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PubMed1990

Transposable element-induced response to artificial selection in Drosophila melanogaster: molecular analysis of selection lines.

Artificial selection lines for abdominal bristle score of Drosophila melanogaster established from P-M hybrid dysgenic crosses showed increases in selection response, heritability and phenotypic variance compared to similar lines started from nondysgenic crosses. To determine whether this increased genetic variance could be due to enhanced transposition of P elements following the dysgenic cross, the cytological locations (sites) of P elements were determined by in situ hybridization for the whole genome of samples of 20 individuals from the parental P strain, 20 individuals from each of the eight dysgenic selection lines, and ten individuals from each of the eight nondysgenic selection lines. Variation among and within the selection lines and the parental P strain in P element insertion sites was exceptionally high. A total of 601 sites were identified, but there was no difference in total number of sites per line, mean number of sites per individual, mean copy number per individual, or site frequency between dysgenic and nondysgenic selection lines, or between lines selected for high and low bristle score. Transposition following nondysgenic crosses may explain additional observations of accelerated selection responses in nondysgenic selection lines. It was not possible to deduce which, if any, of the several hundred insertions in the dysgenic selection lines were responsible for their extreme bristle phenotypes.

Animals↗
PubMedDate not supplied

[The mobile vector method for genetic transformation of animals].

Experimental data on transgenic animal production using transfected sperm are reviewed. Pathways for further improvement of the method for increasing the frequency of transgenic organisms are proposed: modification of the saccharophosphate skeleton and DNA ends; use of nucleic exchange enzymes and directed oligonucleotides; use of adhesive sequences (MAR elements), ori replication, and transposable elements within the transgenes; development of the embryos selection; the use of gene targeting elements; and the use of various DNA conformations. The promising use of spermatozoa as a noninvasive system of gene delivery in transgenesis and prenatal gene therapy are outlined.

Animals↗
PubMed2006

Properties of the various Botmar1 transcripts in imagoes of the bumble bee, Bombus terrestris (Hymenoptera: Apidae).

Botmar1 elements are mariner-like elements (MLEs), class II transposable elements that occur in the genome of the bumble bee, Bombus terrestris. Each haploid B. terrestris genome contains about 230 Botmar1, consisting entirely of 1.3-kb and 0.85-kb elements. During their evolution in the B. terrestris genome, two Botmar1 lineages have been differentiated in terms of their nucleic acid sequences and the differences found in their 5' untranslated regions suggest that they could be transcribed differently in B. terrestris. Here, we show that small amounts of Botmar1 mRNA occur in RNA extracts purified from B. terrestris imagoes. This indicates that the Botmar1 transcription is either weak in imagoes, or is restricted to very few cells. The cloning of several mRNAs reveals that only lineage-2 Botmar1 elements are transcribed. This transcription is specific, and uses cardinal initiators and terminators of eukaryotic elements in the Botmar1 elements. The intrastrand stem-loop folds in the mRNA theoretically synthesized by elements of the first lineage suggest that mRNA maintenance in cells might be self-regulated by RNA interference.

3' Untranslated Regions↗
PubMed2002

Germline transformants spreading out to many insect species.

The past 5 years have witnessed significant advances in our ability to introduce genes into the genomes of insects of medical and agricultural importance. A number of transposable elements now exist that are proving to be sufficiently robust to allow genetic transformation of species within three orders of insects. In particular all of these transposable elements can be used genetically to transform mosquitoes. These developments, together with the use of suitable genes as genetic markers, have enabled several genes and promoters to be transferred between insect species and their effects on the phenotype of the transgenic insect determined. Within a very short period of time, insights into the function of insect promoters in homologous and heterologous insect species are being gained. Furthermore, strategies aimed at ameliorating the harmful effects of pest insects, such as their ability to vector human pathogens, are now being tested in the pest insects themselves. We review the progress that has been made in the development of transgenic technology in pest insect species and conclude that the repertoire of transposable element-based genetic tools, long available to Drosophila geneticists, can now be applied to other insect species. In addition, it is likely that these developments will lead to the generation of pest insects that display a significantly reduced ability to transmit pathogens in the near future.

Animals↗
PubMed1997

Genetic and physical maps of the Alcaligenes eutrophus CH34 megaplasmid pMOL28 and its derivative pMOL50 obtained after temperature-induced mutagenesis and mortality.

We describe the construction of restriction and genetic maps of plasmid pMOL28, which has a size of approximately 180 kb. To do so, partial BamHI-digested DNA of pMOL28 was cloned into cosmid pLAFR3, which can package up to 20-30 kb inserted DNA. Subsequently, a cosmid walking strategy, combined with BamHI or EcoRI restriction analysis and hybridization, was used to construct the restriction maps for both enzymes. On these maps, 35 BamHI fragments and 29 EcoRI fragments were placed, accounting for a total size of approximately 180 kb. We also analyzed several rearranged derivatives of pMOL28 that were obtained after a process of temperature-induced mortality and mutagenesis (TIMM), which is characteristic for Alcaligenes eutrophus CH34 and related strains. The restriction and genetic maps of pMOL50 (222 kb), an enlarged derivative of pMOL28 obtained after TIMM, were constructed. By comparing the pMOL28 and pMOL50 maps, at least two transposable elements were identified which participated in the formation of pMOL50 from pMOL28 during TIMM. These transposable elements were IS1086, which was recently sequenced, and a new element named IS1089, which is located on the 44-kb inserted DNA fragment in pMOL50. Partial sequencing of IS1089 revealed similarity of this element with IS1071 of the chlorobenzoate catabolic transposon Tn5271 of Alcaligenes sp. BR60.

Alcaligenes↗
PubMed2003

A transposable element-mediated gene divergence that directly produces a novel type bovine Bcnt protein including the endonuclease domain of RTE-1.

Ruminant Bcnt protein with a molecular mass of 97 kDa (designated p97Bcnt) includes a region derived from the endonuclease domain of a retrotransposable element RTE-1. Human and mouse Bcnt proteins lack the corresponding region but have a highly conserved 82-amino acid region at the C-terminus that is not present in p97Bcnt. By screening a bovine BAC library, we found two more bcnt-related genes: human-type bcnt (h-type bcnt) and its processed pseudogene. Whereas the pseudogene is localized on chromosome 26, both bcntp97 and the h-type bcnt genes are found on bovine chromosome 18, a synteny region of human chromosome 16 on which human BCNT is localized. Complete nucleotide sequencing of the BAC clone reveals that the bcntp97 and h-type bcnt genes are located just 6 kb apart in a tandem manner. The two h-type bcnt and bcntp97genes are active at both the transcriptional level and the protein level. H-type bovine Bcnt is more like human BCNT than p97Bcnt, when compared at their N-terminal regions. However, phylogenetic analysis using the N-terminal region of the bcnt gene family revealed that the duplication of bovine genes occurred within the bovine lineage with significantly accelerated substitution in bcntp97. This acceleration was not ascribed definitely to positive selection. After duplication, one of the bovine bcnt genes recruited the endonuclease domain of an intronic RTE-1 repeat accompanied by the accelerated substitution at the 5'-ORF, resulting in creation of a novel type of Bcnt protein in bovine.

Amino Acid Sequence↗
PubMed1989

Cloning and characterization of variable-sized gypsy mobile elements in Drosophila melanogaster.

A cosmid genomic library from a known gypsy-induced forked mutation, f1, was screened by 32P-labeled gypsy transposable element. Of more than 250 positive clones we randomly selected 21 for in situ hybridization to wild-type polytene chromosomes. Two clones hybridized to region 15F on the X-chromosome, the cytological position of forked. A third clone hybridized to at least 17 sites on the chromosomes indicating the presence of repetitive sequences in the gypsy flanking DNA. All clones labeled the centromeric regions heavily. Ten clones, including the two hybridizing at 15F, were chosen for further analysis, and restriction mapping allowed us to place them into three groups: (1) full-length, (2) slightly diverging, and (3) highly diverging gypsy elements. Group (2) is missing the XbaI site in both their long terminal repeats (LTRs) as well as the middle HindIII site; four of these gypsy elements also have a approximately 100-bp deletion at the 5' LTR. The group (3) gypsy transposons are missing one LTR and also have highly diverging DNA sequences. The restriction analyses further imply that most of these different gypsy elements are present in more than one copy in the genome of the f1 stock used in this study. The results raise intriguing questions regarding the significance of transposable elements in evolution and biological functions.

Animals↗
PubMed1996

A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes.

Several recent reports indicate that mobile elements are frequently found in and flanking many wild-type plant genes. To determine the extent of this association, we performed computer-based systematic searches to identify mobile elements in the genes of two "model" plants, Oryza sativa (domesticated rice) and Arabidopsis thaliana. Whereas 32 common sequences belonging to nine putative mobile element families were found in the noncoding regions of rice genes, none were found in Arabidopsis genes. Five of the nine families (Gaijin, Castaway, Ditto, Wanderer, and Explorer) are first described in this report, while the other four were described previously (Tourist, Stowaway, p-SINE1, and Amy/LTP). Sequence similarity, structural similarity, and documentation of past mobility strongly suggests that many of the rice common sequences are bona fide mobile elements. Members of four of the new rice mobile element families are similar in some respects to members of the previously identified inverted-repeat element families, Tourist and Stowaway. Together these elements are the most prevalent type of transposons found in the rice genes surveyed and form a unique collection of inverted-repeat transposons we refer to as miniature inverted-repeat transposable elements or MITEs. The sequence and structure of MITEs are clearly distinct from short or long interspersed nuclear elements (SINEs or LINEs), the most common transposable elements associated with mammalian nuclear genes. Mobile elements, therefore, are associated with both animal and plant genes, but the identity of these elements is strikingly different.

Arabidopsis↗
PubMed1992

A micronucleus-limited sequence family in Tetrahymena thermophila: organization and sequence conservation.

During macronuclear development in the ciliated protozoan Tetrahymena thermophila, sequence reorganization including sequence loss occurs. Addressing questions about the organization and nucleotide sequence of micronucleus limited regions can lead to insights about mechanisms of DNA rearrangements during macronuclear development as well as mechanisms for the maintenance of the stability of micronucleus-limited sequence families. We have previously identified a moderately repetitive micronucleus-limited sequence family called X-H (family members hybridize to an approximately 450 bp Xbal-HindIII restriction fragment), completely absent from macronuclear DNA. The first member of this family which we isolated is associated with terminal sequences characteristic of a Tel-1 element, a putative micronuclear transposable element. Two additional family members have been isolated which are not closely associated with Tel-1 terminal sequences. We have nucleotide sequence data for three cloned members of the X-H family. This analysis has demonstrated that the longest cloned members of the X-H family share a region of homology of approximately 2,400 bp and are highly conserved, differing only by small insertions or deletions of 100 bp or less. The sequences from one of the sequenced family members flanking the region of homology are themselves mostly micronucleus-limited.

Animals↗
PubMed2000

Evolutionary dynamics of the SGM transposon family in the Drosophila obscura species group.

SGM (Drosophila subobscura, Drosophila guanche, and Drosophila madeirensis) transposons are a family of transposable elements (TEs) in Drosophila with some functional and structural similarities to miniature inverted-repeat transposable elements (MITEs). These elements were recently active in D. subobscura and D. madeirensis (1-2 MYA), but in D. guanche (3-4 MYA), they gave rise to a species-specifically amplified satellite DNA making up approximately 10% of its genome. SGM elements were already active in the common ancestor of all three species, giving rise to the A-type specific promoter section of the P:-related neogene cluster. SGM sequences are similar to elements found in other obscura group species, such as the ISY elements in D. miranda and the ISamb elements in Drosophila ambigua. SGM elements are composed of different sequence modules, and some of them, i.e., LS and LS-core, are found throughout the Drosophila and Sophophora radiation with similarity to more distantly related TEs. The LS-core module is highly enriched in the noncoding sections of the Drosophila melanogaster genome, suggesting potential regulatory host gene functions. The SGM elements can be considered as a model system elucidating the evolutionary dynamics of mobile elements in their arms race with host-directed silencing mechanisms and their evolutionary impact on the structure and composition of their respective host genomes.

Animals↗
PubMed1989

Developmental and genetic aspects of Mutator excision in maize.

The regulation of excision of Mu elements of the Mutator transposable element family of maize is not well understood. We have used somatic instability of Mu receptor elements from the Bronze 1 and Bronze 2 loci to monitor the frequency and the timing of excision of Mu elements in several tissues. We show that spot size in the aleurone of a bz2::mu1 stock varies between one to approximately 256 cells. This indicates that excision events begin eight divisions prior to full aleurone differentiation and end after the last division of the aleurone. We show that excision is equally biased for late events in all other tissues studied. A locus on chromosome 5 has been identified that affects spot size, possibly by altering the timing of Mu excision. Using somatic excision as an assay of Mutator activity, we found that activity can change in small sectors of the tassel; however, there are no overall activity changes in the tassel during the period of pollen shedding. We also report the recovery of germinal revertants for the bz1::mu1 and bz2::mu1 alleles. One of these revertant alleles was characterized by Southern blot analysis and found to be similar to the progenitor of the mutable allele.

Alleles↗
PubMed1993

Transposition of the maize autonomous element Activator in transgenic Nicotiana plumbaginifolia plants.

The maize autonomous transposable element Ac was introduced into haploid Nicotiana plumbaginifolia via Agrobacterium tumefaciens transformation of leaf disks. All the regenerated transformants (R0) were diploid and either homozygous or heterozygous for the hygromycin resistance gene used to select primary transformants. The Ac excision frequency was determined using the phenotypic assay of restoration of neomycin phosphotransferase activity and expression of kanamycin resistance among progeny seedlings. Some of the R0 plants segregated kanamycin-resistant seedlings in selfed progeny at a high frequency (34 to 100%) and contained one or more transposed Ac elements. In the primary transformants Ac transposition probably occurred during plant regeneration or early development. Other R0 transformants segregated kanamycin-resistant plants at a low frequency (< or = 4%). Two transformants of this latter class, containing a unique unexcised Ac element, were chosen for further study in the expectation that their kanamycin resistant progeny would result from independent germinal transposition events. Southern blot analysis of 32 kanamycin-resistant plants (R1 or R2), selected after respectively one or two selfings of these primary transformants, showed that 27 had a transposed Ac at a new location and 5 did not have any Ac element. Transposed Ac copy number varied from one to six and almost all transposition events were independent. Southern analysis of the R2 and R3 progeny of these kanamycin-resistant plants showed that Ac continued to transpose during four generations, and its activity increased with its copy number. The frequency of Ac transposition, from different loci, remained low (< or = 7%) from R0 to R3 generations when only one Ac copy was present.(ABSTRACT TRUNCATED AT 250 WORDS)

Agrobacterium tumefaciens↗
PubMed1994

Catabolic transposons.

The structure and function of transposable elements that code for catabolic pathways involved in the biodegradation of organic compounds are reviewed. Seven of these catabolic transposons have structural features that place them in the Class I (composite) or Class II (Tn3-family) bacterial elements. One is a conjugative transposon. Another three have been found to have properties of transposable elements but have not been characterized sufficiently to assign to a known class. Structural features of the toluene (Tn4651/Tn4653) and naphthalene (Tn4655) elements that illustrate the enormous potential for acquisition, deletion and rearrangement of DNA within catabolic transposons are discussed. The recently characterized chlorobenzoate (Tn5271) and chlorobenzene (Tn5280) catabolic transposons encode different aromatic ring dioxygenases, however they both illustrate the constraints that must be overcome when recipients of catabolic transposons assemble and regulate complete metabolic pathways for environmental pollutants. The structures of the chlorobenzoate catabolic transposon Tn5271 and the related haloacetate dehalogenase catabolic element of plasmid pUO1 are compared and a hypothesis for their formation is discussed. The structures and activities of catabolic transposons of unknown class coding for the catabolism of halogenated alkanoic acids (DEH) and chlorobiphenyl (Tn4371) are also reviewed.

Biodegradation, Environmental↗
PubMed1993

A 168 bp derivative of Suppressor-mutator/Enhancer is responsible for the maize o2-23 mutation.

From a directed transposon tagging of the maize Opaque-2 gene (O2), we have isolated a stable mutant o2 allele, o2-23. Cloning and molecular analysis of the allele revealed a 168 nucleotide insertion in the third exon of o2. The sequence of this small insertion indicated identity with the 5' and 3' ends of the 8.3 kb Suppressor-mutator/Enhancer (Spm/En) transposable element. This represents the smallest deletion derivative of Spm (dSpm) thus far characterized in maize. Genetic crosses of plants homozygous for o2-23 with plants homozygous for both an o2 null allele (o2-R) and an autonomous Spm produce stable opaque seed having no apparent sectors of vitreous endosperm. DNA fragments of the size expected if the dSpm were to excise were not detectable by Southern analysis, suggesting that this element is unable to transpose. Northern analysis detected an o2-23 mRNA that was much more abundant in o2-23 seeds lacking Spm than in o2-23 seeds containing Spm, consistent with the idea that Spm transacting functions can suppress the accumulation of the o2-23 transcript.

Alleles↗
PubMed1991

Models of repression of transposition in P-M hybrid dysgenesis by P cytotype and by zygotically encoded repressor proteins.

By analytical theory and computer simulation the expected evolutionary dynamics of P transposable element spread in an infinite population are investigated. The analysis is based on the assumption that, unlike transposable elements which move via RNA intermediates, the harmful effects of P elements arise primarily in the act of transposition, and that this causes their evolutionary dynamics to be unusual. It is suggested that a situation of transposition-selection balance will be superceded by the buildup of a cytoplasmically inherited repression or by the elimination of active transposase-encoding elements from the chromosomes, a process which may be accompanied by the evolution of elements which encode proteins which repress transposition.

Animals↗
PubMed2001

Dynamics of mobile element activity in chalcone synthase loci in the common morning glory (Ipomoea purpurea).

Mobile element dynamics in seven alleles of the chalcone synthase D locus (CHS-D) of the common morning glory (Ipomoea purpurea) are analyzed in the context of synonymous nucleotide sequence distances for CHS-D exons. By using a nucleotide sequence of CHS-D from the sister species Ipomoea nil (Japanese morning glory [Johzuka-Hisatomi, Y., Hoshino, A., Mori, T., Habu, Y. & Iida, S. (1999) Genes Genet. Syst. 74, 141-147], it is also possible to determine the relative frequency of insertion and loss of elements within the CHS-D locus between these two species. At least four different types of transposable elements exist upstream of the coding region, or within the single intron of the CHS-D locus in I. purpurea. There are three distinct families of miniature inverted-repeat transposable elements (MITES), and some recent transpositions of Activator/Dissociation (Ac/Ds)-like elements (Tip100), of some short interspersed repetitive elements (SINEs), and of an insertion sequence (InsIpCHSD) found in the neighborhood of this locus. The data provide no compelling evidence of the transposition of the mites since the separation of I. nil and I. purpurea roughly 8 million years ago. Finally, it is shown that the number and frequency of mobile elements are highly heterogeneous among different duplicate CHS loci, suggesting that the dynamics observed at CHS-D are locus-specific.

Acyltransferases↗
PubMed2004

Use of the multipurpose transposon Tn KPK2 for the mutational analysis of chromosomal regions upstream and downstream of the sipF gene in Bradyrhizobium japonicum.

The DNA regions upstream and downstream of the Bradyrhizobium japonicum gene sipF were cloned by in vivo techniques and subsequently sequenced. In order to study the function of the predicted genes, a new transposon for in vitro mutagenesis, Tn KPK2, was constructed. This mutagenesis system has a number of advantages over other transposons. Tn KPK2 itself has no transposase gene, making transposition events stable. Extremely short inverted repeats minimize the length of the transposable element and facilitate the determination of the nucleotide sequence of the flanking regions. Since the transposable element carries a promoterless ' phoA reporter gene, the appearance of functional PhoA fusion proteins indicates that Tn KPK2 has inserted in a gene encoding a periplasmic or secreted protein. Although such events are extremely rare, because the transposon has to insert in-frame, in the correct orientation, and at an appropriate location in the target molecule, a direct screening procedure on agar indicator plates permits the identification of candidate clones from large numbers of colonies. In this study, Tn KPK2 was used for the construction of various symbiotic mutants of B. japonicum. One of the mutant strains, A2-10, which is defective in a gene encoding a protein that comigrates with bacterioferritin ( bcpB), was found to induce the formation of small and ineffective nodules.

Amino Acid Sequence↗
PubMed2003

An active DNA transposon family in rice.

The publication of draft sequences for the two subspecies of Oryza sativa (rice), japonica (cv. Nipponbare) and indica (cv. 93-11), provides a unique opportunity to study the dynamics of transposable elements in this important crop plant. Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element (MITE) from any organism. A sequence classified as a Tourist-like MITE of 430 base pairs, called miniature Ping (mPing), was present in about 70 copies in Nipponbare and in about 14 copies in 93-11. These mPing elements, which are all nearly identical, transpose actively in an indica cell-culture line. Database searches identified a family of related transposase-encoding elements (called Pong), which also transpose actively in the same cells. Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome. Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation.

Amino Acid Sequence↗