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PubMed1983

Analysis of a transposable element in Caenorhabditis elegans.

A transposable element, designated Tc1, has been characterized in Caenorhabditis elegans. Tc1 is 1.7 kilobases long, has an inverted terminal repeat of less than 100 base pairs, and is repeated as a highly conserved element. The copy number and genomic positions of Tc1 are extremely variable among strains, implying that Tc1 is mobile. However, progeny of interstrain crosses did not show hybrid dysgenic traits that might be due to Tc1 transposition.

Animals↗
PubMed1995

The isolation of Ant1, a transposable element from Aspergillus niger.

A transposable element has been isolated from the industrially important fungus Aspergillus niger (strain N402). The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. It had inserted at a TA site and appeared to have duplicated the target site upon insertion. The isolated element was found to be 4798 bp in length and contained 37-bp inverted, imperfect, terminal repeats (ITRs). The sequence of the central region of the element revealed an open reading frame (designated ORF1) which showed similarity, at the amino acid level, to the transposase of the Tc1/mariner class of DNA transposons. Another sequence within the central region of the element showed similarity to the 3' coding and downstream untranslated region of the amyA gene of A. niger. Sequence homology and structural features indicate that this element, which has been named Ant1 (A. niger transposon 1), is related to the Tc1/mariner group of DNA transposons. Ant1 is apparently present as a single copy in strain N402 of A. niger.

Amino Acid Sequence↗
PubMed1987

A new family of the poly-deoxyadenylated class of Drosophila transposable elements identified by a representative member at the dunce locus.

Two transposable elements have been identified at the dunce locus in chromosomes recovered after a premeiotic and interchromosomal conversion event occurred at this gene. One is approximately 8.2 kb and is inserted near the 5' end of the gene. This element was identified by sequence analysis as a member of the B104 (roo) family of copia-like transposable elements. The second resides near the 3' end of the gene and represents a new family of the class of poly-deoxyadenylated [poly(dA)] transposable elements. It is 0.38 kb in length and has one terminus consisting of a stretch of 29 deoxyadenosine residues with a polyadenylation site like those found in mRNA molecules, located about 20 bp away from the poly(dA) stretch. Fourteen base pairs of genome DNA is duplicated at the target site of this element.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMedDate not supplied

[Transposable elements in the Animal Kingdom].

Transposable elements (TEs) are commonly thought to be of universal occurrence in eukaryotes. Analysis of complete higher eukaryotic genomes confirms TE status as substantial genome components and provides insights into their role in shaping the genome structure of extant eukaryotes. This review addresses several recently investigated problems in transposon biology, including potential roles of promoter organization in transposon function and evolution, the ubiquity of TEs in numerous phyla of the animal kingdom, and possible connections between transposon content and the mode of reproduction.

Animals↗
PubMed1995

The distribution of transposable elements on X chromosomes from a natural population of Drosophila simulans.

The distribution of 13 transposable element families along 15 X chromosomes from an African natural population of Drosophila simulans was determined by in situ hybridization to polytene chromosomes. The transposable elements cloned from Drosophila melanogaster all hybridized with Drosophila simulans chromosomes. The number of copies per family was 3.5 times lower in the latter species and correlated with the copy number per family in Drosophila melanogaster. With the exception of 297, the copy number per chromosome followed a Poisson distribution. Element frequencies per chromosome band were generally low. However, several sites of the distal region and the base of the X chromosome had high frequencies of occupation. Elements had higher abundance at the base of the chromosome compared to distal regions. Overall, the distribution of transposable elements in Drosophila simulans is similar to that found in Drosophila melanogaster. These data provide evidence for the operation of a force (or forces) opposing transpositional increase in copy number, and that this force is weaker at the bases of chromosomes, consistent with the idea that recombination between elements at non-homologous sites contains TE copy number. The reduction in copy number of all TE families in Drosophila simulans compared to Drosophila melanogaster can be explained by stronger selection against transposable element multiplication and/or lower rates of transposition in Drosophila simulans.

Africa↗
PubMed1990

Insertion and excision of the transposable element mariner in Drosophila.

The transposable element mariner is active in both germline and somatic cells of Drosophila mauritiana. Activity of the element is greatly enhanced in the presence of Mos1, a genetic factor identified as an autonomous copy of mariner. A strain of D. mauritiana containing Mos1 and other copies of mariner was used to initiate a screen for visible mutations. More than 20 mutations were obtained, including alleles of white, yellow and vermilion. Six alleles were characterized at the molecular level, and all were found to contain a mariner element inserted into the affected gene. Four insertions into the white locus were sequenced to determine the exact site of insertion of mariner. There appears to be little sequence specificity requirement for mariner insertion, other than an absolute requirement for the dinucleotide TA, which is duplicated upon insertion. Sequences of phenotypically wild-type germline and somatic revertants obtained from various white alleles, including the previously isolated wpch allele, were obtained using the polymerase chain reaction. Mariner excision is imprecise in both germline and soma, and the most frequent excision events are the same in the two tissues. Mutant derivatives of wpch were also studied, and were found to exhibit a wide range of molecular structures and phenotypes.

Alleles↗
PubMed2000

Invasion of Drosophila virilis by the Penelope transposable element.

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.

Animals↗
PubMed2003

Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana.

Transposable elements (TEs) comprise a major component of eukaryotic genomes, and exhibit striking deviations from random distribution across the genomes studied, including humans, flies, nematodes, and plants. Although considerable progress has been made in documenting these patterns, the causes are subject to debate. Here, we use the genome sequence of Arabidopsis thaliana to test for the importance of competing models of natural selection against TE insertions. We show that, despite TE accumulation near the centromeres, recombination does not generally correlate with TE abundance, suggesting that selection against ectopic recombination does not influence TE distribution in A. thaliana. In contrast, a consistent negative correlation between gene density and TE abundance, and a strong under-representation of TE insertions in introns suggest that selection against TE disruption of gene expression is playing a more important role in A. thaliana. High rates of self-fertilization may reduce the importance of recombination rate in genome structuring in inbreeding organisms such as A. thaliana and Caenorhabditis elegans.

Arabidopsis↗
PubMed1993

On two transposable elements from Bacillus stearothermophilus.

Two transposable elements, IS5376 and IS5377, were identified in the thermophile Bacillus stearothermophilus CU21 based upon the following criteria: (1) both were found to appear on different plasmids introduced into the same host CU21; (2) signals of homology were found between the genomic DNA of CU21 and each of them; (3) different numbers of Southern hybridization bands were found for the genomic DNA of different strains of B. stearothermophilus; and (4) characteristic inverted repeats at both ends and direct repeats of the target DNA adjacent to them were found for both IS5376 and IS5377. Two open reading frames (ORFs) were detected for IS5376 and one for IS5377. The putative coding products of the ORFs are homologous to those of known ISs from mesophiles and are considered to be transposases. The results of analyses of nucleotide sequence and the deduced amino acid sequence suggest that IS5376 is a member of the IS21 family and that IS5377 is a member of the IS4 family.

Amino Acid Sequence↗
PubMed1989

Characterization and zeste reaction of spontaneously reduced transposable elements in Drosophila melanogaster.

Seven transposable elements (TE), selected from parental stock w 239 Cy, have been characterized. They all carry w+ but have lost both rst+ and the two polytene chromosome bands of a complete TE and are thus cytologically invisible. In situ hybridization with probes from the white-roughest interval shows that the reduced TE's are truncated in the same region, 40-90 kb upstream of the white locus, well proximal to the zeste interaction site. They express the white gene in wild type fashion in all tissues studied (eyes, testis sheaths, and Malpighian tubules) but give zeste reactions varying from yellow to bright red. Thus, by the criterion of the zeste reaction, 40 kb of TE sequences 5' to the transcription start site cannot insulate the white gene from position effects. One single spontaneously reduced TE (TE203) originated from parental stock w TE100 ct. This TE is truncated closer to the white locus (+ 18- +26 kb), but still well separated from the zeste interaction site. In a z1w11E4 background, homozygous TE203 flies have an uneven eye pigmentation, while heterozygotes have eyes that are yellowish red. The Malpighian tubules and testes show wild type pigmentation in both cases, like normal TE's.

Animals↗
PubMed1999

How valuable are model organisms for transposable element studies?

Model organisms have proved to be highly informative for many types of genetic studies involving 'conventional' genes. The results have often been successfully generalized to other closely related organisms and also, perhaps surprisingly frequently, to more distantly related organisms. Because of the wealth of previous knowledge and their availability and convenience, model organisms were often the species of choice for many of the earlier studies of transposable elements. The question arises whether the results of genetic studies of transposable elements in model organisms can be extrapolated in the same ways as those of conventional genes? A number of observations suggest that special care needs to be taken in generalizing the results from model organisms to other species. A hallmark of many transposable elements is their ability to amplify rapidly in species genomes. Rapid spread of a newly invaded element throughout a species range has also been demonstrated. The types and genomic copy numbers of transposable elements have been shown to differ greatly between some closely related species. Horizontal transfer of transposable elements appears to be more frequent than for nonmobile genes. Furthermore, the population structure of some model organisms has been subject to drastic recent changes that may have some bearing on their transposable element genomic complements. In order to initiate discussion of this question, several case studies of transposable elements in well-studied Drosophila species are presented.

Biological Evolution↗
PubMed1999

Transposable element interactions in insects: crossmobilization of hobo and Hermes.

There are four non-drosophilid insect gene vector systems available that have been constructed from the short inverted repeat-type transposable elements Minos, piggyBac, mariner and Hermes. These elements (with the possible exception of piggyBac) are members of transposable element families that appear to be widespread in nature. Because these transposable element families are large it is possible that an insect species targeted for transformation will contain related transposable elements. The data presented here begin to address directly the question of interaction between diverged but related members of transposable element families. We tested the ability of the hAT elements hobo and Hermes to interact and cause crossmobilization. Using plasmid-based and chromosome-based element mobility assays we found that the terminal sequences of hobo and Hermes were almost equally good substrates for hobo transposase. However, this ability to crossmobilize was not reciprocal. Hermes transposase was only rarely able to cause the excision of hobo elements from plasmids and was never observed from germline chromosomes. These results have important implications for transgenic insect studies in the future.

Animals↗
PubMed2000

Molecular and evolutionary analysis of two divergent subfamilies of a novel miniature inverted repeat transposable element in the yellow fever mosquito, Aedes aegypti.

A novel family of miniature inverted repeat transposable elements (MITEs) named Pony was discovered in the yellow fever mosquito, Aedes aegypti. It has all the characteristics of MITEs, including terminal inverted repeats, no coding potential, A+T richness, small size, and the potential to form stable secondary structures. Past mobility of PONY: was indicated by the identification of two Pony insertions which resulted in the duplication of the TA dinucleotide targets. Two highly divergent subfamilies, A and B, were identified in A. aegypti based on sequence comparison and phylogenetic analysis of 38 elements. These subfamilies showed less than 62% sequence similarity. However, within each subfamily, most elements were highly conserved, and multiple subgroups could be identified, indicating recent amplifications from different source genes. Different scenarios are presented to explain the evolutionary history of these subfamilies. Both subfamilies share conserved terminal inverted repeats similar to those of the Tc2 DNA transposons in Caenorhabditis elegans, indicating that Pony may have been borrowing the transposition machinery from a Tc2-like transposon in mosquitoes. In addition to the terminal inverted repeats, full-length and partial subterminal repeats of a sequence motif TTGATTCAWATTCCGRACA represent the majority of the conservation between the two subfamilies, indicating that they may be important structural and/or functional components of the Pony elements. In contrast to known autonomous DNA transposons, both subfamilies of PONY: are highly reiterated in the A. aegypti genome (8,400 and 9, 900 copies, respectively). Together, they constitute approximately 1. 1% of the entire genome. Pony elements were frequently found near other transposable elements or in the noncoding regions of genes. The relative abundance of MITEs varies in eukaryotic genomes, which may have in part contributed to the different organizations of the genomes and reflect different types of interactions between the hosts and these widespread transposable elements.

Aedes↗
PubMed1986

The structure of hobo transposable elements and their insertion sites.

The hobo transposable elements of Drosophila form a family of 3.0-kb elements and their deletion derivatives. Their distribution is consistent with the model that 3.0-kb elements are functionally complete but that smaller hobos are defective and require complete elements in trans for transposition. The sequence of one 3.0-kb element is presented; it has several interesting features, including a 1.9-kb open reading frame downstream from potential TATA and CAT sequences. Comparison of 11 independent insertion sites shows that in every case the hobo element has integrated at and duplicated either the sequence NNNNNNAC or CTTTNNNN. There is evidence that an eight nucleotide sequence internal to hobo that matches both of these sequences has been used as an insertion site for a second hobo element, as the first step in the creation of an internal deletion derivative. Structural similarities between hobo and the eukaryotic transposable elements P, Ac, 1723, and Tam3, found in widely divergent host organisms, suggest that they all transpose by a common mechanism.

Journal Article↗
PubMed2000

High copy numbers of multiple transposable element families in an Australian population of Drosophila simulans.

Sudden mobilization of transposable elements in Drosophila is a well-reported phenomenon but one that usually affects no more than a few elements (one to four). We report here the existence of a D. simulans natural population (Canberra) from Australia, which had high copy numbers for various transposable elements (transposons, LTR retrotransposons and non-LTR retrotransposons). The impact of transposable elements on the host genome and populations is discussed.

Animals↗
PubMed1978

Chloramphenicol resistance in Streptomyces coelicolor A3(2): possible involvement of a transposable element.

The transfer of a Chl element, causing resistance to chloramphenicol in Streptomyces coelicolor A3(2), was studied in NF x SCP1- superfertile crosses. When the Chl element is on the donor side (NF) its transfer to the recombinant cells was virtually total as if the element acted as a second concomitant transfer origin. When the Chl element was on the recipient side (SCP1-) it was never displaced by the immigrant chromosome even when the region facing chl+ was selected for. A fraction of the original Chl- mutants presented a requirement for arginine (ArgB-). A Chl- mutant gave rise spontaneously to ArgB- derivatives at high frequency. The same ArgB- requirement come out at high frequency among Chl- derivatives from a cross NFChl- x SCP1-Chl+ in which neither parent required arginine or produced spontaneously arginine-less derivatives. It is suggested that the Chl element is a "transposable element" (Tn) presumably associated with "insertion sequences" (IS). The insertional inactivation of the Chl element may be accompanied or followed by a deletion in the adjacent ArgB gene.

Arginine↗
PubMed1988

The bacteriophage Mu transposase protein can form high-affinity protein-DNA complexes with the ends of transposable elements of the Tn 3 family.

The 37 kb transposable bacteriophage Mu genome encodes a transposase protein which can recognize and bind to a consensus sequence repeated three times at each extremity of its genome. A subset of this consensus sequence (5'-PuCGAAA(A)-3') is found in the ends of many class II prokaryotic transposable elements. These elements, like phage Mu, cause 5 bp duplications at the site of element insertion, and transpose by a cointegrate mechanism. Using the band retardation assay, we have found that crude protein extracts containing overexpressed Mu transposase can form high-affinity protein-DNA complexes with Mu att R and the ends of the class II elements Tn 3 (right) and IS101. No significant protein-DNA complex formation was observed with DNA fragments containing the right end of the element IS102, or a non-specific pBR322 fragment of similar size. These results suggest that the Mu transposase protein can specifically recognize the ends of other class II transposable elements and that these elements may be evolutionarily related.

Coliphages↗
PubMed1996

Distribution of T1, Q, Pegasus and mariner transposable elements on the polytene chromosomes of PEST, a standard strain of Anopheles gambiae.

The chromosomal locations of four families of transposable elements, T1, Q, Pegasus and mariner, have been determined by in situ hybridization to polytene chromosomes of ovarian nurse cells of the mosquito Anopheles gambiae. As part of this effort, we have developed a vigorous pink-eyed laboratory strain of A. gambiae (PEST), rendered homozygous standard for chromosomal inversions on all autosomes. Ten different individuals of this strain were studied with each transposable element probe. The average number of hybridization sites per genome was 83.9 for T1, 63.4 for Q, 31.5 for Pegasus and 64.7 for mariner, excluding pericentric and centromeric regions. However, some degree of polymorphism was observed within each family such that, considering all ten individuals, 94 different sites were detected for T1, 82 sites for Q, 45 sites for Pegasus and 71 sites for mariner. The mean occupancy per site varied from 0.70 (Pegasus) to 0.91 (mariner), which, while significantly higher than that seen for transposable elements in natural populations of Drosophila melanogaster, is comparable to that seen in established laboratory stocks. In addition, these element families were not randomly distributed. All but Pegasus were concentrated in centromeric heterochromatin and centromere-proximal euchromatin, most showed a deficit of hybridization sites in the distal section of chromosomes, and a significant proportion of sites were coincident between families. These results provide the first detailed examination of the cytogenetic location of transposable elements in a nondrosophilid insect, and, through comparison with the behavior of transposable elements in Drosophila, may provide insight into the interaction between elements and host. The mapped elements are also expected to serve as landmarks useful in integrating the developing physical map of the PEST strain with the chromosomal banding pattern.

Animals↗