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PubMed1997

Characterization of the Sol3 family of nonautonomous transposable elements in tomato and potato.

Sol3 transposons are mobile elements defined by long terminal inverted repeats which are found in tomato and potato. Members of the Sol3 family have been isolated from a variety of solanaceous species including Solanum tuberosum (potato), S. demissum, S. chacoense, Lycopersicon esculentum (tomato), and L. hirsutum. While highly conserved elements are found within different species, Sol3 terminal inverted repeats can also flank unrelated sequences. Southern blot analysis indicates that Sol3 elements are less prevalent in the potato (approximately 50 copies) than in the tomato (>100 copies) genome. No Sol3-hybridizing sequences were observed in tobacco. While a number of Sol3 elements ranging in size from 500 bp to 2 kbp were sequenced, no transposase coding domains could be identified within the internal regions of the elements. The data suggest that the Sol3 represent a heterogeneous family of nonautonomous transposable elements associated with an as-yet-unidentified autonomous transposon.

Base Sequence↗
PubMed1989

Isolation of a transposable element from Neurospora crassa.

A Neurospora crassa strain from Adiopodoumé, Ivory Coast, contains multiple copies of a transposable element, Tad. The element was detected as a 7-kilobase insertion in two independently isolated spontaneous forward mutants of the am (glutamate dehydrogenase) gene. Laboratory strains do not contain Tad. All progeny from crosses of the Adiopodoumé strain to laboratory strains contain multiple copies. When the element was inserted in am, target sequences of 14 and 17 base pairs were duplicated in the two cases analyzed. One mutation, caused by the insertion of Tad at the beginning of the am coding sequence, is genetically stable. The other mutation, caused by insertion upstream of the transcriptional start site, has a reversion frequency of 2.5 x 10(-3). Precise excisions of Tad have not been found.

Base Sequence↗
PubMed1988

A selection cartridge for rapid detection and analysis of spontaneous mutations including insertions of transposable elements in Enterobacteriaceae.

We present a method that allows positive selection and rapid analysis of mutations in Enterobacteriaceae. Mutations are detected in a 2630 bp selection cartridge inserted in two different bacterial multicopy plasmid vectors. Spontaneous mutations in Escherichia coli, Enterobacter cloacae and Citrobacter freundii include insertions, deletions and point mutations. The small size of the target sequence facilitates rapid analysis of DNA rearrangements by cleavage with restriction enzymes and of any type of mutation by DNA sequence analysis. While in E. coli insertions of the mobile elements IS1, IS2 and IS5 were readily found, insertions of putative new transposable elements were detected in Enterobacter cloacae. The selection cartridge can thus serve as a tool for studying the spectrum of insertion mutations in Enterobacteriaceae and probably other Gram-negative bacteria, and the dependency of this spectrum on physiological and environmental factors and the host's genetic background can be investigated.

Base Sequence↗
PubMed2004

Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories.

Among the genus Ipomoea, three morning glories, I. nil the Japanese morning glory), I. purpurea (the common morning glory), and I. tricolor, were domesticated well for floricultural plants, and many spontaneous mutants displaying various flower pigmentation patterns were isolated. Most of these spontaneous mutations were found to be caused by the insertion of DNA transposable elements in the genes for the anthocyanin pigmentation in flowers, and many of them exhibited variegated flowers, such as white flowers with pigmented spots and sectors. Here, we describe the historical background of the mutants displaying variegated flowers and review the genetic and epigenetic regulation in flower pigmentation associated with transposable elements of these morning glories. The flecked, speckled, r-1, and purple mutations in I. nil were caused by insertions of Tpnl and its relatives in the En/Spm superfamily, Tpn2, Tpn3, and Tpn4, into the genes for anthocyanin coloration in flowers,i.e., DFR-B, CHI, CHS-D, and InNHXI, respectively. Similarly, the flaked and pink mutants of I. purpurea have distantly related elements, Tip100 and Tip201, in the Ac/Ds superfamily inserted into the CHS-D and F3'H genes, respectively. The flower variegation patterns can be determined by the frequency and timing of the excision of these transposons, and their stable insertions produce plain color flowers without generating pigmented spots or sectors; furthermore, both genetic and epigenetic regulation appeared to play important roles in determining the frequency and timing of the excision of the transposons. However, flower variegation is not always associated with the excision of an integrated DNA transposon from one of the genes for anthocyanin pigmentation. The mutant Flying Saucers of I. tricolor displaying variegated flowers was found to have the transposon ItMULE inserted into the DFR-B promoter region, but no excision of ITMULEL from the DFR-B could be detected in the variegated flower lines. The instable pearly-vrg allele in cv. Flying Saucers is likely to be an epiallele because the DNA methylation in the DFR-B promoter appeared to be associated with flower pigmentation.

Journal Article↗
PubMed2003

[Negative selection and computer models of the joint evolution of the patterns of polygenes, transposable elements, and origin identity labels].

Computer simulation of the population dynamics of the genomic patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of negative selection for an additive quantitative trait has been performed. It was demonstrated that active polygene alleles disappear very rapidly, whereas the patterns of TEs and OILs continue their evolution determined by strict selective inbreeding and gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. It was demonstrated that the final consensus pattern of OILs consists of the fragments of the original patterns, which contain neither active polygene alleles nor modifier or marker TEs. Neutral TE copies were present in the final pattern, as should be expected in the case of gene drift. Inbreeding coefficient increased steadily but by generation 100 reached values higher than 0.9. All other parameters and initial conditions being the same, the responses to negative and positive selections were asymmetric.

Animals↗
PubMed2003

Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes.

The techniques that are usually used to detect transposable elements (TEs) in nucleic acid sequences rely on sequence similarity with previously characterized elements. However, these methods are likely to miss many elements in various organisms. We tested two strategies for the detection of unknown elements. The first, which we call "TBLASTX strategy," searches for TE sequences by comparing the six-frame translations of the nucleic acid sequences of known TEs with the genomic sequence of interest. The second, "repeat-based strategy," searches genomic sequences for long repeats and clusters them in groups of similar sequences. TE copies from a given family are expected to cluster together. We tested the Drosophila melanogaster genomic sequence and the recently sequenced Anopheles gambiae genome in which most TEs remain unknown. We showed that the "TBLASTX strategy" is very efficient as it detected at least 332 new TE families in D. melanogaster and 400 in A. gambiae. This was unexpected in Drosophila as TEs of this organism have been extensively studied. The "repeat-based strategy" appeared to be very inefficient because of two problems: (i) TE copies are heavily deleted and few copies share homologous regions, and (ii) segmental duplications are frequent and it is not easy to distinguish them from TE copies.

Animals↗
PubMed2003

[Stabilizing selection and computer models of the joint evolution of patterns of polygenes, transposable elements, and origin identity labels].

A computer model of the populations dynamics of the patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of stabilizing selection for an additive quantitative trait (with the target value being 0.4 of the maximum) was analyzed. It was demonstrated that the final plateaus of the trait value and the frequencies of the active values of polygenes are reached rapidly, namely, within five to seven generations (the effective selection period). The inbreeding coefficient during this period also grows rapidly and then gradually increases eventually reaching approximately 0.7. The inbreeding coefficient reaches plateau (at approximately 1.0) only in generations 300-350, which suggests the effect of gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. By generation 100 of selection, the final patterns of TEs and OILs were not formed completely. Fixations and losses, especially those of the OIL pattern, were delayed. In general, however, the population heterogeneity with respect to the patterns studied does not stabilize. This heterogeneity decreases the case of stabilizing selection, although more slowly than in the cases of positive and negative selections.

Animals↗
PubMed1988

Activation of silent transposable elements.

It is well known among maize geneticists that agents that cause chromosome breakage can activate quiescent transposable elements. However, other than temporarily relieving position effect, it is difficult to understand how these events can lead directly to activation. One possibility is that chromosome breakage can initiate a process in the cell resulting in a higher rate of spontaneous mutation. Such a system could be analogous to the SOS response of Escherichia coli in which an error-prone repair system is induced. Chemical mutagens that cause little chromosome breakage but add bulky adducts to the DNA can induce the SOS response. In seed homozygous for a1-m2(8004), wx-m8, no active Spm, that had been treated with ethyl methanesulfonate, we observed activation of Spm at the rate of 1.1 x 10(-4). The spontaneous rate of activation in this material was 1.2 x 10(-5). Most of the activation events occurred as single kernels. This result contrasts with sectors covering at least one-eighth of the ear that would have been expected if activation had occurred as a direct result of mutagenesis in the mature kernel. The late timing of these events suggests that the activation, in most instances, may not be the direct result of chemical mutagenesis.

Crosses, Genetic↗
PubMed2006

The transposable element landscape of the model legume Lotus japonicus.

The largest component of plant and animal genomes characterized to date is transposable elements (TEs). The availability of a significant amount of Lotus japonicus genome sequence has permitted for the first time a comprehensive study of the TE landscape in a legume species. Here we report the results of a combined computer-assisted and experimental analysis of the TEs in the 32.4 Mb of finished TAC clones. While computer-assisted analysis facilitated a determination of TE abundance and diversity, the availability of complete TAC sequences permitted identification of full-length TEs, which facilitated the design of tools for genomewide experimental analysis. In addition to containing all TE types found in previously characterized plant genomes, the TE component of L. japonicus contained several surprises. First, it is the second species (after Oryza sativa) found to be rich in Pack-MULEs, with >1000 elements that have captured and amplified gene fragments. In addition, we have identified what appears to be a legume-specific MULE family that was previously identified only in fungal species. Finally, the L. japonicus genome contains many hundreds, perhaps thousands of Sireviruses: Ty1/copia-like elements with an extra ORF. Significantly, several of the L. japonicus Sireviruses have recently amplified and may still be actively transposing.

Chromosome Mapping↗
PubMed1995

The distribution of the transposable element Bari-1 in the Drosophila melanogaster and Drosophila simulans genomes.

The distribution of the transposable element Bari-1 in D. melanogaster and D. simulans was examined by Southern blot analysis and by in situ hybridization in a large number of strains of different geographical origins and established at different times. Bari-1 copies mostly homogeneous in size and physical map are detected in all strains tested. Both in D. melanogaster and in D. simulans a relatively high level of intraspecific insertion site polymorphism is detectable, suggesting that in both species Bari-1 is or has been actively transposing. The main difference between the two sibling species is the presence of a large tandem array of the element in a well-defined heterochromatic location of the D. melanogaster genome, whereas such a cluster is absent in D. simulans. The presence of Bari-1 elements with apparently identical physical maps in all D. melanogaster and D. simulans strains examined suggests that Bari-1 is not a recent introduction in the genome of the melanogaster complex. Structural analysis reveals unusual features that distinguish it from other inverted repeat transposons, whereas many aspects are similar to the widely distributed Tc1 element of C. elegans.

Animals↗
PubMed1991

Introduction of the transposable element mariner into the germline of Drosophila melanogaster.

A chimeric white gene (wpch) and other constructs containing the transposable element mariner from Drosophila mauritiana were introduced into the germline of Drosophila melanogaster using transformation mediated by the P element. In the absence of other mariner elements, the wpch allele is genetically stable in both germ cells and somatic cells, indicating that the peach element (i.e., the particular copy of mariner inserted in the wpch allele) is inactive. However, in the presence of the active element Mos1, the wpch allele reverts, owing to excision of the peach element, yielding eye-color mosaics and a high rate of germline reversion. In strains containing Mos1 virtually every fly is an eye-color mosaic, and the rate of wpch germline reversion ranges from 10 to 25%, depending on temperature. The overall rates of mariner excision and transposition are approximately sixfold greater than the rates in comparable strains of Drosophila simulans. The activity of the Mos1 element is markedly affected by position effects at the site of Mos1 insertion. In low level mosiac lines, dosage effects of Mos1 are apparent in the heavier level of eye-color mosaicism in Mos1 homozygotes than in heterozygotes. However, saturation occurs in high level mosaic lines, and then dosage effects are not observed. A pBluescribe M13+ plasmid containing Mos1 was injected into the pole plasm of D. melanogaster embryos, and the Mos1 element spontaneously integrated into the germline at high efficiency. These transformed strains of D. melanogaster presently contain numerous copies of mariner and may be useful in transposon tagging and other applications.

Alleles↗
PubMed1993

Expression and biochemical characterization of the DNA binding activity of TcA, the putative transposase of Caenorhabditis elegans transposable element Tc1.

The TcA protein is one of the proteins essential for Tc1 transposition. In order to study the biochemical parameters of Tc1 transposition mechanism, we used TcA protein overproduced in baculovirus system for DNA binding experiments. We show that, despite its relatively strong non specific affinity for DNA, TcA exhibits a better affinity for its Tc1 specific binding sites. The K0.5 is 3.8 nM for the Tc1 whereas in the same type of experiment the K0.5 is 24 nM for calf thymus DNA. The ratio value between specific and non specific DNA binding activity of the TcA protein was also exhibited by other transposases such as those of the bacteriophage Mu, Tn 10 and the Drosophila P element. This nonspecific DNA binding activity may be involved in determining sites of transposable element insertion.

Animals↗
PubMed1980

Insertion of the Drosophila transposable element copia generates a 5 base pair duplication.

To examine the details of insertion for the D. malanogaster transposable element copia, we have isolated three independent pairs of genomic fragments which correspond to occupied and unoccupied target sites for insertion. Restriction endonuclease analysis suggests that sites with and without an element differ by a simple 5000 bp insertion. Direct DNA sequence analysis demonstrates that a 5 bp sequence, present once in the target DNA at the site of insertion, is found on both sides of the element after insertion. The 5 bp sequences which are duplicated are different in each case. Moreover, there does not appear to be any sequence homology among these three independent insertion sites

Animals↗
PubMed1983

Differential induction of altered gene expression by carcinogens at mutant alleles of a Drosophila locus with a transposable element.

Alterations in gene expression by carcinogens were analyzed on three unstable alleles of the white (w+) locus of Drosophilia melanogaster: white-crimson (wc); white-ivory 16 (wi16); and white-unstable 11 (wu11). Two of these alleles (wi16 and wu11) were spontaneous mutant derivatives of wc, which is known to harbor a transposable element. The compounds studied were dimethylnitrosamine, 7,12-dimethylbenz(a)anthracene, and aflatoxin B1. These carcinogens were topically applied on the early larval stages, and the genetic effects assayed were the alterations in eye color either to wild-type (w+) or to other w mutants, initiated both somatically and germinally, as well as the simultaneously induced X-chromosome recessive mutations. The tested compounds influenced the different unstable w alleles in a highly selective manner, both as a function of the inducing agent and the organization of the genome in the target cells. The same treatments raised the somatic reversions to w+ above the corresponding controls for wc and wi16, but not for wu11, whereas the simultaneous induction of other w mutant phenotypes occurred appreciably only with wc. Furthermore, these treatments gave high and variable somatic reversions to w+ with wi16, whereas the simultaneously induced germinal events were uniformly very low. The frequencies of altered expression at the unstable test loci, whether in the soma or germ line, were quantitatively uncorrelated with the mutagenic effects of the treatments in terms of the yield of X-chromosome recessive mutations assayed in the progeny of males emerging from the same treated larvae. There was also an association between the time of the induction of these alterations by the tested carcinogens in the soma and the cellular stage in genomic differentiation. Reversions to w+ were induced preferentially after the onset of genetic determination, whereas changes to the w mutant phenotypes occurred predominantly during the predetermination phases. The genetic properties of transposable elements and the manner of their response to carcinogens supported the hypothesis that nonviral cancer might arise from molecular processes similar to those involved in the evolution of retroviruses.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1984

Dictyostelium transposable element DIRS-1 preferentially inserts into DIRS-1 sequences.

Sequence analysis of genomic clones containing the intact Dictyostelium transposable element DIRS-1 reveals that in five of six cases DIRS-1 has inserted into other DIRS-1 sequences. The nucleotide sequences just beyond the endpoints of the terminal repeats of five different genomic clones can be aligned with different regions of the internal nucleotide sequence of DIRS-1. In the three genomic clones which contain flanking sequences on both sides of the element, both flanking sequences are homologous with DIRS-1. In one of these clones, both extended flanking sequences represent the full 4.1-kilobase EcoRI fragment of DIRS-1, which has been interrupted by the insertion of an intact DIRS-1 element. There is no duplication or deletion (except possibly 1 base) of the DIRS-1 sequence upon insertion of a second DIRS-1 transposon. DIRS-1-into-DIRS-1 insertions can occur in either a colinear or inverted orientation with respect to the target sequence; the target sequence need not be an intact DIRS-1 element. We also describe a cDNA clone which could be derived by transcription of a sequence that resulted from a DIRS-1-into-DIRS-1 insertion and discuss its significance concerning the function of the heat-shock promoters found in the terminal repeats of DIRS-1 and in other DIRS-1-related sequences.

Base Sequence↗
PubMed1994

Transposable elements as population drive mechanisms: specification of critical parameter values.

With a view to the possible use of transposable elements (TEs) as a mechanism to drive genes into insect vector populations, we used a three-parameter density dependent growth equation to examine the critical parameter values that determine whether or not a mobile element will spread and become fixed in a finite diploid vector population. Populations were simulated with parameter values affecting size, reproductive rate, density-dependence, and transposition efficiency of the mobile element. Simulations indicated that an equilibrium was reached quickly, typically in < 50 generations. Even when initially present at < or = 1% of a large population, the mobile element spread quickly and became fixed if transposition efficiency was equal to unity and infertility caused by the element decreased reproductive capacity by as much as 45%. These results were insensitive to the values of basic wild type reproductive rates and density dependence, but population size, transposition efficiency of the element, reproductive rate individuals bearing TEs and initial ratio of TE-bearing to wild individuals modified the outcome. As population size and transposition efficiency decreased in value, TEs became fixed less easily. However, even in populations as small as n = 100, an element with a transposition efficiency > 0.75 that reduces fertility < 25% will become fixed when introduced at a frequency as low as 1% of the total population. These results are consistent with previously reported population genetics models. They suggest that engineered transposons with a wide range of properties may be used to drive genes, such as those for parasite resistance, into wild vector populations.

Animals↗
PubMed2001

Genome evolution: sex and the transposable element.

Mating systems are thought to play an important role in determining the fate of genomic parasites such as transposable elements. This is supported by recent studies which indicate that asexual genomes may be structured very differently to those of sexual species.

Animals↗
PubMed1984

Effects of transposable element insertions on RNA encoded by the white gene of Drosophila.

We have examined the manner in which transposable element insertions affect the expression of the white gene of Drosophila by analyzing polyadenylated RNA of flies with each of nine insertions in or near the gene. In five mutants having insertions in the transcribed sequences of white, transcripts initiating at the white promoter are truncated within the insertions. Two insertions in the 3 kb intron of white alter neither the amount nor the structure of the mature white RNA. An insertion near the 5' end of the gene blocks the accumulation of any white transcripts. Another insertion, located 1.2 kb upstream from the transcribed region of the gene, causes a mutant phenotype yet surprisingly has no obvious effect on the structure or abundance of the major white RNA. We also show that a mutation at each of two other loci that modulate the phenotype of the white-apricot insertion mutant are correlated with small but significant changes in the pattern of white transcripts.

Animals↗