairs seems to have occurred when this element was integrated into the silkworm genome. About 15 copies of K-1.4 are present per haploid genome of various silkworm strains. Genomic loci of some of these elements are different among different strains or even among individual offspring of the same parents. K-1.4 is present also in the genome of Bombyx mandarina. The K-1.4-related sequences are present in some species belonging to the family Saturniidae.

Animals↗
PubMed1990

Insertion of Mu1 elements in the first intron of the Adh1-S gene of maize results in novel RNA processing events.

Maize transposable elements, when inserted in or near genes, alter expression by several transcriptional and post-transcriptional mechanisms. Three independent, unstable insertions of the transposable element Mutator (Mu) into the first intron of the Alcohol dehydrogenase-1 (Adh1) gene have been shown to decrease expression [Strommer et al. (1982). Nature 300, 542-544]. We have developed an approach to elucidate the underlying molecular mechanisms responsible for the mutant phenotypes. Mu1 elements were inserted into Adh1-S intron 1 in vitro to create plasmid facsimiles of the mutant alleles. The Mu1 element was also inserted at novel positions within intron 1 to create new mutations. The Mu1/intron constructions were placed between the Adh1-S promoter/exon 1 segment and a reporter gene (firefly luciferase or beta-glucuronidase), and these chimeric gene constructs were tested in transient assays in maize protoplasts. When compared with the appropriate control, the Mu1 insertions decreased reporter gene expression to levels approximating the alcohol dehydrogenase enzyme activities observed for the Adh1-S mutants in vivo. The Mu1 insertions also showed a polarity effect with luciferase expression increasing as the insertions were placed nearer the 3' splice junction. In addition, Mu1 insertions within a different intron, actin intron 3, also significantly reduced luciferase expression, indicating that Mu1 insertions within introns are likely to diminish expression in many genes. The presence of the Mu1 sequences was correlated with decreased levels of steady-state luciferase transcript. Deletion analysis of the Mu1 element and RNase mapping indicate that the transposable element contains RNA processing signals in its central region that are largely responsible for the decrease in expression.

Actins↗
PubMed1991

Regulation of Drosophila P element transposition.

Drosophila P transposable elements are the best-studied family of eukaryotic non-retroviral transposons. P element transposition is regulated in several different ways and has thus provided a unique system with which to study the control of DNA rearrangements and gene expression in metazoans. Recent genetic and biochemical experiments have begun to shed light on the mechanism of P element transposition and the mechanisms controlling the temporal and spatial patterns of transposition.

Animals↗
PubMed1995

A transposon-like sequence with short terminal inverted repeats in the nuclear genome of Chlamydomonas reinhardtii.

A 1.2 kb DNA sequence, flanked by a potential seven base target-site duplication, was found inserted into a TOC1 transposable element from Chlamydomonas reinhardtii. The insertion sequence, named TOC2, is a member of a family of repeated DNA sequences that is present in all the C. reinhardtii strains tested. It resembles class II transposable elements: it possesses short 14 bp imperfect terminal repeats that begin AGGAGGGT, and sub-terminal direct repeats located within 250 bp of the termini. No large open reading frames were found. The terminal bases and length of target-site duplication are important in classifying transposable elements. On this basis TOC2 does not fall readily into existing families of class II transposable elements found in plants.

Animals↗
PubMed1991

IS801, an insertion sequence element isolated from Pseudomonas syringae pathovar phaseolicola.

A transposable element, designated IS801, was isolated from strain LR781 of Pseudomonas syringae pathovar phaseolicola in two independent events using the entrapment plasmid, pUCD800. IS801 is 1517 base pairs in length and contains open reading frames that potentially encode proteins of 311 and 172 amino acids, as well as smaller proteins. Unlike most other prokaryotic transposable elements, IS801 lacks terminal repeats. Sequence analysis revealed two target pentamers for IS801 insertion that differ by one base pair. One copy of IS801 generated a perfect duplication of its target, TGAAC. The second copy of IS801 was flanked by the target, TGGAC, at one end, and TGAAC at the other end. A third copy of IS801 was cloned from pMMC7105, an indigenous plasmid of strain LR781, and it was flanked by copies of the pentamer TGAAC.

Amino Acid Sequence↗
PubMed1991

DNA sequence of the Doc retroposon in the white-one mutant of Drosophila melanogaster and of secondary insertions in the phenotypically altered derivatives white-honey and white-eosin.

We analysed the structure of the white locus of Drosophila melanogaster in a family of related white mutants. The white-one mutant has bleach white eyes, and a Doc transposable element is inserted into the promotor region of the white locus. The DNA sequence of this Doc insertion was determined, and showed it to be closely related to other Drosophila melanogaster retroposons such as the I factor and the F, G and jockey elements. There are two long open reading frames, which encode a putative nucleic acid binding protein and a putative reverse transcriptase, respectively. Two independent, partially pigmented derivatives were analysed by cloning sequences from this region. In white-honey a transposable element of the retroviral class, B104, is inserted within the Doc element. In white-eosin there is an insertion within the Doc element of a 190 bp sequence that appears to be a member of a novel family of transposable elements. This pogo element is of the same structural class as the Drosophila melanogaster P and hobo elements. These data are consistent with the hypothesis that the Doc retroposon cannot excise, and that, for the white-one mutation, flies with altered phenotypes are most often generated by the insertion of additional transposable elements.

Amino Acid Sequence↗
PubMed1989

cis-acting DNA sequence requirements for P-element transposition.

The P transposable element of Drosophila melanogaster has a complex array of cis-acting DNA sequences necessary for efficient transposition. At the 3' end these sequences extend over more than 150 bp and include 11- and 31-bp sequences found repeated in inverted orientation at the 5' end. The P element's 5' end, however, cannot function as its 3' end. When two 3' P-element ends are present, the more proximal end is used preferentially. We found also that the duplication of the target site does not appear to play a role in forward transposition.

Animals↗
PubMed1995

Molecular characterization of spontaneous mutations at the scarlet locus of Drosophila melanogaster.

Six spontaneous mutations of the scarlet (st) locus of Drosophila melanogaster have been studied at the molecular level. Two of the mutants (st1 and stsp) arose in laboratory populations, while the other four (stcob, stct89, stdct and stdv) were isolated from natural populations. In five of these there is a DNA insertion within the st region and in four cases the insertion has been identified as being a transposable element; these include the retrotransposons 412 and B104/roo, and also jockey a member of the LINE family. In the other case (stdct), the insertion appears to consist of partially duplicated st sequences. In two of the mutants (st1 and stdv) the same transposable element (412) has inserted in the same orientation at exactly the same site within the st gene. The transposable element insertions are found in intron and exon regions of the st gene and also in the putative upstream regulatory region; insertions located in introns or exons result in the production of truncated st transcripts. The results show that the same types of transposable elements that cause spontaneous mutation in laboratory stocks of D. melanogaster also cause mutation in the wild.

ATP-Binding Cassette Transporters↗
PubMed2005

Mobile genetic elements and sexual reproduction.

Transposable elements (TE) are prominent components of most eukaryotic genomes. In addition to their possible participation in the origin of sexual reproduction in eukaryotes, they may be also involved in its maintenance as important contributors to the deleterious mutation load. Comparative analyses of transposon content in the genomes of sexually reproducing and anciently asexual species may help to understand the contribution of different TE classes to the deleterious load. The apparent absence of deleterious retrotransposons from the genomes of ancient asexuals is in agreement with the hypothesis that they may play a special role in the maintenance of sexual reproduction and in early extinction for which most species are destined upon the abandonment of sex.

Animals↗
PubMed2005

Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize.

Helitron transposable elements carrying gene fragments were recently discovered in maize. These elements are frequently specific to certain maize lineages. Here we report evidence supporting the involvement of helitrons in the rapid evolution of the maize genome, in particular in the multiplication of related genic fragments across the genome. We describe a family of four closely related, non-autonomous maize helitrons and their insertion sites at four non-allelic genetic loci across the maize genome: two specific to the B73 inbred, and two to the Mo17 inbred. We propose the phylogeny of this helitron family and provide an approximate timeline of their genomic insertions. One of these elements, the Mo17-specific helitron on chromosome 1 (bin 1.07), is transcriptionally active, probably as a result of insertion in the vicinity of a promoter. Significantly, it produces an alternatively spliced and chimeric transcript joining together genic segments of different chromosomal origin contained within the helitron. This transcript potentially encodes up to four open reading frames. During the course of evolution, transcribed helitrons containing multiple gene fragments may occasionally give rise to new genes with novel biochemical functions by a combinatorial assembly of exons. Thus helitrons not only constantly reshape the genomic organization of maize and profoundly affect its genetic diversity, but also may be involved in the evolution of gene function.

Base Sequence↗
PubMed2003

Excision of the Drosophila mariner transposon Mos1. Comparison with bacterial transposition and V(D)J recombination.

It has been proposed that the modern immune system has evolved from a transposon in an ancient vertebrate. While much is known about the mechanism by which bacterial transposable elements catalyze double-strand breaks at their ends, less is known about how eukaryotic transposable elements carry out these reactions. We have examined the mechanism by which mariner, a eukaryotic transposable element, performs DNA cleavage. We show that the nontransferred strand is cleaved initially, unlike prokaryotic transposons which cleave the transferred strand first. First strand cleavage is not tightly coupled to second strand cleavage and can occur independently of synapsis, as happens in V(D)J recombination but not in transposition of prokaryotic transposons. Unlike V(D)J recombination, however, second strand cleavage of mariner does not occur via a hairpin intermediate.

Animals↗
PubMed1997

CM-gag, a transposable-like element reiterated in the genome of Culex pipiens mosquitoes, contains only a gag gene.

CM-gag elements constitute an homogeneous family of sequences that are reiterated in the genome of Culex pipiens strains from different continents. Apparently complete 1.75 kb CM-gag copies are flanked by target-site duplications and have a polyadenylation signal near their 3' end. They potentially contain a unique gene encoding a putative protein that displays homologies with nucleic acid binding proteins and the gag polypeptide of retroviruses and retrotransposons, but that does not encode a reverse transcriptase. CM-gag elements are similar in their genetic organization to the telomeric transposable sequences Het-A from Drosophila melanogaster, but Southern-hybridization patterns indicate that the former are more probably dispersed in various areas of the mosquito genome. The homogeneity of CM-gag copies that are distributed worldwide suggests that they have most probably been amplified recently. Furthermore, selective constraints against amino acid changes have been acting on these sequences, suggesting that they need to encode the gag-like protein to be incorporated into the chromosomes.

Amino Acid Sequence↗
PubMed2003

The plant MITE mPing is mobilized in anther culture.

Transposable elements constitute a large portion of eukaryotic genomes and contribute to their evolution and diversification. Miniature inverted-repeat transposable elements (MITEs) constitute one of the main groups of transposable elements and are distributed ubiquitously in the genomes of plants and animals such as maize, rice, Arabidopsis, human, insect and nematode. Because active MITEs have not been identified, the transposition mechanism of MITEs and their accumulation in eukaryotic genomes remain poorly understood. Here we describe a new class of MITE, called miniature Ping (mPing), in the genome of Oryza sativa (rice). mPing elements are activated in cells derived from anther culture, where they are excised efficiently from original sites and reinserted into new loci. An mPing-associated Ping element, which has a putative PIF family transposase, is implicated in the recent proliferation of this MITE family in a subspecies of rice.

Base Sequence↗
PubMed1987

Hybrid dysgenesis in D. melanogaster is not a general release mechanism for DNA transpositions.

Many spontaneous mutations are caused by the insertion or excision of DNA elements. Since most mutations are deleterious, evolution should favor a mechanism for genetically controlling the rate of movement of transposable elements in most, if not all, organisms. In Drosophila melanogaster a syndrome of correlated genetic changes, including mutation, chromosome breakage, and sterility, is observed in the hybrid progeny of crosses between different strains. This syndrome, which is termed hybrid dysgenesis, results from the movement of P-DNA elements. What is not clear is whether the movement of other types of transposable elements is under the same coordinated control. In this study the ability of hybrid dysgenesis to increase the rate of excision of 12 DNA elements at 16 mutant alleles and to induce insertion-bearing mutations to change to other mutant states was tested. The data show that hybrid dysgenesis caused by P-element transpositions does not act as a general stimulus for the movement of other Drosophila transposable elements.

Animals↗
PubMed1984

Interspecific DNA transformation in Drosophila.

A DNA fragment that includes the wild-type rosy (ry+) gene of Drosophila melanogaster has been introduced by microinjection into the germ line of the reproductively isolated species Drosophila simulans and incorporated into the D. simulans genome. Transformation was mediated by the transposable element P, which occurs in the genome of most natural populations of D. melanogaster but not in D. simulans. Rubin and Spradling [Rubin, G.M. & Spradling, A.C. (1982) Science 218, 348-353] have previously shown that the ry+ DNA fragment, which is flanked by recognition sequences of P element, can transform the germ line of D. melanogaster. Successful transformation in D. simulans indicates that the P element continues to function as a transposable element in the D. simulans genome. Moreover, the ry+ gene of D. melanogaster functions in the genome of D. simulans to produce normal eye color, despite the estimated 1 to 5 million yr of reproductive isolation since the evolutionary divergence of these species. Interspecific DNA transformation provides a useful method for the study of genetic differences affecting gene expression among related but reproductively isolated species.

Animals↗
PubMed2005

Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila.

To study adaptation, it is essential to identify multiple adaptive mutations and to characterize their molecular, phenotypic, selective, and ecological consequences. Here we describe a genomic screen for adaptive insertions of transposable elements in Drosophila. Using a pilot application of this screen, we have identified an adaptive transposable element insertion, which truncates a gene and apparently generates a functional protein in the process. The insertion of this transposable element confers increased resistance to an organophosphate pesticide and has spread in D. melanogaster recently.

Adaptation, Physiological↗