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PubMed1997

Population genetics models of transposable elements.

The control of transposable element copy number is of considerable theoretical and empirical interest. Under simple models, copy numbers may increase without limit. Mechanisms that can prevent such an increase include those in which the effect of selection increases with copy number, those in which the rate of transposition decreases with copy number, and those where unlimited increase in copy number is prevented by the consequences of functional heterogeneity in the transposable element family. Finite population sizes may attenuate the power of natural selection to act on transposable element copy number in a number of ways that may be of particular importance in laboratory populations. First, a small host population size will create occasional periods in which the variance between individuals in copy number is diminished, and with it the power of natural selection, even when the expected variance is Poisson. Second, small population sizes will produce high-frequency transposable element sites, systematically reducing the variance in copy number. The consequences will be particularly profound when the selective damage of transposable elements follows from their heterozygosity, as when ectopic exchange limits copy number.

Animals↗
PubMed1979

Nomenclature of transposable elements in prokaryotes.

Transposable elements are defined as specific DNA segments that can repeatedly insert into a few or many sites in a genome. They are classified as simple IS elements, more complex Tn transposons and self-replicating episomes. Definitions and nomenclature rules for these three classes of prokaryotic transposable elements are specified.

Cells↗
PubMedDate not supplied

High-frequency precise excision of the Drosophila foldback transposable element.

Precise excision of transposable elements in prokaryotes is a rare event which occurs at a significantly lower rate than transposition and other element-mediated events. Thus, we were intrigued by a eukaryotic transposable element which seemed capable of precise excision at high frequencies. The white-crimson (wc) mutation in Drosophila, a highly unstable allele of the X-linked eye colour locus, white, resulted from the insertion of a member of the foldback (FB) transposable element family. This mutation reverts to its parental phenotype at a frequency of greater than 1 in 10(3) X chromosomes. Characterization of these revertants by Southern blots of genomic DNA indicated that they resulted from loss of the wc insertion. Here we report the nucleotide sequence of the excision point in these revertants, and conclude that the FB element responsible for the wc mutation is capable of precise excision at high frequencies.

Alleles↗
PubMed1990

Invertrons, a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and genomes of adeno-type viruses.

Invertrons are genetic elements composed of DNA with inverted terminal repeats at both ends, covalently bonded to terminal proteins involved in the initiation of DNA replication at both their 5' termini when they exist in the cytoplasm of their host in free form. They function as viruses, linear DNA plasmids, transposable elements, and sometimes combinations of two of these properties. They differ from retroviruses and related retro-type transposons which have direct repeats on both their genomic ends and exploit RNA intermediates for replication of their DNA. A model for replication and integration of invertrons is presented, as well as a model for transposition of transposable elements.

Adenoviridae↗
PubMed1998

Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction.

Anopheles arabiensis, one of the two most potent malaria vectors of the gambiae complex, is characterized by the presence of chromosomal paracentric inversions. Elucidation of the nature and the dynamics of these inversions is of paramount importance for the understanding of the population genetics and evolutionary biology of this mosquito and of the impact on malaria epidemiology. We report here the cloning of the breakpoints of the naturally occurring polymorphic inversion 2Rd' of A. arabiensis. A cDNA clone that cytologically mapped on the proximal breakpoint was the starting material for the isolation of a cosmid clone that spanned the breakpoint. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a repetitive element that exhibits distinct distribution in different A. arabiensis strains. Sequencing analysis of that area revealed elements characteristic of transposable element terminal repeats. We called this presumed transposable element Odysseus. The presence of Odysseus at the junction of the naturally occuring inversion 2Rd' suggests that the inversion may be the result of the transposable element's activity. Characteristics of Odysseus' terminal region as well as its cytological distribution in different strains may indicate a relatively recent activity of Odysseus.

Animals↗
PubMed1987

Isolation and characterization of a 1.7-kb transposable element from a mutator line of maize.

We have cloned and sequenced a 1.7-kb Mu element from a Mutator line of maize and compared its structure to Mu1, a 1.4-kb element. With the exception of a 385-bp block of DNA present in the 1.7-kb element, these transposable elements are structurally similar, sharing terminally inverted and internal direct repeated sequences. Derivation of 1.4-kb elements from the 1.7-kb class via deletion of internal sequence is suggested by the finding that a portion of the extra DNA in Mu1.7 is part of a truncated direct repeat sequence in the 1.4-kb element. An abundant poly(A)+ RNA homologous to a portion of this extra DNA is present in several tissues of both Mutator and non-Mutator lines. Analysis of transcripts from an unstable mutant bronze 1 (bz) allele containing a Mu1.7 element inserted in an exon of the gene detects three species of poly(A)+ RNA that hybridize to a Bz1 (Bronze) gene probe: the largest contains the entire Mu1.7 element in the Bz1 gene transcript; another appears to be a spliced, chimeric transcript; the smallest is normal size Bz1 mRNA. The latter is most likely encoded by the normal-size alleles detected by Southern analysis of tissue expressing purple pigment, suggesting that normal gene function is restored by excision of the Mu1.7 element.

Base Sequence↗
PubMed1995

Distribution of transposable elements in arthropods.

Transposable elements of the DNA-mediated and RNA-mediated classes found in arthropods are briefly described and their distribution reviewed. The distribution patterns of DNA-mediated elements are extremely patchy and the principal cause appears to be the horizontal transfer of elements between host lineages. In the best documented case of mariner elements, these hosts can be in different orders of insects, classes of arthropods, and even other phyla of animals. RNA-mediated elements appear to undergo much longer periods of vertical evolution within host lineages, and evidence for their horizontal transfer remains scant. The evolutionary relationships of many of these transposons have recently been illuminated by phylogenetic analyses of the reverse-transcriptase enzymes of the RNA-mediated elements, and the recognition that the transposases of some of the DNA-mediated elements are distantly related to in the integrases of some of the RNA-mediated elements.

Animals↗
PubMed1988

Insertion and excision of Caenorhabditis elegans transposable element Tc1.

The transposable element Tc1 is responsible for most spontaneous mutations that occur in Caenorhabditis elegans variety Bergerac. We investigated the genetic and molecular properties of Tc1 transposition and excision. We show that Tc1 insertion into the unc-54 myosin heavy-chain gene was strongly site specific. The DNA sequences of independent Tc1 insertion sites were similar to each other, and we present a consensus sequence for Tc1 insertion that describes these similarities. We show that Tc1 excision was usually imprecise. Tc1 excision was imprecise in both germ line and somatic cells. Imprecise excision generated novel unc-54 alleles that had amino acid substitutions, amino acid insertions, and, in certain cases, probably altered mRNA splicing. The DNA sequences remaining after Tc1 somatic excision were the same as those remaining after germ line excision, but the frequency of somatic excision was at least 1,000-fold higher than that of germ line excision. The genetic properties of Tc1 excision, combined with the DNA sequences of the resulting unc-54 alleles, demonstrated that excision was dependent on Tc1 transposition functions in both germ line and somatic cells. Somatic excision was not regulated in the same strain-specific manner as germ-line excision was. In a genetic background where Tc1 transposition and excision in the germ line was not detectable, Tc1 excision in the soma still occurred at high frequency.

Animals↗
PubMed1994

Plant transposable elements and the genome.

Transposable elements are ubiquitous in the plant kingdom and share many common features, both structural and mechanistic, with mobile elements from other eukaryotes. Transposition of these elements can influence plant genes and genomes in many ways. It is also becoming clear that transposable element derived sequences can be a major component of plant genomes. These sequences are probably, therefore, very significant factors in plant evolution.

Biological Evolution↗
PubMed1989

Tagging of a maize gene involved in kernel development by an activated Uq transposable element.

A quiescent Uq transposable element has been activated in a maize plant treated with 5-aza-2'-deoxycytidine. This activated Uq cosegregates with a heritable dominant miniature (Mn) kernel phenotype, indicating its physical association with a maize miniature locus (Mn::Uq). The Mn::Uq mutant is dominant in producing a miniature seed phenotype of variable size and in reducing seedling vigor in the early growth stage. Genetic experiments indicate that the Mn::Uq mutant also affects the activity of the male gametophyte, whereby pollen germination is inhibited, thus lacking pollen tube growth resulting in the male nontransmissibility of this mutant. Proof for the Uq element in this mutant is derived by its ability to transactivate the standard a-ruq reporter allele to yield spotted aleurone tissue. However, the Mn::Uq mutant does not transactivate a normally Uq-responsive c-ruq allele, suggesting a structural difference between the two ruq receptors at the A1 and C1 loci. It is anticipated that cloning of the Uq transposable element would facilitate the molecular cloning and characterization of the maize miniature gene.

DNA Transposable Elements↗
PubMed1996

Identification of functional domains and evolution of Tc1-like transposable elements.

Tc1-like transposable elements from teleost fish have been phylogenetically examined to determine the mechanisms involved in their evolution and conserved domains of function. We identified two new functional domains in these elements. The first is a bipartite nuclear localization signal, indicating that transposons can take advantage of the transport machinery of host cells for nuclear uptake of their transposases. The second is a novel combination of a paired domain-related protein motif juxtaposed to a leucine zipper-like domain located in the putative DNA-binding regions of the transposases. This domain coexists with a special inverted repeat structure in certain transposons in such phylogenetically distant hosts as fish and insects. Our data indicate that reassortment of functional domains and horizontal transmission between species are involved in the formation and spread of new types of transposable elements.

Amino Acid Sequence↗
PubMed1998

Transcriptionally active MuDR, the regulatory element of the mutator transposable element family of Zea mays, is present in some accessions of the Mexican land race Zapalote chico.

To date, mobile Mu transposons and their autonomous regulator MuDR have been found only in the two known Mutator lines of maize and their immediate descendants. To gain insight into the origin, organization, and regulation of Mutator elements, we surveyed exotic maize and related species for cross-hybridization to MuDR. Some accessions of the mexican land race Zapalote chico contain one to several copies of full-length, unmethylated, and transcriptionally active MuDR-like elements plus non-autonomous Mu elements. The sequenced 5.0-kb MuDR-Zc element is 94.6% identical to MuDR, with only 20 amino acid changes in the 93-kD predicted protein encoded by mudrA and ten amino acid changes in the 23-kD predicted protein of mudrB. The terminal inverted repeat (TIR) A of MuDR-Zc is identical to standard MuDR; TIRB is 11.2% divergent from TIRA. In Zapalote chico, mudrA transcripts are very rare, while mudrB transcripts are as abundant as in Mutator lines with a few copies of MuDR. Zapalote chico lines with MuDR-like elements can trans-activate reporter alleles in inactive Mutator backgrounds; they match the characteristic increased forward mutation frequency of standard Mutator lines, but only after outcrossing to another line. Zapalote chico accessions that lack MuDR-like elements and the single copy MuDR a1-mum2 line produce few mutations. New mutants recovered from Zapalote chico are somatically stable.

Base Sequence↗
PubMed1997

Fungal transposable elements and genome evolution.

The transposable elements (TEs) identified in fungal genomes reflect the whole spectrum of eukaryotic transposable elements. Most of our knowledge comes from species representing different ecological situations: plant pathogens, industrial, and field strains, most of them lacking the sexual stage. A number of changes in gene structure and function has been shown to be TE-mediated: inactivation of gene expression upon insertion within or adjacent to a gene, DNA sequence variation through excision and probably extensive chromosomal rearrangements due to recombination between members of a particular family. Moreover, TEs may have other roles in evolution related to their ability to be horizontally transferred and to capture and transpose chromosomal host sequences, thus providing a mechanism for dispersing sequences to new sites. However, the activity of transposable elements and consequently their proliferation within a host genome can be affected, in some fungal species which undergo meiosis, by silencing processes. Our understanding of the biological effects of TEs on the fungal genome has increased dramatically in the past few years but elucidation of the extent to which transposons contribute to genetic variation in nature, providing the flexibility for populations to adapt successfully to environmental changes is an important area for future research.

DNA Transposable Elements↗
PubMed1993

The hobo transposable element of Drosophila can be cross-mobilized in houseflies and excises like the Ac element of maize.

The hobo transposable element from Drosophila melanogaster was found to be capable of excision, resulting in donor sites unlike those reported for any other transposable element currently known in animals. These empty sites most closely resemble those left by the transposable elements Ac and Tam3 in Zea mays and Antirrhinum majus, respectively. Like Ac and Tam3, the hobo element was found to function in a distantly related species, in this case the housefly Musca domestica. Hobo excision in M. domestica was found not to require the expression of hobo-encoded transposase but instead appears to be driven by an endogenous hobo transposase-like activity. DNA sequences displaying high homology to the hobo transposase gene were isolated from the genome of M. domestica and appear to be part of a mobile-element system related to hobo, Ac, and Tam3.

Animals↗
PubMed1979

Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements.

A series of molecular events will explain how genetic elements can transpose from one DNA site to another, generate a short oligonucleotide duplication at both ends of the new insertion site, and replicate in the transposition process. These events include the formation of recombinant molecules which have been postulated to be intermediates in the transposition process. The model explains how the replication of bacteriophage Mu is obligatorily associated with movement to new genetic sites. It postulates that all transposable elements replicate in the transposition process so that they remain at their original site while moving to new sites. According to this model, the mechanism of transposition is very different from the insertion and excision of bacteriophage lambda.

Coliphages↗
PubMed1989

Transposable elements and fitness in Drosophila melanogaster.

Transposable elements constitute a significant fraction of the Drosophila melanogaster genome. The five families of moderately repeated transposable elements identified to date occupy dispersed and variable genomic locations, but have relatively constant copy numbers per individual. What effect to these elements have on the fitness of the individuals harboring them? Experimental evidence relating to this question is reviewed. The relevant data fall into two broad categories. The first involves the determination of the distribution of transposable elements in natural populations, by restriction mapping or in situ hybridization, and the comparison of the observed distribution with different theoretical expectations. The second approach is to study directly the effects of new transposable element-induced mutations on fitness. The P family of transposable elements is a particularly efficient mutagen, and the results of experiments in which initially P-free chromosomes are contaminated with P elements are discussed with regard to P-induced fitness mutations.

Animals↗
PubMed1990

The Mu1 transposable element of maize contains two promoter signals recognized by the Escherichia coli RNA polymerase.

The galactokinase (GalK) expression plasmid vector system pKO-1 has been used to screen for promoter elements in the maize transposable element Mu1 that function in Escherichia coli. Two transcriptional start points, named S1 and S2, were identified, which are located in the two direct repeats of the transposable element. This paper demonstrates that sequence elements exist in a plant transposable element which function as prokaryotic promotors.

Base Sequence↗
PubMed1990

Tad, a LINE-like transposable element of Neurospora, can transpose between nuclei in heterokaryons.

The Tad transposon of Neurospora crassa appears to be a LINE-like element with very restricted distribution within the genus Neurospora. When forced heterokaryons were constructed between strains which did and did not contain Tad, the nuclei of the naive nuclear type rapidly acquired Tad elements. The elements acquired by naive nuclei are active, since they can pass Tad to other naive nuclei in subsequent heterokaryons. When heterokaryons are passaged by serial transfer, the load of acquired Tad elements appears to increase, indicating that transposition is continuing in these heterokaryons, even after all of the naive nuclei have acquired Tad. In normal heterokaryons of Neurospora, nuclei do not fuse. An experiment to test for the possibility that Tad promotes nuclear fusion gave negative results. Thus Tad appears to have a cytoplasmic intermediate in its transposition. When heterokaryon incompatible strains were cocultured, there was no indication that Tad elements could be transferred to the naive strain, suggesting that Tad is not a virus. These data are consistent with the transposition of Tad via RNA and cDNA intermediates, as has been postulated to occur with LINE-like elements.

Base Sequence↗