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At least 613 records · Page 34Linked to original sources
PubMed2005

ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.

We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

Algorithms↗
PubMed2002

Transposable element ISHp608 of Helicobacter pylori: nonrandom geographic distribution, functional organization, and insertion specificity.

A new member of the IS605 transposable element family, designated ISHp608, was found by subtractive hybridization in Helicobacter pylori. Like the three other insertion sequences (ISs) known in this gastric pathogen, it contains two open reading frames (orfA and orfB), each related to putative transposase genes of simpler (one-gene) elements in other prokaryotes; orfB is also related to the Salmonella virulence gene gipA. PCR and hybridization tests showed that ISHp608 is nonrandomly distributed geographically: it was found in 21% of 194 European and African strains, 14% of 175 Bengali strains, 43% of 131 strains from native Peruvians and Alaska natives, but just 1% of 223 East Asian strains. ISHp608 also seemed more abundant in Peruvian gastric cancer strains than gastritis strains (9 of 14 versus 15 of 45, respectively; P = 0.04). Two ISHp608 types differing by approximately 11% in DNA sequence were identified: one was widely distributed geographically, and the other was found only in Peruvian and Alaskan strains. Isolates of a given type differed by < or = 2% in DNA sequence, but several recombinant elements were also found. ISHp608 marked with a resistance gene was found to (i) transpose in Escherichia coli; (ii) generate simple insertions during transposition, not cointegrates; (iii) insert downstream of the motif 5"-TTAC without duplicating target sequences; and (iv) require orfA but not orfB for its transposition. ISHp608 represents a widespread family of novel chimeric mobile DNA elements whose further analysis should provide new insights into transposition mechanisms and into microbial population genetic structure and genome evolution.

Amino Acid Sequence↗
PubMed2002

Experimental evidence that the maize Activator (ac) transposase can act on a non-transposable element promoter to repress reporter gene expression in transient plant assays.

The transposase (TPase) encoded by the maize Activator (Ac) transposable element (TE) has been shown to repress the Ac TPase gene promoter (a form of element 'self-repression'). However, there is a lack of current experimental evidence to suggest that the Ac TPase can repress or activate the expression of non-TE gene promoters. Despite certain attributes of the maize Ac element and its TPase that might argue against such a broader, 'second function', that is, in regulating non-TE genes, the hypothesis that Ac TPase regulates gene expression was nevertheless tested in an in vivo tobacco BY-2 cell system using three different (non-TE) CaMV 35S promoters each linked to a gusA reporter gene. Four experiments were conducted; in each, BY-2 cells were co-transfected with two types of constructs: a CaMV 35S-gusA promoter construct (reporter) and an Ac expression construct (effector). In transient assays, a significant reduction in the magnitude of GUS enzyme activity was observed in the presence of an Ac effector (TPase-encoding) construct, below that observed for the 'no effector construct' treatment. A similar effector versus no effector comparison was made by Fridlender et al., who studied Ac element 'self-repression'. This Ac-associated GUS enzyme activity reduction was observed herein specifically for the gusA promoter construct with the 700 bp native CaMV 35S promoter region (a non-TE promoter). This construct contains 34 putative Ac TPase binding site motifs, 71% of which overlap one another on either DNA strand, motifs which also fall into the class of 'CpG islands' in plants. It is suggested that the Ac TPase can bind to such Ac DNA motifs and CpG islands existing within non-TE promoter regions, and can function as a regulator of transcription. Such a transcriptional mode of regulation has not been shown explicitly herein. The implications of the findings are discussed and a genomic (whole genome) regulation model is presented.

Base Sequence↗
PubMed1988

Transposable element Tc1 of Caenorhabditis elegans recognizes specific target sequences for integration.

The frequency of movement of Tc1, a 1.6-kilobase transposable element in the nematode Caenorhabditis elegans, is under genetic control, and Tc1 insertion sites are widely but nonrandomly distributed. The usually high frequency of insertions at multiple sites in the gene unc-22 suggested that this gene might be particularly rich in preferred target sites. To discover the features of Tc1 target sites, we have sequenced the sites of seven independent Tc1 transpositions into unc-22 and three other sites. Our comparison of these and two other sites from the literature indicates that in all cases Tc1 integrates at the dinucleotide T-A when it is flanked both 5' and 3' by particular preferred nucleotides. Our analysis revealed the following consensus target for Tc1 integration: G-A-K-A-T-A-T-G-T, in which K = G or T. This target site sequence specificity has implications both for the mechanism of Tc1 transposition and the use of Tc1 in cloning genes by transposon-tagging.

Animals↗
PubMed2001

Rates of movement and distribution of transposable elements in Drosophila melanogaster: in situ hybridization vs Southern blotting data.

Genomic copy numbers and the rates of movement of nine families of transposable elements (TEs) of Drosophila melanogaster were estimated in two sets of mutation accumulation lines: Beltsville and Madrid. Southern blotting was used to screen a large number of samples from both genetic backgrounds for TEs. The Madrid lines were also screened by in situ hybridization of TEs to polytene chromosomes, in order to obtain more detailed information about the behaviour of TEs in the euchromatin. Southern blotting data provided evidence of insertions and excision events in both genetic backgrounds, occurring at rates of approximately 10(-5) and 10(-6) per element copy per generation, respectively. In contrast, in situ data from the Madrid background presented a completely different picture, with no evidence for excisions, and a significantly higher rate of transposition (1.01 x 10(-4)). Direct comparison of the two data sets suggests that the Southern blotting technique had serious deficiencies: (i) it underestimated element abundance; (ii) it revealed less than 30% of the new insertions detected by in situ hybridization; and (iii) changes in the size of restriction fragments from any source were spuriously identified as simultaneous insertion-excision events. Our in situ data are consistent with previous studies, and suggest that selection is the main force controlling element spread by transposition.

Animals↗
PubMed1983

RNA from the yeast transposable element Ty1 has both ends in the direct repeats, a structure similar to retrovirus RNA.

The RNA homologous to the yeast transposable element Ty1 is one of the more abundant poly(A)+ RNAs in many strains of the yeast Saccharomyces cerevisiae. The 5' and 3' ends of Ty1 RNA have been determined from analysis of cDNA. The 5' end is 245 bases into the left delta sequence measured from the left side of the Ty1 element. The delta sequence is a direct repeat of about 340 base pairs present at each end of the Ty1 element. The Ty1 transcription includes 93-97 bases of the left delta sequence and continues through the entire internal portion of the element and through about 295 bases of the right delta sequence before reaching the 3' end located 38-46 bases from the right side of the right delta sequence. Because the delta sequences present at each end of a single Ty1 element have identical or very similar DNA sequences, these end points for Ty1 RNA raise several questions about the expression of Ty1 elements. First, what are the initiation and termination signals, because the Ty1 transcript must read through a DNA sequence that is identical to the 3' end at about 50 bases from the 5' end? Second, why is the direction of transcription of the Ty1 element opposite to that of genes that are overexpressed after the insertion of a Ty1 element? Third, because the Ty1 RNA itself has direct repeats of about 45 bases, a structure analogous to retrovirus RNAs, is the Ty1 RNA an intermediate in the transposition of Ty1?

Base Sequence↗
PubMed1988

The defective En-I102 element encodes a product reducing the mutability of the En/Spm transposable element system of Zea mays.

Genetic and molecular analysis has revealed a specific En-element of deletion derivative (En-I102) which reduces En/Spm-induced mutability. In the presence of En-I102 the excision frequency of both the autonomous En-1 element and the inhibitor element Spm-I5719A is reduced and excision occurs later in development. The 3697 bp long En-I102 element is derived from En-1 by an internal deletion of 4590 bp removing nucleotides 1862-6451. The promoter at the left end and sequences required for polyadenylation are retained in En-I102. It is transcribed to yield predominantly a 1.8 kb poly(A) RNA. cDNA analysis of this transcript indicated that it contains the coding capacity for a 386 amino acid polypeptide. This polypeptide shares homology with En/Spm encoded functions and we suggest that it interferes with transposition at the protein level.

Alleles↗
PubMed1997

Transposable elements as sources of variation in animals and plants.

A tremendous wealth of data is accumulating on the variety and distribution of transposable elements (TEs) in natural populations. There is little doubt that TEs provide new genetic variation on a scale, and with a degree of sophistication, previously unimagined. There are many examples of mutations and other types of genetic variation associated with the activity of mobile elements. Mutant phenotypes range from subtle changes in tissue specificity to dramatic alterations in the development and organization of tissues and organs. Such changes can occur because of insertions in coding regions, but the more sophisticated TE-mediated changes are more often the result of insertions into 5' flanking regions and introns. Here, TE-induced variation is viewed from three evolutionary perspectives that are not mutually exclusive. First, variation resulting from the intrinsic parasitic nature of TE activity is examined. Second, we describe possible coadaptations between elements and their hosts that appear to have evolved because of selection to reduce the deleterious effects of new insertions on host fitness. Finally, some possible cases are explored in which the capacity of TEs to generate variation has been exploited by their hosts. The number of well documented cases in which element sequences appear to confer useful traits on the host, although small, is growing rapidly.

Adaptation, Physiological↗
PubMed2006

Transposition of a fungal miniature inverted-repeat transposable element through the action of a Tc1-like transposase.

The mimp1 element previously identified in the ascomycete fungus Fusarium oxysporum has hallmarks of miniature inverted-repeat transposable elements (MITEs): short size, terminal inverted repeats (TIRs), structural homogeneity, and a stable secondary structure. Since mimp1 has no coding capacity, its mobilization requires a transposase-encoding element. On the basis of the similarity of TIRs and target-site preference with the autonomous Tc1-like element impala, together with a correlated distribution of both elements among the Fusarium genus, we investigated the ability of mimp1 to jump upon expression of the impala transposase provided in trans. Under these conditions, we present evidence that mimp1 transposes by a cut-and-paste mechanism into TA dinucleotides, which are duplicated upon insertion. Our results also show that mimp1 reinserts very frequently in genic regions for at least one-third of the cases. We also show that the mimp1/impala double-component system is fully functional in the heterologous species F. graminearum, allowing the development of a highly efficient tool for gene tagging in filamentous fungi.

Base Sequence↗
PubMed2006

The evolutionary history of the transposable element Penelope in the Drosophila virilis group of species.

We have used phylogenetic techniques to study the evolutionary history of the Penelope transposable element in the Drosophila virilis species group. Two divergent types of Penelope have been detected, one previously described, clade I, and a new one which we have termed clade III. The phylogeny of some copies of the Penelope clade I element was partially consistent with the species phylogeny of the D. montana subphylad, suggesting cospeciation and allowing the estimation of the evolutionary rate of Penelope. Divergence times of elements found in different species are younger than the age of the species, suggesting horizontal transfer events.

Animals↗
PubMed1983

Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome.

We have isolated and characterized several members of the P transposable element family from a Drosophila melanogaster P strain. Large 2.9 kb elements are present as multiple highly conserved copies together with smaller (0.5-1.6 kb), heterogeneous elements. The complete DNA sequences of the 2.9 kb element and four small elements (previously isolated from hybrid-dysgenesis-induced mutations of the white locus) have been determined. Each small element appears to have arisen from the 2.9 kb element by a different internal deletion. P elements have 31 bp perfect inverse terminal repeats and upon insertion duplicate an 8 bp sequence found only once at the site of insertion. Three of the insertions into the white locus occurred at the same nucleotide, indicating a high degree of local site specificity for insertion. The basis of this specificity has been investigated by DNA sequence analysis of the sites where 18 P elements are found. A revertant of one of the white locus mutants has been found to result from precise excision of the P element, restoring the wild-type DNA sequence.

Animals↗
PubMed1991

Chromosome breakage by pairs of closely linked transposable elements of the Ac-Ds family in maize.

Chromosome breaks and hence chromosomal rearrangements often occur in maize stocks harboring transposable elements (TEs), yet it is not clear what types of TE structures promote breakage. We have shown previously that chromosomes containing a complex transposon structure consisting of an Ac (Activator) element closely linked in direct orientation to a terminally deleted or fractured Ac (fAc) element have a strong tendency to break during endosperm development. Here we show that pairs of closely linked transposons with intact ends, either two Ac elements--a common product of Ac transposition--or an Ac and a Ds (Dissociation) element, can constitute chromosome-breaking structures, and that the frequency of breakage is inversely related to intertransposon distance. Similar structures may also be implicated in chromosome breaks in other eukaryotic TE systems known to produce chromosomal rearrangements. The present findings are discussed in light of a model of chromosome breakage that is based on the transposition of a partially replicated macrotransposon delimited by the outside ends of the two linked TEs.

Chromosome Aberrations↗
PubMed1986

The Drosophila melanogaster gypsy transposable element encodes putative gene products homologous to retroviral proteins.

We determined the complete nucleotide sequence of the gypsy element present at the forked locus of Drosophila melanogaster in the f1 allele. The gypsy element shares more homology with vertebrate retroviruses than with the copia element of D. melanogaster or the Ty element of Saccharomyces cerevisiae, both in overall organization and at the DNA sequence level. This transposable element is 7,469 base pairs long and encodes three putative protein products. The long terminal repeats are 482 nucleotides long and contain transcription initiation and termination signals; sequences homologous to the polypurine tract and tRNA primer binding site of retroviruses are located adjacent to the long terminal repeats. The central region of the element contains three different open reading frames. The second one encodes a putative protein which shows extensive amino acid homology to retroviral proteins, including gag-specific protease, reverse transcriptase, and DNA endonuclease.

Amino Acid Sequence↗
PubMed2001

Transposable elements are found in a large number of human protein-coding genes.

To study the genome-wide impact of transposable elements (TEs) on the evolution of protein-coding regions, we examined 13 799 human genes and found 533 (approximately 4%) cases of TEs within protein-coding regions. The majority of these TEs (approximately 89.5%) reside within 'introns' and were recruited into coding regions as novel exons. We found that TE integration often has an effect on gene function. In particular, there were two mouse genes whose coding regions consist largely of TEs, suggesting that TE insertion might create new genes. Thus, there is increasing evidence for an important role of TEs in gene evolution. Because many TEs are taxon-specific, their integration into coding regions could accelerate species divergence.

Animals↗
PubMed1989

Essential large transcripts of the maize Spm transposable element are generated by alternative splicing.

We used in vitro mutagenesis and cDNA cloning to identify new Suppressor-mutator (Spm) transposable element genes. Frameshift mutations in the ORFs of the tnpA gene's first intron markedly reduce Spm activity in transgenic tobacco, indicating that intron sequences encode essential gene products. Evidence is given that Spm encodes large alternatively spliced transcripts, designated tnpB (4.9 kb), tnpC (5.7 kb), and tnpD (5.8 kb), comprising all of the tnpA exons, most of the tnpA intron 1 ORF1 sequence, and either none, part, or all of the intron 1 ORF2 sequence. Two alternative splice donor sites were identified at the end of exon 1, and the structure of the different exon 1 sequences suggests that Spm employs a novel mode of translational regulation.

DNA↗
PubMed2006

Cooperation is fleeting in the world of transposable elements.

Composite transposons are key vehicles for the worldwide spreading of genes that allow bacteria to survive toxic compounds. Composite transposons consist of two smaller transposable elements called insertion sequences (ISs), which flank the genes that permit such survival. Each IS in a composite transposon can either transpose alone, selfishly, or it can transpose cooperatively, jointly with the other IS. Cooperative transposition can enhance an IS's chance of survival, but it also carries the risk of transposon destruction. I use game theory to show that the conditions under which cooperative transposition is an evolutionarily stable strategy (ESS) are not biologically realistic. I then analyze the distribution of thousands of ISs in more than 200 bacterial genomes to test the following prediction of the game-theoretical model: if cooperative transposition was an ESS, then the closely spaced ISs that characterize composite transposons should be more abundant in genomes than expected by chance. The data show that this is not the case. Cooperativity can only be maintained in a transitional, far-from-equilibrium state shortly after a selection pressure first arises. This is the case in the spreading of antibiotic resistance, where we are witnessing a fleeting moment in evolution, a moment in which cooperation among selfish DNA molecules has provided a means of survival. Because such cooperation does not pay in the long run, the vehicles of such survival will eventually disappear again. My analysis demonstrates that game theory can help explain behavioral strategies even for mobile DNA.

Animals↗
PubMed1990

Distribution of hobo transposable elements in the genus Drosophila.

This study describes the distribution of hobo-hybridizing sequences in the genus Drosophila. Southern blot analysis of 134 species revealed that hobo sequences are limited to the melanogaster and montium subgroups of the melanogaster-species group. Of the hobo-bearing species, only D. melanogaster and two of its sibling species, D. simulans and D. mauritiana, were found to contain potentially complete hobo elements. The distribution of hobo sequences is one of the narrowest distributions thus far described for any Drosophila transposable element.

Animals↗
PubMed2006

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.

MOTIVATION: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of TEs, which provides the main mechanism of mutation in some genomes, is an essential component of genome evolution. In this study we introduce a new concept of domain, a segmentation unit useful for describing the architecture of different copies of TEs. Our method extracts occurrences of a terminus-defined family of TEs, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relative to the presence or the absence of domains, the method results in a graphical view of sequences segmented into domains. RESULTS: Analysis of the new non-autonomous TE AtREP21 in the model plant Arabidopsis thaliana reveals copies of very different sizes and various combinations of domains which show the potential of our method. AVAILABILITY: DomainOrganizer web page is available at www.irisa.fr/symbiose/DomainOrganizer/.

Algorithms↗