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PubMed1995

LTR-retrotransposons and MITEs: important players in the evolution of plant genomes.

Retrotransposons are an abundant and ancient component of plant genomes, yet recent evidence indicates that element activity in many modern plants is restricted to times of stress. Stress activation of plant retrotransposons may be a significant factor in somaclonal variation, in addition to providing an important means to isolate new active elements. Long terminal repeat retrotransposons and a second class of elements we have called miniature inverted-repeat transposable elements (MITEs) have recently been found to be associated with the genes of diverse plants where some contribute regulatory sequences. Because of their sequence diversity and small size, MITEs may be a valuable evolutionary tool for altering patterns of gene expression.

Animals↗
PubMed1994

Neighboring plasmid sequences can affect Mini-Mu DNA transposition in the absence of expression of the bacteriophage Mu semi-essential early region.

Bacteriophage Mu DNA, like other transposable elements, requires DNA sequences at both extremities to transpose. It has been previously demonstrated that the transposition activity of various transposons can be influenced by sequences outside their ends. We have found that alterations in the neighboring plasmid sequences near the right extremity of a Mini-Mu, inserted in the plasmid pSC101, can exert an influence on the efficiency of Mini-Mu DNA transposition when an induced helper Mu prophage contains a polar insertion in its semi-essential early region (SEER). The SEER of Mu is known to contain several genes that can affect DNA transposition, and our results suggest that some function(s), located in the SEER of Mu, may be required for optimizing transposition (and thus, replication) of Mu genomes from restrictive locations during the lytic cycle.

Bacteriophage mu↗
PubMed2001

Sensitivity to diethylether anesthesia of fruit flies primarily depends on the genotypes of the sodium channel gene rather than the states of the membranes and the mechanisms might be different from heat-induced paralysis.

The para locus of Drosophila melanogaster encodes the alpha subunit of a voltage-sensitive sodium channel. Many of the mutants develop paralysis at the high temperature (37 degrees C) and are hypersensitive to diethylether anesthesia. We examined whether the two aspects of the phenotype are mediated by a same mechanism that involves the sodium channel molecule by investigating properties of the three para alleles (para(hd838), para(ts1) and para(ts3)). Larvae of the all para strains showed almost normal sensitivities to diethylether anesthesia while adult flies of them showed hypersensitivities to that in the following manner: para(hd838)<==para(ts1)<para(ts3)<Canton-S. Larvae of the two para strains showed hypersensitivities to heat-induced paralysis in the following manner: para(ts1)=para(ts3)<para(hd838)=Canton-S, while adult flies of the all para strains showed hypersensitivities to that in the following manner: para(ts1)=para(ts3)<para(hd838)<Canton-S. The distinct phenotype of para(hd838) from para(ts1) or para(ts3) observed in the larval and adult heat-induced paralysis, would be the reflection of the difference of the mutation sites between in para(hd838) and para(ts1) or para(ts3). In addition, because the rank of sensitivity in the adult anesthesia and heat-induced paralysis were reversed between para(hd838) and para(ts1) or para(ts3), the mechanisms of diethylether anesthesia and heat-induced paralysis are not the same. There would be the anesthesia-specific mechanisms because the sensitivity to anesthesia became more remarkable in para(hd838) than in para(ts1) or para(ts3). para(hd838) has an insertion of P-element, one of a transposable element, in the second intron of the para sodium channel gene. Excision of the P-element from the para locus of the para(hd838) conferred the flies the wild-typic phenotype and reduction of the para gene in para(hd838) dramatically enhanced the hypersensitivity to anesthesia, suggesting that the phenotype of the strain was caused exclusively by the mutation of the para locus. The susceptibility to anesthesia also depends on the temperature at which the flies were assayed, not at which they were cultured, but the dependence on the assay temperature was smaller than that on the genotype. By these findings we could assure that the sensitivity to diethylether anesthesia of para(hd838) primarily depends on the genotypes of the sodium channel gene rather than other reasons such as the fluidity of the membranes.

Journal Article↗
PubMed2004

Eukaryotic gene regulation by targeted chromatin re-modeling at dispersed, middle-repetitive sequence elements.

RNA interference might have evolved to minimize the deleterious impact of transposable elements and viruses on eukaryotic genomes, because mutations in genes within the RNAi pathway cause mobilization of transposons in nematodes and flies. Although the first examples of RNAi involved post-transcriptional gene silencing, recently the pathway has been shown to act at the transcriptional level. It does so by establishing a chromatin configuration on the target DNA that has many of the hallmarks of heterochromatin, thus preventing its transcription. Members of dispersed, repeated sequence families appear to have been utilized by the RNAi machinery to regulate nearby genes in yeast. The unusual genomic distribution of three repeated element families in the chicken, fruit-fly and nematode genomes prompts speculation that some of these repeats have been co-opted to control gene expression, either locally or over extended chromosomal domains.

Animals↗
PubMed2026

Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.

Plant genomes are filled with retrotransposons and their derivatives, constantly undergoing sequence diversification and structural rearrangement. Among them, short, non-autonomous retrotransposons lack full coding capacity and often form subfamilies. As a result, non-autonomous retrotransposons are incompletely identified in most to all genome assemblies.Here, we capitalize on our comprehensive understanding of the transposable element (TE) landscape in sugar beet (Beta vulgaris) to assess the extent of the blind spot for non-autonomous long terminal repeat (LTR) retrotransposons. This use case serves to answer if all of these sequences are derivatives of easier-to-identify full-length elements or if there is more variability that is currently overlooked.For this we applied a semi-automated structural discovery workflow followed by in-depth manual verification to characterize non-autonomous LTR retrotransposons in sugar beet. We retrieve more than 100 non-autonomous LTR retrotransposon families that lack complete autonomous coding capacity, including canonical terminal-repeat retrotransposons in miniature (TRIMs), elongated non-coding derivatives and families retaining fragmented coding remnants. The identified families span a broad range, including elements exceeding 15,000&#xa0;bp in length and display evidence for reshuffling and modular evolution. Only a subset of families could be confidently linked to autonomous retrotransposons, showing sequence diversification within the non-autonomous LTR retrotransposon fraction beyond the autonomous genomic templates.We highlight that a large fraction of non-autonomous LTR retrotransposons is incompletely recovered with the current TE identification workflows, even if the output is well-curated and condensed into TE libraries and suggest procedures to remedy this gap. This study gives a genome-wide view into the non-autonomous LTR retrotransposon landscape of a single plant genome and highlights the importance of structure-based approaches for their identification and classification.

LTR retrotransposons↗
PubMed1989

Chromosome-breaking structure in maize involving a fractured Ac element.

Chromosome breakage in maize can result from an interaction between certain transposable elements. When an Ac (Activator) element and a state I Ds (Dissociation) element are present together in the genome, either linked or unlinked, breaks occur regularly at the locus of the Ds element. We show here that breaks occur with high frequency at or near the locus of a structure consisting of a 2.5-kilobase (kb) terminally deleted or fractured Ac element very tightly linked to a second, intact 4.6-kb Ac element. This structure has the features of a macrotransposon and may behave like one. Loss of the tight linkage abolishes chromosome breakage. A model based on transposition of the macrotransposon is proposed to explain the chromosome-breaking properties of Ac and Ds.

Alleles↗
PubMed1997

Transposition of the IS21-related element IS1415 in Rhodococcus erythropolis.

Three copies of the IS21-related transposable element IS1415 were identified in Rhodococcus erythropolis NI86/21. Adjacent to one of the IS1415 copies, a 47-bp sequence nearly identical to the conserved 5' end of integrons was found. Accurate transposition of IS1415 carrying a chloramphenicol resistance gene (Tn5561) was demonstrated following delivery from a suicide vector to R. erythropolis SQ1.

Amino Acid Sequence↗
PubMed1994

Involvement of SRE element of Ty1 transposon in TEC1-dependent transcriptional activation.

Some Ty1 transposable element insertion mutations of Saccharomyces cerevisiae activate transcription of adjacent genes in a cell-type dependent manner. This activation requires at least STE12 and TEC1 gene products. The binding site for the STE12 protein is located in the sterile responsive element (SRE), which is just downstream the 5' LTR of Ty1 and contains one copy of the pheromone response element (PRE). This report defines the sequences in Ty1 required for TEC1-dependent activation using a TDH3::lacZ reporter gene in which the UAS was replaced by different portions of a Ty1 or Ty2 element. The Ty1 SRE seems to be sufficient to ensure the TEC1 and STE12-mediated activation whereas Ty2 SRE can activate the expression of the adjacent genes in the absence of both proteins. Adjacent to the PRE element, there is a region (PAE) with extensive sequence divergence in Ty1 and Ty2 SREs. Swapping experiments between Ty1 and Ty2 sequences show that Ty1 PAE is required for the activation of adjacent gene expression in a TEC1 and STE12-dependent manner. The use of a LexA::TEC1 construct indicates that the chimeric protein has no activation ability suggesting that TEC1 could act in conjunction with another factor.

Base Sequence↗
PubMed1995

P DNA element movement in somatic cells reduces lifespan in Drosophila melanogaster: evidence in support of the somatic mutation theory of aging.

Evidence is presented in support of the hypothesis that P DNA element movement in somatic cells of Drosophila melanogaster induces genetic damage that significantly reduces lifespan. The lifespan of D. melanogaster males was significantly reduced by the somatic movement of a single P element in the presence of P[ry+ delta 2-3](99B) transposase. In addition, the P[ry+ SalI](89D) repressor of P[ry+ delta 2-3](99B) somatic transposase was observed to reduce the effect of P element movement on lifespan. Finally, the frequency of somatic-cell chromosome breakage was significantly increased in neuroblasts of males with somatically active P elements. These results show that lifespan in D. melanogaster is decreased with increased somatic genetic damage from DNA-element movement. Although this conclusion does not confirm that transposable element movement is a cause of natural senescence, this conclusion is clear evidence in support of a close relationship between somatic genetic damage and aging.

Aging↗
PubMed1993

Transposition pattern of the maize element Ds in Arabidopsis thaliana.

As part of establishing an efficient transposon tagging system in Arabidopsis using the maize elements Ac and Ds, we have analyzed the inheritance and pattern of Ds transposition in four independent Arabidopsis transformants. A low proportion (33%) of plants inheriting the marker used to monitor excision contained a transposed Ds. Selection for the transposed Ds increased this to at least 49%. Overall, 68% of Ds transpositions inherited with the excision marker were to genetically linked sites; however, the distribution of transposed elements varied around the different donor sites. Mapping of transposed Ds elements that were genetically unlinked to the donor site showed that a proportion (3 of 11 tested) integrated into sites which were still physically linked.

Arabidopsis↗
PubMed2001

Occurrence of Tn4371-related mobile elements and sequences in (chloro)biphenyl-degrading bacteria.

Tn4371, a 55-kb transposable element involved in the degradation and biphenyl or 4-chlorobiphenyl identified in Ralstonia eutropha A5, displays a modular structure including a phage-like integrase gene (int), a Pseudomonas-like (chloro)biphenyl catabolic gene cluster (bph), and RP4- and Ti-plasmid-like transfer genes (trb) (C. Merlin, D. Springael, and A. Toussaint, Plasmid 41:40-54, 1999). Southern blot hybridization was used to examine the presence of different regions of Tn4371 in a collection of (chloro)biphenyl-degrading bacteria originating from different habitats and belonging to different bacterial genera. Tn4371-related sequences were never detected on endogenous plasmids. Although the gene probes containing only bph sequences hybridized to genomic DNA from most strains tested, a limited selection of strains, all beta-proteobacteria, displayed hybridization patterns similar to the Tn4371 bph cluster. Homology between Tn4371 and DNA of two of those strains, originating from the same area as strain A5, extended outside the catabolic genes and covered the putative transfer region of Tn4371. On the other hand, none of the (chloro)biphenyl degraders hybridized with the outer left part of Tn4371 containing the int gene. The bph catabolic determinant of the two strains displaying homology to the Tn4371 transfer genes and a third strain isolated from the A5 area could be mobilized to a R. eutropha recipient, after insertion into an endogenous or introduced IncP1 plasmid. The mobilized DNA of those strains included all Tn4371 homologous sequences previously identified in their genome. Our observations show that the bph genes present on Tn4371 are highly conserved between different (chloro)biphenyl-degrading hosts, isolated globally but belonging mainly to the beta-proteobacteria. On the other hand, Tn4371-related mobile elements carrying bph genes are apparently only found in isolates from the environment that provided the Tn4371-bearing isolate A5.

Bacteria↗
PubMed1999

A P element-homologous sequence in the house fly, Musca domestica.

Sequences homologous to the P transposable element have been identified in Musca domestica. Sequence analysis of a genomic clone (Md-P1) indicates that, although the house fly P element has lost its coding capacity, the basic general structure of drosophilid P elements is present. The house fly P element sequence shares a number of structural features with that from the blow fly, Lucilia cuprina, including a large intron separating exons 1 and 2, two additional introns interrupting exon 2 and the apparent absence of inverted repeat termini. Within a relatively well-conserved central region, the house fly sequence shows 59% similarity to the D. melanogaster P element, but distal regions are more diverged. Southern blot analysis of several strains indicated the presence of at least four P element copies.

Amino Acid Sequence↗
PubMed1987

A series of Tn5 variants with various drug-resistance markers and suicide vector for transposon mutagenesis.

A series of variants of transposon Tn5 were constructed by replacement of the 2.7-kb central segment which encodes kanamycin resistance with various other resistance-coding genes: tetracycline, chloramphenicol, gentamicin, trimethoprim, streptomycin or ampicillin. A thermosensitive replication mutant of the broad-host-range transmissible plasmid R388 was also constructed for use as a suicide vector for the delivery of transposable elements.

DNA Transposable Elements↗
PubMed1999

Transposition of the piggyBac element in embryos of Drosophila melanogaster, Aedes aegypti and Trichoplusia ni.

The Lepidopteran transposable element piggyBac is being recognized as a useful vector for genetic engineering in a variety of insect species. This transposon can mediate transformation in the Dipteran species Ceratitis capitata, and can potentially serve as a versatile vector for transformation of a wide variety of insect species. Using a plasmid-based interplasmid transposition assay, we have demonstrated that this transposon, of the short inverted terminal repeat type, is capable of transposition in embryos of three different insect species, Drosophila melanogaster, the yellow fever mosquito Aedes aegypti, and its host of origin, Trichoplusia ni. This assay can confirm the potential utility of piggyBac as a gene transfer tool in a given insect species, and provides an experimental model for assessing molecular mechanisms of transposon movement.

Aedes↗
PubMed2002

Aberrant transposition of a Tc1-mariner element, impala, in the fungus Fusarium oxysporum.

We previously determined that the impalaD transposable element of Fusarium oxysporum was able to mobilize a non autonomous copy of impala ( niaD::imp::hph), inserted in the niaD gene encoding nitrate reductase. Generally, mobilization results in the recovery of Nia(+) revertants at low frequency. In the course of this study, we recovered a transformant that gave rise to Nia(+) revertants at a high rate. These revertants displayed atypical phenotypes and showed a niaD hybridization pattern different from that in more typical revertants. Molecular analysis of the structure of the transformant and atypical revertants indicated that (i) in the transformant, two copies of impala, one defective and one active, were inserted at the same genomic locus in a head-to-head orientation; and (ii) all the revertants analyzed presented the same chromosomal rearrangement, an inversion resulting in the replacement of the niaD promoter by a new sequence containing a cryptic promoter. We also frequently observed additional DNA rearrangements (deletion or inversion) in these revertants. The sequences at the rearrangement junctions indicated the occurrence of a transposition event that used the ITRs (Inverted Terminal Repeats) of separate transposons arranged in direct orientation. These features can be interpreted as the consequences of an aberrant transposition process. Such a process may account for the rearrangements observed in some genomic regions containing multiple transposon ends, and could serve as a mechanism for the generation of genetic diversity.

Base Sequence↗