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PubMed1989

Interaction of the mottler of white with transposable element alleles at the white locus in Drosophila melanogaster.

The mottler of white (mw) locus has been determined to interact with alleles of the white (w) eye color locus which are a subset of the transposable element insertion mutants. The transposable elements belong to six different types, including copia, and are located at several sites within the w gene. Three X-ray-induced revertants of white-apricot (wa) no longer respond to mw, indicating that the transposable element must be present for mw to act. The mottling property of the original allele was analyzed by combining the mw mutant with extra copies of wa, either in a tandem duplication or in a transposable segment on chromosome two. Because neither duplication alters the mottling pattern, the event that results in the mottled pattern must occur at mw and not at w. The pattern of a deficiency for the locus heterozygous with the original allele differs from that of mw/mw females, confirming that this unique mottling property occurs at mw. A new allele of mw was induced in hybrid dysgenic crosses. It is not mottled, slightly enhances wa as a heterozygote, and further enhances as a homozygote or hemizygote. An analysis of RNA from wa with mw shows a reduction of the full-length normal RNA and a concomitant increase in certain RNAs that terminate within the copia element. These results suggest that several retrotransposon-induced alleles share an RNA processing function encoded by mw.

Alleles↗

PubMed1998

Isolation and characterization of a new transposable element in Chlamydomonas reinhardtii.

A new transposable element, Tcr3, was identified in the unicellular green alga Chlamydomonas reinhardtii. The Tcr3 element contained imperfect terminal inverted repeat sequences of 56 bp and created a 2 bp target site duplication upon insertion. Insertion of Tcr3 into the 3'-untranslated region of the NIT8 gene, which is essential for nitrate assimilation, prevented expression of the gene. Excision of the Tcr3 element correlated with reversion of the mutant phenotype and left behind a 3 bp footprint. Tcr3 was found in all Chlamydomonas isolates tested and should prove to be useful for transposon-tagging experiments in Chlamydomonas.

Animals↗

PubMed1994

Gene marker loss induced by the transposable element, En, in maize.

The En/Spm transposable element system in maize includes the functional element, En/Spm and the receptor element I/dSpm. An En receptor has been found that shows En-induced breakage. This En-responsive receptor (designated I836518) is located on the short arm of chromosome 9, proximal to Wx. In the presence of En, markers distal to the receptor show a loss of gene expression. Kernels heterozygous for aleurone and endosperm marker genes have a variegated appearance. The hypothesis is advanced that this variegation represents a physical loss of the chromosome segments carrying the genes distal to the receptor position. It is the first case of an En-controlled breakage event.

Chromosome Mapping↗

PubMed1997

Topological constraints on transvection between white genes within the transposing element TE35B in Drosophila melanogaster.

The transposable element TE35B carries two copies of the white (w) gene at 35B1.2 on the second chromosome. These w genes are suppressed in zeste-1 (z1) mutant background in a synapsis-dependent manner. Single-copy derivatives of the original TE35B stock give red eyes when heterozygous, but zeste eyes when homozygous. TE35B derivatives carrying single, double or triple copies of w were crossed to generate flies carrying from two to five ectopic w genes. Within this range, z1-mediated suppression is insensitive to copynumber and does not distinguish between w genes that are in cis or in trans. Suppression does not require the juxtaposition of even numbers of w genes, but is extremely sensitive to chromosomal topology. When arranged in a tight cluster, in triple-copy TE derivatives, w genes are nonsuppressible. Breakpoints falling within TE35B and separating two functional w genes act as partial suppressors of z1. Similarly, breakpoints immediately proximal or distal to both w genes give partial suppression. This transvection-dependent downregulation of w genes may result from mis-activation of the X-chromosome dosage compensation mechanism.

ATP-Binding Cassette Transporters↗

PubMed2004

Detection of transposable elements by their compositional bias.

BACKGROUND: Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be used as a tool for detection and analysis of TE sequences. RESULTS: We compared the composition of TE sequences and host gene sequences using probabilistic models of nucleotide sequences. We used hidden Markov models (HMM), which take into account the base composition of the sequences (occurrences of words n nucleotides long, with n ranging here from 1 to 4) and the heterogeneity between coding and non-coding parts of sequences. We analyzed three sets of sequences containing class I TEs, class II TEs and genes respectively in three species: Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. Each of these sets had a distinct, homogeneous composition, enabling us to distinguish between the two classes of TE and the genes. However the particular base composition of the TEs differed in the three species studied. CONCLUSIONS: This approach can be used to detect and annotate TEs in genomic sequences and complements the current homology-based TE detection methods. Furthermore, the HMM method is able to identify the parts of a sequence in which the nucleotide composition resembles that of a coding region of a TE. This is useful for the detailed annotation of TE sequences, which may contain an ancient, highly diverged coding region that is no longer fully functional.

Animals↗

PubMed1997

Characterization of the maize Mutator transposable element MURA transposase as a DNA-binding protein.

The autonomous MuDR element of the Mutator (Mu) transposable element family of maize encodes at least two proteins, MURA and MURB. Based on amino acid sequence similarity, previous studies have reported that MURA is likely to be a transposase. The functional characterization of MURA has been hindered by the instability of its cDNA, mudrA, in Escherichia coli. In this study, we report the first successful stabilization and expression of MURA in Saccharomyces cerevisiae. Gel mobility shift assays demonstrate that MURA is a DNA-binding protein that specifically binds to sequences within the highly conserved Mu element terminal inverted repeats (TIRs). DNase I and 1,10-phenanthroline-copper footprinting of MURA-Mu1 TIR complexes indicate that MURA binds to a conserved approximately 32-bp region in the TIR of Mu1. In addition, MURA can bind to the same region in the TIRs of all tested actively transposing Mu elements but binds poorly to the diverged Mu TIRs of inactive elements. Previous studies have reported a correlation between Mu transposon inactivation and methylation of the Mu element TIRs. Gel mobility shift assays demonstrate that MURA can interact differentially with unmethylated, hemimethylated, and homomethylated TIR substrates. The significance of MURA's interaction with the TIRs of Mu elements is discussed in the context of what is known about the regulation and mechanisms of Mutator activities in maize.

Base Sequence↗

PubMed1985

Dehalogenase genes of Pseudomonas putida PP3 on chromosomally located transposable elements.

Pseudomonas putida PP3 utilizes halogenated alkanoic acids (HAA) such as 2,2-DCPA as its sole carbon and energy sources. Spontaneous HHA- mutants, isolated by selection for resistance to the toxic analogs monochloroacetic acid and dichloroacetic acid, arose at frequencies several orders of magnitude higher than expected for spontaneous mutations. Analysis of the five classes of mutants isolated suggested that the dehalogenase and HAA permease genes were on chromosomally located transposable elements and that the spontaneous mutations involved excision of these elements. This suggestion was confirmed by the observation that one of the elements can transpose to a target DNA molecule. The frequency of the excision event was strongly influenced by environmental conditions. Possible relationships between expression of cryptic genes and their location on transposable elements are discussed.

DNA Transposable Elements↗

PubMed2002

Transposable elements and the lines of Blaschko: a new perspective.

BACKGROUND: Transposable elements or retrotransposons are particles of retroviral origin that are interspersed in large numbers in the genome of plants and animals. They may affect the activity of adjacent genes by methylation or demethylation, resulting in silencing or activation of gene expression. In animals such as mice or dogs, retrotransposons may give rise to phenotypic variation in the form of variegated coat patterns reminiscent of the lines of Blaschko as observed in human skin. OBJECTIVE AND METHODS: Because the human genome does likewise contain large amounts of retrotransposons, it is conceivable that these elements may cause similar skin lesions in human skin. The group of genodermatoses following the lines of Blaschko was therefore screened for phenotypes suggesting such an epigenetic origin. RESULTS: As possible examples, the inflammatory linear verrucous epidermal nevus as well as cases of pigmentary mosaicism arranged in hypermelanotic or hypomelanotic streaks following the lines of Blaschko may be taken into consideration. Such phenotypes usually occur sporadically but may affect, by way of exception, several members of a family. CONCLUSION: These linear skin disorders would possibly visualize the action of a transposable element that is partly expressed and partly silenced at an early developmental stage.

Animals↗

PubMed1995

The insertion sequence element ISRm2011-2 belongs to the IS630-Tc1 family of transposable elements and is abundant in Rhizobium meliloti.

The insertion sequence (IS) element ISRm2011-2 of Rhizobium meliloti (Rm) is characterized by 19-bp imperfect terminal inverted repeats (three mismatches) and a size of 1053 bp. Upon transposition, ISRm2011-2 generates a putative target duplication of 2 bp. ISRm2011-2 carries two major overlapping open reading frames (ORFA and B) with a coding capacity of 135 and 201 amino acids (aa), respectively. A potential translational frameshifting window (5'-AAAAAAAG) is located in the overlapping region of both ORFs. The putative fusion product of both proteins, which probably represents the mature transposase, has a predicted molecular mass of 35.8 kDa and a pI of 10.5. Comparison of the deduced aa sequence of ORFA with database entries revealed homology to putative transposases of some IS elements of the IS3 family, as well as to eukaryotic transcription factors. The protein encoded by ORFB shows homology to transposases (Tps) of the recently proposed IS630-Tc1 family which includes Tps of both prokaryotic and eukaryotic transposable elements. Analyses of the distribution of ISRm2011-2 in natural Rm populations showed that this IS element is abundant in Rm strains.

Amino Acid Sequence↗

PubMed1995

Guest: a 98 bp inverted repeat transposable element in Neurospora crassa.

The region immediately 3' of histidine-3 has been cloned and sequenced from two laboratory strains of the ascomycete fungus Neurospora crassa; St Lawrence 74A and Lindegren, which have different derivations from wild collections. Amongst the differences distinguishing these sequences are insertions ranging in size from 20 to 101 bp present only in St Lawrence. The largest of these is flanked by a 3 bp direct repeat, has terminal inverted repeats (TIR) and shares features with several known transposable elements. At 98 bp, it may be the smallest transposable element yet found in eukaryotes. There are multiple copies of the TIR in the Neurospora genome, similar but not identical to the one sequenced. PCR amplification of Neurospora genomic DNA, using 26 bp of the TIR as a single primer, gave products of discrete sizes ranging from 100 bp to about 1.3 kb, suggesting that the element isolated (Guest) may be a deletion derivative of a family of larger transposable elements. Guest appears to be the first transposable element reported in fungi that is not a retrotransposon.

Base Sequence↗

PubMed1994

The basis for germline specificity of the hobo transposable element in Drosophila melanogaster.

Previous results suggested that the hobo transposable element is active predominantly in the germline of Drosophila. We investigate germline restriction of hobo transposition by testing in vitro modified elements for their ability to mobilize marked elements in vivo. Although intact hobo elements are germline specific, an hsp70 promoter-hobo transposase fusion is active in the soma. Analysis of the hsp70-promoted transcript does not provide evidence for splicing. Moreover, the hobo promoter confers germline bias to a highly sensitive reporter, delta 2-3 P transposase. These results indicate that hobo transposition is germline specific due to regulation of transposase production at the level of transcription. Thus, although hobo is similar to the P transposable element in organization and tissue specificity, it differs in the underlying mechanism governing germline specific activity.

Animals↗

PubMed1983

Homologue destabilization by a putative transposable element in Drosophila melanogaster.

We postulate the presence of a transposable element, designated the L factor, to explain the properties of an unstable X chromosome and its derivatives. These chromosomes generate recessive lethal mutations at high rates, as does a stable X chromosome that has been associated with them for only one generation. The stable X chromosome does not become highly mutable in the absence of the unstable X chromosome, even when autosomes from the unstable stock are present. These facts suggest that the L factor is confined to the X chromosome and that it transposes to other X chromosomes paired with it. We propose the term "homologue destabilization" to denote the change in the stable chromosome brought about by this transposition. The lethal mutations caused by the L factor occur preferentially in the region around the cut wing locus (ct) and are sometimes associated with recognizable chromosome aberrations. The breakpoints of these aberrations are most often in the vicinity of ct, implying that the L factor is located near ct on the unstable chromosome, but it may reside at other sites as well. Alternately, the ct region may simply be a preferred target for the insertion of this transposable element.

Animals↗

PubMed1992

Horizontal transfer of hobo transposable elements within the Drosophila melanogaster species complex: evidence from DNA sequencing.

The hobo family of transposable elements, one of three transposable-element families that cause hybrid dysgenesis in Drosophila melanogaster, appears to be present in all members of the D. melanogaster species complex: D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. Some hobo-hybridizing sequences are also found in the other members of the melanogaster subgroup and in many members of the related montium subgroup. Surveys of older isofemale lines of D. melanogaster suggest that complete hobo elements were absent prior to 50 years ago and that hobo has recently been introduced into the species by horizontal transfer. To test the horizontal transfer hypothesis, the 2.6-kb XhoI fragments of hobo elements from D. melanogaster, D. simulans, and D. mauritiana were cloned and sequenced. The DNA sequences reveal an extremely low level of divergence and support the conclusion that the active hobo element has been horizontally transferred into or among these species in the recent past.

Animals↗

PubMed2005

Two novel transposable elements in a cytochrome P450 gene govern anthocyanin biosynthesis of commercial petunias.

The gene Hf1 plays a key role in the expression of floral color in petunias. Hf1 encodes a flavonoid-3',5'-hydroxylase (F3'5'H). The recessive allele (hf1) in an inbred line of petunia is known to be generated by the insertion of a transposable element (Psl). We isolated a novel Mutator-like transposable element (named dTph9) from the hf1 allele of a commercial petunia with red flowers. Another novel transposable element (named rTph1) was found in hf1 of another red petunia. rTph1 shared features with the copia-like retrotransposable element family. These novel elements were inserted independently in the third exon of the Hf1 gene, at different positions. The hf1 allele harboring dTph9 or rTph1 cannot produce an active F3'5'H enzyme because there are stop codons in the dTph9 and rTph1 sequences. Southern analysis showed that these elements were present in relatively low copy numbers and that mutation of the Hf1 locus was associated with the transposition of both elements. We conclude that a loss-of-function mutation of the petunia Hf1 gene is caused by the insertion of at least two different transposable elements, other than Psl, within the Hf1 gene.

Alleles↗

PubMed1996

Rates of movement of transposable elements in Drosophila melanogaster.

Mobilization rates of nine families of transposable elements (P, hobo, FB, gypsy, 412, copia, blood, 297, and jockey) were estimated by using 182 lines. Lines were started from a completely isogenic population of Drosophila melanogaster, carrying the marker sepia as an indicator of possible contamination, and have been accumulating spontaneous mutations independently for 80 generations of brother-sister (or two double-first-cousin) matings. Transposable element movements have been analyzed in complete genomes by the Southern technique. Mobilization was a rare event, with an average rate of 10(-5) per site per generation. The most active element was FB. In contrast, the retroelements gypsy and blood did not move at all. Most changes in restriction patterns were consistent with rearrangements rather than with true transposition. The euchromatic or heterochromatic location of elements was tested by comparing insertion patterns from adults and salivary glands. Certain putative rearrangements involved heterochromatic copies of the retroelements 412, copia or 297. Clustering of movement across families was observed, suggesting that movement of different families may be non-independent. As association between modified insertion patterns and mutant effects on quantitative traits shows that spontaneous transposition events cause continuous variation.

Animals↗

PubMedDate not supplied

Permanent fixation of a transposable element insert in the A2 gene of maize (Zea mays L.).

Transposable elements are considered to be responsible for creating genetic variation that contributes to evolutionary change. The pervasiveness of transposable elements in certain breeding lines of maize suggests that part of the observed genetic variation in those lines might be the result of transposition activity. Stable genetic variation often results from the allelic differences created by footprints generated in the host genes upon element excision; such variation can also result from insertions that are permanently fixed at a particular locus. The 1.3-kb element within the a2-m1 (class II state) allele of maize is one example of a stable insertion. Though the l element never excises from the A2 gene, it interacts with the TNPA (transposase A) product of the En/Spm element. In this study, we tested whether continued interaction of the l element with TNPA would lead to excision of l or other change of this allele. Our screening of 220,000 kernels did not yield any new states of a2-m1 in the presence of an active autonomous En/Spm element, indicating that this l element is highly stable and permanently fixed at this locus. The probable implications of l-element stability are discussed.

Base Sequence↗

PubMed2006

Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes.

Autonomous transposable elements, generally considered as junk and selfish, encode transposition proteins that can bind, copy, break, join or degrade nucleic acids as well as process or interact with other proteins. Such a repertoire of activities might be of interest for the host cell. There is indeed substantial evidence that mobile DNA can serve as a dynamic reservoir for new cellular functions. Transposable element genes encoding transposase, integrase, reverse transcriptase as well as structural and envelope proteins have been repeatedly recruited by their host during evolution in most eukaryotic lineages. Such domesticated sequences protect us against infections, are necessary for our reproduction, allow the replication of our chromosomes and control cell proliferation and death; others are essential for plant development. Many new candidates for domesticated sequences have been revealed by sequencing projects. Their functional analysis will uncover new aspects of evolutionary alchemy, the turning of junk into gold within genomes.

Animals↗

PubMed1992

The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. II. Inferences on the nature of selection against elements.

Data were collected on the distribution of nine families of transposable elements among a sample of autosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of biotinylated probes to polytene chromosomes. There is no general tendency for elements to accumulate at the tips of chromosomes. Elements tend to be present in excess of random expectation in the euchromatin proximal to the centromeres of the major autosomes, and on chromosome four. There is considerable heterogeneity between different families in the extent of this excess. The overall abundance of element families is inversely related to the extent to which they accumulate proximally. The level of proximal accumulation for the major autosomes is similar to that on the fourth chromosome, but less than that for the X chromosome. There is an overall deficiency of elements in the mid-section of the X compared with the mid-sections of the major autosomes, with considerable heterogeneity between families. The magnitude of this deficiency is positively related to the extent to which elements accumulate proximally. No such deficiency is seen if the proximal regions of the X and autosomes are compared. There is a small and non-significant excess of elements in third chromosomes carrying inversions. There is some between-year heterogeneity in element abundance. The implications of these findings are discussed, and it is concluded that they generally support the hypothesis that transposable element abundance is regulated primarily by the deleterious fitness consequences of meiotic ectopic exchange between elements. If this is the case, such exchange must be very infrequent in the proximal euchromatin, and the elements detected in population surveys of this kind must be inserted into sites where they have negligible mutational effects on fitness.

Animals↗