Tnr8, a foldback transposable element from rice

An insertion sequence 418 bp in length was found in one member of rice retroposon p-SINE1 in Oryza glaberrima. This sequence had long terminal inverted repeats (TIRs) and is flanked by direct repeats of a 9-bp sequence at the target site, indicative that the insertion sequence is a rice transposable element, which we named Tnr8. Interestingly, each TIR sequence consisted of a unique 9-bp terminal sequence and six tandem repeats of a sequence about 30 bp in length, like the foldback transposable element first identified in Drosophila. A homology search of databases and analysis by PCR revealed that a large number of Tnr8 members with sequence variations were present in the rice genome. Some of these members were not present at given loci in several rice species with the AA genome. These findings suggest that the Tnr8 family members transposed long ago, but some appear to have mobilized after rice strains with the AA genome diverged. The Tnr8 members are thought to be involved in rearrangements of the rice genome.     

DNA sequence analysis of a Drosophila foldback transposable element rearrangement

Summary The complete nucleotide sequence of a DNA rearrangement associated with the foldback 4 (FB 4) transposable element is presented. The results demonstrate that the entire loop sequence and almost all of one of the inverted terminal repeats is absent. Moreover, the sequence of the remaining inverted repeat suggests that the FB elements might undergo inversions via recombinations between the two inverted repeats of a single element.     

Distribution and conservation of the foldback transposable element inDrosophila

Summary Foldback elements are a family of transposable elements described inDrosophila melanogaster. The members of this dispersed repetitive family have terminal inverted repeats that sometimes flank a central region. The inverted repeats of all the family members are homologous.The study of the distribution and conservation of the foldback elements in differentDrosophila species shows that this distribution is different from that of the hybrid dysgenesis systems (PM and IR). Sequences homologous to foldback elements were observed by Southern blots and in situ hybridization in all species of themelanogaster subgroup and in some species of themontium andtakahashii subgroups. The element was probably already present before the radiation of these subgroups. No evidence of horizontal transmission of the foldback element could be observed.     

New foldback transposable element TFB1 found in histone genes of the midge Chironomus thummi

A new Foldback transposable element (TFB1) has been found in the histone H1-H3 intergenic region in the midge Chironomus thummi thummi. TFB1 has long terminal inverted repeats, composed of short, degenerate subrepeats and is flanked by nine or ten base-pair "target site" duplications. TFB1 is present in at least two adjacent histone gene units in Ch. th. thummi, indicating a homogenization of histone gene repeats. The copy number and chromosomal distribution of TFB1 are different in the closely related subspecies Ch. th. thummi and Ch. th. piger. showing that amplification, elimination and transposition of TFB1 have occurred recently during evolution.     

Specificity and regulation of the mutator transposable element system in maize

The Mutator transposable element system is exceptional in many of its basic attributes. The high frequency and low specificity of mutant induction are both unusual and useful characteristics of the Mutator system. Other basic features are at least equally fascinating: the existence of multiple Mu element subfamilies with apparently unrelated internal sequences; the lack of correlation between Mu element transposition and excision; the complex inheritance of Mutator activity; the tight developmental regulation of Afufaror‐conditioned events; and the coordinated processes of element modification/inactivation, to name a few.

Molecular and genetic studies over the last 10 years have begun to explain many of these interesting properties and have uncovered new mysteries of Mutator biology. Both positive and negative regulators of the system have been identified and characterized to varying degrees. Insertion specificity has been observed at several levels. Recent accomplishments include the isolation of an autonomous Mu element and the discovery of maize lines with altered developmental regulation of Mutator‐derived mutability. This review defines the Mutator system, describes the status of current experimentation in the Mutator field, proposes models that may explain some aspects of Mutator behavior, and details future studies that will help elucidate the nature of the Mutator phenomenon.     

ISL1: a new transposable element in Lactobacillus casei

Summary The genome structures of a temperate Lactobacillus phage, FSW, and its virulent mutants, FSVs, were examined by restriction, heteroduplex and nucleotide-sequence analyses. The results showed that two out of three FSVs had the same 1.3 kbp insertion (designated as ISL1) at different positions in the FSW sequence. ISL1 was 1,256 bp long and contained at least two long open reading frames of 279 and 822 bases on one strand. Inverted repeats were found at the termini of the ISL1 which was bracketed by 3 bp direct repeats of the FSW sequence. From this evidence, we concluded that ISL1 was a transposable element in Lactobacillus casei.     

Folbos, a new foldback element in rice

A new class I foldback element, Folbos, has been discovered in O. sativa L. Its long terminal inverted repeats (IVRs) are 303 and 331 bp long and the left one encodes a short open reading frame of 76 codons. The IVRs consist of inner and outer domains, the latter built up of 6 tandem repeats of about 30 bp each. The central region is represented by 90 bp conservative stretch adjacent to a variable length (19-33 bp) A-tail, which in most cases includes the sequence 5'-TGACTT-3'. Folbos targets AT-rich regions and the insertion results in 7 bp target site duplications. Half of the copies found in annotated sequences of O. sativa japonica cv. Nipponbare are positioned in close proximity to (< 1kb) or within the transcribed regions, thus they have the potential to contribute to plant genome evolution.     

On the divergence of members of a transposable element family

Statistical properties of the amount of divergence of members of a transposable element family are studied. The analysis is based on the model proposed by Langley et al. [5], describing the evolution of a family of selectively neutral transposable elements in a finite haploid population of size 2N. By considering the time back to the most recent common ancestor of two copies, both the probability of identity and the moments of the number of sites that differ between two sampled copies are obtained. Our analytic results are consistent with the numerical results of Ohta [8] for a similar model. The effects of gene conversion are also examined. In agreement with Slatkin [9], we find that gene conversion has a minimal effect on the probability of identity providing that the rate of deletion is sufficiently large.     

Complete foldback transposable elements encode a novel protein found in Drosophila melanogaster.

An apparently complete foldback (FB) transposable element homologous to FB white-crimson (FBwc) was analyzed. A complete FB element could encode one or more proteins required for regulation of FB transposition. The central DNA region (the loop) and the junctions between the loop and the inverted terminal repeats were sequenced. Three open reading frames (ORFs) are present in the loop, and a novel 308 bp inverted repeat is present at the junctions. No significant homologies were found when the DNA sequences of the loop region and the novel inverted repeat were screened against the Gene data bank. Antibodies were prepared in guinea-pigs against a peptide present near the amino terminus of ORF1, the longest ORF. A 71,000 dalton protein was isolated from an extract of Drosophila melanogaster early-stage embryos on an anti-ORF1 peptide-affinity column. Immunohistochemical studies of adult flies demonstrate localization of this protein in egg chambers.     

The map-1 gene family in root-knot nematodes, Meloidogyne spp.: a set of taxonomically restricted genes specific to clonal species

Taxonomically restricted genes (TRGs), i.e., genes that are restricted to a limited subset of phylogenetically related organisms, may be important in adaptation. In parasitic organisms, TRG-encoded proteins are possible determinants of the specificity of host-parasite interactions. In the root-knot nematode (RKN) Meloidogyne incognita, the map-1 gene family encodes expansin-like proteins that are secreted into plant tissues during parasitism, thought to act as effectors to promote successful root infection. MAP-1 proteins exhibit a modular architecture, with variable number and arrangement of 58 and 13-aa domains in their central part. Here, we address the evolutionary origins of this gene family using a combination of bioinformatics and molecular biology approaches. Map-1 genes were solely identified in one single member of the phylum Nematoda, i.e., the genus Meloidogyne, and not detected in any other nematode, thus indicating that the map-1 gene family is indeed a TRG family. A phylogenetic analysis of the distribution of map-1 genes in RKNs further showed that these genes are specifically present in species that reproduce by mitotic parthenogenesis, with the exception of M. floridensis, and could not be detected in RKNs reproducing by either meiotic parthenogenesis or amphimixis. These results highlight the divergence between mitotic and meiotic RKN species as a critical transition in the evolutionary history of these parasites. Analysis of the sequence conservation and organization of repeated domains in map-1 genes suggests that gene duplication(s) together with domain loss/duplication have contributed to the evolution of the map-1 family, and that some strong selection mechanism may be acting upon these genes to maintain their functional role(s) in the specificity of the plant-RKN interactions.     

Flipper, a mobile Fot1-like transposable element in Botrytis cinerea

A transposable element, Flipper, was isolated from the phytopathogenic fungus Botrytis cinerea. The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. The Flipper sequence is 1842 bp long with perfect inverted terminal repeats (ITRs) of 48 bp and an open reading frame (ORF) of 533 amino acids, potentially encoding for a transposase; the element is flanked by the dinucleotide TA. The encoded protein is very similar to the putative transposases of three elements from other phytopathogenic fungi, Fot1 from Fusarium oxysporum, and Pot2 and MGR586 from Magnaporthe grisea. The number of Flipper elements in strains of B. cinerea varied from 0 to 20 copies per genome. Analysis of the descendants of one cross showed that the segregation ratio of Flipper elements was 2:2 and that the copies were not linked. Received: 4 December 1996 / Accepted: 21 January 1997     

The pogo transposable element family of Drosophila melanogaster.

Summary A 190 by insertion is associated with the white-eosin mutation in Drosophila melanogaster. This insertion is a member of a family of transposable elements, pogo elements, which is of the same class as the P and hobo elements of D. melanogaster. Strains typically have many copies of a 190 by element, 10–15 elements 1.1–1.5 kb in size and several copies of a 2.1 kb element. The smaller elements all appear to be derived from the largest by single internal deletions so that all elements share terminal sequences. They either always insert at the dinucleotide TA and have perfect 21 bp terminal inverse repeats, or have 22 by inverse repeats and produce no duplication upon insertion. Analysis by DNA blotting of their distribution and occupancy of insertion sites in different strains suggests that they may be less mobile than P or hobo. The DNA sequence of the largest element has two long open reading frames on one strand which are joined by splicing as indicated by cDNA analysis. RNAs of this strand are made, whose sizes are similar to the major size classes of elements. A protein predicted by the DNA sequence has significant homology with a human centrosomal-associated protein, CENP-B. Homologous sequences were not detected in other Drosophila species, suggesting that this transposable element family may be restricted to D. melanogaster.     

Kiddo, a new transposable element family closely associated with rice genes

The promoter region of the rice ubiquitin2 (rubq2) gene was found to be polymorphic between japonica (T309) and indica (IR24) lines as the result of a 270-bp deletion in T309. A TTATA footprint in the T309 rubq2 promoter suggested that an excision event had occurred, and inspection of the 270-bp region present in IR24 revealed that it had all the characteristics of a miniature inverted repeat transposable element (MITE). Database searches showed that this element is a member of a new MITE family, which we have named Kiddo. Thirty-five complete Kiddo sequences were identified in existing rice genomic sequence databases. They could be arranged into four groups, within-group sequence identity was over 90%, with 65-75% identity between groups. The high sequence similarity within a group indicates that some Kiddo members were recently mobile and may still be active. An additional 24 decayed Kiddo sequences were detected. Interestingly, approximately 80% of 18 Kiddo members from annotated accessions lie within 530 bp of a coding sequence. That approximately 40% of Kiddo members present in genic regions reside in introns suggests that Kiddo transposition entails the use of both DNA and RNA intermediates, and may provide some insight into the origins of individual groups. DNA blot analysis showed that Kiddo is a rice-specific element, although one sequence with limited (72%) similarity to Kiddo group A was detected as a wheat EST. Kiddo family members may represent new molecular and phylogenetic markers, as well as representing valuable materials for studying the molecular mechanisms of MITE transposition.     

FARE, a new family of foldback transposons in Arabidopsis

A new family of transposons, FARE, has been identified in Arabidopsis. The structure of these elements is typical of foldback transposons, a distinct subset of mobile DNA elements found in both plants and animals. The ends of FARE elements are long, conserved inverted repeat sequences typically 550 bp in length. These inverted repeats are modular in organization and are predicted to confer extensive secondary structure to the elements. FARE elements are present in high copy number, are heterogeneous in size, and can be divided into two subgroups. FARE1's average 1.1 kb in length and are composed entirely of the long inverted repeats. FARE2's are larger, up to 16.7 kb in length, and contain a large internal region in addition to the inverted repeat ends. The internal region is predicted to encode three proteins, one of which bears homology to a known transposase. FARE1.1 was isolated as an insertion polymorphism between the ecotypes Columbia and Nossen. This, coupled with the presence of 9-bp target-site duplications, strongly suggests that FARE elements have transposed recently. The termini of FARE elements and other foldback transposons are imperfect palindromic sequences, a unique organization that further distinguishes these elements from other mobile DNAs.     

The Tol1 element of the medaka fish, a member of the hAT transposable element family, jumps in Caenorhabditis elegans

Tol1 is a DNA-based transposable element residing in the genome of the medaka fish Oryzias latipes, and has been proven to be transposed in various vertebrate species, including mammals. This element belongs to the hAT (hobo/Activator/Tam3) transposable element family, whose members are distributed in a wide range of organisms. It is thus possible that Tol1 is mobile in organisms other than vertebrates. We here show that transposition of this element occurs in the nematode Caenorhabditis elegans. A donor plasmid containing a Tol1 element and a helper plasmid carrying the transposase gene were delivered into gonad cells and, after several generations of culturing, were recovered from worms. PCR analysis of the donor plasmid, using primers that encompassed the Tol1 element, revealed excision of the Tol1 portion from the plasmid. Analysis of genomic DNA of the worms by the inverse PCR method provided evidence that Tol1 had been integrated into the C. elegans chromosomes. Vertebrates and C. elegans are phylogenetically distantly related organisms in that the former are deuterostomes and the latter a protostome animal. Our results indicate (1) the transposition reaction of the Tol1 element requires, besides the transposase, no factors from host cells, or (2) the host factors, even if required, are those that are common to protostomes and deuterostomes. The results also have significance for the development of a gene transfer vector and other biotechnology tools for C. elegans.     

High conservation of the differentially amplified MPA2 satellite DNA family in parthenogenetic root-knot nematodes

Sequence variability and distribution of a newly characterized MPA2 satellite DNA family are described in five root-knot nematode species of the genus Meloidogyne, the mitotic parthenogens M. paranaensis, M. incognita, M. arenaria and M. javanica, and the meiotic/mitotic M. hapla (isolates A and B, respectively). The lack of distinctive mutations and the considerable contribution (40.8%) of ancestral changes disclose an ancient satellite DNA which existed in the common ancestor of extant parthenogenetic species in the same or similar form and remained preserved for a period of at least 43 My. Nonuniformly distributed polymorphic sites along the satellite monomer suggest differences in constraints acting on particular sequence segments. Sequence diversity is clearly unaffected by significant differences in genomic abundance of the MPA2 satellite DNA in the examined species. Observed results suggest that the dynamics of this satellite DNA family might be in the first instance a consequence of characteristics of its nucleotide sequence and possible constraints imposed on it. Under conditions of mitotic and meiotic parthenogenesis, slow accumulation of mutations and slow replacement of old MPA2 sequence variants with new ones may be equivalent to the dynamics of some satellite DNA sequences conserved for extremely long evolutionary periods in sexual species.     

TESD: a transposable element dynamics simulation environment

Various mathematical models have been used to explore the dynamics of transposable elements (TEs) within their host genomes. However, numerous factors can influence their dynamics, and we know only little about the dynamics of TEs when they first began to invade populations. In addition, the influence of population structuring has only recently been investigated. Transposable Element Simulator Dynamics, a population genomics simulation environment, has therefore been developed to provide a simple tool for analyzing the dynamics of TEs in a community based on (i) various TE parameters, such as the transposition and excision rates, the recombination rate and the coefficient of selection against TE insertions; and (ii) population parameters, such as population size and migration rates. The simulations can be used to illustrate the dynamic fate of TEs in structured populations, can be extended by using more specific molecular or demographic models, and can be useful for teaching population genetics and genomics. AVAILABILITY: TESD is distributed under GPL from the P?le Bioinformatique Lyonnais (PBIL) web server at http://pbil.univ-lyon1.fr/software/TESD